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Haller F, Jimenez K, Baumgartner M, Lang M, Klotz A, Jambrich M, Busslinger G, Müllauer L, Khare V, Gasche C. Nfe2l2/NRF2 Deletion Attenuates Tumorigenesis and Increases Bacterial Diversity in a Mouse Model of Lynch Syndrome. Cancer Prev Res (Phila) 2024; 17:311-324. [PMID: 38643981 DOI: 10.1158/1940-6207.capr-23-0478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/29/2024] [Accepted: 04/18/2024] [Indexed: 04/23/2024]
Abstract
Lynch syndrome (LS) is the most prevalent heritable form of colorectal cancer. Its early onset and high lifetime risk for colorectal cancer emphasize the necessity for effective chemoprevention. NFE2L2 (NRF2) is often considered a potential druggable target, and many chemopreventive compounds induce NRF2. However, although NRF2 counteracts oxidative stress, it is also overexpressed in colorectal cancer and may promote tumorigenesis. In this study, we evaluated the role of NRF2 in the prevention of LS-associated neoplasia. We found increased levels of NRF2 in intestinal epithelia of mice with intestinal epithelium-specific Msh2 deletion (MSH2ΔIEC) compared with C57BL/6 (wild-type) mice, as well as an increase in downstream NRF2 targets NAD(P)H dehydrogenase (quinone 1) and glutamate-cysteine ligase catalytic subunit. Likewise, NRF2 levels were increased in human MSH2-deficient LS tumors compared with healthy human controls. In silico analysis of a publicly accessible RNA sequencing LS dataset also found an increase in downstream NRF2 targets. Upon crossing MSH2ΔIEC with Nrf2null (MSH2ΔIECNrf2null) mice, we unexpectedly found reduced tumorigenesis in MSH2ΔIECNrf2null mice compared with MSH2ΔIEC mice after 40 weeks, which occurred despite an increase in oxidative damage in MSH2ΔIECNrf2null mice. The loss of NRF2 impaired proliferation as seen by Ki67 intestinal staining and in organoid cultures. This was accompanied by diminished WNT/β-catenin signaling, but apoptosis was unaffected. Microbial α-diversity increased over time with the loss of NRF2 based upon 16S rRNA gene amplicon sequencing of murine fecal samples. Altogether, we show that NRF2 protein levels are increased in MSH2 deficiency and associated neoplasia, but the loss of NRF2 attenuates tumorigenesis. Activation of NRF2 may not be a feasible strategy for chemoprevention in LS. Prevention Relevance: Patients with LS have an early onset and high lifetime risk for colorectal cancer. In this study, we show that NRF2 protein levels are increased in MSH2 deficiency and associated neoplasia, but the loss of NRF2 attenuates tumorigenesis. This suggests that NRF2 may not be a tumor suppressor in this specific context.
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Affiliation(s)
- Felix Haller
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Kristine Jimenez
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Maximilian Baumgartner
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Michaela Lang
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anton Klotz
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Manuela Jambrich
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Georg Busslinger
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Leonhard Müllauer
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Vineeta Khare
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Christoph Gasche
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
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2
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Martin LC, O'Hare MA, Ghielmetti G, Twesigomwe D, Kerr TJ, Gumbo R, Buss PE, Kitchin N, Hemmings SMJ, Miller MA, Goosen WJ. Short-read full-length 16S rRNA amplicon sequencing for characterisation of the respiratory bacteriome of captive and free-ranging African elephants (Loxodonta africana). Sci Rep 2024; 14:14768. [PMID: 38926469 PMCID: PMC11208578 DOI: 10.1038/s41598-024-65841-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 06/24/2024] [Indexed: 06/28/2024] Open
Abstract
Hypervariable region sequencing of the 16S ribosomal RNA (rRNA) gene plays a critical role in microbial ecology by offering insights into bacterial communities within specific niches. While providing valuable genus-level information, its reliance on data from targeted genetic regions limits its overall utility. Recent advances in sequencing technologies have enabled characterisation of the full-length 16S rRNA gene, enhancing species-level classification. Although current short-read platforms are cost-effective and precise, they lack full-length 16S rRNA amplicon sequencing capability. This study aimed to evaluate the feasibility of a modified 150 bp paired-end full-length 16S rRNA amplicon short-read sequencing technique on the Illumina iSeq 100 and 16S rRNA amplicon assembly workflow by utilising a standard mock microbial community and subsequently performing exploratory characterisation of captive (zoo) and free-ranging African elephant (Loxodonta africana) respiratory microbiota. Our findings demonstrate that, despite generating assembled amplicons averaging 869 bp in length, this sequencing technique provides taxonomic assignments consistent with the theoretical composition of the mock community and respiratory microbiota of other mammals. Tentative bacterial signatures, potentially representing distinct respiratory tract compartments (trunk and lower respiratory tract) were visually identified, necessitating further investigation to gain deeper insights into their implication for elephant physiology and health.
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Affiliation(s)
- Lauren C Martin
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Unit, Cape Town, South Africa
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Michaela A O'Hare
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Unit, Cape Town, South Africa
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Giovanni Ghielmetti
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 270, 8057, Zurich, Switzerland
| | - David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tanya J Kerr
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Rachiel Gumbo
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Peter E Buss
- South African National Parks, Veterinary Wildlife Services, Kruger National Park, Skukuza, South Africa
| | - Natasha Kitchin
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Unit, Cape Town, South Africa
| | - Sian M J Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Unit, Cape Town, South Africa
| | - Michele A Miller
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Wynand J Goosen
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa.
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3
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Niu Y, Heddes M, Altaha B, Birkner M, Kleigrewe K, Meng C, Haller D, Kiessling S. Targeting the intestinal circadian clock by meal timing ameliorates gastrointestinal inflammation. Cell Mol Immunol 2024:10.1038/s41423-024-01189-z. [PMID: 38918576 DOI: 10.1038/s41423-024-01189-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
Abstract
The expression of clock genes has been observed to be impaired in biopsies from patients with inflammatory bowel disease (IBD). Disruption of circadian rhythms, which occurs in shift workers, has been linked to an increased risk of gastrointestinal diseases, including IBD. The peripheral circadian clock in intestinal epithelial cells (IECs) was previously shown to balance gastrointestinal homeostasis by regulating the microbiome. Here, we demonstrated that the intestinal clock is disrupted in an IBD-relevant mouse model (IL-10-/-). A lack of the intestinal clock gene (Bmal1) in intestinal epithelial cells (IECs) in a chemically and a novel genetically induced colitis model (DSS, Bmal1IEC-/-xIL-10-/-) promoted colitis and dramatically reduced survival rates. Germ-free Bmal1IEC-/- mice colonized with disease-associated microbiota from IL-10-/- mice exhibited increased inflammatory responses, highlighting the importance of the local intestinal clock for microbiota-induced IBD development. Targeting the intestinal clock directly by timed restricted feeding (RF) in IL-10-/- mice restored intestinal clock functions, including immune cell recruitment and microbial rhythmicity; improved inflammatory responses; dramatically enhanced survival rates and rescued the histopathological phenotype. In contrast, RF failed to improve IBD symptoms in Bmal1IEC-/-xIL-10-/- mice, demonstrating the significance of the intestinal clock in determining the beneficial effect of RF. Overall, we provide evidence that intestinal clock dysfunction triggers host immune imbalance and promotes the development and progression of IBD-like colitis. Enhancing intestinal clock function by RF modulates the pathogenesis of IBD and thus could become a novel strategy to ameliorate symptoms in IBD patients.
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Affiliation(s)
- Yunhui Niu
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354, Freising, Germany
- Chair of Nutrition and Immunology, School of Life Sciences, Technical University of Munich, Gregor-Mendel-Str. 2, 85354, Freising, Germany
| | - Marjolein Heddes
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354, Freising, Germany
- Chair of Nutrition and Immunology, School of Life Sciences, Technical University of Munich, Gregor-Mendel-Str. 2, 85354, Freising, Germany
| | - Baraa Altaha
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354, Freising, Germany
- Chair of Nutrition and Immunology, School of Life Sciences, Technical University of Munich, Gregor-Mendel-Str. 2, 85354, Freising, Germany
| | - Michael Birkner
- Chair of Nutrition and Immunology, School of Life Sciences, Technical University of Munich, Gregor-Mendel-Str. 2, 85354, Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Gregor-Mendel-Str. 4, 85354, Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Gregor-Mendel-Str. 4, 85354, Freising, Germany
| | - Dirk Haller
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354, Freising, Germany
- Chair of Nutrition and Immunology, School of Life Sciences, Technical University of Munich, Gregor-Mendel-Str. 2, 85354, Freising, Germany
| | - Silke Kiessling
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354, Freising, Germany.
- Chair of Nutrition and Immunology, School of Life Sciences, Technical University of Munich, Gregor-Mendel-Str. 2, 85354, Freising, Germany.
- Faculty of Health and Medical Sciences, University of Surrey, Stag Hill Campus, GU27XP, Guildford, UK.
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Li C, Liu C, Li H, Liao H, Xu L, Yao M, Li X. The microgeo: an R package rapidly displays the biogeography of soil microbial community traits on maps. FEMS Microbiol Ecol 2024; 100:fiae087. [PMID: 38866720 PMCID: PMC11212663 DOI: 10.1093/femsec/fiae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/26/2024] [Accepted: 06/11/2024] [Indexed: 06/14/2024] Open
Abstract
Many R packages provide statistical approaches for elucidating the diversity of soil microbes, yet they still struggle to visualize microbial traits on a geographical map. This creates challenges in interpreting microbial biogeography on a regional scale, especially when the spatial scale is large or the distribution of sampling sites is uneven. Here, we developed a lightweight, flexible, and user-friendly R package called microgeo. This package integrates many functions involved in reading, manipulating, and visualizing geographical boundary data; downloading spatial datasets; and calculating microbial traits and rendering them onto a geographical map using grid-based visualization, spatial interpolation, or machine learning. Using this R package, users can visualize any trait calculated by microgeo or other tools on a map and can analyze microbiome data in conjunction with metadata derived from a geographical map. In contrast to other R packages that statistically analyze microbiome data, microgeo provides more-intuitive approaches in illustrating the biogeography of soil microbes on a large geographical scale, serving as an important supplement to statistically driven comparisons and facilitating the biogeographic analysis of publicly accessible microbiome data at a large spatial scale in a more convenient and efficient manner. The microgeo R package can be installed from the Gitee (https://gitee.com/bioape/microgeo) and GitHub (https://github.com/ChaonanLi/microgeo) repositories. Detailed tutorials for the microgeo R package are available at https://chaonanli.github.io/microgeo.
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Affiliation(s)
- Chaonan Li
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang 621000, China
| | - Chi Liu
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hankang Li
- Department of Electrical Engineering and Computer Science, University of California, Irvine, CA 92697, United States
| | - Haijun Liao
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang 621000, China
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Normal University of Sichuan Province, Mianyang Normal University, Mianyang 621000, China
| | - Lin Xu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Minjie Yao
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiangzhen Li
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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5
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Mahar JE, Wille M, Harvey E, Moritz CC, Holmes EC. The diverse liver viromes of Australian geckos and skinks are dominated by hepaciviruses and picornaviruses and reflect host taxonomy and habitat. Virus Evol 2024; 10:veae044. [PMID: 38854849 PMCID: PMC11160328 DOI: 10.1093/ve/veae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/28/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024] Open
Abstract
Lizards have diverse ecologies and evolutionary histories, and represent a promising group to explore how hosts shape virome structure and virus evolution. Yet, little is known about the viromes of these animals. In Australia, squamates (lizards and snakes) comprise the most diverse order of vertebrates, and Australia hosts the highest diversity of lizards globally, with the greatest breadth of habitat use. We used meta-transcriptomic sequencing to determine the virome of nine co-distributed, tropical lizard species from three taxonomic families in Australia and analyzed these data to identify host traits associated with viral abundance and diversity. We show that lizards carry a large diversity of viruses, identifying more than thirty novel, highly divergent vertebrate-associated viruses. These viruses were from nine viral families, including several that contain well known pathogens, such as the Flaviviridae, Picornaviridae, Bornaviridae, Iridoviridae, and Rhabdoviridae. Members of the Flaviviridae were particularly abundant across species sampled here, largely belonging to the genus Hepacivirus: fourteen novel hepaciviruses were identified, broadening the known diversity of this group and better defining its evolution by uncovering new reptilian clades. The evolutionary histories of the viruses studied here frequently aligned with the biogeographic and phylogenetic histories of the hosts, indicating that exogenous viruses may help infer host evolutionary history if sampling is strategic and sampling density high enough. Notably, analysis of alpha and beta diversity revealed that virome composition and richness in the animals sampled here was shaped by host taxonomy and habitat. In sum, we identified a diverse range of reptile viruses that broadly contributes to our understanding of virus-host ecology and evolution.
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Affiliation(s)
- Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Michelle Wille
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Craig C Moritz
- Research School of Biology & Centre for Biodiversity Analysis, The Australian National University, Canberra, ACT 2600, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
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6
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Messaritakis I, Koulouris A, Boukla E, Vogiatzoglou K, Lagkouvardos I, Intze E, Sfakianaki M, Chondrozoumaki M, Karagianni M, Athanasakis E, Xynos E, Tsiaoussis J, Christodoulakis M, Flamourakis ME, Tsagkataki ES, Giannikaki L, Chliara E, Mavroudis D, Tzardi M, Souglakos J. Exploring Gut Microbiome Composition and Circulating Microbial DNA Fragments in Patients with Stage II/III Colorectal Cancer: A Comprehensive Analysis. Cancers (Basel) 2024; 16:1923. [PMID: 38792001 PMCID: PMC11119035 DOI: 10.3390/cancers16101923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) significantly contributes to cancer-related mortality, necessitating the exploration of prognostic factors beyond TNM staging. This study investigates the composition of the gut microbiome and microbial DNA fragments in stage II/III CRC. METHODS A cohort of 142 patients with stage II/III CRC and 91 healthy controls underwent comprehensive microbiome analysis. Fecal samples were collected for 16S rRNA sequencing, and blood samples were tested for the presence of microbial DNA fragments. De novo clustering analysis categorized individuals based on their microbial profiles. Alpha and beta diversity metrics were calculated, and taxonomic profiling was conducted. RESULTS Patients with CRC exhibited distinct microbial composition compared to controls. Beta diversity analysis confirmed CRC-specific microbial profiles. Taxonomic profiling revealed unique taxonomies in the patient cohort. De novo clustering separated individuals into distinct groups, with specific microbial DNA fragment detection associated with certain patient clusters. CONCLUSIONS The gut microbiota can differentiate patients with CRC from healthy individuals. Detecting microbial DNA fragments in the bloodstream may be linked to CRC prognosis. These findings suggest that the gut microbiome could serve as a prognostic factor in stage II/III CRC. Identifying specific microbial markers associated with CRC prognosis has potential clinical implications, including personalized treatment strategies and reduced healthcare costs. Further research is needed to validate these findings and uncover underlying mechanisms.
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Affiliation(s)
- Ippokratis Messaritakis
- Laboratory of Translational Oncology, Medical School, University of Crete, 70013 Heraklion, Greece; (A.K.); (M.C.); (D.M.)
| | - Andreas Koulouris
- Laboratory of Translational Oncology, Medical School, University of Crete, 70013 Heraklion, Greece; (A.K.); (M.C.); (D.M.)
| | - Eleni Boukla
- Laboratory of Translational Oncology, Medical School, University of Crete, 70013 Heraklion, Greece; (A.K.); (M.C.); (D.M.)
| | - Konstantinos Vogiatzoglou
- Laboratory of Translational Oncology, Medical School, University of Crete, 70013 Heraklion, Greece; (A.K.); (M.C.); (D.M.)
| | - Ilias Lagkouvardos
- Department of Clinical Microbiology, School of Medicine, University of Crete, 70013 Heraklion, Greece; (I.L.); (E.I.)
| | - Evangelia Intze
- Department of Clinical Microbiology, School of Medicine, University of Crete, 70013 Heraklion, Greece; (I.L.); (E.I.)
| | - Maria Sfakianaki
- Laboratory of Translational Oncology, Medical School, University of Crete, 70013 Heraklion, Greece; (A.K.); (M.C.); (D.M.)
| | - Maria Chondrozoumaki
- Laboratory of Translational Oncology, Medical School, University of Crete, 70013 Heraklion, Greece; (A.K.); (M.C.); (D.M.)
| | - Michaela Karagianni
- Laboratory of Translational Oncology, Medical School, University of Crete, 70013 Heraklion, Greece; (A.K.); (M.C.); (D.M.)
| | - Elias Athanasakis
- Department of General Surgery, Heraklion University Hospital, 71100 Heraklion, Greece;
| | - Evangelos Xynos
- Department of Surgery, Creta Interclinic Hospital of Heraklion, 71305 Heraklion, Greece
| | - John Tsiaoussis
- Department of Anatomy, School of Medicine, University of Crete, 70013 Heraklion, Greece;
| | | | | | - Eleni S. Tsagkataki
- Department of General Surgery, Venizeleio General Hospital, 71409 Heraklion, Greece (M.E.F.)
| | - Linda Giannikaki
- Histopathology, Venizeleio General Hospital, 71409 Heraklion, Greece
| | - Evdoxia Chliara
- Histopathology, Venizeleio General Hospital, 71409 Heraklion, Greece
| | - Dimitrios Mavroudis
- Laboratory of Translational Oncology, Medical School, University of Crete, 70013 Heraklion, Greece; (A.K.); (M.C.); (D.M.)
