51
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Rosés C, Nieto JA, Viadel B, Gallego E, Romo-Hualde A, Streitenberger S, Milagro FI, Barceló A. An In Vitro Protocol to Study the Modulatory Effects of a Food or Biocompound on Human Gut Microbiome and Metabolome. Foods 2021; 10:foods10123020. [PMID: 34945571 PMCID: PMC8701939 DOI: 10.3390/foods10123020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
The gut microbiota plays a key role in gastrointestinal immune and metabolic functions and is influenced by dietary composition. An in vitro protocol simulating the physiological conditions of the digestive system helps to study the effects of foods/biocompounds on gut microbiome and metabolome. The Dynamic-Colonic Gastrointestinal Digester consists of five interconnected compartments, double jacket vessels that simulate the physiological conditions of the stomach, the small intestine and the three colonic sections, which are the ascending colon, transverse colon and descending colon. Human faeces are required to reproduce the conditions and culture medium of the human colon, allowing the growth of the intestinal microbiota. After a stabilization period of 12 days, a food/biocompound can be introduced to study its modulatory effects during the next 14 days (treatment period). At the end of the stabilization and treatment period, samples taken from the colon compartments are analysed. The 16S rRNA gene analysis reveals the microbiota composition. The untargeted metabolomics analysis gives more than 10,000 features (metabolites/compounds). The present protocol allows in vitro testing of the modulatory effects of foods or biocompounds on gut microbiota composition and metabolic activity.
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Affiliation(s)
- Carles Rosés
- Servei de Genòmica, Universitat Autònoma de Barcelona, Bellaterra, 08193 Cerdanyola del Vallés, Spain;
| | - Juan Antonio Nieto
- Ainia, In Vitro Digestion Assays, Parque Tecnológico de Valencia, 46980 Paterna, Spain; (J.A.N.); (B.V.); (E.G.)
| | - Blanca Viadel
- Ainia, In Vitro Digestion Assays, Parque Tecnológico de Valencia, 46980 Paterna, Spain; (J.A.N.); (B.V.); (E.G.)
| | - Elisa Gallego
- Ainia, In Vitro Digestion Assays, Parque Tecnológico de Valencia, 46980 Paterna, Spain; (J.A.N.); (B.V.); (E.G.)
| | - Ana Romo-Hualde
- Centre for Nutrition Research, Department of Nutrition, Food Sciences and Physiology, University of Navarra, 31008 Pamplona, Spain; (A.R.-H.); (F.I.M.)
| | | | - Fermín I. Milagro
- Centre for Nutrition Research, Department of Nutrition, Food Sciences and Physiology, University of Navarra, 31008 Pamplona, Spain; (A.R.-H.); (F.I.M.)
- Navarra Institute for Health Research (IdISNA), 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Anna Barceló
- Servei de Genòmica, Universitat Autònoma de Barcelona, Bellaterra, 08193 Cerdanyola del Vallés, Spain;
- Correspondence:
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52
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Vandeputte D, De Commer L, Tito RY, Kathagen G, Sabino J, Vermeire S, Faust K, Raes J. Temporal variability in quantitative human gut microbiome profiles and implications for clinical research. Nat Commun 2021; 12:6740. [PMID: 34795283 PMCID: PMC8602282 DOI: 10.1038/s41467-021-27098-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/26/2021] [Indexed: 01/04/2023] Open
Abstract
While clinical gut microbiota research is ever-expanding, extending reference knowledge of healthy between- and within-subject gut microbiota variation and its drivers remains essential; in particular, temporal variability is under-explored, and a comparison with cross-sectional variation is missing. Here, we perform daily quantitative microbiome profiling on 713 fecal samples from 20 Belgian women over six weeks, combined with extensive anthropometric measurements, blood panels, dietary data, and stool characteristics. We show substantial temporal variation for most major gut genera; we find that for 78% of microbial genera, day-to-day absolute abundance variation is substantially larger within than between individuals, with up to 100-fold shifts over the study period. Diversity, and especially evenness indicators also fluctuate substantially. Relative abundance profiles show similar but less pronounced temporal variation. Stool moisture, and to a lesser extent diet, are the only significant host covariates of temporal microbiota variation, while menstrual cycle parameters did not show significant effects. We find that the dysbiotic Bact2 enterotype shows increased between- and within-subject compositional variability. Our results suggest that to increase diagnostic as well as target discovery power, studies could adopt a repeated measurement design and/or focus analysis on community-wide microbiome descriptors and indices.
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Affiliation(s)
- Doris Vandeputte
- grid.415751.3KU Leuven – University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium ,grid.511066.5VIB, Center for Microbiology, Kasteelpark Arenberg 31, B-3000 Leuven, Belgium
| | - Lindsey De Commer
- grid.415751.3KU Leuven – University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Raul Y. Tito
- grid.415751.3KU Leuven – University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium ,grid.511066.5VIB, Center for Microbiology, Kasteelpark Arenberg 31, B-3000 Leuven, Belgium
| | - Gunter Kathagen
- grid.415751.3KU Leuven – University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium ,grid.511066.5VIB, Center for Microbiology, Kasteelpark Arenberg 31, B-3000 Leuven, Belgium
| | - João Sabino
- grid.5596.f0000 0001 0668 7884Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven B-3000 Leuven, Belgium
| | - Séverine Vermeire
- grid.5596.f0000 0001 0668 7884Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven B-3000 Leuven, Belgium
| | - Karoline Faust
- grid.415751.3KU Leuven – University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Jeroen Raes
- KU Leuven - University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Herestraat 49, B-3000, Leuven, Belgium. .,VIB, Center for Microbiology, Kasteelpark Arenberg 31, B-3000, Leuven, Belgium.
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53
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Yang Q, Rutherfurd-Markwick K, Mutukumira AN. Identification of dominant lactic acid bacteria and yeast in rice sourdough produced in New Zealand. Curr Res Food Sci 2021; 4:729-736. [PMID: 34729499 PMCID: PMC8546371 DOI: 10.1016/j.crfs.2021.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/07/2021] [Accepted: 10/06/2021] [Indexed: 11/21/2022] Open
Abstract
This study characterised a commercial New Zealand gluten free (GF) rice sourdough and its starter culture composition. Acidity of the mother sourdough, dough before proofing and dough after proofing was determined during the production of rice sourdough bread, and colour was measured for the baked bread. Yeast and lactic acid bacteria (LAB) were enumerated in the rice sourdough samples and representative colonies characterised using API kits and sequenced by the Internal Transcribed Spacer and 16 S rRNA region. Sourdough LAB isolates were identified as Lactobacillus (L.) papraplantarum DSM 10667 and L. fermentarum CIP 102980 and the yeast isolates as Saccharomyces (S.) cerevisiae CBS 1171. Dough acidity increased significantly (p < 0.05) during fermentation due to the metabolic activities of the sourdough cultures. After baking, the colour of the rice sourdough bread crust was similar to that of unleavened wheat bread (golden brown). The improved colour of the rice sourdough bread crust may be a result of combined use of sourdough technique and optimal baking conditions. The results of this study may allow bakers to improve the overall quality of GF rice sourdough baked bread by selecting suitable fermentation and baking parameters. Gluten-free rice sourdough bread. Rice sourdough fermentation of gluten-free bread improved bread crust colour Rice sourdough LAB identified as Lactobacillus paraplantarum CIP 102980 and Lactobacillus fermentarum DSM 10667 Yeast isolated from rice sourdough was identified as S. cerevisiae CBS 1171.
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Affiliation(s)
- Qiwei Yang
- School of Food and Advanced Technology, Massey University, Auckland, 0745, New Zealand
| | - Kay Rutherfurd-Markwick
- School of Health Sciences, College of Health, Massey University, Auckland, 0745, New Zealand
| | - Anthony N. Mutukumira
- School of Food and Advanced Technology, Massey University, Auckland, 0745, New Zealand
- Corresponding author.
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54
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Lloréns-Rico V, Gregory AC, Van Weyenbergh J, Jansen S, Van Buyten T, Qian J, Braz M, Menezes SM, Van Mol P, Vanderbeke L, Dooms C, Gunst J, Hermans G, Meersseman P, Wauters E, Neyts J, Lambrechts D, Wauters J, Raes J. Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host. Nat Commun 2021; 12:6243. [PMID: 34716338 PMCID: PMC8556379 DOI: 10.1038/s41467-021-26500-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/06/2021] [Indexed: 12/11/2022] Open
Abstract
Understanding the pathology of COVID-19 is a global research priority. Early evidence suggests that the respiratory microbiome may be playing a role in disease progression, yet current studies report contradictory results. Here, we examine potential confounders in COVID-19 respiratory microbiome studies by analyzing the upper (n = 58) and lower (n = 35) respiratory tract microbiome in well-phenotyped COVID-19 patients and controls combining microbiome sequencing, viral load determination, and immunoprofiling. We find that time in the intensive care unit and type of oxygen support, as well as associated treatments such as antibiotic usage, explain the most variation within the upper respiratory tract microbiome, while SARS-CoV-2 viral load has a reduced impact. Specifically, mechanical ventilation is linked to altered community structure and significant shifts in oral taxa previously associated with COVID-19. Single-cell transcriptomics of the lower respiratory tract of COVID-19 patients identifies specific oral bacteria in physical association with proinflammatory immune cells, which show higher levels of inflammatory markers. Overall, our findings suggest confounders are driving contradictory results in current COVID-19 microbiome studies and careful attention needs to be paid to ICU stay and type of oxygen support, as bacteria favored in these conditions may contribute to the inflammatory phenotypes observed in severe COVID-19 patients.
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Affiliation(s)
- Verónica Lloréns-Rico
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Ann C Gregory
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Johan Van Weyenbergh
- Laboratory for Clinical and Evolutionary Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Sander Jansen
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Tina Van Buyten
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Junbin Qian
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Marcos Braz
- Laboratory for Clinical and Evolutionary Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Soraya Maria Menezes
- Laboratory for Clinical and Evolutionary Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Pierre Van Mol
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Pneumology, University Hospitals Leuven, Leuven, Belgium
| | - Lore Vanderbeke
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Christophe Dooms
- Department of Pneumology, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Jan Gunst
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Greet Hermans
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Philippe Meersseman
- Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Els Wauters
- Department of Pneumology, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Joost Wauters
- Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, 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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55
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Aslani F, Geisen S, Ning D, Tedersoo L, Bahram M. Towards revealing the global diversity and community assembly of soil eukaryotes. Ecol Lett 2021; 25:65-76. [PMID: 34697894 DOI: 10.1111/ele.13904] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/01/2021] [Accepted: 10/11/2021] [Indexed: 01/01/2023]
Abstract
Soil fungi, protists, and animals (i.e., the eukaryome) play a critical role in key ecosystem functions in terrestrial ecosystems. Yet, we lack a holistic understanding of the processes shaping the global distribution of the eukaryome. We conducted a molecular analysis of 193 composite soil samples spanning the world's major biomes. Our analysis showed that the importance of selection processes was higher in the community assemblage of smaller-bodied and wider niche breadth organisms. Soil pH and mean annual precipitation were the primary determinants of the community structure of eukaryotic microbes and animals, respectively. We further found contrasting latitudinal diversity patterns and strengths for soil eukaryotic microbes and animals. Our results point to a potential link between body size and niche breadth of soil eukaryotes and the relative effect of ecological processes and environmental factors in driving their biogeographic patterns.
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Affiliation(s)
- Farzad Aslani
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Daliang Ning
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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56
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Lazic T, Pierri C, Corriero G, Balech B, Cardone F, Deflorio M, Fosso B, Gissi C, Marzano M, Nonnis Marzano F, Pesole G, Santamaria M, Gristina M. Evaluating the Efficiency of DNA Metabarcoding to Analyze the Diet of Hippocampus guttulatus (Teleostea: Syngnathidae). Life (Basel) 2021; 11:life11100998. [PMID: 34685370 PMCID: PMC8540156 DOI: 10.3390/life11100998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 12/14/2022] Open
Abstract
Seahorses are considered a flagship species for conservation efforts and due to their conservation status, improving knowledge on their dietary composition while applying a non-invasive approach, could be useful. Using Hippocampus guttulatus as a case study, the present study represents pioneering research into investigating the diet of seahorses by NGS-based DNA metabarcoding of fecal samples. The study developed and tested the protocol for fecal DNA metabarcoding during the feeding trials where captive seahorses were fed on a diet of known composition; the process was subsequently applied on fecal samples collected from wild individuals. The analysis of samples collected during the feeding trials indicated the reliability of the applied molecular approach by allowing the characterization of the effectively ingested prey. In the field study, among detected prey species, results revealed that the majority of the seahorse samples contained taxa such as Amphipoda, Decapoda, Isopoda, and Calanoida, while less common prey taxa were Gastropoda and Polyplacophora. As only a small amount of starting fecal material is needed and the sampling procedure is neither invasive nor lethal. The present study indicates DNA metabarcoding as useful for investigating seahorse diet and could help define management and conservation actions.
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Affiliation(s)
- Tamara Lazic
- Department of Biology, University of Bari, 70125 Bari, Italy; (T.L.); (G.C.)
| | - Cataldo Pierri
- Department of Biology, University of Bari, 70125 Bari, Italy; (T.L.); (G.C.)
- Correspondence:
| | - Giuseppe Corriero
- Department of Biology, University of Bari, 70125 Bari, Italy; (T.L.); (G.C.)
| | - Bachir Balech
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
| | - Frine Cardone
- Department of Integrated Marine Ecology, Zoological Station Anton Dohrn, 80127 Naples, Italy;
| | - Michele Deflorio
- Department of Veterinary Medicine, University of Bari, 70125 Bari, Italy;
| | - Bruno Fosso
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
| | - Carmela Gissi
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70125 Bari, Italy
| | - Marinella Marzano
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
| | - Francesco Nonnis Marzano
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43121 Parma, Italy;
| | - Graziano Pesole
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70125 Bari, Italy
| | - Monica Santamaria
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
| | - Michele Gristina
- Institute of Anthropic Impacts and Sustainability in Marine Environment (IAS), National Council of Research (CNR), 90100 Palermo, Italy;
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57
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Loos D, Zhang L, Beemelmanns C, Kurzai O, Panagiotou G. DAnIEL: A User-Friendly Web Server for Fungal ITS Amplicon Sequencing Data. Front Microbiol 2021; 12:720513. [PMID: 34484161 PMCID: PMC8416086 DOI: 10.3389/fmicb.2021.720513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/26/2021] [Indexed: 01/04/2023] Open
Abstract
Trillions of microbes representing all kingdoms of life are resident in, and on, humans holding essential roles for the host development and physiology. The last decade over a dozen online tools and servers, accessible via public domain, have been developed for the analysis of bacterial sequences; however, the analysis of fungi is still in its infancy. Here, we present a web server dedicated to the comprehensive analysis of the human mycobiome for (i) translating raw sequencing reads to data tables and high-standard figures, (ii) integrating statistical analysis and machine learning with a manually curated relational database and (iii) comparing the user’s uploaded datasets with publicly available from the Sequence Read Archive. Using 1,266 publicly available Internal transcribed spacers (ITS) samples, we demonstrated the utility of DAnIEL web server on large scale datasets and show the differences in fungal communities between human skin and soil sites.
