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Kühn J, Brandsch C, Bailer AC, Kiourtzidis M, Hirche F, Yu Chen C, Markó L, Bartolomaeus TUP, Löber U, Michel S, Wensch-Dorendorf M, Forslund-Startceva SK, Stangl GI. UV light exposure vs. vitamin D supplementation: a comparison of health benefits and vitamin D metabolism in a pig model. J Nutr Biochem 2024:109746. [PMID: 39178919 DOI: 10.1016/j.jnutbio.2024.109746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 08/12/2024] [Accepted: 08/16/2024] [Indexed: 08/26/2024]
Abstract
There is limited data on the effect of UV light exposure versus orally ingested vitamin D3 on vitamin D metabolism and health. A 4-week study with 16 pigs (as a model for human physiology) was conducted. The pigs were either supplemented with 20 µg/d vitamin D3 or exposed to UV light for 19 min/d to standardise plasma 25-hydroxyvitamin D3 levels. Important differences were higher levels of stored vitamin D3 in skin and subcutaneous fat, higher plasma concentrations of 3-epi-25-hydroxyvitamin D3 and increases of cutaneous lumisterol3 in UV-exposed pigs compared to supplemented pigs. UV light exposure compared to vitamin D3 supplementation resulted in lower hepatic cholesterol, higher circulating plasma nitrite, a marker of the blood pressure-lowering nitric oxide, and a reduction in the release of pro- and anti-inflammatory cytokines from stimulated peripheral blood mononuclear cells. However, plasma metabolome and stool microbiome analyses did not reveal any differences between the two groups. To conclude, the current data show important health relevant differences between oral vitamin D3 supplementation and UV light exposure. The findings may also partly explain the different vitamin D effects on health parameters obtained from association and intervention studies.
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Affiliation(s)
- Julia Kühn
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle Saale, Germany.
| | - Corinna Brandsch
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle Saale, Germany
| | - Anja C Bailer
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle Saale, Germany; Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD), Halle-Jena-Leipzig, Germany
| | - Mikis Kiourtzidis
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle Saale, Germany; Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD), Halle-Jena-Leipzig, Germany
| | - Frank Hirche
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle Saale, Germany
| | - Chia- Yu Chen
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany; Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Berlin, Germany
| | - Lajos Markó
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany; Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Berlin, Germany
| | - Theda U P Bartolomaeus
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany; Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Berlin, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany; Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Berlin, Germany
| | - Samira Michel
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle Saale, Germany
| | - Monika Wensch-Dorendorf
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle Saale, Germany
| | - Sofia K Forslund-Startceva
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany; Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Berlin, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Gabriele I Stangl
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle Saale, Germany; Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD), Halle-Jena-Leipzig, Germany
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2
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Deleu S, Jacobs I, Vazquez Castellanos JF, Verstockt S, Trindade de Carvalho B, Subotić A, Verstockt B, Arnauts K, Deprez L, Vissers E, Lenfant M, Vandermeulen G, De Hertogh G, Verbeke K, Matteoli G, Huys GRB, Thevelein JM, Raes J, Vermeire S. Effect of Mutant and Engineered High-Acetate-Producing Saccharomyces cerevisiae var. boulardii Strains in Dextran Sodium Sulphate-Induced Colitis. Nutrients 2024; 16:2668. [PMID: 39203805 PMCID: PMC11357622 DOI: 10.3390/nu16162668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/02/2024] [Accepted: 08/07/2024] [Indexed: 09/03/2024] Open
Abstract
Acetate-producing Saccharomyces cerevisiae var. boulardii strains could exert improved effects on ulcerative colitis, which here, was preclinically evaluated in an acute dextran sodium sulphate induced model of colitis. Nine-week-old female mice were divided into 12 groups, receiving either drinking water or 2.75% dextran sodium sulphate for 7 days, combined with a daily gavage of various treatments with different levels of acetate accumulation: sham control (phosphate buffered saline, no acetate), non-probiotic control (Baker's yeast, no acetate), probiotic control (Enterol®, transient acetate), and additionally several Saccharomyces cerevisiae var. boulardii strains with respectively no, high, and extra-high acetate accumulation. Disease activity was monitored daily, and feces samples were collected at different timepoints. On day 14, the mice were sacrificed, upon which blood and colonic tissue were collected for analysis. Disease activity in inflamed mice was lower when treated with the high-acetate-producing strain compared to sham and non-probiotic controls. The non-acetate-producing strain showed higher disease activity compared to the acetate-producing strains. Accordingly, higher histologic inflammation was observed in non- or transient-acetate-producing strains compared to the sham control, whereas this increase was not observed for high- and extra-high-acetate-producing strains upon induction of inflammation. These anti-inflammatory findings were confirmed by transcriptomic analysis of differentially expressed genes. Moreover, only the strain with the highest acetate production was superior in maintaining a stable gut microbial alpha-diversity upon inflammation. These findings support new possibilities for acetate-mediated management of inflammation in inflammatory bowel disease by administrating high-acetate-producing Saccharomyces cerevisae var. boulardii strains.
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Affiliation(s)
- Sara Deleu
- TARGID, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (S.D.); (E.V.)
| | - Inge Jacobs
- TARGID, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (S.D.); (E.V.)
| | - Jorge F. Vazquez Castellanos
- VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium (G.R.B.H.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Sare Verstockt
- TARGID, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (S.D.); (E.V.)
| | | | - Ana Subotić
- NovelYeast bv, Bio-Incubator BIO4, Gaston Geenslaan 3, Leuven-Heverlee, 3001 Leuven, Belgium
| | - Bram Verstockt
- TARGID, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (S.D.); (E.V.)
- Department of Gastroenterology and Hepatology, UZ Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Kaline Arnauts
- TARGID, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (S.D.); (E.V.)
| | - Lowie Deprez
- TARGID, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (S.D.); (E.V.)
| | - Eva Vissers
- TARGID, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (S.D.); (E.V.)
| | - Matthias Lenfant
- TARGID, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (S.D.); (E.V.)
- Department of Gastroenterology and Hepatology, UZ Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Greet Vandermeulen
- TARGID, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (S.D.); (E.V.)
| | - Gert De Hertogh
- TARGID, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (S.D.); (E.V.)
- Laboratory of Morphology and Molecular Pathology, UZ Leuven, 3000 Leuven, Belgium
| | - Kristin Verbeke
- TARGID, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (S.D.); (E.V.)
| | - Gianluca Matteoli
- TARGID, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (S.D.); (E.V.)
| | - Geert R. B. Huys
- VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium (G.R.B.H.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Johan M. Thevelein
- NovelYeast bv, Bio-Incubator BIO4, Gaston Geenslaan 3, Leuven-Heverlee, 3001 Leuven, Belgium
| | - Jeroen Raes
- VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium (G.R.B.H.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Séverine Vermeire
- TARGID, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (S.D.); (E.V.)
- Department of Gastroenterology and Hepatology, UZ Leuven, KU Leuven, 3000 Leuven, Belgium
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3
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Chen W, Chen X, Zhang Y, Wu H, Zhao D. Variation on gut microbiota diversity of endangered red pandas ( Ailurus fulgens) living in captivity acrosss geographical latitudes. Front Microbiol 2024; 15:1420305. [PMID: 39165571 PMCID: PMC11333448 DOI: 10.3389/fmicb.2024.1420305] [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: 04/19/2024] [Accepted: 07/17/2024] [Indexed: 08/22/2024] Open
Abstract
The gut microbiome plays important roles in metabolic and immune system related to the health of host. This study applied non-invasive sampling and 16S rDNA high-throughput sequencing to study the gut microbiota structure of red pandas (Ailurus fulgens) for the first time under different geographical latitudes in captivity. The results showed that the two predominant phyla Firmicutes (59.30%) and Proteobacteria (38.58%) constituted 97.88% of the total microbiota in all the fecal samples from north group (red pandas from Tianjin Zoo and Jinan Zoo) and south group (red pandas from Nanjing Hongshan Forest Zoo). The relative abundance of Cyanobacteria in north group was significantly higher than that in south group. At the genus level, Escherichia-Shigella (24.82%) and Clostridium_sensu_stricto_1 (23.00%) were common dominant genera. The relative abundance of norank_f__norank_o__Chloroplast, Terrisporobacter and Anaeroplasma from south group was significantly higher than that of north group. Alpha and Beta analysis consistently showed significant differences between north group and south group, however, the main functions of intestinal microbiota were basically the same, which play an important role in metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in different environments, and amino acid biosynthesis. The variations in gut microbiota between the northern and southern populations of the same species, both kept in captivity, which are primarily driven by significant differences in climate and diet. These findings provide a deeper understanding of the gut microbiota in red pandas and have important implications for their conservation, particularly in optimizing diet and environmental conditions in captivity.
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Affiliation(s)
| | | | | | - Hong Wu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Dapeng Zhao
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
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4
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Zhao Z, Amano C, Reinthaler T, Baltar F, Orellana MV, Herndl GJ. Metaproteomic analysis decodes trophic interactions of microorganisms in the dark ocean. Nat Commun 2024; 15:6411. [PMID: 39080340 PMCID: PMC11289388 DOI: 10.1038/s41467-024-50867-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: 07/14/2023] [Accepted: 07/24/2024] [Indexed: 08/02/2024] Open
Abstract
Proteins in the open ocean represent a significant source of organic matter, and their profiles reflect the metabolic activities of marine microorganisms. Here, by analyzing metaproteomic samples collected from the Pacific, Atlantic and Southern Ocean, we reveal size-fractionated patterns of the structure and function of the marine microbiota protein pool in the water column, particularly in the dark ocean (>200 m). Zooplankton proteins contributed three times more than algal proteins to the deep-sea community metaproteome. Gammaproteobacteria exhibited high metabolic activity in the deep-sea, contributing up to 30% of bacterial proteins. Close virus-host interactions of this taxon might explain the dominance of gammaproteobacterial proteins in the dissolved fraction. A high urease expression in nitrifiers suggested links between their dark carbon fixation and zooplankton urea production. In summary, our results uncover the taxonomic contribution of the microbiota to the oceanic protein pool, revealing protein fluxes from particles to the dissolved organic matter pool.
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Affiliation(s)
- Zihao Zhao
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria.
| | - Chie Amano
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Federico Baltar
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Mónica V Orellana
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria.
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands.
- Environmental & Climate Research Hub, University of Vienna, Vienna, Austria.
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5
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Kayongo A, Ntayi ML, Olweny G, Kyalo E, Ndawula J, Ssengooba W, Kigozi E, Kalyesubula R, Munana R, Namaganda J, Caroline M, Sekibira R, Bagaya BS, Kateete DP, Joloba ML, Jjingo D, Sande OJ, Mayanja-Kizza H. Airway microbiome signature accurately discriminates Mycobacterium tuberculosis infection status. iScience 2024; 27:110142. [PMID: 38904070 PMCID: PMC11187240 DOI: 10.1016/j.isci.2024.110142] [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: 01/29/2024] [Revised: 03/05/2024] [Accepted: 05/27/2024] [Indexed: 06/22/2024] Open
Abstract
Mycobacterium tuberculosis remains one of the deadliest infectious agents globally. Amidst efforts to control TB, long treatment duration, drug toxicity, and resistance underscore the need for novel therapeutic strategies. Despite advances in understanding the interplay between microbiome and disease in humans, the specific role of the microbiome in predicting disease susceptibility and discriminating infection status in tuberculosis still needs to be fully investigated. We investigated the impact of M.tb infection and M.tb-specific IFNγ immune responses on airway microbiome diversity by performing TB GeneXpert and QuantiFERON-GOLD assays during the follow-up phase of a longitudinal HIV-Lung Microbiome cohort of individuals recruited from two large independent cohorts in rural Uganda. M.tb rather than IFNγ immune response mainly drove a significant reduction in airway microbiome diversity. A microbiome signature comprising Streptococcus, Neisseria, Fusobacterium, Prevotella, Schaalia, Actinomyces, Cutibacterium, Brevibacillus, Microbacterium, and Beijerinckiacea accurately discriminated active TB from Latent TB and M.tb-uninfected individuals.
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Affiliation(s)
- Alex Kayongo
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Moses Levi Ntayi
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Geoffrey Olweny
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Edward Kyalo
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Josephine Ndawula
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Willy Ssengooba
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Robert Kalyesubula
- Department of Research, African Community Center for Social Sustainability (ACCESS), Nakaseke 256, Uganda
- Department of Medicine, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Richard Munana
- Department of Research, African Community Center for Social Sustainability (ACCESS), Nakaseke 256, Uganda
| | - Jesca Namaganda
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Musiime Caroline
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Rogers Sekibira
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Bernard Sentalo Bagaya
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - David Patrick Kateete
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Moses Lutaakome Joloba
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Daudi Jjingo
- College of Computing and Information Sciences, Computer Science, Makerere University, Kampala 256, Uganda
- African Center of Excellence in Bioinformatics and Data Science, Infectious Diseases Institute, Kampala 256, Uganda
| | - Obondo James Sande
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Harriet Mayanja-Kizza
- Department of Medicine, Makerere University, College of Health Sciences, Kampala 256, Uganda
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Tunbenjasiri K, Pongking T, Sitthirach C, Kongsintaweesuk S, Roytrakul S, Charoenlappanit S, Klungsaeng S, Anutrakulchai S, Chalermwat C, Pairojkul C, Pinlaor S, Pinlaor P. Metagenomics and metaproteomics alterations are associated with kidney disease in opisthorchiasis hamsters fed a high-fat and high-fructose diet. PLoS One 2024; 19:e0301907. [PMID: 38814931 PMCID: PMC11139331 DOI: 10.1371/journal.pone.0301907] [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: 10/02/2023] [Accepted: 03/24/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND Opisthorchis viverrini (O. viverrini, Ov) infection and consumption of high-fat and high-fructose (HFF) diet exacerbate liver and kidney disease. Here, we investigated the effects of a combination of O. viverrini infection and HFF diet on kidney pathology via changes in the gut microbiome and host proteome in hamsters. METHODOLOGY/PRINCIPAL FINDINGS Twenty animals were divided into four groups; 1) fed a normal diet not infected with O. viverrini (normal group), 2) fed an HFF diet and not infected with O. viverrini (HFF), 3) fed a normal diet and infected with O. viverrini (Ov), and 4) fed an HFF diet and infected with O. viverrini (HFFOv). DNA was extracted from fecal samples and the V3-V4 region of the bacterial 16S rRNA gene sequenced on an Illumina MiSeq sequencing platform. In addition, LC/MS-MS analysis was done. Histopathological studies and biochemical assays were also conducted. The results indicated that the HFFOv group exhibited the most severe kidney injury, manifested as elevated KIM-1 expression and accumulation of fibrosis in kidney tissue. The microbiome of the HFFOv group was more diverse than in the HFF group: there were increased numbers of Ruminococcaceae, Lachnospiraceae, Desulfovibrionaceae and Akkermansiaceae, but fewer Eggerthellaceae. In total, 243 host proteins were identified across all groups. Analysis using STITCH predicted that host proteome changes may lead to leaking of the gut, allowing molecules such as soluble CD14 and p-cresol to pass through to promote kidney disease. In addition, differential expression of TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 (Tab2, involving renal inflammation and injury) are predicted to be associated with kidney disease. CONCLUSIONS/SIGNIFICANCE The combination of HFF diet and O. viverrini infection may promote kidney injury through alterations in the gut microbiome and host proteome. This knowledge may suggest an effective strategy to prevent kidney disease beyond the early stages.