- Department of Medical Oncology, University Hospital of Heraklion, 71110 Heraklion, Greece
| | - Maria Tzardi
- Laboratory of Pathology, University General Hospital of Heraklion, 70013 Heraklion, Greece;
| | - John Souglakos
- Laboratory of Translational Oncology, Medical School, University of Crete, 70013 Heraklion, Greece; (A.K.); (M.C.); (D.M.)
- Department of Medical Oncology, University Hospital of Heraklion, 71110 Heraklion, Greece
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7
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Sadiq S, Harvey E, Mifsud JCO, Minasny B, McBratney AB, Pozza LE, Mahar JE, Holmes EC. Australian terrestrial environments harbour extensive RNA virus diversity. Virology 2024; 593:110007. [PMID: 38346363 DOI: 10.1016/j.virol.2024.110007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 03/13/2024]
Abstract
Australia is home to a diverse range of unique native fauna and flora. To address whether Australian ecosystems also harbour unique viruses, we performed meta-transcriptomic sequencing of 16 farmland and sediment samples taken from the east and west coasts of Australia. We identified 2460 putatively novel RNA viruses across 18 orders, the vast majority of which belonged to the microbe-associated phylum Lenarviricota. In many orders, such as the Nodamuvirales and Ghabrivirales, the novel viruses identified here comprised entirely new clades. Novel viruses also fell between established genera or families, such as in the Cystoviridae and Picornavirales, while highly divergent lineages were identified in the Sobelivirales and Ghabrivirales. Viral read abundance and alpha diversity were influenced by sampling site, soil type and land use, but not by depth from the surface. In sum, Australian soils and sediments are home to remarkable viral diversity, reflecting the biodiversity of local fauna and flora.
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Affiliation(s)
- Sabrina Sadiq
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Budiman Minasny
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Alex B McBratney
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Liana E Pozza
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
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8
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Ramaboli MC, Ocvirk S, Khan Mirzaei M, Eberhart BL, Valdivia-Garcia M, Metwaly A, Neuhaus K, Barker G, Ru J, Nesengani LT, Mahdi-Joest D, Wilson AS, Joni SK, Layman DC, Zheng J, Mandal R, Chen Q, Perez MR, Fortuin S, Gaunt B, Wishart D, Methé B, Haller D, Li JV, Deng L, Swart R, O'Keefe SJD. Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer. Nat Commun 2024; 15:3379. [PMID: 38643180 PMCID: PMC11032404 DOI: 10.1038/s41467-024-46265-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/15/2024] [Indexed: 04/22/2024] Open
Abstract
Transition from traditional high-fiber to Western diets in urbanizing communities of Sub-Saharan Africa is associated with increased risk of non-communicable diseases (NCD), exemplified by colorectal cancer (CRC) risk. To investigate how urbanization gives rise to microbial patterns that may be amenable by dietary intervention, we analyzed diet intake, fecal 16 S bacteriome, virome, and metabolome in a cross-sectional study in healthy rural and urban Xhosa people (South Africa). Urban Xhosa individuals had higher intakes of energy (urban: 3,578 ± 455; rural: 2,185 ± 179 kcal/d), fat and animal protein. This was associated with lower fecal bacteriome diversity and a shift from genera favoring degradation of complex carbohydrates (e.g., Prevotella) to taxa previously shown to be associated with bile acid metabolism and CRC. Urban Xhosa individuals had higher fecal levels of deoxycholic acid, shown to be associated with higher CRC risk, but similar short-chain fatty acid concentrations compared with rural individuals. Fecal virome composition was associated with distinct gut bacterial communities across urbanization, characterized by different dominant host bacteria (urban: Bacteriodota; rural: unassigned taxa) and variable correlation with fecal metabolites and dietary nutrients. Food and skin microbiota samples showed compositional differences along the urbanization gradient. Rural-urban dietary transition in South Africa is linked to major changes in the gut microbiome and metabolome. Further studies are needed to prove cause and identify whether restoration of specific components of the traditional diet will arrest the accelerating rise in NCDs in Sub-Saharan Africa.
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Affiliation(s)
- M C Ramaboli
- African Microbiome Institute, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - S Ocvirk
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Intestinal Microbiology Research Group, German Institute of Human Nutrition, Potsdam, Germany
- ZIEL - Institute for Food and Health, Technical University of Munich, Freising, Germany
| | - M Khan Mirzaei
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg, Germany
- Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - B L Eberhart
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - M Valdivia-Garcia
- Section of Nutrition, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - A Metwaly
- Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - K Neuhaus
- Core Facility Microbiome, ZIEL - Institute for Food and Health, Technical University of Munich, Freising, Germany
| | - G Barker
- Section of Nutrition, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - J Ru
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg, Germany
- Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - L T Nesengani
- Department of Agriculture and Animal Health, University of South Africa, Pretoria, South Africa
| | - D Mahdi-Joest
- Intestinal Microbiology Research Group, German Institute of Human Nutrition, Potsdam, Germany
| | - A S Wilson
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - S K Joni
- Department of Nutrition and Dietetics, School of Public Health, University of the Western Cape, Cape Town, South Africa
| | - D C Layman
- Department of Nutrition and Dietetics, School of Public Health, University of the Western Cape, Cape Town, South Africa
| | - J Zheng
- The Metabolomics Innovation Centre & Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - R Mandal
- The Metabolomics Innovation Centre & Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Q Chen
- Section of Nutrition, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - M R Perez
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - S Fortuin
- African Microbiome Institute, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - B Gaunt
- Zithulele Hospital, Mqanduli District, Mqanduli, Eastern Cape Province, South Africa
| | - D Wishart
- The Metabolomics Innovation Centre & Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - B Methé
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - D Haller
- ZIEL - Institute for Food and Health, Technical University of Munich, Freising, Germany
- Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - J V Li
- Section of Nutrition, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - L Deng
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg, Germany
- Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - R Swart
- Department of Nutrition and Dietetics, School of Public Health, University of the Western Cape, Cape Town, South Africa
| | - S J D O'Keefe
- African Microbiome Institute, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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9
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Heppner N, Reitmeier S, Heddes M, Merino MV, Schwartz L, Dietrich A, List M, Gigl M, Meng C, van der Veen DR, Schirmer M, Kleigrewe K, Omer H, Kiessling S, Haller D. Diurnal rhythmicity of infant fecal microbiota and metabolites: A randomized controlled interventional trial with infant formula. Cell Host Microbe 2024; 32:573-587.e5. [PMID: 38569545 DOI: 10.1016/j.chom.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/13/2024] [Accepted: 02/26/2024] [Indexed: 04/05/2024]
Abstract
Microbiota assembly in the infant gut is influenced by diet. Breastfeeding and human breastmilk oligosaccharides promote the colonization of beneficial bifidobacteria. Infant formulas are supplemented with bifidobacteria or complex oligosaccharides, notably galacto-oligosaccharides (GOS), to mimic breast milk. To compare microbiota development across feeding modes, this randomized controlled intervention study (German Clinical Trial DRKS00012313) longitudinally sampled infant stool during the first year of life, revealing similar fecal bacterial communities between formula- and breast-fed infants (N = 210) but differences across age. Infant formula containing GOS sustained high levels of bifidobacteria compared with formula containing B. longum and B. breve or placebo. Metabolite and bacterial profiling revealed 24-h oscillations and circadian networks. Rhythmicity in bacterial diversity, specific taxa, and functional pathways increased with age and was strongest following breastfeeding and GOS supplementation. Circadian rhythms in dominant taxa were further maintained ex vivo in a chemostat model. Hence, microbiota rhythmicity develops early in life and is impacted by diet.
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Affiliation(s)
- Nina Heppner
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Sandra Reitmeier
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Marjolein Heddes
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Michael Vig Merino
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Leon Schwartz
- Data Science in Systems Biology, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Alexander Dietrich
- Data Science in Systems Biology, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Markus List
- Data Science in Systems Biology, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Michael Gigl
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Daan R van der Veen
- Faculty of Health and Biomedical Science, University of Surrey, 388 Stag Hill Campus, Guildford 17 GU27XH, UK
| | - Melanie Schirmer
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Hélène Omer
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Silke Kiessling
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany; Faculty of Health and Biomedical Science, University of Surrey, 388 Stag Hill Campus, Guildford 17 GU27XH, UK
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
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10
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Siasios P, Giosi E, Ouranos K, Christoforidi M, Dimopoulou I, Leshi E, Exindari M, Anastassopoulou C, Gioula G. Oropharyngeal Microbiome Analysis in Patients with Varying SARS-CoV-2 Infection Severity: A Prospective Cohort Study. J Pers Med 2024; 14:369. [PMID: 38672996 PMCID: PMC11051038 DOI: 10.3390/jpm14040369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/16/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Patients with COVID-19 infection have distinct oropharyngeal microbiota composition and diversity metrics according to disease severity. However, these findings are not consistent across the literature. We conducted a multicenter, prospective study in patients with COVID-19 requiring outpatient versus inpatient management to explore the microbial abundance of taxa at the phylum, family, genus, and species level, and we utilized alpha and beta diversity indices to further describe our findings. We collected oropharyngeal washing specimens at the time of study entry, which coincided with the COVID-19 diagnosis, to conduct all analyses. We included 43 patients in the study, of whom 16 were managed as outpatients and 27 required hospitalization. Proteobacteria, Actinobacteria, Bacteroidetes, Saccharibacteria TM7, Fusobacteria, and Spirochaetes were the most abundant phyla among patients, while 61 different families were detected, of which the Streptococcaceae and Staphylococcaceae families were the most predominant. A total of 132 microbial genera were detected, with Streptococcus being the predominant genus in outpatients, in contrast to hospitalized patients, in whom the Staphylococcus genus was predominant. LeFSe analysis identified 57 microbial species in the oropharyngeal washings of study participants that could discriminate the severity of symptoms of COVID-19 infections. Alpha diversity analysis did not reveal a difference in the abundance of bacterial species between the groups, but beta diversity analysis established distinct microbial communities between inpatients and outpatients. Our study provides information on the complex association between the oropharyngeal microbiota and SARS-CoV-2 infection. Although our study cannot establish causation, knowledge of specific taxonomic changes with increasing SARS-CoV-2 infection severity can provide us with novel clues for the prognostic classification of COVID-19 patients.
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Affiliation(s)
- Panagiotis Siasios
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Evangelia Giosi
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Konstantinos Ouranos
- Department of Medicine, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Maria Christoforidi
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Ifigenia Dimopoulou
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Enada Leshi
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Maria Exindari
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Cleo Anastassopoulou
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Georgia Gioula
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
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11
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Tang Y, Nie H, Zhang Y, Wei Y, Huang Y, Zhuang Y, Yang W, Zhu Y. Effects of Sjogren's syndrome and high sugar diet on oral microbiome in patients with rampant caries: a clinical study. BMC Oral Health 2024; 24:361. [PMID: 38515087 PMCID: PMC10956276 DOI: 10.1186/s12903-024-04150-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/15/2024] [Indexed: 03/23/2024] Open
Abstract
OBJECTIVE The purpose of this study was to assess the composition of the oral microbial flora of adults with rampant caries in China to provide guidance for treatment. PATIENTS AND METHODS Sixty human salivary and supragingival plaque samples were collected. They were characterized into four groups: patients with rampant caries with Sjogren's syndrome (RC-SS) or high-sugar diet (RC-HD), common dental caries (DC), and healthy individuals (HP). The 16S rRNA V3-V4 region of the bacterial DNA was detected by Illumina sequencing. PCoA based on OTU with Bray-Curtis algorithm, the abundance of each level, LEfSe analysis, network analysis, and PICRUSt analysis were carried out between the four groups and two sample types. Clinical and demographic data were compared using analysis of variance (ANOVA) or the nonparametric Kruskal-Wallis rank-sum test, depending on the normality of the data, using GraphPad Prism 8 (P < 0.05). RESULTS OTU principal component analysis revealed a significant difference between healthy individuals and those with RC-SS. In the saliva of patients with rampant caries, the relative abundance of Firmicutes increased significantly at the phylum level. Further, Streptocpccus, Veillonella, Prevotella, and Dialister increased, while Neisseria and Haemophilus decreased at the genus level. Veillonella increased in the plaque samples of patients with rampant caries. CONCLUSION Both salivary and dental plaque composition were significantly different between healthy individuals and patients with rampant caries. This study provides a microbiological basis for exploring the etiology of rampant caries. CLINICAL RELEVANCE This study provides basic information on the flora of the oral cavity in adults with rampant caries in China. These findings could serve as a reference for the treatment of this disease.
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Affiliation(s)
- Yifei Tang
- Department of Endodontic, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, China
| | - Hua Nie
- Department of Endodontic, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, China
| | - Yu Zhang
- Department of Endodontic, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, China
| | - Yuan Wei
- Department of Endodontic, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, China
| | - Yequan Huang
- Department of Endodontic, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, China
| | - Yuan Zhuang
- Department of Endodontic, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, China
| | - Weidong Yang
- Department of Endodontic, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, China.
| | - Yanan Zhu
- Department of Endodontic, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, China.
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12
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Xie Z, He W, Gobbi A, Bertram HC, Nielsen DS. The effect of in vitro simulated colonic pH gradients on microbial activity and metabolite production using common prebiotics as substrates. BMC Microbiol 2024; 24:83. [PMID: 38468200 PMCID: PMC10926653 DOI: 10.1186/s12866-024-03235-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND The interplay between gut microbiota (GM) and the metabolization of dietary components leading to the production of short-chain fatty acids (SCFAs) is affected by a range of factors including colonic pH and carbohydrate source. However, there is still only limited knowledge on how the GM activity and metabolite production in the gastrointestinal tract could be influenced by pH and the pH gradient increases along the colon. RESULTS Here we investigate the effect of pH gradients corresponding to levels typically found in the colon on GM composition and metabolite production using substrates inulin, lactose, galactooligosaccharides (GOS), and fructooligosaccharide (FOS) in an in vitro colon setup. We investigated 3 different pH regimes (low, 5.2 increasing to 6.4; medium, 5.6 increasing to 6.8 and high, 6.0 increasing to 7.2) for each fecal inoculum and found that colonic pH gradients significantly influenced in vitro simulated GM structure, but the influence of fecal donor and substrate was more pronounced. Low pH regimes strongly influenced GM with the decreased relative abundance of Bacteroides spp. and increased Bifidobacterium spp. Higher in vitro simulated colonic pH promoted the production of SCFAs in a donor- and substrate-dependent manner. The butyrate producer Butyricimonas was enriched at higher pH conditions, where also butyrate production was increased for inulin. The relative abundance of Phascolarctobacterium, Bacteroides, and Rikenellaceae also increased at higher colonic pH, which was accompanied by increased production of propionate with GOS and FOS as substrates. CONCLUSIONS Together, our results show that colonic substrates such as dietary fibres influence GM composition and metabolite production, not only by being selectively utilized by specific microbes, but also because of their SCFA production, which in turn also influences colonic pH and overall GM composition and activity. Our work provides details about the effect of the gradients of rising pH from the proximal to distal colon on fermenting dietary substrates in vitro and highlights the importance of considering pH in GM research.
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Affiliation(s)
- Zhuqing Xie
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark.
| | - Weiwei He
- Department of Food Science, Aarhus University, Aarhus N, Denmark
- Present Address: State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Alex Gobbi
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Present Address: European Food and Safety Authority, Parma, Italy
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13
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Czech M, Schneider S, Peltokangas N, El Khawanky N, Ghimire S, Andrieux G, Hülsdünker J, Krausz M, Proietti M, Braun LM, Rückert T, Langenbach M, Schmidt D, Martin I, Wenger V, de Vega E, Haring E, Pourjam M, Pfeifer D, Schmitt-Graeff A, Grimbacher B, Aumann K, Kircher B, Tilg H, Raffatellu M, Thiele Orberg E, Häcker G, Duyster J, Köhler N, Holler E, Nachbaur D, Boerries M, Gerner RR, Grün D, Zeiser R. Lipocalin-2 expression identifies an intestinal regulatory neutrophil population during acute graft-versus-host disease. Sci Transl Med 2024; 16:eadi1501. [PMID: 38381845 DOI: 10.1126/scitranslmed.adi1501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/24/2024] [Indexed: 02/23/2024]
Abstract
Acute graft-versus-host disease (aGVHD) is a life-threatening complication of allogeneic hematopoietic cell transplantation (allo-HCT), for which therapeutic options are limited. Strategies to promote intestinal tissue tolerance during aGVHD may improve patient outcomes. Using single-cell RNA sequencing, we identified a lipocalin-2 (LCN2)-expressing neutrophil population in mice with intestinal aGVHD. Transfer of LCN2-overexpressing neutrophils or treatment with recombinant LCN2 reduced aGVHD severity, whereas the lack of epithelial or hematopoietic LCN2 enhanced aGVHD severity and caused microbiome alterations. Mechanistically, LCN2 induced insulin-like growth factor 1 receptor (IGF-1R) signaling in macrophages through the LCN2 receptor SLC22A17, which increased interleukin-10 (IL-10) production and reduced major histocompatibility complex class II (MHCII) expression. Transfer of LCN2-pretreated macrophages reduced aGVHD severity but did not reduce graft-versus-leukemia effects. Furthermore, LCN2 expression correlated with IL-10 expression in intestinal biopsies in multiple cohorts of patients with aGVHD, and LCN2 induced IGF-1R signaling in human macrophages. Collectively, we identified a LCN2-expressing intestinal neutrophil population that reduced aGVHD severity by decreasing MHCII expression and increasing IL-10 production in macrophages. This work provides the foundation for administration of LCN2 as a therapeutic approach for aGVHD.
