DOCSLIB.ORG

Effects of Commercial Feed Additives on the Gut Microbiota of Food

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

EFFECTS OF COMMERCIAL FEED ADDITIVES ON THE GUT MICROBIOTA OF FOOD ANIMALS BY PRAKASH POUDEL A dissertation submitted in partial fulfillment of the requirements for the Doctor of Philosophy Major in Animal Science South Dakota State University 2019 DocuSign Envelope ID: 33CCE236-EF21-4AF6-8A80-6DC42FC018CE ii DISSERTATION ACCEPTANCE PAGE Prakash Poudel This dissertation is approved as a creditable and independent investigation by a candidate for the Doctor of Philosophy degree and is acceptable for meeting the dissertation requirements for this degree. Acceptance of this does not imply that the conclusions reached by the candidate are necessarily the conclusions of the major department. Benoit St-Pierre Advisor Date Joseph P Cassady Department Head Date Dean, Graduate School Date iii ACKNOWLEDGEMENT First of all, I would like to express my thanks to my advisor, Dr. Benoit St-Pierre, for accepting me as a PhD student in your team and providing me the valuable guidance, encouragement, support and knowledge throughout the study of my PhD at South Dakota State University. I extremely felt fortunate to have a professor like you who cared so much about my research activities, always responded my queries, and supported to execute laboratory works in no time. The journey of my study was possible due to your patience and encouragement. You taught me to be an expert on microbiota and a true researcher. Many thanks again for your guidance towards my future career. I am also indebted to receive a great support from my supervisory committee members, Dr. Crystal Levesque, Dr. Joy Scaria, and Dr. Kunsoon Park. Thank you all for your time, directions, support, advices, and inputs towards my research projects. Special thank goes to Dr. Samuel Ryan for supporting on animal trial on Swine facility at SDSU. At this moment, I would also like to thank my previous advisor Dr. David Casper and fellow graduate students Kelly Froehlich and Subash Acharya for helping me to collect rumen samples from the calves on EO experiment. I really appreciate the support and assistance I got from my past and present lab colleagues Vinay, Lee, Angie and other graduate student for sampling and data analysis. I would also like to thank swine facility at SDSU for allowing me to carry out the nursery pig research. I would thankful to Vitech Bio-Chem Corporation, CA for providing the funding of two Peptiva experiments carried out on piglets. iv Finally, I would like to express my heartful gratitude to my beloved wife Kalpana, daughter Anweshi, and son Ayansh, and other family members for their endless support, patience, understanding, and love throughout my study period without which this great accomplishment would not have been possible. Thank you for all those and love you so much. v TABLE OF CONTENTS LIST OF ABBREVIATIONS…………………………………………..……………......xi LIST OF FIGURES……………………………………………….……..……………...xiii LIST OF TABLES……………………………………………………..…………...…...xiv ABSTRACT…………………………………………………………………………….xvi Chapter 1: Literature Review ……………………………………………………………..1 1. Meeting the Food Demand of a Growing World Population .....................................2 1.1 Current Situation and Future Outlook .................................................................2 1.2 Role of the livestock sector .................................................................................3 2. Challenges for livestock production: health and welfare of young animals ...............5 2.1 Overview of challenges.......................................................................................5 2.2 Dairy production .................................................................................................6 2.3 Swine production .............................................................................................. 10 3. The gut microbiome ............................................................................................... 12 3.1 Importance........................................................................................................ 12 3.2 Rumen Microbial ecology ................................................................................. 14 3.3 Microbial succession in the gastrointestinal tract ............................................... 15 3.4 Eubiosis vs dysbiosis ........................................................................................ 17 4. Manipulating the gut microbiome ........................................................................... 18 4.1 Antibiotics ........................................................................................................ 19 vi 4.2 Essential oils ..................................................................................................... 21 4.3 Peptides ............................................................................................................ 26 4.4 Enzymes as supplements in animal feed ............................................................ 29 4.5 Prebiotics in animal diets .................................................................................. 32 5. Hypothesis and Research Objectives ...................................................................... 33 References ................................................................................................................. 34 Chapter 2: Feeding essential oils to neonatal Holstein dairy calves results in increased ruminal Prevotellaceae abundance and propionate concentrations…………...57 Abstract ..................................................................................................................... 58 2. Materials and Methods ........................................................................................ 61 2.1 Sample collection ............................................................................................. 61 2.2 SCFA analysis .................................................................................................. 62 2.3 Microbial DNA isolation and PCR amplification .............................................. 63 2.4 Computational analysis of PCR generated 16S rRNA amplicon sequences ....... 64 2.5 Computational analysis for alpha and beta diversity .......................................... 65 2.6 Statistical Analyses ........................................................................................... 66 3. Results ................................................................................................................ 66 3.1 Comparative analysis of ruminal SCFA between EO supplemented and non-supplemented diets .......................................................................................... 66 vii 3.2 Effects of EO on the taxonomic composition of ruminal bacteria in growing calves ..................................................................................................................... 67 3.3 Effects of EO on the ruminal bacterial community structure in growing calves . 68 3.4 Identification of potential associations between main OTUs and ruminant performance parameters .......................................................................................... 69 4. Discussion .......................................................................................................... 71 5. Conclusion .......................................................................................................... 76 References ................................................................................................................. 85 Chapter 3: Dietary inclusion of a peptide-based feed additive can accelerate the maturation of the fecal bacterial microbiome in weaned pigs……………..…………….93 Abstract ..................................................................................................................... 94 1. Introduction ........................................................................................................ 96 2. Materials and Methods ........................................................................................ 99 2.1 Animal performance trial and sample collection................................................ 99 2.2 Microbial DNA isolation and PCR amplification of the 16S rRNA gene ......... 101 2.3 Computational analysis of PCR generated 16S rRNA amplicon sequences ..... 101 2.4 Statistical analyses .......................................................................................... 103 3. Results .............................................................................................................. 104 3.1 Effect of low inclusion of Peptiva on swine performance during the nursery phase .................................................................................................................... 104 viii 3.2 Effect of diet composition and Peptiva supplementation on the fecal bacterial profile of weaned pigs .......................................................................................... 104 3.3 Comparative analysis of fecal bacterial composition by alpha and beta diversity ............................................................................................................................. 105 3.4 Identification of weaned pig OTUs responding to distinct dietary treatments .. 106 3.5 Associations between main OTUs and dietary treatments................................ 107 4. Discussion ........................................................................................................ 107 4.1 Bacterial succession from Lactobacillaceae
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.
  • Bovine Host Genome Acts on Speci C Metabolism, Communication and Genetic Processes of Rumen Microbes Host-Genomically Linked To