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Affiliation(s)
- Keerapach Tunbenjasiri
- Biomedical Science Program, Graduate School, Khon Kaen University, Khon Kaen, Thailand
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, Thailand
| | - Thatsanapong Pongking
- Biomedical Science Program, Graduate School, Khon Kaen University, Khon Kaen, Thailand
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, Thailand
| | - Chutima Sitthirach
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, Thailand
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Suppakrit Kongsintaweesuk
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, Thailand
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Sitiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sawanya Charoenlappanit
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sirinapha Klungsaeng
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, Thailand
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sirirat Anutrakulchai
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, Thailand
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Chalongchai Chalermwat
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Chawalit Pairojkul
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Somchai Pinlaor
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, Thailand
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Porntip Pinlaor
- Chronic Kidney Disease Prevention in Northeastern Thailand, Khon Kaen University, Khon Kaen, Thailand
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
- Department of Microbiology, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
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7
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Caenepeel C, Deleu S, Vazquez Castellanos JF, Arnauts K, Braekeleire S, Machiels K, Baert F, Mana F, Pouillon L, Hindryckx P, Lobaton T, Louis E, Franchimont D, Verstockt B, Ferrante M, Sabino J, Vieira-Silva S, Falony G, Raes J, Vermeire S. Rigorous Donor Selection for Fecal Microbiota Transplantation in Active Ulcerative Colitis: Key Lessons From a Randomized Controlled Trial Halted for Futility. Clin Gastroenterol Hepatol 2024:S1542-3565(24)00492-0. [PMID: 38788915 DOI: 10.1016/j.cgh.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/03/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND & AIMS Rigorous donor preselection on microbiota level, strict anaerobic processing, and repeated fecal microbiota transplantation (FMT) administration were hypothesized to improve FMT induction of remission in ulcerative colitis (UC). METHODS The RESTORE-UC trial was a multi-centric, double-blind, sham-controlled, randomized trial. Patients with moderate to severe UC (defined by total Mayo 4-10) were randomly allocated to receive 4 anaerobic-prepared allogenic or autologous donor FMTs. Allogenic donor material was selected after a rigorous screening based on microbial cell count, enterotype, and the abundance of specific genera. The primary endpoint was steroid-free clinical remission (total Mayo ≤2, no sub-score >1) at week 8. A pre-planned futility analysis was performed after 66% (n = 72) of intended inclusions (n = 108). Quantitative microbiome profiling (n = 44) was performed at weeks 0 and 8. RESULTS In total, 72 patients were included, of which 66 received at least 1 FMT (allogenic FMT, n = 30 and autologous FMT, n = 36). At week 8, respectively, 3 and 5 patients reached the primary endpoint of steroid-free clinical remission (P = .72), indicating no treatment difference of at least 5% in favor of allogenic FMT. Hence, the study was stopped due to futility. Microbiome analysis showed numerically more enterotype transitions upon allogenic FMT compared with autologous FMT, and more transitions were observed when patients were treated with a different enterotype than their own at baseline (P = .01). Primary response was associated with lower total Mayo scores, lower bacterial cell counts, and higher Bacteroides 2 prevalence at baseline. CONCLUSION The RESTORE-UC trial did not meet its primary endpoint of increased steroid-free clinical remission at week 8. Further research should additionally consider patient selection, sterilized sham-control, increased frequency, density, and viability of FMT prior to administration. CLINICALTRIALS gov, Number: NCT03110289.
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Affiliation(s)
- Clara Caenepeel
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium; University Hospitals Leuven, Department of Gastroenterology and Hepatology, Leuven, Belgium
| | - Sara Deleu
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Jorge Francisco Vazquez Castellanos
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium; Center for Microbiology, VIB, Leuven, Belgium
| | - Kaline Arnauts
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Sara Braekeleire
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Kathleen Machiels
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Filip Baert
- AZ Delta Roeselare, Department of Gastroenterology and Hepatology, Roeselare, Belgium
| | - Fazia Mana
- University Hospitals Brussels, Department of Gastroenterology and Hepatology, Brussels, Belgium
| | - Lieven Pouillon
- Imelda Hospital Bonheiden, Department of Gastroenterology and Hepatology, Bonheiden, Belgium
| | - Pieter Hindryckx
- Ghent University Hospital, Department of Gastroenterology, Ghent, Belgium
| | - Triana Lobaton
- Ghent University Hospital, Department of Gastroenterology, Ghent, Belgium; Department of Internal Medicine and Paediatrics, Ghent University, Gent, Belgium
| | - Edouard Louis
- Liège University Hospital, CHU Liège, Department of Gastroenterology and Hepatology, Liège, Belgium
| | - Denis Franchimont
- Erasmus Hospital Brussels, Department of Gastroenterology and Hepatology, Brussels, Belgium
| | - Bram Verstockt
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium; University Hospitals Leuven, Department of Gastroenterology and Hepatology, Leuven, Belgium
| | - Marc Ferrante
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium; University Hospitals Leuven, Department of Gastroenterology and Hepatology, Leuven, Belgium
| | - João Sabino
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium; University Hospitals Leuven, Department of Gastroenterology and Hepatology, Leuven, Belgium
| | - Sara Vieira-Silva
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium; Institute of Medical Microbiology and Hygiene and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany; Institute of Molecular Biology (IMB), Mainz, Germany
| | - Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium; Center for Microbiology, VIB, Leuven, Belgium; Institute of Medical Microbiology and Hygiene and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium; Center for Microbiology, VIB, Leuven, Belgium
| | - Séverine Vermeire
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium; University Hospitals Leuven, Department of Gastroenterology and Hepatology, Leuven, Belgium.
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8
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Tito RY, Verbandt S, Aguirre Vazquez M, Lahti L, Verspecht C, Lloréns-Rico V, Vieira-Silva S, Arts J, Falony G, Dekker E, Reumers J, Tejpar S, Raes J. Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development. Nat Med 2024; 30:1339-1348. [PMID: 38689063 PMCID: PMC11108775 DOI: 10.1038/s41591-024-02963-2] [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: 11/18/2022] [Accepted: 03/29/2024] [Indexed: 05/02/2024]
Abstract
Despite substantial progress in cancer microbiome research, recognized confounders and advances in absolute microbiome quantification remain underused; this raises concerns regarding potential spurious associations. Here we study the fecal microbiota of 589 patients at different colorectal cancer (CRC) stages and compare observations with up to 15 published studies (4,439 patients and controls total). Using quantitative microbiome profiling based on 16S ribosomal RNA amplicon sequencing, combined with rigorous confounder control, we identified transit time, fecal calprotectin (intestinal inflammation) and body mass index as primary microbial covariates, superseding variance explained by CRC diagnostic groups. Well-established microbiome CRC targets, such as Fusobacterium nucleatum, did not significantly associate with CRC diagnostic groups (healthy, adenoma and carcinoma) when controlling for these covariates. In contrast, the associations of Anaerococcus vaginalis, Dialister pneumosintes, Parvimonas micra, Peptostreptococcus anaerobius, Porphyromonas asaccharolytica and Prevotella intermedia remained robust, highlighting their future target potential. Finally, control individuals (age 22-80 years, mean 57.7 years, standard deviation 11.3) meeting criteria for colonoscopy (for example, through a positive fecal immunochemical test) but without colonic lesions are enriched for the dysbiotic Bacteroides2 enterotype, emphasizing uncertainties in defining healthy controls in cancer microbiome research. Together, these results indicate the importance of quantitative microbiome profiling and covariate control for biomarker identification in CRC microbiome studies.
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Affiliation(s)
- Raúl Y Tito
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Sara Verbandt
- Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Marta Aguirre Vazquez
- Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Leo Lahti
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Computing, University of Turku, Turku, Finland
| | - Chloe Verspecht
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Verónica Lloréns-Rico
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Systems Biology of Host-Microbiome Interactions Laboratory, Principe Felipe Research Center (CIPF), Valencia, Spain
| | - Sara Vieira-Silva
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Institute of Medical Microbiology and Hygiene and Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
| | - Janine Arts
- Oncology, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Institute of Medical Microbiology and Hygiene and Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Evelien Dekker
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Joke Reumers
- Therapeutics Discovery, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Sabine Tejpar
- Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium.
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium.
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9
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Gad M, Cao M, Qin D, Sun Q, Yu CP, Hu A. Development, validation, and application of a microbial community-based index of biotic integrity for assessing the ecological status of a peri-urban watershed in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 910:168659. [PMID: 37979863 DOI: 10.1016/j.scitotenv.2023.168659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 11/20/2023]
Abstract
This study represents the pioneering effort in employing 16S rRNA-bacteria and 18S rRNA-microeukaryotes to construct the microbial community-based index of biotic integrity (MC-IBI) for assessing the ecological health of riverine ecosystems. The MC-IBI was developed, validated, and implemented using water samples from the Changle River watershed, encompassing both wet and dry seasons. A total of 205 metrics, containing microbial diversity, composition, pollution tolerance/sensitivity, and functional categories, were selected as candidates for evaluation. Following a rigorous screening process, five core metrics were identified as key indicators, namely Pielou's evenness of microeukaryotes, %Cryptophyceae, %Proteobacteria, %Oxyphotobacteria, and % 16S rRNA gene-human pathogens. Moreover, redundancy analysis revealed three metrics (i.e., Pielou's evenness, % 16S rRNA gene-human pathogens, and % Proteobacteria) were positively correlated with impairment conditions. In contrast, two metrics (i.e., %Oxyphotobacteria and %Cryptophyceae) were associated positively with reference conditions. Notably, the developed MC-IBI demonstrates clear discrimination between reference and impaired sites and significantly correlates with environmental parameters and land use patterns. A path model analysis revealed that land use patterns (i.e., build-up land, cropland) negatively impacted the MC-IBI scores. The application of the MC-IBI method yielded an assessment of the ecological conditions at the 73 sampling locations within the Changle River watershed, assigning them into categories of "Very good" (4.1 %), "Good" (4.1 %), "Moderate" (5.5 %), "Poor" (21.9 %), and "Very poor" (64.4 %). This bioassessment framework presents an innovative approach toward the preservation, maintenance, and management of riverine ecosystems.
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Affiliation(s)
- Mahmoud Gad
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Water Pollution Research Department, National Research Centre, Giza 12622, Egypt
| | - Meixian Cao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dan Qin
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qian Sun
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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10
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Gilbert BTP, Tadeo RYT, Lamacchia C, Studer O, Courvoisier D, Raes J, Finckh A. Gut microbiome and intestinal inflammation in preclinical stages of rheumatoid arthritis. RMD Open 2024; 10:e003589. [PMID: 38296308 PMCID: PMC10836359 DOI: 10.1136/rmdopen-2023-003589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/15/2024] [Indexed: 02/05/2024] Open
Abstract
BACKGROUND Faecal Prevotellaceae, and other microbes, have been associated with rheumatoid arthritis (RA) and preclinical RA. We have performed a quantitative microbiome profiling study in preclinical stages of RA. METHODS First-degree relatives of patients with RA (RA-FDRs) from the SCREEN-RA cohort were categorised into four groups: controls, healthy asymptomatic RA-FDRs; high genetic risk, asymptomatic RA-FDRs with two copies of the shared epitope; autoimmunity, asymptomatic RA-FDRs with RA-associated autoimmunity; and symptomatic, clinically suspect arthralgias or untreated new-onset RA.Faecal samples were collected and frozen. 16S sequencing was performed, processed with DADA2 pipeline and Silva database. Cell counts (cytometry) and faecal calprotectin (enzyme-linked immunosorbent assay, ELISA) were also obtained. Microbial community analyses were conducted using non-parametric tests, such as permutational multivariate analysis of variance (PERMANOVA), Wilcoxon and Kruskal-Wallis, or Aldex2. RESULTS A total of 371 individuals were included and categorised according to their preclinical stage of the disease. Groups had similar age, gender and body mass index. We found no significant differences in the quantitative microbiome profiles by preclinical stages (PERMANOVA, R2=0.00798, p=0.56) and, in particular, no group differences in Prevotellaceae abundance. Results were similar when using relative microbiome profiling data (PERMANOVA, R2=0.0073, p=0.83) or Aldex2 on 16S sequence counts. Regarding faecal calprotectin, we found no differences between groups (p=0.3). CONCLUSIONS We could not identify microbiome profiles associated with preclinical stages of RA. Only in a subgroup of individuals with the most pronounced phenotypes did we modestly retrieve the previously reported associations.
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Affiliation(s)
- Benoît Thomas P Gilbert
- Division of Rheumatology, HUG, Geneva, Switzerland
- Geneva Centre for Inflammation Research, UNIGE, Geneva, Switzerland
| | - Raul Yhossef Tito Tadeo
- KU Leuven, Department of Microbiology, Immunology, and Transplantation, Rega Institute for Medical Research, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, B-3000 Leuven, Belgium
| | - Celine Lamacchia
- Division of Rheumatology, HUG, Geneva, Switzerland
- Geneva Centre for Inflammation Research, UNIGE, Geneva, Switzerland
| | - Olivia Studer
- Division of Rheumatology, HUG, Geneva, Switzerland
- Geneva Centre for Inflammation Research, UNIGE, Geneva, Switzerland
| | - Delphine Courvoisier
- Division of Rheumatology, HUG, Geneva, Switzerland
- Geneva Centre for Inflammation Research, UNIGE, Geneva, Switzerland
| | - Jeroen Raes
- KU Leuven, Department of Microbiology, Immunology, and Transplantation, Rega Institute for Medical Research, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, B-3000 Leuven, Belgium
| | - Axel Finckh
- Division of Rheumatology, HUG, Geneva, Switzerland
- Geneva Centre for Inflammation Research, UNIGE, Geneva, Switzerland
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11
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Zhang L, Adyari B, Hou L, Yang X, Gad M, Wang Y, Ma C, Sun Q, Tang Q, Zhang Y, Yu CP, Hu A. Mass-immigration shapes the antibiotic resistome of wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168193. [PMID: 37914134 DOI: 10.1016/j.scitotenv.2023.168193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023]
Abstract
Wastewater treatment plants (WWTPs) are the hotspots for the spread of antibiotic resistance genes (ARGs) into the environment. Nevertheless, a comprehensive assessment of the city-level and short-term daily (inter-day) variations of ARG profiles in the whole process (influent-INF, activated sludge-AS and effluent-EF) of WWTPs is still lacking. Here, 285 ARGs and ten mobile gene elements were monitored in seven WWTPs in Xiamen for seven days via high-throughput qPCR. The average daily load of ARGs to WWTPs was about 1.32 × 1020 copies/d, and a total of 1.56 × 1018 copies/d was discharged to the environment across the entire city. Stochastic processes were the main force determining the assembly of ARG communities during sampling campaign, with their relative importance ranked in the order of INF > EFF > AS. There're little daily variations in ARG richness, abundance, β-diversity composition as well as assembly mechanisms. The results of SourceTracker, variation partitioning analysis, and hierarchical partitioning analysis indicated that bacteria and ARGs from upstream treatment processes played an increasingly dominant role in shaping ARG communities in AS and EFF, respectively, suggesting the importance of mass-immigration of bacteria and ARGs from the source on ARG transport in wastewater treatment processes. This emphasizes the need to revise the way we mitigate ARG contamination but focus on the source of ARGs in urban wastewater.
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Affiliation(s)
- Lanping Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Bob Adyari
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Department of Environmental Engineering, Universitas Pertamina, Jakarta 12220, Indonesia
| | - Liyuan Hou
- Department of Civil and Environmental Engineering, Utah State University, UT 84322, USA; Utah Water Research Laboratory, Utah State University, Logan, UT 84322, USA
| | - Xiaoyong Yang
- School of Environmental and Material Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Mahmoud Gad
- Water Pollution Research Department, National Research Centre, Giza 12622, Egypt
| | - Yuwen Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Cong Ma
- Xiamen Municipal Environmental Technology Co., Ltd., Xiamen 361001, China
| | - Qian Sun
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qiang Tang
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Yifeng Zhang
- Department of Environmental and Resource Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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12
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Cerk K, Ugalde‐Salas P, Nedjad CG, Lecomte M, Muller C, Sherman DJ, Hildebrand F, Labarthe S, Frioux C. Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing. Microb Biotechnol 2024; 17:e14396. [PMID: 38243750 PMCID: PMC10832553 DOI: 10.1111/1751-7915.14396] [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: 01/09/2023] [Revised: 11/27/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024] Open
Abstract
Building models is essential for understanding the functions and dynamics of microbial communities. Metabolic models built on genome-scale metabolic network reconstructions (GENREs) are especially relevant as a means to decipher the complex interactions occurring among species. Model reconstruction increasingly relies on metagenomics, which permits direct characterisation of naturally occurring communities that may contain organisms that cannot be isolated or cultured. In this review, we provide an overview of the field of metabolic modelling and its increasing reliance on and synergy with metagenomics and bioinformatics. We survey the means of assigning functions and reconstructing metabolic networks from (meta-)genomes, and present the variety and mathematical fundamentals of metabolic models that foster the understanding of microbial dynamics. We emphasise the characterisation of interactions and the scaling of model construction to large communities, two important bottlenecks in the applicability of these models. We give an overview of the current state of the art in metagenome sequencing and bioinformatics analysis, focusing on the reconstruction of genomes in microbial communities. Metagenomics benefits tremendously from third-generation sequencing, and we discuss the opportunities of long-read sequencing, strain-level characterisation and eukaryotic metagenomics. We aim at providing algorithmic and mathematical support, together with tool and application resources, that permit bridging the gap between metagenomics and metabolic modelling.