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Affiliation(s)
- Marie Czech
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Sophia Schneider
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Nina Peltokangas
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, 97078 Würzburg, Germany
| | - Nadia El Khawanky
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Department of Medicine III, University Hospital rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, 81675 Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, 81675 Munich, Germany
| | - Sakhila Ghimire
- Department of Internal Medicine III, Haematology and Internal Oncology, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Jan Hülsdünker
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Máté Krausz
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, Albert-Ludwigs-University, 79106 Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Institute for Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Michele Proietti
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, Albert-Ludwigs-University, 79106 Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, Hannover Medical School, 30625 Hannover, Germany
- RESIST-Cluster of Excellence 2155, Hannover Medical School, 30625 Hannover, Germany
| | - Lukas M Braun
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Tamina Rückert
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Marlene Langenbach
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Dominik Schmidt
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Ina Martin
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Valentin Wenger
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Enrique de Vega
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Eileen Haring
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Mohsen Pourjam
- Core Facility Microbiome, ZIEL Institute of Food and Health, Technical University of Munich, 85354 Freising, Germany
| | - Dietmar Pfeifer
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | | | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, Albert-Ludwigs-University, 79106 Freiburg, Germany
- DZIF-German Center for Infection Research, Satellite Center Freiburg, 79106 Freiburg, Germany
- RESIST-Cluster of Excellence 2155 to Hannover Medical School, Satellite Center Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Konrad Aumann
- Department of Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Brigitte Kircher
- Department of Internal Medicine V, Hematology and Oncology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Hepatology and Endocrinology and Metabolism, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Manuela Raffatellu
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, CA 92123-0735, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, CA 92093, USA
| | - Erik Thiele Orberg
- Department of Internal Medicine III, Haematology and Internal Oncology, University Hospital Regensburg, 93053 Regensburg, Germany
- German Cancer Consortium (DKTK), partner-site Munich, a partnership between DKFZ and Klinikum rechts der Isar, 81675 Munich, Germany
- Bavarian Cancer Research Center (BZKF), 93053 Regensburg, Germany
| | - Georg Häcker
- Institute of Medical Microbiology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Justus Duyster
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK), Partner site Freiburg, a partnership between DKFZ and Medical Center, University of Freiburg, 79106 Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg Germany
| | - Natalie Köhler
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Ernst Holler
- Department of Internal Medicine III, Haematology and Internal Oncology, University Hospital Regensburg, 93053 Regensburg, Germany
| | - David Nachbaur
- Department of Internal Medicine V, Hematology and Oncology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- German Cancer Consortium (DKTK), Partner site Freiburg, a partnership between DKFZ and Medical Center, University of Freiburg, 79106 Freiburg, Germany
| | - Romana R Gerner
- Department of Medicine III, University Hospital rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, 81675 Munich, Germany
- TUM School of Life Sciences Weihenstephan, ZIEL Institute for Food & Health, 85354 Freising-Weihenstephan, Germany
| | - Dominic Grün
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, 97078 Würzburg, Germany
| | - Robert Zeiser
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK), Partner site Freiburg, a partnership between DKFZ and Medical Center, University of Freiburg, 79106 Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg Germany
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14
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Ye RZ, Li YY, Xu DL, Wang BH, Wang XY, Zhang MZ, Wang N, Gao WY, Li C, Han XY, Du LF, Xia LY, Song K, Xu Q, Liu J, Cheng N, Li ZH, Du YD, Yu HJ, Shi XY, Jiang JF, Sun Y, Cui XM, Ding SJ, Zhao L, Cao WC. Virome diversity shaped by genetic evolution and ecological landscape of Haemaphysalis longicornis. MICROBIOME 2024; 12:35. [PMID: 38378577 PMCID: PMC10880243 DOI: 10.1186/s40168-024-01753-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/04/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND Haemaphysalis longicornis is drawing attentions for its geographic invasion, extending population, and emerging disease threat. However, there are still substantial gaps in our knowledge of viral composition in relation to genetic diversity of H. longicornis and ecological factors, which are important for us to understand interactions between virus and vector, as well as between vector and ecological elements. RESULTS We conducted the meta-transcriptomic sequencing of 136 pools of H. longicornis and identified 508 RNA viruses of 48 viral species, 22 of which have never been reported. Phylogenetic analysis of mitochondrion sequences divided the ticks into two genetic clades, each of which was geographically clustered and significantly associated with ecological factors, including altitude, precipitation, and normalized difference vegetation index. The two clades showed significant difference in virome diversity and shared about one fifth number of viral species that might have evolved to "generalists." Notably, Bandavirus dabieense, the pathogen of severe fever with thrombocytopenia syndrome was only detected in ticks of clade 1, and half number of clade 2-specific viruses were aquatic-animal-associated. CONCLUSIONS These findings highlight that the virome diversity is shaped by internal genetic evolution and external ecological landscape of H. longicornis and provide the new foundation for promoting the studies on virus-vector-ecology interaction and eventually for evaluating the risk of H. longicornis for transmitting the viruses to humans and animals. Video Abstract.
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Affiliation(s)
- Run-Ze Ye
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Yu-Yu Li
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Da-Li Xu
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- Shandong Provincial Key Laboratory of Communicable Disease Control and Prevention, Department of Communicable Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, Shandong, People's Republic of China
| | - Bai-Hui Wang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Xiao-Yang Wang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Ming-Zhu Zhang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Ning Wang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Wan-Ying Gao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Cheng Li
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Xiao-Yu Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Li-Feng Du
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Luo-Yuan Xia
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Ke Song
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Qing Xu
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Jing Liu
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Nuo Cheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Ze-Hui Li
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Yi-Di Du
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Hui-Jun Yu
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Xiao-Yu Shi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Yi Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
| | - Shu-Jun Ding
- Shandong Provincial Key Laboratory of Communicable Disease Control and Prevention, Department of Communicable Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, Shandong, People's Republic of China.
| | - Lin Zhao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China.
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China.
| | - Wu-Chun Cao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China.
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
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Stroeva AR, Klyukina AA, Vidishcheva ON, Poludetkina EN, Solovyeva MA, Pyrkin VO, Gavirova LA, Birkeland NK, Akhmanov GG, Bonch-Osmolovskaya EA, Merkel AY. Structure of Benthic Microbial Communities in the Northeastern Part of the Barents Sea. Microorganisms 2024; 12:387. [PMID: 38399791 PMCID: PMC10892650 DOI: 10.3390/microorganisms12020387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The Barents Sea shelf is one of the most economically promising regions in the Arctic in terms of its resources and geographic location. However, benthic microbial communities of the northeastern Barents Sea are still barely studied. Here, we present a detailed systematic description of the structures of microbial communities located in the sediments and bottom water of the northeastern Barents Sea based on 16S rRNA profiling and a qPCR assessment of the total prokaryotic abundance in 177 samples. Beta- and alpha-diversity analyses revealed a clear difference between the microbial communities of diverse sediment layers and bottom-water fractions. We identified 101 microbial taxa whose representatives had statistically reliable distribution patterns between these ecotopes. Analysis of the correlation between microbial community structure and geological data yielded a number of important results-correlations were found between the abundance of individual microbial taxa and bottom relief, thickness of marine sediments, presence of hydrotrolite interlayers, and the values of pH and Eh. We also demonstrated that a relatively high abundance of prokaryotes in sediments can be caused by the proliferation of Deltaproteobacteria representatives, in particular, sulfate and iron reducers.
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Affiliation(s)
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | | | | | | | | | | | - Nils-Kåre Birkeland
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway
| | | | - Elizaveta A. Bonch-Osmolovskaya
- Lomonosov Moscow State University, 119234 Moscow, Russia
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Alexander Y. Merkel
- Lomonosov Moscow State University, 119234 Moscow, Russia
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
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16
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Schult D, Maurer HC, Frolova M, Ringelhan M, Mayr U, Ulrich J, Heilmaier M, Rasch S, Lahmer T, Reitmeier S, Hennig C, Gassner C, Thur N, Will T, Janssen KP, Steiger K, Jesinghaus M, Neuhaus K, Quante M, Haller D, Abdelhafez M, Schmid RM, Middelhoff M. Systematic Evaluation of Clinical, Nutritional, and Fecal Microbial Factors for Their Association With Colorectal Polyps. Clin Transl Gastroenterol 2024; 15:e00660. [PMID: 38088370 PMCID: PMC10887443 DOI: 10.14309/ctg.0000000000000660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/29/2023] [Indexed: 02/25/2024] Open
Abstract
INTRODUCTION The identification of risk factors for precursor lesions of colorectal cancer (CRC) holds great promise in the context of prevention. With this study, we aimed to identify patient characteristics associated with colorectal polyps (CPs) and polyp features of potential malignant progression. Furthermore, a potential association with gut microbiota in this context was investigated. METHODS In this single-center study, a total of 162 patients with CPs and 91 control patients were included. Multiple variables including information on lifestyle, diet, serum parameters, and gut microbiota, analyzed by 16S-rRNA gene amplicon sequencing and functional imputations (Picrust2), were related to different aspects of CPs. RESULTS We observed that elevated serum alkaline phosphatase (AP) levels were significantly associated with the presence of high-grade dysplastic polyps. This association was further seen for patients with CRC. Thereby, AP correlated with other parameters of liver function. We did not observe significant changes in the gut microbiota between patients with CP and their respective controls. However, a trend toward a lower alpha-diversity was seen in patients with CRC. Interestingly, AP was identified as a possible clinical effect modifier of stool sample beta diversity. DISCUSSION We show for the first time an increased AP in premalignant CP. Furthermore, AP showed a significant influence on the microbial composition of the intestine. Relatively elevated liver enzymes, especially AP, may contribute to the detection of precancerous dysplastic or neoplastic changes in colorectal lesions. The association between elevated AP, premalignant CP, and the microbiome merits further study.
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Affiliation(s)
- David Schult
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - H. Carlo Maurer
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Marina Frolova
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Marc Ringelhan
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Ulrich Mayr
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Jörg Ulrich
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Markus Heilmaier
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Sebastian Rasch
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Tobias Lahmer
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Sandra Reitmeier
- ZIEL—Institute for Food & Health, Technische Universität München, Freising, Germany
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Chiara Hennig
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Christina Gassner
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Niklas Thur
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Theresa Will
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Katja Steiger
- Institute of Pathology, Technische Universität München, Munich, Germany
| | - Moritz Jesinghaus
- Institute of Pathology, Technische Universität München, Munich, Germany
- Institute of Pathology, University Hospital Marburg, Marburg, Germany
| | - Klaus Neuhaus
- ZIEL—Institute for Food & Health, Technische Universität München, Freising, Germany
| | - Michael Quante
- Department of Internal Medicine II, Universitätsklinikum Freiburg, Universität Freiburg, Freiburg, Germany
| | - Dirk Haller
- ZIEL—Institute for Food & Health, Technische Universität München, Freising, Germany
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Mohamed Abdelhafez
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Roland M. Schmid
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Moritz Middelhoff
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
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17
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Viehof A, Haange SB, Streidl T, Schubert K, Engelmann B, Haller D, Rolle-Kampczyk U, von Bergen M, Clavel T. The human intestinal bacterium Eggerthella lenta influences gut metabolomes in gnotobiotic mice. MICROBIOME RESEARCH REPORTS 2024; 3:14. [PMID: 38841406 PMCID: PMC11149096 DOI: 10.20517/mrr.2023.65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 06/07/2024]
Abstract
The intestinal microbiota and its metabolites are known to influence host metabolic health. However, little is known about the role of specific microbes. In this work, we used the minimal consortium Oligo-Mouse-Microbiota (OMM12) to study the function of Coriobacteriia under defined conditions in gnotobiotic mice. OMM12 mice with or without the addition of the dominant gut bacterium Eggerthella lenta (E. lenta) were fed with diets varying in fat content and primary bile acids. E. lenta stably colonised the mouse caecum at high relative abundances (median: 27.5%). This was accompanied by decreased occurrence of Akkermansia muciniphila and Enterococcus faecalis, but results did not reach statistical significance in all groups depending on diet and inter-individual differences. Changes in host parameters (anthropometry, blood glucose, and cholesterol) and liver proteomes were primarily due to diet. In contrast, metabolomes in colon content differed significantly between the colonisation groups. The presence of E. lenta was associated with elevated levels of latifolicinin C acid and decreased creatine, sarcosine, N,N-dimethylarginine, and N-Acetyl-DL-methionine. In conclusion, E. lenta altered specific metabolites in the colon but did not have significant effects on the mice or liver proteomes under the conditions tested due to marked inter-individual differences.
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Affiliation(s)
- Alina Viehof
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen 52074, Germany
| | - Sven-Bastiaan Haange
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research (UFZ), Leipzig 04318, Germany
| | - Theresa Streidl
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen 52074, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research (UFZ), Leipzig 04318, Germany
| | - Beatrice Engelmann
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research (UFZ), Leipzig 04318, Germany
| | - Dirk Haller
- ZIEL Institute for Food and Health, Technical University of Munich, Freising 85354, Germany
- Chair of Nutrition and Immunology, Technical University of Munich, Freising 85354, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research (UFZ), Leipzig 04318, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research (UFZ), Leipzig 04318, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig 04103, Germany
- Institute of Biochemistry, University of Leipzig, Leipzig 04109, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen 52074, Germany
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18
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Rønning SB, Carlsen H, Rocha SDC, Rud I, Solberg N, Høst V, Veiseth-Kent E, Arnesen H, Bergum S, Kirkhus B, Böcker U, Abedali N, Rundblad A, Bålsrud P, Måge I, Holven KB, Ulven SM, Pedersen ME. Dietary intake of micronized avian eggshell membrane in aged mice reduces circulating inflammatory markers, increases microbiota diversity, and attenuates skeletal muscle aging. Front Nutr 2024; 10:1336477. [PMID: 38288061 PMCID: PMC10822908 DOI: 10.3389/fnut.2023.1336477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 12/27/2023] [Indexed: 01/31/2024] Open
Abstract
Introduction Avian eggshell membrane (ESM) is a complex extracellular matrix comprising collagens, glycoproteins, proteoglycans, and hyaluronic acid. We have previously demonstrated that ESM possesses anti-inflammatory properties in vitro and regulates wound healing processes in vivo. The present study aimed to investigate if oral intake of micronized ESM could attenuate skeletal muscle aging associated with beneficial alterations in gut microbiota profile and reduced inflammation. Methods Elderly male C57BL/6 mice were fed an AIN93G diet supplemented with 0, 0.1, 1, or 8% ESM. Young mice were used as reference. The digestibility of ESM was investigated using the static in vitro digestion model INFOGEST for older people and adults, and the gut microbiota profile was analyzed in mice. In addition, we performed a small-scale pre-clinical human study with healthy home-dwelling elderly (>70 years) who received capsules with a placebo or 500 mg ESM every day for 4 weeks and studied the effect on circulating inflammatory markers. Results and discussion Intake of ESM in elderly mice impacted and attenuated several well-known hallmarks of aging, such as a reduction in the number of skeletal muscle fibers, the appearance of centronucleated fibers, a decrease in type IIa/IIx fiber type proportion, reduced gene expression of satellite cell markers Sdc3 and Pax7 and increased gene expression of the muscle atrophy marker Fbxo32. Similarly, a transition toward the phenotypic characteristics of young mice was observed for several proteins involved in cellular processes and metabolism. The digestibility of ESM was poor, especially for the elderly condition. Furthermore, our experiments showed that mice fed with 8% ESM had increased gut microbiota diversity and altered microbiota composition compared with the other groups. ESM in the diet also lowered the expression of the inflammation marker TNFA in mice and in vitro in THP-1 macrophages. In the human study, intake of ESM capsules significantly reduced the inflammatory marker CRP. Altogether, our results suggest that ESM, a natural extracellular biomaterial, may be attractive as a nutraceutical candidate with a possible effect on skeletal muscle aging possibly through its immunomodulating effect or gut microbiota.
