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Sex Differences in Colonization of Gut Microbiota from a Man with Short
www.nature.com/scientificreports OPEN Sex differences in colonization of gut microbiota from a man with short-term vegetarian and inulin- Received: 28 June 2016 Accepted: 11 October 2016 supplemented diet in germ-free Published: 31 October 2016 mice Jing-jing Wang1, Jing Wang2, Xiao-yan Pang2, Li-ping Zhao2, Ling Tian1,* & Xing-peng Wang1,* Gnotobiotic mouse model is generally used to evaluate the efficacy of gut microbiota. Sex differences of gut microbiota are acknowledged, yet the effect of recipient’s gender on the bacterial colonization remains unclear. Here we inoculated male and female germ-free C57BL/6J mice with fecal bacteria from a man with short-term vegetarian and inulin-supplemented diet. We sequenced bacterial 16S rRNA genes V3-V4 region from donor’s feces and recipient’s colonic content. Shannon diversity index showed female recipients have higher bacteria diversity than males. Weighted UniFrac principal coordinates analysis revealed the overall structures of male recipient’s gut microbiota were significantly separated from those of females, and closer to the donor. Redundancy analysis identified 46 operational taxonomic units (OTUs) differed between the sexes. The relative abundance of 13 OTUs were higher in males, such as Parabacteroides distasonis and Blautia faecis, while 33 OTUs were overrepresented in females, including Clostridium groups and Escherichia fergusonii/Shigella sonnei. Moreover, the interactions of these differential OTUs were sexually distinct. These findings demonstrated that the intestine of male and female mice preferred to accommodate microbiota differently. Therefore, it is necessary to designate the gender of gnotobiotic mice for complete evaluation of modulatory effects of gut microbiota from human feces upon diseases. -
Functional Comparison of Bacteria from the Human Gut and Closely
Functional comparison of bacteria from the human gut and closely related non-gut bacteria reveals the importance of conjugation and a paucity of motility and chemotaxis functions in the gut environment Dragana Dobrijevic, Anne-Laure Abraham, Alexandre Jamet, Emmanuelle Maguin, Maarten van de Guchte To cite this version: Dragana Dobrijevic, Anne-Laure Abraham, Alexandre Jamet, Emmanuelle Maguin, Maarten van de Guchte. Functional comparison of bacteria from the human gut and closely related non-gut bacte- ria reveals the importance of conjugation and a paucity of motility and chemotaxis functions in the gut environment. PLoS ONE, Public Library of Science, 2016, 11 (7), pp.e0159030. 10.1371/jour- nal.pone.0159030. hal-01353535 HAL Id: hal-01353535 https://hal.archives-ouvertes.fr/hal-01353535 Submitted on 11 Aug 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License RESEARCH ARTICLE Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals -
Computational Methods for the Identification and Quantification Of
Computational methods for the identification and quantification of microbial organisms in metagenomes Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) am Fachbereich Mathematik und Informatik der Freien Universit¨atBerlin von Martin Michael Serenus Lindner Berlin August 2014 Betreuer: PD Dr. Bernhard Renard Erstgutachter: PD Dr. Bernhard Renard Zweitgutachter: Jun.-Prof. Dr. Tobias Marschall Tag der Disputation: 15. Oktober 2014 ii Abstract Metagenomics allows analyzing genomic material taken directly from the environ- ment. In contrast to classical genomics, no purification of single organisms is per- formed and therefore the extracted genomic material reflects the composition of the original microbial community. The possible applications of metagenomics are mani- fold and the field has become increasingly popular due to the recent improvements in sequencing technologies. One of the most fundamental challenges in metagenomics is the identification and quantification of organisms in a sample, called taxonomic profiling. In this work, we present approaches to the following current problems in taxo- nomic profiling: First, differentiation between closely related organisms in metage- nomic samples is still challenging. Second, the identification of novel organisms in metagenomic samples poses problems to current taxonomic profiling methods, especially when there is no suitable reference genome available. The contribution of this thesis comprises three major projects. First, we introduce the Genome Abundance Similarity Correction (GASiC) algorithm, a method that allows differentiating between and quantifying highly similar microbial organisms in a metagenomic sample. The method first estimates the similarities between the available reference genomes with a simulation approach. Based on the similarities, GASiC corrects the observed abundances of each reference genome using a non- negative lasso approach. -
