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Vojvoda Zeljko T, Kajan K, Jalžić B, Hu A, Cukrov N, Marguš M, Cukrov N, Marković T, Sabatino R, Di Cesare A, Orlić S. Genome-centric metagenomes unveiling the hidden resistome in an anchialine cave. ENVIRONMENTAL MICROBIOME 2024; 19:67. [PMID: 39252078 PMCID: PMC11386340 DOI: 10.1186/s40793-024-00612-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 09/02/2024] [Indexed: 09/11/2024]
Abstract
BACKGROUND Antibiotic resistance is a critical global concern, posing significant challenges to human health and medical treatments. Studying antibiotic resistance genes (ARGs) is essential not only in clinical settings but also in diverse environmental contexts. However, ARGs in unique environments such as anchialine caves, which connect both fresh and marine water, remain largely unexplored despite their intriguing ecological characteristics. RESULTS We present the first study that comprehensively explores the occurrence and distribution of ARGs and mobile genetic elements (MGEs) within an anchialine cave. Utilizing metagenomic sequencing we uncovered a wide array of ARGs with the bacitracin resistance gene, bacA and multidrug resistance genes, being the most dominant. The cave's microbial community and associated resistome were significantly influenced by the salinity gradient. The discovery of novel β-lactamase variants revealed the cave's potential as a reservoir for previously undetected resistance genes. ARGs in the cave demonstrated horizontal transfer potential via plasmids, unveiling ecological implications. CONCLUSIONS These findings highlight the need for further exploration of the resistome in unique environments like anchialine caves. The interconnected dynamics of ARGs and MGEs within anchialine caves offer valuable insights into potential reservoirs and mechanisms of antibiotic resistance in natural ecosystems. This study not only advances our fundamental understanding but also highlights the need for a comprehensive approach to address antibiotic resistance in diverse ecological settings.
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Affiliation(s)
- Tanja Vojvoda Zeljko
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička Cesta 54, 10000, Zagreb, Croatia
| | - Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
| | - Branko Jalžić
- Croatian Biospeleological Society, 10000, Zagreb, Croatia
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Neven Cukrov
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička Cesta 54, 10000, Zagreb, Croatia
| | - Marija Marguš
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička Cesta 54, 10000, Zagreb, Croatia
| | - Nuša Cukrov
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička Cesta 54, 10000, Zagreb, Croatia
| | | | - Raffaella Sabatino
- Molecular Ecology Group (MEG), National Research Council of Italy (CNR), Water Research Institute (IRSA), Largo Tonolli 50, 28922, Verbania, Italy
- National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133, Palermo, Italy
| | - Andrea Di Cesare
- Molecular Ecology Group (MEG), National Research Council of Italy (CNR), Water Research Institute (IRSA), Largo Tonolli 50, 28922, Verbania, Italy
- National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133, Palermo, Italy
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000, Zagreb, Croatia.
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia.
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Khadem S, Berry D, Al-Khlifeh E. Climate influences the gut eukaryome of wild rodents in the Great Rift Valley of Jordan. Parasit Vectors 2024; 17:358. [PMID: 39180136 PMCID: PMC11342738 DOI: 10.1186/s13071-024-06451-x] [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: 05/31/2024] [Accepted: 08/13/2024] [Indexed: 08/26/2024] Open
Abstract
BACKGROUND The mammalian gut microbiome includes a community of eukaryotes with significant taxonomic and functional diversity termed the eukaryome. The molecular analysis of eukaryotic diversity in microbiomes of wild mammals is still in its early stages due to the recent emergence of interest in this field. This study aimed to fill this knowledge gap by collecting data on eukaryotic species found in the intestines of wild rodents. Because little is known about the influence of climate on the gut eukaryome, we compared the composition of the gut eukaryotes in two rodent species, Mus musculus domesticus and Acomys cahirinus, which inhabit a transect crossing a temperate and tropical zone on the Jordanian side of the Great Rift Valley (GRV). METHODS We used high-throughput amplicon sequencing targeting the 18S rRNA gene in fecal samples from rodents to identify eukaryotic organisms, their relative abundance, and their potential for pathogenicity. RESULTS Nematodes and protozoa were the most prevalent species in the eukaryome communities, whereas fungi made up 6.5% of the total. Sixty percent of the eukaryotic ASVs belonged to taxa that included known pathogens. Eighty percent of the rodents were infected with pinworms, specifically Syphacia obvelata. Eukaryotic species diversity differed significantly between bioclimatic zones (p = 0.001). Nippostrongylus brasiliensis and Aspiculuris tetraptera were found to be present exclusively in the Sudanian zone rodents. This area has not reported any cases of Trichuris infections. Yet, Capillaria infestations were unique to the Mediterranean region, while Trichuris vulpis infestations were also prevalent in the Mediterranean and Irano-Turanian regions. CONCLUSIONS This study highlights the importance of considering host species diversity and environmental factors when studying eukaryome composition in wild mammals. These data will be valuable as a reference to eukaryome study.
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Affiliation(s)
- Sanaz Khadem
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Enas Al-Khlifeh
- Laboratory of Immunology, Department of Medical Laboratory Science, Al-Balqa Applied University, Al-Salt, Jordan.
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Bellach L, Kautzky-Willer A, Heneis K, Leutner M, Kautzky A. The Effects of Caloric Restriction and Clinical Psychological Intervention on the Interplay of Gut Microbial Composition and Stress in Women. Nutrients 2024; 16:2584. [PMID: 39203721 PMCID: PMC11357322 DOI: 10.3390/nu16162584] [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: 07/01/2024] [Revised: 07/23/2024] [Accepted: 08/03/2024] [Indexed: 09/03/2024] Open
Abstract
Both mental and metabolic disorders are steadily becoming more prevalent, increasing interest in non-pharmacological lifestyle interventions targeting both types of disorders. However, the combined effect of diet and psychological interventions on the gut microbiome and mental health outcomes remains underexplored. Thus, in this study, we randomized 41 women into two caloric restriction (CR) dietary groups, namely very-low-calorie diet (VLCD) and F.X. Mayr diet (FXM). The patients were then further randomized to either receive clinical psychological intervention (CPI) or no CPI. Blood and fecal samples were collected before and after two weeks of CR. Psychometric outcomes were assessed using the Perceived Stress Scale (PSS), Brief Symptom Index (BSI), and Burnout Dimension Inventory (BODI). Stool samples underwent 16S-rRNA sequencing. Upon two weeks of CR, α-diversity decreased overall and longitudinal PERMANOVA models revealed significant shifts in β-diversity according to diet, CPI, age, and body-mass-index. Furthermore, Agathobacter, Fusicatenibacter, and Subdoligranulum decreased in abundance. However, the Oscillibacter genus was enriched solely in FXM. CPI had a negligible effect on the microbiome. Dimension reduction models revealed clusters of taxa which distinctly associated with psychometric outcomes. Members of the Oscillospiraceae family were linked to favorable psychometric outcomes after two weeks of CR. Despite α-diversity reductions after CR, enrichment of Oscillospiraceae spp., solely seen in FXM, correlated with improved psychometric outcomes. This study suggests a promising direction for future interventions targeting mental health through gut microbial modulation.
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Affiliation(s)
- Luise Bellach
- Department of Internal Medicine III, Division of Endocrinology and Metabolism, Medical University of Vienna, 1090 Vienna, Austria
| | - Alexandra Kautzky-Willer
- Department of Internal Medicine III, Division of Endocrinology and Metabolism, Medical University of Vienna, 1090 Vienna, Austria
| | - Kathrin Heneis
- Department of Internal Medicine III, Division of Endocrinology and Metabolism, Medical University of Vienna, 1090 Vienna, Austria
| | - Michael Leutner
- Department of Internal Medicine III, Division of Endocrinology and Metabolism, Medical University of Vienna, 1090 Vienna, Austria
| | - Alexander Kautzky
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, 1090 Vienna, Austria
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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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Effenberger M, Grander C, Hausmann B, Enrich B, Pjevac P, Zoller H, Tilg H. Apelin and the gut microbiome: Potential interaction in human MASLD. Dig Liver Dis 2024; 56:932-940. [PMID: 38087672 DOI: 10.1016/j.dld.2023.11.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 05/28/2024]
Abstract
BACKGROUND Metabolic dysfunction-associated steatotic liver disease (MASLD) is a leading cause of chronic liver disease with increasing numbers worldwide. Adipokines like apelin (APLN) can act as key players in the complex pathophysiology of MASLD. AIMS Investigating the role of APLN in MASLD. METHODS Fecal and blood samples were collected in a MASLD cohort and healthy controls (HC). MASLD patients with liver fibrosis and MASLD-associated hepatocellular carcinoma (HCC) were included into the study. Systemic concentration of Apelin, Apelin receptor (APLNR) and circulating cytokines were measured in serum samples. RESULTS Apelin concentration correlated with the Fib-4 score and was elevated in MASLD patients (mild fibrosis, mF (Fib-4 <3.25) and severe fibrosis, sF (Fib-4 >3.25)) as well as in MASLD-associated HCC patients compared to HC. In accordance APLNR and circulating cytokines were also elevated in mF and sF. In contrast apelin levels were negatively associated with liver survival at three and five years. Changes in taxa composition at phylum level showed an increase of Enterobactericae, Prevotellaceae and Lactobacillaceae in patients with sF compared to mF. We could also observe an association between apelin concentrations and bacterial lineages (phyla). CONCLUSIONS Circulating apelin is associated with liver fibrosis and HCC. In addition, there might exist an interaction between systemic apelin and the gut microbiome.
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Affiliation(s)
- Maria Effenberger
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Christoph Grander
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria.
| | - 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
| | - Barbara Enrich
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria; Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Heinz Zoller
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
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Oesterle I, Ayeni KI, Ezekiel CN, Berry D, Rompel A, Warth B. Insights into the early-life chemical exposome of Nigerian infants and potential correlations with the developing gut microbiome. ENVIRONMENT INTERNATIONAL 2024; 188:108766. [PMID: 38801800 DOI: 10.1016/j.envint.2024.108766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
Early-life exposure to natural and synthetic chemicals can impact acute and chronic health conditions. Here, a suspect screening workflow anchored on high-resolution mass spectrometry was applied to elucidate xenobiotics in breast milk and matching stool samples collected from Nigerian mother-infant pairs (n = 11) at three time points. Potential correlations between xenobiotic exposure and the developing gut microbiome, as determined by 16S rRNA gene amplicon sequencing, were subsequently explored. Overall, 12,192 and 16,461 features were acquired in the breast milk and stool samples, respectively. Following quality control and suspect screening, 562 and 864 features remained, respectively, with 149 of these features present in both matrices. Taking advantage of 242 authentic reference standards measured for confirmatory purposes of food bio-actives and toxicants, 34 features in breast milk and 68 features in stool were identified and semi-quantified. Moreover, 51 and 78 features were annotated with spectral library matching, as well as 416 and 652 by in silico fragmentation tools in breast milk and stool, respectively. The analytical workflow proved its versatility to simultaneously determine a diverse panel of chemical classes including mycotoxins, endocrine-disrupting chemicals (EDCs), antibiotics, plasticizers, perfluorinated alkylated substances (PFAS), and pesticides, although it was originally optimized for polyphenols. Spearman rank correlation of the identified features revealed significant correlations between chemicals of the same classification such as polyphenols. One-way ANOVA and differential abundance analysis of the data obtained from stool samples revealed that molecules of plant-based origin elevated as complementary foods were introduced to the infants' diets. Annotated compounds in the stool, such as tricetin, positively correlated with the genus Blautia. Moreover, vulgaxanthin negatively correlated with Escherichia-Shigella. Despite the limited sample size, this exploratory study provides high-quality exposure data of matched biospecimens obtained from mother-infant pairs in sub-Saharan Africa and shows potential correlations between the chemical exposome and the gut microbiome.