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Affiliation(s)
- Daniel Loos
- Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Lu Zhang
- Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Christine Beemelmanns
- Chemical Biology of Microbe-Host Interactions Group, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Oliver Kurzai
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany.,National Reference Center for Invasive Fungal Infections NRZMyk, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany.,Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam, China
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58
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Hou L, Wang H, Chen Q, Su JQ, Gad M, Li J, Mulla SI, Yu CP, Hu A. Fecal pollution mediates the dominance of stochastic assembly of antibiotic resistome in an urban lagoon (Yundang lagoon), China. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:126083. [PMID: 34000699 DOI: 10.1016/j.jhazmat.2021.126083] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/19/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Sewage and fecal pollution cause antibiotic resistance genes (ARGs) pollution in urban lagoons. Seasonality also affects ARG dynamics. However, knowledge of factors controlling ARG community assembly across seasons is still limited. Here, we revealed the seasonal variation of ARGs and depict the underlying assembly processes and drivers via high-throughput quantitative PCR in an urban lagoon, China. A higher richness and abundance of ARGs were observed in summer and winter compared to spring and fall (Kruskal-Wallis test, P < 0.05). Both ARG and prokaryotic communities were mainly governed by stochastic processes, however, these processes drove ARGs and prokaryotes differently across seasons. Stochastic processes played a more dominant role in shaping ARG communities in summer (average stochasticity: 83%) and winter (75%), resulting in a stable antibiotic resistome. However, no such seasonal pattern of stochastic processes was determined for prokaryotes, indicating a decoupling of the assembly process of ARGs and prokaryotes. Moreover, fecal microorganisms (e.g., Bacteroidetes and Faecalibacterium) mediated the stochastic processes of ARG profiles, via enhancement of prokaryotic biomass and mobile genetic element abundances. The tnpA-07 transposase was the key for the horizontal gene transfer. These findings will enhance our understanding of how fecal pollution shapes ARG community assembly in urban lagoons.
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Affiliation(s)
- Liyuan Hou
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hongjie 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
| | - Qingfu Chen
- Yundang Lake Management Center, Xiamen, Fujian 361004, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China
| | - 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
| | - Jiangwei Li
- 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
| | - Sikandar I Mulla
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Department of Biochemistry, School of Applied Sciences, Reva University, Bangalore 560064, India
| | - 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
| | - 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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59
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Thapa S, Sheu JC, Venkatachalam A, Runge JK, Luna RA, Calarge CA. Gut microbiome in adolescent depression. J Affect Disord 2021; 292:500-507. [PMID: 34146902 PMCID: PMC8282757 DOI: 10.1016/j.jad.2021.05.107] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/02/2021] [Accepted: 05/31/2021] [Indexed: 01/01/2023]
Abstract
OBJECTIVES To examine the association of major depressive disorder (MDD) and selective serotonin reuptake inhibitor (SSRI) use with gut microbiome in older adolescents and younger adults. METHODS Fifteen to 20-year-old participants within a month of starting an SSRI and unmedicated controls were enrolled in a longitudinal study. They underwent a diagnostic evaluation comprising self-completed and rater-administered questionnaires and clinical interview. They also provided a stool sample, which was stored at -80°C until DNA extraction. Microbial DNA was extracted with the MoBio PowerSoil kit, and the V4 region of the 16S rRNA was amplified and sequenced. Raw sequence data was processed with the LotuS pipeline. Only samples with no antibiotic exposure in the last 6 months and with >1000 quality filtered reads were included in the analysis. RESULTS 160 participants (57.5% female, mean age 20.0±1.9 years, 29% taking SSRIs) were enrolled, comprising 110 MDD patients (60% in acute episode), 27 healthy controls, and 23 psychiatric controls. No significant group differences were observed in bacterial richness or alpha and beta diversity. Differential abundance analysis of bacterial taxa found no significant group differences at the phylum and genus levels. Neither being in a major depressive episode vs. remission nor using SSRIs was associated with differential bacterial composition. CONCLUSIONS In this sizeable sample of older adolescents, neither MDD nor SSRI use was associated with differences in gut bacterial microbiome. In this age group, the bi-directional interaction between the gut bacteria and brain may be more nuanced than in adults, requiring further investigation.
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Affiliation(s)
- Santosh Thapa
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Jessica C Sheu
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Alamelu Venkatachalam
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Jessica K Runge
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Ruth Ann Luna
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Chadi A Calarge
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA.
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Abstract
Technological advances in community sequencing have steadily increased the taxonomic resolution at which microbes can be delineated. In high-resolution metagenomics, bacterial strains can now be resolved, enhancing medical microbiology and the description of microbial evolution in vivo. In the Hildebrand lab, we are researching novel approaches to further increase the phylogenetic resolution of metagenomics. I propose that ultra-resolution metagenomics will be the next qualitative level of community sequencing, classified by the accurate resolution of ultra-rare genetic events, such as subclonal mutations present in all populations of evolving cells. This will be used to quantify evolutionary processes at ecologically relevant scales, monitor the progress of infections within a patient, and accurately track pathogens in food and infection chains. However, to develop this next metagenomic generation, we first need to understand the currently imposed limits of sequencing technologies, metagenomic strain delineation, and genome reconstructions.
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Affiliation(s)
- Falk Hildebrand
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
- Digital Biology, Earlham Institute, Norwich, United Kingdom
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61
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Si J, Froussart E, Viaene T, Vázquez-Castellanos JF, Hamonts K, Tang L, Beirinckx S, De Keyser A, Deckers T, Amery F, Vandenabeele S, Raes J, Goormachtig S. Interactions between soil compositions and the wheat root microbiome under drought stress: From an in silico to in planta perspective. Comput Struct Biotechnol J 2021; 19:4235-4247. [PMID: 34429844 PMCID: PMC8353387 DOI: 10.1016/j.csbj.2021.07.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/29/2022] Open
Abstract
As wheat (Triticum aestivum) is an important staple food across the world, preservation of stable yields and increased productivity are major objectives in breeding programs. Drought is a global concern because its adverse impact is expected to be amplified in the future due to the current climate change. Here, we analyzed the effects of edaphic, environmental, and host factors on the wheat root microbiomes collected in soils from six regions in Belgium. Amplicon sequencing analysis of unplanted soil and wheat root endosphere samples indicated that the microbial community variations can be significantly explained by soil pH, microbial biomass, wheat genotype, and soil sodium and iron levels. Under drought stress, the biodiversity in the soil decreased significantly, but increased in the root endosphere community, where specific soil parameters seemingly determine the enrichment of bacterial groups. Indeed, we identified a cluster of drought-enriched bacteria that significantly correlated with soil compositions. Interestingly, integration of a functional analysis further revealed a strong correlation between the same cluster of bacteria and β-glucosidase and osmoprotectant proteins, two functions known to be involved in coping with drought stress. By means of this in silico analysis, we identified amplicon sequence variants (ASVs) that could potentially protect the plant from drought stress and validated them in planta. Yet, ASVs based on 16S rRNA sequencing data did not completely distinguish individual isolates because of their intrinsic short sequences. Our findings support the efforts to maintain stable crop yields under drought conditions through implementation of root microbiome analyses.
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Affiliation(s)
- Jiyeon Si
- Laboratory of Molecular Bacteriology. Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Center for Microbiology, VIB, 3000 Leuven, Belgium
- Medical Science Research Institute, School of Medicine, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Emilie Froussart
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 90e2 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | | | - Jorge F. Vázquez-Castellanos
- Laboratory of Molecular Bacteriology. Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Center for Microbiology, VIB, 3000 Leuven, Belgium
| | | | - Lin Tang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 90e2 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Stien Beirinckx
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 90e2 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Annick De Keyser
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 90e2 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | | | - Fien Amery
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | | | - Jeroen Raes
- Laboratory of Molecular Bacteriology. Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Center for Microbiology, VIB, 3000 Leuven, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 90e2 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
- Corresponding author at: VIB-UGhent Center for Plant Systems Biology, 9052 Ghent, Belgium.
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62
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Cuevas-Sierra A, Milagro FI, Aranaz P, Martínez JA, Riezu-Boj JI. Gut Microbiota Differences According to Ultra-Processed Food Consumption in a Spanish Population. Nutrients 2021; 13:2710. [PMID: 34444870 PMCID: PMC8398738 DOI: 10.3390/nu13082710] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 01/02/2023] Open
Abstract
Ultra-processed foods (UPFs) consumption could affect gut microbiota diversity and profile. We aimed to evaluate the effects of UPFs on microbiota, considering the role of sex. The consumption of UPFs (using NOVA criteria) was assessed with a validated 137-item food-frequency questionnaire. Participants (n = 359) were classified into less than three servings per day (n = 96) of UPFs and more than five (n = 90). Women and men were subclassified following the same criteria. 16S rRNA sequencing was performed from DNA fecal samples, and differences in microbiota were analyzed using EdgeR. The relationship between UPFs and bacteria was assessed by Spearman correlation and comparison of tertiles of consumption. Women who consumed more than five servings/day of UPFs presented an increase in Acidaminococcus, Butyrivibrio, Gemmiger, Shigella, Anaerofilum, Parabacteroides, Bifidobacterium, Enterobacteriales, Bifidobacteriales and Actinobacteria and a decrease in Melainabacter and Lachnospira. Bifidobacterium, Bifidobacteriales and Actinobacteria was positively associated with pizza and Actinobacteria with industrially processed dairy in women. Men who consumed more than five servings/day presented an increase of Granulicatella, Blautia, Carnobacteriaceae, Bacteroidaceae, Peptostreptococcaceae, Bacteroidia and Bacteroidetes and a decrease of Anaerostipes and Clostridiaceae. Bacteroidia and Bacteroidetes correlated positively with industrially processed meat. This study suggests that UPFs may affect microbiota composition differently in women and men.
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Affiliation(s)
- Amanda Cuevas-Sierra
- Department of Nutrition, Food Sciences and Physiology, University of Navarra, 31008 Pamplona, Spain; (A.C.-S.); (J.A.M.); (J.I.R.-B.)
- Center for Nutrition Research, University of Navarra, 31008 Pamplona, Spain;
| | - Fermín I. Milagro
- Department of Nutrition, Food Sciences and Physiology, University of Navarra, 31008 Pamplona, Spain; (A.C.-S.); (J.A.M.); (J.I.R.-B.)
- Center for Nutrition Research, University of Navarra, 31008 Pamplona, Spain;
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y Nutrición (CIBERobn), Institute of Health Carlos III, 28029 Madrid, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Paula Aranaz
- Center for Nutrition Research, University of Navarra, 31008 Pamplona, Spain;
| | - Jose Alfredo Martínez
- Department of Nutrition, Food Sciences and Physiology, University of Navarra, 31008 Pamplona, Spain; (A.C.-S.); (J.A.M.); (J.I.R.-B.)
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y Nutrición (CIBERobn), Institute of Health Carlos III, 28029 Madrid, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - José I. Riezu-Boj
- Department of Nutrition, Food Sciences and Physiology, University of Navarra, 31008 Pamplona, Spain; (A.C.-S.); (J.A.M.); (J.I.R.-B.)
- Center for Nutrition Research, University of Navarra, 31008 Pamplona, Spain;
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
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64
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Junius S, Mavrogiannis AV, Lemaitre P, Gerbaux M, Staels F, Malviya V, Burton O, Gergelits V, Singh K, Tito Tadeo RY, Raes J, Humblet-Baron S, Liston A, Schlenner SM. Unstable regulatory T cells, enriched for naïve and Nrp1 neg cells, are purged after fate challenge. Sci Immunol 2021; 6:6/61/eabe4723. [PMID: 34301799 DOI: 10.1126/sciimmunol.abe4723] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 04/27/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022]
Abstract
Regulatory T cells (Tregs) are indispensable for the control of immune homeostasis and have clinical potential as a cell therapy for treating autoimmunity. Tregs can lose expression of the lineage-defining Foxp3 transcription factor and acquire effector T cell (Teff) characteristics, a process referred to as Treg plasticity. The extent and reversibility of such plasticity during immune responses remain unknown. Here, using a murine genetic fate-mapping system, we show that Treg stability is maintained even during exposure to a complex microbial/antigenic environment. Furthermore, we demonstrate that the observed plasticity of Tregs after adoptive transfer into a lymphopenic environment is a property limited to only a subset of the Treg population, with the nonconverting majority of Tregs being resistant to plasticity upon secondary stability challenge. The unstable Treg fraction is a complex mixture of phenotypically distinct Tregs, enriched for naïve and neuropilin-1-negative Tregs, and includes peripherally induced Tregs and recent thymic emigrant Tregs These results suggest that a "purging" process can be used to purify stable Tregs that are capable of robust fate retention, with potential implications for improving cell transfer therapy.
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Affiliation(s)
- Steffie Junius
- KU Leuven-University of Leuven, Department of Microbiology, Immunology and Transplantation, Leuven 3000, Belgium.,VIB Center for Brain and Disease Research, Leuven 3000, Belgium
| | - Adamantios V Mavrogiannis
- KU Leuven-University of Leuven, Department of Microbiology, Immunology and Transplantation, Leuven 3000, Belgium
| | - Pierre Lemaitre
- KU Leuven-University of Leuven, Department of Microbiology, Immunology and Transplantation, Leuven 3000, Belgium
| | - Margaux Gerbaux
- KU Leuven-University of Leuven, Department of Microbiology, Immunology and Transplantation, Leuven 3000, Belgium.,Pediatric Department, Academic Children Hospital Queen Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Frederik Staels
- KU Leuven-University of Leuven, Department of Microbiology, Immunology and Transplantation, Leuven 3000, Belgium.,VIB Center for Brain and Disease Research, Leuven 3000, Belgium
| | - Vanshika Malviya
- KU Leuven-University of Leuven, Department of Microbiology, Immunology and Transplantation, Leuven 3000, Belgium
| | - Oliver Burton
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Václav Gergelits
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Kailash Singh
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Raul Yhossef Tito Tadeo
- KU Leuven-University of Leuven, Department of Microbiology, Immunology and Transplantation, Leuven 3000, Belgium.,VIB-KU Leuven Center for Microbiology, VIB, Leuven 3000, Belgium
| | - Jeroen Raes
- KU Leuven-University of Leuven, Department of Microbiology, Immunology and Transplantation, Leuven 3000, Belgium.,VIB-KU Leuven Center for Microbiology, VIB, Leuven 3000, Belgium
| | - Stephanie Humblet-Baron
- KU Leuven-University of Leuven, Department of Microbiology, Immunology and Transplantation, Leuven 3000, Belgium
| | - Adrian Liston
- KU Leuven-University of Leuven, Department of Microbiology, Immunology and Transplantation, Leuven 3000, Belgium. .,VIB Center for Brain and Disease Research, Leuven 3000, Belgium.,Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Susan M Schlenner
- KU Leuven-University of Leuven, Department of Microbiology, Immunology and Transplantation, Leuven 3000, Belgium.
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65
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Suriano F, Vieira-Silva S, Falony G, Roumain M, Paquot A, Pelicaen R, Régnier M, Delzenne NM, Raes J, Muccioli GG, Van Hul M, Cani PD. Novel insights into the genetically obese (ob/ob) and diabetic (db/db) mice: two sides of the same coin. MICROBIOME 2021; 9:147. [PMID: 34183063 PMCID: PMC8240277 DOI: 10.1186/s40168-021-01097-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/19/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Leptin-deficient ob/ob mice and leptin receptor-deficient db/db mice are commonly used mice models mimicking the conditions of obesity and type 2 diabetes development. However, although ob/ob and db/db mice are similarly gaining weight and developing massive obesity, db/db mice are more diabetic than ob/ob mice. It remains still unclear why targeting the same pathway-leptin signaling-leads to the development of two different phenotypes. Given that gut microbes dialogue with the host via different metabolites (e.g., short-chain fatty acids) but also contribute to the regulation of bile acids metabolism, we investigated whether inflammatory markers, bacterial components, bile acids, short-chain fatty acids, and gut microbes could contribute to explain the specific phenotype discriminating the onset of an obese and/or a diabetic state in ob/ob and db/db mice. RESULTS Six-week-old ob/ob and db/db mice were followed for 7 weeks; they had comparable body weight, fat mass, and lean mass gain, confirming their severely obese status. However, as expected, the glucose metabolism and the glucose-induced insulin secretion were significantly different between ob/ob and db/db mice. Strikingly, the fat distribution was different, with db/db mice having more subcutaneous and ob/ob mice having more epididymal fat. In addition, liver steatosis was more pronounced in the ob/ob mice than in db/db mice. We also found very distinct inflammatory profiles between ob/ob and db/db mice, with a more pronounced inflammatory tone in the liver for ob/ob mice as compared to a higher inflammatory tone in the (subcutaneous) adipose tissue for db/db mice. When analyzing the gut microbiota composition, we found that the quantity of 19 microbial taxa was in some way affected by the genotype. Furthermore, we also show that serum LPS concentration, hepatic bile acid content, and cecal short-chain fatty acid profiles were differently affected by the two genotypes. CONCLUSION Taken together, our results elucidate potential mechanisms implicated in the development of an obese or a diabetic state in two genetic models characterized by an altered leptin signaling. We propose that these differences could be linked to specific inflammatory tones, serum LPS concentration, bile acid metabolism, short-chain fatty acid profile, and gut microbiota composition. Video abstract.