Microbiota-Directed Fibre Activates Both Targeted and Secondary
ARTICLE https://doi.org/10.1038/s41467-020-19585-0 OPEN Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut ✉ Leszek Michalak 1, John Christian Gaby1 , Leidy Lagos2, Sabina Leanti La Rosa 1, Torgeir R. Hvidsten 1, Catherine Tétard-Jones3, William G. T. Willats3, Nicolas Terrapon 4,5, Vincent Lombard4,5, Bernard Henrissat 4,5,6, Johannes Dröge7, Magnus Øverlie Arntzen 1, Live Heldal Hagen 1, ✉ ✉ Margareth Øverland2, Phillip B. Pope 1,2,8 & Bjørge Westereng 1,8 1234567890():,; Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have tailored an acetylated galactoglucomannan (AcGGM) fibre to match unique enzymatic capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut commensals. Here, we test the accuracy of AcGGM within the complex endogenous gut microbiome of pigs, wherein we resolve 355 metagenome-assembled genomes together with quantitative metaproteomes. In AcGGM-fed pigs, both target populations differentially express AcGGM-specific polysaccharide utilization loci, including novel, mannan-specific esterases that are critical to its deconstruction. However, AcGGM-inclusion also manifests a “butterfly effect”, whereby numerous metabolic changes and interdependent cross-feeding pathways occur in neighboring non-mannanolytic populations that produce short-chain fatty acids. Our findings show how intricate structural features and acetylation patterns of dietary fibre can be customized to specific bacterial populations, with potential to create greater modulatory effects at large. 1 Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway. -
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Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut Downloaded from: https://research.chalmers.se, 2021-10-02 23:09 UTC Citation for the original published paper (version of record): Michalak, L., Gaby, J., Lagos, L. et al (2020) Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut Nature Communications, 11(1) http://dx.doi.org/10.1038/s41467-020-19585-0 N.B. When citing this work, cite the original published paper. research.chalmers.se offers the possibility of retrieving research publications produced at Chalmers University of Technology. It covers all kind of research output: articles, dissertations, conference papers, reports etc. since 2004. research.chalmers.se is administrated and maintained by Chalmers Library (article starts on next page) ARTICLE https://doi.org/10.1038/s41467-020-19585-0 OPEN Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut ✉ Leszek Michalak 1, John Christian Gaby1 , Leidy Lagos2, Sabina Leanti La Rosa 1, Torgeir R. Hvidsten 1, Catherine Tétard-Jones3, William G. T. Willats3, Nicolas Terrapon 4,5, Vincent Lombard4,5, Bernard Henrissat 4,5,6, Johannes Dröge7, Magnus Øverlie Arntzen 1, Live Heldal Hagen 1, ✉ ✉ Margareth Øverland2, Phillip B. Pope 1,2,8 & Bjørge Westereng 1,8 1234567890():,; Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have tailored an acetylated galactoglucomannan (AcGGM) fibre to match unique enzymatic capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut commensals. -
Gut Microbiome-Related Effects of Berberine and Probiotics on Type 2 Diabetes (The PREMOTE Study)
ARTICLE https://doi.org/10.1038/s41467-020-18414-8 OPEN Gut microbiome-related effects of berberine and probiotics on type 2 diabetes (the PREMOTE study) Yifei Zhang 1,19, Yanyun Gu1,19, Huahui Ren2,19, Shujie Wang 1,19, Huanzi Zhong 2,19, Xinjie Zhao3, Jing Ma4, Xuejiang Gu5, Yaoming Xue6, Shan Huang7, Jialin Yang8, Li Chen9, Gang Chen10, Shen Qu11, Jun Liang12, Li Qin13, Qin Huang14, Yongde Peng15,QiLi3, Xiaolin Wang3, Ping Kong2, Guixue Hou 2, Mengyu Gao2, Zhun Shi2, Xuelin Li1, Yixuan Qiu1, Yuanqiang Zou2, Huanming Yang2,16, Jian Wang2,16, ✉ ✉ Guowang Xu3, Shenghan Lai17, Junhua Li 2,18 , Guang Ning1 & Weiqing Wang1 1234567890():,; Human gut microbiome is a promising target for managing type 2 diabetes (T2D). Measures altering gut microbiota like oral intake of probiotics or berberine (BBR), a bacteriostatic agent, merit metabolic homoeostasis. We hence conducted a randomized, double-blind, placebo- controlled trial with newly diagnosed T2D patients from 20 centres in China. Four-hundred- nine eligible participants were enroled, randomly assigned (1:1:1:1) and completed a 12-week treatment of either BBR-alone, probiotics+BBR, probiotics-alone, or placebo, after a one-week run-in of gentamycin pretreatment. The changes in glycated haemoglobin, as the primary outcome, in the probiotics+BBR (least-squares mean [95% CI], −1.04[−1.19, −0.89]%) and BBR-alone group (−0.99[−1.16, −0.83]%) were significantly greater than that in the placebo and probiotics-alone groups (−0.59[−0.75, −0.44]%, −0.53[−0.68, −0.37]%, P < 0.001). BBR treatment induced more gastrointestinal side effects. -
Systemic Igg Repertoire As a Biomarker for Translocating Gut Microbiota Members