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Affiliation(s)
- Klara Cerk
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | | | - Chabname Ghassemi Nedjad
- Inria, University of Bordeaux, INRAETalenceFrance
- University of Bordeaux, CNRS, Bordeaux INP, LaBRI, UMR 5800TalenceFrance
| | - Maxime Lecomte
- Inria, University of Bordeaux, INRAETalenceFrance
- INRAE STLO¸University of RennesRennesFrance
| | | | | | - Falk Hildebrand
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | - Simon Labarthe
- Inria, University of Bordeaux, INRAETalenceFrance
- INRAE, University of Bordeaux, BIOGECO, UMR 1202CestasFrance
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13
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Quesada-Vázquez S, Castells-Nobau A, Latorre J, Oliveras-Cañellas N, Puig-Parnau I, Tejera N, Tobajas Y, Baudin J, Hildebrand F, Beraza N, Burcelin R, Martinez-Gili L, Chilloux J, Dumas ME, Federici M, Hoyles L, Caimari A, Del Bas JM, Escoté X, Fernández-Real JM, Mayneris-Perxachs J. Potential therapeutic implications of histidine catabolism by the gut microbiota in NAFLD patients with morbid obesity. Cell Rep Med 2023; 4:101341. [PMID: 38118419 PMCID: PMC10772641 DOI: 10.1016/j.xcrm.2023.101341] [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: 01/05/2023] [Revised: 07/18/2023] [Accepted: 11/22/2023] [Indexed: 12/22/2023]
Abstract
The gut microbiota contributes to the pathophysiology of non-alcoholic fatty liver disease (NAFLD). Histidine is a key energy source for the microbiota, scavenging it from the host. Its role in NAFLD is poorly known. Plasma metabolomics, liver transcriptomics, and fecal metagenomics were performed in three human cohorts coupled with hepatocyte, rodent, and Drosophila models. Machine learning analyses identified plasma histidine as being strongly inversely associated with steatosis and linked to a hepatic transcriptomic signature involved in insulin signaling, inflammation, and trace amine-associated receptor 1. Circulating histidine was inversely associated with Proteobacteria and positively with bacteria lacking the histidine utilization (Hut) system. Histidine supplementation improved NAFLD in different animal models (diet-induced NAFLD in mouse and flies, ob/ob mouse, and ovariectomized rats) and reduced de novo lipogenesis. Fecal microbiota transplantation (FMT) from low-histidine donors and mono-colonization of germ-free flies with Enterobacter cloacae increased triglyceride accumulation and reduced histidine content. The interplay among microbiota, histidine catabolism, and NAFLD opens therapeutic opportunities.
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Affiliation(s)
| | - Anna Castells-Nobau
- Department of Diabetes, Endocrinology, and Nutrition, Dr. Josep Trueta Hospital, Girona, Spain; Nutrition, Eumetabolism, and Health Group, Girona Biomedical Research Institute (IDIBGI), Girona, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Jèssica Latorre
- Department of Diabetes, Endocrinology, and Nutrition, Dr. Josep Trueta Hospital, Girona, Spain
| | - Núria Oliveras-Cañellas
- Department of Diabetes, Endocrinology, and Nutrition, Dr. Josep Trueta Hospital, Girona, Spain; Nutrition, Eumetabolism, and Health Group, Girona Biomedical Research Institute (IDIBGI), Girona, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Irene Puig-Parnau
- Department of Diabetes, Endocrinology, and Nutrition, Dr. Josep Trueta Hospital, Girona, Spain; Nutrition, Eumetabolism, and Health Group, Girona Biomedical Research Institute (IDIBGI), Girona, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Noemi Tejera
- Microbes in the Food Chain, Institute Strategic Program, Microbes and Gut Health, Institute Strategic Program - Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Yaiza Tobajas
- Eurecat, Centre Tecnològic de Catalunya, Unitat de Nutrició i Salut, Reus, Spain
| | - Julio Baudin
- Eurecat, Centre Tecnològic de Catalunya, Unitat de Nutrició i Salut, Reus, Spain
| | - Falk Hildebrand
- Microbes in the Food Chain, Institute Strategic Program, Microbes and Gut Health, Institute Strategic Program - Quadram Institute Bioscience, Norwich Research Park, Norwich, UK; Digital Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk NR4 7UZ, UK
| | - Naiara Beraza
- Microbes in the Food Chain, Institute Strategic Program, Microbes and Gut Health, Institute Strategic Program - Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Rémy Burcelin
- Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France; Université Paul Sabatier (UPS), Unité Mixte de Recherche (UMR), Toulouse, France; Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Team 2: 'Intestinal Risk Factors, Diabetes, Dyslipidemia, and Heart Failure', F-31432 Toulouse Cedex 4, France
| | - Laura Martinez-Gili
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Julien Chilloux
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Marc-Emmanuel Dumas
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Imperial College London, Du Cane Road, London W12 0NN, UK; Section of Genomic and Environmental Medicine, National Heart & Lung Institute, Imperial College London, Dovehouse Street, London SW3 6LY, UK; European Genomic Institute for Diabetes, CNRS UMR 8199, INSERM UMR 1283, Institut Pasteur de Lille, Lille University Hospital, University of Lille, 59045 Lille, France; McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montréal, QC H3A 0G1, Canada
| | - Massimo Federici
- Department of Systems Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Lesley Hoyles
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK
| | - Antoni Caimari
- Eurecat, Centre Tecnològic de Catalunya, Unitat de Nutrició i Salut, Reus, Spain
| | - Josep M Del Bas
- Eurecat, Centre Tecnològic de Catalunya, Unitat de Nutrició i Salut, Reus, Spain
| | - Xavier Escoté
- Eurecat, Centre Tecnològic de Catalunya, Unitat de Nutrició i Salut, Reus, Spain.
| | - José-Manuel Fernández-Real
- Department of Diabetes, Endocrinology, and Nutrition, Dr. Josep Trueta Hospital, Girona, Spain; Nutrition, Eumetabolism, and Health Group, Girona Biomedical Research Institute (IDIBGI), Girona, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain.
| | - Jordi Mayneris-Perxachs
- Department of Diabetes, Endocrinology, and Nutrition, Dr. Josep Trueta Hospital, Girona, Spain; Nutrition, Eumetabolism, and Health Group, Girona Biomedical Research Institute (IDIBGI), Girona, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain.
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14
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Frioux C, Ansorge R, Özkurt E, Ghassemi Nedjad C, Fritscher J, Quince C, Waszak SM, Hildebrand F. Enterosignatures define common bacterial guilds in the human gut microbiome. Cell Host Microbe 2023; 31:1111-1125.e6. [PMID: 37339626 DOI: 10.1016/j.chom.2023.05.024] [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: 01/26/2023] [Revised: 04/03/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023]
Abstract
The human gut microbiome composition is generally in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states detrimental to host health. To disentangle the inherent complexity and capture the ecological spectrum of microbiome variability, we used 5,230 gut metagenomes to characterize signatures of bacteria commonly co-occurring, termed enterosignatures (ESs). We find five generalizable ESs dominated by either Bacteroides, Firmicutes, Prevotella, Bifidobacterium, or Escherichia. This model confirms key ecological characteristics known from previous enterotype concepts, while enabling the detection of gradual shifts in community structures. Temporal analysis implies that the Bacteroides-associated ES is "core" in the resilience of westernized gut microbiomes, while combinations with other ESs often complement the functional spectrum. The model reliably detects atypical gut microbiomes correlated with adverse host health conditions and/or the presence of pathobionts. ESs provide an interpretable and generic model that enables an intuitive characterization of gut microbiome composition in health and disease.
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Affiliation(s)
- Clémence Frioux
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK; Inria, University of Bordeaux, INRAE, 33400 Talence, France.
| | - Rebecca Ansorge
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | - Ezgi Özkurt
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | | | - Joachim Fritscher
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | - Christopher Quince
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo 0318, Norway; Department of Neurology, University of California, San Francisco, San Francisco, CA 94148, USA; Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Falk Hildebrand
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK.
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15
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Lyimu WM, Leta S, Everaert N, Paeshuyse J. Influence of Live Attenuated Salmonella Vaccines on Cecal Microbiome Composition and Microbiota Abundances in Young Broiler Chickens. Vaccines (Basel) 2023; 11:1116. [PMID: 37376505 DOI: 10.3390/vaccines11061116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Salmonellosis is a global food safety challenge caused by Salmonella, a gram-negative bacterium of zoonotic importance. Poultry is considered a major reservoir for the pathogen, and humans are exposed through consumption of raw or undercooked products derived from them. Prophylaxis of Salmonella in poultry farms generally mainly involves biosecurity measures, flock testing and culling, use of antibiotics, and vaccination programs. For decades, the use of antibiotics has been a common practice to limit poultry contamination with important pathogenic bacteria such as Salmonella at the farm level. However, due to an increasing prevalence of resistance, non-therapeutic use of antibiotics in animal production has been banned in many parts of the world. This has prompted the search for non-antimicrobial alternatives. Live vaccines are among the developed and currently used methods for Salmonella control. However, their mechanism of action, particularly the effect they might have on commensal gut microbiota, is not well understood. In this study, three different commercial live attenuated Salmonella vaccines (AviPro® Salmonella Vac T, AviPro® Salmonella DUO, and AviPro® Salmonella Vac E) were used to orally vaccinate broiler chickens, and cecal contents were collected for microbiomes analysis by 16S rRNA next generation sequencing. Quantitative real-time PCR (qPCR) was used to study the cecal immune-related genes expression in the treatment groups, while Salmonella-specific antibodies were analyzed from sera and cecal extracts by enzyme-linked immunosorbent assay (ELISA). We show that vaccination with live attenuated Salmonella vaccines had a significant influence on the variability of the broiler cecal microbiota (p = 0.016). Furthermore, the vaccines AviPro® Salmonella Vac T and AviPro® Salmonella DUO, but not AviPro® Salmonella Vac E, had a significant effect (p = 0.024) on microbiota composition. This suggests that the live vaccine type used can differently alter the microbiota profiles, driving the gut colonization resistance and immune responses to pathogenic bacteria, and might impact the overall chicken health and productivity. Further investigation is, however, required to confirm this.
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Affiliation(s)
- Wilfred Michael Lyimu
- Laboratory of Host-Pathogen Interactions in Livestock, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Samson Leta
- Laboratory of Host-Pathogen Interactions in Livestock, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
- Department of Biomedical Sciences, College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu P.O. Box 34, Ethiopia
| | - Nadia Everaert
- The Nutrition and Animal Microbiota Ecosystems Laboratory, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Jan Paeshuyse
- Laboratory of Host-Pathogen Interactions in Livestock, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
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16
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Shen K, Din AU, Sinha B, Zhou Y, Qian F, Shen B. Translational informatics for human microbiota: data resources, models and applications. Brief Bioinform 2023; 24:7152256. [PMID: 37141135 DOI: 10.1093/bib/bbad168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
With the rapid development of human intestinal microbiology and diverse microbiome-related studies and investigations, a large amount of data have been generated and accumulated. Meanwhile, different computational and bioinformatics models have been developed for pattern recognition and knowledge discovery using these data. Given the heterogeneity of these resources and models, we aimed to provide a landscape of the data resources, a comparison of the computational models and a summary of the translational informatics applied to microbiota data. We first review the existing databases, knowledge bases, knowledge graphs and standardizations of microbiome data. Then, the high-throughput sequencing techniques for the microbiome and the informatics tools for their analyses are compared. Finally, translational informatics for the microbiome, including biomarker discovery, personalized treatment and smart healthcare for complex diseases, are discussed.
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Affiliation(s)
- Ke Shen
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Ahmad Ud Din
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Baivab Sinha
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Yi Zhou
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Fuliang Qian
- Center for Systems Biology, Suzhou Medical College of Soochow University, Suzhou 215123, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou 215123, China
| | - Bairong Shen
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
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17
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Plantinga AM, Kamp KJ, Wu Q, Chen L, Yoo L, Burr RL, Cain KC, Raftery D, Neto FC, Badu S, So SY, Savidge T, Shulman RJ, Heitkemper MM. Exploration of associations among dietary tryptophan, microbiome composition and function, and symptom severity in irritable bowel syndrome. Neurogastroenterol Motil 2023; 35:e14545. [PMID: 36780542 PMCID: PMC10953042 DOI: 10.1111/nmo.14545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/30/2022] [Accepted: 01/24/2023] [Indexed: 02/15/2023]
Abstract
BACKGROUND Imbalance of the tryptophan (TRP) pathway may influence symptoms among patients with irritable bowel syndrome (IBS). This study explored relationships among different components that contribute to TRP metabolism (dietary intake, stool metabolite levels, predicted microbiome metabolic capability) in females with IBS and healthy controls (HCs). Within the IBS group, we also investigated relationships between TRP metabolic determinants, Bifidobacterium abundance, and symptoms of IBS. METHODS Participants with IBS (Rome III) and HCs completed a 28-day diary of gastrointestinal symptoms and a 3-day food record for TRP intake. They provided a stool sample for shotgun metagenomics, 16 S rRNA analyses, and quantitative measurement of TRP by mass spectrometry. RESULTS Our cohort included 115 females, 69 with IBS and 46 HCs, with a mean age of 28.5 years (SD 7.4). TRP intake (p = 0.71) and stool TRP level (p = 0.27) did not differ between IBS and HC. Bifidobacterium abundance was lower in the IBS group than in HCs (p = 0.004). Predicted TRP metabolism gene content was higher in IBS than HCs (FDR-corrected q = 0.006), whereas predicted biosynthesis gene content was lower (q = 0.045). Within the IBS group, there was no association between symptom severity and TRP intake or stool TRP, but there was a significant interaction between Bifidobacterium abundance and TRP intake (q = 0.029) in predicting stool character. CONCLUSIONS Dietary TRP intake, microbiome composition, and differences in TRP metabolism constitute a complex interplay of factors that could modulate IBS symptom severity.
