DOCSLIB.ORG

Ruminococcaceae Genus Bacteroides Anaerotruncus Species B

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Cultivating Changing Gut Microbial Communities Lauri O. Byerley, RDN, LDN, FAND Associate Professor Louisiana State University Health Sciences Center Department of Physiology Disclaimer Research Funding Through the Years: • NCI • NIAAA • US Army • American Institute of Cancer Research • California Walnut Commission • American Public University • Louisiana State University Health Sciences Center Hippocrates….”All Diseases begin in the gut” Collaborators: DAVID WELSH CHRISTOPHER TAYLOR BRITTANY LORENZO SHELIA BANKS MENG LUO MONICA PONDER (VIRGINIA TECH) EUGENE BLANCHARD Seminar Layout • Learning objectives • Definition of terms • Introduction • Microbe view of the gut • Why cultivating microbes is important • Detecting gut microbes • Feeding our gut microbes • Proof of concept – Can we cultivate specific microbes? • Summary Learning Objectives • Diagram the GI tract from a microbe’s perspective • Describe why we should cultivate gut microbes • Explain the process by which microbes are detected • Produce a list of several different fiber types and several foods/ingredients associated with each fiber type • Describe alterations in gut microbiota following dietary changes • List the most appropriate foods to cultivate our gut microbiome Definition of Terms • Microbiota – a collection or community of microbes. Includes bacteria, fungi, archaea and viruses • Microbiome – refers to the genomes of all the microbes in a community • Metagenomics ‐ a technique that reveals biological functions of an entire community • Metabolomics – measurement of metabolites https://media.npr.org/assets/img/2016/08 /09/e‐coli_wide‐ b2909f1ef2e257a4c5fa01112174ab941c24 7871‐s800‐c85.jpg Introduction • We are more bacteria than human… • More bacteria in and on our body than human cells • Healthy human has approximately 40 trillion bacteria in gut • 500 to 1,000 species encompassing 10,000 strains • Humans – 23,000 genes • Microbiome – estimated 3,300,000 genes (150 fold more) • Mutual relationship http://www.global‐engage.com/wp‐content/uploads/2017/04/human‐microbiome‐NGS.jpg Microbiome – “Human Organ” • Weight ‐ approximately 1‐2 kg • No distinct structure ‐ organized system of cells like the immune system • Each person has a unique microbiome • So unique we may be able to track forensically http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1500832/ Microbes view of our gut • Major barriers for microbes entering the gut: • low pH • Saliva • Bile • Immune system • Finding a place to attach to intestinal wall • Surviving a widely varied diet https://elearning.kullabs.com/img/note_images/b7nZNAW6sMPqqMTg.jpg Keep these things in mind when cultivating our gut microbiome Microbial Biomass & pH Figure 1(A) Small intestine mucosal immune system landscape. M Zaeem Cader, and Arthur Kaser Gut 2013;62:1653-1664 Figure 1(B) Colon (large intestine) mucosal immune system. M Zaeem Cader, and Arthur Kaser Gut 2013;62:1653-1664 What is happening in the gut? For those microbes that manage to colonize the gut: • gut flora perform regular tasks of digestion, vitamin production, many others • Gene transfer between the myriad of species in the gut can generate new combinations including ones resistant to drugs “superbugs” https://i2.wp.com/thescientificparent.or g/wp‐content/uploads/2017/03/GI‐ Tract‐Small.png?fit=816%2C971&ssl=1 Why is Cultivating Important? Many Functions of Our Gut Bacteria https://www.researchgate.net/profile/Brigitta_Brinkman/publication/281518789/figure/fig1/AS:313058971930624@1451650483890/Main‐functions‐of‐bacteria‐in‐the‐gut‐ Bacteria‐benefit‐the‐host‐in‐many‐ways‐Besides.png Who Are the Players? Scientific Classification or Taxonomic Rank • Don’t get hung up on this – just know it exists • King Play Chess On Fine Green Silk • 3 Kingdoms: • Bacteria • Archaea King Play • Eukaryota Chess Kingdom Bacteria Bacteria On Fine Phylum Bacteriodetes Firmicutes Green Class Bacteriodetes Clostridia Silk Order Bacteriodales Clostridiales Family Bacteroidaceae Ruminococcaceae Genus Bacteroides Anaerotruncus Species B. fragilis A. colihominis Methods • We cannot grow most bacteria in the lab • We must detect DNA • Fecal samples collected from the descending colon • DNA isolated • V3 hypervariable region of 16S rRNA gene deep sequenced on an Illumina MiSeq. • Data analyzed using the UPARSE and QIIME pipeline and SAS. Species Name LOB1NTBMCA LOB1PFW LOB2PFW None;Other;Other;Other;Other;Other;Other 00 0 k__Bacteria;Other;Other;Other;Other;Other;Other 0.004396 0.001905 0.003637 k__Bacteria;p__Actinobacteria;Other;Other;Other;Other;Other 7.14E‐05 0 0.000222 k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;Other;Other;Other 0 0 0 k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces;Other 