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Affiliation(s)
- Francesco Suriano
- Metabolism and Nutrition Research group, Louvain Drug Research Institute (LDRI), Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), UCLouvain, Université catholique de Louvain, Av. E. Mounier, 73 B1.73.11, 1200, Brussels, Belgium
| | - Sara Vieira-Silva
- Department of Microbiology and Immunology, Rega Institute for Medical Research, VIB Center for Microbiology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Gwen Falony
- Department of Microbiology and Immunology, Rega Institute for Medical Research, VIB Center for Microbiology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Martin Roumain
- Bioanalysis and Pharmacology of Bioactive Lipids Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Adrien Paquot
- Bioanalysis and Pharmacology of Bioactive Lipids Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Rudy Pelicaen
- Metabolism and Nutrition Research group, Louvain Drug Research Institute (LDRI), Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), UCLouvain, Université catholique de Louvain, Av. E. Mounier, 73 B1.73.11, 1200, Brussels, Belgium
| | - Marion Régnier
- Metabolism and Nutrition Research group, Louvain Drug Research Institute (LDRI), Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), UCLouvain, Université catholique de Louvain, Av. E. Mounier, 73 B1.73.11, 1200, Brussels, Belgium
| | - Nathalie M Delzenne
- Metabolism and Nutrition Research group, Louvain Drug Research Institute (LDRI), Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), UCLouvain, Université catholique de Louvain, Av. E. Mounier, 73 B1.73.11, 1200, Brussels, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute for Medical Research, VIB Center for Microbiology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Giulio G Muccioli
- Bioanalysis and Pharmacology of Bioactive Lipids Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Matthias Van Hul
- Metabolism and Nutrition Research group, Louvain Drug Research Institute (LDRI), Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), UCLouvain, Université catholique de Louvain, Av. E. Mounier, 73 B1.73.11, 1200, Brussels, Belgium
| | - Patrice D Cani
- Metabolism and Nutrition Research group, Louvain Drug Research Institute (LDRI), Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), UCLouvain, Université catholique de Louvain, Av. E. Mounier, 73 B1.73.11, 1200, Brussels, Belgium.
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Hildebrand F, Gossmann TI, Frioux C, Özkurt E, Myers PN, Ferretti P, Kuhn M, Bahram M, Nielsen HB, Bork P. Dispersal strategies shape persistence and evolution of human gut bacteria. Cell Host Microbe 2021; 29:1167-1176.e9. [PMID: 34111423 PMCID: PMC8288446 DOI: 10.1016/j.chom.2021.05.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/19/2021] [Accepted: 05/14/2021] [Indexed: 02/07/2023]
Abstract
Human gut bacterial strains can co-exist with their hosts for decades, but little is known about how these microbes persist and disperse, and evolve thereby. Here, we examined these processes in 5,278 adult and infant fecal metagenomes, longitudinally sampled in individuals and families. Our analyses revealed that a subset of gut species is extremely persistent in individuals, families, and geographic regions, represented often by locally successful strains of the phylum Bacteroidota. These “tenacious” bacteria show high levels of genetic adaptation to the human host but a high probability of loss upon antibiotic interventions. By contrast, heredipersistent bacteria, notably Firmicutes, often rely on dispersal strategies with weak phylogeographic patterns but strong family transmissions, likely related to sporulation. These analyses describe how different dispersal strategies can lead to the long-term persistence of human gut microbes with implications for gut flora modulations. Bacterial strains may persist within family members through transfer Bacteria adapt dispersal strategies: heredipersistent, spatiopersistent, and tenacious Dispersal strategies correlate with genetic bottlenecks and effective population size
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Affiliation(s)
- Falk Hildebrand
- Gut Microbes and Health, Quadram Institute Bioscience, NR4 7UQ Norwich, UK; Digital Biology, Earlham Institute, NR4 7UZ Norwich, UK; European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.
| | - Toni I Gossmann
- Department of Animal Behaviour, Bielefeld University, Bielefeld DE-33501, Germany
| | - Clémence Frioux
- Gut Microbes and Health, Quadram Institute Bioscience, NR4 7UQ Norwich, UK; Inria, INRAE, CNRS, Univ. Bordeaux, 33405 Talence, France
| | - Ezgi Özkurt
- Gut Microbes and Health, Quadram Institute Bioscience, NR4 7UQ Norwich, UK; Digital Biology, Earlham Institute, NR4 7UZ Norwich, UK
| | - Pernille Neve Myers
- Clinical Microbiomics A/S, Copenhagen, Denmark; Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Pamela Ferretti
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Michael Kuhn
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 750 07 Uppsala, Sweden; Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014 Tartu, Estonia
| | | | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany; Max Delbrück Center for Molecular Medicine, Berlin, Germany; Yonsei Frontier Lab (YFL), Yonsei University, Seoul 03722, South Korea; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
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Mohamad-Zainal NSL, Ramli N, Zolkefli N, Mustapha NA, Hassan MA, Maeda T. Survivability of Alcaligenaceae and Chromatiaceae as palm oil mill effluent pollution bioindicators under fluctuations of temperature, pH and total suspended solid. J Biosci Bioeng 2021; 132:174-182. [PMID: 34074597 DOI: 10.1016/j.jbiosc.2021.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/09/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022]
Abstract
Alcaligenaceae and Chromatiaceae were previously reported as the specific pollution bioindicators in the receiving river water contaminated by palm oil mill effluent (POME) final discharge. Considering the inevitable sensitivity of bacteria under environmental stresses, it is crucial to assess the survivability of both bacteria in the fluctuated environmental factors, proving their credibility as POME pollution bioindicators in the environment. In this study, the survivability of Alcaligenaceae and Chromatiaceae from facultative pond, algae (aerobic) pond and final discharge were evaluated under varying sets of temperature (25-40°C), pH (pH 7-9) and low/high total suspended solid (TSS) contents of POME collected during low/high crop seasons of oil palm, respectively. Following treatment, the viability status and compositions of the bacterial community were assessed using flow cytometry-based assay and high-throughput Illumina MiSeq, respectively, in correlation with the changes of physicochemical properties. The changes in temperature, pH and TSS indeed changed the physicochemical properties of POME. The functionality of bacterial cells was also shifted where the viable cells and high nucleic acid contents reduced at elevated levels of temperature and pH but increased at high TSS content. Interestingly, the Alcaligenaceae and Chromatiaceae continuously detected in the samples which accounted for more than 0.5% of relative abundance, with a positive correlation with biological oxygen demand (BOD5) concentration. Therefore, either Alcaligenaceae or Chromatiaceae or both could be regarded as the reliable and specific bacterial indicators to indicate the pollution in river water due to POME final discharge despite the fluctuations in temperature, pH and TSS.
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Affiliation(s)
- Noor Shaidatul Lyana Mohamad-Zainal
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Norhayati Ramli
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Laboratory of Biopolymer and Derivatives, Institute of Tropical Forestry and Forest Products (INTROP), Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Nurhasliza Zolkefli
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Nurul Asyifah Mustapha
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu-ku, Fukuoka 808-0196, Japan
| | - Mohd Ali Hassan
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu-ku, Fukuoka 808-0196, Japan
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Lee SY, Lee DY, Kang HJ, Kang JH, Jang HW, Kim BK, Hur SJ. Analysis of in vitro digestion using human gut microbiota in adult and elderly individuals. Food Chem 2021; 362:130228. [PMID: 34198129 DOI: 10.1016/j.foodchem.2021.130228] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 04/19/2021] [Accepted: 05/25/2021] [Indexed: 11/29/2022]
Abstract
In vitro human digestion models are widely used to determine the digestibility of bioactive substances and to perform drug delivery analyses. To develop the most accurate in vitro human digestion model reported to date, we simulated all digestion conditions, including pH and digestion time, with changes in the amount of digestive enzymes, motility, and proportion of human gut microbiota in adult and elderly individuals. Using this newly developed model, the digestibility of vitamin E emulsified by lard was found to be significantly different between adults and the elderly. Therefore, this model can accurately simulate oral, gastric, and intestinal (with gut microbiota effects) digestion of bioactive substances and can aid in analyzing drug delivery in adults and elderly individuals.
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Affiliation(s)
- Seung Yun Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Da Young Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Hea Jin Kang
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Ji Hyeop Kang
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Hae Won Jang
- Department of Food Science & Biotechnology, Sungshin Women's University, Seoul 01133, Republic of Korea
| | - Bum Keun Kim
- Research Group of Food Processing, Korea Food Research Institute, Wanju 55365, Republic of Korea
| | - Sun Jin Hur
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea.
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69
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Ansorge R, Birolo G, James SA, Telatin A. Dadaist2: A Toolkit to Automate and Simplify Statistical Analysis and Plotting of Metabarcoding Experiments. Int J Mol Sci 2021; 22:5309. [PMID: 34069990 PMCID: PMC8157834 DOI: 10.3390/ijms22105309] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/14/2022] Open
Abstract
The taxonomic composition of microbial communities can be assessed using universal marker amplicon sequencing. The most common taxonomic markers are the 16S rDNA for bacterial communities and the internal transcribed spacer (ITS) region for fungal communities, but various other markers are used for barcoding eukaryotes. A crucial step in the bioinformatic analysis of amplicon sequences is the identification of representative sequences. This can be achieved using a clustering approach or by denoising raw sequencing reads. DADA2 is a widely adopted algorithm, released as an R library, that denoises marker-specific amplicons from next-generation sequencing and produces a set of representative sequences referred to as 'Amplicon Sequence Variants' (ASV). Here, we present Dadaist2, a modular pipeline, providing a complete suite for the analysis that ranges from raw sequencing reads to the statistics of numerical ecology. Dadaist2 implements a new approach that is specifically optimised for amplicons with variable lengths, such as the fungal ITS. The pipeline focuses on streamlining the data flow from the command line to R, with multiple options for statistical analysis and plotting, both interactive and automatic.
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Affiliation(s)
- Rebecca Ansorge
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (R.A.); (S.A.J.)
| | - Giovanni Birolo
- Medical Sciences Department, University of Turin, 10126 Turin, Italy;
| | - Stephen A. James
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (R.A.); (S.A.J.)
| | - Andrea Telatin
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (R.A.); (S.A.J.)
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70
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Engevik MA, Engevik AC, Engevik KA, Auchtung JM, Chang-Graham AL, Ruan W, Luna RA, Hyser JM, Spinler JK, Versalovic J. Mucin-Degrading Microbes Release Monosaccharides That Chemoattract Clostridioides difficile and Facilitate Colonization of the Human Intestinal Mucus Layer. ACS Infect Dis 2021; 7:1126-1142. [PMID: 33176423 DOI: 10.1021/acsinfecdis.0c00634] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
It is widely accepted that the pathogen Clostridioides difficile exploits an intestinal environment with an altered microbiota, but the details of these microbe-microbe interactions are unclear. Adherence and colonization of mucus has been demonstrated for several enteric pathogens and it is possible that mucin-associated microbes may be working in concert with C. difficile. We showed that C. difficile ribotype-027 adheres to MUC2 glycans and using fecal bioreactors, we identified that C. difficile associates with several mucin-degrading microbes. C. difficile was found to chemotax toward intestinal mucus and its glycan components, demonstrating that C. difficile senses the mucus layer. Although C. difficile lacks the glycosyl hydrolases required to degrade mucin glycans, coculturing C. difficile with the mucin-degrading Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Ruminococcus torques allowed C. difficile to grow in media that lacked glucose but contained purified MUC2. Collectively, these studies expand our knowledge on how intestinal microbes support C. difficile.
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Affiliation(s)
- Melinda A. Engevik
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - Amy C. Engevik
- Department of Surgery, Vanderbilt University School of Medicine, Nashville Tennessee 37232, United States
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville Tennessee 37232, United States
| | - Kristen A. Engevik
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
| | - Jennifer M. Auchtung
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Food Science and Technology, University of Nebraska—Lincoln, Lincoln Nebraska 68588, United States
| | - Alexandra L. Chang-Graham
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
| | - Wenly Ruan
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - Ruth Ann Luna
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - Joseph M. Hyser
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
| | - Jennifer K. Spinler
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - James Versalovic
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
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71
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Garcia-Ibañez P, Roses C, Agudelo A, Milagro FI, Barceló AM, Viadel B, Nieto JA, Moreno DA, Carvajal M. The Influence of Red Cabbage Extract Nanoencapsulated with Brassica Plasma Membrane Vesicles on the Gut Microbiome of Obese Volunteers. Foods 2021; 10:foods10051038. [PMID: 34068672 PMCID: PMC8151636 DOI: 10.3390/foods10051038] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/30/2021] [Accepted: 05/07/2021] [Indexed: 12/28/2022] Open
Abstract
The aim of the study was to evaluate the influence of the red cabbage extracts on the bioaccessibility of their isothiocyanates, and their effect on the intestinal microbiota using a dynamic model of human digestion treated with the gut microbiome of obese adults. The elicitation of red cabbage plants with methyl jasmonate (MeJA) duplicated the content of glucosinolates (GSLs) in the plant organs used for elaborating the encapsulated formula. The use of plasma membrane vesicles, according to a proper methodology and technology, showed a high retention of sulforaphane (SFN) and indol-3-carbinol (I3C) over the course of the 14-day digestion study. The microbiome was scarcely affected by the treatments in terms of microbiota composition or the Bacteroidetes/Firmicutes ratio, but a 3 to 4-fold increase was observed in the production of butyric acid with the encapsulated extract treatment. Based on our pilot red cabbage extract study, the consumption of this extract, mainly encapsulated, may play a potential role in the management of obesity in adults.
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Affiliation(s)
- Paula Garcia-Ibañez
- Aquaporins Group, Centro de Edafología y Biología Aplicada del Segura, CEBAS-CSIC, Campus Universitario de Espinardo-25, E-30100 Murcia, Spain; (P.G.-I.); (M.C.)