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Affiliation(s)
| | | | - Qinglong Wu
- Baylor College of Medicine and Texas Children’s Hospital, Houston, TX
| | - Li Chen
- University of Washington, Seattle, WA
| | - Linda Yoo
- University of Washington, Seattle, WA
| | | | | | | | | | - Shyam Badu
- Baylor College of Medicine and Texas Children’s Hospital, Houston, TX
| | - Sik Yu So
- Baylor College of Medicine and Texas Children’s Hospital, Houston, TX
| | - Tor Savidge
- Baylor College of Medicine and Texas Children’s Hospital, Houston, TX
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18
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Métris KL, Métris J. Aircraft surveys for air eDNA: probing biodiversity in the sky. PeerJ 2023; 11:e15171. [PMID: 37077310 PMCID: PMC10108859 DOI: 10.7717/peerj.15171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/13/2023] [Indexed: 04/21/2023] Open
Abstract
Air is a medium for dispersal of environmental DNA (eDNA) carried in bioaerosols, yet the atmosphere is mostly unexplored as a source of genetic material encompassing all domains of life. In this study, we designed and deployed a robust, sterilizable hardware system for airborne nucleic acid capture featuring active filtration of a quantifiable, controllable volume of air and a high-integrity chamber to protect the sample from loss or contamination. We used our hardware system on an aircraft across multiple height transects over major aerosolization sources to collect air eDNA, coupled with high-throughput amplicon sequencing using multiple DNA metabarcoding markers targeting bacteria, plants, and vertebrates to test the hypothesis of large-scale genetic presence of these bioaerosols throughout the planetary boundary layer in the lower troposphere. Here, we demonstrate that the multi-taxa DNA assemblages inventoried up to 2,500 m using our airplane-mounted hardware system are reflective of major aerosolization sources in the survey area and show previously unreported airborne species detections (i.e., Allium sativum L). We also pioneer an aerial survey flight grid standardized for atmospheric sampling of genetic material and aeroallergens using a light aircraft and limited resources. Our results show that air eDNA from terrestrial bacteria, plants, and vertebrates is detectable up to high altitude using our airborne air sampler and demonstrate the usefulness of light aircraft in monitoring campaigns. However, our work also underscores the need for improved marker choices and reference databases for species in the air column, particularly eukaryotes. Taken together, our findings reveal strong connectivity or mixing of terrestrial-associated eDNA from ground level aerosolization sources and the atmosphere, and we recommend that parameters and indices considering lifting action, atmospheric instability, and potential for convection be incorporated in future surveys for air eDNA. Overall, this work establishes a foundation for light aircraft campaigns to comprehensively and economically inventory bioaerosol emissions and impacts at scale, enabling transformative future opportunities in airborne DNA technology.
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Affiliation(s)
- Kimberly L. Métris
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States
- Airborne Science LLC, Clemson, SC, United States
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19
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Salas-Perez F, Assmann TS, Ramos-Lopez O, Martínez JA, Riezu-Boj JI, Milagro FI. Crosstalk between Gut Microbiota and Epigenetic Markers in Obesity Development: Relationship between Ruminococcus, BMI, and MACROD2/ SEL1L2 Methylation. Nutrients 2023; 15:nu15071550. [PMID: 37049393 PMCID: PMC10097304 DOI: 10.3390/nu15071550] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
Changes in gut microbiota composition and in epigenetic mechanisms have been proposed to play important roles in energy homeostasis, and the onset and development of obesity. However, the crosstalk between epigenetic markers and the gut microbiome in obesity remains unclear. The main objective of this study was to establish a link between the gut microbiota and DNA methylation patterns in subjects with obesity by identifying differentially methylated DNA regions (DMRs) that could be potentially regulated by the gut microbiota. DNA methylation and bacterial DNA sequencing analysis were performed on 342 subjects with a BMI between 18 and 40 kg/m2. DNA methylation analyses identified a total of 2648 DMRs associated with BMI, while ten bacterial genera were associated with BMI. Interestingly, only the abundance of Ruminococcus was associated with one BMI-related DMR, which is located between the MACROD2/SEL1L2 genes. The Ruminococcus abundance negatively correlated with BMI, while the hypermethylated DMR was associated with reduced MACROD2 protein levels in serum. Additionally, the mediation test showed that 19% of the effect of Ruminococcus abundance on BMI is mediated by the methylation of the MACROD2/SEL1L2 DMR. These findings support the hypothesis that a crosstalk between gut microbiota and epigenetic markers may be contributing to obesity development.
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Affiliation(s)
| | - Taís Silveira Assmann
- Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Federal University of do Rio Grande do Sul, Porto Alegre 90035-003, Brazil
| | - Omar Ramos-Lopez
- Medicine and Psychology School, Autonomous University of Baja California, Tijuana 22390, Mexico
| | - J Alfredo Martínez
- Center for Nutrition Research, University of Navarra, 31008 Pamplona, Spain
- Department of Nutrition, Food Science and Physiology, University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y la Nutrición (CIBERobn), Carlos III Health Institute, 28029 Madrid, Spain
| | - Jose Ignacio Riezu-Boj
- Center for Nutrition Research, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Fermín I Milagro
- Center for Nutrition Research, University of Navarra, 31008 Pamplona, Spain
- Department of Nutrition, Food Science and Physiology, University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y la Nutrición (CIBERobn), Carlos III Health Institute, 28029 Madrid, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
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20
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Kayongo A, Bartolomaeus TUP, Birkner T, Markó L, Löber U, Kigozi E, Atugonza C, Munana R, Mawanda D, Sekibira R, Uwimaana E, Alupo P, Kalyesubula R, Knauf F, Siddharthan T, Bagaya BS, Kateete DP, Joloba ML, Sewankambo NK, Jjingo D, Kirenga B, Checkley W, Forslund SK. Sputum Microbiome and Chronic Obstructive Pulmonary Disease in a Rural Ugandan Cohort of Well-Controlled HIV Infection. Microbiol Spectr 2023; 11:e0213921. [PMID: 36790203 PMCID: PMC10100697 DOI: 10.1128/spectrum.02139-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
Sub-Saharan Africa has increased morbidity and mortality related to chronic obstructive pulmonary disease (COPD). COPD among people living with HIV (PLWH) has not been well studied in this region, where HIV/AIDS is endemic. Increasing evidence suggests that respiratory microbial composition plays a role in COPD severity. Therefore, we aimed to investigate microbiome patterns and associations among PLWH with COPD in Sub-Saharan Africa. We conducted a cross-sectional study of 200 adults stratified by HIV and COPD in rural Uganda. Induced sputum samples were collected as an easy-to-obtain proxy for the lower respiratory tract microbiota. We performed 16S rRNA gene sequencing and used PICRUSt2 (version 2.2.3) to infer the functional profiles of the microbial community. We used a statistical tool to detect changes in specific taxa that searches and adjusts for confounding factors such as antiretroviral therapy (ART), age, sex, and other participant characteristics. We could cluster the microbial community into three community types whose distribution was shown to be significantly impacted by HIV. Some genera, e.g., Veillonella, Actinomyces, Atopobium, and Filifactor, were significantly enriched in HIV-infected individuals, while the COPD status was significantly associated with Gammaproteobacteria and Selenomonas abundance. Furthermore, reduced bacterial richness and significant enrichment in Campylobacter were associated with HIV-COPD comorbidity. Functional prediction using PICRUSt2 revealed a significant depletion in glutamate degradation capacity pathways in HIV-positive patients. A comparison of our findings with an HIV cohort from the United Kingdom revealed significant differences in the sputum microbiome composition, irrespective of viral suppression. IMPORTANCE Even with ART available, HIV-infected individuals are at high risk of suffering comorbidities, as shown by the high prevalence of noninfectious lung diseases in the HIV population. Recent studies have suggested a role for the respiratory microbiota in driving chronic lung inflammation. The respiratory microbiota was significantly altered among PLWH, with disease persisting up to 3 years post-ART initiation and HIV suppression. The community structure and diversity of the sputum microbiota in COPD are associated with disease severity and clinical outcomes, both in stable COPD and during exacerbations. Therefore, a better understanding of the sputum microbiome among PLWH could improve COPD prognostic and risk stratification strategies. In this study, we observed that in a virologically suppressed HIV cohort in rural Uganda, we could show differences in sputum microbiota stratified by HIV and COPD, reduced bacterial richness, and significant enrichment in Campylobacter associated with HIV-COPD comorbidity.
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Affiliation(s)
- Alex Kayongo
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Theda Ulrike Patricia Bartolomaeus
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Till Birkner
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Lajos Markó
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Ulrike Löber
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Edgar Kigozi
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Carolyne Atugonza
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Richard Munana
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Denis Mawanda
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Rogers Sekibira
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Esther Uwimaana
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Patricia Alupo
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Robert Kalyesubula
- African Community Center for Social Sustainability (ACCESS), Department of Research, Nakaseke, Uganda
- Makerere University, College of Health Sciences, Department of Medicine, Kampala, Uganda
| | - Felix Knauf
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Trishul Siddharthan
- University of Miami, School of Medicine, Division of pulmonary and critical care medicine, Miami, Florida, USA
| | - Bernard S. Bagaya
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - David P. Kateete
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Moses L. Joloba
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Nelson K. Sewankambo
- Makerere University, College of Health Sciences, Department of Medicine, Kampala, Uganda
| | - Daudi Jjingo
- Makerere University, College of Computing and Information Sciences, Department of Computer Science, Kampala, Uganda
- African Center of Excellence in Bioinformatics and Data Science, Infectious Diseases Institute, Kampala, Uganda
| | - Bruce Kirenga
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Makerere University, College of Health Sciences, Department of Medicine, Kampala, Uganda
| | - William Checkley
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Center for Global Non-Communicable Disease Research and Training, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sofia K. Forslund
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
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21
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Devolder L, Pauwels A, Van Remoortel A, Falony G, Vieira-Silva S, Nagels G, De Keyser J, Raes J, D’Hooghe MB. Gut microbiome composition is associated with long-term disability worsening in multiple sclerosis. Gut Microbes 2023; 15:2180316. [PMID: 36803643 PMCID: PMC9980703 DOI: 10.1080/19490976.2023.2180316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Predicting the long-term outcome of multiple sclerosis (MS) remains an important challenge to this day. As the gut microbiota is emerging as a potential player in MS, we investigated in this study whether gut microbial composition at baseline is related to long-term disability worsening in a longitudinal cohort of 111 MS patients. Fecal samples and extensive host metadata were collected at baseline and 3 months post-baseline, with additional repeated neurological measurements performed over (median) 4.4 y. Worsening (with EDSS-Plus) occurred in 39/95 patients (outcome undetermined for 16 individuals). The inflammation-associated, dysbiotic Bacteroides 2 enterotype (Bact2) was detected at baseline in 43.6% of worsened patients, while only 16.1% of non-worsened patients harbored Bact2. This association was independent of identified confounders, and Bact2 was more strongly associated with EDSS-Plus than neurofilament light chain (NfL) plasma levels. Furthermore, using fecal sampling performed 3 months post-baseline, we observed Bact2 to be relatively stable, suggesting its potential use as a prognostic biomarker in MS clinical practice.
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Affiliation(s)
- Lindsay Devolder
- Laboratory of Molecular Bacteriology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium,Center for Microbiology, VIB Center for Microbiology, VIB, Leuven, Belgium,Center for Neurosciences, Vrije Universiteit Brussel, Jette, Belgium
| | - Ayla Pauwels
- Laboratory of Molecular Bacteriology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium,Center for Microbiology, VIB Center for Microbiology, VIB, Leuven, Belgium,Center for Neurosciences, Vrije Universiteit Brussel, Jette, Belgium,Department of Neurology, Universitair Ziekenhuis Brussel, Jette, Belgium,National Multiple Sclerosis Center, Melsbroek, Belgium
| | | | - Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium,Center for Microbiology, VIB Center for Microbiology, VIB, Leuven, Belgium,Institute of Medical Microbiology and Hygiene, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sara Vieira-Silva
- Laboratory of Molecular Bacteriology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium,Center for Microbiology, VIB Center for Microbiology, VIB, Leuven, Belgium,Institute of Medical Microbiology and Hygiene, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Guy Nagels
- Center for Neurosciences, Vrije Universiteit Brussel, Jette, Belgium,Department of Neurology, Universitair Ziekenhuis Brussel, Jette, Belgium,St. Edmund Hall, University of Oxford, Oxford, UK
| | - Jacques De Keyser
- Center for Neurosciences, Vrije Universiteit Brussel, Jette, Belgium,Department of Neurology, Universitair Ziekenhuis Brussel, Jette, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium,Center for Microbiology, VIB Center for Microbiology, VIB, Leuven, Belgium,CONTACT Jeroen Raes Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Marie B. D’Hooghe
- Center for Neurosciences, Vrije Universiteit Brussel, Jette, Belgium,Department of Neurology, Universitair Ziekenhuis Brussel, Jette, Belgium,National Multiple Sclerosis Center, Melsbroek, Belgium,Marie B. D’hooghe National Multiple Sclerosis Center, Melsbroek, Belgium
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22
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van de Velde C, Joseph C, Simoens K, Raes J, Bernaerts K, Faust K. Technical versus biological variability in a synthetic human gut community. Gut Microbes 2023; 15:2155019. [PMID: 36580382 PMCID: PMC9809966 DOI: 10.1080/19490976.2022.2155019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Synthetic communities grown in well-controlled conditions are an important tool to decipher the mechanisms driving community dynamics. However, replicate time series of synthetic human gut communities in chemostats are rare, and it is thus still an open question to what extent stochasticity impacts gut community dynamics. Here, we address this question with a synthetic human gut bacterial community using an automated fermentation system that allows for a larger number of biological replicates. We collected six biological replicates for a community initially consisting of five common gut bacterial species that fill different metabolic niches. After an initial 12 hours in batch mode, we switched to chemostat mode and observed the community to stabilize after 2-3 days. Community profiling with 16S rRNA resulted in high variability across replicate vessels and high technical variability, while the variability across replicates was significantly lower for flow cytometric data. Both techniques agree on the decrease in the abundance of Bacteroides thetaiotaomicron, accompanied by an initial increase in Blautia hydrogenotrophica. These changes occurred together with reproducible metabolic shifts, namely a fast depletion of glucose and trehalose concentration in batch followed by a decrease in formic acid and pyruvic acid concentrations within the first 12 hours after the switch to chemostat mode. In conclusion, the observed variability in the synthetic bacterial human gut community, as assessed with 16S rRNA gene sequencing, is largely due to technical variability. The low variability seen in HPLC and flow cytometry data suggests a highly deterministic system.
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Affiliation(s)
- Charlotte van de Velde
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, LeuvenB-3000, Belgium
| | - Clémence Joseph
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, LeuvenB-3000, Belgium
| | - Kenneth Simoens
- KU Leuven, Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), LeuvenB-3001, Belgium
| | - Jeroen Raes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, LeuvenB-3000, Belgium,Center for Microbiology, VIB-KU Leuven, Leuven, Belgium
| | - Kristel Bernaerts
- KU Leuven, Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), LeuvenB-3001, Belgium
| | - Karoline Faust
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, LeuvenB-3000, Belgium,CONTACT Karoline Faust Rega institute, Herestraat 49, Leuven3000, Belgium
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23
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Bergen N, Krämer P, Romberg J, Wichels A, Gerlach G, Brinkhoff T. Shell Disease Syndrome Is Associated with Reduced and Shifted Epibacterial Diversity on the Carapace of the Crustacean Cancer pagurus. Microbiol Spectr 2022; 10:e0341922. [PMID: 36342282 PMCID: PMC9769784 DOI: 10.1128/spectrum.03419-22] [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: 08/26/2022] [Accepted: 09/09/2022] [Indexed: 11/09/2022] Open
Abstract
Cancer pagurus is highly susceptible to shell disease syndrome. However, little is known about concomitant changes in the epibacterial community. We compared the bacterial communities of black spot affected and nonaffected areas of the carapace by amplicon sequencing of 16S rRNA genes and 16S rRNA. Within each spot, bacterial communities of affected areas were less diverse compared to communities from nonaffected areas. Communities of different affected spots were, however, more divergent from each other, compared to those of different nonaffected areas. This indicates a reduced and shifted microbial community composition caused by the black spot disease. Different communities found in black spots likely indicate different stages of the disease. In affected areas, Flavobacteriaceae rose to one of the most abundant and active families due to the increase of Aquimarina spp., suggesting a significant role in shell disease syndrome. We isolated 75 bacterial strains from diseased and healthy areas, which are primarily affiliated with Proteobacteria and Bacteroidetes, reflecting the dominant phyla detected by amplicon sequencing. The ability to degrade chitin was mainly found for Gammaproteobacteria and Aquimarina spp. within the Flavobacteriia, while the ability to use N-acetylglucosamine, the monomer of the polysaccharide chitin, was observed for most isolates, including many Alphaproteobacteria. One-third of the isolates, including most Aquimarina spp., showed antagonistic properties, indicating a high potential for interactions between the bacterial populations. The combination of bacterial community analysis and the physiological properties of the isolates provided insights into a functional complex epibacterial community on the carapace of C. pagurus. IMPORTANCE In recent years, shell disease syndrome has been detected for several ecologically and economically important crustacean species. Large proportions of populations are affected, e.g., >60% of the widely distributed species Cancer pagurus in different North Sea areas. Bacteria play a significant role in the development of different forms of shell disease, all characterized by microbial chitinolytic degradation of the outer shell. By comparing the bacterial communities of healthy and diseased areas of the shell of C. pagurus, we demonstrated that the disease causes a reduced bacterial diversity within affected areas, a phenomenon co-occurring also with many other diseases. Furthermore, the community composition dramatically changed with some taxa rising to high relative abundances and showing increased activity, indicating strong participation in shell disease. Characterization of bacterial isolates obtained from affected and nonaffected spots provided deeper insights into their physiological properties and thus the possible role within the microbiome.