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Affiliation(s)
| | - Harald Carlsen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Ida Rud
- Nofima AS, Food Division, Ås, Norway
| | | | | | | | - Henriette Arnesen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | | | | | | | - Nada Abedali
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Amanda Rundblad
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Pia Bålsrud
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | - Kirsten Bjørklund Holven
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- National Advisory Unit on Familial Hypercholesterolemia, Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
| | - Stine Marie Ulven
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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Halkjær SI, Refslund Danielsen M, de Knegt VE, Andersen LO, Stensvold CR, Nielsen HV, Mirsepasi-Lauridsen HC, Krogfelt KA, Cortes D, Petersen AM. Multi-strain probiotics during pregnancy in women with obesity influence infant gut microbiome development: results from a randomized, double-blind placebo-controlled study. Gut Microbes 2024; 16:2337968. [PMID: 38591920 PMCID: PMC11005804 DOI: 10.1080/19490976.2024.2337968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/10/2024] Open
Abstract
Probiotics have been described to influence host health and prevent the risk of obesity by gut microbiome (GM) modulation. In a randomized double-blinded placebo-controlled feasibility study, we investigated whether Vivomixx® multi-strain probiotics administered to 50 women with obesity during pregnancy altered the GM composition and perinatal health outcomes of their infants up to 9 months after birth. The mothers and infants were followed up with four visits after birth: at 3 d, and at 3, 6, and 9 months after delivery. The infants were monitored by anthropometric measurements, fecal sample analysis, and questionnaires regarding health and diet.The study setup after birth was feasible, and the women and infants were willing to participate in additional study visits and collection of fecal samples during the 9-month follow-up. In total, 47 newborns were included for microbiome analysis.Maternal prenatal Vivomixx® administration did not alter infant GM diversity nor differential abundance, and the probiotic strains were not vertically transferred. However, the infant GM exhibited a decreased prevalence of the obesity-associated genera, Collinsella, in the probiotic group and of the metabolic health-associated Akkermansia in the placebo group, indicating that indirect community-scale effects of Vivomixx® on the GM of the mothers could be transferred to the infant.Moreover, 3 d after birth, the GM of the infant was influenced by mode of delivery and antibiotics administered during birth. Vaginally delivered infants had increased diversity and relative abundance of the metabolic health-associated Bifidobacterium and Bacteroides while having a decreased relative abundance of Enterococcus compared with infants delivered by cesarean section. Maternal antibiotic administration during birth resulted in a decreased relative abundance of Bifidobacteriumin the GM of the infants. In conclusion, this study observed potential effects on obesity-associated infant GM after maternal probiotic supplementation.
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Affiliation(s)
- Sofie Ingdam Halkjær
- Gastrounit,Medical Division, Copenhagen University Hospital Amager and Hvidovre, Hvidovre, Denmark
| | | | - Victoria E. de Knegt
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Amager and Hvidovre, Hvidovre, Denmark
| | - Lee O’Brien Andersen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Henrik Vedel Nielsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Hengameh Chloé Mirsepasi-Lauridsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Karen Angeliki Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Dina Cortes
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Amager and Hvidovre, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Munk Petersen
- Gastrounit,Medical Division, Copenhagen University Hospital Amager and Hvidovre, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Microbiology, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark
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20
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Robinson CRP, Dolezal AG, Newton ILG. Host species and geography impact bee-associated RNA virus communities with evidence for isolation by distance in viral populations. ISME COMMUNICATIONS 2024; 4:ycad003. [PMID: 38304079 PMCID: PMC10833078 DOI: 10.1093/ismeco/ycad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 02/03/2024]
Abstract
Virus symbionts are important mediators of ecosystem function, yet we know little of their diversity and ecology in natural populations. The alarming decline of pollinating insects in many regions of the globe, especially the European honey bee, Apis mellifera, has been driven in part by worldwide transmission of virus pathogens. Previous work has examined the transmission of known honey bee virus pathogens to wild bee populations, but only a handful of studies have investigated the native viromes associated with wild bees, limiting epidemiological predictors associated with viral pathogenesis. Further, variation among different bee species might have important consequences in the acquisition and maintenance of bee-associated virome diversity. We utilized comparative metatranscriptomics to develop a baseline description of the RNA viromes associated with wild bee pollinators and to document viral diversity, community composition, and structure. Our sampling includes five wild-caught, native bee species that vary in social behavior as well as managed honey bees. We describe 26 putatively new RNA virus species based on RNA-dependent RNA polymerase phylogeny and show that each sampled bee species was associated with a specific virus community composition, even among sympatric populations of distinct host species. From 17 samples of a single host species, we recovered a single virus species despite over 600 km of distance between host populations and found strong evidence for isolation by distance in associated viral populations. Our work adds to the small number of studies examining viral prevalence and community composition in wild bees.
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Affiliation(s)
- Chris R P Robinson
- Department of Biology, Indiana University, Bloomington, IN 47405, United States
| | - Adam G Dolezal
- Department of Entomology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
| | - Irene L G Newton
- Department of Biology, Indiana University, Bloomington, IN 47405, United States
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21
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Lee SJ, Kim D, Ann HW, Han M, Lee JA, Lee Y, Ahn S, Seo HW, Kim JH, Ahn JY, Jeong SJ, Ku NS, Yeom JS, Ryu CM, Choi JY. DECIPHERING GUT MICROBIOTA IN PATIENTS WITH SEVERE SEPSIS AND SEPTIC SHOCK. Shock 2024; 61:28-33. [PMID: 37878472 DOI: 10.1097/shk.0000000000002241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
ABSTRACT Introduction: Gut microbiota dysbiosis is associated with susceptibility to sepsis and poor outcomes. However, changes to the intestinal microbiota during sepsis and their value as biomarkers are unclear. In this study, we compared the intestinal microbiota of patients with sepsis and healthy controls. Methods: Stool was collected from patients with sepsis (subdivided according to mortality) and controls. Microbiome diversity and composition were analyzed by 16S rRNA gene pyrosequencing. The α-diversity of the intestinal microbiome was determined using operational taxonomic unit counts and the Chao1, Shannon, and ACE indices. Adjusted Cox regression analyses assessed 6-month mortality risk factors. Results: Fifty-nine patients (14 in-hospital deaths) and 29 healthy controls were enrolled. Operational taxonomic unit counts and Chao1 and ACE indices were lower in the nonsurvivor than in the other groups. The controls showed a higher Shannon and lower Simpson index than did the sepsis group. The genus Blautia was more abundant in controls than in the sepsis group, and Faecalibacterium less abundant in the nonsurvivor than in the other groups. Regression analysis associated low Shannon index with 6-month mortality. Conclusions: Survivors of sepsis, nonsurvivors, and healthy controls have different gut microbiomes, and a low Shannon index is a risk factor for 6-month mortality.
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Affiliation(s)
| | - Dajeong Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Hea Won Ann
- Division of Infectious Diseases, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Min Han
- Division of Infectious Diseases, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Ah Lee
- Division of Infectious Diseases, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yongseop Lee
- Division of Infectious Diseases, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sangmin Ahn
- Division of Infectious Diseases, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hwi Won Seo
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Jung Ho Kim
- Division of Infectious Diseases, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jin Young Ahn
- Division of Infectious Diseases, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Su Jin Jeong
- Division of Infectious Diseases, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Nam Su Ku
- Division of Infectious Diseases, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Joon-Sup Yeom
- Division of Infectious Diseases, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Choong-Min Ryu
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Jun Yong Choi
- Division of Infectious Diseases, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
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22
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Buchenauer L, Haange SB, Bauer M, Rolle-Kampczyk UE, Wagner M, Stucke J, Elter E, Fink B, Vass M, von Bergen M, Schulz A, Zenclussen AC, Junge KM, Stangl GI, Polte T. Maternal exposure of mice to glyphosate induces depression- and anxiety-like behavior in the offspring via alterations of the gut-brain axis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167034. [PMID: 37709081 DOI: 10.1016/j.scitotenv.2023.167034] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/24/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The past decade has been characterized by increased awareness and de-stigmatization of mental health issues, in particular the most common neuropsychiatric disorders depression and anxiety. Further, with growing understanding of neurodevelopmental disorders such as attention deficit and hyperactivity disorder and autism spectrum disorder, the number of diagnosed patients has increased. The pathogenesis of these behavioral disorders is multifactorial and early-life exposure to environmental chemicals has been proposed to be a relevant risk factor that might mediate these effects by disturbances on the gut-brain-axis. However, for glyphosate, the most widely used pesticide worldwide, there are only limited and inconsistent findings that link chronic low-dose exposure in particular during early life to neurobehavioral disorders. Here, we explored the impact of maternal oral glyphosate exposure (0.5 and 50 mg/kg body weight/day) during pregnancy and the lactational period on offspring's behavior, brain gene expression and gut microbiota using a cross-generational mouse model. Behavioral analyses revealed a depression- and anxiety-like behavior as well as social deficits most notably in adult female offspring of glyphosate-exposed dams. Furthermore, the expression of tryptophan hydroxylase 2, an enzyme discussed to be linked to behavioral problems, was reduced in the hippocampus of female offspring and correlated to a glyphosate-induced DNA hypermethylation of the gene. Moreover, maternal glyphosate exposure significantly altered the gut microbiota in the female offspring including a decreased abundance of Akkermansia and increased abundance of Alistipes and Blautia, bacteria involved in tryptophan metabolism and associated with depression- and anxiety-like disorders. Our results suggest that glyphosate might influence the gut-brain axis crosstalk following in-utero and lactational exposure. This study underlines the importance of understanding the impact of exposure to pesticides on the gut-brain axis and further emphasizes the need for microbiome analyses to be compulsorily included in health risk assessments of pesticides.
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Affiliation(s)
- Lisa Buchenauer
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany; University of Leipzig, Leipzig University Medical Center, Department of Dermatology, Venerology and Allergology, Leipzig, Germany
| | - Sven-Bastiaan Haange
- Helmholtz Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany
| | - Mario Bauer
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany
| | - Ulrike E Rolle-Kampczyk
- Helmholtz Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany
| | - Marita Wagner
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany; University of Leipzig, Leipzig University Medical Center, Department of Dermatology, Venerology and Allergology, Leipzig, Germany
| | - Johanna Stucke
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany; University of Leipzig, Leipzig University Medical Center, Department of Dermatology, Venerology and Allergology, Leipzig, Germany
| | - Elena Elter
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany; University of Leipzig, Leipzig University Medical Center, Department of Dermatology, Venerology and Allergology, Leipzig, Germany
| | - Beate Fink
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany
| | - Maren Vass
- University of Leipzig, Leipzig University Medical Center, Department of Dermatology, Venerology and Allergology, Leipzig, Germany
| | - Martin von Bergen
- Helmholtz Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany; University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Angela Schulz
- University of Leipzig, Medical Faculty, Rudolf Schönheimer Institute of Biochemistry, Leipzig, Germany
| | - Ana C Zenclussen
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany; Perinatal Immunology, Saxonian Incubator for Clinical Translation (SIKT), Medical Faculty, University Leipzig, 04103 Leipzig, Germany
| | - Kristin M Junge
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany; AKAD University Stuttgart, School of Health and Social Sciences, Stuttgart, Germany
| | - Gabriele I Stangl
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Tobias Polte
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany; University of Leipzig, Leipzig University Medical Center, Department of Dermatology, Venerology and Allergology, Leipzig, Germany.
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23
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Hülpüsch C, Rauer L, Nussbaumer T, Schwierzeck V, Bhattacharyya M, Erhart V, Traidl-Hoffmann C, Reiger M, Neumann AU. Benchmarking MicrobIEM - a user-friendly tool for decontamination of microbiome sequencing data. BMC Biol 2023; 21:269. [PMID: 37996810 PMCID: PMC10666409 DOI: 10.1186/s12915-023-01737-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 10/16/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Microbiome analysis is becoming a standard component in many scientific studies, but also requires extensive quality control of the 16S rRNA gene sequencing data prior to analysis. In particular, when investigating low-biomass microbial environments such as human skin, contaminants distort the true microbiome sample composition and need to be removed bioinformatically. We introduce MicrobIEM, a novel tool to bioinformatically remove contaminants using negative controls. RESULTS We benchmarked MicrobIEM against five established decontamination approaches in four 16S rRNA amplicon sequencing datasets: three serially diluted mock communities (108-103 cells, 0.4-80% contamination) with even or staggered taxon compositions and a skin microbiome dataset. Results depended strongly on user-selected algorithm parameters. Overall, sample-based algorithms separated mock and contaminant sequences best in the even mock, whereas control-based algorithms performed better in the two staggered mocks, particularly in low-biomass samples (≤ 106 cells). We show that a correct decontamination benchmarking requires realistic staggered mock communities and unbiased evaluation measures such as Youden's index. In the skin dataset, the Decontam prevalence filter and MicrobIEM's ratio filter effectively reduced common contaminants while keeping skin-associated genera. CONCLUSIONS MicrobIEM's ratio filter for decontamination performs better or as good as established bioinformatic decontamination tools. In contrast to established tools, MicrobIEM additionally provides interactive plots and supports selecting appropriate filtering parameters via a user-friendly graphical user interface. Therefore, MicrobIEM is the first quality control tool for microbiome experts without coding experience.
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Affiliation(s)
- Claudia Hülpüsch
- Environmental Medicine, Faculty of Medicine, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany
- Chair of Environmental Medicine, Technical University of Munich, Munich, Germany
- CK CARE, Christine Kühne Center for Allergy Research and Education, Davos, Switzerland
| | - Luise Rauer
- Environmental Medicine, Faculty of Medicine, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany
- Chair of Environmental Medicine, Technical University of Munich, Munich, Germany
- Institute of Environmental Medicine, Helmholtz Munich, Augsburg, Germany
| | - Thomas Nussbaumer
- Institute of Environmental Medicine, Helmholtz Munich, Augsburg, Germany
| | - Vera Schwierzeck
- Institute of Environmental Medicine, Helmholtz Munich, Augsburg, Germany
- Institute of Hygiene, University Hospital Muenster, Muenster, Germany
| | - Madhumita Bhattacharyya
- Environmental Medicine, Faculty of Medicine, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany
- Chair of Environmental Medicine, Technical University of Munich, Munich, Germany
| | - Veronika Erhart
- Environmental Medicine, Faculty of Medicine, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany
| | - Claudia Traidl-Hoffmann
- Environmental Medicine, Faculty of Medicine, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany
- Chair of Environmental Medicine, Technical University of Munich, Munich, Germany
- CK CARE, Christine Kühne Center for Allergy Research and Education, Davos, Switzerland
- Institute of Environmental Medicine, Helmholtz Munich, Augsburg, Germany
- ZIEL - Institute for Food & Health, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Matthias Reiger
- Environmental Medicine, Faculty of Medicine, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany
- Chair of Environmental Medicine, Technical University of Munich, Munich, Germany
- Institute of Environmental Medicine, Helmholtz Munich, Augsburg, Germany
| | - Avidan U Neumann
- Environmental Medicine, Faculty of Medicine, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany.
- Institute of Environmental Medicine, Helmholtz Munich, Augsburg, Germany.
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24
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Trinh S, Keller L, Herpertz-Dahlmann B, Seitz J. [Fecal Microbiota Transplants in the Context of (Child and Adolescent) Psychiatric Disorders]. ZEITSCHRIFT FUR KINDER- UND JUGENDPSYCHIATRIE UND PSYCHOTHERAPIE 2023; 51:431-440. [PMID: 36892328 DOI: 10.1024/1422-4917/a000928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Fecal Microbiota Transplants in the Context of (Child and Adolescent) Psychiatric Disorders Abstract: There has recently been a significant increase in interest in gut microbiota and its interaction with the brain (gut-brain axis). Not only are the findings of microbiome research interesting for basic scientists, they also offer relevant insights for clinical practice. A causal relationship between gut microbiome and various somatic diseases such as diabetes mellitus, inflammatory bowel diseases, and obesity as well as psychiatric diseases such as major depression, anxiety disorders, and eating disorders seems plausible. To study the causal relationship of intestinal bacteria with individual phenotypes, researchers apply so-called stool transplantations (fecal microbiota transplantations) in the preclinical context. For this purpose, they transfer microbiota samples from patients into laboratory animals to observe possible changes in phenotype. In the clinical context, fecal microbiota transplantation is already being used with therapeutic intentions for selected diseases, for example, recurrent infections with Clostridioides difficile or inflammatory bowel diseases; they have already become part of the official clinical guidelines for C. difficile. For many other diseases, however, including mental illnesses, the potential of using fecal transplantations for therapeutic purposes is still being explored. Previous findings suggest that the intestinal microbiome, particularly fecal microbiota transplantations, represent a promising starting point for new therapeutic approaches.