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Affiliation(s)
- Ian Oesterle
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, 1090 Vienna, Austria; Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, 1090 Wien, Austria(1); University of Vienna, Vienna Doctoral School of Chemistry (DoSChem), 1090 Vienna, Austria
| | - Kolawole I Ayeni
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, 1090 Vienna, Austria; Department of Microbiology, Babcock University, Ilishan-Remo, Ogun State, Nigeria
| | - Chibundu N Ezekiel
- Department of Microbiology, Babcock University, Ilishan-Remo, Ogun State, Nigeria; University of Natural Resources and Life Sciences Vienna (BOKU), Department of Agrobiotechnology (IFA-Tulln), Institute for Bioanalytics and Agro-Metabolomics, Konrad-Lorenz Str. 20, 3430 Tulln, Austria
| | - David Berry
- University of Vienna, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, 1030 Vienna, Austria
| | - Annette Rompel
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, 1090 Wien, Austria(1); University of Vienna, Vienna Doctoral School of Chemistry (DoSChem), 1090 Vienna, Austria
| | - Benedikt Warth
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, 1090 Vienna, Austria; University of Vienna, Vienna Doctoral School of Chemistry (DoSChem), 1090 Vienna, Austria; Exposome Austria, Research Infrastructure and National EIRENE Node, Austria.
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Rojas-Pinzon PA, Prommer J, Sedlacek CJ, Sandén T, Spiegel H, Pjevac P, Fuchslueger L, Giguere AT. Inhibition profile of three biological nitrification inhibitors and their response to soil pH modification in two contrasting soils. FEMS Microbiol Ecol 2024; 100:fiae072. [PMID: 38702852 PMCID: PMC11110862 DOI: 10.1093/femsec/fiae072] [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: 12/18/2023] [Revised: 03/28/2024] [Accepted: 05/02/2024] [Indexed: 05/06/2024] Open
Abstract
Up to 70% of the nitrogen (N) fertilizer applied to agricultural soils is lost through microbially mediated processes, such as nitrification. This can be counteracted by synthetic and biological compounds that inhibit nitrification. However, for many biological nitrification inhibitors (BNIs), the interaction with soil properties, nitrifier specificity, and effective concentrations are unclear. Here, we investigated three synthetic nitrification inhibitors (SNIs) (DCD, DMPP, and nitrapyrin) and three BNIs [methyl 3(4-hydroxyphenyl) propionate (MHPP), methyl 3(4-hydroxyphenyl) acrylate (MHPA), and limonene] in two agricultural soils differing in pH and nitrifier communities. The efficacies of SNIs and BNIs were resilient to short-term pH changes in the neutral pH soil, whereas the efficacy of some BNIs increased by neutralizing the alkaline soil. Among the BNIs, MHPA showed the highest inhibition and was, together with MHPP, identified as a putative AOB/comammox-selective inhibitor. Additionally, MHPA and limonene effectively inhibited nitrification at concentrations comparable to those used for DCD. Moreover, we identified the effective concentrations at which 50% and 80% of inhibition is observed (EC50 and EC80) for the BNIs, and similar EC80 values were observed in both soils. Overall, our results show that these BNIs could potentially serve as effective alternatives to SNIs currently used.
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Affiliation(s)
- Paula A Rojas-Pinzon
- Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Judith Prommer
- Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Christopher J Sedlacek
- Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Taru Sandén
- Department for Soil Health and Plant Nutrition, Austrian Agency for Health and Food Safety (AGES), Spargelfeldstraße 191, 1220 Vienna, Austria
| | - Heide Spiegel
- Department for Soil Health and Plant Nutrition, Austrian Agency for Health and Food Safety (AGES), Spargelfeldstraße 191, 1220 Vienna, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Environment and Climate Hub, University of Vienna, Augasse 2/6, 1090 Vienna, Austria
| | - Lucia Fuchslueger
- Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Environment and Climate Hub, University of Vienna, Augasse 2/6, 1090 Vienna, Austria
| | - Andrew T Giguere
- Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
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Barrajon-Santos V, Nepel M, Hausmann B, Voglmayr H, Woebken D, Mayer VE. Dynamics and drivers of fungal communities in a multipartite ant-plant association. BMC Biol 2024; 22:112. [PMID: 38745290 PMCID: PMC11093746 DOI: 10.1186/s12915-024-01897-y] [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: 09/08/2023] [Accepted: 04/18/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Fungi and ants belong to the most important organisms in terrestrial ecosystems on Earth. In nutrient-poor niches of tropical rainforests, they have developed steady ecological relationships as a successful survival strategy. In tropical ant-plant mutualisms worldwide, where resident ants provide the host plants with defense and nutrients in exchange for shelter and food, fungi are regularly found in the ant nesting space, inhabiting ant-made dark-colored piles ("patches"). Unlike the extensively investigated fungus-growing insects, where the fungi serve as the primary food source, the purpose of this ant-fungi association is less clear. To decipher the roles of fungi in these structures within ant nests, it is crucial to first understand the dynamics and drivers that influence fungal patch communities during ant colony development. RESULTS In this study, we investigated how the ant colony age and the ant-plant species affect the fungal community in the patches. As model we selected one of the most common mutualisms in the Tropics of America, the Azteca-Cecropia complex. By amplicon sequencing of the internal transcribed spacer 2 (ITS2) region, we analyzed the patch fungal communities of 93 Azteca spp. colonies inhabiting Cecropia spp. trees. Our study demonstrates that the fungal diversity in patches increases as the ant colony grows and that a change in the prevalent fungal taxa occurs between initial and established patches. In addition, the ant species significantly influences the composition of the fungal community in established ant colonies, rather than the host plant species. CONCLUSIONS The fungal patch communities become more complex as the ant colony develops, due to an acquisition of fungi from the environment and a substrate diversification. Our results suggest a successional progression of the fungal communities in the patches during ant colony growth and place the ant colony as the main driver shaping such communities. The findings of this study demonstrate the unexpectedly complex nature of ant-plant mutualisms in tropical regions at a micro scale.
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Affiliation(s)
- Veronica Barrajon-Santos
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria.
| | - Maximilian Nepel
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- Present Address: Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland, New Zealand
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - Hermann Voglmayr
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Veronika E Mayer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.
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Foessleitner P, Pjevac P, Granser S, Wisgrill L, Pummer L, Eckel F, Seki D, Berry D, Hausmann B, Farr A. The maternal microbiome in pregnancy, delivery, and early-stage development of neonatal microbiome after cesarean section: A prospective longitudinal study. Acta Obstet Gynecol Scand 2024; 103:832-841. [PMID: 38268221 PMCID: PMC11019516 DOI: 10.1111/aogs.14773] [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: 05/29/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 01/26/2024]
Abstract
INTRODUCTION Changes within the maternal microbiome during the last trimester of pregnancy and the determinants of the subsequent neonatal microbiome establishment after delivery by elective cesarean section are described. MATERIAL AND METHODS Maternal vaginal and rectal microbiome samples were collected in the last trimester and before cesarean section; intrauterine cavity, placenta, neonatal buccal mucosa, skin, and meconium samples were obtained at birth; neonatal sample collection was repeated 2-3 days postnatally. Microbial community composition was analyzed by 16S rRNA gene amplicon sequencing. Relative abundance measurements of amplicon sequencing variants and sum counts at higher taxonomic levels were compared to test for significant overlap or differences in microbial community compositions. CLINICALTRIALS gov ID: NCT04489056. RESULTS A total of 30 mothers and their neonates were included with available microbiome samples for all maternal, intrauterine cavity and placenta samples, as well as for 18 of 30 neonates. The composition of maternal vaginal and rectal microbiomes during the last trimester of healthy pregnancies did not significantly change (permutational multivariate analysis of variance [PERMANOVA], p > 0.05). No robust microbial signature was detected in the intrauterine cavity, placenta, neonatal buccal mucosa, skin swabs, or meconium samples collected at birth. After birth, the neonatal microbiome was rapidly established, and significantly different microbial communities were detectable 2-3 days postnatally in neonate buccal mucosa and stool samples (PERMANOVA, p < 0.01). CONCLUSIONS Maternal vaginal and rectal microbiomes in healthy pregnancies remain stable during the third trimester. No microbial colonization of the neonate was observed before birth in healthy pregnancies. Neonatal microbiomes in infants delivered by cesarean section displayed a taxonomic composition distinct from maternal vaginal and rectal microbiomes at birth, indicating that postnatal exposure to the extrauterine environment is the driving source of initial neonatal microbiome development in this cohort.
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Affiliation(s)
- Philipp Foessleitner
- Department of Obstetrics and Gynecology, Division of Obstetrics and Feto‐Maternal MedicineMedical University of Vienna, and Comprehensive Center for Pediatrics (CCP), Medical University of ViennaViennaAustria
| | - Petra Pjevac
- Joint Microbiome FacilityMedical University of Vienna and University of ViennaViennaAustria
- University of ViennaCenter for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem ScienceViennaAustria
| | - Sonja Granser
- Department of Obstetrics and Gynecology, Division of Obstetrics and Feto‐Maternal MedicineMedical University of Vienna, and Comprehensive Center for Pediatrics (CCP), Medical University of ViennaViennaAustria
| | - Lukas Wisgrill
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Intensive Care Medicine, and Neuropediatrics, and Comprehensive Center for Pediatrics (CCP)Medical University of ViennaViennaAustria
| | - Lisa Pummer
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Intensive Care Medicine, and Neuropediatrics, and Comprehensive Center for Pediatrics (CCP)Medical University of ViennaViennaAustria
| | - Fanny Eckel
- Department of Obstetrics and Gynecology, Division of Obstetrics and Feto‐Maternal MedicineMedical University of Vienna, and Comprehensive Center for Pediatrics (CCP), Medical University of ViennaViennaAustria
| | - David Seki
- University of ViennaCenter for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem ScienceViennaAustria
- Department of Laboratory MedicineMedical University of ViennaViennaAustria
| | - David Berry
- Joint Microbiome FacilityMedical University of Vienna and University of ViennaViennaAustria
- University of ViennaCenter for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem ScienceViennaAustria
| | - Bela Hausmann
- Joint Microbiome FacilityMedical University of Vienna and University of ViennaViennaAustria
- Department of Laboratory MedicineMedical University of ViennaViennaAustria
| | - Alex Farr
- Department of Obstetrics and Gynecology, Division of Obstetrics and Feto‐Maternal MedicineMedical University of Vienna, and Comprehensive Center for Pediatrics (CCP), Medical University of ViennaViennaAustria
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10
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Hu H, Kristensen JM, Herbold CW, Pjevac P, Kitzinger K, Hausmann B, Dueholm MKD, Nielsen PH, Wagner M. Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants. MICROBIOME 2024; 12:55. [PMID: 38493180 PMCID: PMC10943839 DOI: 10.1186/s40168-024-01769-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/23/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), and their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance and diversity of Patescibacteria due to the low coverage of commonly used PCR primers for this highly divergent bacterial phylum. Therefore, our current understanding of the global diversity, distribution, and ecological role of Patescibacteria in WWTPs is very incomplete. This is particularly relevant as Patescibacteria are considered to be associated with microbial host cells and can therefore influence the abundance and temporal variability of other microbial groups that are important for WWTP functioning. RESULTS Here, we evaluated the in silico coverage of widely used 16S rRNA gene-targeted primer pairs and redesigned a primer pair targeting the V4 region of bacterial and archaeal 16S rRNA genes to expand its coverage for Patescibacteria. We then experimentally evaluated and compared the performance of the original and modified V4-targeted primers on 565 WWTP samples from the MiDAS global sample collection. Using the modified primer pair, the percentage of ASVs classified as Patescibacteria increased from 5.9 to 23.8%, and the number of detected patescibacterial genera increased from 560 to 1576, while the detected diversity of the remaining microbial community remained similar. Due to this significantly improved coverage of Patescibacteria, we identified 23 core genera of Patescibacteria in WWTPs and described the global distribution pattern of these unusual microbes in these systems. Finally, correlation network analysis revealed potential host organisms that might be associated with Patescibacteria in WWTPs. Interestingly, strong indications were found for an association between Patescibacteria of the Saccharimonadia and globally abundant polyphosphate-accumulating organisms of the genus Ca. Phosphoribacter. CONCLUSIONS Our study (i) provides an improved 16S rRNA gene V4 region-targeted amplicon primer pair inclusive of Patescibacteria with little impact on the detection of other taxa, (ii) reveals the diversity and distribution patterns of Patescibacteria in WWTPs on a global scale, and (iii) provides new insights into the ecological role and potential hosts of Patescibacteria in WWTPs. Video Abstract.
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Affiliation(s)
- Huifeng Hu
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Universitätsring 1, 1010, Vienna, Austria
| | - Jannie Munk Kristensen
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Craig William Herbold
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Te Kura Putaiao Koiora, School of Biological Sciences, Te Whare Wananga o Waitaha, University of Canterbury, Otautahi, Christchurch, Aotearoa, New Zealand
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna , University of Vienna, Vienna, Austria
| | - Katharina Kitzinger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna , University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjaer Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
- Joint Microbiome Facility of the Medical University of Vienna , University of Vienna, Vienna, Austria.