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Affiliation(s)
- Nils Bergen
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Philipp Krämer
- Institute for Biology and Environmental Science, University of Oldenburg, Oldenburg, Germany
| | - Julia Romberg
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Antje Wichels
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Gabriele Gerlach
- Institute for Biology and Environmental Science, University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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24
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Riezu-Boj JI, Barajas M, Pérez-Sánchez T, Pajares MJ, Araña M, Milagro FI, Urtasun R. Lactiplantibacillus plantarum DSM20174 Attenuates the Progression of Non-Alcoholic Fatty Liver Disease by Modulating Gut Microbiota, Improving Metabolic Risk Factors, and Attenuating Adipose Inflammation. Nutrients 2022; 14:nu14245212. [PMID: 36558371 PMCID: PMC9787191 DOI: 10.3390/nu14245212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/26/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease, reaching epidemic proportions worldwide. Targeting the gut-adipose tissue-liver axis by modulating the gut microbiota can be a promising therapeutic approach in NAFLD. Lactiplantibacillus plantarum, a potent lactic-acid-producing bacterium, has been shown to attenuate NAFLD. However, to our knowledge, the possible effect of the Lactiplantibacillus plantarum strain DSM20174 (L.p. DSM20174) on the gut-adipose tissue axis, diminishing inflammatory mediators as fuel for NAFLD progression, is still unknown. Using a NAFLD mouse model fed a high-fat, high-fructose (HFHF) diet for 10 weeks, we show that L.p DSM20174 supplementation of HFHF mice prevented weight gain, improved glucose and lipid homeostasis, and reduced white adipose inflammation and NAFLD progression. Furthermore, 16S rRNA gene sequencing of the faecal microbiota suggested that treatment of HFHF-fed mice with L.p DSM20174 changed the diversity and altered specific bacterial taxa at the levels of family, genus, and species in the gut microbiota. In conclusion, the beneficial effects of L.p DSM20174 in preventing fatty liver progression may be related to modulations in the composition and potential function of gut microbiota associated with lower metabolic risk factors and a reduced M1-like/M2-like ratio of macrophages and proinflammatory cytokine expression in white adipose tissue and liver.
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Affiliation(s)
- José I. Riezu-Boj
- Department of Nutrition, Food Sciences, and Physiology, University of Navarra, 31008 Pamplona, Spain
- Center for Nutrition Research, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Miguel Barajas
- Biochemistry Area, Department of Health Science, Public University of Navarre, 31008 Pamplona, Spain
| | - Tania Pérez-Sánchez
- Biochemistry Area, Department of Health Science, Public University of Navarre, 31008 Pamplona, Spain
| | - María J. Pajares
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Biochemistry Area, Department of Health Science, Public University of Navarre, 31008 Pamplona, Spain
| | - Miriam Araña
- Biochemistry Area, Department of Health Science, Public University of Navarre, 31008 Pamplona, Spain
| | - Fermín I. Milagro
- Department of Nutrition, Food Sciences, and Physiology, University of Navarra, 31008 Pamplona, Spain
- Center for Nutrition Research, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: (F.I.M.); (R.U.); Tel.: +34-948-425600 (F.I.M.); +34-948-169000 (R.U.)
| | - Raquel Urtasun
- Biochemistry Area, Department of Health Science, Public University of Navarre, 31008 Pamplona, Spain
- Correspondence: (F.I.M.); (R.U.); Tel.: +34-948-425600 (F.I.M.); +34-948-169000 (R.U.)
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25
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Is There a Universal Endurance Microbiota? Microorganisms 2022; 10:microorganisms10112213. [DOI: 10.3390/microorganisms10112213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/31/2022] [Accepted: 11/05/2022] [Indexed: 11/12/2022] Open
Abstract
Billions of microbes sculpt the gut ecosystem, affecting physiology. Since endurance athletes’ performance is often physiology-limited, understanding the composition and interactions within athletes’ gut microbiota could improve performance. Individual studies describe differences in the relative abundance of bacterial taxa in endurance athletes, suggesting the existence of an “endurance microbiota”, yet the taxa identified are mostly non-overlapping. To narrow down the source of this variation, we created a bioinformatics workflow and reanalyzed fecal microbiota from four 16S rRNA gene sequence datasets associated with endurance athletes and controls, examining diversity, relative abundance, correlations, and association networks. There were no significant differences in alpha diversity among all datasets and only one out of four datasets showed a significant overall difference in bacterial community abundance. When bacteria were examined individually, there were no genera with significantly different relative abundance in all four datasets. Two genera were significantly different in two datasets (Veillonella and Romboutsia). No changes in correlated abundances were consistent across datasets. A power analysis using the variance in relative abundance detected in each dataset indicated that much larger sample sizes will be necessary to detect a modest difference in relative abundance especially given the multitude of covariates. Our analysis confirms several challenges when comparing microbiota in general, and indicates that microbes consistently or universally associated with human endurance remain elusive.
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26
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Özkurt E, Fritscher J, Soranzo N, Ng DYK, Davey RP, Bahram M, Hildebrand F. LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis. MICROBIOME 2022; 10:176. [PMID: 36258257 PMCID: PMC9580208 DOI: 10.1186/s40168-022-01365-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 09/01/2022] [Indexed: 05/02/2023]
Abstract
BACKGROUND Amplicon sequencing is an established and cost-efficient method for profiling microbiomes. However, many available tools to process this data require both bioinformatics skills and high computational power to process big datasets. Furthermore, there are only few tools that allow for long read amplicon data analysis. To bridge this gap, we developed the LotuS2 (less OTU scripts 2) pipeline, enabling user-friendly, resource friendly, and versatile analysis of raw amplicon sequences. RESULTS In LotuS2, six different sequence clustering algorithms as well as extensive pre- and post-processing options allow for flexible data analysis by both experts, where parameters can be fully adjusted, and novices, where defaults are provided for different scenarios. We benchmarked three independent gut and soil datasets, where LotuS2 was on average 29 times faster compared to other pipelines, yet could better reproduce the alpha- and beta-diversity of technical replicate samples. Further benchmarking a mock community with known taxon composition showed that, compared to the other pipelines, LotuS2 recovered a higher fraction of correctly identified taxa and a higher fraction of reads assigned to true taxa (48% and 57% at species; 83% and 98% at genus level, respectively). At ASV/OTU level, precision and F-score were highest for LotuS2, as was the fraction of correctly reported 16S sequences. CONCLUSION LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. AVAILABILITY LotuS2 is available from GitHub, conda, or via a Galaxy web interface, documented at http://lotus2.earlham.ac.uk/ . Video Abstract.
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Affiliation(s)
- Ezgi Özkurt
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | - Joachim Fritscher
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | - Nicola Soranzo
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | - Duncan Y K Ng
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Robert P Davey
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51, Uppsala, Sweden
- Institute of Ecology and Earth Sciences, University of Tartu, Lai St, 40, Tartu, Estonia
| | - Falk Hildebrand
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK.
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27
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Si J, Vázquez-Castellanos JF, Gregory AC, Decommer L, Rymenans L, Proost S, Centelles Lodeiro J, Weger M, Notdurfter M, Leitner C, Santer P, Rungger G, Willeit J, Willeit P, Pechlaner R, Grabherr F, Kiechl S, Tilg H, Raes J. Long-term life history predicts current gut microbiome in a population-based cohort study. NATURE AGING 2022; 2:885-895. [PMID: 37118287 PMCID: PMC10154234 DOI: 10.1038/s43587-022-00286-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/25/2022] [Indexed: 04/30/2023]
Abstract
Extensive scientific and clinical microbiome studies have explored contemporary variation and dynamics of the gut microbiome in human health and disease1-3, yet the role of long-term life history effects has been underinvestigated. Here, we analyzed the current, quantitative microbiome composition in the older adult Bruneck Study cohort (Italians, Bruneck, n = 304 (male, 154; female, 150); age 65-98 years) with extensive clinical, demographic, lifestyle and nutritional data collected over the past 26 years4. Multivariate analysis of historical variables indicated that medication history, historical physical activity, past dietary habits and specific past laboratory blood parameters explain a significant fraction of current quantitative microbiome variation in older adults, enlarging the explanatory power of contemporary covariates by 33.4%. Prediction of current enterotype by a combination of past and contemporary host variables revealed good levels of predictability (area under the curve (AUC), 0.78-0.83), with Prevotella and dysbiotic Bacteroides 2 being the best predicted enterotypes. These findings demonstrate long-term life history effects on the microbiota and provide insights into lifestyle variables and their role in maintaining a healthy gut microbiota in later life.
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Affiliation(s)
- Jiyeon Si
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
| | - Jorge F Vázquez-Castellanos
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Ann C Gregory
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Lindsey Decommer
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Leen Rymenans
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Sebastian Proost
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Javier Centelles Lodeiro
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Martin Weger
- Medizinische Klinik II, Klinikum Ingolstadt, Ingolstadt, Germany
| | | | - Christoph Leitner
- Department of Internal Medicine, Hospital of Bruneck, Bruneck, Italy
| | - Peter Santer
- Department of Laboratory Medicine, Hospital of Bruneck, Bruneck, Italy
| | | | - Johann Willeit
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Peter Willeit
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
- Clinical Epidemiology Team, Institute of Health Economics, Medical University of Innsbruck, Innsbruck, Austria
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Raimund Pechlaner
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Felix Grabherr
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University Innsbruck, Innsbruck, Austria
| | - Stefan Kiechl
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
- VASCage, Research Centre on Vascular Ageing and Stroke, Innsbruck, Austria
| | - Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University Innsbruck, Innsbruck, Austria.
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium.
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
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28
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Bidirectional Interactions between Arboviruses and the Bacterial and Viral Microbiota in Aedes aegypti and Culex quinquefasciatus. mBio 2022; 13:e0102122. [PMID: 36069449 PMCID: PMC9600335 DOI: 10.1128/mbio.01021-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mosquitoes are important vectors for many arboviruses. It is becoming increasingly clear that various symbiotic microorganisms (including bacteria and insect-specific viruses; ISVs) in mosquitoes have the potential to modulate the ability of mosquitoes to transmit arboviruses. In this study, we compared the bacteriome and virome (both eukaryotic viruses and bacteriophages) of female adult Aedes aegypti and Culex quinquefasciatus mosquitoes fed with sucrose/water, blood, or blood spiked with Zika virus (ZIKV) or West Nile virus (WNV), respectively. Furthermore, we investigated associations between the microbiota and vector competence. We show that the influence of arboviruses on the mosquito microbiome—and vice versa—is distinct for each combination of arbovirus/mosquito species. The presence of ZIKV resulted in a temporarily increased Aedes ISV diversity. However, this effect was distinct for different ISVs: some ISVs decreased following the blood meal (Aedes aegypti totivirus), whereas other ISVs increased only when the blood contained ZIKV (Guadeloupe mosquito virus). Also, the diversity of the Aedes bacteriome depended on the diet and the presence of ZIKV, with a lower diversity observed for mosquitoes receiving blood without ZIKV. In Cx. quinquefasciatus, some ISVs increased in WNV-infected mosquitoes (Guadeloupe Culex tymo-like virus). Particularly, the presence of Wenzhou sobemo-like virus 3 (WSLV3) was associated with the absence of infectious WNV in mosquito heads, suggesting that WSLV3 might affect vector competence for WNV. Distinct profiles of bacteriophages were identified in Culex mosquitoes depending on diet, despite the lack of clear changes in the bacteriome. Overall, our data demonstrate a complex three-way interaction among arboviruses, resident microbiota, and the host, which is distinct for different arbovirus–mosquito combinations. A better understanding of these interactions may lead to the identification of microbiota able to suppress the ability of arbovirus transmission to humans, and hence improved arbovirus control measures.
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29
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Kaiyrlykyzy A, Kozhakhmetov S, Babenko D, Zholdasbekova G, Alzhanova D, Olzhayev F, Baibulatova A, Kushugulova AR, Askarova S. Study of gut microbiota alterations in Alzheimer's dementia patients from Kazakhstan. Sci Rep 2022; 12:15115. [PMID: 36068280 PMCID: PMC9448737 DOI: 10.1038/s41598-022-19393-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/29/2022] [Indexed: 11/30/2022] Open
Abstract
We have investigated the diversity and composition of gut microbiotas isolated from AD (Alzheimer's disease) patients (n = 41) and healthy seniors (n = 43) from Nur-Sultan city (Kazakhstan). The composition of the gut microbiota was characterized by 16S ribosomal RNA sequencing. Our results demonstrated significant differences in bacterial abundance at phylum, class, order, and genus levels in AD patients compared to healthy aged individuals. Relative abundance analysis has revealed increased amount of taxa belonging to Acidobacteriota, Verrucomicrobiota, Planctomycetota and Synergistota phyla in AD patients. Among bacterial genera, microbiotas of AD participants were characterized by a decreased amount of Bifidobacterium, Clostridia bacterium, Castellaniella, Erysipelotrichaceae UCG-003, Roseburia, Tuzzerella, Lactobacillaceae and Monoglobus. Differential abundance analysis determined enriched genera of Christensenellaceae R-7 group, Prevotella, Alloprevotella, Eubacterium coprostanoligenes group, Ruminococcus, Flavobacterium, Ohtaekwangia, Akkermansia, Bacteroides sp. Marseille-P3166 in AD patients, whereas Levilactobacillus, Lactiplantibacillus, Tyzzerella, Eubacterium siraeum group, Monoglobus, Bacteroides, Erysipelotrichaceae UCG-003, Veillonella, Faecalibacterium, Roseburia, Haemophilus were depleted. We have also found correlations between some bacteria taxa and blood serum biochemical parameters. Adiponectin was correlated with Acidimicrobiia, Faecalibacterium, Actinobacteria, Oscillospiraceae, Prevotella and Christensenellaceae R-7. The Christensenellaceae R-7 group and Acidobacteriota were correlated with total bilirubin, while Firmicutes, Acidobacteriales bacterium, Castellaniella alcaligenes, Lachnospiraceae, Christensenellaceae and Klebsiella pneumoniae were correlated with the level of CRP in the blood of AD patients. In addition, we report the correlations found between disease severity and certain fecal bacteria. This is the first reported study demonstrating gut microbiota alterations in AD in the Central Asian region.
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Affiliation(s)
- Aiym Kaiyrlykyzy
- Laboratory of Bioengineering and Regenerative Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.,Graduate School of Public Health, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Samat Kozhakhmetov
- Laboratory of Human Microbiome and Longevity, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.,Kazakhstan Society of Human Microbiome Researchers, Nur-Sultan, Kazakhstan
| | - Dmitriy Babenko
- Medical University Karaganda, Karagandy, Kazakhstan.,Innovative Center ArtScience, Nur-Sultan, Kazakhstan
| | | | - Dinara Alzhanova
- Department of Neurology, Medical University Astana, Nur-Sultan, Kazakhstan
| | - Farkhad Olzhayev
- Laboratory of Bioengineering and Regenerative Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Aida Baibulatova
- Laboratory of Bioengineering and Regenerative Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Almagul R Kushugulova
- Laboratory of Human Microbiome and Longevity, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan. .,Kazakhstan Society of Human Microbiome Researchers, Nur-Sultan, Kazakhstan.
| | - Sholpan Askarova
- Laboratory of Bioengineering and Regenerative Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.