0 0 0 k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium;s__ 0 0.000159 0 • Excel spreadsheet with numbers • Use these numbers to determine significant differences http://learn.genetics.utah.edu/content/microbiome/study/image How to analyze data? s/microbesdoing.jpg Fig. 4 Alpha diversity: species richness (number of taxa) within a single microbial ecosystem. How many different microbial species could be detected in one sample? Beta diversity: diversity in microbial community between different environments (difference in taxonomic abundance profiles from different samples). How different is the microbial composition in one environment compared to another? https://www.researchgate.net/profile/Patrice_Cani/publication/2Atherosclerosis 2018 268, 117-126DOI:81288066/figure/fig5/AS:271086130561031@1441643378758/Mice‐Fed‐ (10.1016/j.atherosclerosis.2017.11.023) a‐Lard‐Diet‐Have‐Increased‐Adiposity‐ and‐Distinct‐Gut‐Microbiota‐Composition.png Microbe Communities • Microbes act in communities • Microbes react to their surroundings • Shift when the environment changes • Change quickly http://learn.genetics.utah.edu/conte nt/microbiome/intro/images/microb es.jpg Factors Affect Human Gut Microbiome • Age • Activity/Exercise • Emotional State/Stress • Diet • Gender • Climate • Occupation • Hygiene • Antibiotics • Medications • Living with animals • Where you live • Diurnal Variation http://learn.genetics.utah.edu/content/microbiome/changing/images/change6.jpg Diet is a big player for the gut microbiome Diet Influences the Gut Microbiome • We acquire microbiome at birth • Long‐term diet effects: Bacteroides (Genus) Prevotella (Genus) Diet (Phyla ‐ Bacteriodetes) (Phyla – Baceriodetes) High animal protein, high fat, low High Low carbohydrate (Atkins, Paleo) High carbohydrates, low animal Low High protein, low fat • Japanese harbor organisms that aids in seaweed digestion • African children – high Bacteroidetes and deplete of Firmicutes to maximize energy uptake from fiber‐rich diet • vegetarians have gut flora that are better equipped to break down plant roughage, making otherwise indigestible molecules such as cellulose available for humans Scientific Evidence – Diet Influences Gut Microbiome Carnivore Omnivore Hervifore Meugge BD et al. Science. 2011 May 20; 332(6032): 970–974. Partitioning of People Into Enterotypes • Difficult studies because increases in one macronutrient typically associated with decrease in another • Higher complex carbohydrate diet – more Prevotella • Higher fat/protein diet – more Bacteroides Wu GD, et al. Science 334:105, 2011 Macronutrient composition rapidly impacts microbiome Changes within 24 hours Wu GD et al. Science. 2011 Oct 7; 334(6052): 105–108. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368382/ Macronutrient composition rapidly impacts microbiome Plant‐based Animal‐based Diet Diet Similarity of each individual’s gut microbiota to their baseline communities (β‐diversity, Jensen‐Shannon distance) decreased on the animal‐based diet (dates with q<0.05 identified with asterisks; Bonferroni‐corrected, two‐sided Mann‐Whitney U test). David, LA Et al Nature. 2014 Jan 23; 505(7484): Community differences were apparent one day after a tracing dye 559–563. showed the animal‐based diet reached the gut (blue arrows depict https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957 appearance of food dyes added to first and last diet day meals 428/bin/nihms536070f1.jpg Scientific Evidence ‐ Diet Influences Gut Microbiome 16S rRNA gene surveys reveal a clear separation of two children populations investigated. BF = Children from a rural African village of Burkina Faso (BF) Diet is • low in fat and animal protein • rich in starch, fiber, and plant polysaccharides • predominantly vegetarian EU = European children Diet is • typical western diet high in animal protein, sugar, starch, and fat • low in fiber. Carlotta De Filippo et al. PNAS 2010;107:33:14691-14696 ©2010 by National Academy of Sciences Diet Influences Microbiome • Changes occur rapidly ‐ within 24 hours of eating a high fat/low fiber or low fat/high fiber diet • Changes are significant • Changes are modest • Changes only last for at least 10 days The adult gut microbiome is characterized as existing in a steady state that requires a major disturbance to permanently alter that Microbiome is strongly associated state. Short-term diet interventions may transiently alter the gut microbiome community with long‐term diet. structure, but long-term diet changes are required to shift to a new steady-state. Voreades N., Kozil, A, Weir TL. Front Microbiol. 2014; 5: 494. What is our microbes favorite food? Fiber Dietary Fiber: Non-digestible soluble and insoluble carbohydrates ( > 3 monomeric units), and lignin
Recommended publications
  • Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis

    Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis

    International Journal of Molecular Sciences Review Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis David Johane Machate 1, Priscila Silva Figueiredo 2 , Gabriela Marcelino 2 , Rita de Cássia Avellaneda Guimarães 2,*, Priscila Aiko Hiane 2 , Danielle Bogo 2, Verônica Assalin Zorgetto Pinheiro 2, Lincoln Carlos Silva de Oliveira 3 and Arnildo Pott 1 1 Graduate Program in Biotechnology and Biodiversity in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; [email protected] (D.J.M.); [email protected] (A.P.) 2 Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; pri.fi[email protected] (P.S.F.); [email protected] (G.M.); [email protected] (P.A.H.); [email protected] (D.B.); [email protected] (V.A.Z.P.) 3 Chemistry Institute, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; [email protected] * Correspondence: [email protected]; Tel.: +55-67-3345-7416 Received: 9 March 2020; Accepted: 27 March 2020; Published: 8 June 2020 Abstract: Long-term high-fat dietary intake plays a crucial role in the composition of gut microbiota in animal models and human subjects, which affect directly short-chain fatty acid (SCFA) production and host health. This review aims to highlight the interplay of fatty acid (FA) intake and gut microbiota composition and its interaction with hosts in health promotion and obesity prevention and its related metabolic dysbiosis.
  • Appendix III: OTU's Found to Be Differentially Abundant Between CD and Control Patients Via Metagenomeseq Analysis

    Appendix III: OTU's Found to Be Differentially Abundant Between CD and Control Patients Via Metagenomeseq Analysis

    Appendix III: OTU's found to be differentially abundant between CD and control patients via metagenomeSeq analysis OTU Log2 (FC CD / FDR Adjusted Phylum Class Order Family Genus Species Number Control) p value 518372 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 2.16 5.69E-08 194497 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.15 8.93E-06 175761 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 5.74 1.99E-05 193709 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.40 2.14E-05 4464079 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides NA 7.79 0.000123188 20421 Firmicutes Clostridia Clostridiales Lachnospiraceae Coprococcus NA 1.19 0.00013719 3044876 Firmicutes Clostridia Clostridiales Lachnospiraceae [Ruminococcus] gnavus -4.32 0.000194983 184000 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 2.81 0.000306032 4392484 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides NA 5.53 0.000339948 528715 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 2.17 0.000722263 186707 Firmicutes Clostridia Clostridiales NA NA NA 2.28 0.001028539 193101 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 1.90 0.001230738 339685 Firmicutes Clostridia Clostridiales Peptococcaceae Peptococcus NA 3.52 0.001382447 101237 Firmicutes Clostridia Clostridiales NA NA NA 2.64 0.001415109 347690 Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillospira NA 3.18 0.00152075 2110315 Firmicutes Clostridia
  • Development of the Equine Hindgut Microbiome in Semi-Feral and Domestic Conventionally-Managed Foals Meredith K

    Development of the Equine Hindgut Microbiome in Semi-Feral and Domestic Conventionally-Managed Foals Meredith K