bioRxiv preprint doi: https://doi.org/10.1101/2021.08.17.456549; this version posted August 18, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. Systemic IgG repertoire as a biomarker for translocating gut microbiota members Ivan Vujkovic-Cvijin1,2,†,*, Hugh Welles1,2, Connie W.Y. Ha3,‡, Lutfi Huq1,§, Shreni Mistry2, Jason M. Brenchley4, Giorgio Trinchieri5, Suzanne Devkota3, Yasmine Belkaid1,2* 1Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20892, USA. 2NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA. 3F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA. 4Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20892, USA. 5Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA. † Present address: Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA ‡ Present address: The Benioff Center for Microbiome Medicine, University of California - San Francisco, San Francisco, CA 94143, USA. § Present address: Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD 20892, USA. *Co-corresponding authors: Ivan Vujkovic-Cvijin ([email protected]); Yasmine Belkaid ([email protected]) 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.08.17.456549; this version posted August 18, 2021. -
Host Adaptation in Gut Firmicutes Is Associated with Sporulation Loss and Altered Transmission Cycle Hilary P
Browne et al. Genome Biology (2021) 22:204 https://doi.org/10.1186/s13059-021-02428-6 RESEARCH Open Access Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle Hilary P. Browne1*, Alexandre Almeida2,3, Nitin Kumar1, Kevin Vervier1, Anne T. Adoum2, Elisa Viciani1, Nicholas J. R. Dawson1, Samuel C. Forster1,4,5, Claire Cormie2, David Goulding2 and Trevor D. Lawley1* * Correspondence: [email protected]. uk; [email protected] Abstract 1Host-Microbiota Interactions Laboratory, Wellcome Sanger Background: Human-to-human transmission of symbiotic, anaerobic bacteria is a Institute, Hinxton, UK fundamental evolutionary adaptation essential for membership of the human gut Full list of author information is microbiota. However, despite its importance, the genomic and biological adaptations available at the end of the article underpinning symbiont transmission remain poorly understood. The Firmicutes are a dominant phylum within the intestinal microbiota that are capable of producing resistant endospores that maintain viability within the environment and germinate within the intestine to facilitate transmission. However, the impact of host transmission on the evolutionary and adaptive processes within the intestinal microbiota remains unknown. Results: We analyze 1358 genomes of Firmicutes bacteria derived from host and environment-associated habitats. Characterization of genomes as spore-forming based on the presence of sporulation-predictive genes reveals multiple losses of sporulation in many distinct lineages. Loss of sporulation in gut Firmicutes is associated with features of host-adaptation such as genome reduction and specialized metabolic capabilities. Consistent with these data, analysis of 9966 gut metagenomes from adults around the world demonstrates that bacteria now incapable of sporulation are more abundant within individuals but less prevalent in the human population compared to spore-forming bacteria. -
And Population-Level Microbiome Analysis of the Wasp Spider Argiope
bioRxiv preprint doi: https://doi.org/10.1101/822437; this version posted October 29, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Tissue- and population-level microbiome analysis of the wasp spider 2 Argiope bruennichi identifies a novel dominant bacterial symbiont 3 Monica M. Sheffer1*, Gabriele Uhl1, Stefan Prost2,3, Tillmann Lueders4, Tim Urich5, Mia 4 M. Bengtsson5* 5 6 1Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany 7 2LOEWE-Center for Translational Biodiversity Genomics, Senckenberg Museum, 60325 8 Frankfurt, Germany 9 3South African National Biodiversity Institute, National Zoological Gardens of South 10 Africa, Pretoria 0001, South Africa 11 4Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, 12 95448 Bayreuth, Germany 13 5Institute of Microbiology, University of Greifswald, 17487 Greifswald, Germany 14 15 *corresponding authors: 16 E-Mail: [email protected] 17 Zoological Institute and Museum, University of Greifswald, Loitzer Str. 26, 17489 18 Greifswald, Germany 19 E-Mail: [email protected] 20 Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17487 21 Greifswald, Germany 22 1 bioRxiv preprint doi: https://doi.org/10.1101/822437; this version posted October 29, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. -
Caloric Restriction Disrupts the Microbiota and Colonization Resistance