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Blackman AC, Thapa S, Venkatachalam A, Horvath TD, Runge JK, Haidacher SJ, Hoch KM, Haag AM, Luna RA, Anagnostou A. Insights into Microbiome and Metabolic Signatures of Children Undergoing Peanut Oral Immunotherapy. CHILDREN 2022; 9:children9081192. [PMID: 36010081 PMCID: PMC9406383 DOI: 10.3390/children9081192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022]
Abstract
Background: Peanut oral immunotherapy has emerged as a novel, active management approach for peanut-allergic sufferers, but limited data exist currently on the role of the microbiome in successful desensitization. Objective: We examined the oral and gut microbiome in a cohort of 17 children undergoing peanut oral immunotherapy with the aim to identify the microbiome signatures associated with successful desensitization. We also set out to characterize their fecal metabolic profiles after successful therapy. Methods: Participants gradually built up their daily dose from 2 mg (starting dose) to 300 mg (maintenance dose) within approximately 40 weeks. We collected a buccal and stool specimen from each subject at two different time points: at baseline and post-therapy (1 month after reaching maintenance). The oral (buccal) and gut (fecal) microbiome was characterized based on sequencing of 16S rRNA gene amplicons with Illumina MiSeq. Fecal short chain fatty acid levels were measured using liquid chromatography-tandem mass spectrometry. Results: We report increased alpha diversity of the oral microbiome post-therapy and have also identified a significant increase in the relative abundance of oral Actinobacteria, associated with the desensitized state. However, the baseline gut microbiome did not differ from the post-therapy. Additionally, fecal short chain fatty acids increased after therapy, but not significantly. Conclusion: Our research adds to the limited current knowledge on microbiome and metabolic signatures in pediatric patients completing oral immunotherapy. Post-therapy increased trends of fecal fatty acid levels support a role in modulating the allergic response and potentially exerting protective and anti-inflammatory effects alongside successful desensitization. A better understanding of the microbiome-related mechanisms underlying desensitization may allow development of smarter therapeutic approaches in the near future. Clinical implication: The oral microbiome composition is altered following successful peanut oral immunotherapy, with a significant increase in alpha diversity and the relative abundance of phylum Actinobacteria. Capsule summary: Significant microbiome changes in children completing peanut immunotherapy include increase in alpha-diversity and overrepresentation of Actinobacteria in the oral microbiome, and increased trends for fecal short chain fatty acids, suggesting a protective effect against the allergic response.
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Affiliation(s)
- Andrea C. Blackman
- Department of Pediatrics, Section of Immunology, Allergy and Retrovirology, Texas Children’s Hospital, Houston, TX 77030, USA
- Section of Allergy, Immunology & Retrovirology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Santosh Thapa
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Alamelu Venkatachalam
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Thomas D. Horvath
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Jessica K. Runge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Sigmund J. Haidacher
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Kathleen M. Hoch
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Anthony M. Haag
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Ruth Ann Luna
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Aikaterini Anagnostou
- Department of Pediatrics, Section of Immunology, Allergy and Retrovirology, Texas Children’s Hospital, Houston, TX 77030, USA
- Section of Allergy, Immunology & Retrovirology, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: ; Tel.: +1-832-824-1319
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Martens PJ, Centelles-Lodeiro J, Ellis D, Cook DP, Sassi G, Verlinden L, Verstuyf A, Raes J, Mathieu C, Gysemans C. High Serum Vitamin D Concentrations, Induced via Diet, Trigger Immune and Intestinal Microbiota Alterations Leading to Type 1 Diabetes Protection in NOD Mice. Front Immunol 2022; 13:902678. [PMID: 35784365 PMCID: PMC9241442 DOI: 10.3389/fimmu.2022.902678] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
The hormonally-active form of vitamin D, 1,25-dihydroxyvitamin D3, can modulate both innate and adaptive immunity, through binding to the nuclear vitamin D receptor expressed in most immune cells. A high dose of regular vitamin D protected non-obese diabetic (NOD) mice against type 1 diabetes (T1D), when initiated at birth and given lifelong. However, considerable controversy exists on the level of circulating vitamin D (25-hydroxyvitamin D3, 25(OH)D3) needed to modulate the immune system in autoimmune-prone subjects and protect against T1D onset. Here, we evaluated the impact of two doses of dietary vitamin D supplementation (400 and 800 IU/day), given to female NOD mice from 3 until 25 weeks of age, on disease development, peripheral and gut immune system, gut epithelial barrier function, and gut bacterial taxonomy. Whereas serum 25(OH)D3 concentrations were 2.6- (400 IU/day) and 3.9-fold (800 IU/day) higher with dietary vitamin D supplementation compared to normal chow (NC), only the 800 IU/day vitamin D-supplemented diet delayed and reduced T1D incidence compared to NC. Flow cytometry analyses revealed an increased frequency of FoxP3+ Treg cells in the spleen of mice receiving the 800 IU/day vitamin D-supplemented diet. This vitamin D-induced increase in FoxP3+ Treg cells, also expressing the ecto-5’-nucleotidase CD73, only persisted in the spleen of mice at 25 weeks of age. At this time point, the frequency of IL-10-secreting CD4+ T cells was also increased in all studied immune organs. High-dose vitamin D supplementation was unable to correct gut leakiness nor did it significantly modify the increased gut microbial diversity and richness over time observed in NOD mice receiving NC. Intriguingly, the rise in alpha-diversity during maturation occurred especially in mice not progressing to hyperglycaemia. Principal coordinates analysis identified that both diet and disease status significantly influenced the inter-individual microbiota variation at the genus level. The abundance of the genera Ruminoclostridium_9 and Marvinbryantia gradually increased or decreased, respectively in faecal samples of mice on the 800 IU/day vitamin D-supplemented diet compared to mice on the 400 IU/day vitamin D-supplemented diet or NC, irrespective of disease outcome. In summary, dietary vitamin D reduced T1D incidence in female NOD mice at a dose of 800, but not of 400, IU/day, and was accompanied by an expansion of Treg cells in various lymphoid organs and an altered intestinal microbiota signature.
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Affiliation(s)
- Pieter-Jan Martens
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Javier Centelles-Lodeiro
- Laboratory of Molecular Bacteriology, Rega-Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Darcy Ellis
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Dana Paulina Cook
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Gabriele Sassi
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Lieve Verlinden
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Annemieke Verstuyf
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Rega-Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Chantal Mathieu
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Conny Gysemans
- Clinical and Experimental Endocrinology (CEE), Katholieke Universiteit Leuven, Leuven, Belgium
- *Correspondence: Conny Gysemans,
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Maillard F, Fernandez CW, Mundra S, Heckman KA, Kolka RK, Kauserud H, Kennedy PG. Warming drives a 'hummockification' of microbial communities associated with decomposing mycorrhizal fungal necromass in peatlands. THE NEW PHYTOLOGIST 2022; 234:2032-2043. [PMID: 34559896 DOI: 10.1111/nph.17755] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Dead fungal mycelium (necromass) represents a critical component of soil carbon (C) and nutrient cycles. Assessing how the microbial communities associated with decomposing fungal necromass change as global temperatures rise will help in determining how these belowground organic matter inputs contribute to ecosystem responses. In this study, we characterized the structure of bacterial and fungal communities associated with multiple types of decaying mycorrhizal fungal necromass incubated within mesh bags across a 9°C whole ecosystem temperature enhancement in a boreal peatland. We found major taxonomic and functional shifts in the microbial communities present on decaying mycorrhizal fungal necromass in response to warming. These changes were most pronounced in hollow microsites, which showed convergence towards the necromass-associated microbial communities present in unwarmed hummocks. We also observed a high colonization of ericoid mycorrhizal fungal necromass by fungi from the same genera as the necromass. These results indicate that microbial communities associated with mycorrhizal fungal necromass decomposition are likely to change significantly with future climate warming, which may have strong impacts on soil biogeochemical cycles in peatlands. Additionally, the high enrichment of congeneric fungal decomposers on ericoid mycorrhizal necromass may help to explain the increase in ericoid shrub dominance in warming peatlands.
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Affiliation(s)
- François Maillard
- Department of Plant & Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Christopher W Fernandez
- Department of Plant & Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
- Department of Forestry, Michigan State University, East Lansing, MI, 48824, USA
| | - Sunil Mundra
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, Oslo, NO-0316, Norway
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, Abu-Dhabi, UAE
| | | | - Randall K Kolka
- USDA Forest Service Northern Research Station, Grand Rapids, MN, 55744, USA
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, Oslo, NO-0316, Norway
| | - Peter G Kennedy
- Department of Plant & Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
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Mundra S, Kauserud H, Økland T, Nordbakken J, Ransedokken Y, Kjønaas OJ. Shift in tree species changes the belowground biota of boreal forests. THE NEW PHYTOLOGIST 2022; 234:2073-2087. [PMID: 35307841 PMCID: PMC9325058 DOI: 10.1111/nph.18109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The replacement of native birch with Norway spruce has been initiated in Norway to increase long-term carbon storage in forests. However, there is limited knowledge on the impacts that aboveground changes will have on the belowground microbiota. We examined which effects a tree species shift from birch to spruce stands has on belowground microbial communities, soil fungal biomass and relationships with vegetation biomass and soil organic carbon (SOC). Replacement of birch with spruce negatively influenced soil bacterial and fungal richness and strongly altered microbial community composition in the forest floor layer, most strikingly for fungi. Tree species-mediated variation in soil properties was a major factor explaining variation in bacterial communities. For fungi, both soil chemistry and understorey vegetation were important community structuring factors, particularly for ectomycorrhizal fungi. The relative abundance of ectomycorrhizal fungi and the ectomycorrhizal : saprotrophic fungal ratio were higher in spruce compared to birch stands, particularly in the deeper mineral soil layers, and vice versa for saprotrophs. The positive relationship between ergosterol (fungal biomass) and SOC stock in the forest floor layer suggests higher carbon sequestration potential in spruce forest soil, alternatively, that the larger carbon stock leads to an increase in soil fungal biomass.
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Affiliation(s)
- Sunil Mundra
- Section for Genetics and Evolutionary Biology (EvoGene)Department of BiosciencesUniversity of OsloPO Box 1066 BlindernOsloNO‐0316Norway
- Department of BiologyCollege of ScienceUnited Arab Emirates UniversityPO Box 15551Al‐Ain, Abu‐DhabiUnited Arab Emirates
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EvoGene)Department of BiosciencesUniversity of OsloPO Box 1066 BlindernOsloNO‐0316Norway
| | - Tonje Økland
- Norwegian Institute of Bioeconomy ResearchPO Box 115ÅsNO‐1431Norway
| | | | - Yngvild Ransedokken
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesPO Box 5003ÅsNO‐1432Norway
| | - O. Janne Kjønaas
- Norwegian Institute of Bioeconomy ResearchPO Box 115ÅsNO‐1431Norway
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Biclot A, Huys GRB, Bacigalupe R, D’hoe K, Vandeputte D, Falony G, Tito RY, Raes J. Effect of cryopreservation medium conditions on growth and isolation of gut anaerobes from human faecal samples. MICROBIOME 2022; 10:80. [PMID: 35644616 PMCID: PMC9150342 DOI: 10.1186/s40168-022-01267-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/03/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Novel strategies for anaerobic bacterial isolations from human faecal samples and various initiatives to generate culture collections of gut-derived bacteria have instigated considerable interest for the development of novel microbiota-based treatments. Early in the process of building a culture collection, optimal faecal sample preservation is essential to safeguard the viability of the broadest taxonomic diversity range possible. In contrast to the much more established faecal storage conditions for meta-omics applications, the impact of stool sample preservation conditions on bacterial growth recovery and isolation remains largely unexplored. In this study, aliquoted faecal samples from eleven healthy human volunteers selected based on a range of physicochemical and microbiological gradients were cryopreserved at - 80 °C either without the addition of any medium (dry condition) or in different Cary-Blair medium conditions with or without a cryoprotectant, i.e. 20% (v/v) glycerol or 5% (v/v) DMSO. Faecal aliquots were subjected to bulk 16S rRNA gene sequencing as well as dilution plating on modified Gifu Anaerobic Medium after preservation for culturable fraction profiling and generation of bacterial culture collections. RESULTS Analyses of compositional variation showed that cryopreservation medium conditions affected quantitative recovery but not the overall community composition of cultured fractions. Post-preservation sample dilution and richness of the uncultured source samples were the major drivers of the cultured fraction richness at genus level. However, preservation conditions differentially affected recovery of specific genera. Presence-absence analysis indicated that twenty-two of the 45 most abundant common genera (>0.01% abundance, dilution 10-4) were recovered in cultured fractions from all preservation conditions, while nine genera were only detected in fractions from a single preservation condition. Overall, the highest number of common genera (i.e. 35/45) in cultured fractions were recovered from sample aliquots preserved without medium and in the presence of Cary-Blair medium containing 5% (v/v) DMSO. Also, in the culture collection generated from the cultured fractions, these two preservation conditions yielded the highest species richness (72 and 66, respectively). CONCLUSION Our results demonstrate that preservation methods partly determine richness and taxonomic diversity of gut anaerobes recovered from faecal samples. Complementing the current standard practice of cryopreserving stool samples in dry conditions with other preservation conditions, such as Cary-Blair medium with DMSO, could increase the species diversity of gut-associated culture collections. Video abstract.
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Affiliation(s)
- Anaïs Biclot
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Geert R. B. Huys
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Rodrigo Bacigalupe
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Kevin D’hoe
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Doris Vandeputte
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Present address: Meinig School of Biomedical Engineering, Cornell, USA
| | - Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Raul Y. Tito
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
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Horvath TD, Ihekweazu FD, Haidacher SJ, Ruan W, Engevik KA, Fultz R, Hoch KM, Luna RA, Oezguen N, Spinler JK, Haag AM, Versalovic J, Engevik MA. Bacteroides ovatus colonization influences the abundance of intestinal short chain fatty acids and neurotransmitters. iScience 2022; 25:104158. [PMID: 35494230 PMCID: PMC9038548 DOI: 10.1016/j.isci.2022.104158] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 11/01/2021] [Accepted: 03/23/2022] [Indexed: 12/18/2022] Open
Abstract
Gut microbes can synthesize multiple neuro-active metabolites. We profiled neuro-active compounds produced by the gut commensal Bacteroides ovatus in vitro and in vivo by LC-MS/MS. We found that B. ovatus generates acetic acid, propionic acid, isobutyric acid, and isovaleric acid. In vitro, B. ovatus consumed tryptophan and glutamate and synthesized the neuro-active compounds glutamine and GABA. Consistent with our LC-MS/MS-based in vitro data, we observed elevated levels of acetic acid, propionic acid, isobutyric acid, and isovaleric acid in the intestines of B. ovatus mono-associated mice compared with germ-free controls. B. ovatus mono-association also increased the concentrations of intestinal GABA and decreased the concentrations of tryptophan and glutamine compared with germ-free controls. Computational network analysis revealed unique links between SCFAs, neuro-active compounds, and colonization status. These results highlight connections between microbial colonization and intestinal neurotransmitter concentrations, suggesting that B. ovatus selectively influences the presence of intestinal neurotransmitters.
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Affiliation(s)
- Thomas D. Horvath
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Faith D. Ihekweazu
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Section of Gastroenterology, Hepatology, and Nutrition, Texas Children’s Hospital, Houston, TX, USA
| | - Sigmund J. Haidacher
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Wenly Ruan
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Section of Gastroenterology, Hepatology, and Nutrition, Texas Children’s Hospital, Houston, TX, USA
| | - Kristen A. Engevik
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Robert Fultz
- Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch, Galveston, TX, USA
| | - Kathleen M. Hoch
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Ruth Ann Luna
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Numan Oezguen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Jennifer K. Spinler
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Anthony M. Haag
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Melinda A. Engevik
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina, 173 Ashley Ave, BSB 621, Charleston, SC 29425, USA
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van de Velde CC, Joseph C, Biclot A, Huys GRB, Pinheiro VB, Bernaerts K, Raes J, Faust K. Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification. ISME COMMUNICATIONS 2022; 2:40. [PMID: 37938658 PMCID: PMC9723706 DOI: 10.1038/s43705-022-00123-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 03/26/2022] [Accepted: 04/14/2022] [Indexed: 09/07/2023]
Abstract
A bottleneck for microbial community experiments with many samples and/or replicates is the fast quantification of individual taxon abundances, which is commonly achieved through sequencing marker genes such as the 16S rRNA gene. Here, we propose a new approach for high-throughput and high-quality enumeration of human gut bacteria in a defined community, combining flow cytometry and supervised classification to identify and quantify species mixed in silico and in defined communities in vitro. We identified species in a 5-species in silico community with an F1 score of 71%. In addition, we demonstrate in vitro that our method performs equally well or better than 16S rRNA gene sequencing in two-species cocultures and agrees with 16S rRNA gene sequencing data on the most abundant species in a four-species community. We found that shape and size differences alone are insufficient to distinguish species, and that it is thus necessary to exploit the multivariate nature of flow cytometry data. Finally, we observed that variability of flow cytometry data across replicates differs between gut bacterial species. In conclusion, the performance of supervised classification of gut species in flow cytometry data is species-dependent, but is for some combinations accurate enough to serve as a faster alternative to 16S rRNA gene sequencing.