- Phytochemistry and Healthy Foods Lab, Department of Food Science Technology, Centro de Edafología y Biología Aplicada del Segura, CEBAS-CSIC, Campus de Espinardo-25, E-30100 Murcia, Spain
| | - Carles Roses
- Servei de Genòmica I Bioinformàtica, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (C.R.); (A.M.B.)
| | - Agatha Agudelo
- Sakata Seed Ibérica S.L., Pl. Poeta Vicente Gaos, 6 Bajo, 46021 Valencia, Spain;
- Biotechnology Department, Universidad Politécnica de Valencia, UPV, Camino de Vera s/n, 46022 Valencia, Spain
| | - Fermin I. Milagro
- Center for Nutrition Research, Department of Nutrition, Food Sciences and Physiology, University of Navarra, 31008 Pamplona, Spain;
- Navarra Institute for Health Research (IdISNA), 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de la Salud Carlos III, 289029 Madrid, Spain
| | - Ana M. Barceló
- Servei de Genòmica I Bioinformàtica, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (C.R.); (A.M.B.)
| | - Blanca Viadel
- AINIA, Technology Centre, C/Benjamin Franklin 5-11, Parque Tecnológico de Valencia, 46980 Paterna, Valencia, Spain; (B.V.); (J.A.N.)
| | - Juan Antonio Nieto
- AINIA, Technology Centre, C/Benjamin Franklin 5-11, Parque Tecnológico de Valencia, 46980 Paterna, Valencia, Spain; (B.V.); (J.A.N.)
| | - Diego A. Moreno
- Phytochemistry and Healthy Foods Lab, Department of Food Science Technology, Centro de Edafología y Biología Aplicada del Segura, CEBAS-CSIC, Campus de Espinardo-25, E-30100 Murcia, Spain
- Correspondence:
| | - Micaela Carvajal
- Aquaporins Group, Centro de Edafología y Biología Aplicada del Segura, CEBAS-CSIC, Campus Universitario de Espinardo-25, E-30100 Murcia, Spain; (P.G.-I.); (M.C.)
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72
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Thapa S, Venkatachalam A, Khan N, Naqvi M, Balderas M, Runge JK, Haag A, Hoch KM, Glaze DG, Luna RA, Motil KJ. Assessment of the gut bacterial microbiome and metabolome of girls and women with Rett Syndrome. PLoS One 2021; 16:e0251231. [PMID: 33956889 PMCID: PMC8101921 DOI: 10.1371/journal.pone.0251231] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/22/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Gastrointestinal problems affect the health and quality of life of individuals with Rett syndrome (RTT) and pose a medical hardship for their caregivers. We hypothesized that the variability in the RTT phenotype contributes to the dysbiosis of the gut microbiome and metabolome in RTT, predisposing these individuals to gastrointestinal dysfunction. OBJECTIVES We characterized the gut bacterial microbiome and metabolome in girls and young women with RTT (n = 44) and unaffected controls (n = 21), and examined the relation between the composition of the microbiome and variations in the RTT phenotype. METHODS Demographics and clinical information, including growth and anthropometric measurements, pubertal status, symptoms, clinical severity score, bowel movement, medication use, and dietary intakes were collected from the participants. Fecal samples were collected for analysis of the gut microbiome using Illumina MiSeq-based next-generation sequencing of the 16S rRNA gene followed by bioinformatics analysis of microbial composition, diversity, and community structure. Selected end-products of microbial protein metabolism were characterized by liquid chromatography-mass spectrometry. RESULTS The gut bacterial microbiome differed within the RTT cohort based on pubertal status (p<0.02) and clinical severity scores (p<0.02) of the individuals and the type of diet (p<0.01) consumed. Although the composition of the gut microbiome did not differ between RTT and unaffected individuals, concentrations of protein end-products of the gut bacterial metabolome, including γ-aminobutyric acid (GABA) (p<0.001), tyrosine (p<0.02), and glutamate (p<0.06), were lower in the RTT cohort. Differences in the microbiome within RTT groups, based on symptomatic anxiety, hyperventilation, abdominal distention, or changes in stool frequency and consistency, were not detected. CONCLUSIONS Although variability in the RTT phenotype contributes to the dysbiosis of the gut microbiome, we presently cannot infer causality between gut bacterial dysbiosis and gastrointestinal dysfunction. Nevertheless, alterations in the gut metabolome may provide clues to the pathophysiology of gastrointestinal problems in RTT.
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Affiliation(s)
- Santosh Thapa
- Department of Pathology, Medical Metagenomics Laboratory, Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, Texas, United States of America
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alamelu Venkatachalam
- Department of Pathology, Medical Metagenomics Laboratory, Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, Texas, United States of America
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Nabeel Khan
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Mohammed Naqvi
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Miriam Balderas
- Department of Pathology, Medical Metagenomics Laboratory, Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, Texas, United States of America
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jessica K. Runge
- Department of Pathology, Medical Metagenomics Laboratory, Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, Texas, United States of America
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anthony Haag
- Department of Pathology, Metabolomics and Proteomics Laboratory, Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, Texas, United States of America
| | - Kathleen M. Hoch
- Department of Pathology, Metabolomics and Proteomics Laboratory, Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, Texas, United States of America
| | - Daniel G. Glaze
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neurology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ruth Ann Luna
- Department of Pathology, Medical Metagenomics Laboratory, Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, Texas, United States of America
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kathleen J. Motil
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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Maurice S, Arnault G, Nordén J, Botnen SS, Miettinen O, Kauserud H. Fungal sporocarps house diverse and host-specific communities of fungicolous fungi. THE ISME JOURNAL 2021; 15:1445-1457. [PMID: 33432137 PMCID: PMC8115690 DOI: 10.1038/s41396-020-00862-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 11/16/2022]
Abstract
Sporocarps (fruit bodies) are the sexual reproductive stage in the life cycle of many fungi. They are highly nutritious and consequently vulnerable to grazing by birds and small mammals, and invertebrates, and can be infected by microbial and fungal parasites and pathogens. The complexity of communities thriving inside sporocarps is largely unknown. In this study, we revealed the diversity, taxonomic composition and host preference of fungicolous fungi (i.e., fungi that feed on other fungi) in sporocarps. We carried out DNA metabarcoding of the ITS2 region from 176 sporocarps of 11 wood-decay fungal host species, all collected within a forest in northeast Finland. We assessed the influence of sporocarp traits, such as lifespan, morphology and size, on the fungicolous fungal community. The level of colonisation by fungicolous fungi, measured as the proportion of non-host ITS2 reads, varied between 2.8-39.8% across the 11 host species and was largely dominated by Ascomycota. Host species was the major determinant of the community composition and diversity of fungicolous fungi, suggesting that host adaptation is important for many fungicolous fungi. Furthermore, the alpha diversity was consistently higher in short-lived and resupinate sporocarps compared to long-lived and pileate ones, perhaps due to a more hostile environment for fungal growth in the latter too. The fungicolous fungi represented numerous lineages in the fungal tree of life, among which a significant portion was poorly represented with reference sequences in databases.
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Affiliation(s)
- Sundy Maurice
- Section for Genetics and Evolutionary Biology, University of Oslo, Blindernveien 31, 0316, Oslo, Norway.
| | - Gontran Arnault
- Section for Genetics and Evolutionary Biology, University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Jenni Nordén
- Norwegian Institute for Nature Research, Gaustadalléen 21, 0349, Oslo, Norway
| | - Synnøve Smebye Botnen
- Section for Genetics and Evolutionary Biology, University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Otto Miettinen
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014, Helsinki, Finland
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology, University of Oslo, Blindernveien 31, 0316, Oslo, Norway
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Kaczmarczyk M, Löber U, Adamek K, Węgrzyn D, Skonieczna-Żydecka K, Malinowski D, Łoniewski I, Markó L, Ulas T, Forslund SK, Łoniewska B. The gut microbiota is associated with the small intestinal paracellular permeability and the development of the immune system in healthy children during the first two years of life. J Transl Med 2021; 19:177. [PMID: 33910577 PMCID: PMC8082808 DOI: 10.1186/s12967-021-02839-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The intestinal barrier plays an important role in the defense against infections, and nutritional, endocrine, and immune functions. The gut microbiota playing an important role in development of the gastrointestinal tract can impact intestinal permeability and immunity during early life, but data concerning this problem are scarce. METHODS We analyzed the microbiota in fecal samples (101 samples in total) collected longitudinally over 24 months from 21 newborns to investigate whether the markers of small intestinal paracellular permeability (zonulin) and immune system development (calprotectin) are linked to the gut microbiota. The results were validated using data from an independent cohort that included the calprotectin and gut microbiota in children during the first year of life. RESULTS Zonulin levels tended to increase for up to 6 months after childbirth and stabilize thereafter remaining at a high level while calprotectin concentration was high after childbirth and began to decline from 6 months of life. The gut microbiota composition and the related metabolic potentials changed during the first 2 years of life and were correlated with zonulin and calprotectin levels. Faecal calprotectin correlated inversely with alpha diversity (Shannon index, r = - 0.30, FDR P (Q) = 0.039). It also correlated with seven taxa; i.a. negatively with Ruminococcaceae (r = - 0.34, Q = 0.046), and Clostridiales (r = - 0.34, Q = 0.048) and positively with Staphylococcus (r = 0.38, Q = 0.023) and Staphylococcaceae (r = 0.35, Q = 0.04), whereas zonulin correlated with 19 taxa; i.a. with Bacillales (r = - 0.52, Q = 0.0004), Clostridiales (r = 0.48, Q = 0.001) and the Ruminococcus (torques group) (r = 0.40, Q = 0.026). When time intervals were considered only changes in abundance of the Ruminococcus (torques group) were associated with changes in calprotectin (β = 2.94, SE = 0.8, Q = 0.015). The dynamics of stool calprotectin was negatively associated with changes in two MetaCyc pathways: pyruvate fermentation to butanoate (β = - 4.54, SE = 1.08, Q = 0.028) and Clostridium acetobutylicum fermentation (β = - 4.48, SE = 1.16, Q = 0.026). CONCLUSIONS The small intestinal paracellular permeability, immune system-related markers and gut microbiota change dynamically during the first 2 years of life. The Ruminococcus (torques group) seems to be especially involved in controlling paracellular permeability. Staphylococcus, Staphylococcaceae, Ruminococcaceae, and Clostridiales, may be potential biomarkers of the immune system. Despite observed correlations their clear causation and health consequences were not proven. Mechanistic studies are required.
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Affiliation(s)
- Mariusz Kaczmarczyk
- Department of Clinical Biochemistry, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
| | - Ulrike Löber
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Karolina Adamek
- Department of Neonatal Diseases, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
| | - Dagmara Węgrzyn
- Department of Neonatal Diseases, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
| | | | - Damian Malinowski
- Department of Pharmacology, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
| | - Igor Łoniewski
- Department of Biochemical Sciences, Pomeranian Medical University in Szczecin, 71-460, Szczecin, Poland.
- Department of Human Nutrition and Metabolomics, Broniewskiego 24, 71-460, Szczecin, Poland.
| | - Lajos Markó
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
| | - Thomas Ulas
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, 53127, Bonn, Germany
| | - Sofia K Forslund
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
| | - Beata Łoniewska
- Department of Neonatal Diseases, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
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Kushugulova A, Löber U, Akpanova S, Rysbekov K, Kozhakhmetov S, Khassenbekova Z, Essex M, Nurgozhina A, Nurgaziyev M, Babenko D, Markó L, Forslund SK. Dynamic Changes in Microbiome Composition Following Mare's Milk Intake for Prevention of Collateral Antibiotic Effect. Front Cell Infect Microbiol 2021; 11:622735. [PMID: 33968795 PMCID: PMC8097163 DOI: 10.3389/fcimb.2021.622735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/01/2021] [Indexed: 01/22/2023] Open
Abstract
Introduction Probiotics and prebiotics are widely used for recovery of the human gut microbiome after antibiotic treatment. High antibiotic usage is especially common in children with developing microbiome. We hypothesized that dry Mare’s milk, which is rich in biologically active substances without containing live bacteria, could be used as a prebiotic in promoting microbial diversity following antibiotic treatment in children. The present pilot study aims to determine the impacts of dry Mare’s milk on the diversity of gut bacterial communities when administered during antibiotic treatment and throughout the subsequent recovery phase. Methods Six children aged 4 to 5 years and diagnosed with bilateral bronchopneumonia were prescribed cephalosporin antibiotics. During the 60 days of the study, three children consumed dry Mare’s milk whereas the other three did not. Fecal samples were collected daily during antibiotic therapy and every 5 days after antibiotic therapy. Total DNA was isolated and taxonomic composition of gut microbiota was analyzed by 16S rRNA amplicon sequencing. To assess the immune status of the gut, stool samples were analyzed by bead-based multiplex assays. Results Mare’s milk treatment seems to prevent the bloom of Mollicutes, while preventing the loss of Coriobacteriales. Immunological analysis of the stool reveals an effect of Mare’s milk on local immune parameters under the present conditions.
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Affiliation(s)
- Almagul 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.,SaumalBioTech, Nur-Sultan, Kazakhstan
| | - Ulrike Löber
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Saniya Akpanova
- Department of Pediatric Diseases with Courses in Cardio-Rheumatology and Gastroenterology, Nur-sultan (Astana) Medical University, Nur-Sultan, Kazakhstan
| | - Kairat Rysbekov
- Department of Pediatric Diseases with Courses in Cardio-Rheumatology and Gastroenterology, Nur-sultan (Astana) Medical University, Nur-Sultan, 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.,SaumalBioTech, Nur-Sultan, Kazakhstan
| | | | - Morgan Essex
- 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.,Laboratory of Innate Immunity, Department of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin, Berlin, Germany
| | - Ayaulym Nurgozhina
- 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
| | - Madiyar Nurgaziyev
- 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
- Research Center Karaganda Medical University, Karagandy, Kazakhstan
| | - Lajos Markó
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Sofia K Forslund
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany.,Structural and Computational Biology Unit, The European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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76
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Daisley BA, Reid G. BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities. mSystems 2021; 6:e00082-21. [PMID: 33824193 PMCID: PMC8546966 DOI: 10.1128/msystems.00082-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/08/2021] [Indexed: 01/04/2023] Open
Abstract
High-throughput 16S rRNA gene sequencing technologies have robust potential to improve our understanding of bee (Hymenoptera: Apoidea)-associated microbial communities and their impact on hive health and disease. Despite recent computation algorithms now permitting exact inferencing of high-resolution exact amplicon sequence variants (ASVs), the taxonomic classification of these ASVs remains a challenge due to inadequate reference databases. To address this, we assemble a comprehensive data set of all publicly available bee-associated 16S rRNA gene sequences, systematically annotate poorly resolved identities via inclusion of 618 placeholder labels for uncultivated microbial dark matter, and correct for phylogenetic inconsistencies using a complementary set of distance-based and maximum likelihood correction strategies. To benchmark the resultant database (BEExact), we compare performance against all existing reference databases in silico using a variety of classifier algorithms to produce probabilistic confidence scores. We also validate realistic classification rates on an independent set of ∼234 million short-read sequences derived from 32 studies encompassing 50 different bee types (36 eusocial and 14 solitary). Species-level classification rates on short-read ASVs range from 80 to 90% using BEExact (with ∼20% due to "bxid" placeholder names), whereas only ∼30% at best can be resolved with current universal databases. A series of data-driven recommendations are developed for future studies. We conclude that BEExact (https://github.com/bdaisley/BEExact) enables accurate and standardized microbiota profiling across a broad range of bee species-two factors of key importance to reproducibility and meaningful knowledge exchange within the scientific community that together, can enhance the overall utility and ecological relevance of routine 16S rRNA gene-based sequencing endeavors.IMPORTANCE The failure of current universal taxonomic databases to support the rapidly expanding field of bee microbiota research has led to many investigators relying on "in-house" reference sets or manual classification of sequence reads (usually based on BLAST searches), often with vague identity thresholds and subjective taxonomy choices. This time-consuming, error- and bias-prone process lacks standardization, cripples the potential for comparative cross-study analysis, and in many cases is likely to incorrectly sway study conclusions. BEExact is structured on and leverages several complementary bioinformatic techniques to enable refined inference of bee host-associated microbial communities without any other methodological modifications necessary. It also bridges the gap between current practical outcomes (i.e., phylotype-to-genus level constraints with 97% operational taxonomic units [OTUs]) and the theoretical resolution (i.e., species-to-strain level classification with 100% ASVs) attainable in future microbiota investigations. Other niche habitats could also likely benefit from customized database curation via implementation of the novel approaches introduced in this study.