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Affiliation(s)
- Stefanie Trinh
- Institut für Neuroanatomie, Uniklinik RWTH Aachen, Deutschland
| | - Lara Keller
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Uniklinik RWTH Aachen, Deutschland
| | - Beate Herpertz-Dahlmann
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Uniklinik RWTH Aachen, Deutschland
| | - Jochen Seitz
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Uniklinik RWTH Aachen, Deutschland
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25
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Joachim L, Göttert S, Sax A, Steiger K, Neuhaus K, Heinrich P, Fan K, Orberg ET, Kleigrewe K, Ruland J, Bassermann F, Herr W, Posch C, Heidegger S, Poeck H. The microbial metabolite desaminotyrosine enhances T-cell priming and cancer immunotherapy with immune checkpoint inhibitors. EBioMedicine 2023; 97:104834. [PMID: 37865045 PMCID: PMC10597767 DOI: 10.1016/j.ebiom.2023.104834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/23/2023] Open
Abstract
BACKGROUND Inter-individual differences in response to immune checkpoint inhibitors (ICI) remain a major challenge in cancer treatment. The composition of the gut microbiome has been associated with differential ICI outcome, but the underlying molecular mechanisms remain unclear, and therapeutic modulation challenging. METHODS We established an in vivo model to treat C57Bl/6j mice with the type-I interferon (IFN-I)-modulating, bacterial-derived metabolite desaminotyrosine (DAT) to improve ICI therapy. Broad spectrum antibiotics were used to mimic gut microbial dysbiosis and associated ICI resistance. We utilized genetic mouse models to address the role of host IFN-I in DAT-modulated antitumour immunity. Changes in gut microbiota were assessed using 16S-rRNA sequencing analyses. FINDINGS We found that oral supplementation of mice with the microbial metabolite DAT delays tumour growth and promotes ICI immunotherapy with anti-CTLA-4 or anti-PD-1. DAT-enhanced antitumour immunity was associated with more activated T cells and natural killer cells in the tumour microenvironment and was dependent on host IFN-I signalling. Consistent with this, DAT potently enhanced expansion of antigen-specific T cells following vaccination with an IFN-I-inducing adjuvant. DAT supplementation in mice compensated for the negative effects of broad-spectrum antibiotic-induced dysbiosis on anti-CTLA-4-mediated antitumour immunity. Oral administration of DAT altered the gut microbial composition in mice with increased abundance of bacterial taxa that are associated with beneficial response to ICI immunotherapy. INTERPRETATION We introduce the therapeutic use of an IFN-I-modulating bacterial-derived metabolite to overcome resistance to ICI. This approach is a promising strategy particularly for patients with a history of broad-spectrum antibiotic use and associated loss of gut microbial diversity. FUNDING Melanoma Research Alliance, Deutsche Forschungsgemeinschaft, German Cancer Aid, Wilhelm Sander Foundation, Novartis Foundation.
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Affiliation(s)
- Laura Joachim
- Department of Medicine III, School of Medicine, Technical University of Munich, Munich, Germany; Centre for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Sascha Göttert
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Anna Sax
- Department of Medicine III, School of Medicine, Technical University of Munich, Munich, Germany; Centre for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Katja Steiger
- Institute of Pathology, School of Medicine, Technical University of Munich, Munich, Germany; German Cancer Consortium (DKTK), Partner-site Munich and German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Paul Heinrich
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany; Leibniz Institute for Immunotherapy (LIT), Regensburg, Germany
| | - Kaiji Fan
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Erik Thiele Orberg
- Department of Medicine III, School of Medicine, Technical University of Munich, Munich, Germany; Centre for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany; German Cancer Consortium (DKTK), Partner-site Munich and German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Karin Kleigrewe
- Bavarian Centre for Biomolecular Mass Spectrometry, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Jürgen Ruland
- Centre for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany; German Cancer Consortium (DKTK), Partner-site Munich and German Cancer Research Centre (DKFZ), Heidelberg, Germany; Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Florian Bassermann
- Department of Medicine III, School of Medicine, Technical University of Munich, Munich, Germany; Centre for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany; German Cancer Consortium (DKTK), Partner-site Munich and German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Wolfgang Herr
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Christian Posch
- Department of Dermatology and Allergy, School of Medicine, Technical University of Munich, Munich, Germany; Faculty of Medicine, Sigmund Freud University Vienna, Vienna, Austria
| | - Simon Heidegger
- Department of Medicine III, School of Medicine, Technical University of Munich, Munich, Germany; Centre for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.
| | - Hendrik Poeck
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany; Leibniz Institute for Immunotherapy (LIT), Regensburg, Germany; Centre for Immunomedicine in Transplantation and Oncology (CITO), Regensburg, Germany; Bavarian Cancer Research Centre (BZKF), Regensburg, Germany.
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26
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Kister B, Viehof A, Rolle-Kampczyk U, Schwentker A, Treichel NS, Jennings SA, Wirtz TH, Blank LM, Hornef MW, von Bergen M, Clavel T, Kuepfer L. A physiologically based model of bile acid metabolism in mice. iScience 2023; 26:107922. [PMID: 37817939 PMCID: PMC10561051 DOI: 10.1016/j.isci.2023.107922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/04/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
Bile acid (BA) metabolism is a complex system that includes a wide variety of primary and secondary, as well as conjugated and unconjugated BAs that undergo continuous enterohepatic circulation (EHC). Alterations in both composition and dynamics of BAs have been associated with various diseases. However, a mechanistic understanding of the relationship between altered BA metabolism and related diseases is lacking. Computational modeling may support functional analyses of the physiological processes involved in the EHC of BAs along the gut-liver axis. In this study, we developed a physiologically based model of murine BA metabolism describing synthesis, hepatic and microbial transformations, systemic distribution, excretion, and EHC of BAs at the whole-body level. For model development, BA metabolism of specific pathogen-free (SPF) mice was characterized in vivo by measuring BA levels and composition in various organs, expression of transporters along the gut, and cecal microbiota composition. We found significantly different BA levels between male and female mice that could only be explained by adjusted expression of the hepatic enzymes and transporters in the model. Of note, this finding was in agreement with experimental observations. The model for SPF mice could also describe equivalent experimental data in germ-free mice by specifically switching off microbial activity in the intestine. The here presented model can therefore facilitate and guide functional analyses of BA metabolism in mice, e.g., the effect of pathophysiological alterations on BA metabolism and translation of results from mouse studies to a clinically relevant context through cross-species extrapolation.
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Affiliation(s)
- Bastian Kister
- Institute for Systems Medicine with Focus on Organ Interaction, University Hospital RWTH Aachen, Aachen, Germany
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Alina Viehof
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Annika Schwentker
- Institute of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Nicole Simone Treichel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Susan A.V. Jennings
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Theresa H. Wirtz
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Lars M. Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Mathias W. Hornef
- Institute of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Leipzig, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Lars Kuepfer
- Institute for Systems Medicine with Focus on Organ Interaction, University Hospital RWTH Aachen, Aachen, Germany
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27
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Rigas D, Grivas N, Nelli A, Gouva E, Skoufos I, Kormas K, Tzora A, Lagkouvardos I. Persistent Dysbiosis, Parasite Rise and Growth Impairment in Aquacultured European Seabass after Oxytetracycline Treatment. Microorganisms 2023; 11:2302. [PMID: 37764146 PMCID: PMC10534334 DOI: 10.3390/microorganisms11092302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
The use of antibiotics in open-water aquaculture is often unavoidable when faced with pathogens with high mortality rates. In addition, seasonal pathogen surges have become more common and more intense over the years. Apart from the apparent cost of antibiotic treatment, it has been observed that, in aquaculture practice, the surviving fish often display measurable growth impairment. To understand the role of gut microbiota on the observed growth impairment, in this study, we follow the incidence of Photobacterium damselae subsp. piscicida in a seabass commercial open-water aquaculture setting in Galaxidi (Greece). Fish around 10 months of age were fed with feed containing oxytetracycline (120 mg/kg/day) for twelve days, followed by a twelve-day withdrawal period, and another eighteen days of treatment. The fish were sampled 19 days before the start of the first treatment and one month after the end of the second treatment cycle. Sequencing of the 16S rRNA gene was used to measure changes in the gut microbiome. Overall, the gut microbiota community, even a month after treatment, was highly dysbiotic and characterized by very low alpha diversity. High abundances of alkalophilic bacteria in the post-antibiotic-treated fish indicated a rise in pH that was coupled with a significant increase in gut parasites. This study's results indicate that oxytetracycline (OTC) treatment causes persistent dysbiosis even one month after withdrawal and provides a more suitable environment for an increase in parasites. These findings highlight the need for interventions to restore a healthy and protective gut microbiome.
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Affiliation(s)
| | - Nikos Grivas
- Galaxidi Marine Farm S.A., 33200 Galaxidi, Greece
| | - Aikaterini Nelli
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, School of Agriculture, University of Ioannina, 47100 Arta, Greece
| | - Evangelia Gouva
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, School of Agriculture, University of Ioannina, 47100 Arta, Greece
| | - Ioannis Skoufos
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, School of Agriculture, University of Ioannina, 47100 Arta, Greece
| | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, 38446 Volos, Greece
- Agricultural Development Institute, University Research and Innovation Centre "IASON", Argonafton & Filellinon, 38221 Volos, Greece
| | - Athina Tzora
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, School of Agriculture, University of Ioannina, 47100 Arta, Greece
| | - Ilias Lagkouvardos
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, School of Agriculture, University of Ioannina, 47100 Arta, Greece
- Department of Microbiology and Microbial Pathogenesis, School of Medicine, University of Crete, 71500 Heraklion, Greece
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Gorgulho J, Roderburg C, Beier F, Bokemeyer C, Brümmendorf TH, Luedde T, Loosen SH. Peripheral blood CD3+HLADR+ cells and associated gut microbiome species predict response and overall survival to immune checkpoint blockade. Front Immunol 2023; 14:1206953. [PMID: 37705980 PMCID: PMC10495594 DOI: 10.3389/fimmu.2023.1206953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 08/02/2023] [Indexed: 09/15/2023] Open
Abstract
Background The search for biomarkers to identify ideal candidates for immune checkpoint inhibitor (ICI) therapy is fundamental. In this study, we analyze peripheral blood CD3+HLADR+ cells (activated T-cells) as a novel biomarker for ICI therapy and how its association to certain gut microbiome species can indicate individual treatment outcomes. Methods Flow cytometry analysis of peripheral mononuclear blood cells (PBMCs) was performed on n=70 patients undergoing ICI therapy for solid malignancies to quantify HLA-DR on circulating CD3+ cells. 16s-rRNA sequencing of stool samples was performed on n=37 patients to assess relative abundance of gut microbiota. Results Patients with a higher frequency of CD3+HLADR+ cells before treatment initiation showed a significantly reduced tumor response and overall survival (OS), a worst response and experienced less toxicities to ICI therapy. As such, patients with a frequency of CD3+HLADR+ cells above an ideal cut-off value of 18.55% had a median OS of only 132 days compared to 569 days for patients below. Patients with increasing CD3+HLADR+ cell counts during therapy had a significantly improved OS. An immune signature score comprising CD3+HLADR+ cells and the neutrophil-lymphocyte ratio (NLR) was highly significant for predicting OS before and during therapy. When allied to the relative abundance of microbiota from the Burkholderiales order and the species Bacteroides vulgatus, two immune-microbial scores revealed a promising predictive and prognostic power. Conclusion We identify the frequencies and dynamics of CD3+HLADR+ cells as an easily accessible prognostic marker to predict outcome to ICIs, and how these could be associated with immune modulating microbiome species. Two unprecedented immune-microbial scores comprising CD3+HLADR+, NLR and relative abundance of gut bacteria from the Burkhorderiales order or Bacteroides vulgatus species could accurately predict OS to immune checkpoint blockade.
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Affiliation(s)
- Joao Gorgulho
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section of Pneumology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Roderburg
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIOABCD), Aachen, Germany
| | - Fabian Beier
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIOABCD), Aachen, Germany
- Department of Medicine IV, University Hospital Rheinisch Westfällisch Technische Hochschule (RWTH) Aachen, Aachen, Germany
| | - Carsten Bokemeyer
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section of Pneumology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Tim H. Brümmendorf
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIOABCD), Aachen, Germany
- Department of Medicine IV, University Hospital Rheinisch Westfällisch Technische Hochschule (RWTH) Aachen, Aachen, Germany
| | - Tom Luedde
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIOABCD), Aachen, Germany
| | - Sven H. Loosen
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIOABCD), Aachen, Germany
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Arnesen H, Markussen T, Birchenough G, Birkeland S, Nyström EEL, Hansson GC, Carlsen H, Boysen P. Microbial experience through housing in a farmyard-type environment alters intestinal barrier properties in mouse colons. Sci Rep 2023; 13:13701. [PMID: 37607995 PMCID: PMC10444815 DOI: 10.1038/s41598-023-40640-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/14/2023] [Indexed: 08/24/2023] Open
Abstract
To close the gap between ultra-hygienic research mouse models and the much more environmentally exposed conditions of humans, we have established a system where laboratory mice are raised under a full set of environmental factors present in a naturalistic, farmyard-type habitat-a process we have called feralization. In previous studies we have shown that feralized (Fer) mice were protected against colorectal cancer when compared to conventionally reared laboratory mice (Lab). However, the protective mechanisms remain to be elucidated. Disruption of the protective intestinal barrier is an acknowledged player in colorectal carcinogenesis, and in the current study we assessed colonic mucosal barrier properties in healthy, feralized C57BL/6JRj male mice. While we found no effect of feralization on mucus layer properties, higher expression of genes encoding the mucus components Fcgbp and Clca1 still suggested mucus enforcement due to feralization. Genes encoding other proteins known to be involved in bacterial defense (Itln1, Ang1, Retnlb) and inflammatory mechanisms (Zbp1, Gsdmc2) were also higher expressed in feralized mice, further suggesting that the Fer mice have an altered intestinal mucosal barrier. These findings demonstrate that microbial experience conferred by housing in a farmyard-type environment alters the intestinal barrier properties in mice possibly leading to a more robust protection against disease. Future studies to unravel regulatory roles of feralization on intestinal barrier should aim to conduct proteomic analyses and in vivo performance of the feralized mice intestinal barrier.
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Affiliation(s)
- Henriette Arnesen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Turhan Markussen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - George Birchenough
- Mucin Biology Group, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Signe Birkeland
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Elisabeth E L Nyström
- Mucin Biology Group, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Gunnar C Hansson
- Mucin Biology Group, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Harald Carlsen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Preben Boysen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway.
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Amar Y, Rogner D, Silva RL, Foesel BU, Ud-Dean M, Lagkouvardos I, Steimle-Grauer SA, Niedermeier S, Kublik S, Jargosch M, Heinig M, Thomas J, Eyerich S, Wikström JD, Schloter M, Eyerich K, Biedermann T, Köberle M. Darier's disease exhibits a unique cutaneous microbial dysbiosis associated with inflammation and body malodour. MICROBIOME 2023; 11:162. [PMID: 37496039 PMCID: PMC10369845 DOI: 10.1186/s40168-023-01587-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/01/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Darier's disease (DD) is a genodermatosis caused by mutations of the ATP2A2 gene leading to disrupted keratinocyte adhesion. Recurrent episodes of skin inflammation and infections with a typical malodour in DD indicate a role for microbial dysbiosis. Here, for the first time, we investigated the DD skin microbiome using a metabarcoding approach of 115 skin swabs from 14 patients and 14 healthy volunteers. Furthermore, we analyzed its changes in the context of DD malodour and the cutaneous DD transcriptome. RESULTS We identified a disease-specific cutaneous microbiome with a loss of microbial diversity and of potentially beneficial commensals. Expansion of inflammation-associated microbes such as Staphylococcus aureus and Staphylococcus warneri strongly correlated with disease severity. DD dysbiosis was further characterized by abundant species belonging to Corynebacteria, Staphylococci and Streptococci groups displaying strong associations with malodour intensity. Transcriptome analyses showed marked upregulation of epidermal repair, inflammatory and immune defence pathways reflecting epithelial and immune response mechanisms to DD dysbiotic microbiome. In contrast, barrier genes including claudin-4 and cadherin-4 were downregulated. CONCLUSIONS These findings allow a better understanding of Darier exacerbations, highlighting the role of cutaneous dysbiosis in DD inflammation and associated malodour. Our data also suggest potential biomarkers and targets of intervention for DD. Video Abstract.