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11
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Kajan K, Fuchs BM, Orlić S. Insight into planktonic protistan and fungal communities across the nutrient-depleted environment of the South Pacific Subtropical Gyre. Microbiol Spectr 2024; 12:e0301623. [PMID: 38334383 PMCID: PMC10913754 DOI: 10.1128/spectrum.03016-23] [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: 08/04/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
Ocean microorganisms constitute ~70% of the marine biomass, contribute to ~50% of the Earth's primary production, and play a vital role in global biogeochemical cycles. The marine heterotrophic and mixotrophic protistan and fungal communities have often been overlooked mainly due to limitations in morphological species identification. Despite the accumulation of studies on biogeographic patterns observed in microbial communities, our understanding of the abundance and distribution patterns within the microbial community of the largest subtropical gyre, the South Pacific Gyre (SPG), remains incomplete. Here, we investigated the diversity and vertical composition of protistan and fungal communities in the water column of the ultra-oligotrophic SPG. Our results showed apparent differences in protistan community diversity in the photic and aphotic regions. The entire protistan community diversity was significantly affected by temperature, salinity, oxygen, and nutrient concentrations, while the parasitic community diversity was also affected by chlorophyll a concentration. The parasitic protists were assigned to the class Syndiniales accounting for over 98% of the total parasitic protists, exhibiting higher relative sequence abundance along the water depth and displaying consistent patterns among different sampling stations. In contrast to the protistan community, the fungal community along the SPG primarily clustered based on the sampling station and pelagic zones. In particular, our study reveals a significant presence of parasitic protists and functionally diverse fungi in SPG and their potential impact on carbon cycling in the gyre.IMPORTANCEOur findings carry important implications for understanding the distribution patterns of the previously unrecognized occurrence of parasitic protists and functionally diverse fungi in the nutrient-limited South Pacific Gyre. In particular, our study reveals a significant presence of parasitic Syndiniales, predominantly abundant in the upper 300 m of the aphotic zone in the gyre, and a distinct presence of fungal communities in the aphotic zone at the central part of the gyre. These findings strongly suggest that these communities play a substantial role in yet insufficiently described microbial food web. Moreover, our research enhances our understanding of their contribution to the dynamics of the food webs in oligotrophic gyres and is valuable for projecting the ecological consequences of future climate warming.
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Affiliation(s)
- Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
| | - Bernhard M. Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
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12
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Metze D, Schnecker J, de Carlan CLN, Bhattarai B, Verbruggen E, Ostonen I, Janssens IA, Sigurdsson BD, Hausmann B, Kaiser C, Richter A. Soil warming increases the number of growing bacterial taxa but not their growth rates. SCIENCE ADVANCES 2024; 10:eadk6295. [PMID: 38394199 PMCID: PMC10889357 DOI: 10.1126/sciadv.adk6295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Soil microorganisms control the fate of soil organic carbon. Warming may accelerate their activities putting large carbon stocks at risk of decomposition. Existing knowledge about microbial responses to warming is based on community-level measurements, leaving the underlying mechanisms unexplored and hindering predictions. In a long-term soil warming experiment in a Subarctic grassland, we investigated how active populations of bacteria and archaea responded to elevated soil temperatures (+6°C) and the influence of plant roots, by measuring taxon-specific growth rates using quantitative stable isotope probing and 18O water vapor equilibration. Contrary to prior assumptions, increased community growth was associated with a greater number of active bacterial taxa rather than generally faster-growing populations. We also found that root presence enhanced bacterial growth at ambient temperatures but not at elevated temperatures, indicating a shift in plant-microbe interactions. Our results, thus, reveal a mechanism of how soil bacteria respond to warming that cannot be inferred from community-level measurements.
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Affiliation(s)
- Dennis Metze
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Biplabi Bhattarai
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Erik Verbruggen
- Research Group Plants and Ecosystems, University of Antwerp, Antwerp, Belgium
| | - Ivika Ostonen
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ivan A. Janssens
- Research Group Plants and Ecosystems, University of Antwerp, Antwerp, Belgium
| | - Bjarni D. Sigurdsson
- Faculty of Environmental and Forest Sciences, Agricultural University of Iceland, Hvanneyri, Borgarnes, Iceland
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- International Institute for Applied Systems Analysis, Advancing Systems Analysis Program, Laxenburg, Austria
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13
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Ayeni K, Seki D, Pjevac P, Hausmann B, Krausová M, Braun D, Wisgrill L, Berry D, Warth B, Ezekiel CN. Biomonitoring of Dietary Mycotoxin Exposure and Associated Impact on the Gut Microbiome in Nigerian Infants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2236-2246. [PMID: 38252460 PMCID: PMC10851434 DOI: 10.1021/acs.est.3c07786] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/06/2024] [Accepted: 01/09/2024] [Indexed: 01/23/2024]
Abstract
Mycotoxins are toxic chemicals that adversely affect human health. Here, we assessed the influence of mycotoxin exposure on the longitudinal development of early life intestinal microbiota of Nigerian neonates and infants (NIs). Human biomonitoring assays based on liquid chromatography tandem mass spectrometry were applied to quantify mycotoxins in breast milk (n = 68) consumed by the NIs, their stool (n = 82), and urine samples (n = 15), which were collected longitudinally from month 1-18 postdelivery. Microbial community composition was characterized by 16S rRNA gene amplicon sequencing of stool samples and was correlated to mycotoxin exposure patterns. Fumonisin B1 (FB1), FB2, and alternariol monomethyl ether (AME) were frequently quantified in stool samples between months 6 and 18. Aflatoxin M1 (AFM1), AME, and citrinin were quantified in breast milk samples at low concentrations. AFM1, FB1, and ochratoxin A were quantified in urine samples at relatively high concentrations. Klebsiella and Escherichia/Shigella were dominant in very early life stool samples (month 1), whereas Bifidobacterium was dominant between months 3 and 6. The total mycotoxin levels in stool were significantly associated with NIs' gut microbiome composition (PERMANOVA, p < 0.05). However, no significant correlation was observed between specific microbiota and the detection of certain mycotoxins. Albeit a small cohort, this study demonstrates that mycotoxins may influence early life gut microbiome composition.
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Affiliation(s)
- Kolawole
I. Ayeni
- Department
of Microbiology, Babcock University, Ilishan Remo PMB 4003, Ogun State, Nigeria
- University
of Vienna, Faculty of Chemistry, Department of Food Chemistry and
Toxicology, Währinger
Straße 38, Vienna 1090, Austria
| | - David Seki
- Joint
Microbiome Facility of the Medical University of Vienna and the University
of Vienna, Djerassiplatz 1, Vienna 1030, Austria
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna 1090, Austria
| | - Petra Pjevac
- Joint
Microbiome Facility of the Medical University of Vienna and the University
of Vienna, Djerassiplatz 1, Vienna 1030, Austria
- Department
of Microbiology and Ecosystem Science, Centre for Microbiology and
Environmental Systems Science, University
of Vienna, Djerassiplatz
1, Vienna 1030, Austria
| | - Bela Hausmann
- Joint
Microbiome Facility of the Medical University of Vienna and the University
of Vienna, Djerassiplatz 1, Vienna 1030, Austria
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna 1090, Austria
| | - Magdaléna Krausová
- University
of Vienna, Faculty of Chemistry, Department of Food Chemistry and
Toxicology, Währinger
Straße 38, Vienna 1090, Austria
| | - Dominik Braun
- University
of Vienna, Faculty of Chemistry, Department of Food Chemistry and
Toxicology, Währinger
Straße 38, Vienna 1090, Austria
| | - Lukas Wisgrill
- Division
of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive
Center for Pediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna 1090, Austria
- Exposome
Austria, Research Infrastructure and National EIRENE Node, Vienna 1090, Austria
| | - David Berry
- Joint
Microbiome Facility of the Medical University of Vienna and the University
of Vienna, Djerassiplatz 1, Vienna 1030, Austria
- Department
of Microbiology and Ecosystem Science, Centre for Microbiology and
Environmental Systems Science, University
of Vienna, Djerassiplatz
1, Vienna 1030, Austria
| | - Benedikt Warth
- University
of Vienna, Faculty of Chemistry, Department of Food Chemistry and
Toxicology, Währinger
Straße 38, Vienna 1090, Austria
- Exposome
Austria, Research Infrastructure and National EIRENE Node, Vienna 1090, Austria
| | - Chibundu N. Ezekiel
- Department
of Microbiology, Babcock University, Ilishan Remo PMB 4003, Ogun State, Nigeria
- University
of Natural Resources and Life Sciences Vienna (BOKU), Department of
Agrobiotechnology (IFA-Tulln), Institute for Bioanalytics and Agro-Metabolomics, Konrad-LorenzStr. 20, Tulln 3430, Austria
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14
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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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15
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Simon E, Guseva K, Darcy S, Alteio L, Pjevac P, Schmidt H, Jenab K, Ranits C, Kaiser C. Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates. THE ISME JOURNAL 2024; 18:wrae156. [PMID: 39105276 PMCID: PMC11325450 DOI: 10.1093/ismejo/wrae156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/29/2024] [Accepted: 08/05/2024] [Indexed: 08/07/2024]
Abstract
Soils provide essential ecosystem services and represent the most diverse habitat on Earth. It has been suggested that the presence of various physico-chemically heterogeneous microhabitats supports the enormous diversity of microbial communities in soil. However, little is known about the relationship between microbial communities and their immediate environment at the micro- to millimetre scale. In this study, we examined whether bacteria, archaea, and fungi organize into distinct communities in individual 2-mm-sized soil aggregates and compared them to communities of homogenized bulk soil samples. Furthermore, we investigated their relationship to their local environment by concomitantly determining microbial community structure and physico-chemical properties from the same individual aggregates. Aggregate communities displayed exceptionally high beta-diversity, with 3-4 aggregates collectively capturing more diversity than their homogenized parent soil core. Up to 20%-30% of ASVs (particularly rare ones) were unique to individual aggregates selected within a few centimetres. Aggregates and bulk soil samples showed partly different dominant phyla, indicating that taxa that are potentially driving biogeochemical processes at the small scale may not be recognized when analysing larger soil volumes. Microbial community composition and richness of individual aggregates were closely related to aggregate-specific carbon and nitrogen content, carbon stable-isotope composition, and soil moisture, indicating that aggregates provide a stable environment for sufficient time to allow co-development of communities and their environment. We conclude that the soil microbiome is a metacommunity of variable subcommunities. Our study highlights the necessity to study small, spatially coherent soil samples to better understand controls of community structure and community-mediated processes in soils.
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Affiliation(s)
- Eva Simon
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Ksenia Guseva
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Sean Darcy
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Lauren Alteio
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, 3430 Tulln, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Vienna, Austria
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Kian Jenab
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Christian Ranits
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
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16
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Riva A, Rasoulimehrabani H, Cruz-Rubio JM, Schnorr SL, von Baeckmann C, Inan D, Nikolov G, Herbold CW, Hausmann B, Pjevac P, Schintlmeister A, Spittler A, Palatinszky M, Kadunic A, Hieger N, Del Favero G, von Bergen M, Jehmlich N, Watzka M, Lee KS, Wiesenbauer J, Khadem S, Viernstein H, Stocker R, Wagner M, Kaiser C, Richter A, Kleitz F, Berry D. Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting. Nat Commun 2023; 14:8210. [PMID: 38097563 PMCID: PMC10721620 DOI: 10.1038/s41467-023-43448-z] [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: 09/24/2023] [Accepted: 11/09/2023] [Indexed: 12/17/2023] Open
Abstract
Prebiotics are defined as non-digestible dietary components that promote the growth of beneficial gut microorganisms. In many cases, however, this capability is not systematically evaluated. Here, we develop a methodology for determining prebiotic-responsive bacteria using the popular dietary supplement inulin. We first identify microbes with a capacity to bind inulin using mesoporous silica nanoparticles functionalized with inulin. 16S rRNA gene amplicon sequencing of sorted cells revealed that the ability to bind inulin was widespread in the microbiota. We further evaluate which taxa are metabolically stimulated by inulin and find that diverse taxa from the phyla Firmicutes and Actinobacteria respond to inulin, and several isolates of these taxa can degrade inulin. Incubation with another prebiotic, xylooligosaccharides (XOS), in contrast, shows a more robust bifidogenic effect. Interestingly, the Coriobacteriia Eggerthella lenta and Gordonibacter urolithinfaciens are indirectly stimulated by the inulin degradation process, expanding our knowledge of inulin-responsive bacteria.