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Affiliation(s)
- Brendan A Daisley
- Department of Microbiology & Immunology, The University of Western Ontario, London, Ontario, Canada
- Canadian Centre for Human Microbiome and Probiotics Research, London, Ontario, Canada
| | - Gregor Reid
- Department of Microbiology & Immunology, The University of Western Ontario, London, Ontario, Canada
- Canadian Centre for Human Microbiome and Probiotics Research, London, Ontario, Canada
- Department of Surgery, Schulich School of Medicine, London, Ontario, Canada
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77
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Zhu Z, Difford GF, Noel SJ, Lassen J, Løvendahl P, Højberg O. Stability Assessment of the Rumen Bacterial and Archaeal Communities in Dairy Cows Within a Single Lactation and Its Association With Host Phenotype. Front Microbiol 2021; 12:636223. [PMID: 33927700 PMCID: PMC8076905 DOI: 10.3389/fmicb.2021.636223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/28/2021] [Indexed: 01/09/2023] Open
Abstract
Better characterization of changes in the rumen microbiota in dairy cows over the lactation period is crucial for understanding how microbial factors may potentially be interacting with host phenotypes. In the present study, we characterized the rumen bacterial and archaeal community composition of 60 lactating Holstein dairy cows (33 multiparous and 27 primiparous), sampled twice within the same lactation with a 122 days interval. Firmicutes and Bacteroidetes dominated the rumen bacterial community and showed no difference in relative abundance between samplings. Two less abundant bacterial phyla (SR1 and Proteobacteria) and an archaeal order (Methanosarcinales), on the other hand, decreased significantly from the mid-lactation to the late-lactation period. Moreover, between-sampling stability assessment of individual operational taxonomic units (OTUs), evaluated by concordance correlation coefficient (C-value) analysis, revealed the majority of the bacterial OTUs (6,187 out of 6,363) and all the 79 archaeal OTUs to be unstable over the investigated lactation period. The remaining 176 stable bacterial OTUs were mainly assigned to Prevotella, unclassified Prevotellaceae, and unclassified Bacteroidales. Milk phenotype-based screening analysis detected 32 bacterial OTUs, mainly assigned to unclassified Bacteroidetes and Lachnospiraceae, associated with milk fat percentage, and 6 OTUs, assigned to Ruminococcus and unclassified Ruminococcaceae, associated with milk protein percentage. These OTUs were only observed in the multiparous cows. None of the archaeal OTUs was observed to be associated with the investigated phenotypic parameters, including methane production. Co-occurrence analysis of the rumen bacterial and archaeal communities revealed Fibrobacter to be positively correlated with the archaeal genus vadinCA11 (Pearson r = 0.76) and unclassified Methanomassiliicoccaceae (Pearson r = 0.64); vadinCA11, on the other hand, was negatively correlated with Methanobrevibacter (Pearson r = –0.56). In conclusion, the rumen bacterial and archaeal communities of dairy cows displayed distinct stability at different taxonomic levels. Moreover, specific members of the rumen bacterial community were observed to be associated with milk phenotype parameters, however, only in multiparous cows, indicating that dairy cow parity could be one of the driving factors for host–microbe interactions.
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Affiliation(s)
- Zhigang Zhu
- Department of Animal Science, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
| | - Gareth Frank Difford
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
| | - Samantha Joan Noel
- Department of Animal Science, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
| | - Jan Lassen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
| | - Peter Løvendahl
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
| | - Ole Højberg
- Department of Animal Science, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
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78
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Gilroy R, Ravi A, Getino M, Pursley I, Horton DL, Alikhan NF, Baker D, Gharbi K, Hall N, Watson M, Adriaenssens EM, Foster-Nyarko E, Jarju S, Secka A, Antonio M, Oren A, Chaudhuri RR, La Ragione R, Hildebrand F, Pallen MJ. Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. PeerJ 2021; 9:e10941. [PMID: 33868800 PMCID: PMC8035907 DOI: 10.7717/peerj.10941] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/22/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. RESULTS We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii. CONCLUSIONS Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.
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Affiliation(s)
| | | | - Maria Getino
- School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Isabella Pursley
- School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Daniel L. Horton
- School of Veterinary Medicine, University of Surrey, Guildford, UK
| | | | - Dave Baker
- Quadram Institute Bioscience, Norwich, UK
| | - Karim Gharbi
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
| | - Mick Watson
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | - Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Arss Secka
- West Africa Livestock Innovation Centre, Banjul, The Gambia
| | - Martin Antonio
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Roy R. Chaudhuri
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | | | - Falk Hildebrand
- Quadram Institute Bioscience, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, UK
- University of East Anglia, Norwich, UK
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79
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Gao B, Chi L, Zhu Y, Shi X, Tu P, Li B, Yin J, Gao N, Shen W, Schnabl B. An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies. Biomolecules 2021; 11:530. [PMID: 33918473 PMCID: PMC8066849 DOI: 10.3390/biom11040530] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome is a microbial ecosystem which expresses 100 times more genes than the human host and plays an essential role in human health and disease pathogenesis. Since most intestinal microbial species are difficult to culture, next generation sequencing technologies have been widely applied to study the gut microbiome, including 16S rRNA, 18S rRNA, internal transcribed spacer (ITS) sequencing, shotgun metagenomic sequencing, metatranscriptomic sequencing and viromic sequencing. Various software tools were developed to analyze different sequencing data. In this review, we summarize commonly used computational tools for gut microbiome data analysis, which extended our understanding of the gut microbiome in health and diseases.
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Affiliation(s)
- Bei Gao
- Department of Marine Science, School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China;
| | - Liang Chi
- Metaorganism Immunity Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Yixin Zhu
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
| | - Xiaochun Shi
- Department of Environmental Ecological Engineering, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China; (X.S.); (W.S.)
| | - Pengcheng Tu
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China;
| | - Bing Li
- Suzhou Industrial Park Environmental Law Enforcement Brigade (Environmental Monitoring Station), Suzhou 215021, China;
| | - Jun Yin
- Department of Hydrometeorology, School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China;
| | - Nan Gao
- Department of Biotechnology, School of Biological and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China;
| | - Weishou Shen
- Department of Environmental Ecological Engineering, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China; (X.S.); (W.S.)
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Nanjing 210044, China
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA 92161, USA
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80
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Li J, Hu A, Bai S, Yang X, Sun Q, Liao X, Yu CP. Characterization and Performance of Lactate-Feeding Consortia for Reductive Dechlorination of Trichloroethene. Microorganisms 2021; 9:microorganisms9040751. [PMID: 33918519 PMCID: PMC8065584 DOI: 10.3390/microorganisms9040751] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022] Open
Abstract
Understanding the underlying mechanism that drives the microbial community mediated by substrates is crucial to enhance the biostimulation in trichloroethene (TCE)-contaminated sites. Here, we investigated the performance of stable TCE-dechlorinating consortia by monitoring the variations in TCE-related metabolites and explored their underlying assembly mechanisms using 16S rDNA amplicon sequencing and bioinformatics analyses. The monitoring results indicated that three stable TCE-dechlorinating consortia were successfully enriched by lactate-containing anaerobic media. The statistical analysis results demonstrated that the microbial communities of the enrichment cultures changed along with time and were distinguished by their sample sources. The deterministic and stochastic processes were simultaneously responsible for shaping the TCE-dechlorinating community assembly. The indicator patterns shifted with the exhaustion of the carbon source and the pollutants, and the tceA-carrying Dehalococcoides, as an indicator for the final stage samples, responded positively to TCE removal during the incubation period. Pseudomonas, Desulforhabdus, Desulfovibrio and Methanofollis were identified as keystone populations in the TCE-dechlorinating process by co-occurrence network analysis. The results of this study indicate that lactate can be an effective substrate for stimulated bioremediation of TCE-contaminated sites, and the reduction of the stochastic forces or enhancement of the deterministic interventions may promote more effective biostimulation.
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Affiliation(s)
- Jiangwei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (J.L.); (A.H.); (X.Y.); (Q.S.); (X.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (J.L.); (A.H.); (X.Y.); (Q.S.); (X.L.)
| | - Shijie Bai
- Institute of Deep Sea Science and Engineering, Chinese Academic of Sciences, Sanya 572000, China;
| | - Xiaoyong Yang
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (J.L.); (A.H.); (X.Y.); (Q.S.); (X.L.)
| | - Qian Sun
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (J.L.); (A.H.); (X.Y.); (Q.S.); (X.L.)
| | - Xu Liao
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (J.L.); (A.H.); (X.Y.); (Q.S.); (X.L.)
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (J.L.); (A.H.); (X.Y.); (Q.S.); (X.L.)
- Water Innovation, Low Carbon and Environmental Sustainability Research Center, National Taiwan University, Taipei 10617, Taiwan
- Correspondence:
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81
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Fasting alters the gut microbiome reducing blood pressure and body weight in metabolic syndrome patients. Nat Commun 2021; 12:1970. [PMID: 33785752 PMCID: PMC8010079 DOI: 10.1038/s41467-021-22097-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
Periods of fasting and refeeding may reduce cardiometabolic risk elevated by Western diet. Here we show in the substudy of NCT02099968, investigating the clinical parameters, the immunome and gut microbiome exploratory endpoints, that in hypertensive metabolic syndrome patients, a 5-day fast followed by a modified Dietary Approach to Stop Hypertension diet reduces systolic blood pressure, need for antihypertensive medications, body-mass index at three months post intervention compared to a modified Dietary Approach to Stop Hypertension diet alone. Fasting alters the gut microbiome, impacting bacterial taxa and gene modules associated with short-chain fatty acid production. Cross-system analyses reveal a positive correlation of circulating mucosa-associated invariant T cells, non-classical monocytes and CD4+ effector T cells with systolic blood pressure. Furthermore, regulatory T cells positively correlate with body-mass index and weight. Machine learning analysis of baseline immunome or microbiome data predicts sustained systolic blood pressure response within the fasting group, identifying CD8+ effector T cells, Th17 cells and regulatory T cells or Desulfovibrionaceae, Hydrogenoanaerobacterium, Akkermansia, and Ruminococcaceae as important contributors to the model. Here we report that the high-resolution multi-omics data highlight fasting as a promising non-pharmacological intervention for the treatment of high blood pressure in metabolic syndrome patients. Nutritional modification including fasting has been shown to reduce cardiometabolic risk linked to western diet. Here the authors show implementation of fasting resulted in alterations to the intestinal microbiota, and circulating immune cells, improving blood pressure and body weight in patients with metabolic syndrome.
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82
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Bedarf JR, Beraza N, Khazneh H, Özkurt E, Baker D, Borger V, Wüllner U, Hildebrand F. Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson's disease individuals. MICROBIOME 2021; 9:75. [PMID: 33771222 PMCID: PMC8004470 DOI: 10.1186/s40168-021-01012-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 02/02/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to the neuro-inflammatory changes seen in Parkinson's disease (PD) and Alzheimer's disease (AD) or as a "brain microbiome" in the context of healthy patients' brain samples. METHODS Using 16S rRNA gene sequencing, we tested the hypothesis that there is a bacterial brain microbiome. We evaluated brain samples from healthy human subjects and individuals suffering from PD (olfactory bulb and pre-frontal cortex), as well as murine brains. In line with state-of-the-art recommendations, we included several negative and positive controls in our analysis and estimated total bacterial biomass by 16S rRNA gene qPCR. RESULTS Amplicon sequencing did detect bacterial signals in both human and murine samples, but estimated bacterial biomass was extremely low in all samples. Stringent reanalyses implied bacterial signals being explained by a combination of exogenous DNA contamination (54.8%) and false positive amplification of host DNA (34.2%, off-target amplicons). Several seemingly brain-enriched microbes in our dataset turned out to be false-positive signals upon closer examination. We identified off-target amplification as a major confounding factor in low-bacterial/high-host-DNA scenarios. These amplified human or mouse DNA sequences were clustered and falsely assigned to bacterial taxa in the majority of tested amplicon sequencing pipelines. Off-target amplicons seemed to be related to the tissue's sterility and could also be found in independent brain 16S rRNA gene sequences. CONCLUSIONS Taxonomic signals obtained from (extremely) low biomass samples by 16S rRNA gene sequencing must be scrutinized closely to exclude the possibility of off-target amplifications, amplicons that can only appear enriched in biological samples, but are sometimes assigned to bacterial taxa. Sequences must be explicitly matched against any possible background genomes present in large quantities (i.e., the host genome). Using close scrutiny in our approach, we find no evidence supporting the hypothetical presence of either a brain microbiome or a bacterial infection in PD brains. Video abstract.
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Affiliation(s)
- Janis R. Bedarf
- Department of Neurology, University Hospital Bonn, Venusberg Campus 1, 53127 Bonn, Germany
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA UK
| | - Naiara Beraza
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA UK
| | - Hassan Khazneh
- Department of Neurology, University Hospital Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - Ezgi Özkurt
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UA UK
| | - David Baker
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA UK
| | - Valeri Borger
- Department of Neurosurgery, University Hospital Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - Ullrich Wüllner
- Department of Neurology, University Hospital Bonn, Venusberg Campus 1, 53127 Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Venusberg Campus 2, 53127 Bonn, Germany
| | - Falk Hildebrand
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UA UK
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83
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Romano S, Savva GM, Bedarf JR, Charles IG, Hildebrand F, Narbad A. Meta-analysis of the Parkinson's disease gut microbiome suggests alterations linked to intestinal inflammation. NPJ Parkinsons Dis 2021. [PMID: 33692356 DOI: 10.1101/2020.08.10.20171397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
The gut microbiota is emerging as an important modulator of neurodegenerative diseases, and accumulating evidence has linked gut microbes to Parkinson's disease (PD) symptomatology and pathophysiology. PD is often preceded by gastrointestinal symptoms and alterations of the enteric nervous system accompany the disease. Several studies have analyzed the gut microbiome in PD, but a consensus on the features of the PD-specific microbiota is missing. Here, we conduct a meta-analysis re-analyzing the ten currently available 16S microbiome datasets to investigate whether common alterations in the gut microbiota of PD patients exist across cohorts. We found significant alterations in the PD-associated microbiome, which are robust to study-specific technical heterogeneities, although differences in microbiome structure between PD and controls are small. Enrichment of the genera Lactobacillus, Akkermansia, and Bifidobacterium and depletion of bacteria belonging to the Lachnospiraceae family and the Faecalibacterium genus, both important short-chain fatty acids producers, emerged as the most consistent PD gut microbiome alterations. This dysbiosis might result in a pro-inflammatory status which could be linked to the recurrent gastrointestinal symptoms affecting PD patients.