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Affiliation(s)
- Charlotte C van de Velde
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium
| | - Clémence Joseph
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium
| | - Anaïs Biclot
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium
- VIB-KU Leuven, Center for Microbiology, B-3000, Leuven, Belgium
| | - Geert R B Huys
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium
- VIB-KU Leuven, Center for Microbiology, B-3000, Leuven, Belgium
| | - Vitor B Pinheiro
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, B-3000, Leuven, Belgium
| | - Kristel Bernaerts
- KU Leuven, Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), B-3001, Leuven, Belgium
| | - Jeroen Raes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium
- VIB-KU Leuven, Center for Microbiology, B-3000, Leuven, Belgium
| | - Karoline Faust
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium.
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Gohar D, Põldmaa K, Tedersoo L, Aslani F, Furneaux B, Henkel TW, Saar I, Smith ME, Bahram M. Global diversity and distribution of mushroom-inhabiting bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:254-264. [PMID: 35102713 DOI: 10.1111/1758-2229.13045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Mushroom-forming fungi are important sources of food and medicine in many regions of the world, and their development and health are known to depend on various microbes. Recent studies have examined the structure of mushroom-inhabiting bacterial (MIB) communities and their association with local environmental variables, but global-scale diversity and determinants of these communities remain poorly understood. Here we examined the MIB global diversity and community composition in relation to climate, soil and host factors. We found a core global mushroom microbiome, accounting for 30% of sequence reads, while comprising a few bacterial genera such as Halomonas, Serratia, Bacillus, Cutibacterium, Bradyrhizobium and Burkholderia. Our analysis further revealed an important role of host phylogeny in shaping the communities of MIB, whereas the effects of climate and soil factors remained negligible. The results suggest that the communities of MIB and free-living bacteria are structured by contrasting community assembly processes and that fungal-bacterial interactions are an important determinant of MIB community structure.
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Affiliation(s)
- Daniyal Gohar
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
| | - Kadri Põldmaa
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
- Natural History Museum and Botanical Garden, University of Tartu, Vanemuise 46, Tartu, 51003, Estonia
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
| | - Farzad Aslani
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
- School of Environmental and Rural Sciences, University of New England, Armidale, NSW, Australia
| | - Brendan Furneaux
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Terry W Henkel
- Department of Biological Sciences, Humboldt State University, Arcata, CA, USA
| | - Irja Saar
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, Uppsala, 756 51, Sweden
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Bahram M, Espenberg M, Pärn J, Lehtovirta-Morley L, Anslan S, Kasak K, Kõljalg U, Liira J, Maddison M, Moora M, Niinemets Ü, Öpik M, Pärtel M, Soosaar K, Zobel M, Hildebrand F, Tedersoo L, Mander Ü. Structure and function of the soil microbiome underlying N 2O emissions from global wetlands. Nat Commun 2022; 13:1430. [PMID: 35301304 PMCID: PMC8931052 DOI: 10.1038/s41467-022-29161-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 02/23/2022] [Indexed: 01/16/2023] Open
Abstract
Wetland soils are the greatest source of nitrous oxide (N2O), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the N2O emissions from wetland soils are poorly understood. Using in situ N2O measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and N2O emissions. We show that N2O emissions are higher in drained and warm wetland soils, and are correlated with functional diversity of microbes. We further provide evidence that despite their much lower abundance compared to bacteria, nitrifying archaeal abundance is a key factor explaining N2O emissions from wetland soils globally. Our data suggest that ongoing global warming and intensifying environmental change may boost archaeal nitrifiers, collectively transforming wetland soils to a greater source of N2O.
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Affiliation(s)
- Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia. .,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Mikk Espenberg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Jaan Pärn
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | | | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kuno Kasak
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Jaan Liira
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Maddison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ülo Niinemets
- Institute of Agricultural & Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kaido Soosaar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Falk Hildebrand
- Quadram Institute Bioscience, Norwich, Norfolk, UK.,Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - Leho Tedersoo
- College of Science, King Saud University, Riyadh, Saudi Arabia.,Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Ülo Mander
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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Qi X, Ye J, Wen Y, Liu L, Cheng B, Cheng S, Yao Y, Zhang F. Evaluating the Effects of Diet-Gut Microbiota Interactions on Sleep Traits Using the UK Biobank Cohort. Nutrients 2022; 14:1134. [PMID: 35334789 PMCID: PMC8951611 DOI: 10.3390/nu14061134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 12/11/2022] Open
Abstract
Previous studies showed that diet and gut microbiota had a correlation with sleep. However, the potential interaction effects of diet and gut microbiota on sleep are still unclear. The phenotypic data of insomnia (including 374,505 subjects) and sleep duration (including 372,805 subjects) were obtained from the UK Biobank cohort. The Single Nucleotide Polymorphisms (SNPs) associated with 114 gut microbiota, 84 dietary habits, and 4 dietary compositions were derived from the published Genome-wide Association Study (GWAS). We used Linkage Disequilibrium Score Regression (LDSC) to estimate the genetic correlation and colocalization analysis to assess whether dietary habits and insomnia/sleep duration shared a causal variant in a region of the genome. Using UK Biobank genotype data, the polygenetic risk score of gut microbiota, dietary habits, and dietary compositions were calculated for each subject. Logistic regression and linear regression models were used to assess the potential effects of diet-gut microbiota interactions on sleep phenotypes, including insomnia and sleep duration. Insomnia and sleep duration were used as dependent variables, and sex, age, the Townsend Deprivation Index scores, and smoking and drinking habits were selected as covariates in the regression analysis. All statistical analyses were conducted using R-3.5.1 software. Significant genetic correlations were discovered between insomnia/sleep duration and dietary habits. Further, we found several significant dietary compositions-gut microbiota interactions associated with sleep, such as fat × G_Collinsella_RNT (p = 1.843 × 10-2) and protein × G_Collinsella_HB (p = 7.11 × 10-3). Besides, multiple dietary habits-gut microbiota interactions were identified for sleep, such as overall beef intake × G_Desulfovibrio_RNT (p = 3.26 × 10-4), cups of coffee per day × G_Escherichia_Shigella_RNT (p = 1.14 × 10-3), and pieces of dried fruit per day × G_Bifidobacterium_RNT (p = 5.80 × 10-3). This study reported multiple diet-gut microbiota interactions associated with sleep, which may provide insights into the biological mechanisms of diet and gut microbiota affecting sleep.
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Affiliation(s)
- Xin Qi
- Precision Medicine Center, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China;
| | - Jing Ye
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (J.Y.); (Y.W.); (L.L.); (B.C.); (S.C.); (Y.Y.)
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (J.Y.); (Y.W.); (L.L.); (B.C.); (S.C.); (Y.Y.)
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (J.Y.); (Y.W.); (L.L.); (B.C.); (S.C.); (Y.Y.)
| | - Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (J.Y.); (Y.W.); (L.L.); (B.C.); (S.C.); (Y.Y.)
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (J.Y.); (Y.W.); (L.L.); (B.C.); (S.C.); (Y.Y.)
| | - Yao Yao
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (J.Y.); (Y.W.); (L.L.); (B.C.); (S.C.); (Y.Y.)
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (J.Y.); (Y.W.); (L.L.); (B.C.); (S.C.); (Y.Y.)
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Ebrahim Z, Proost S, Tito RY, Raes J, Glorieux G, Moosa MR, Blaauw R. The Effect of ß-Glucan Prebiotic on Kidney Function, Uremic Toxins and Gut Microbiome in Stage 3 to 5 Chronic Kidney Disease (CKD) Predialysis Participants: A Randomized Controlled Trial. Nutrients 2022; 14:nu14040805. [PMID: 35215453 PMCID: PMC8880761 DOI: 10.3390/nu14040805] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/16/2021] [Accepted: 02/08/2022] [Indexed: 12/21/2022] Open
Abstract
There is growing evidence that gut dysbiosis contributes to the progression of chronic kidney disease (CKD) owing to several mechanisms, including microbiota-derived uremic toxins, diet and immune-mediated factors. The aim of this study was to investigate the effect of a ß-glucan prebiotic on kidney function, uremic toxins and the gut microbiome in stage 3 to 5 CKD participants. Fifty-nine participants were randomized to either the ß-glucan prebiotic intervention group (n = 30) or the control group (n = 29). The primary outcomes were to assess kidney function (urea, creatinine and glomerular filtration rate), plasma levels of total and free levels of uremic toxins (p-cresyl sulfate (pCS), indoxyl-sulfate (IxS), p-cresyl glucuronide (pCG) and indoxyl 3-acetic acid (IAA) and gut microbiota using 16S rRNA sequencing at baseline, week 8 and week 14. The intervention group (age 40.6 ± 11.4 y) and the control group (age 41.3 ± 12.0 y) did not differ in age or any other socio-demographic variables at baseline. There were no significant changes in kidney function over 14 weeks. There was a significant reduction in uremic toxin levels at different time points, in free IxS at 8 weeks (p = 0.003) and 14 weeks (p < 0.001), free pCS (p = 0.006) at 14 weeks and total and free pCG (p < 0.001, p < 0.001, respectively) and at 14 weeks. There were no differences in relative abundances of genera between groups. Enterotyping revealed that the population consisted of only two of the four enterotypes: Bacteroides 2 and Prevotella. The redundancy analysis showed a few factors significantly affected the gut microbiome: these included triglyceride levels (p < 0.001), body mass index (p = 0.002), high- density lipoprotein (p < 0.001) and the prebiotic intervention (p = 0.002). The ß-glucan prebiotic significantly altered uremic toxin levels of intestinal origin and favorably affected the gut microbiome.
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Affiliation(s)
- Zarina Ebrahim
- Division of Human Nutrition, Department of Global Health, Stellenbosch University, Cape Town 8000, South Africa;
- Correspondence: (Z.E.); (S.P.)
| | - Sebastian Proost
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (R.Y.T.); (J.R.)
- Center for Microbiology, VIB, 3000 Leuven, Belgium
- Correspondence: (Z.E.); (S.P.)
| | - Raul Yhossef Tito
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (R.Y.T.); (J.R.)
- Center for Microbiology, VIB, 3000 Leuven, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (R.Y.T.); (J.R.)
- Center for Microbiology, VIB, 3000 Leuven, Belgium
| | - Griet Glorieux
- Department of Internal Medicine and Pediatrics, Nephrology Section, Ghent University Hospital, 9000 Ghent, Belgium;
| | | | - Renée Blaauw
- Division of Human Nutrition, Department of Global Health, Stellenbosch University, Cape Town 8000, South Africa;
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Kubinski R, Djamen-Kepaou JY, Zhanabaev T, Hernandez-Garcia A, Bauer S, Hildebrand F, Korcsmaros T, Karam S, Jantchou P, Kafi K, Martin RD. Benchmark of Data Processing Methods and Machine Learning Models for Gut Microbiome-Based Diagnosis of Inflammatory Bowel Disease. Front Genet 2022; 13:784397. [PMID: 35251123 PMCID: PMC8895431 DOI: 10.3389/fgene.2022.784397] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/13/2022] [Indexed: 12/14/2022] Open
Abstract
Patients with inflammatory bowel disease (IBD) wait months and undergo numerous invasive procedures between the initial appearance of symptoms and receiving a diagnosis. In order to reduce time until diagnosis and improve patient wellbeing, machine learning algorithms capable of diagnosing IBD from the gut microbiome's composition are currently being explored. To date, these models have had limited clinical application due to decreased performance when applied to a new cohort of patient samples. Various methods have been developed to analyze microbiome data which may improve the generalizability of machine learning IBD diagnostic tests. With an abundance of methods, there is a need to benchmark the performance and generalizability of various machine learning pipelines (from data processing to training a machine learning model) for microbiome-based IBD diagnostic tools. We collected fifteen 16S rRNA microbiome datasets (7,707 samples) from North America to benchmark combinations of gut microbiome features, data normalization and transformation methods, batch effect correction methods, and machine learning models. Pipeline generalizability to new cohorts of patients was evaluated with two binary classification metrics following leave-one-dataset-out cross (LODO) validation, where all samples from one study were left out of the training set and tested upon. We demonstrate that taxonomic features processed with a compositional transformation method and batch effect correction with the naive zero-centering method attain the best classification performance. In addition, machine learning models that identify non-linear decision boundaries between labels are more generalizable than those that are linearly constrained. Lastly, we illustrate the importance of generating a curated training dataset to ensure similar performance across patient demographics. These findings will help improve the generalizability of machine learning models as we move towards non-invasive diagnostic and disease management tools for patients with IBD.
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Affiliation(s)
| | | | | | - Alex Hernandez-Garcia
- Mila, Quebec Artificial Intelligence Institute, University of Montreal, Montréal, QC, Canada
| | - Stefan Bauer
- Max Planck Institute for Intelligent Systems, Tübingen, Germany
| | - Falk Hildebrand
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
- Earlham Institute, Norwich, United Kingdom
| | - Tamas Korcsmaros
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
- Earlham Institute, Norwich, United Kingdom
| | - Sani Karam
- Phyla Technologies Inc, Montréal, QC, Canada
| | - Prévost Jantchou
- Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Kamran Kafi
- Phyla Technologies Inc, Montréal, QC, Canada
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Changes in Wastewater Treatment Performance and the Microbial Community during the Bioaugmentation of a Denitrifying Pseudomonas Strain in the Low Carbon–Nitrogen Ratio Sequencing Batch Reactor. WATER 2022. [DOI: 10.3390/w14040540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The low carbon–nitrogen ratio (C/N) of influent wastewater results in the insufficient carbon source for the process of denitrification in urban wastewater treatment plants (WWTPs). A denitrifying bacterial strain, Pseudomonas sp. JMSTP, was isolated and demonstrated effective denitrification ability under a low C/N ratio of 1.5–4 (w/w) in anoxic conditions. Sequencing batch reactor (SBR) studies were conducted to test the bioaugmentation of JMSTP on total nitrogen (TN) removal under the influent COD/N ratio of 3/1. After the second bioaugmentation, the TN of effluent in the bioaugmented SBR was significantly lower than that in the control SBR. Redundancy analysis results showed that there was a positive correlation between Pseudomonas sp. abundance and TN removal in the bioaugmented SBR. Microbial community analysis showed that, especially after the second bioaugmentation, the abundance of Pseudomonas sp. decreased rapidly, but it was still much higher than that in the control SBR. Correlation network analysis showed that after the addition, Pseudomonas sp. had no significant co-occurrence relationship with other native bacteria, owing to the quick increase and decrease. Our results suggest that JMSTP shows the potential to enhance TN removal through bioaugmentation. Since the effect of bioaugmentation gradually diminishes, further research is still needed to investigate its long-lasting applications.