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Affiliation(s)
- Alessandra Riva
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Chair of Nutrition and Immunology, School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Hamid Rasoulimehrabani
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - José Manuel Cruz-Rubio
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria
| | - Stephanie L Schnorr
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Cornelia von Baeckmann
- Department of Functional Materials and Catalysis, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Deniz Inan
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Georgi Nikolov
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - 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
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Andreas Spittler
- Core Facility Flow Cytometry and Surgical Research Laboratories, Medical University of Vienna, Vienna, Austria
| | - Márton Palatinszky
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Aida Kadunic
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Norbert Hieger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Giorgia Del Favero
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Martin von Bergen
- Helmholtz Centre for Environmental Research, Department of Molecular Systems Biology, Leipzig, Germany
| | - Nico Jehmlich
- Helmholtz Centre for Environmental Research, Department of Molecular Systems Biology, Leipzig, Germany
| | - Margarete Watzka
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Kang Soo Lee
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Julia Wiesenbauer
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Sanaz Khadem
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Helmut Viernstein
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria
| | - Roman Stocker
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Freddy Kleitz
- Department of Functional Materials and Catalysis, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
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17
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Sanchez-Vicente S, Tokarz R. Tick-Borne Co-Infections: Challenges in Molecular and Serologic Diagnoses. Pathogens 2023; 12:1371. [PMID: 38003835 PMCID: PMC10674443 DOI: 10.3390/pathogens12111371] [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: 11/01/2023] [Revised: 11/14/2023] [Accepted: 11/18/2023] [Indexed: 11/26/2023] Open
Abstract
Co-infections are a poorly understood aspect of tick-borne diseases. In the United States alone, nineteen different tick-borne pathogens have been identified. The majority of these agents are transmitted by only two tick species, Ixodes scapularis and Amblyomma americanum. Surveillance studies have demonstrated the presence of multiple pathogens in individual ticks suggesting a risk of polymicrobial transmission to humans. However, relatively few studies have explored this relationship and its impact on human disease. One of the key factors for this deficiency are the intrinsic limitations associated with molecular and serologic assays employed for the diagnosis of tick-borne diseases. Limitations in the sensitivity, specificity and most importantly, the capacity for inclusion of multiple agents within a single assay represent the primary challenges for the accurate detection of polymicrobial tick-borne infections. This review will focus on outlining these limitations and discuss potential solutions for the enhanced diagnosis of tick-borne co-infections.
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Affiliation(s)
- Santiago Sanchez-Vicente
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA;
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA;
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
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18
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Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Boettcher T, Cheng JX, Wagner M. The Parkinson's drug entacapone disrupts gut microbiome homeostasis via iron sequestration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.12.566429. [PMID: 38014294 PMCID: PMC10680583 DOI: 10.1101/2023.11.12.566429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Increasing evidence shows that many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, much less is known about the mechanisms by which drugs target the microbiome and how drugs affect microbial function. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single cell chemical imaging to investigate the impact of two widely prescribed nervous system targeted drugs on the gut microbiome. Ex vivo supplementation of physiologically relevant concentrations of entacapone or loxapine succinate to faecal samples significantly impacted the abundance of up to one third of the microbial species present. Importantly, we demonstrate that the impact of these drugs on microbial metabolism is much more pronounced than their impact on abundances, with low concentrations of drugs reducing the activity, but not the abundance of key microbiome members like Bacteroides, Ruminococcus or Clostridium species. We further demonstrate that entacapone impacts the microbiome due to its ability to complex and deplete available iron, and that microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Remarkably, entacapone-induced iron starvation selected for iron-scavenging organisms carrying antimicrobial resistance and virulence genes. Collectively, our study unveils the impact of two under-investigated drugs on whole microbiomes and identifies metal sequestration as a mechanism of drug-induced microbiome disturbance.
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19
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Kostešić E, Mitrović M, Kajan K, Marković T, Hausmann B, Orlić S, Pjevac P. Microbial Diversity and Activity of Biofilms from Geothermal Springs in Croatia. MICROBIAL ECOLOGY 2023; 86:2305-2319. [PMID: 37209180 PMCID: PMC10640420 DOI: 10.1007/s00248-023-02239-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/07/2023] [Indexed: 05/22/2023]
Abstract
Hot spring biofilms are stable, highly complex microbial structures. They form at dynamic redox and light gradients and are composed of microorganisms adapted to the extreme temperatures and fluctuating geochemical conditions of geothermal environments. In Croatia, a large number of poorly investigated geothermal springs host biofilm communities. Here, we investigated the microbial community composition of biofilms collected over several seasons at 12 geothermal springs and wells. We found biofilm microbial communities to be temporally stable and highly dominated by Cyanobacteria in all but one high-temperature sampling site (Bizovac well). Of the physiochemical parameters recorded, temperature had the strongest influence on biofilm microbial community composition. Besides Cyanobacteria, the biofilms were mainly inhabited by Chloroflexota, Gammaproteobacteria, and Bacteroidota. In a series of incubations with Cyanobacteria-dominated biofilms from Tuhelj spring and Chloroflexota- and Pseudomonadota-dominated biofilms from Bizovac well, we stimulated either chemoorganotrophic or chemolithotrophic community members, to determine the fraction of microorganisms dependent on organic carbon (in situ predominantly produced via photosynthesis) versus energy derived from geochemical redox gradients (here simulated by addition of thiosulfate). We found surprisingly similar levels of activity in response to all substrates in these two distinct biofilm communities, and observed microbial community composition and hot spring geochemistry to be poor predictors of microbial activity in the study systems.
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Affiliation(s)
- Ema Kostešić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Maja Mitrović
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia
| | | | - 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
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
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20
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Al-khlifeh E, Khadem S, Hausmann B, Berry D. Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley. Front Microbiol 2023; 14:1258775. [PMID: 37954239 PMCID: PMC10637782 DOI: 10.3389/fmicb.2023.1258775] [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: 07/14/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023] Open
Abstract
Host phylogeny and the environment play vital roles in shaping animal microbiomes. However, the effects of these variables on the diversity and richness of the gut microbiome in different bioclimatic zones remain underexplored. In this study, we investigated the effects of host phylogeny and bioclimatic zone on the diversity and composition of the gut microbiota of two heterospecific rodent species, the spiny mouse Acomys cahirinus and the house mouse Mus musculus, in three bioclimatic zones of the African Great Rift Valley (GRV). We confirmed host phylogeny using the D-loop sequencing method and analyzed the influence of host phylogeny and bioclimatic zone parameters on the rodent gut microbiome using high-throughput amplicon sequencing of 16S rRNA gene fragments. Phylogenetic analysis supported the morphological identification of the rodents and revealed a marked genetic difference between the two heterospecific species. We found that bioclimatic zone had a significant effect on the gut microbiota composition while host phylogeny did not. Microbial alpha diversity of heterospecific hosts was highest in the Mediterranean forest bioclimatic zone, followed by the Irano-Turanian shrubland, and was lowest in the Sudanian savanna tropical zone. The beta diversity of the two rodent species showed significant differences across the Mediterranean, Irano-Turanian, and Sudanian regions. The phyla Firmicutes and Bacteroidetes were highly abundant, and Deferribacterota, Cyanobacteria and Proteobacteria were also prominent. Amplicon sequence variants (ASVs) were identified that were unique to the Sudanian bioclimatic zone. The core microbiota families recovered in this study were consistent among heterospecific hosts. However, diversity decreased in conspecific host populations found at lower altitudes in Sudanian bioclimatic zone. The composition of the gut microbiota is linked to the adaptation of the host to its environment, and this study underscores the importance of incorporating climatic factors such as elevation and ambient temperature, in empirical microbiome research and is the first to describe the rodent gut microbiome from the GRV.
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Affiliation(s)
- Enas Al-khlifeh
- Laboratory of Immunology, Department of Medical Laboratory Science, Al-Balqa Applied University, Al-Salt, Jordan
| | - Sanaz Khadem
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
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21
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Mödl B, Awad M, Zwolanek D, Scharf I, Schwertner K, Milovanovic D, Moser D, Schmidt K, Pjevac P, Hausmann B, Krauß D, Mohr T, Svinka J, Kenner L, Casanova E, Timelthaler G, Sibilia M, Krieger S, Eferl R. Defects in microvillus crosslinking sensitize to colitis and inflammatory bowel disease. EMBO Rep 2023; 24:e57084. [PMID: 37691494 PMCID: PMC10561180 DOI: 10.15252/embr.202357084] [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: 02/28/2023] [Revised: 08/04/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023] Open
Abstract
Intestinal epithelial cells are covered by the brush border, which consists of densely packed microvilli. The Intermicrovillar Adhesion Complex (IMAC) links the microvilli and is required for proper brush border organization. Whether microvillus crosslinking is involved in the intestinal barrier function or colitis is currently unknown. We investigate the role of microvillus crosslinking in colitis in mice with deletion of the IMAC component CDHR5. Electron microscopy shows pronounced brush border defects in CDHR5-deficient mice. The defects result in severe mucosal damage after exposure to the colitis-inducing agent DSS. DSS increases the permeability of the mucus layer and brings bacteria in direct contact with the disorganized brush border of CDHR5-deficient mice. This correlates with bacterial invasion into the epithelial cell layer which precedes epithelial apoptosis and inflammation. Single-cell RNA sequencing data of patients with ulcerative colitis reveals downregulation of CDHR5 in enterocytes of diseased areas. Our results provide experimental evidence that a combination of microvillus crosslinking defects with increased permeability of the mucus layer sensitizes to inflammatory bowel disease.
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Affiliation(s)
- Bernadette Mödl
- Center for Cancer ResearchMedical University of Vienna & Comprehensive Cancer Center (CCC)ViennaAustria
| | - Monira Awad
- Center for Cancer ResearchMedical University of Vienna & Comprehensive Cancer Center (CCC)ViennaAustria
| | - Daniela Zwolanek
- Center for Cancer ResearchMedical University of Vienna & Comprehensive Cancer Center (CCC)ViennaAustria
| | - Irene Scharf
- Center for Cancer ResearchMedical University of Vienna & Comprehensive Cancer Center (CCC)ViennaAustria
| | - Katharina Schwertner
- Center for Cancer ResearchMedical University of Vienna & Comprehensive Cancer Center (CCC)ViennaAustria
| | - Danijela Milovanovic
- Department of Experimental and Translational Pathology, Institute of Clinical PathologyMedical University of ViennaViennaAustria
| | - Doris Moser
- Department of Cranio‐Maxillofacial and Oral SurgeryMedical University of ViennaViennaAustria
| | - Katy Schmidt
- Cell Imaging & Ultrastructure ResearchUniversity of ViennaViennaAustria
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of ViennaViennaAustria
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaAustria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of ViennaViennaAustria
- Department of Laboratory MedicineMedical University of ViennaViennaAustria
| | - Dana Krauß
- Center for Cancer ResearchMedical University of Vienna & Comprehensive Cancer Center (CCC)ViennaAustria
| | - Thomas Mohr
- Center for Cancer ResearchMedical University of Vienna & Comprehensive Cancer Center (CCC)ViennaAustria
- Department of Analytical ChemistryUniversity of ViennaViennaAustria
- Joint Metabolome FacilityUniversity of Vienna and Medical University ViennaViennaAustria
| | - Jasmin Svinka
- Center for Cancer ResearchMedical University of Vienna & Comprehensive Cancer Center (CCC)ViennaAustria
| | - Lukas Kenner
- Department of Experimental and Translational Pathology, Institute of Clinical PathologyMedical University of ViennaViennaAustria
- Department of Laboratory Animal PathologyUniversity of Veterinary Medicine ViennaViennaAustria
| | - Emilio Casanova
- Center of Physiology and Pharmacology, Institute of PharmacologyMedical University of Vienna & Comprehensive Cancer Center (CCC)ViennaAustria
| | - Gerald Timelthaler
- Center for Cancer ResearchMedical University of Vienna & Comprehensive Cancer Center (CCC)ViennaAustria
| | - Maria Sibilia
- Center for Cancer ResearchMedical University of Vienna & Comprehensive Cancer Center (CCC)ViennaAustria
| | - Sigurd Krieger
- Department of Experimental and Translational Pathology, Institute of Clinical PathologyMedical University of ViennaViennaAustria
| | - Robert Eferl
- Center for Cancer ResearchMedical University of Vienna & Comprehensive Cancer Center (CCC)ViennaAustria
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22
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Metze D, Schnecker J, Canarini A, Fuchslueger L, Koch BJ, Stone BW, Hungate BA, Hausmann B, Schmidt H, Schaumberger A, Bahn M, Kaiser C, Richter A. Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions. Nat Commun 2023; 14:5895. [PMID: 37736743 PMCID: PMC10516970 DOI: 10.1038/s41467-023-41524-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Climate change increases the frequency and intensity of drought events, affecting soil functions including carbon sequestration and nutrient cycling, which are driven by growing microorganisms. Yet we know little about microbial responses to drought due to methodological limitations. Here, we estimate microbial growth rates in montane grassland soils exposed to ambient conditions, drought, and potential future climate conditions (i.e., soils exposed to 6 years of elevated temperatures and elevated CO2 levels). For this purpose, we combined 18O-water vapor equilibration with quantitative stable isotope probing (termed 'vapor-qSIP') to measure taxon-specific microbial growth in dry soils. In our experiments, drought caused >90% of bacterial and archaeal taxa to stop dividing and reduced the growth rates of persisting ones. Under drought, growing taxa accounted for only 4% of the total community as compared to 35% in the controls. Drought-tolerant communities were dominated by specialized members of the Actinobacteriota, particularly the genus Streptomyces. Six years of pre-exposure to future climate conditions (3 °C warming and + 300 ppm atmospheric CO2) alleviated drought effects on microbial growth, through more drought-tolerant taxa across major phyla, accounting for 9% of the total community. Our results provide insights into the response of active microbes to drought today and in a future climate, and highlight the importance of studying drought in combination with future climate conditions to capture interactive effects and improve predictions of future soil-climate feedbacks.