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Affiliation(s)
- Stefano Romano
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
| | - George M Savva
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Janis R Bedarf
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Department of Neurology, University of Bonn, Bonn, Germany
| | - Ian G Charles
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
| | - Falk Hildebrand
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- Earlham Institute, Norwich Research Park, Norwich, UK.
| | - Arjan Narbad
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
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84
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Mundra S, Kjønaas OJ, Morgado LN, Krabberød AK, Ransedokken Y, Kauserud H. Soil depth matters: shift in composition and inter-kingdom co-occurrence patterns of microorganisms in forest soils. FEMS Microbiol Ecol 2021; 97:fiab022. [PMID: 33547899 PMCID: PMC7948073 DOI: 10.1093/femsec/fiab022] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/04/2021] [Indexed: 02/01/2023] Open
Abstract
Soil depth represents a strong physiochemical gradient that greatly affects soil-dwelling microorganisms. Fungal communities are typically structured by soil depth, but how other microorganisms are structured is less known. Here, we tested whether depth-dependent variation in soil chemistry affects the distribution and co-occurrence patterns of soil microbial communities. This was investigated by DNA metabarcoding in conjunction with network analyses of bacteria, fungi, as well as other micro-eukaryotes, sampled in four different soil depths in Norwegian birch forests. Strong compositional turnover in microbial assemblages with soil depth was detected for all organismal groups. Significantly greater microbial diversity and fungal biomass appeared in the nutrient-rich organic layer, with sharp decrease towards the less nutrient-rich mineral zones. The proportions of copiotrophic bacteria, Arthropoda and Apicomplexa were markedly higher in the organic layer, while patterns were opposite for oligotrophic bacteria, Cercozoa, Ascomycota and ectomycorrhizal fungi. Network analyses indicated more intensive inter-kingdom co-occurrence patterns in the upper mineral layer (0-5 cm) compared to the above organic and the lower mineral soil, signifying substantial influence of soil depth on biotic interactions. This study supports the view that different microbial groups are adapted to different forest soil strata, with varying level of interactions along the depth gradient.
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Affiliation(s)
- Sunil Mundra
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, Abu-Dhabi, UAE
| | - O Janne Kjønaas
- NIBIO, Department of Terrestrial Ecology, NO-1431 Ås, Norway
| | - Luis N Morgado
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
- Naturalis Biodiversity Center, 2300 RA Leiden, the Netherlands
| | - Anders Kristian Krabberød
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Yngvild Ransedokken
- Faculty of Environmental and Natural Resource Management, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
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85
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Meta-analysis of the Parkinson's disease gut microbiome suggests alterations linked to intestinal inflammation. NPJ Parkinsons Dis 2021; 7:27. [PMID: 33692356 PMCID: PMC7946946 DOI: 10.1038/s41531-021-00156-z] [Citation(s) in RCA: 307] [Impact Index Per Article: 102.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/08/2021] [Indexed: 02/06/2023] Open
Abstract
The gut microbiota is emerging as an important modulator of neurodegenerative diseases, and accumulating evidence has linked gut microbes to Parkinson's disease (PD) symptomatology and pathophysiology. PD is often preceded by gastrointestinal symptoms and alterations of the enteric nervous system accompany the disease. Several studies have analyzed the gut microbiome in PD, but a consensus on the features of the PD-specific microbiota is missing. Here, we conduct a meta-analysis re-analyzing the ten currently available 16S microbiome datasets to investigate whether common alterations in the gut microbiota of PD patients exist across cohorts. We found significant alterations in the PD-associated microbiome, which are robust to study-specific technical heterogeneities, although differences in microbiome structure between PD and controls are small. Enrichment of the genera Lactobacillus, Akkermansia, and Bifidobacterium and depletion of bacteria belonging to the Lachnospiraceae family and the Faecalibacterium genus, both important short-chain fatty acids producers, emerged as the most consistent PD gut microbiome alterations. This dysbiosis might result in a pro-inflammatory status which could be linked to the recurrent gastrointestinal symptoms affecting PD patients.
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86
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Chun YS, Kim SY, Kim M, Lim JY, Shin BK, Kim YS, Lee DY, Seo JA, Choi HK. Mycobiome analysis for distinguishing the geographical origins of sesame seeds. Food Res Int 2021; 143:110271. [PMID: 33992372 DOI: 10.1016/j.foodres.2021.110271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 02/15/2021] [Accepted: 02/22/2021] [Indexed: 11/19/2022]
Abstract
Sesame (Sesamum indicum) is one of the most widely cultivated crops in Asia and Africa. The identification of the geographical origins of sesame seeds is important for the detection of fraudulent samples. This study was conducted to build a prediction model and suggest potential biomarkers for distinguishing the geographical origins of sesame seeds using mycobiome (fungal microbiome) analysis coupled with multivariate statistical analysis. Sesame seeds were collected from 25 cities in Korea, six cities in China, and five sites in other countries (Ethiopia, India, Nigeria, and Pakistan). According to the expression of fungal internal transcribed spacer (ITS) sequences in sesame seeds, 21 fungal genera were identified in sesame seeds from various countries. The optimal partial least squares-discriminant analysis model was established by applying two components with unit variance scaling. Based on seven-fold cross validation, the predictive model had 94.4% (Korea vs. China/other countries), 91.7% (China vs. Korea/other countries), and 88.9% (other countries vs. Korea/China) accuracy in determining the geographical origins of sesame seeds. Alternaria, Aspergillus, and Macrophomina were suggested as the potential fungal genera to differentiate the geographical origins of sesame seeds. This study demonstrated that mycobiome analysis could be used as a complementary method for distinguishing the geographical origins of raw sesame seeds.
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Affiliation(s)
- Yoon Shik Chun
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Seok-Young Kim
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Minjoo Kim
- School of Systems Biomedical Science, Soongsil University, Seoul, Republic of Korea
| | - Jae Yun Lim
- School of Systems Biomedical Science, Soongsil University, Seoul, Republic of Korea
| | - Byeung Kon Shin
- National Agricultural Products Quality Management Service, Gimcheon, Republic of Korea
| | - Young-Suk Kim
- Department of Food Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Do Yup Lee
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jeong-Ah Seo
- School of Systems Biomedical Science, Soongsil University, Seoul, Republic of Korea.
| | - Hyung-Kyoon Choi
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea.
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87
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Engevik MA, Danhof HA, Auchtung J, Endres BT, Ruan W, Bassères E, Engevik AC, Wu Q, Nicholson M, Luna RA, Garey KW, Crawford SE, Estes MK, Lux R, Yacyshyn MB, Yacyshyn B, Savidge T, Britton RA, Versalovic J. Fusobacteriumnucleatum Adheres to Clostridioides difficile via the RadD Adhesin to Enhance Biofilm Formation in Intestinal Mucus. Gastroenterology 2021; 160:1301-1314.e8. [PMID: 33227279 PMCID: PMC7956072 DOI: 10.1053/j.gastro.2020.11.034] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/02/2020] [Accepted: 11/13/2020] [Indexed: 01/01/2023]
Abstract
BACKGROUND & AIMS Although Clostridioides difficile infection (CDI) is known to involve the disruption of the gut microbiota, little is understood regarding how mucus-associated microbes interact with C difficile. We hypothesized that select mucus-associated bacteria would promote C difficile colonization and biofilm formation. METHODS To create a model of the human intestinal mucus layer and gut microbiota, we used bioreactors inoculated with healthy human feces, treated with clindamycin and infected with C difficile with the addition of human MUC2-coated coverslips. RESULTS C difficile was found to colonize and form biofilms on MUC2-coated coverslips, and 16S rRNA sequencing showed a unique biofilm profile with substantial cocolonization with Fusobacterium species. Consistent with our bioreactor data, publicly available data sets and patient stool samples showed that a subset of patients with C difficile infection harbored high levels of Fusobacterium species. We observed colocalization of C difficile and F nucleatum in an aggregation assay using adult patients and stool of pediatric patients with inflammatory bowel disease and in tissue sections of patients with CDI. C difficile strains were found to coaggregate with F nucleatum subspecies in vitro; an effect that was inhibited by blocking or mutating the adhesin RadD on Fusobacterium and removal of flagella on C difficile. Aggregation was shown to be unique between F nucleatum and C difficile, because other gut commensals did not aggregate with C difficile. Addition of F nucleatum also enhanced C difficile biofilm formation and extracellular polysaccharide production. CONCLUSIONS Collectively, these data show a unique interaction of between pathogenic C difficile and F nucleatum in the intestinal mucus layer.
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Affiliation(s)
- Melinda A. Engevik
- Department of Pathology & Immunology, Baylor College of
Medicine,Texas Children’s Microbiome Center, Department of
Pathology, Texas Children's Hospital
| | - Heather A. Danhof
- Department of Molecular Virology and Microbiology, Baylor
College of Medicine
| | - Jennifer Auchtung
- Department of Molecular Virology and Microbiology, Baylor
College of Medicine,Department of Food Science and Technology, University of
Nebraska-Lincoln
| | - Bradley T. Endres
- Department of Pharmacy Practice and Translational Research,
University of Houston College of Pharmacy
| | - Wenly Ruan
- Department of Pathology & Immunology, Baylor College of
Medicine,Texas Children’s Microbiome Center, Department of
Pathology, Texas Children's Hospital
| | - Eugénie Bassères
- Department of Pharmacy Practice and Translational Research,
University of Houston College of Pharmacy
| | - Amy C. Engevik
- Department of Surgical Sciences, Vanderbilt University
Medical Center
| | - Qinglong Wu
- Department of Pathology & Immunology, Baylor College of
Medicine,Texas Children’s Microbiome Center, Department of
Pathology, Texas Children's Hospital
| | | | - Ruth Ann Luna
- Department of Pathology & Immunology, Baylor College of
Medicine,Texas Children’s Microbiome Center, Department of
Pathology, Texas Children's Hospital
| | - Kevin W. Garey
- Department of Pharmacy Practice and Translational Research,
University of Houston College of Pharmacy
| | - Sue E. Crawford
- Department of Molecular Virology and Microbiology, Baylor
College of Medicine
| | - Mary K. Estes
- Department of Molecular Virology and Microbiology, Baylor
College of Medicine,Department of Surgical Sciences, Vanderbilt University
Medical Center
| | - Renate Lux
- Department of Periodontics, University of California Los
Angeles School of Dentistry
| | - Mary Beth Yacyshyn
- Department of Medicine Division of Digestive Diseases
University of Cincinnati College of Medicine
| | - Bruce Yacyshyn
- Department of Medicine Division of Digestive Diseases
University of Cincinnati College of Medicine
| | - Tor Savidge
- Department of Pathology & Immunology, Baylor College of
Medicine,Texas Children’s Microbiome Center, Department of
Pathology, Texas Children's Hospital
| | - Robert A. Britton
- Department of Molecular Virology and Microbiology, Baylor
College of Medicine
| | - James Versalovic
- Department of Pathology & Immunology, Baylor College of
Medicine,Texas Children’s Microbiome Center, Department of
Pathology, Texas Children's Hospital
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88
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Gut Microbiota Bacterial Species Associated with Mediterranean Diet-Related Food Groups in a Northern Spanish Population. Nutrients 2021; 13:nu13020636. [PMID: 33669303 PMCID: PMC7920039 DOI: 10.3390/nu13020636] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/05/2021] [Accepted: 02/13/2021] [Indexed: 12/11/2022] Open
Abstract
The MD (Mediterranean diet) is recognized as one of the healthiest diets worldwide and is associated with the prevention of cardiovascular and metabolic diseases. Dietary habits are considered one of the strongest modulators of gut microbiota, which seem to play a significant role in health status of the host. The purpose of the present study was to evaluate interactive associations between gut microbiota composition and habitual dietary intake in 360 Spanish adults from the Obekit cohort (normal weight, overweight, and obese participants). Dietary intake and adherence to the MD tests were administered and fecal samples were collected from each participant. Fecal 16S rRNA (ribosomal Ribonucleic Acid) gene sequencing was performed and checked against the dietary habits. MetagenomeSeq was the statistical tool applied to analyze data at the species taxonomic level. Results from this study identified several beneficial bacteria that were more abundant in the individuals with higher adherence to the MD. Bifidobacterium animalis was the species with the strongest association with the MD. Some SCFA (Short Chain Fatty Acids) -producing bacteria were also associated with MD. In conclusion, this study showed that MD, fiber, legumes, vegetable, fruit, and nut intake are associated with an increase in butyrate-producing taxa such as Roseburia faecis, Ruminococcus bromii, and Oscillospira (Flavonifractor) plautii.
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89
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Diet- and sex-related changes of gut microbiota composition and functional profiles after 4 months of weight loss intervention. Eur J Nutr 2021; 60:3279-3301. [PMID: 33591390 DOI: 10.1007/s00394-021-02508-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/02/2021] [Indexed: 12/12/2022]
Abstract
PURPOSE Obesity has been related to intestinal dysbiosis and the modification of gut microbiota composition by dietary strategies becomes a promising strategy to help manage obesity. The aim of the current study was to evaluate the effect of two weight-loss diets on the composition and functional profile of gut microbiota. METHODS 55 men and 124 women with BMI > 25 kg/m2 were randomly assigned to moderately high-protein (MHP) or low-fat (LF) diet. Differences in fecal bacteria abundance (based on 16 s rRNA sequencing) between before and after 4 months of calorie restriction was analyzed using EdgeR tool in MicrobiomeAnalyst platform. Bacterial functional profile was predicted using Tax4Fun and metagenomeSeq analysis. Significant KEGG Orthology (KO) terms were selected for the metabolomic study using chromatography. RESULTS After the intervention, MHP-men showed a significant decrease in Negativicutes, Selenomonadales, Dielma and Dielma fastidiosa. LF-men showed a significant increase in Bacilli, Lactobacillales, Christensenellaceae, Peptococcaceae, and Streptococcaceae, Peptococcus, Streptococcus and Christensenella, Duncaniella dubosii_CP039396_93.49%, Roseburia sp_AB744234_98.96% and Alistipes inops_KJ572413_99.57%. MHP-women increased Pasteurellales, Phascolarctobacterium succinatutens, Ruthenibacterium lactatiformans_LR215981_99.55% and decreased in Phascolarctobacterium succinatutens_NR112902_99.56%. Finally, LF-women presented a significant decrease in Bacteroides clarus and Erysipelothrix inopinata_CP060715_84.4%. Surprisingly, no matching bacterial changes were found between these four groups. A total of 42 KO, 10 metabolic pathways and 107 related metabolites related were found implicated in these bacterial changes. Seven metabolites were confirmed in plasma. CONCLUSION Weight-loss-related-changes in gut microbiome composition and the functional profile occur in a sex- and diet-related manner, showing that women and men could differentially benefit from the consumption of MHP and LF diets. TRIAL REGISTRATION NCT02737267, 10th March 2016 retrospectively registered.
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90
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Aguilera-Lizarraga J, Florens MV, Viola MF, Jain P, Decraecker L, Appeltans I, Cuende-Estevez M, Fabre N, Van Beek K, Perna E, Balemans D, Stakenborg N, Theofanous S, Bosmans G, Mondelaers SU, Matteoli G, Ibiza Martínez S, Lopez-Lopez C, Jaramillo-Polanco J, Talavera K, Alpizar YA, Feyerabend TB, Rodewald HR, Farre R, Redegeld FA, Si J, Raes J, Breynaert C, Schrijvers R, Bosteels C, Lambrecht BN, Boyd SD, Hoh RA, Cabooter D, Nelis M, Augustijns P, Hendrix S, Strid J, Bisschops R, Reed DE, Vanner SJ, Denadai-Souza A, Wouters MM, Boeckxstaens GE. Local immune response to food antigens drives meal-induced abdominal pain. Nature 2021; 590:151-156. [PMID: 33442055 DOI: 10.1038/s41586-020-03118-2] [Citation(s) in RCA: 144] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 11/27/2020] [Indexed: 12/19/2022]
Abstract
Up to 20% of people worldwide develop gastrointestinal symptoms following a meal1, leading to decreased quality of life, substantial morbidity and high medical costs. Although the interest of both the scientific and lay communities in this issue has increased markedly in recent years, with the worldwide introduction of gluten-free and other diets, the underlying mechanisms of food-induced abdominal complaints remain largely unknown. Here we show that a bacterial infection and bacterial toxins can trigger an immune response that leads to the production of dietary-antigen-specific IgE antibodies in mice, which are limited to the intestine. Following subsequent oral ingestion of the respective dietary antigen, an IgE- and mast-cell-dependent mechanism induced increased visceral pain. This aberrant pain signalling resulted from histamine receptor H1-mediated sensitization of visceral afferents. Moreover, injection of food antigens (gluten, wheat, soy and milk) into the rectosigmoid mucosa of patients with irritable bowel syndrome induced local oedema and mast cell activation. Our results identify and characterize a peripheral mechanism that underlies food-induced abdominal pain, thereby creating new possibilities for the treatment of irritable bowel syndrome and related abdominal pain disorders.