    Bovine Host Genome Acts on Speci C Metabolism, Communication and Genetic Processes of Rumen Microbes Host-Genomically Linked To

    Bovine host genome acts on specic metabolism, communication and genetic processes of rumen microbes host-genomically linked to methane emissions Marina Martínez-Álvaro SRUC https://orcid.org/0000-0003-2295-5839 Marc Auffret SRUC Carol-Anne Duthie SRUC Richard Dewhurst SRUC Matthew Cleveland Genus plc Mick Watson Roslin Institute https://orcid.org/0000-0003-4211-0358 Rainer Roehe ( [email protected] ) SRUC https://orcid.org/0000-0002-4880-3756 Article Keywords: bovine host genome, rumen, CH4 Posted Date: May 17th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-290150/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License 1 Bovine host genome acts on specific metabolism, communication and 2 genetic processes of rumen microbes host-genomically linked to methane 3 emissions 4 Marina Martínez-Álvaro1, Marc D. Auffret1, Carol-Anne Duthie1, Richard J. Dewhurst1, 5 Matthew A. Cleveland2, Mick Watson3 and Rainer Roehe*1 6 1Scotland’s Rural College, Edinburgh, UK 7 2Genus plc, DeForest, WI, USA 8 3The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of 9 Edinburgh, UK 10 11 *Corresponding author. Email: [email protected] 12 13 14 Introductory paragraph 15 Whereas recent studies in different species showed that the host genome shapes the microbial 16 community profile, our new research strategy revealed substantial host genomic control of 17 comprehensive functional microbial processes in the rumen of bovines by utilising microbial 18 gene profiles from whole metagenomic sequencing. Of 1,107/225/1,141 rumen microbial 19 genera/metagenome assembled uncultured genomes (RUGs)/genes identified, 203/16/352 20 were significantly (P<2.02 x10-5) heritable (0.13 to 0.61), revealing substantial variation in 21 host genomic control.
  • The Critical Role of Dietary Foliage in Maintaining the Gut Microbiome And