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Affiliation(s)
- Dennis Metze
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria.
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alberto Canarini
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Lucia Fuchslueger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Benjamin J Koch
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bram W Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Schaumberger
- Agricultural Research and Education Centre Raumberg-Gumpenstein, Irdning, Austria
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- International Institute for Applied Systems Analysis, Advancing Systems Analysis Program, Laxenburg, Austria.
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23
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Čačković A, Kajan K, Selak L, Marković T, Brozičević A, Pjevac P, Orlić S. Hydrochemical and Seasonally Conditioned Changes of Microbial Communities in the Tufa-Forming Freshwater Network Ecosystem. mSphere 2023:e0060222. [PMID: 37097185 DOI: 10.1128/msphere.00602-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Freshwater network ecosystems consist of interconnected lotic and lentic environments within the same catchment area. Using Plitvice Lakes as an example, we studied the changes in environmental conditions and microbial communities (bacteria and fungi) that occur with downstream flow. Water samples from tributaries, interlake streams, connections of the cascading lakes, and the Korana River, the main outflow of the system, were characterized using amplicon sequencing of bacterial 16S rRNA and fungal ITS2 genes. Our results show that different environmental conditions and bacterial and fungal communities prevail among the three stream types within the freshwater network ecosystem during multiple sampling seasons. Microbial community differences were also confirmed along the longitudinal gradient between the most distant sampling sites. The higher impact of "mass effect" was evident during spring and winter, while "species sorting" and "environmental selection" was more pronounced during summer. Prokaryotic community assembly was majorly influenced by deterministic processes, while fungal community assembly was highly dominated by stochastic processes, more precisely by the undominated fraction, which is not dominated by any process. Despite the differences between stream types, the microbial community of Plitvice Lakes is shown to be very stable by the core microbiome that makes up the majority of stream communities. Our results suggest microbial community succession along the river-lake continuum of microbial communities in small freshwater network ecosystems with developed tufa barriers. IMPORTANCE Plitvice Lakes represent a rare freshwater ecosystem consisting of a complex network of lakes and waterfalls connecting them, as well as rivers and streams supplying water to the lake basin. The unique geomorphological, hydrological, biogeochemical, and biological phenomenon of Plitvice Lakes lies in the biodynamic process of forming tufa barriers. In addition to microbial communities, abiotic water factors also have a major influence on the formation of tufa. Therefore, it is important to understand how changes in environmental conditions and microbial community assembly affect the functioning of the ecosystem of a freshwater network with developed tufa barriers.
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Affiliation(s)
- Andrea Čačković
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
| | - Lorena Selak
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Andrijana Brozičević
- Scientific Research Center "Dr. Ivo Pevalek," Plitvice Lakes National Park, Plitvička Jezera, Croatia
| | - Petra Pjevac
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna, Vienna, Austria
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
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24
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Tauber J, Möstl D, Vierheilig J, Saracevic E, Svardal K, Krampe J. Biological Methanation in an Anaerobic Biofilm Reactor—Trace Element and Mineral Requirements for Stable Operation. Processes (Basel) 2023. [DOI: 10.3390/pr11041013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Biological methanation of carbon dioxide using hydrogen makes it possible to improve the methane and energy content of biogas produced from sewage sludge and organic residuals and to reach the requirements for injection into the natural gas network. Biofilm reactors, so-called trickling bed reactors, offer a relatively simple, energy-efficient, and reliable technique for upgrading biogas via ex-situ methanation. A mesophilic lab-scale biofilm reactor was operated continuously for nine months to upgrade biogas from anaerobic sewage sludge digestion to a methane content >98%. To supply essential trace elements to the biomass, a stock solution was fed to the trickling liquid. Besides standard parameters and gas quality, concentrations of Na, K, Ca, Mg, Ni, and Fe were measured in the liquid and the biofilm using ICP-OES (inductively coupled plasma optical emission spectrometry) to examine the biofilms load-dependent uptake rate and to calculate quantities required for a stable operation. Additionally, microbial community dynamics were monitored by amplicon sequencing (16S rRNA gene). It was found that all investigated (trace) elements are taken up by the biomass. Some are absorbed depending on the load, others independently of it. For example, a biomass-specific uptake of 0.13 mg·g−1·d−1 for Ni and up to 50 mg·g−1·d−1 for Mg were measured.
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25
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Retter A, Haas JC, Birk S, Stumpp C, Hausmann B, Griebler C, Karwautz C. From the Mountain to the Valley: Drivers of Groundwater Prokaryotic Communities along an Alpine River Corridor. Microorganisms 2023; 11:microorganisms11030779. [PMID: 36985351 PMCID: PMC10055094 DOI: 10.3390/microorganisms11030779] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/08/2023] [Accepted: 03/11/2023] [Indexed: 03/19/2023] Open
Abstract
Rivers are the “tip of the iceberg”, with the underlying groundwater being the unseen freshwater majority. Microbial community composition and the dynamics of shallow groundwater ecosystems are thus crucial, due to their potential impact on ecosystem processes and functioning. In early summer and late autumn, samples of river water from 14 stations and groundwater from 45 wells were analyzed along a 300 km transect of the Mur River valley, from the Austrian alps to the flats at the Slovenian border. The active and total prokaryotic communities were characterized using high-throughput gene amplicon sequencing. Key physico-chemical parameters and stress indicators were recorded. The dataset was used to challenge ecological concepts and assembly processes in shallow aquifers. The groundwater microbiome is analyzed regarding its composition, change with land use, and difference to the river. Community composition and species turnover differed significantly. At high altitudes, dispersal limitation was the main driver of groundwater community assembly, whereas in the lowland, homogeneous selection explained the larger share. Land use was a key determinant of the groundwater microbiome composition. The alpine region was more diverse and richer in prokaryotic taxa, with some early diverging archaeal lineages being highly abundant. This dataset shows a longitudinal change in prokaryotic communities that is dependent on regional differences affected by geomorphology and land use.
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Affiliation(s)
- Alice Retter
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Wien, Austria
| | | | - Steffen Birk
- Institute of Earth Sciences, NAWI Graz Geocenter, University of Graz, 8010 Graz, Austria
| | - Christine Stumpp
- Institute of Soil Physics and Rural Water Management, University of Natural Resources and Life Sciences (BOKU), 1180 Wien, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Wien, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Wien, Austria
| | - Christian Griebler
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Wien, Austria
| | - Clemens Karwautz
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Wien, Austria
- Correspondence:
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26
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Doulidis PG, Galler AI, Hausmann B, Berry D, Rodríguez-Rojas A, Burgener IA. Gut microbiome signatures of Yorkshire Terrier enteropathy during disease and remission. Sci Rep 2023; 13:4337. [PMID: 36927871 PMCID: PMC10018597 DOI: 10.1038/s41598-023-31024-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
The role of the gut microbiome in developing Inflammatory Bowel Disease (IBD) in humans and dogs has received attention in recent years. Evidence suggests that IBD is associated with alterations in gut microbial composition, but further research is needed in veterinary medicine. The impact of IBD treatment on the gut microbiome needs to be better understood, especially in a breed-specific form of IBD in Yorkshire Terriers known as Yorkshire Terrier Enteropathy (YTE). This study aimed to investigate the difference in gut microbiome composition between YTE dogs during disease and remission and healthy Yorkshire Terriers. Our results showed a significant increase in specific taxa such as Clostridium sensu stricto 1, Escherichia-Shigella, and Streptococcus, and a decrease in Bacteroides, Prevotella, Alloprevotella, and Phascolarctobacterium in YTE dogs compared to healthy controls. No significant difference was found between the microbiome of dogs in remission and those with active disease, suggesting that the gut microbiome is affected beyond clinical recovery.
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Affiliation(s)
- Pavlos G Doulidis
- Department for Small Animal Internal Medicine, Clinic for Small Animals and Horses, University of Veterinary Medicine, Vienna, Austria
| | - Alexandra I Galler
- Department for Small Animal Internal Medicine, Clinic for Small Animals and Horses, University of Veterinary Medicine, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna, University of Vienna, Vienna, Austria.,Division of Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - David Berry
- Joint Microbiome Facility of the Medical University of Vienna, University of Vienna, Vienna, Austria.,Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Alexandro Rodríguez-Rojas
- Department for Small Animal Internal Medicine, Clinic for Small Animals and Horses, University of Veterinary Medicine, Vienna, Austria
| | - Iwan A Burgener
- Department for Small Animal Internal Medicine, Clinic for Small Animals and Horses, University of Veterinary Medicine, Vienna, Austria.
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Osvatic JT, Yuen B, Kunert M, Wilkins L, Hausmann B, Girguis P, Lundin K, Taylor J, Jospin G, Petersen JM. Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis. THE ISME JOURNAL 2023; 17:453-466. [PMID: 36639537 PMCID: PMC9938160 DOI: 10.1038/s41396-022-01355-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023]
Abstract
Chemosynthetic symbioses between bacteria and invertebrates occur worldwide from coastal sediments to the deep sea. Most host groups are restricted to either shallow or deep waters. In contrast, Lucinidae, the most species-rich family of chemosymbiotic invertebrates, has both shallow- and deep-sea representatives. Multiple lucinid species have independently colonized the deep sea, which provides a unique framework for understanding the role microbial symbionts play in evolutionary transitions between shallow and deep waters. Lucinids acquire their symbionts from their surroundings during early development, which may allow them to flexibly acquire symbionts that are adapted to local environments. Via metagenomic analyses of museum and other samples collected over decades, we investigated the biodiversity and metabolic capabilities of the symbionts of 22 mostly deep-water lucinid species. We aimed to test the theory that the symbiont played a role in adaptation to life in deep-sea habitats. We identified 16 symbiont species, mostly within the previously described genus Ca. Thiodiazotropha. Most genomic functions were shared by both shallow-water and deep-sea Ca. Thiodiazotropha, though nitrogen fixation was exclusive to shallow-water species. We discovered multiple cases of symbiont switching near deep-sea hydrothermal vents and cold seeps, where distantly related hosts convergently acquired novel symbionts from a different bacterial order. Finally, analyses of selection revealed consistently stronger purifying selection on symbiont genomes in two extreme habitats - hydrothermal vents and an oxygen-minimum zone. Our findings reveal that shifts in symbiont metabolic capability and, in some cases, acquisition of a novel symbiont accompanied adaptation of lucinids to challenging deep-sea habitats.