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Affiliation(s)
- Javier Aguilera-Lizarraga
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Morgane V Florens
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Maria Francesca Viola
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Piyush Jain
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Lisse Decraecker
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Iris Appeltans
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Maria Cuende-Estevez
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Naomi Fabre
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Kim Van Beek
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Eluisa Perna
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Dafne Balemans
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Nathalie Stakenborg
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Stavroula Theofanous
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Goele Bosmans
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Stéphanie U Mondelaers
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Gianluca Matteoli
- Laboratory for Mucosal Immunology, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Sales Ibiza Martínez
- Laboratory for Mucosal Immunology, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium.,Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Cintya Lopez-Lopez
- Gastrointestinal Diseases Research Unit, Queen's University, Kingston, Ontario, Canada
| | | | - Karel Talavera
- Laboratory for Ion Channel Research, VIB Center for Brain and Disease Research, KU Leuven Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Yeranddy A Alpizar
- Neuroscience Research group, BIOMED, Hasselt University, Hasselt, Belgium
| | | | - Hans-Reimer Rodewald
- Division of Cellular Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Ricard Farre
- Mucosal Permeability Lab, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Frank A Redegeld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Jiyeon Si
- KU Leuven Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium.,VIB KU Leuven Center for Microbiology, Leuven, Belgium
| | - Jeroen Raes
- KU Leuven Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium.,VIB KU Leuven Center for Microbiology, Leuven, Belgium
| | - Christine Breynaert
- Allergy and Clinical Immunology Research Group, KU Leuven Department of Microbiology, Immunology and Transplantation, Leuven, Belgium
| | - Rik Schrijvers
- Allergy and Clinical Immunology Research Group, KU Leuven Department of Microbiology, Immunology and Transplantation, Leuven, Belgium
| | - Cédric Bosteels
- Laboratory of Immunoregulation, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Bart N Lambrecht
- Laboratory of Immunoregulation, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Department of Pulmonary Medicine, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Ramona A Hoh
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Deirdre Cabooter
- KU Leuven Department of Pharmaceutical and Pharmacological Sciences, Leuven, Belgium
| | - Maxim Nelis
- KU Leuven Department of Pharmaceutical and Pharmacological Sciences, Leuven, Belgium
| | - Patrick Augustijns
- KU Leuven Department of Pharmaceutical and Pharmacological Sciences, Leuven, Belgium
| | - Sven Hendrix
- Department of Morphology, Biomedical Research Institute, Hasselt University, Hasselt, Belgium.,Medical School Hamburg, Hamburg, Germany
| | - Jessica Strid
- Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Raf Bisschops
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - David E Reed
- Gastrointestinal Diseases Research Unit, Queen's University, Kingston, Ontario, Canada
| | - Stephen J Vanner
- Gastrointestinal Diseases Research Unit, Queen's University, Kingston, Ontario, Canada
| | - Alexandre Denadai-Souza
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Mira M Wouters
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium
| | - Guy E Boeckxstaens
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Leuven, Belgium.
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91
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Kamp KJ, Cain KC, Utleg A, Burr RL, Raftery D, Luna RA, Shulman RJ, Heitkemper MM. Bile Acids and Microbiome Among Individuals With Irritable Bowel Syndrome and Healthy Volunteers. Biol Res Nurs 2021; 23:65-74. [PMID: 32666807 PMCID: PMC7874368 DOI: 10.1177/1099800420941255] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder. High bile acid (BA) profiles have been associated with abdominal pain symptoms, mucosal inflammation, and diarrhea in a subgroup of those with IBS. The purpose of this study was to compare: 1) fecal primary and secondary BAs in women with and without IBS; and 2) symptoms, gut microbiome, and diet between women with high and normal BAs (i.e., similar to healthy [HC] women). Women (ages 18-45) with IBS and HCs were recruited from healthcare providers or the community. Participants kept a 28-day symptom diary, completed a 3-day food journal, and collected a stool sample for microbiome analysis (16 S rRNA gene sequencing). Primary and secondary BA levels were determined by mass spectrometry. Primary BAs did not differ between IBS (n = 45) and HC (n = 28) groups; women with IBS had significantly increased conjugated secondary BAs (glycodeoxycholic acid [p = 0.006], taurodeoxycholic acid [p = 0.006], and glycolithocholic acid [p = 0.01]). Sixty percent of women with IBS had normal BAs whereas 40% had high BAs. Women with high fecal BAs were predominantly IBS-Diarrhea or IBS-Mixed and consumed less fiber and vegetable protein and more animal protein compared to women with IBS whose fecal BAs levels were comparable to HCs. Those with high conjugated secondary fecal BAs also had a greater Firmicutes/Bacteroidetes ratio, less abundance of phylum Bacteroidetes and genus Gemmiger, and more abundance of family Erysipelotrichaceae compared to IBS women with normal BAs. Determination of fecal BA levels provides additional insights into pathophysiological links between diet and microbiome in IBS.
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Affiliation(s)
- Kendra J Kamp
- Division of Gastroenterology, School of Medicine, 7284University of Washington, Seattle, WA, USA
| | - Kevin C Cain
- Department of Biostatistics, School of Public Health, 7284University of Washington, Seattle, WA, USA
| | - Angelita Utleg
- School of Nursing, 7284University of Washington, Seattle, WA, USA
| | - Robert L Burr
- Department of Biobehavioral Nursing and Health Informatics, School of Nursing, 7284University of Washington, Seattle, WA, USA
| | - Daniel Raftery
- Department of Anesthesiology & Pain Medicine, 7284University of Washington, Seattle, WA, USA
| | | | | | - Margaret M Heitkemper
- Department of Biobehavioral Nursing and Health Informatics, School of Nursing, 7284University of Washington, Seattle, WA, USA
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92
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Bahram M, Netherway T, Frioux C, Ferretti P, Coelho LP, Geisen S, Bork P, Hildebrand F. Metagenomic assessment of the global diversity and distribution of bacteria and fungi. Environ Microbiol 2021; 23:316-326. [PMID: 33185929 PMCID: PMC7898879 DOI: 10.1111/1462-2920.15314] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 10/22/2020] [Accepted: 11/09/2020] [Indexed: 12/17/2022]
Abstract
Bacteria and fungi are of uttermost importance in determining environmental and host functioning. Despite close interactions between animals, plants, their associated microbiomes, and the environment they inhabit, the distribution and role of bacteria and especially fungi across host and environments as well as the cross-habitat determinants of their community compositions remain little investigated. Using a uniquely broad global dataset of 13 483 metagenomes, we analysed the microbiome structure and function of 25 host-associated and environmental habitats, focusing on potential interactions between bacteria and fungi. We found that the metagenomic relative abundance ratio of bacteria-to-fungi is a distinctive microbial feature of habitats. Compared with fungi, the cross-habitat distribution pattern of bacteria was more strongly driven by habitat type. Fungal diversity was depleted in host-associated communities compared with those in the environment, particularly terrestrial habitats, whereas this diversity pattern was less pronounced for bacteria. The relative gene functional potential of bacteria or fungi reflected their diversity patterns and appeared to depend on a balance between substrate availability and biotic interactions. Alongside helping to identify hotspots and sources of microbial diversity, our study provides support for differences in assembly patterns and processes between bacterial and fungal communities across different habitats.
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Affiliation(s)
- Mohammad Bahram
- Department of EcologySwedish University of Agricultural SciencesUppsalaUlls väg 16, 756 51Sweden
- Department of BotanyInstitute of Ecology and Earth Sciences, University of TartuTartu40 Lai St.Estonia
| | - Tarquin Netherway
- Department of EcologySwedish University of Agricultural SciencesUppsalaUlls väg 16, 756 51Sweden
| | - Clémence Frioux
- Gut Microbes and HealthQuadram Institute BioscienceNorwich, NorfolkUK
- Digital BiologyEarlham InstituteNorwich, NorfolkUK
| | - Pamela Ferretti
- Structural and Computational BiologyEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Luis Pedro Coelho
- Structural and Computational BiologyEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Stefan Geisen
- Department of Terrestrial EcologyNetherlands Institute of Ecology NIOO‐KNAWWageningen6708 PBThe Netherlands
| | - Peer Bork
- Structural and Computational BiologyEuropean Molecular Biology LaboratoryHeidelbergGermany
- Max Delbrück Centre for Molecular MedicineBerlinGermany
| | - Falk Hildebrand
- Gut Microbes and HealthQuadram Institute BioscienceNorwich, NorfolkUK
- Digital BiologyEarlham InstituteNorwich, NorfolkUK
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93
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Belcour A, Frioux C, Aite M, Bretaudeau A, Hildebrand F, Siegel A. Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. eLife 2020; 9:e61968. [PMID: 33372654 PMCID: PMC7861615 DOI: 10.7554/elife.61968] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/25/2020] [Indexed: 12/13/2022] Open
Abstract
To capture the functional diversity of microbiota, one must identify metabolic functions and species of interest within hundreds or thousands of microorganisms. We present Metage2Metabo (M2M) a resource that meets the need for de novo functional screening of genome-scale metabolic networks (GSMNs) at the scale of a metagenome, and the identification of critical species with respect to metabolic cooperation. M2M comprises a flexible pipeline for the characterisation of individual metabolisms and collective metabolic complementarity. In addition, M2M identifies key species, that are meaningful members of the community for functions of interest. We demonstrate that M2M is applicable to collections of genomes as well as metagenome-assembled genomes, permits an efficient GSMN reconstruction with Pathway Tools, and assesses the cooperation potential between species. M2M identifies key organisms by reducing the complexity of a large-scale microbiota into minimal communities with equivalent properties, suitable for further analyses.
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Affiliation(s)
| | - Clémence Frioux
- Univ Rennes, Inria, CNRS, IRISARennesFrance
- Inria Bordeaux Sud-OuestTalenceFrance
- Gut Microbes and Heath, Quadram InstituteNorwichUnited Kingdom
- Digital Biology, Earlham InstituteNorwichUnited Kingdom
| | | | - Anthony Bretaudeau
- Univ Rennes, Inria, CNRS, IRISARennesFrance
- Inria, UMR IGEPP, BioInformatics Platform for Agroecosystems Arthropods (BIPAA)RennesFrance
- Inria, IRISA, GenOuest Core FacilityRennesFrance
| | - Falk Hildebrand
- Gut Microbes and Heath, Quadram InstituteNorwichUnited Kingdom
- Digital Biology, Earlham InstituteNorwichUnited Kingdom
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94
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Assmann TS, Cuevas-Sierra A, Riezu-Boj JI, Milagro FI, Martínez JA. Comprehensive Analysis Reveals Novel Interactions between Circulating MicroRNAs and Gut Microbiota Composition in Human Obesity. Int J Mol Sci 2020; 21:ijms21249509. [PMID: 33327530 PMCID: PMC7765005 DOI: 10.3390/ijms21249509] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/10/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022] Open
Abstract
Background: The determinants that mediate the interactions between microRNAs and the gut microbiome impacting on obesity are scarcely understood. Thus, the aim of this study was to investigate possible interactions between circulating microRNAs and gut microbiota composition in obesity. Method: The sample comprised 78 subjects with obesity (cases, body mass index (BMI): 30–40 kg/m2) and 25 eutrophic individuals (controls, BMI ≤ 25 kg/m2). The expression of 96 microRNAs was investigated in plasma of all individuals using miRCURY LNA miRNA Custom PCR Panels. Bacterial DNA sequencing was performed following the Illumina 16S protocol. The FDR correction was used for multiple comparison analyses. Results: A total of 26 circulating microRNAs and 12 bacterial species were found differentially expressed between cases and controls. Interestingly, an interaction among three miRNAs (miR-130b-3p, miR-185-5p and miR-21-5p) with Bacteroides eggerthi and BMI levels was evidenced (r2 = 0.148, p = 0.004). Moreover, these microRNAs regulate genes that participate in metabolism-related pathways, including fatty acid degradation, insulin signaling and glycerolipid metabolism. Conclusions: This study characterized an interaction between the abundance of 4 bacterial species and 14 circulating microRNAs in relation to obesity. Moreover, the current study also suggests that miRNAs may serve as a communication mechanism between the gut microbiome and human hosts.
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Affiliation(s)
- Taís Silveira Assmann
- Center for Nutrition Research, Department of Nutrition, Food Science and Physiology, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain; (T.S.A.); (A.C.-S.); (J.I.R.-B.); (J.A.M.)
| | - Amanda Cuevas-Sierra
- Center for Nutrition Research, Department of Nutrition, Food Science and Physiology, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain; (T.S.A.); (A.C.-S.); (J.I.R.-B.); (J.A.M.)
| | - José Ignacio Riezu-Boj
- Center for Nutrition Research, Department of Nutrition, Food Science and Physiology, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain; (T.S.A.); (A.C.-S.); (J.I.R.-B.); (J.A.M.)
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y Nutrición (CIBERobn), Carlos III Health Institute, 28029 Madrid, Spain
- IdiSNA—Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Fermín I. Milagro
- Center for Nutrition Research, Department of Nutrition, Food Science and Physiology, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain; (T.S.A.); (A.C.-S.); (J.I.R.-B.); (J.A.M.)
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y Nutrición (CIBERobn), Carlos III Health Institute, 28029 Madrid, Spain
- IdiSNA—Navarra Institute for Health Research, 31008 Pamplona, Spain
- Correspondence:
| | - J. Alfredo Martínez
- Center for Nutrition Research, Department of Nutrition, Food Science and Physiology, University of Navarra, Irunlarrea 1, 31008 Pamplona, Spain; (T.S.A.); (A.C.-S.); (J.I.R.-B.); (J.A.M.)
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y Nutrición (CIBERobn), Carlos III Health Institute, 28029 Madrid, Spain
- IdiSNA—Navarra Institute for Health Research, 31008 Pamplona, Spain
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95
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Hupfauf S, Etemadi M, Fernández-Delgado Juárez M, Gómez-Brandón M, Insam H, Podmirseg SM. CoMA - an intuitive and user-friendly pipeline for amplicon-sequencing data analysis. PLoS One 2020; 15:e0243241. [PMID: 33264369 PMCID: PMC7710066 DOI: 10.1371/journal.pone.0243241] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/17/2020] [Indexed: 12/23/2022] Open
Abstract
In recent years, there has been a veritable boost in next-generation sequencing (NGS) of gene amplicons in biological and medical studies. Huge amounts of data are produced and need to be analyzed adequately. Various online and offline analysis tools are available; however, most of them require extensive expertise in computer science or bioinformatics, and often a Linux-based operating system. Here, we introduce "CoMA-Comparative Microbiome Analysis" as a free and intuitive analysis pipeline for amplicon-sequencing data, compatible with any common operating system. Moreover, the tool offers various useful services including data pre-processing, quality checking, clustering to operational taxonomic units (OTUs), taxonomic assignment, data post-processing, data visualization, and statistical appraisal. The workflow results in highly esthetic and publication-ready graphics, as well as output files in standardized formats (e.g. tab-delimited OTU-table, BIOM, NEWICK tree) that can be used for more sophisticated analyses. The CoMA output was validated by a benchmark test, using three mock communities with different sample characteristics (primer set, amplicon length, diversity). The performance was compared with that of Mothur, QIIME and QIIME2-DADA2, popular packages for NGS data analysis. Furthermore, the functionality of CoMA is demonstrated on a practical example, investigating microbial communities from three different soils (grassland, forest, swamp). All tools performed well in the benchmark test and were able to reveal the majority of all genera in the mock communities. Also for the soil samples, the results of CoMA were congruent to those of the other pipelines, in particular when looking at the key microbial players.