Article Caloric restriction disrupts the microbiota and colonization resistance https://doi.org/10.1038/s41586-021-03663-4 Reiner Jumpertz von Schwartzenberg1,2,3,13, Jordan E. Bisanz4,13, Svetlana Lyalina5, Peter Spanogiannopoulos4, Qi Yan Ang4, Jingwei Cai6, Sophia Dickmann1, Marie Friedrich1, Received: 28 November 2017 Su-Yang Liu7, Stephanie L. Collins6, Danielle Ingebrigtsen8, Steve Miller8, Jessie A. Turnbaugh4, Accepted: 21 May 2021 Andrew D. Patterson6, Katherine S. Pollard5,9,10,11,12, Knut Mai1,2, Joachim Spranger1,2,3,14 ✉ & Peter J. Turnbaugh4,14 ✉ Published online: 23 June 2021 Check for updates Diet is a major factor that shapes the gut microbiome1, but the consequences of diet-induced changes in the microbiome for host pathophysiology remain poorly understood. We conducted a randomized human intervention study using a very-low-calorie diet (NCT01105143). Although metabolic health was improved, severe calorie restriction led to a decrease in bacterial abundance and restructuring of the gut microbiome. Transplantation of post-diet microbiota to mice decreased their body weight and adiposity relative to mice that received pre-diet microbiota. Weight loss was associated with impaired nutrient absorption and enrichment in Clostridioides difcile, which was consistent with a decrease in bile acids and was sufcient to replicate metabolic phenotypes in mice in a toxin-dependent manner. These results emphasize the importance of diet–microbiome interactions in modulating host energy balance and the need to understand the role of diet in the interplay between pathogenic and benefcial symbionts. Very-low-calorie diets (VLCDs) involve extreme calorie restriction Data Fig. 1g). Glucose regulation reverted after CONVD despite the (approximately 800 kcal per day, typically in liquid form2). -
Carbohydrate and Bacterial Binding Specificity of Human Intelectin-1
Carbohydrate and Bacterial Binding Specificity of Human Intelectin-1 By Christine R. Isabella M.S. Biochemistry University of Wisconsin – Madison, 2017 B.S. Molecular and Cellular Biology University of Puget Sound, 2012 SUBMITTED TO THE DEPARTMENT OF CHEMISTRY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN CHEMISTRY AT THE MASSACHUSETTS INSTITUTE OF TECHNOLOGY February 2021 Ó 2021 Massachusetts Institute of Technology. All Rights Reserved. Signature of Author: _____________________________________________________________ Department of Chemistry January 11, 2021 Certified By: ___________________________________________________________________ Laura L. Kiessling Novartis Professor of Chemistry Thesis Supervisor Accepted By: ___________________________________________________________________ Adam P. Willard Associate Professor of Chemistry Chair, Department Committee on Graduate Students 1 This doctoral thesis has been examined by a committee of professors from the Department of Chemistry as follows: Barbara Imperiali _______________________________________________________________ Thesis Committee Chair Class of 1922 Professor of Biology and Chemistry Laura L. Kiessling _______________________________________________________________ Thesis Supervisor Novartis Professor of Chemistry Ronald T. Raines ________________________________________________________________ Thesis Committee Member Roger and Georges Firmenich Professor of Natural Products Chemistry Eric J. Alm ____________________________________________________________________ -
Functional Comparison of Bacteria from the Human Gut and Closely
RESEARCH ARTICLE Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment Dragana Dobrijevic¤, Anne-Laure Abraham, Alexandre Jamet, Emmanuelle Maguin, a11111 Maarten van de Guchte* Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France ¤ Current address: Department of Biochemical Engineering, University College London, London, WC1H 0AH, United Kingdom * [email protected] OPEN ACCESS Citation: Dobrijevic D, Abraham A-L, Jamet A, Abstract Maguin E, van de Guchte M (2016) Functional Comparison of Bacteria from the Human Gut and The human GI tract is a complex and still poorly understood environment, inhabited by Closely Related Non-Gut Bacteria Reveals the one of the densest microbial communities on earth. The gut microbiota is shaped by mil- Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment. lennia of evolution to co-exist with the host in commensal or symbiotic relationships. Mem- PLoS ONE 11(7): e0159030. doi:10.1371/journal. bers of the gut microbiota perform specific molecular functions important in the human gut pone.0159030 environment. This can be illustrated by the presence of a highly expanded repertoire of Editor: Francesco Cappello, University of Palermo, proteins involved in carbohydrate metabolism, in phase with the large diversity of polysac- ITALY charides originating from the diet or from the host itself that can be encountered in this Received: April 15, 2016 environment. In order to identify other bacterial functions that are important in the human Accepted: June 24, 2016 gut environment, we investigated the distribution of functional groups of proteins in a group of human gut bacteria and their close non-gut relatives.