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Affiliation(s)
- Yacine Amar
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Danielle Rogner
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Rafaela L Silva
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Bärbel U Foesel
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Deutsches Forschungszentrum Für Gesundheit Und Umwelt (GmbH), 85764, Neuherberg, Germany
| | - Minhaz Ud-Dean
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Ilias Lagkouvardos
- Core Facility Microbiome, Technical University of Munich, 85354, Freising, Germany
| | - Susanne A Steimle-Grauer
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Sebastian Niedermeier
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Deutsches Forschungszentrum Für Gesundheit Und Umwelt (GmbH), 85764, Neuherberg, Germany
| | - Manja Jargosch
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Jenny Thomas
- Center of Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Zentrum München, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Stefanie Eyerich
- Center of Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Zentrum München, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Jakob D Wikström
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Dermato-Venereology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Deutsches Forschungszentrum Für Gesundheit Und Umwelt (GmbH), 85764, Neuherberg, Germany
| | - Kilian Eyerich
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Dermatology and Venereology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Tilo Biedermann
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany.
| | - Martin Köberle
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
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Zavarzina DG, Merkel AY, Klyukina AA, Elizarov IM, Pikhtereva VA, Rusakov VS, Chistyakova NI, Ziganshin RH, Maslov AA, Gavrilov SN. Iron or sulfur respiration-an adaptive choice determining the fitness of a natronophilic bacterium Dethiobacter alkaliphilus in geochemically contrasting environments. Front Microbiol 2023; 14:1108245. [PMID: 37520367 PMCID: PMC10376724 DOI: 10.3389/fmicb.2023.1108245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Haloalkaliphilic microorganisms are double extremophiles functioning optimally at high salinity and pH. Their typical habitats are soda lakes, geologically ancient yet widespread ecosystems supposed to harbor relict microbial communities. We compared metabolic features and their determinants in two strains of the natronophilic species Dethiobacter alkaliphilus, the only cultured representative of the class "Dethiobacteria" (Bacillota). The strains of D. alkaliphilus were previously isolated from geographically remote Mongolian and Kenyan soda lakes. The type strain AHT1T was described as a facultative chemolithoautotrophic sulfidogen reducing or disproportionating sulfur or thiosulfate, while strain Z-1002 was isolated as a chemolithoautotrophic iron reducer. Here, we uncovered the iron reducing ability of strain AHT1T and the ability of strain Z-1002 for thiosulfate reduction and anaerobic Fe(II) oxidation. Key catabolic processes sustaining the growth of both D. alkaliphilus strains appeared to fit the geochemical settings of two contrasting natural alkaline environments, sulfur-enriched soda lakes and iron-enriched serpentinites. This hypothesis was supported by a meta-analysis of Dethiobacterial genomes and by the enrichment of a novel phylotype from a subsurface alkaline aquifer under Fe(III)-reducing conditions. Genome analysis revealed multiheme c-type cytochromes to be the most probable determinants of iron and sulfur redox transformations in D. alkaliphilus. Phylogeny reconstruction showed that all the respiratory processes in this organism are likely provided by evolutionarily related early forms of unconventional octaheme tetrathionate and sulfite reductases and their structural analogs, OmhA/OcwA Fe(III)-reductases. Several phylogenetically related determinants of anaerobic Fe(II) oxidation were identified in the Z-1002 genome, and the oxidation process was experimentally demonstrated. Proteomic profiling revealed two distinct sets of multiheme cytochromes upregulated in iron(III)- or thiosulfate-respiring cells and the cytochromes peculiar for Fe(II) oxidizing cells. We suggest that maintaining high variation in multiheme cytochromes is an effective adaptive strategy to occupy geochemically contrasting alkaline environments. We propose that sulfur-enriched soda lakes could be secondary habitats for D. alkaliphilus compared to Fe-rich serpentinites, and that the ongoing evolution of Dethiobacterales could retrace the evolutionary path that may have occurred in prokaryotes at a turning point in the biosphere's history, when the intensification of the sulfur cycle outweighed the global significance of the iron cycle.
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Affiliation(s)
- Daria G. Zavarzina
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Yu Merkel
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ivan M. Elizarov
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Valeria A. Pikhtereva
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Maslov
- Faculty of Geology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey N. Gavrilov
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Gu F, Larsen N, Pascale N, Petersen SA, Khakimov B, Respondek F, Jespersen L. Age-related effects on the modulation of gut microbiota by pectins and their derivatives: an in vitro study. Front Microbiol 2023; 14:1207837. [PMID: 37476669 PMCID: PMC10354267 DOI: 10.3389/fmicb.2023.1207837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/13/2023] [Indexed: 07/22/2023] Open
Abstract
Introduction The present study investigates whether supplementation with pectin-type polysaccharides has potential to improve aging-associated dysbiosis of the gut microbiota. The influence of different types of pectins on the gut microbiota composition and short-chain fatty acids (SCFAs) profiles of elderly was compared to younger adults. Methods Pectins studied included a pectin polysaccharide (PEC), a partially hydrolyzed pectin (PPH), and a pectin oligosaccharide (POS). Additionally, inulin was used as a reference prebiotic substrate. Individual fecal samples were collected from healthy elderly volunteers (70-75 years) and younger adults (30-35 years). In vitro fermentations were performed using the CoMiniGut model with controlled temperature and pH. Samples were withdrawn at baseline and after 24 h fermentation for measurement of SCFAs production and microbiota composition by 16S rRNA gene sequencing. Results and Discussion The results showed that fermentations with PEC and PPH resulted in a specific stimulation of Faecalibacterium prausnitzii regardless of the age groups. Collinsella aerofaciens became a dominating species in the young adult group with fermentations of all three pectins, which was not observed in the elderly group. No significant differences in SCFAs production were found among the pectins, indicating a high level of functional redundancy. Pectins boosted various bacterial groups differently from the reference prebiotic substrate (inulin). We also found inulin had reduced butyrogenic and bifidogenic effects in the elderly group compared to the younger adult group. In conclusion, the in vitro modulating effects of pectins on elderly gut microbiota showed potential of using pectins to improve age-related dysbiosis.
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Affiliation(s)
- Fangjie Gu
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
- CP Kelco ApS, Lille Skensved, Denmark
| | - Nadja Larsen
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Bekzod Khakimov
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | | | - Lene Jespersen
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
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Skoufos I, Nelli A, Venardou B, Lagkouvardos I, Giannenas I, Magklaras G, Zacharis C, Jin L, Wang J, Gouva E, Skoufos S, Bonos E, Tzora A. Use of an Innovative Silage of Agro-Industrial Waste By-Products in Pig Nutrition: A Pilot Study of Its Effects on the Pig Gastrointestinal Microbiota. Microorganisms 2023; 11:1723. [PMID: 37512895 PMCID: PMC10384456 DOI: 10.3390/microorganisms11071723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
The aim of this study was to evaluate whether dietary supplementation with an innovative silage (IS) created using 60% olive mill waste, 20% grape pomace, and 20% deproteinised feta cheese waste solids can modulate the composition of the intestinal microbiota in weaned (Exp. 1) and finishing (Exp. 2) pigs. In Exp. 1 (40 day supplementation), forty-five crossbred weaned pigs were randomly assigned to the 0% (Control), 5%, or 10% IS groups (15 replicates/experimental diet). In Exp. 2 (60 day supplementation), eighteen finishing pigs from Exp. 1 were fed the control diet for 8 weeks before being re-assigned to their original experimental groups and fed with the 0% (Control), 5%, or 10% IS diets (six replicates/experimental diet). Performance parameters were recorded. Ileal and caecal digesta and mucosa were collected at the end of each experiment for microbiota analysis using 16S rRNA gene sequencing (five pigs/experimental diet for Exp. 1 and six pigs/experimental diet for Exp. 2). No significant effects on pig growth parameters were observed in both experiments. In Exp. 1, 5% IS supplementation increased the relative abundance of the Prevotellaceae family, Coprococcus genus, and Alloprevotella rava (OTU_48) and reduced the relative abundance of Lactobacillus genus in the caecum compared to the control and/or 10% IS diets (p < 0.05). In Exp. 2, 5% IS supplementation led to compositionally more diverse and different ileal and caecal microbiota compared to the control group (p < 0.05; p = 0.066 for β-diversity in ileum). Supplementation with the 5% IS increased the relative abundance of Clostridium celatum/disporicum/saudiense (OTU_3) in the ileum and caecum and Bifidobacterium pseudolongum (OTU_17) in the caecum and reduced the relative abundance of Streptococcus gallolyticus/alactolyticus (OTU_2) in the caecum compared to the control diet (p < 0.05). Similar effects on C. celatum/disporicum/saudiense and S. gallolyticus/alactolyticus were observed with the 10% IS diet in the caecum (p < 0.05). IS has the potential to beneficially alter the composition of the gastrointestinal microbiota in pigs.
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Affiliation(s)
- Ioannis Skoufos
- Laboratory of Animal Science, Nutrition and Biotechnology, Department of Agriculture, School of Agriculture, University of Ioannina, Kostakioi Artas, 47100 Arta, Greece
| | - Aikaterini Nelli
- Laboratory of Animal Health, Hygiene and Food Quality, Department of Agriculture, School of Agriculture, University of Ioannina, Kostakioi Artas, 47100 Arta, Greece
| | - Brigkita Venardou
- Laboratory of Animal Health, Hygiene and Food Quality, Department of Agriculture, School of Agriculture, University of Ioannina, Kostakioi Artas, 47100 Arta, Greece
| | - Ilias Lagkouvardos
- Laboratory of Animal Health, Hygiene and Food Quality, Department of Agriculture, School of Agriculture, University of Ioannina, Kostakioi Artas, 47100 Arta, Greece
| | - Ilias Giannenas
- Laboratory of Nutrition, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Georgios Magklaras
- Laboratory of Animal Science, Nutrition and Biotechnology, Department of Agriculture, School of Agriculture, University of Ioannina, Kostakioi Artas, 47100 Arta, Greece
| | - Christos Zacharis
- Laboratory of Animal Science, Nutrition and Biotechnology, Department of Agriculture, School of Agriculture, University of Ioannina, Kostakioi Artas, 47100 Arta, Greece
| | - Lizhi Jin
- Meritech (Asia Pacific) Biotech Pte Ltd., Singapore 079903, Singapore
| | - Jin Wang
- National Center for International Research on Animal Gut Nutrition, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Evangelia Gouva
- Laboratory of Animal Health, Hygiene and Food Quality, Department of Agriculture, School of Agriculture, University of Ioannina, Kostakioi Artas, 47100 Arta, Greece
| | - Stylianos Skoufos
- Laboratory of Animal Health, Hygiene and Food Quality, Department of Agriculture, School of Agriculture, University of Ioannina, Kostakioi Artas, 47100 Arta, Greece
| | - Eleftherios Bonos
- Laboratory of Animal Science, Nutrition and Biotechnology, Department of Agriculture, School of Agriculture, University of Ioannina, Kostakioi Artas, 47100 Arta, Greece
| | - Athina Tzora
- Laboratory of Animal Health, Hygiene and Food Quality, Department of Agriculture, School of Agriculture, University of Ioannina, Kostakioi Artas, 47100 Arta, Greece
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Angstmann H, Pfeiffer S, Kublik S, Ehrhardt B, Uliczka K, Rabe KF, Roeder T, Wagner C, Schloter M, Krauss-Etschmann S. The microbial composition of larval airways from Drosophila melanogaster differ between specimens from laboratory and natural habitats. ENVIRONMENTAL MICROBIOME 2023; 18:55. [PMID: 37370177 DOI: 10.1186/s40793-023-00506-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/19/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND The fruit fly Drosophila melanogaster lives in natural habitats and has also long been used as a model organism in biological research. In this study, we used a molecular barcoding approach to analyse the airways microbiome of larvae of D. melanogaster, which were obtained from eggs of flies of the laboratory strain w1118 and from immune deficient flies (NF-kB-K), and from wild-caught flies. To assess intergenerational transmission of microbes, all eggs were incubated under the same semi-sterile conditions. RESULTS The airway microbiome of larvae from both lab-strains was dominated by the two families Acetobacteraceae and Lactobacillaceae, while larvae from wild-caught flies were dominated by Lactobacillaceae, Anaplasmataceae and Leuconostocaceae. Barcodes linked to Anaplasmataceae could be further assigned to Wolbachia sp., which is a widespread intracellular pathogen in arthropods. For Leuconostoceae, the most abundant reads were assigned to Weissella sp. Both Wolbachia and Weissella affect the development of the insects. Finally, a relative high abundance of Serratia sp. was found in larvae from immune deficient relish-/- compared to w1118 and wild-caught fly airways. CONCLUSIONS Our results show for the first time that larvae from D. melanogaster harbor an airway microbiome, which is of low complexity and strongly influenced by the environmental conditions and to a lesser extent by the immune status. Furthermore, our data indicate an intergenerational transmission of the microbiome as shaped by the environment.
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Affiliation(s)
- Hanna Angstmann
- Division of Experimental Asthma Research, Early Life Origins of Chronic Lung Disease, Research Center Borstel, German Center for Lung Research (DZL), Airway Research Center North (ARCN), Leibniz Lung Center, Borstel, Germany
| | - Stefan Pfeiffer
- ZIEL - Institute for Food and Health, Technical University of Munich, Freising, Germany
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Birte Ehrhardt
- Division of Experimental Asthma Research, Early Life Origins of Chronic Lung Disease, Research Center Borstel, German Center for Lung Research (DZL), Airway Research Center North (ARCN), Leibniz Lung Center, Borstel, Germany
| | - Karin Uliczka
- Division of Experimental Asthma Research, Early Life Origins of Chronic Lung Disease, Research Center Borstel, German Center for Lung Research (DZL), Airway Research Center North (ARCN), Leibniz Lung Center, Borstel, Germany
| | - Klaus F Rabe
- Department of Pneumology, Lungen Clinic, Grosshansdorf, Germany
- Department of Medicine, Christian Albrechts University, Germany Member of the German Center for Lung Research, Kiel, Germany
| | - Thomas Roeder
- Division of Molecular Physiology, Institute of Zoology, Christian-Albrechts University, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Kiel, Germany
| | - Christina Wagner
- Division of Experimental Asthma Research, Early Life Origins of Chronic Lung Disease, Research Center Borstel, German Center for Lung Research (DZL), Airway Research Center North (ARCN), Leibniz Lung Center, Borstel, Germany
| | - Michael Schloter
- ZIEL - Institute for Food and Health, Technical University of Munich, Freising, Germany
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Susanne Krauss-Etschmann
- Division of Experimental Asthma Research, Early Life Origins of Chronic Lung Disease, Research Center Borstel, German Center for Lung Research (DZL), Airway Research Center North (ARCN), Leibniz Lung Center, Borstel, Germany.
- Department of Medicine, Institute for Experimental Medicine, Christian Albrechts University, Kiel, Germany.
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Trinh S, Kogel V, Kneisel L, Müller-Limberger E, Herpertz-Dahlmann B, Beyer C, Seitz J. Gut Microbiota and Brain Alterations after Refeeding in a Translational Anorexia Nervosa Rat Model. Int J Mol Sci 2023; 24:ijms24119496. [PMID: 37298445 DOI: 10.3390/ijms24119496] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023] Open
Abstract
The gut microbiota composition is causally involved in the regulation of body weight. Through the gut-brain axis, microbiota play a role in psychiatric disorders including anorexia nervosa (AN). Previously, we showed microbiome changes to be associated with brain volume and astrocyte reductions after chronic starvation in an AN animal model. Here, we analyzed whether these alterations are reversible after refeeding. The activity-based anorexia (ABA) model is a well-established animal model that mimics several symptoms of AN. Fecal samples and the brain were analyzed. Like previous results, significant alterations in the microbiome were observed after starvation. After refeeding, including the normalization of food intake and body weight, α- and β-diversity, as well as the relative abundance of specific genera, were largely normalized in starved rats. Brain parameters appeared to normalize alongside microbial restitution with some aberrations in the white matter. We confirmed our previous findings of microbial dysbiosis during starvation and showed a high degree of reversibility. Thus, microbiome alterations in the ABA model appear to be mostly starvation-related. These findings support the usefulness of the ABA model in investigating starvation-induced effects on the microbiota-gut-brain axis to help comprehend the pathomechanisms of AN and potentially develop microbiome-targeted treatments for patients.
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Affiliation(s)
- Stefanie Trinh
- Institute of Neuroanatomy, RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | - Vanessa Kogel
- Institute of Neuroanatomy, RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | - Lilly Kneisel
- Institute of Neuroanatomy, RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | | | - Beate Herpertz-Dahlmann
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, RWTH Aachen University, Neuenhofer Weg 21, 52074 Aachen, Germany
| | - Cordian Beyer
- Institute of Neuroanatomy, RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | - Jochen Seitz
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, RWTH Aachen University, Neuenhofer Weg 21, 52074 Aachen, Germany
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Endika MF, Barnett DJM, Klostermann CE, Schols HA, Arts ICW, Penders J, Nauta A, Smidt H, Venema K. Microbiota-dependent influence of prebiotics on the resilience of infant gut microbiota to amoxicillin/clavulanate perturbation in an in vitro colon model. Front Microbiol 2023; 14:1131953. [PMID: 37275167 PMCID: PMC10232780 DOI: 10.3389/fmicb.2023.1131953] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 04/21/2023] [Indexed: 06/07/2023] Open
Abstract
Antibiotic exposure disturbs the developing infant gut microbiota. The capacity of the gut microbiota to recover from this disturbance (resilience) depends on the type of antibiotic. In this study, infant gut microbiota was exposed to a combination of amoxicillin and clavulanate (amoxicillin/clavulanate) in an in vitro colon model (TIM-2) with fecal-derived microbiota from 1-month-old (1-M; a mixed-taxa community type) as well as 3-month-old (3-M; Bifidobacterium dominated community type) breastfed infants. We investigated the effect of two common infant prebiotics, 2'-fucosyllactose (2'-FL) or galacto-oligosaccharides (GOS), on the resilience of infant gut microbiota to amoxicillin/clavulanate-induced changes in microbiota composition and activity. Amoxicillin/clavulanate treatment decreased alpha diversity and induced a temporary shift of microbiota to a community dominated by enterobacteria. Moreover, antibiotic treatment increased succinate and lactate in both 1- and 3-M colon models, while decreasing the production of short-chain (SCFA) and branched-chain fatty acids (BFCA). The prebiotic effect on the microbiota recovery depended on the fermenting capacity of antibiotic-exposed microbiota. In the 1-M colon model, the supplementation of 2'-FL supported the recovery of microbiota and restored the production of propionate and butyrate. In the 3-M colon model, GOS supplementation supported the recovery of microbiota and increased the production of acetate and butyrate.