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Affiliation(s)
- Jay T. Osvatic
- grid.10420.370000 0001 2286 1424University of Vienna, Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, Division of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria ,University of Venna, Doctoral School in Microbiology and Environmental Science, Djerassiplatz 1, 1030 Vienna, Austria
| | - Benedict Yuen
- grid.10420.370000 0001 2286 1424University of Vienna, Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, Division of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria
| | - Martin Kunert
- grid.10420.370000 0001 2286 1424University of Vienna, Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, Division of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria
| | - Laetitia Wilkins
- grid.419529.20000 0004 0491 3210Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28209 Bremen, Germany
| | - Bela Hausmann
- grid.10420.370000 0001 2286 1424Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Vienna, Austria ,grid.22937.3d0000 0000 9259 8492Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Peter Girguis
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA
| | - Kennet Lundin
- grid.516430.50000 0001 0059 3334Gothenburg Natural History Museum, Box 7283, 40235 Gothenburg, Sweden ,grid.8761.80000 0000 9919 9582Gothenburg Global Biodiversity Centre, Box 461, 40530 Gothenburg, Sweden
| | - John Taylor
- grid.35937.3b0000 0001 2270 9879Natural History Museum, Cromwell Rd, London, SW7 5BD UK
| | | | - Jillian M. Petersen
- grid.10420.370000 0001 2286 1424University of Vienna, Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, Division of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria
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28
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Graffius S, Garzón JFG, Zehl M, Pjevac P, Kirkegaard R, Flieder M, Loy A, Rattei T, Ostrovsky A, Zotchev SB. Secondary Metabolite Production Potential in a Microbiome of the Freshwater Sponge Spongilla lacustris. Microbiol Spectr 2023; 11:e0435322. [PMID: 36728429 PMCID: PMC10100984 DOI: 10.1128/spectrum.04353-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/17/2023] [Indexed: 02/03/2023] Open
Abstract
Marine and freshwater sponges harbor diverse communities of bacteria with vast potential to produce secondary metabolites that may play an important role in protecting the host from predators and infections. In this work, we initially used cultivation and metagenomics to investigate the microbial community of the freshwater sponge Spongilla lacustris collected in an Austrian lake. Representatives of 41 bacterial genera were isolated from the sponge sample and classified according to their 16S rRNA gene sequences. The genomes of 33 representative isolates and the 20 recovered metagenome-assembled genomes (MAGs) contained in total 306 secondary metabolite biosynthesis gene clusters (BGCs). Comparative 16S rRNA gene and genome analyses showed very little taxon overlap between the recovered isolates and the sponge community as revealed by cultivation-independent methods. Both culture-independent and -dependent analyses suggested high biosynthetic potential of the S. lacustris microbiome, which was confirmed experimentally even at the subspecies level for two Streptomyces isolates. To our knowledge, this is the most thorough description of the secondary metabolite production potential of a freshwater sponge microbiome to date. IMPORTANCE A large body of research is dedicated to marine sponges, filter-feeding animals harboring rich bacterial microbiomes believed to play an important role in protecting the host from predators and infections. Freshwater sponges have received so far much less attention with respect to their microbiomes, members of which may produce bioactive secondary metabolites with potential to be developed into drugs to treat a variety of diseases. In this work, we investigated the potential of bacteria associated with the freshwater sponge Spongilla lacustris to biosynthesize diverse secondary metabolites. Using culture-dependent and -independent methods, we discovered over 300 biosynthetic gene clusters in sponge-associated bacteria and proved production of several compounds by selected isolates using genome mining. Our results illustrate the importance of a complex approach when dealing with microbiomes of multicellular organisms that may contain producers of medically important secondary metabolites.
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Affiliation(s)
- Sophie Graffius
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Vienna, Austria
| | | | - Martin Zehl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Rasmus Kirkegaard
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Mathias Flieder
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational System Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Andrew Ostrovsky
- Department of Palaeontology, Faculty of Earth Sciences, Geography and Astronomy, Geozentrum, University of Vienna, Vienna, Austria
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Sergey B. Zotchev
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Vienna, Austria
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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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Lemberger U, Pjevac P, Hausmann B, Berry D, Moser D, Jahrreis V, Özsoy M, Shariat SF, Veser J. The microbiome of kidney stones and urine of patients with nephrolithiasis. Urolithiasis 2023; 51:27. [PMID: 36596939 PMCID: PMC9810570 DOI: 10.1007/s00240-022-01403-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 12/27/2022] [Indexed: 01/05/2023]
Abstract
The incidence of nephrolithiasis is rising worldwide. Although it is a multifactorial disease, lifestyle plays a major role in its etiology. Another considerable factor could be an aberrant microbiome. In our observational single-center study, we aimed to investigate the composition of bacteria in kidney stones and urine focusing on patients with features of metabolic syndrome. Catheterized urine and kidney stones were collected prospectively from 100 consecutive patients undergoing endoscopic nephrolithotomy between 2020 and 2021 at our clinic. Microbiome composition was analyzed via 16S rRNA gene amplicon sequencing. Detection of bacteria was successful in 24% of the analyzed kidney stones. These patients had a prolonged length of stay compared to patients without verifiable bacteria in their stones (2.9 vs 1.5 days). Patients with features of metabolic syndrome were characterized by kidney stones colonized with classical gastrointestinal bacteria and displayed a significant enrichment of Enterococcaceae and Enterobacteriaceae. Stones of patients without features of metabolic syndrome characterized by Ureaplasma and Staphylococcaceae. Patients with bacteria in their kidney stones exhibit a longer length of stay, possibly due to more complex care. Patients presenting with features of metabolic syndrome displayed a distinct stone microbiome compared to metabolically fit patients. Understanding the role of bacteria in stone formation could enable targeted therapy, prevention of post-operative complications and new therapeutic strategies.
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Affiliation(s)
- Ursula Lemberger
- Research Laboratory, Department of Urology, Medical University of Vienna, Waeringerguertel 18-20, 1090, Vienna, Austria.
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the 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
| | - 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
| | - David Berry
- Joint Microbiome Facility of the Medical University of Vienna and the 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
| | - Daniel Moser
- Research Laboratory, Department of Urology, Medical University of Vienna, Waeringerguertel 18-20, 1090, Vienna, Austria
| | - Victoria Jahrreis
- Research Laboratory, Department of Urology, Medical University of Vienna, Waeringerguertel 18-20, 1090, Vienna, Austria
| | - Mehmet Özsoy
- Research Laboratory, Department of Urology, Medical University of Vienna, Waeringerguertel 18-20, 1090, Vienna, Austria
| | - Shahrokh F Shariat
- Research Laboratory, Department of Urology, Medical University of Vienna, Waeringerguertel 18-20, 1090, Vienna, Austria
- Departments of Urology, Weill Cornell Medical College, New York, USA
- Department of Urology, University of Texas Southwestern, Dallas, TX, USA
- Department of Urology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute for Urology, University of Jordan, Amman, Jordan
| | - Julian Veser
- Research Laboratory, Department of Urology, Medical University of Vienna, Waeringerguertel 18-20, 1090, Vienna, Austria
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Bartosik TJ, Campion NJ, Freisl K, Liu DT, Gangl K, Stanek V, Tu A, Pjevac P, Hausmann B, Eckl-Dorna J, Schneider S. The nasal microbiome in patients suffering from non-steroidal anti-inflammatory drugs-exacerbated respiratory disease in absence of corticosteroids. Front Immunol 2023; 14:1112345. [PMID: 37122714 PMCID: PMC10140405 DOI: 10.3389/fimmu.2023.1112345] [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: 11/30/2022] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is a chronic inflammatory disease phenotypically classified by the absence (CRSsNP) or presence of nasal polyps (CRSwNP). The latter may also be associated with asthma and hypersensitivity towards non-steroidal anti-inflammatory drugs (NSAID) as a triad termed NSAID-exacerbated respiratory disease (N-ERD). The role of the microbiome in these different disease entities with regard to the underlying inflammatory process and disease burden is yet not fully understood. To address this question, we measured clinical parameters and collected nasal samples (nasal mucosal fluids, microbiome swabs from middle meatus and anterior naris) of patients suffering from CRSsNP (n=20), CRSwNP (n=20) or N-ERD (n=20) as well as from patients without CRS (=disease controls, n=20). Importantly, all subjects refrained from taking local or systemic corticosteroids or immunosuppressants for at least two weeks prior to sampling. The nasal microbiome was analyzed using 16S rRNA gene amplicon sequencing, and levels of 33 inflammatory cytokines were determined in nasal mucosal fluids using the MSD platform. Patients suffering from N-ERD and CRSwNP showed significantly worse smell perception and significantly higher levels of type 2 associated cytokines IL-5, IL-9, Eotaxin and CCL17. Across all 4 patient groups, Corynebacteria and Staphylococci showed the highest relative abundances. Although no significant difference in alpha and beta diversity was observed between the control and the CRS groups, pairwise testing revealed a higher relative abundance of Staphylococci in the middle meatus in N-ERD patients as compared to CRSwNP (p<0.001), CRSsNP (p<0.01) and disease controls (p<0.05) and of Lawsonella in patients suffering from CRSwNP in middle meatus and anterior naris in comparison to CRSsNP (p<0.0001 for both locations) and disease controls (p<0.01 and p<0.0001). Furthermore, we observed a positive correlation of Staphylococci with IL-5 (Pearson r=0.548) and a negative correlation for Corynebacteria and Eotaxin-3 (r=-0.540). Thus, in patients refraining from oral and nasal corticosteroid therapy for at least two weeks known to alter microbiome composition, we did not observe differences in microbiome alpha or beta diversity between various CRS entities and disease controls. However, our data suggest a close association between increased bacterial colonization with Staphylococci and decreased colonization by Corynebacteria as well as increased type 2 inflammation.
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Affiliation(s)
- Tina J. Bartosik
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
| | - Nicholas J. Campion
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
| | - Kilian Freisl
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
| | - David T. Liu
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
| | - Katharina Gangl
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
| | - Victoria Stanek
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
| | - Aldine Tu
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - 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
| | - Julia Eckl-Dorna
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
- *Correspondence: Julia Eckl-Dorna,
| | - Sven Schneider
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
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Overbeeke A, Hausmann B, Nikolov G, Pereira FC, Herbold CW, Berry D. Nutrient niche specificity for glycosaminoglycans is reflected in polysaccharide utilization locus architecture of gut Bacteroides species. Front Microbiol 2022; 13:1033355. [PMID: 36523841 PMCID: PMC9745678 DOI: 10.3389/fmicb.2022.1033355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/11/2022] [Indexed: 09/24/2023] Open
Abstract
INTRODUCTION Glycosaminoglycans (GAGs) present in the mucosal layer can be used as nutrients by certain intestinal bacteria, particularly members of the Bacteroides. GAG abundances are altered in some diseases such as inflammatory bowel diseases, which may affect microbial composition and activity, and it is therefore important to understand GAG utilization by members of the gut microbiota. METHODS We used growth assays, transcriptomics, and comparative genomics to evaluate chondroitin sulfate (CS) and hyaluronan (HA) degradation ability by multiple gut Bacteroides species. RESULTS AND DISCUSSION We found that not all Bacteroides species able to degrade CS could also degrade HA, despite having lyases which act on both compounds. We propose that in the model organism Bacteroides thetaiotaomicron, the lyase BT_3328 in combination with surface binding proteins BT_3329 and BT_3330 and potentially BT_4411 are involved in HA breakdown. Furthermore, degradation of both compounds provides public goods for other Bacteroides, including non-degraders, suggesting that cooperative degradation as well as cross-feeding may be widespread in the mucosal glycan utilization clade.