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Affiliation(s)
- Sebastian Hupfauf
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Mohammad Etemadi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran
| | | | - María Gómez-Brandón
- Department of Ecology and Animal Biology, GEA Group, University of Vigo, Vigo, Spain
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
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96
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Isaacs‐Ten A, Echeandia M, Moreno‐Gonzalez M, Brion A, Goldson A, Philo M, Patterson AM, Parker A, Galduroz M, Baker D, Rushbrook SM, Hildebrand F, Beraza N. Intestinal Microbiome-Macrophage Crosstalk Contributes to Cholestatic Liver Disease by Promoting Intestinal Permeability in Mice. Hepatology 2020; 72:2090-2108. [PMID: 32168395 PMCID: PMC7839474 DOI: 10.1002/hep.31228] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/30/2020] [Accepted: 02/14/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS Mounting evidence supports an association between cholestatic liver disease and changes in the composition of the microbiome. Still, the role of the microbiome in the pathogenesis of this condition remains largely undefined. APPROACH AND RESULTS To address this, we have used two experimental models, administering alpha-naphtylisocyanate or feeding a 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine diet, to induce cholestatic liver disease in germ-free mice and germ-free mice conventionalized with the microbiome from wild-type, specific pathogen-free animals. Next, we have inhibited macrophage activation by depleting these cells using clodronate liposomes and inhibiting the inflammasome with a specific inhibitor of NOD-, LRR-, and pyrin domain-containing protein 3. Our results demonstrate that cholestasis, the accumulation of bile acids in the liver, fails to promote liver injury in the absence of the microbiome in vivo. Additional in vitro studies supported that endotoxin sensitizes hepatocytes to bile-acid-induced cell death. We also demonstrate that during cholestasis, macrophages contribute to promoting intestinal permeability and to altered microbiome composition through activation of the inflammasome, overall leading to increased endotoxin flux into the cholestatic liver. CONCLUSIONS We demonstrate that the intestinal microbiome contributes to cholestasis-mediated cell death and inflammation through mechanisms involving activation of the inflammasome in macrophages.
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Affiliation(s)
- Anna Isaacs‐Ten
- Gut Microbes and Health Institute Strategic ProgrammeQuadram Institute BioscienceNorwich Research ParkNorwichUnited Kingdom
| | - Marta Echeandia
- Gut Microbes and Health Institute Strategic ProgrammeQuadram Institute BioscienceNorwich Research ParkNorwichUnited Kingdom
| | - Mar Moreno‐Gonzalez
- Gut Microbes and Health Institute Strategic ProgrammeQuadram Institute BioscienceNorwich Research ParkNorwichUnited Kingdom
| | - Arlaine Brion
- Analytical Science UnitQuadram Institute BioscienceNorwich Research ParkNorwichUnited Kingdom
| | - Andrew Goldson
- Analytical Science UnitQuadram Institute BioscienceNorwich Research ParkNorwichUnited Kingdom
| | - Mark Philo
- Analytical Science UnitQuadram Institute BioscienceNorwich Research ParkNorwichUnited Kingdom
| | - Angela M. Patterson
- Gut Microbes and Health Institute Strategic ProgrammeQuadram Institute BioscienceNorwich Research ParkNorwichUnited Kingdom
| | - Aimee Parker
- Gut Microbes and Health Institute Strategic ProgrammeQuadram Institute BioscienceNorwich Research ParkNorwichUnited Kingdom
| | - Mikel Galduroz
- Gut Microbes and Health Institute Strategic ProgrammeQuadram Institute BioscienceNorwich Research ParkNorwichUnited Kingdom
| | - David Baker
- Science OperationsQuadram Institute Bioscience, Norwich Research ParkNorwichUnited Kingdom
| | - Simon M. Rushbrook
- Department of GastroenterologyNorfolk and Norwich University HospitalNorwichUnited Kingdom
| | - Falk Hildebrand
- Gut Microbes and Health Institute Strategic ProgrammeQuadram Institute BioscienceNorwich Research ParkNorwichUnited Kingdom,Digital BiologyEarlham InstituteNorwichUnited Kingdom
| | - Naiara Beraza
- Gut Microbes and Health Institute Strategic ProgrammeQuadram Institute BioscienceNorwich Research ParkNorwichUnited Kingdom,Food Innovation and Health Institute Strategic ProgrammeQuadram Institute BioscienceNorwich Research ParkNorwichUnited Kingdom
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97
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Willers M, Ulas T, Völlger L, Vogl T, Heinemann AS, Pirr S, Pagel J, Fehlhaber B, Halle O, Schöning J, Schreek S, Löber U, Essex M, Hombach P, Graspeuntner S, Basic M, Bleich A, Cloppenborg-Schmidt K, Künzel S, Jonigk D, Rupp J, Hansen G, Förster R, Baines JF, Härtel C, Schultze JL, Forslund SK, Roth J, Viemann D. S100A8 and S100A9 Are Important for Postnatal Development of Gut Microbiota and Immune System in Mice and Infants. Gastroenterology 2020; 159:2130-2145.e5. [PMID: 32805279 DOI: 10.1053/j.gastro.2020.08.019] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/14/2020] [Accepted: 08/09/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS After birth, the immune system matures via interactions with microbes in the gut. The S100 calcium binding proteins S100A8 and S100A9, and their extracellular complex form, S100A8-A9, are found in high amounts in human breast milk. We studied levels of S100A8-A9 in fecal samples (also called fecal calprotectin) from newborns and during infancy, and their effects on development of the intestinal microbiota and mucosal immune system. METHODS We collected stool samples (n = 517) from full-term (n = 72) and preterm infants (n = 49) at different timepoints over the first year of life (days 1, 3, 10, 30, 90, 180, and 360). We measured levels of S100A8-A9 by enzyme-linked immunosorbent assay and analyzed fecal microbiomes by 16S sRNA gene sequencing. We also obtained small and large intestine biopsies from 8 adults and 10 newborn infants without inflammatory bowel diseases (controls) and 8 infants with necrotizing enterocolitis and measured levels of S100A8 by immunofluorescence microscopy. Children were followed for 2.5 years and anthropometric data and medical information on infections were collected. We performed studies with newborn C57BL/6J wild-type and S100a9-/- mice (which also lack S100A8). Some mice were fed or given intraperitoneal injections of S100A8 or subcutaneous injections of Staphylococcus aureus. Blood and intestine, mesenterial and celiac lymph nodes were collected; cells and cytokines were measured by flow cytometry and studied in cell culture assays. Colon contents from mice were analyzed by culture-based microbiology assays. RESULTS Loss of S100A8 and S100A9 in mice altered the phenotypes of colonic lamina propria macrophages, compared with wild-type mice. Intestinal tissues from neonatal S100-knockout mice had reduced levels of CX3CR1 protein, and Il10 and Tgfb1 mRNAs, compared with wild-type mice, and fewer T-regulatory cells. S100-knockout mice weighed 21% more than wild-type mice at age 8 weeks and a higher proportion developed fatal sepsis during the neonatal period. S100-knockout mice had alterations in their fecal microbiomes, with higher abundance of Enterobacteriaceae. Feeding mice S100 at birth prevented the expansion of Enterobacteriaceae, increased numbers of T-regulatory cells and levels of CX3CR1 protein and Il10 mRNA in intestine tissues, and reduced body weight and death from neonatal sepsis. Fecal samples from term infants, but not preterm infants, had significantly higher levels of S100A8-A9 during the first 3 months of life than fecal samples from adults; levels decreased to adult levels after weaning. Fecal samples from infants born by cesarean delivery had lower levels of S100A8-A9 than from infants born by vaginal delivery. S100 proteins were expressed by lamina propria macrophages in intestinal tissues from infants, at higher levels than in intestinal tissues from adults. High fecal levels of S100 proteins, from 30 days to 1 year of age, were associated with higher abundance of Actinobacteria and Bifidobacteriaceae, and lower abundance of Gammaproteobacteria-particularly opportunistic Enterobacteriaceae. A low level of S100 proteins in infants' fecal samples associated with development of sepsis and obesity by age 2 years. CONCLUSION S100A8 and S100A9 regulate development of the intestinal microbiota and immune system in neonates. Nutritional supplementation with these proteins might aide in development of preterm infants and prevent microbiota-associated disorders in later years.
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Affiliation(s)
- Maike Willers
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Thomas Ulas
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, Bonn, Germany; PRECISE, Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Lena Völlger
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Thomas Vogl
- Institute of Immunology, University of Münster, Münster, Germany
| | - Anna S Heinemann
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Sabine Pirr
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Julia Pagel
- Department of Pediatrics, University of Lübeck, Lübeck, Germany
| | - Beate Fehlhaber
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Olga Halle
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Jennifer Schöning
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Sabine Schreek
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Morgan Essex
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Hombach
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, Bonn, Germany
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Marijana Basic
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Hannover, Germany
| | - Andre Bleich
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Hannover, Germany
| | | | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Danny Jonigk
- Department of Pathology, Hannover Medical School, Hannover, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Gesine Hansen
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Reinhold Förster
- Institute of Immunology, Hannover Medical School, Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - John F Baines
- Institute of Experimental Medicine, University of Kiel, Kiel, Germany; Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Christoph Härtel
- PRIMAL Consortium, Hannover Medical School, Hannover, Germany; Department of Pediatrics, University Hospital of Würzburg, Würzburg, Germany
| | - Joachim L Schultze
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, Bonn, Germany; PRECISE, Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Sofia K Forslund
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany; European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Johannes Roth
- Institute of Immunology, University of Münster, Münster, Germany
| | - Dorothee Viemann
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany; PRIMAL Consortium, Hannover Medical School, Hannover, Germany.
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98
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Weißbecker C, Schnabel B, Heintz-Buschart A. Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology. Gigascience 2020; 9:6011256. [PMID: 33252655 PMCID: PMC7702218 DOI: 10.1093/gigascience/giaa135] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/20/2020] [Accepted: 11/05/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Amplicon sequencing of phylogenetic marker genes, e.g., 16S, 18S, or ITS ribosomal RNA sequences, is still the most commonly used method to determine the composition of microbial communities. Microbial ecologists often have expert knowledge on their biological question and data analysis in general, and most research institutes have computational infrastructures to use the bioinformatics command line tools and workflows for amplicon sequencing analysis, but requirements of bioinformatics skills often limit the efficient and up-to-date use of computational resources. RESULTS We present dadasnake, a user-friendly, 1-command Snakemake pipeline that wraps the preprocessing of sequencing reads and the delineation of exact sequence variants by using the favorably benchmarked and widely used DADA2 algorithm with a taxonomic classification and the post-processing of the resultant tables, including hand-off in standard formats. The suitability of the provided default configurations is demonstrated using mock community data from bacteria and archaea, as well as fungi. CONCLUSIONS By use of Snakemake, dadasnake makes efficient use of high-performance computing infrastructures. Easy user configuration guarantees flexibility of all steps, including the processing of data from multiple sequencing platforms. It is easy to install dadasnake via conda environments. dadasnake is available at https://github.com/a-h-b/dadasnake.
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Affiliation(s)
- Christina Weißbecker
- Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Soil Ecology; Theodor-Lieser-Str. 4, 06120 Halle, Germany
| | - Beatrix Schnabel
- Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Soil Ecology; Theodor-Lieser-Str. 4, 06120 Halle, Germany
| | - Anna Heintz-Buschart
- Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Soil Ecology; Theodor-Lieser-Str. 4, 06120 Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Metagenomics Support Unit; Puschstr. 4, 04103 Leipzig, Germany
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99
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Abstract
BACKGROUND The human microbiome evolves rapidly in early life with contributions from various factors such as diet, delivery mode, medical history, antibiotics exposure, genetics, immunomodulators and the environment. A high use of antibiotics in pediatric outpatient settings has been well documented, and improvement in antibiotic selection is required to reduce the risks of antibiotic resistance and disruption of the microbiome. METHODS We performed an exploratory study using 16S rRNA gene-based sequencing to characterize the gut and nasopharyngeal microbiome of children (n = 50) age 1-6 years of age in a pediatric otolaryngology practice. RESULTS Relative abundance of Haemophilus and Moraxella were higher in nasopharyngeal swabs, while Prevotella, Bacteroides, Porphyromonas and Faecalibacterium were highly abundant in rectal swabs. The gut microbiome composition in children <2 years old was different compared with children ≥2 years age. Gut bacterial diversity increased with an increase in age of the children. Children taking probiotics had a notable increase in abundance of potentially beneficial gut bacteria such as Bacteroides and Akkermansia. The nasopharyngeal microbiome differed between children who received antibiotics in the 3 months before sample collection compared with those that did not. Haemophilus spp. was highly abundant in children who received antibiotics 3 months before sampling. CONCLUSIONS The pediatric nasopharyngeal and rectal microbiomes differ in bacterial composition and diversity. The increased abundance of Haemophilus spp. in the nasopharyngeal microbiome of children who received antibiotics during the 3 months before sampling suggests a potential impact of antibiotics in colonization with the otopathogen and may be relevant to clinical practice.
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100
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Spinler JK, Oezguen N, Runge JK, Luna RA, Karri V, Yang J, Hirschi KD. Dietary impact of a plant-derived microRNA on the gut microbiome. ACTA ACUST UNITED AC 2020; 2. [PMID: 33542959 PMCID: PMC7856875 DOI: 10.1186/s41544-020-00053-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background: Global estimations of 4 billion people living on plant-based diets signify tremendous diversity in plant consumption and their assorted miRNAs, which presents a challenging model to experimentally address how plant-based miRNAs impact the microbiome. Here we establish baseline gut microbiome composition for a mouse model deficient in the specific mammalian miR-146a shown to alter gut microbiomes. We then asses the effect on the gut microbiome when miR-146a-deficient mice are fed a transgenic plant-based diet expressing the murine-derived miR-146a. Mice deficient in miR-146a were maintained either on a baseline diet until 7 weeks of age (day 0) and then fed either vector or miR-146a-expressing plant-based diets for 21 days. The gut microbiomes of mice were examined by comparing the V4 region of 16S rRNA gene sequences of DNA isolated from fecal samples at days 0 (baseline diet) and 21 (vector or miR-146a expressing plant-based diets). Results: Beta-diversity analysis demonstrated that the transition from baseline chow to a plant-based diet resulted in significant longitudinal shifts in microbial community structure attributable to increased fiber intake. Bipartite network analysis suggests that miR-146a-deficient mice fed a plant diet rich in miR-146a have a microbiome population modestly different than mice fed an isogenic control plant diet deficient in miR-146a. Conclusion: A mouse diet composed of a transgenic plant expressing a mouse miR-146a may fine tune microbial communities but does not appear to have global effects on microbiome structure and composition.
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Affiliation(s)
- Jennifer K Spinler
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA.,Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, 1102 Bates Ave, Houston, TX 77030, USA
| | - Numan Oezguen
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA.,Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, 1102 Bates Ave, Houston, TX 77030, USA
| | - Jessica K Runge
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA.,Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, 1102 Bates Ave, Houston, TX 77030, USA
| | - Ruth Ann Luna
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA.,Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, 1102 Bates Ave, Houston, TX 77030, USA
| | | | - Jian Yang
- Pediatrics-Nutrition, Children's Nutrition Research, Baylor College of Medicine, 1100 Bates Ave, Houston, TX 77030, USA
| | - Kendal D Hirschi
- Pediatrics-Nutrition, Children's Nutrition Research, Baylor College of Medicine, 1100 Bates Ave, Houston, TX 77030, USA
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