    Tavenner et al. Animal Microbiome (2020) 2:43 Animal Microbiome https://doi.org/10.1186/s42523-020-00060-6 RESEARCH ARTICLE Open Access Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals Meredith K. Tavenner1, Sue M. McDonnell2 and Amy S. Biddle1* Abstract Background: Early development of the gut microbiome is an essential part of neonate health in animals. It is unclear whether the acquisition of gut microbes is different between domesticated animals and their wild counterparts. In this study, fecal samples from ten domestic conventionally managed (DCM) Standardbred and ten semi-feral managed (SFM) Shetland-type pony foals and dams were compared using 16S rRNA sequencing to identify differences in the development of the foal hindgut microbiome related to time and management. Results: Gut microbiome diversity of dams was lower than foals overall and within groups, and foals from both groups at Week 1 had less diverse gut microbiomes than subsequent weeks. The core microbiomes of SFM dams and foals had more taxa overall, and greater numbers of taxa within species groups when compared to DCM dams and foals. The gut microbiomes of SFM foals demonstrated enhanced diversity of key groups: Verrucomicrobia (RFP12), Ruminococcaceae, Fusobacterium spp., and Bacteroides spp., based on age and management. Lactic acid bacteria Lactobacillus spp. and other Lactobacillaceae genera were enriched only in DCM foals, specifically during their second and third week of life. Predicted microbiome functions estimated computationally suggested that SFM foals had higher mean sequence counts for taxa contributing to the digestion of lipids, simple and complex carbohydrates, and protein.
  • WO 2018/064165 A2 (.Pdf)

    WO 2018/064165 A2 (.Pdf)

    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/064165 A2 05 April 2018 (05.04.2018) W !P O PCT (51) International Patent Classification: Published: A61K 35/74 (20 15.0 1) C12N 1/21 (2006 .01) — without international search report and to be republished (21) International Application Number: upon receipt of that report (Rule 48.2(g)) PCT/US2017/053717 — with sequence listing part of description (Rule 5.2(a)) (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 62/400,372 27 September 2016 (27.09.2016) US 62/508,885 19 May 2017 (19.05.2017) US 62/557,566 12 September 2017 (12.09.2017) US (71) Applicant: BOARD OF REGENTS, THE UNIVERSI¬ TY OF TEXAS SYSTEM [US/US]; 210 West 7th St., Austin, TX 78701 (US). (72) Inventors: WARGO, Jennifer; 1814 Bissonnet St., Hous ton, TX 77005 (US). GOPALAKRISHNAN, Vanch- eswaran; 7900 Cambridge, Apt. 10-lb, Houston, TX 77054 (US). (74) Agent: BYRD, Marshall, P.; Parker Highlander PLLC, 1120 S. Capital Of Texas Highway, Bldg. One, Suite 200, Austin, TX 78746 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
  • Download (PDF)

    Download (PDF)

    Supplemental Table 1. OTU (Operational Taxonomic Unit) level taxonomic analysis of gut microbiota Case-control Average ± STDEV (%) Wilcoxon OTU Phylum Class Order Family Genus Patient (n = 15) Control (n = 16) p OTU_366 Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillospira 0.0189 ± 0.0217 0.00174 ± 0.00429 0.004** OTU_155 Firmicutes Clostridia Clostridiales Ruminococcaceae Ruminococcus 0.0554 ± 0.0769 0.0161 ± 0.0461 0.006** OTU_352 Firmicutes Clostridia Clostridiales Ruminococcaceae Ruminococcus 0.0119 ± 0.0111 0.00227 ± 0.00413 0.007** OTU_719 Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillospira 0.00150 ± 0.00190 0.000159 ± 0.000341 0.007** OTU_620 Firmicutes Clostridia Clostridiales Ruminococcaceae Unclassified 0.00573 ± 0.0115 0.0000333 ± 0.000129 0.008** OTU_47 Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnospira 1.44 ± 2.04 0.183 ± 0.337 0.011* OTU_769 Firmicutes Clostridia Clostridiales Ruminococcaceae Unclassified 0.000857 ± 0.00175 0 0.014* OTU_747 Firmicutes Clostridia Clostridiales Ruminococcaceae Anaerotruncus 0.000771 ± 0.00190 0 0.014* OTU_748 Firmicutes Clostridia Clostridiales Ruminococcaceae Unclassified 0.0135 ± 0.0141 0.00266 ± 0.00420 0.015* OTU_81 Bacteroidetes Bacteroidia Bacteroidales [Barnesiellaceae] Unclassified 0.434 ± 0.436 0.0708 ± 0.126 0.017* OTU_214 Firmicutes Clostridia Clostridiales Ruminococcaceae Unclassified 0.0254 ± 0.0368 0.00496 ± 0.00959 0.020* OTU_113 Actinobacteria Coriobacteriia Coriobacteriales Coriobacteriaceae Unclassified 0 0.189 ± 0.363 0.021* OTU_100 Bacteroidetes
  • The Isolation of Novel Lachnospiraceae Strains and the Evaluation of Their Potential Roles in Colonization Resistance Against Clostridium Difficile