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Affiliation(s)
- Annelieke Overbeeke
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility, Medical University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Georgi Nikolov
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Fatima C. Pereira
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Craig W. Herbold
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Joint Microbiome Facility, Medical University of Vienna, Vienna, Austria
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Selak L, Marković T, Pjevac P, Orlić S. Microbial marker for seawater intrusion in a coastal Mediterranean shallow Lake, Lake Vrana, Croatia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157859. [PMID: 35940271 DOI: 10.1016/j.scitotenv.2022.157859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/24/2022] [Accepted: 08/02/2022] [Indexed: 05/13/2023]
Abstract
Climate change-induced rising sea levels and prolonged dry periods impose a global threat to the freshwater scarcity on the coastline: salinization. Lake Vrana is the largest surface freshwater resource in mid-Dalmatia, while the local springs are heavily used in agriculture. The karstified carbonate ridge that separates this shallow lake from the Adriatic Sea enables seawater intrusion if the lakes' precipitation-evaporation balance is disturbed. In this study, the impact of anthropogenic activities and drought exuberated salinization on microbial communities was tracked in Lake Vrana and its inlets, using 16S rRNA gene sequencing. The lack of precipitation and high water temperatures in summer months introduced an imbalance in the water regime of the lake, allowing for seawater intrusion, mainly via the karst conduit Jugovir. The determined microbial community spatial differences in the lake itself and the main drainage canals were driven by salinity, drought, and nutrient loading. Particle-associated and free-living microorganisms both strongly responded to the ecosystem perturbations, and their co-occurrence was driven by the salinization event. Notably, a bloom of halotolerant taxa, predominant the sulfur-oxidizing genus Sulfurovum, emerged with increased salinity and sulfate concentrations, having the potential to be used as an indicator for salinization of shallow coastal lakes. Following summer salinization, lake water column homogenization took from a couple of weeks up to a few months, while the entire system displayed increased salinity despite increased precipitation. This study represents a valuable contribution to understanding the impact of the Freshwater Salinization Syndrome on Mediterranean lakes' microbial communities and the ecosystem resilience.
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Affiliation(s)
- Lorena Selak
- Division of Materials Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Tamara Marković
- Croatian Geological Survey, Milan Sachs 2 Street, 10000 Zagreb, Croatia
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; University of Vienna, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia.
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Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer. Leukemia 2022; 36:2705-2714. [PMID: 36224329 DOI: 10.1038/s41375-022-01712-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 11/08/2022]
Abstract
The composition of the gut microbiome influences the clinical course after allogeneic hematopoietic stem cell transplantation (HSCT), but little is known about the relevance of skin microorganisms. In a single-center, observational study, we recruited a cohort of 50 patients before undergoing conditioning treatment and took both stool and skin samples up to one year after HSCT. We could confirm intestinal dysbiosis following HSCT and report that the skin microbiome is likewise perturbed in HSCT-recipients. Overall bacterial colonization of the skin was decreased after conditioning. Particularly patients that developed acute skin graft-versus-host disease (aGVHD) presented with an overabundance of Staphylococcus spp. In addition, a loss in alpha diversity was indicative of aGVHD development already before disease onset and correlated with disease severity. Further, co-localization of CD45+ leukocytes and staphylococci was observed in the skin of aGVHD patients even before disease development and paralleled with upregulated genes required for antigen-presentation in mononuclear phagocytes. Overall, our data reveal disturbances of the skin microbiome as well as cutaneous immune response in HSCT recipients with changes associated with cutaneous aGVHD.
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Impaired Mucosal Homeostasis in Short-Term Fiber Deprivation Is Due to Reduced Mucus Production Rather Than Overgrowth of Mucus-Degrading Bacteria. Nutrients 2022; 14:nu14183802. [PMID: 36145178 PMCID: PMC9501499 DOI: 10.3390/nu14183802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/25/2022] Open
Abstract
The gut mucosal environment is key in host health; protecting against pathogens and providing a niche for beneficial bacteria, thereby facilitating a mutualistic balance between host and microbiome. Lack of dietary fiber results in erosion of the mucosal layer, suggested to be a result of increased mucus-degrading gut bacteria. This study aimed to use quantitative analyses to investigate the diet-induced imbalance of mucosal homeostasis. Seven days of fiber-deficiency affected intestinal anatomy and physiology, seen by reduced intestinal length and loss of the colonic crypt-structure. Moreover, the mucus layer was diminished, muc2 expression decreased, and impaired mucus secretion was detected by stable isotope probing. Quantitative microbiome profiling of the gut microbiota showed a diet-induced reduction in bacterial load and decreased diversity across the intestinal tract, including taxa with fiber-degrading and butyrate-producing capabilities. Most importantly, there was little change in the absolute abundance of known mucus-degrading bacteria, although, due to the general loss of taxa, relative abundance would erroneously indicate an increase in mucus degraders. These findings underscore the importance of using quantitative methods in microbiome research, suggesting erosion of the mucus layer during fiber deprivation is due to diminished mucus production rather than overgrowth of mucus degraders.
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36
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Mitrović M, Kostešić E, Marković T, Selak L, Hausmann B, Pjevac P, Orlić S. Microbial community composition and hydrochemistry of underexplored geothermal waters in Croatia. Syst Appl Microbiol 2022; 45:126359. [PMID: 36150364 DOI: 10.1016/j.syapm.2022.126359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/28/2022] [Accepted: 09/07/2022] [Indexed: 10/31/2022]
Abstract
In Croatia, a variety of geothermal springs with a wide temperature range and varied hydrochemical conditions exist, and they may harbor different niches for the distribution of microbial communities. In this study, 19 different sites, mainly located in central and eastern Croatia, were selected for primary characterization of spring hydrochemistry and microbial community composition. Using 16S rRNA gene amplicon sequencing, it was found that the bacterial communities that dominated most geothermal waters were related to Proteobacteria and Campylobacteria, while most archaeal sequences were related to Crenarchaeota. At the genus level, the prokaryotic community was highly site-specific and was often dominated by a single genus, including sites dominated by Hydrogenophilus, Sulfuricurvum, Sulfurovum, Thiofaba and Nitrospira, while the most abundant archaeal genera were affiliated to the ammonia-oxidizing archaea, Candidatus Nitrosotenuis and Candidatus Nitrososphaera. Whereas the microbial communities were overall highly location-specific, temperature, pH, ammonia, nitrate, total nitrogen, sulfate and hydrogen sulfide, as well as dissolved organic and inorganic carbon, were the abiotic factors that significantly affected microbial community composition. Furthermore, an aquifer-type effect was observed in the community composition, but there was no pronounced seasonal variability for geothermal spring communities (i.e. the community structure was mainly stable during the three seasons sampled). These results surprisingly pointed to stable and geographically unique microbial communities that were adapted to different geothermal water environments throughout Croatia. Knowing which microbial communities are present in these extreme habitats is essential for future research. They will allow us to explore further the microbial metabolisms prevailing at these geothermal sites that have high potential for biotechnological uses, as well as the establishment of the links between microbial community structure and the physicochemical environment of geothermal waters.
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Affiliation(s)
- Maja Mitrović
- Ruđer Bošković Institute, Division of Materials Chemistry, Laboratory for Precipitation Processes, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Ema Kostešić
- Ruđer Bošković Institute, Division of Materials Chemistry, Laboratory for Precipitation Processes, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Tamara Marković
- Croatian Geological Survey, Milan Sachs 2 Street, 10 000 Zagreb, Croatia
| | - Lorena Selak
- Ruđer Bošković Institute, Division of Materials Chemistry, Laboratory for Precipitation Processes, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; University of Vienna, Department of Microbiology and Ecosystem Science, Divison of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria
| | - Sandi Orlić
- Ruđer Bošković Institute, Division of Materials Chemistry, Laboratory for Precipitation Processes, Bijenička cesta 54, 10 000 Zagreb, Croatia; Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia.
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How to Verify Non-Presence-The Challenge of Axenic Algae Cultivation. Cells 2022; 11:cells11162594. [PMID: 36010670 PMCID: PMC9406910 DOI: 10.3390/cells11162594] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 01/04/2023] Open
Abstract
Many phycological applications require the growth and maintenance of pure algae cultures. In some research areas, such as biochemistry and physiology, axenic growth is essential to avoid misinterpretations caused by contaminants. Nonetheless, axenicity-defined as the state of only a single strain being present, free of any other organism-needs to be verified. We compare the available methods to assess axenicity. We first purified unialgal Limnospira fusiformis cultures with an established series of axenicity treatments, and by including two additional treatment steps. The presumable axenic cultures were then tested for their axenic state by applying conventional tests on LB (lysogeny broth) agar-plates, 16S rRNA gene amplicon sequencing, flow-cytometry and epifluorescence microscopy. Only the plate tests indicated axenic conditions. We found a linear relationship between total cell counts of contaminants achieved by flow cytometry and epifluorescence microscopy, with flow cytometry counts being consistently higher. In addition, 16S rRNA gene amplicon sequencing demonstrated its superiority by not only being an efficient tool for axenicity testing, but also for identification of persistent contaminants. Although classic plate tests are still commonly used to verify axenicity, we found the LB-agar-plate technique to be inappropriate. Cultivation-independent methods are highly recommended to test for axenic conditions. A combination of flow-cytometry and 16S rRNA gene amplicon sequencing complement each other and will yield the most reliable result.
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Hu YJ, Satten GA. A rarefaction-without-resampling extension of PERMANOVA for testing presence-absence associations in the microbiome. Bioinformatics 2022; 38:3689-3697. [PMID: 35723568 PMCID: PMC9991891 DOI: 10.1093/bioinformatics/btac399] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 12/15/2022] Open
Abstract
MOTIVATION PERMANOVA is currently the most commonly used method for testing community-level hypotheses about microbiome associations with covariates of interest. PERMANOVA can test for associations that result from changes in which taxa are present or absent by using the Jaccard or unweighted UniFrac distance. However, such presence-absence analyses face a unique challenge: confounding by library size (total sample read count), which occurs when library size is associated with covariates in the analysis. It is known that rarefaction (subsampling to a common library size) controls this bias but at the potential costs of information loss and the introduction of a stochastic component into the analysis. RESULTS Here, we develop a non-stochastic approach to PERMANOVA presence-absence analyses that aggregates information over all potential rarefaction replicates without actual resampling, when the Jaccard or unweighted UniFrac distance is used. We compare this new approach to three possible ways of aggregating PERMANOVA over multiple rarefactions obtained from resampling: averaging the distance matrix, averaging the (element-wise) squared distance matrix and averaging the F-statistic. Our simulations indicate that our non-stochastic approach is robust to confounding by library size and outperforms each of the stochastic resampling approaches. We also show that, when overdispersion is low, averaging the (element-wise) squared distance outperforms averaging the unsquared distance, currently implemented in the R package vegan. We illustrate our methods using an analysis of data on inflammatory bowel disease in which samples from case participants have systematically smaller library sizes than samples from control participants. AVAILABILITY AND IMPLEMENTATION We have implemented all the approaches described above, including the function for calculating the analytical average of the squared or unsquared distance matrix, in our R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Glen A Satten
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA 30322, USA
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Amorim K, Loick-Wilde N, Yuen B, Osvatic JT, Wäge-Recchioni J, Hausmann B, Petersen JM, Fabian J, Wodarg D, Zettler ML. Chemoautotrophy, symbiosis and sedimented diatoms support high biomass of benthic molluscs in the Namibian shelf. Sci Rep 2022; 12:9731. [PMID: 35697901 PMCID: PMC9192762 DOI: 10.1038/s41598-022-13571-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/17/2022] [Indexed: 11/26/2022] Open
Abstract
The molluscs Lucinoma capensis, Lembulus bicuspidatus and Nassarius vinctus are highly abundant in Namibian oxygen minimum zone sediments. To understand which nutritional strategies allow them to reach such impressive abundances in this extreme habitat we investigated their trophic diversity, including a chemosymbiosis in L. capensis, focussing on nitrogen biochemical pathways of the symbionts. We combined results of bulk nitrogen and carbon (δ13C and δ15N) and of compound-specific isotope analyses of amino acid nitrogen (AAs-δ15NPhe and δ15NGlu), with 16S rRNA gene sequencing of L. capensis tissues and also with exploratory results of ammonium, nitrate and nitrite turnover. The trophic position (TP) of the bivalve L. capensis is placed between autotrophy and mixotrophy, consistent with its proposed symbiosis with sulfur-oxidizing Candidatus Thiodiazotropha sp. symbionts. The symbionts are here revealed to perform nitrate reduction and ammonium uptake, with clear indications of ammonium host-symbionts recycling, but surprisingly unable to fix nitrogen. The TP of the bivalve L. bicuspidatus is placed in between mixotrophy and herbivory. The TP of the gastropod N. vinctus reflected omnivory. Multiple lines of evidences in combination with current ecosystem knowledge point to sedimented diatoms as important components of L. bicuspidatus and N. vinctus' diet, likely supplemented at times with chemoautotrophic bacteria. This study highlights the importance of benthic-pelagic coupling that fosters the dietary base for macrozoobenthos in the OMZ. It further unveils that, in contrast to all shallow water lucinid symbionts, deeper water lucinid symbionts rely on ammonium assimilation rather than dinitrogen fixation to obtain nitrogen for growth.