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Affiliation(s)
- Martha F. Endika
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - David J. M. Barnett
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
- Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Cynthia E. Klostermann
- Biobased Chemistry and Technology, Wageningen University and Research, Wageningen, Netherlands
| | - Henk A. Schols
- Laboratory of Food Chemistry, Wageningen University and Research, Wageningen, Netherlands
| | - Ilja C. W. Arts
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
| | - John Penders
- Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, Netherlands
| | | | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Koen Venema
- Centre for Healthy Eating and Food Innovation (HEFI), Maastricht University—Campus Venlo, Venlo, Netherlands
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Rötzer V, Wenderlein J, Wiesinger A, Versen F, Rauch E, Straubinger RK, Zeiler E. Bovine Udder Health: From Standard Diagnostic Methods to New Approaches-A Practical Investigation of Various Udder Health Parameters in Combination with 16S rRNA Sequencing. Microorganisms 2023; 11:1311. [PMID: 37317285 DOI: 10.3390/microorganisms11051311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
Bovine udder health is an important factor for animal wellbeing and the dairy farm economy. Thus, researchers aim to understand factors causing mastitis. The gold standard for diagnosing mastitis in cows is the conventional culturing of milk samples. However, during the last few years, the use of molecular methods has increased. These methods, especially sequencing, provide a deeper insight into the diversity of the bacterial community. Yet, inconsistent results regarding the mammary microbiome have been published. This study aimed to evaluate the udder health of eight dairy cows at seven days postpartum with the standard methods in veterinary practice. Additionally, swabs from the teat canal and milk samples were analyzed using 16S rRNA gene amplicon sequencing. The sensitive low-biomass milk samples displayed only a few contaminations even though they were sampled in a field environment. In healthy udders, no bacterial communities were detected by the bacterial culture nor the 16S rRNA gene amplicons. The results from the standard examination of the cows, the cell count, and the bacteriological examination were comparable with the results from 16S rRNA gene amplicon sequencing when cows displayed subclinical or latent mastitis. Besides the pathogen detected in bacterial culturing, a second bacterial strain with low but significant abundance was detected by sequencing, which might aid in the understanding of mastitis incidence. In general, molecular biological approaches might lead to promising insights into pathological events in the udder and might help to understand the pathomechanism and infection source via epidemiological analyses.
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Affiliation(s)
- Verena Rötzer
- Faculty of Sustainable Agriculture and Energy Systems, University of Applied Science Weihenstephan-Triesdorf, 85354 Freising, Germany
- Chair of Animal Welfare, Ethology, Animal Hygiene and Animal Husbandry, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Jasmin Wenderlein
- Chair of Bacteriology and Mycology, Institute for Infectious Diseases and Zoonoses, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Anna Wiesinger
- Chair of Bacteriology and Mycology, Institute for Infectious Diseases and Zoonoses, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Felix Versen
- Faculty of Sustainable Agriculture and Energy Systems, University of Applied Science Weihenstephan-Triesdorf, 85354 Freising, Germany
| | - Elke Rauch
- Chair of Animal Welfare, Ethology, Animal Hygiene and Animal Husbandry, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Reinhard K Straubinger
- Chair of Bacteriology and Mycology, Institute for Infectious Diseases and Zoonoses, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Eva Zeiler
- Faculty of Sustainable Agriculture and Energy Systems, University of Applied Science Weihenstephan-Triesdorf, 85354 Freising, Germany
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Oosterlinck B, Ceuleers H, Arras W, De Man JG, Geboes K, De Schepper H, Peeters M, Lebeer S, Skieceviciene J, Hold GL, Kupcinskas J, Link A, De Winter BY, Smet A. Mucin-microbiome signatures shape the tumor microenvironment in gastric cancer. MICROBIOME 2023; 11:86. [PMID: 37085819 PMCID: PMC10120190 DOI: 10.1186/s40168-023-01534-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS We aimed to identify mucin-microbiome signatures shaping the tumor microenvironment in gastric adenocarcinomas and clinical outcomes. METHODS We performed high-throughput profiling of the mucin phenotypes present in 108 gastric adenocarcinomas and 20 functional dyspepsia cases using validated mucin-based RT-qPCRs with subsequent immunohistochemistry validation and correlated the data with clinical outcome parameters. The gastric microbiota was assessed by 16S rRNA gene sequencing, taxonomy, and community composition determined, microbial networks analyzed, and the metagenome inferred in association with mucin phenotypes and expression. RESULTS Gastric adenocarcinomas with an intestinal mucin environment or high-level MUC13 expression are associated with poor survival. On the contrary, gastric MUC5AC or MUC6 abundance was associated with a more favorable outcome. The oral taxa Neisseria, Prevotella, and Veillonella had centralities in tumors with intestinal and mixed phenotypes and were associated with MUC13 overexpression, highlighting their role as potential drivers in MUC13 signaling in GC. Furthermore, dense bacterial networks were observed in intestinal and mixed mucin phenotype tumors whereas the lowest community complexity was shown in null mucin phenotype tumors due to higher Helicobacter abundance resulting in a more decreased diversity. Enrichment of oral or intestinal microbes was mucin phenotype dependent. More specifically, intestinal mucin phenotype tumors favored the establishment of pro-inflammatory oral taxa forming strong co-occurrence networks. CONCLUSIONS Our results emphasize key roles for mucins in gastric cancer prognosis and shaping microbial networks in the tumor microenvironment. Specifically, the enriched oral taxa associated with aberrant MUC13 expression can be potential biomarkers in predicting disease outcomes. Video Abstract.
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Affiliation(s)
- Baptiste Oosterlinck
- Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Wilrijk, Belgium
- Infla-Med Research Consortium of Excellence, University of Antwerp, Antwerp, Belgium
| | - Hannah Ceuleers
- Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Wilrijk, Belgium
- Infla-Med Research Consortium of Excellence, University of Antwerp, Antwerp, Belgium
| | - Wout Arras
- Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Wilrijk, Belgium
- Infla-Med Research Consortium of Excellence, University of Antwerp, Antwerp, Belgium
| | - Joris G De Man
- Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Wilrijk, Belgium
- Infla-Med Research Consortium of Excellence, University of Antwerp, Antwerp, Belgium
| | - Karen Geboes
- Pathology Department, Gent University Hospital, Ghent, Belgium
| | - Heiko De Schepper
- Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Wilrijk, Belgium
- Infla-Med Research Consortium of Excellence, University of Antwerp, Antwerp, Belgium
- Division of Gastroenterology and Hepatology, Antwerp University Hospital, Edegem, Belgium
| | - Marc Peeters
- Department of Oncology, Antwerp University Hospital, Edegem, Belgium
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Jurgita Skieceviciene
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Georgina L Hold
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Juozas Kupcinskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-Von-Guericke University, Magdeburg, Germany
| | - Benedicte Y De Winter
- Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Wilrijk, Belgium
- Infla-Med Research Consortium of Excellence, University of Antwerp, Antwerp, Belgium
- Division of Gastroenterology and Hepatology, Antwerp University Hospital, Edegem, Belgium
| | - Annemieke Smet
- Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Wilrijk, Belgium.
- Infla-Med Research Consortium of Excellence, University of Antwerp, Antwerp, Belgium.
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Metwaly A, Jovic J, Waldschmitt N, Khaloian S, Heimes H, Häcker D, Ahmed M, Hammoudi N, Le Bourhis L, Mayorgas A, Siebert K, Basic M, Schwerd T, Allez M, Panes J, Salas A, Bleich A, Zeissig S, Schnupf P, Cominelli F, Haller D. Diet prevents the expansion of segmented filamentous bacteria and ileo-colonic inflammation in a model of Crohn's disease. MICROBIOME 2023; 11:66. [PMID: 37004103 PMCID: PMC10064692 DOI: 10.1186/s40168-023-01508-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 02/25/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Crohn's disease (CD) is associated with changes in the microbiota, and murine models of CD-like ileo-colonic inflammation depend on the presence of microbial triggers. Increased abundance of unknown Clostridiales and the microscopic detection of filamentous structures close to the epithelium of Tnf ΔARE mice, a mouse model of CD-like ileitis pointed towards segmented filamentous bacteria (SFB), a commensal mucosal adherent bacterium involved in ileal inflammation. RESULTS We show that the abundance of SFB strongly correlates with the severity of CD-like ileal inflammation in two mouse models of ileal inflammation, including Tnf ΔARE and SAMP/Yit mice. SFB mono-colonization of germ-free Tnf ΔARE mice confirmed the causal link and resulted in severe ileo-colonic inflammation, characterized by elevated tissue levels of Tnf and Il-17A, neutrophil infiltration and loss of Paneth and goblet cell function. Co-colonization of SFB in human-microbiota associated Tnf ΔARE mice confirmed that SFB presence is indispensable for disease development. Screening of 468 ileal and colonic mucosal biopsies from adult and pediatric IBD patients, using previously published and newly designed human SFB-specific primer sets, showed no presence of SFB in human tissue samples, suggesting a species-specific functionality of the pathobiont. Simulating the human relevant therapeutic effect of exclusive enteral nutrition (EEN), EEN-like purified diet antagonized SFB colonization and prevented disease development in Tnf ΔARE mice, providing functional evidence for the protective mechanism of diet in modulating microbiota-dependent inflammation in IBD. CONCLUSIONS We identified a novel pathogenic role of SFB in driving severe CD-like ileo-colonic inflammation characterized by loss of Paneth and goblet cell functions in Tnf ΔARE mice. A purified diet antagonized SFB colonization and prevented disease development in Tnf ΔARE mice in contrast to a fiber-containing chow diet, clearly demonstrating the important role of diet in modulating a novel IBD-relevant pathobiont and supporting a direct link between diet and microbial communities in mediating protective functions. Video Abstract.
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Affiliation(s)
- Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Jelena Jovic
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Nadine Waldschmitt
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Sevana Khaloian
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Helena Heimes
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Deborah Häcker
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Mohamed Ahmed
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Nassim Hammoudi
- APHP, Hôpital Saint Louis, Department of Gastroenterology, INSERM UMRS 1160, Paris Diderot, Sorbonne Paris-Cité University, Paris, France
- Université Paris Cité, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
| | - Lionel Le Bourhis
- Université Paris Cité, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
| | - Aida Mayorgas
- Department of Experimental Pathology, Instituto de Investigaciones Biomédicas de Barcelona CSIC, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Kolja Siebert
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Marijana Basic
- Hannover Medical School, Institute for Laboratory Animal Science, Hannover, Germany
| | - Tobias Schwerd
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Matthieu Allez
- APHP, Hôpital Saint Louis, Department of Gastroenterology, INSERM UMRS 1160, Paris Diderot, Sorbonne Paris-Cité University, Paris, France
- Université Paris Cité, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
| | - Julian Panes
- Department of Experimental Pathology, Instituto de Investigaciones Biomédicas de Barcelona CSIC, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Azucena Salas
- Department of Experimental Pathology, Instituto de Investigaciones Biomédicas de Barcelona CSIC, IDIBAPS, CIBERehd, Barcelona, Spain
| | - André Bleich
- Hannover Medical School, Institute for Laboratory Animal Science, Hannover, Germany
| | - Sebastian Zeissig
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Pamela Schnupf
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Fabio Cominelli
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany.
- ZIEL-Institute for Food and Health, Technical University of Munich, Freising, Germany.
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Corinthian Currants Supplementation Restores Serum Polar Phenolic Compounds, Reduces IL-1beta, and Exerts Beneficial Effects on Gut Microbiota in the Streptozotocin-Induced Type-1 Diabetic Rat. Metabolites 2023; 13:metabo13030415. [PMID: 36984855 PMCID: PMC10051135 DOI: 10.3390/metabo13030415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
The present study aimed at investigating the possible benefits of a dietary intervention with Corinthian currants, a rich source of phenolic compounds, on type 1 diabetes (T1D) using the animal model of the streptozotocin-(STZ)-induced diabetic rat. Male Wistar rats were randomly assigned into four groups: control animals, which received a control diet (CD) or a diet supplemented with 10% w/w Corinthian currants (CCD), and diabetic animals, which received a control diet (DCD) or a currant diet (DCCD) for 4 weeks. Plasma biochemical parameters, insulin, polar phenolic compounds, and inflammatory factors were determined. Microbiota populations in tissue and intestinal fluid of the caecum, as well as fecal microbiota populations and short-chain fatty acids (SCFAs), were measured. Fecal microbiota was further analyzed by 16S rRNA sequencing. The results of the study showed that a Corinthian currant-supplemented diet restored serum polar phenolic compounds and decreased interleukin-1b (IL-1b) (p < 0.05) both in control and diabetic animals. Increased caecal lactobacilli counts (p < 0.05) and maintenance of enterococci levels within normal range were observed in the intestinal fluid of the DCCD group (p < 0.05 compared to DCD). Higher acetic acid levels were detected in the feces of diabetic rats that received the currant diet compared to the animals that received the control diet (p < 0.05). Corinthian currant could serve as a beneficial dietary component in the condition of T1D based on the results coming from the animal model of the STZ-induced T1D rat.
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Lin S, Xu X, Holck J, Wittrup Agger J, Wilkens C, Xie Z, Khakimov B, Nielsen DS, Meyer AS. Soluble, Diferuloylated Corn Bran Glucuronoarabinoxylans Modulate the Human Gut Microbiota In Vitro. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3885-3897. [PMID: 36787634 DOI: 10.1021/acs.jafc.2c08338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Corn bran is exceptionally rich in substituted glucuronoarabinoxylan polysaccharides, which are monoferuloylated and cross-linked by diferulic acid moieties. Here, we assessed the potential prebiotic activity of three enzymatically solubilized corn bran glucuronoarabinoxylans: medium feruloylated (FGAX-M), laccase cross-linked FGAX-M (FGAX-H), and alkali-treated FGAX-M devoid of feruloyl substitutions (FGAX-B). We examined the influence of these soluble FGAX samples on the gut microbiome composition and functionality during in vitro simulated colon fermentations, determined by 16S rRNA gene amplicon sequencing and assessment of short-chain fatty acid (SCFAs) production. All FGAX samples induced changes in the relative composition of the microbiota and the SCFA levels after 24 h of in vitro fermentation. The changes induced by FGAX-M and FGAX-H tended to be more profound and more similar to the changes induced by inulin than changes conferred by FGAX-B. The microbiota changes induced by FGAX-M and FGAX-H correlated with an increase in the relative abundance of Anaerostipes and with increased butyric acid production, while the changes induced by the FGAX-B sample were less compelling. The results imply that solubilized, substituted diferuloylated corn bran glucuronoarabinoxylans may be potential prebiotic candidates and that both single feruloylations and diferuloyl cross-links influence the prebiotic potential of these arabinoxylan compounds.
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Affiliation(s)
- Shang Lin
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, DK-2800 Kongens Lyngby, Denmark
| | - Xinming Xu
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, DK-2800 Kongens Lyngby, Denmark
| | - Jesper Holck
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, DK-2800 Kongens Lyngby, Denmark
| | - Jane Wittrup Agger
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, DK-2800 Kongens Lyngby, Denmark
| | - Casper Wilkens
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, DK-2800 Kongens Lyngby, Denmark
| | - Zhuqing Xie
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Bekzod Khakimov
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Anne S Meyer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, DK-2800 Kongens Lyngby, Denmark
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Li C, Liu S, Zhou H, Zhu W, Cui M, Li J, Wang J, Liu J, Zhu J, Li W, Bi Y, Carr MJ, Holmes EC, Shi W. Metatranscriptomic Sequencing Reveals Host Species as an Important Factor Shaping the Mosquito Virome. Microbiol Spectr 2023; 11:e0465522. [PMID: 36786616 PMCID: PMC10101097 DOI: 10.1128/spectrum.04655-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/18/2023] [Indexed: 02/15/2023] Open
Abstract
Mosquitoes are important vector hosts for numerous viral pathogens and harbor a large number of mosquito-specific viruses as well as human-infecting viruses. Previous studies have mainly focused on the discovery of mosquito viruses, and our understanding of major ecological factors associated with virome structure in mosquitoes remains limited. We utilized metatranscriptomic sequencing to characterize the viromes of five mosquito species sampled across eight locations in Yunnan Province, China. This revealed the presence of 52 viral species, of which 19 were novel, belonging to 15 viral families/clades. Of particular note was Culex hepacivirus 1, clustering within the avian clade of hepaciviruses. Notably, both the viromic diversity and abundance of Aedes genus mosquitoes were significantly higher than those of the Culex genus, while Aedes albopictus mosquitoes harbored a higher diversity than Aedes aegypti mosquitoes. Our findings thus point to discernible differences in viromic structure between mosquito genera and even between mosquito species within the same genus. Importantly, such differences were not attributable to differences in sampling between geographical location. Our study also revealed the ubiquitous presence of the endosymbiont bacterium Wolbachia, with the genetic diversity and abundance also varying between mosquito species. In conclusion, our results suggested that the mosquito host species play an important role in shaping the virome's structure. IMPORTANCE This study revealed the huge capability of mosquitoes in harboring a rich diversity of RNA viruses, although relevant studies have characterized the intensively unparalleled diversity of RNA viruses previously. Furthermore, our findings showed discernible differences not only in viromic structure between mosquito genera and even between mosquito species within the same genus but also in the genetic diversity and abundance of Wolbachia between different mosquito populations. These findings emphasize the importance of host genetic background in shaping the virome composition of mosquitoes.