    The Isolation of Novel Lachnospiraceae Strains and the Evaluation of Their Potential Roles in Colonization Resistance Against Clostridium Difficile

    The isolation of novel Lachnospiraceae strains and the evaluation of their potential roles in colonization resistance against Clostridium difficile Diane Yuan Wang Honors Thesis in Biology Department of Ecology and Evolutionary Biology College of Literature, Science, & the Arts University of Michigan, Ann Arbor April 1st, 2014 Sponsor: Vincent B. Young, M.D., Ph.D. Associate Professor of Internal Medicine Associate Professor of Microbiology and Immunology Medical School Co-Sponsor: Aaron A. King, Ph.D. Associate Professor of Ecology & Evolutionary Associate Professor of Mathematics College of Literature, Science, & the Arts Reader: Blaise R. Boles, Ph.D. Assistant Professor of Molecular, Cellular and Developmental Biology College of Literature, Science, & the Arts 1 Table of Contents Abstract 3 Introduction 4 Clostridium difficile 4 Colonization Resistance 5 Lachnospiraceae 6 Objectives 7 Materials & Methods 9 Sample Collection 9 Bacterial Isolation and Selective Growth Conditions 9 Design of Lachnospiraceae 16S rRNA-encoding gene primers 9 DNA extraction and 16S ribosomal rRNA-encoding gene sequencing 10 Phylogenetic analyses 11 Direct inhibition 11 Bile salt hydrolase (BSH) detection 12 PCR assay for bile acid 7α-dehydroxylase detection 12 Tables & Figures Table 1 13 Table 2 15 Table 3 21 Table 4 25 Figure 1 16 Figure 2 19 Figure 3 20 Figure 4 24 Figure 5 26 Results 14 Isolation of novel Lachnospiraceae strains 14 Direct inhibition 17 Bile acid physiology 22 Discussion 27 Acknowledgments 33 References 34 2 Abstract Background: Antibiotic disruption of the gastrointestinal tract’s indigenous microbiota can lead to one of the most common nosocomial infections, Clostridium difficile, which has an annual cost exceeding $4.8 billion dollars.
  • The Gut Microbiota and Disease

    The Gut Microbiota and Disease

    The Gut Microbiota and Disease: Segmented Filament Bacteria Exacerbates Kidney Disease in a Lupus Mouse Model Armin Munir1, Giancarlo Valiente1,2, Takuma Wada3, Jeffrey Hampton1, Lai-Chu Wu1,4, Aharon Freud5,6, Wael Jarjour1 1Division of Rheumatology and Immunology, The Ohio State Wexner Medical Center, 2Medical Scientist Training Program, The Ohio State University College of Medicine, 3Rheumatology and Applied Immunology, Saitama Medical University, 4Department of Biological Chemistry and Pharmacology, The Ohio State University, 5The James Cancer Hospital and Solove Research Institute, 6Department of Pathology, The Ohio State Wexner Medical Center Introduction Increased Glomerulonephritis in +SFB Mice ↑Inflammatory Cytokine Levels in +SFB Mice Gut Microbiome 16S rRNA Heat Map 15 weeks old 30 weeks old -SFB +SFB -SFB +SFB Background: -SFB +SFB Commensal organisms are a vital component to the host organism. A B C Lachnoclostridium uncultured bacterium Segmented Filament Bacteria (SFB) is a commensal bacterium found Lachnospiraceae NC2004 group uncultured bacterium A Lachnospiraceae NK4A136 group uncultured bacterium in many animal species. SFB has been shown to exacerbate Roseburia uncultured bacterium Ruminiclostridium 6 uncultured bacterium inflammatory arthritis but has not been implicated in Systemic Lupus Anaerostipes ambiguous taxa Lachnoclostridium ambiguous taxa Erythematosus (SLE). The focus of our study was to understand the Lachnospiraceae GCA-9000066575 uncultured bacterium Family XIII AD3011 group ambiguous taxa broader relationship
  • PDF 2672 Kb) Additional File 4: Figure S2