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Affiliation(s)
- K Amorim
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany.
| | - N Loick-Wilde
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - B Yuen
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - J T Osvatic
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - J Wäge-Recchioni
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - B Hausmann
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - J M Petersen
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - J Fabian
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - D Wodarg
- Department of Marine Chemistry, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - M L Zettler
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
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40
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Karl CM, Vidakovic A, Pjevac P, Hausmann B, Schleining G, Ley JP, Berry D, Hans J, Wendelin M, König J, Somoza V, Lieder B. Individual Sweet Taste Perception Influences Salivary Characteristics After Orosensory Stimulation With Sucrose and Noncaloric Sweeteners. Front Nutr 2022; 9:831726. [PMID: 35694162 PMCID: PMC9174746 DOI: 10.3389/fnut.2022.831726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/23/2022] [Indexed: 12/05/2022] Open
Abstract
Emerging evidence points to a major role of salivary flow and viscoelastic properties in taste perception and mouthfeel. It has been proposed that sweet-tasting compounds influence salivary characteristics. However, whether perceived differences in the sensory properties of structurally diverse sweet-tasting compounds contribute to salivary flow and saliva viscoelasticity as part of mouthfeel and overall sweet taste perception remains to be clarified. In this study, we hypothesized that the sensory diversity of sweeteners would differentially change salivary characteristics in response to oral sweet taste stimulation. Therefore, we investigated salivary flow and saliva viscoelasticity from 21 healthy test subjects after orosensory stimulation with sucrose, rebaudioside M (RebM), sucralose, and neohesperidin dihydrochalcone (NHDC) in a crossover design and considered the basal level of selected influencing factors, including the basal oral microbiome. All test compounds enhanced the salivary flow rate by up to 1.51 ± 0.12 g/min for RebM compared to 1.10 ± 0.09 g/min for water within the 1st min after stimulation. The increase in flow rate was moderately correlated with the individually perceived sweet taste (r = 0.3, p < 0.01) but did not differ between the test compounds. The complex viscosity of saliva was not affected by the test compounds, but the analysis of covariance showed that it was associated (p < 0.05) with mucin 5B (Muc5B) concentration. The oral microbiome was of typical composition and diversity but was strongly individual-dependent (permutational analysis of variance (PERMANOVA): R 2 = 0.76, p < 0.001) and was not associated with changes in salivary characteristics. In conclusion, this study indicates an impact of individual sweet taste impressions on the flow rate without measurable changes in the complex viscosity of saliva, which may contribute to the overall taste perception and mouthfeel of sweet-tasting compounds.
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Affiliation(s)
- Corinna M. Karl
- Christian Doppler Laboratory for Taste Research, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Department of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Ana Vidakovic
- Christian Doppler Laboratory for Taste Research, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - 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
| | - Gerhard Schleining
- Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - David Berry
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | | | - Jürgen König
- Department of Nutritional Sciences, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Veronika Somoza
- Department of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Chair of Nutritional Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Barbara Lieder
- Christian Doppler Laboratory for Taste Research, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Department of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
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41
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Rangel F, Enes P, Gasco L, Gai F, Hausmann B, Berry D, Oliva-Teles A, Serra CR, Pereira FC. Differential Modulation of the European Sea Bass Gut Microbiota by Distinct Insect Meals. Front Microbiol 2022; 13:831034. [PMID: 35495644 PMCID: PMC9041418 DOI: 10.3389/fmicb.2022.831034] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/22/2022] [Indexed: 01/04/2023] Open
Abstract
The aquaculture industry is one of the fastest-growing sectors in animal food production. However, farming of carnivorous fish strongly relies on the use of wild fish-based meals, a practice that is environmentally and economically unsustainable. Insect-based diets constitute a strong candidate for fishmeal substitution, due to their high nutritional value and low environmental footprint. Nevertheless, data on the impact of insect meal (IM) on the gut microbiome of farmed fish are so far inconclusive, and very scarce in what concerns modulation of microbial-mediated functions. Here we use high-throughput 16S rRNA gene amplicon sequencing and quantitative PCR to evaluate the impact of different IMs on the composition and chitinolytic potential of the European sea bass gut digesta- and mucosa-associated communities. Our results show that insect-based diets of distinct origins differently impact the gut microbiota of the European sea bass (Dicentrarchus labrax). We detected clear modulatory effects of IM on the gut microbiota, which were more pronounced in the digesta, where communities differed considerably among the diets tested. Major community shifts were associated with the use of black soldier fly larvae (Hermetia illucens, HM) and pupal exuviae (HEM) feeds and were characterized by an increase in the relative abundance of the Firmicutes families Bacillaceae, Enterococcaceae, and Lachnospiraceae and the Actinobacteria family Actinomycetaceae, which all include taxa considered beneficial for fish health. Modulation of the digesta community by HEM was characterized by a sharp increase in Paenibacillus and a decrease of several Gammaproteobacteria and Bacteroidota members. In turn, a mealworm larvae-based diet (Tenebrio molitor, TM) had only a modest impact on microbiota composition. Further, using quantitative PCR, we demonstrate that shifts induced by HEM were accompanied by an increase in copy number of chitinase ChiA-encoding genes, predominantly originating from Paenibacillus species with effective chitinolytic activity. Our study reveals an HEM-driven increase in chitin-degrading taxa and associated chitinolytic activity, uncovering potential benefits of adopting exuviae-supplemented diets, a waste product of insect rearing, as a functional ingredient.
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Affiliation(s)
- Fábio Rangel
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- CIMAR/CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Paula Enes
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- CIMAR/CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Laura Gasco
- Department of Agricultural, Forest and Food Sciences, University of Turin, Torino, Italy
| | - Francesco Gai
- Institute of Science of Food Production, National Research Council, Torino, Italy
| | - 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
| | - David Berry
- Joint Microbiome Facility of the Medical University of Vienna and the 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
| | - Aires Oliva-Teles
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- CIMAR/CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Claudia R. Serra
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- CIMAR/CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Fátima C. Pereira
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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42
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Wang L, Wang N, Zhao Y, Lu G. Toxoplasma gondii causes changes in the host's expression of cancer‑associated miRNAs. Oncol Lett 2022; 23:149. [PMID: 35350589 PMCID: PMC8941548 DOI: 10.3892/ol.2022.13267] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/21/2022] [Indexed: 11/16/2022] Open
Abstract
Throughout the world, numerous individuals are infected with Toxoplasma gondii, which may improve immunity against cancer. Furthermore, microRNAs (miRs) may be differentially expressed in the host upon infection with T. gondii. In the present study, RNA-sequencing analysis and reverse transcription-quantitative PCR revealed that miR-429-3p, miR-145a-5p, miR-211-5p, miR-31-3p and miR-135a-5p were determined to be downregulated, while miR-21a-3p, miR-135b-5p, miR-210-5p and miR-146-3p were upregulated in mice post-infection with T. gondii. Antitumor genes [TNF receptor superfamily member 11b, large tumor suppressor kinase (Lats)2 and Lats1] were identified as targets of miR-429-3p, miR-145a-5p, miR-211-5p, miR-31-3p and miR-135a-5p with a luciferase reporter assay. In addition, the protein levels of Lats2 and Lats1 were detected to be higher in T. gondii-infected mice than in the control group. Therefore, these results provide favorable evidence for the suppression of cancer upon T. gondii infection and may give novel ideas for the treatment of tumors.
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Affiliation(s)
- Lin Wang
- Department of Epilepsy Center, Ji Nan Children's Hospital, Jinan, Shandong 250022, P.R. China
| | - Ning Wang
- Department of Clinical Laboratory, Qingdao Third People's Hospital, Qingdao, Shandong 266041, P.R. China
| | - Ying Zhao
- Department of Pathogen Biology, School of Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250062, P.R. China
| | - Gang Lu
- Department of Pathogen Biology, School of Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250062, P.R. China
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43
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Fillinger L, Hürkamp K, Stumpp C, Weber N, Forster D, Hausmann B, Schultz L, Griebler C. Spatial and Annual Variation in Microbial Abundance, Community Composition, and Diversity Associated With Alpine Surface Snow. Front Microbiol 2021; 12:781904. [PMID: 34912321 PMCID: PMC8667604 DOI: 10.3389/fmicb.2021.781904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/08/2021] [Indexed: 01/04/2023] Open
Abstract
Understanding microbial community dynamics in the alpine cryosphere is an important step toward assessing climate change impacts on these fragile ecosystems and meltwater-fed environments downstream. In this study, we analyzed microbial community composition, variation in community alpha and beta diversity, and the number of prokaryotic cells and virus-like particles (VLP) in seasonal snowpack from two consecutive years at three high altitude mountain summits along a longitudinal transect across the European Alps. Numbers of prokaryotic cells and VLP both ranged around 104 and 105 per mL of snow meltwater on average, with variation generally within one order of magnitude between sites and years. VLP-to-prokaryotic cell ratios spanned two orders of magnitude, with median values close to 1, and little variation between sites and years in the majority of cases. Estimates of microbial community alpha diversity inferred from Hill numbers revealed low contributions of common and abundant microbial taxa to the total taxon richness, and thus low community evenness. Similar to prokaryotic cell and VLP numbers, differences in alpha diversity between years and sites were generally relatively modest. In contrast, community composition displayed strong variation between sites and especially between years. Analyses of taxonomic and phylogenetic community composition showed that differences between sites within years were mainly characterized by changes in abundances of microbial taxa from similar phylogenetic clades, whereas shifts between years were due to significant phylogenetic turnover. Our findings on the spatiotemporal dynamics and magnitude of variation of microbial abundances, community diversity, and composition in surface snow may help define baseline levels to assess future impacts of climate change on the alpine cryosphere.
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Affiliation(s)
- Lucas Fillinger
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Kerstin Hürkamp
- Institute of Radiation Medicine, Helmholtz Zentrum München, Neuherberg, Germany
| | - Christine Stumpp
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Nina Weber
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Dominik Forster
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Neuherberg, Germany
| | - 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
| | - Lotta Schultz
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Christian Griebler
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Neuherberg, Germany
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44
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Seki D, Mayer M, Hausmann B, Pjevac P, Giordano V, Goeral K, Unterasinger L, Klebermaß-Schrehof K, De Paepe K, Van de Wiele T, Spittler A, Kasprian G, Warth B, Berger A, Berry D, Wisgrill L. Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage. Cell Host Microbe 2021; 29:1558-1572.e6. [PMID: 34480872 PMCID: PMC8525911 DOI: 10.1016/j.chom.2021.08.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/30/2021] [Accepted: 08/09/2021] [Indexed: 02/08/2023]
Abstract
Premature infants are at substantial risk for suffering from perinatal white matter injury. Though the gut microbiota has been implicated in early-life development, a detailed understanding of the gut-microbiota-immune-brain axis in premature neonates is lacking. Here, we profiled the gut microbiota, immunological, and neurophysiological development of 60 extremely premature infants, which received standard hospital care including antibiotics and probiotics. We found that maturation of electrocortical activity is suppressed in infants with severe brain damage. This is accompanied by elevated γδ T cell levels and increased T cell secretion of vascular endothelial growth factor and reduced secretion of neuroprotectants. Notably, Klebsiella overgrowth in the gut is highly predictive for brain damage and is associated with a pro-inflammatory immunological tone. These results suggest that aberrant development of the gut-microbiota-immune-brain axis may drive or exacerbate brain injury in extremely premature neonates and represents a promising target for novel intervention strategies.
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Affiliation(s)
- David Seki
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria; Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Margareta Mayer
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1090 Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria; Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1090 Vienna, Austria
| | - Vito Giordano
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Katharina Goeral
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Lukas Unterasinger
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Katrin Klebermaß-Schrehof
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Kim De Paepe
- Department of Biotechnology, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, 9000 Ghent, Belgium
| | - Tom Van de Wiele
- Department of Biotechnology, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, 9000 Ghent, Belgium
| | - Andreas Spittler
- Core Facility Flow Cytometry & Department of Surgery, Research Lab, Medical University of Vienna, 1090 Vienna, Austria
| | - Gregor Kasprian
- Division of Neuroradiology and Musculoskeletal Radiology, Department of Radiology, Medical University of Vienna, 1090 Vienna, Austria
| | - Benedikt Warth
- Department of Food Chemistry and Toxicology, University of Vienna, 1090 Vienna, Austria
| | - Angelika Berger
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria; Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1090 Vienna, Austria.
| | - Lukas Wisgrill
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria.
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