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Gad M, Hou L, Cao M, Adyari B, Zhang L, Qin D, Yu CP, Sun Q, Hu A. Tracking microeukaryotic footprint in a peri-urban watershed, China through machine-learning approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150401. [PMID: 34562761 DOI: 10.1016/j.scitotenv.2021.150401] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/17/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Microeukaryotes play a significant role in biogeochemical cycling and can serve as bioindicators of water quality in freshwater ecosystems. However, there is a knowledge gap on how freshwater microeukaryotic communities are assembled, especially that how terrestrial microeukaryotes influence freshwater microeukaryotic assemblages. Here, we used a combination of 18S rRNA gene amplicon sequencing and community-based microbial source tracking (MST) approaches (i.e., SourceTracker and FEAST) to assess the contribution of microeukaryotes from surrounding environments (i.e., soils, river sediments, swine wastewater, influents and effluents of decentralized wastewater treatment plants) to planktonic microeukaryotes in the main channel, tributaries and reservoir of a peri-urban watershed, China in wet and dry seasons. The results indicated that SAR (~ 49% of the total communities), Opithokonta (~ 34%), Archaeplastida (~ 9%), and Amoebozoa (~ 2%) were dominant taxa in the watershed. The community-based MST analysis revealed that sewage effluents (7.96 - 21.84%), influents (2.23 - 13.97%), and river sediments (2.56 - 11.71%) were the major exogenous sources of riverine microeukaryotes. At the spatial scale, the downstream of the watershed (i.e., main channel and tributaries) received higher proportions of exogenous microeukaryotic OTUs compared to the upstream reservoirs, while at the seasonal scale, the sewage effluents and influents contributed higher exogenous microeukaryotes to river water in wet season than in dry season. Moreover, the swine and domestic wastewater led to the presence of Apicomplexa in wet season only, implying rainfall runoff may enhance the spread of parasitic microeukaryotes. Taken together, our study provides novel insights into the immigration patterns of microeukaryotes and their dominant supergroups between terrestrial and riverine habitats.
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Affiliation(s)
- Mahmoud Gad
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Water Pollution Research Department, National Research Centre, Giza 12622, Egypt
| | - Liyuan Hou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Meixian Cao
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bob Adyari
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Environmental Engineering, Universitas Pertamina, Jakarta 12220, Indonesia
| | - Lanping Zhang
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dan Qin
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Qian Sun
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Anyi Hu
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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Pryszlak A, Wenzel T, Seitz KW, Hildebrand F, Kartal E, Cosenza MR, Benes V, Bork P, Merten CA. Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics. CELL REPORTS METHODS 2022; 2:None. [PMID: 35118437 PMCID: PMC8787643 DOI: 10.1016/j.crmeth.2021.100137] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/05/2021] [Accepted: 12/07/2021] [Indexed: 11/25/2022]
Abstract
We report a droplet microfluidic method to target and sort individual cells directly from complex microbiome samples and to prepare these cells for bulk whole-genome sequencing without cultivation. We characterize this approach by recovering bacteria spiked into human stool samples at a ratio as low as 1:250 and by successfully enriching endogenous Bacteroides vulgatus to the level required for de novo assembly of high-quality genomes. Although microbiome strains are increasingly demanded for biomedical applications, a vast majority of species and strains are uncultivated and without reference genomes. We address this shortcoming by encapsulating complex microbiome samples directly into microfluidic droplets and amplifying a target-specific genomic fragment using a custom molecular TaqMan probe. We separate those positive droplets by droplet sorting, selectively enriching single target strain cells. Finally, we present a protocol to purify the genomic DNA while specifically removing amplicons and cell debris for high-quality genome sequencing.
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Affiliation(s)
- Anna Pryszlak
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tobias Wenzel
- European Molecular Biology Laboratory, Heidelberg, Germany
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Falk Hildebrand
- European Molecular Biology Laboratory, Heidelberg, Germany
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
- Digital Biology, Earlham Institute, Norwich, UK
| | - Ece Kartal
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Vladimir Benes
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- University of Würzburg, Würzburg, Germany
| | - Christoph A. Merten
- European Molecular Biology Laboratory, Heidelberg, Germany
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Goosen C, Proost S, Tito RY, Baumgartner J, Barnabas SL, Cotton MF, Zimmermann MB, Raes J, Blaauw R. The effect of oral iron supplementation on the gut microbiota, gut inflammation, and iron status in iron-depleted South African school-age children with virally suppressed HIV and without HIV. Eur J Nutr 2022; 61:2067-2078. [PMID: 34997267 DOI: 10.1007/s00394-021-02793-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/20/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE Both HIV and oral iron interventions may alter gut microbiota composition and increase gut inflammation. We determined the effect of oral iron supplementation on gut microbiota composition, gut inflammation, and iron status in iron-depleted South Africa school-aged children living with HIV (HIV+) but virally suppressed on antiretroviral therapy and children without HIV (HIV-ve). METHODS In this before-after intervention study with case-control comparisons, we provided 55 mg elemental iron from ferrous sulphate, once daily for 3 months, to 33 virally suppressed (< 50 HIV RNA copies/mL) HIV+ and 31 HIV-ve children. At baseline and endpoint, we assessed microbial composition of faecal samples (16S rRNA sequencing), and markers of gut inflammation (faecal calprotectin), anaemia (haemoglobin) and iron status (plasma ferritin, soluble transferrin receptor). This study was nested within a larger trial registered at clinicaltrials.gov as NCT03572010. RESULTS HIV+ (11.3y SD ± 1.8, 46% male) and HIV-ve (11.1y SD ± 1.7, 52% male) groups did not significantly differ in age or sex ratio. Following iron supplementation, improvements were observed in haemoglobin (HIV+ : 118 to 124 g/L, P = 0.003; HIV-ve: 120 to 124 g/L, P = 0.003), plasma ferritin (HIV+ : 15 to 34 µg/L, P < 0.001; HIV-ve: 18 to 37 µg/L, P < 0.001), and soluble transferrin receptor (HIV+ : 7.1 to 5.9 mg/L, P < 0.001; HIV-ve: 6.6 to 5.7 mg/L, P < 0.001), with no significant change in the relative abundance of any genera, alpha diversity of the gut microbiota (HIV+ : P = 0.37; HIV-ve: P = 0.77), or faecal calprotectin (HIV+ : P = 0.42; HIV-ve: P = 0.80). CONCLUSION Our findings suggest that oral iron supplementation can significantly improve haemoglobin and iron status without increasing pathogenic gut microbial taxa or gut inflammation in iron-depleted virally suppressed HIV+ and HIV-ve school-age children.
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Affiliation(s)
- Charlene Goosen
- Division of Human Nutrition, Department of Global Health, Stellenbosch University, Cape Town, South Africa.
| | - Sebastian Proost
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Raul Y Tito
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Jeannine Baumgartner
- Laboratory of Human Nutrition, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Shaun L Barnabas
- Family Centre for Research With Ubuntu, Department of Paediatrics and Child Health, Stellenbosch University, Cape Town, South Africa
| | - Mark F Cotton
- Family Centre for Research With Ubuntu, Department of Paediatrics and Child Health, Stellenbosch University, Cape Town, South Africa
| | - Michael B Zimmermann
- Laboratory of Human Nutrition, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.
- Center for Microbiology, VIB, Leuven, Belgium.
| | - Renée Blaauw
- Division of Human Nutrition, Department of Global Health, Stellenbosch University, Cape Town, South Africa
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Fournier P, Pellan L, Barroso-Bergadà D, Bohan DA, Candresse T, Delmotte F, Dufour MC, Lauvergeat V, Le Marrec C, Marais A, Martins G, Masneuf-Pomarède I, Rey P, Sherman D, This P, Frioux C, Labarthe S, Vacher C. The functional microbiome of grapevine throughout plant evolutionary history and lifetime. ADV ECOL RES 2022. [DOI: 10.1016/bs.aecr.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Valles-Colomer M, Bacigalupe R, Vieira-Silva S, Suzuki S, Darzi Y, Tito RY, Yamada T, Segata N, Raes J, Falony G. Variation and transmission of the human gut microbiota across multiple familial generations. Nat Microbiol 2022; 7:87-96. [PMID: 34969979 PMCID: PMC8727295 DOI: 10.1038/s41564-021-01021-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022]
Abstract
Although the composition and functional potential of the human gut microbiota evolve over the lifespan, kinship has been identified as a key covariate of microbial community diversification. However, to date, sharing of microbiota features within families has mostly been assessed between parents and their direct offspring. Here we investigate the potential transmission and persistence of familial microbiome patterns and microbial genotypes in a family cohort (n = 102) spanning 3 to 5 generations over the same female bloodline. We observe microbiome community composition associated with kinship, with seven low abundant genera displaying familial distribution patterns. While kinship and current cohabitation emerge as closely entangled variables, our explorative analyses of microbial genotype distribution and transmission estimates point at the latter as a key covariate of strain dissemination. Highest potential transmission rates are estimated between sisters and mother-daughter pairs, decreasing with increasing daughter's age and being higher among cohabiting pairs than those living apart. Although rare, we detect potential transmission events spanning three and four generations, primarily involving species of the genera Alistipes and Bacteroides. Overall, while our analyses confirm the existence of family-bound microbiome community profiles, transmission or co-acquisition of bacterial strains appears to be strongly linked to cohabitation.
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Affiliation(s)
- Mireia Valles-Colomer
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Department for Integrative Biology, University of Trento, Trento, Italy
| | - Rodrigo Bacigalupe
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Sara Vieira-Silva
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Shinya Suzuki
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Youssef Darzi
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Raul Y Tito
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Takuji Yamada
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Nicola Segata
- European Institute of Oncology Istituto di Ricovero e Cura a Carattere Scientifico, Milan, Italy
- Department for Integrative Biology, University of Trento, Trento, Italy
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium.
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium.
| | - Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
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Analyzing the human gut mycobiome – a short guide for beginners. Comput Struct Biotechnol J 2022; 20:608-614. [PMID: 35116136 PMCID: PMC8790610 DOI: 10.1016/j.csbj.2022.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/04/2022] [Accepted: 01/08/2022] [Indexed: 12/30/2022] Open
Abstract
The human body is a dynamic ecosystem consisting of millions of microbes which are often comprised under the term microbiome. Compared to bacteria, which count for the overwhelming majority of the microbiome, the number of human-associated fungi is small and often underestimated. Nonetheless, they can be found in different host niches such as the gut, the oral cavity and the skin. The fungal community has several potential roles in health and disease of the human host. In this review we will focus on intestinal fungi and their interaction with the host as well as bacteria. We also summarize technical challenges and possible biases researchers must be aware of when conducting mycobiome analysis.
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Abstract
Disturbances in the primary colonization of the infant gut can result in lifelong consequences and have been associated with a range of host conditions. Although early-life factors have been shown to affect infant gut microbiota development, our current understanding of human gut colonization in early life remains limited. To gain more insights into the unique dynamics of this rapidly evolving ecosystem, we investigated the microbiota over the first year of life in eight densely sampled infants (n = 303 total samples). To evaluate the gut microbiota maturation transition toward an adult configuration, we compared the microbiome composition of the infants to that of the Flemish Gut Flora Project (FGFP) population (n = 1,106). We observed the infant gut microbiota to mature through three distinct, conserved stages of ecosystem development. Across these successional gut microbiota maturation stages, the genus predominance was observed to shift from Escherichia over Bifidobacterium to Bacteroides. Both disease and antibiotic treatment were observed to be associated occasionally with gut microbiota maturation stage regression, a transient setback in microbiota maturation dynamics. Although the studied microbiota trajectories evolved to more adult-like constellations, microbiome community typing against the background of the FGFP cohort clustered all infant samples within the (in adults) potentially dysbiotic Bacteroides 2 (Bact2) enterotype. We confirmed the similarities between infant gut microbial colonization and adult dysbiosis. Profound knowledge about the primary gut colonization process in infants might provide crucial insights into how the secondary colonization of a dysbiotic adult gut can be redirected.
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Wauters L, Tito RY, Ceulemans M, Lambaerts M, Accarie A, Rymenans L, Verspecht C, Toth J, Mols R, Augustijns P, Tack J, Vanuytsel T, Raes J. Duodenal Dysbiosis and Relation to the Efficacy of Proton Pump Inhibitors in Functional Dyspepsia. Int J Mol Sci 2021; 22:ijms222413609. [PMID: 34948413 PMCID: PMC8708077 DOI: 10.3390/ijms222413609] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 12/11/2022] Open
Abstract
Proton pump inhibitors (PPI) may improve symptoms in functional dyspepsia (FD) through duodenal eosinophil-reducing effects. However, the contribution of the microbiome to FD symptoms and its interaction with PPI remains elusive. Aseptic duodenal brushings and biopsies were performed before and after PPI intake (4 weeks Pantoprazole 40 mg daily, FD-starters and controls) or withdrawal (2 months, FD-stoppers) for 16S-rRNA sequencing. Between- and within-group changes in genera or diversity and associations with symptoms or duodenal factors were analyzed. In total, 30 controls, 28 FD-starters and 19 FD-stoppers were followed. Mucus-associated Porphyromonas was lower in FD-starters vs. controls and correlated with symptoms in FD and duodenal eosinophils in both groups, while Streptococcus correlated with eosinophils in controls. Although clinical and eosinophil-reducing effects of PPI therapy were unrelated to microbiota changes in FD-starters, increased Streptococcus was associated with duodenal PPI effects in controls and remained higher despite withdrawal of long-term PPI therapy in FD-stoppers. Thus, duodenal microbiome analysis demonstrated differential mucus-associated genera, with a potential role of Porphyromonas in FD pathophysiology. While beneficial effects of short-term PPI therapy were not associated with microbial changes in FD-starters, increased Streptococcus and its association with PPIeffects in controls suggest a role for duodenal dysbiosis after long-term PPI therapy.
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Affiliation(s)
- Lucas Wauters
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, 3000 Leuven, Belgium; (L.W.); (J.T.)
- Translational Research in Gastrointestinal Disorders (TARGID), KU Leuven, 3000 Leuven, Belgium; (M.C.); (M.L.); (A.A.); (J.T.)
- VIB Center for Microbiology, 3000 Leuven, Belgium; (R.Y.T.); (L.R.); (C.V.)
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Raúl Y. Tito
- VIB Center for Microbiology, 3000 Leuven, Belgium; (R.Y.T.); (L.R.); (C.V.)
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Matthias Ceulemans
- Translational Research in Gastrointestinal Disorders (TARGID), KU Leuven, 3000 Leuven, Belgium; (M.C.); (M.L.); (A.A.); (J.T.)
| | - Maarten Lambaerts
- Translational Research in Gastrointestinal Disorders (TARGID), KU Leuven, 3000 Leuven, Belgium; (M.C.); (M.L.); (A.A.); (J.T.)
| | - Alison Accarie
- Translational Research in Gastrointestinal Disorders (TARGID), KU Leuven, 3000 Leuven, Belgium; (M.C.); (M.L.); (A.A.); (J.T.)
| | - Leen Rymenans
- VIB Center for Microbiology, 3000 Leuven, Belgium; (R.Y.T.); (L.R.); (C.V.)
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Chloë Verspecht
- VIB Center for Microbiology, 3000 Leuven, Belgium; (R.Y.T.); (L.R.); (C.V.)
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Joran Toth
- Translational Research in Gastrointestinal Disorders (TARGID), KU Leuven, 3000 Leuven, Belgium; (M.C.); (M.L.); (A.A.); (J.T.)
| | - Raf Mols
- Drug Delivery and Disposition, KU Leuven, 3000 Leuven, Belgium; (R.M.); (P.A.)
| | - Patrick Augustijns
- Drug Delivery and Disposition, KU Leuven, 3000 Leuven, Belgium; (R.M.); (P.A.)
| | - Jan Tack
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, 3000 Leuven, Belgium; (L.W.); (J.T.)
- Translational Research in Gastrointestinal Disorders (TARGID), KU Leuven, 3000 Leuven, Belgium; (M.C.); (M.L.); (A.A.); (J.T.)
| | - Tim Vanuytsel
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, 3000 Leuven, Belgium; (L.W.); (J.T.)
- Translational Research in Gastrointestinal Disorders (TARGID), KU Leuven, 3000 Leuven, Belgium; (M.C.); (M.L.); (A.A.); (J.T.)
- Correspondence: (T.V.); (J.R.)
| | - Jeroen Raes
- VIB Center for Microbiology, 3000 Leuven, Belgium; (R.Y.T.); (L.R.); (C.V.)
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Correspondence: (T.V.); (J.R.)
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