    PDF 2672 Kb) Additional File 4: Figure S2

    Schnorr et al. BMC Microbiology (2019) 19:164 https://doi.org/10.1186/s12866-019-1540-5 RESEARCHARTICLE Open Access Taxonomic features and comparisons of the gut microbiome from two edible fungus-farming termites (Macrotermes falciger; M. natalensis) harvested in the Vhembe district of Limpopo, South Africa Stephanie L. Schnorr1,2,3,4* , Courtney A. Hofman2,3, Shandukani R. Netshifhefhe5,6, Frances D. Duncan5, Tanvi P. Honap2,3, Julie Lesnik7† and Cecil M. Lewis2,3*† Abstract Background: Termites are an important food resource for many human populations around the world, and are a good supply of nutrients. The fungus-farming ‘higher’ termite members of Macrotermitinae are also consumed by modern great apes and are implicated as critical dietary resources for early hominins. While the chemical nutritional composition of edible termites is well known, their microbiomes are unexplored in the context of human health. Here we sequenced the V4 region of the 16S rRNA gene of gut microbiota extracted from the whole intestinal tract of two Macrotermes sp. soldiers collected from the Limpopo region of South Africa. Results: Major and minor soldier subcastes of M. falciger exhibit consistent differences in taxonomic representation, and are variable in microbial presence and abundance patterns when compared to another edible but less preferred species, M. natalensis. Subcaste differences include alternate patterns in sulfate-reducing bacteria and methanogenic Euryarchaeota abundance, and differences in abundance between Alistipes and Ruminococcaceae. M. falciger minor soldiers and M. natalensis soldiers have similar microbial profiles, likely from close proximity to the termite worker castes, particularly during foraging and fungus garden cultivation.
  • The Impact of Tiny Organisms: Microbial Communities and Disease States

    The Impact of Tiny Organisms: Microbial Communities and Disease States

    University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2016 The Impact of Tiny Organisms: Microbial Communities and Disease States Christel Sjöland Chehoud University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Microbiology Commons Recommended Citation Chehoud, Christel Sjöland, "The Impact of Tiny Organisms: Microbial Communities and Disease States" (2016). Publicly Accessible Penn Dissertations. 1645. https://repository.upenn.edu/edissertations/1645 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1645 For more information, please contact [email protected]. The Impact of Tiny Organisms: Microbial Communities and Disease States Abstract In the last decade, primarily through the use of sequencing, much has been learned about the trillions of microorganisms that reside in human hosts. These microorganisms play a wide range of roles including helping our immune systems develop, digesting our food, and protecting us from the invasion of pathogenic organisms. My thesis focuses on the characterization of fungal, viral, and bacterial communities in humans, investigating the use of defined microbial communities to cure diseases in animal models, and examining the effects of human microbiome modifications through fecal microbiota transfers. In the first part of this thesis, I use deep sequencing of ribosomal RNA gene tags to characterize the composition of the bacterial, fungal, and archaeal microbiota in pediatric patients with Inflammatory Bowel Disease and healthy controls. Archaeal reads were rare in the pediatric samples, whereas an abundant amount of fungal reads was recovered. Pediatric IBD was found to be associated with reduced diversity in both fungal and bacterial gut microbiota, and specific Candida taxa were increased in abundance in the IBD samples.
  • Faecalibacterium Prausnitzii: from Microbiology to Diagnostics and Prognostics

    Faecalibacterium Prausnitzii: from Microbiology to Diagnostics and Prognostics

    The ISME Journal (2017) 11, 841–852 © 2017 International Society for Microbial Ecology All rights reserved 1751-7362/17 www.nature.com/ismej MINI REVIEW Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics Mireia Lopez-Siles1, Sylvia H Duncan2, L Jesús Garcia-Gil1 and Margarita Martinez-Medina1 1Laboratori de Microbiologia Molecular, Departament de Biologia, Universitat de Girona, Girona, Spain and 2Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK There is an increasing interest in Faecalibacterium prausnitzii, one of the most abundant bacterial species found in the gut, given its potentially important role in promoting gut health. Although some studies have phenotypically characterized strains of this species, it remains a challenge to determine which factors have a key role in maintaining the abundance of this bacterium in the gut. Besides, phylogenetic analysis has shown that at least two different F. prausnitzii phylogroups can be found within this species and their distribution is different between healthy subjects and patients with gut disorders. It also remains unknown whether or not there are other phylogroups within this species, and also if other Faecalibacterium species exist. Finally, many studies have shown that F. prausnitzii abundance is reduced in different intestinal disorders. It has been proposed that F. prausnitzii monitoring may therefore serve as biomarker to assist in gut diseases diagnostics. In this mini- review, we aim to serve as an overview of F. prausnitzii phylogeny, ecophysiology and diversity. In addition, strategies to modulate the abundance of F. prausnitzii in the gut as well as its application as a biomarker for diagnostics and prognostics of gut diseases are discussed.
  • Meta Analysis of Microbiome Studies Identifies Shared and Disease