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Affiliation(s)
- Cixiu Li
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Shuqi Liu
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Hong Zhou
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Wei Zhu
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Mingxue Cui
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Juan Li
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Jiao Wang
- Mengla County Center for Disease Control and Prevention, Mengla, China
| | - Jiangyun Liu
- Mengla County Center for Disease Control and Prevention, Mengla, China
| | - Jin Zhu
- Xishuangbanna Prefecture Center for Disease Control and Prevention, Jinghong, China
| | - Weiping Li
- Xishuangbanna Prefecture Center for Disease Control and Prevention, Jinghong, China
| | - Yuhai Bi
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Michael J. Carr
- National Virus Reference Laboratory, School of Medicine, University College Dublin, Dublin, Ireland
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Weifeng Shi
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
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Le-Trilling VTK, Ebel JF, Baier F, Wohlgemuth K, Pfeifer KR, Mookhoek A, Krebs P, Determann M, Katschinski B, Adamczyk A, Lange E, Klopfleisch R, Lange CM, Sokolova V, Trilling M, Westendorf AM. Acute cytomegalovirus infection modulates the intestinal microbiota and targets intestinal epithelial cells. Eur J Immunol 2023; 53:e2249940. [PMID: 36250419 DOI: 10.1002/eji.202249940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/29/2022] [Accepted: 10/14/2022] [Indexed: 02/04/2023]
Abstract
Primary and recurrent cytomegalovirus (CMV) infections frequently cause CMV colitis in immunocompromised as well as inflammatory bowel disease (IBD) patients. Additionally, colitis occasionally occurs upon primary CMV infection in patients who are apparently immunocompetent. In both cases, the underlying pathophysiologic mechanisms are largely elusive - in part due to the lack of adequate access to specimens. We employed the mouse cytomegalovirus (MCMV) model to assess the association between CMV and colitis. During acute primary MCMV infection of immunocompetent mice, the gut microbial composition was affected as manifested by an altered ratio of the Firmicutes to Bacteroidetes phyla. Interestingly, these microbial changes coincided with high-titer MCMV replication in the colon, crypt hyperplasia, increased colonic pro-inflammatory cytokine levels, and a transient increase in the expression of the antimicrobial protein Regenerating islet-derived protein 3 gamma (Reg3γ). Further analyses revealed that murine and human intestinal epithelial cell lines, as well as primary intestinal crypt cells and organoids represent direct targets of CMV infection causing increased cell death. Accordingly, in vivo MCMV infection disrupted the intestinal epithelial barrier and increased apoptosis of intestinal epithelial cells. In summary, our data show that CMV transiently induces colitis in immunocompetent hosts by altering the intestinal homeostasis.
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Affiliation(s)
| | - Jana-Fabienne Ebel
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Franziska Baier
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kerstin Wohlgemuth
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kai Robin Pfeifer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Aart Mookhoek
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Philippe Krebs
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Madita Determann
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Benjamin Katschinski
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Alexandra Adamczyk
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Erik Lange
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Robert Klopfleisch
- Institute of Veterinary Pathology, Free University of Berlin, Berlin, Germany
| | - Christian M Lange
- Department of Gastroenterology and Hepatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Viktoriya Sokolova
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany
| | - Mirko Trilling
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Astrid M Westendorf
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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Early life gut microbiota profiles linked to synbiotic formula effects: a randomized clinical trial in European infants. Am J Clin Nutr 2023; 117:326-339. [PMID: 36811568 DOI: 10.1016/j.ajcnut.2022.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 11/05/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Microbial colonization of the gastrointestinal tract after birth is an essential event that influences infant health with life-long consequences. Therefore, it is important to investigate strategies to positively modulate colonization in early life. OBJECTIVES This randomized, controlled intervention study included 540 infants to investigate the effects of a synbiotic intervention formula (IF) containing Limosilactobacillus fermentum CECT5716 and galacto-oligosaccharides on the fecal microbiome. METHODS The fecal microbiota from infants was analyzed by 16S rRNA amplicon sequencing at 4, 12, and 24 months of age. Metabolites (e.g., short-chain fatty acids) and other milieu parameters (e.g., pH, humidity, and IgA) were also measured in stool samples. RESULTS Microbiota profiles changed with age, with major differences in diversity and composition. Significant effects of the synbiotic IF compared with control formula (CF) were visible at month 4, including higher occurrence of Bifidobacterium spp. and Lactobacillaceae and lower occurrence of Blautia spp., as well as Ruminoccocus gnavus and relatives. This was accompanied by lower fecal pH and concentrations of butyrate. After de novo clustering at 4 months of age, overall phylogenetic profiles of the infants receiving IF were closer to reference profiles of those fed with human milk than infants fed CF. The changes owing to IF were associated with fecal microbiota states characterized by lower occurrence of Bacteroides compared with higher levels of Firmicutes (valid name Bacillota), Proteobacteria (valid name Pseudomonadota), and Bifidobacterium at 4 months of age. These microbiota states were linked to higher prevalence of infants born by Cesarean section. CONCLUSIONS The synbiotic intervention influenced fecal microbiota and milieu parameters at an early age depending on the overall microbiota profiles of the infants, sharing a few similarities with breastfed infants. This trial was registered at clinicaltrials.gov as NCT02221687.
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Sauter D, Steuer A, Wasmund K, Hausmann B, Szewzyk U, Sperlich A, Gnirss R, Cooper M, Wintgens T. Microbial communities and processes in biofilters for post-treatment of ozonated wastewater treatment plant effluent. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159265. [PMID: 36206900 DOI: 10.1016/j.scitotenv.2022.159265] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/30/2022] [Accepted: 10/02/2022] [Indexed: 06/16/2023]
Abstract
Ozonation is an established solution for organic micropollutant (OMP) abatement in tertiary wastewater treatment. Biofiltration is the most common process for the biological post-treatment step, which is generally required to remove undesired oxidation products from the reaction of ozone with water matrix compounds. This study comparatively investigates the effect of filter media on the removal of organic contaminants and on biofilm properties for biologically activated carbon (BAC) and anthracite biofilters. Biofilms were analysed in two pilot-scale filters that have been operated for >50,000 bed volumes as post-treatment for ozonated wastewater treatment plant effluent. In parallel, the removal performance of bulk organics and OMP, including differentiation of adsorption and biotransformation through sodium azide inhibition, were carried out in bench-scale filter columns filled with material from the pilot filters. The use of BAC instead of anthracite resulted in an improved removal of organic bulk parameters, dissolved oxygen, and OMP. The OMP removal observed in the BAC filter but not in the anthracite filter was based on adsorption for most of the investigated compounds. For valsartan, however, biotransformation was found to be the dominant pathway, indicating that conditions for biotransformation of certain OMP are better on BAC than on anthracite. Adenosine triphosphate analyses in the media-attached biofilms of the pilot filters showed that biomass concentrations in the BAC filter were significantly higher than in the anthracite filter. The microbial communities (16S rRNA gene sequencing) appeared to be similar with respect to the types of organisms occurring on both filter materials. Alpha diversity also exhibited little variation between filter media. Beta diversity analysis, however, revealed that filter media and bed depth substantially influenced the biofilm composition. In practice, the impact of filter media on biofilm properties and biotransformation processes should be considered for the design of biofilters.
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Affiliation(s)
- Daniel Sauter
- Berliner Wasserbetriebe, Neue Juedenstr. 1, 10179 Berlin, Germany
| | - Andrea Steuer
- Chair of Environmental Microbiology, Institute of Environmental Technology, Technische Universität Berlin, Ernst-Reuter-Platz 1, 10587 Berlin, Germany
| | - Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University Vienna, Djerassiplatz 1, A-1030 Vienna, Austria; School of Biological Science, University of Portsmouth, King Henry Building, King Henry I St, PO12DY Portsmouth, UK
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Ulrich Szewzyk
- Chair of Environmental Microbiology, Institute of Environmental Technology, Technische Universität Berlin, Ernst-Reuter-Platz 1, 10587 Berlin, Germany
| | | | - Regina Gnirss
- Berliner Wasserbetriebe, Neue Juedenstr. 1, 10179 Berlin, Germany
| | - Myriel Cooper
- Chair of Environmental Microbiology, Institute of Environmental Technology, Technische Universität Berlin, Ernst-Reuter-Platz 1, 10587 Berlin, Germany
| | - Thomas Wintgens
- RWTH Aachen University, Institut für Siedlungswasserwirtschaft, Mies-van-der-Rohe-Str. 1, 52074 Aachen, Germany; School of Life Sciences, Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland, Hofackerstrasse 40, 4132 Muttenz, Switzerland.
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The Development of the Bacterial Community of Brown Trout ( Salmo trutta) during Ontogeny. Microorganisms 2023; 11:microorganisms11010211. [PMID: 36677503 PMCID: PMC9863972 DOI: 10.3390/microorganisms11010211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish's bacterial community (BC) and thus increase embryo mortality. Yet, knowledge of the physiological BC during ontogeny in general is scarce. In this project, the BC of brown trout has been investigated in a period from unfertilized egg to 95 days post fertilization (dpf) using 16S rRNA gene amplicon sequencing. Developmental changes differed between early and late ontogeny and major differences in BC occurred especially during early developmental stages. Thus, analysis was conducted separately for 0 to 67 dpf and from 67 to 95 dpf. All analyzed stages were sampled in toto to avoid bias due to different sampling methods in different developmental stages. The most abundant phylum in the BC of all developmental stages was Pseudomonadota, while only two families (Comamonadaceae and Moraxellaceae) occurred in all developmental stages. The early developmental stages until 67 dpf displayed greater shifts in their BC regarding bacterial richness, microbial diversity, and taxonomic composition. Thereafter, in the fry stages, the BC seemed to stabilize and changes were moderate. In future studies, a reduction in the sampling time frames during early development, an increase in sampling numbers, and an attempt for biological reproduction in order to characterize the causes of these variations is recommended.
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Li N, Li C, Hu T, Li J, Zhou H, Ji J, Wu J, Kang W, Holmes EC, Shi W, Xu S. Nationwide genomic surveillance reveals the prevalence and evolution of honeybee viruses in China. MICROBIOME 2023; 11:6. [PMID: 36631833 PMCID: PMC9832778 DOI: 10.1186/s40168-022-01446-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/08/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND The economic and environmental value of honeybees has been severely challenged in recent years by the collapse of their colonies worldwide, often caused by outbreaks of infectious diseases. However, our understanding of the diversity, prevalence, and transmission of honeybee viruses is largely obscure due to a lack of large-scale and longitudinal genomic surveillance on a global scale. RESULTS We report the meta-transcriptomic sequencing of nearly 2000 samples of the two most important economic and widely maintained honeybee species, as well as an associated ectoparasite mite, collected across China during 2016-2019. We document the natural diversity and evolution of honeybee viruses in China, providing evidence that multiple viruses commonly co-circulate within individual bee colonies. We also expanded the genomic data for 12 important honeybee viruses and revealed novel genetic variants and lineages associated with China. We identified more than 23 novel viruses from the honeybee and mite viromes, with some exhibiting ongoing replication in their respective hosts. Together, these data provide additional support to the idea that mites are an important reservoir and spill-over host for honeybee viruses. CONCLUSIONS Our data show that honeybee viruses are more widespread, prevalent, and genetically diverse than previously realized. The information provided is important in mitigating viral infectious diseases in honeybees, in turn helping to maintain sustainable productive agriculture on a global scale. Video Abstract.
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Affiliation(s)
- Nannan Li
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Cixiu Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Tao Hu
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Juan Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Hong Zhou
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Jingkai Ji
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Jiangli Wu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Weipeng Kang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Edward C Holmes
- Sydeny Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Weifeng Shi
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China.
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China.
| | - Shufa Xu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Wiesinger A, Wenderlein J, Ulrich S, Hiereth S, Chitimia-Dobler L, Straubinger RK. Revealing the Tick Microbiome: Insights into Midgut and Salivary Gland Microbiota of Female Ixodes ricinus Ticks. Int J Mol Sci 2023; 24:ijms24021100. [PMID: 36674613 PMCID: PMC9864629 DOI: 10.3390/ijms24021100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/09/2023] Open
Abstract
The ectoparasite Ixodes ricinus is an important vector for many tick-borne diseases (TBD) in the northern hemisphere, such as Lyme borreliosis, rickettsiosis, human granulocytic anaplasmosis, or tick-borne encephalitis virus. As climate change will lead to rising temperatures in the next years, we expect an increase in tick activity, tick population, and thus in the spread of TBD. Consequently, it has never been more critical to understand relationships within the microbial communities in ticks that might contribute to the tick's fitness and the occurrence of TBD. Therefore, we analyzed the microbiota in different tick tissues such as midgut, salivary glands, and residual tick material, as well as the microbiota in complete Ixodes ricinus ticks using 16S rRNA gene amplicon sequencing. By using a newly developed DNA extraction protocol for tick tissue samples and a self-designed mock community, we were able to detect endosymbionts and pathogens that have been described in the literature previously. Further, this study displayed the usefulness of including a mock community during bioinformatic analysis to identify essential bacteria within the tick.
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Affiliation(s)
- Anna Wiesinger
- Chair of Bacteriology and Mycology, Institute for Infectious Diseases and Zoonosis, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Jasmin Wenderlein
- Chair of Bacteriology and Mycology, Institute for Infectious Diseases and Zoonosis, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Sebastian Ulrich
- Chair of Bacteriology and Mycology, Institute for Infectious Diseases and Zoonosis, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Stephanie Hiereth
- Chair of Bacteriology and Mycology, Institute for Infectious Diseases and Zoonosis, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Lidia Chitimia-Dobler
- Bundeswehr Institute of Microbiology (InstMikroBioBw), Neuherbergstraße 11, 80937 Munich, Germany
| | - Reinhard K. Straubinger
- Chair of Bacteriology and Mycology, Institute for Infectious Diseases and Zoonosis, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
- Correspondence:
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Nelli A, Venardou B, Skoufos I, Voidarou C(C, Lagkouvardos I, Tzora A. An Insight into Goat Cheese: The Tales of Artisanal and Industrial Gidotyri Microbiota. Microorganisms 2023; 11:microorganisms11010123. [PMID: 36677415 PMCID: PMC9863150 DOI: 10.3390/microorganisms11010123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
The purpose of this study was to determine for the first time the microbiota in artisanal-type and industrial-type Gidotyri cheeses and investigate the influence of the cheese-making practices on their composition using culture-independent techniques. The microbiota present in artisanal with commercial starters (Artisanal_CS, n = 15), artisanal with in-house starters (Artisanal_IHS, n = 10) and industrial (Ind., n = 9) Gidotyri cheese samples were analyzed using a targeted metagenomic approach (16S rRNA gene). The Ind. Gidotyri cheese microbiota were less complex, dominated by the Streptococcaceae family (91%) that was more abundant compared to the artisanal Gidotyri cheeses (p < 0.05). Artisanal cheeses were more diverse compositionally with specific bacterial species being prevalent to each subtype. Particularly, Loigolactobacillus coryniformis (OTU 175), Secundilactobacillus malefermentans (OTU 48), and Streptococcus parauberis (OTU 50) were more prevalent in Artisanal_IHS cheeses compared to Artisanal_CS (p ≤ 0.001) and Ind. (p < 0.01) Gidotyri cheeses. Carnobacterium maltaromaticum (OTU 23) and Enterobacter hormaechei subsp. hoffmannii (OTU 268) were more prevalent in Artisanal_CS cheeses compared to Artisanal_IHS cheeses (p < 0.05) and Ind. cheeses (p < 0.05). Hafnia alvei (OTU 13) and Acinetobacter colistiniresistens (OTU 111) tended to be more prevalent in Artisanal_CS compared to the other two cheese groups (p < 0.10). In conclusion, higher microbial diversity was observed in the artisanal-type Gidotyri cheeses, with possible bacterial markers specific to each subtype identified with potential application to traceability of the manufacturing processes’ authenticity and cheese quality.
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50
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Carbohydrate Sources Influence the Microbiota and Flavour Profile of a Lupine-Based Moromi Fermentation. Foods 2023; 12:foods12010197. [PMID: 36613413 PMCID: PMC9818829 DOI: 10.3390/foods12010197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 01/03/2023] Open
Abstract
Lupine-based seasoning sauce is produced similarly to soy sauces and therefore generates a comparable microbiota and aroma profile. While the koji state is dominated by Aspergillus oryzae, the microbiome of the moromi differs to soy moromi, especially in yeast composition due to the absence of Zygosaccharomyces rouxii and Debaryomyces hansenii as the dominant yeast. In this study, we monitored the addition of a carbohydrate source on the microbiome and aroma profile of the resulting sauce. Compared to previous studies, the usage of a yeast starter culture resulted in a sparsely diverse microbiota that was dominated by D. hansenii and T. halophilus. This led to a pH below 5 even after four months of incubation and most of the measured aroma compounds were pyrazines and acids. The addition of wheat and buckwheat resulted in a temporary change in the yeast consortium with the appearance of Z. rouxii and additional bacterial genera. The aroma profile differs in the presence of pyrazines and esters. Since no significant differences in the taste and odour of wheat-added and buckwheat-added sauce was sensed, both substrates influence the lupine sauce in a similar way.
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