    Meta Analysis of Microbiome Studies Identifies Shared and Disease

    bioRxiv preprint doi: https://doi.org/10.1101/134031; this version posted May 8, 2017. 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 4.0 International license. Meta analysis of microbiome studies identifies shared and disease-specific patterns Claire Duvallet1,2, Sean Gibbons1,2,3, Thomas Gurry1,2,3, Rafael Irizarry4,5, and Eric Alm1,2,3,* 1Department of Biological Engineering, MIT 2Center for Microbiome Informatics and Therapeutics 3The Broad Institute of MIT and Harvard 4Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute 5Department of Biostatistics, Harvard T.H. Chan School of Public Health *Corresponding author, [email protected] Contents 1 Abstract2 2 Introduction3 3 Results4 3.1 Most disease states show altered microbiomes ........... 5 3.2 Loss of beneficial microbes or enrichment of pathogens? . 5 3.3 A core set of microbes associated with health and disease . 7 3.4 Comparing studies within and across diseases separates signal from noise ............................... 9 4 Conclusion 10 5 Methods 12 5.1 Dataset collection ........................... 12 5.2 16S processing ............................ 12 5.3 Statistical analyses .......................... 13 5.4 Microbiome community analyses . 13 5.5 Code and data availability ...................... 13 6 Table and Figures 14 1 bioRxiv preprint doi: https://doi.org/10.1101/134031; this version posted May 8, 2017. 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.
  • Effect of Fructans, Prebiotics and Fibres on the Human Gut Microbiome Assessed by 16S Rrna-Based Approaches: a Review

    Effect of Fructans, Prebiotics and Fibres on the Human Gut Microbiome Assessed by 16S Rrna-Based Approaches: a Review

    Wageningen Academic Beneficial Microbes, 2020; 11(2): 101-129 Publishers Effect of fructans, prebiotics and fibres on the human gut microbiome assessed by 16S rRNA-based approaches: a review K.S. Swanson1, W.M. de Vos2,3, E.C. Martens4, J.A. Gilbert5,6, R.S. Menon7, A. Soto-Vaca7, J. Hautvast8#, P.D. Meyer9, K. Borewicz2, E.E. Vaughan10* and J.L. Slavin11 1Division of Nutritional Sciences, University of Illinois at Urbana-Champaign,1207 W. Gregory Drive, Urbana, IL 61801, USA; 2Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, the Netherlands; 3Human Microbiome Research Programme, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, 00014, Helsinki, Finland; 4Department of Microbiology and Immunology, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, MI 48130, USA; 5Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL 60637, USA; 6Bioscience Division, Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL 60439, USA; 7The Bell Institute of Health and Nutrition, General Mills Inc., 9000 Plymouth Ave N, Minneapolis, MN 55427, USA; 8Division Human Nutrition, Department Agrotechnology and Food Sciences, P.O. Box 17, 6700 AA, Wageningen University; 9Nutrition & Scientific Writing Consultant, Porfierdijk 27, 4706 MH Roosendaal, the Netherlands; 10Sensus (Royal Cosun), Oostelijke Havendijk 15, 4704 RA, Roosendaal, the Netherlands; 11Department of Food Science and Nutrition, University of Minnesota, 1334 Eckles Ave, St. Paul, MN 55108, USA; [email protected]; #Emeritus Professor Received: 27 May 2019 / Accepted: 15 December 2019 © 2020 Wageningen Academic Publishers OPEN ACCESS REVIEW ARTICLE Abstract The inherent and diverse capacity of dietary fibres, nondigestible oligosaccharides (NDOs) and prebiotics to modify the gut microbiota and markedly influence health status of the host has attracted rising interest.