    The Critical Role of Dietary Foliage in Maintaining the Gut Microbiome And

    View metadata, citation and similar papers at core.ac.uk brought to you by CORE www.nature.com/scientificreportsprovided by IUPUIScholarWorks OPEN The critical role of dietary foliage in maintaining the gut microbiome and metabolome of folivorous Received: 31 May 2018 Accepted: 13 September 2018 sifakas Published: xx xx xxxx Lydia K. Greene 1,2, Erin A. McKenney3,4, Thomas M. O’Connell5 & Christine M. Drea1,2,3 The gut microbiome (GMB) of folivores metabolizes dietary fber into nutrients, including short- chain fatty acids (SCFAs); however, experiments probing the consequences of foliage quality on host GMBs are lacking. We therefore examined GMB structure and function via amplicon sequencing and Nuclear Magnetic Resonance spectroscopy in 31 captive sifakas (Propithecus coquereli) during dietary manipulations associated with husbandry. Supplementing standard diets with diverse foliage blends, versus with a single plant species, promoted more diverse GMBs, enriched for taxa implicated in plant-fber metabolism, but depleted in taxa implicated in starch metabolism and bile tolerance. The consumption of diverse blends was associated with greater concentrations of colonic SCFAs. Abundant foliage, via forest access, promoted compositionally distinct and more stable GMBs, but reduced concentrations of SCFAs, possibly refecting selection of high-quality leaves. In 11 subjects denied forest access, we examined the temporal pace of microbial shifts when supplemental foliage was abruptly switched between diverse blends and single species. The sifaka GMB responded within days, with community diversity and composition closely tracking foliage diversity. By providing experimental evidence that the folivore GMB is sensitive to minor changes in dietary foliage, we reveal the fragility of specialist GMBs, with implications for managing the wellbeing of endangered wildlife.
  • Individuality in Gut Microbiota Composition Is a Complex Polygenic Trait Shaped by Multiple Environmental and Host Genetic Factors

    Individuality in Gut Microbiota Composition Is a Complex Polygenic Trait Shaped by Multiple Environmental and Host Genetic Factors

    Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors Andrew K. Bensona,1, Scott A. Kellyb, Ryan Leggea, Fangrui Maa, Soo Jen Lowa, Jaehyoung Kima, Min Zhanga, Phaik Lyn Oha, Derrick Nehrenbergb, Kunjie Huab, Stephen D. Kachmanc, Etsuko N. Moriyamad, Jens Waltera, Daniel A. Petersona, and Daniel Pompb,e aDepartment of Food Science and Technology and Core for Applied Genomics and Ecology, University of Nebraska, Lincoln, NE 68583-0919; bDepartment of Genetics, Carolina Center for Genome Science, University of North Carolina, Chapel Hill, NC 27599-7545; cDepartment of Statistics, University of Nebraska, Lincoln, NE 68583-0963; dSchool of Biological Sciences and Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588-0118; and eDepartment of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7461 Edited by Trudy F. C. Mackay, North Carolina State University, Raleigh, NC, and approved September 8, 2010 (received for review June 10, 2010) In vertebrates, including humans, individuals harbor gut microbial to be multifactorial, with both environmental and genetic compo- communities whose species composition and relative proportions nents (11–13), and the contribution of the gut microbiota is cur- of dominant microbial groups are tremendously varied. Although rently viewed as an environmental factor (14). Although a number external and stochastic factors clearly contribute to the individu- of studies have suggested that composition of the gut microbiota ality of the microbiota, the fundamental principles dictating how may be subject to host genetic forces, existing evidence is conflicting environmental factors and host genetic factors combine to shape and confounded by the genetic diversity of vertebrate (especially this complex ecosystem are largely unknown and require system- human) populations and strong environmental effects (15–19).
  • The Effect of Early Life Nutrition on Rumen Microbial Community Development and Impact on Lifetime Performance in Ruminants

    The Effect of Early Life Nutrition on Rumen Microbial Community Development and Impact on Lifetime Performance in Ruminants

    Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and private study only. The thesis may not be reproduced elsewhere without the permission of the Author. THE EFFECT OF EARLY LIFE NUTRITION ON RUMEN MICROBIAL COMMUNITY DEVELOPMENT AND IMPACT ON LIFETIME PERFORMANCE IN RUMINANTS A thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy In Veterinary Sciences At Massey University Palmerston North New Zealand Omar Cristobal Carballo 2019 Abstract Manipulation of the rumen microbiota in adult ruminants has been intended to improve animal performance and decrease greenhouse gas emissions, but results have only shown a short- or non-lasting effect after intervention. Changes in the ruminal microbiota during rumen development have recently shown promising results in the short-term. Therefore, the purpose of the present body of work was to determine how dietary management and chemical interventions, during rumen development, modify the ruminal microbial community composition, and whether these changes affect rumen fermentation and development, and consequently, performance in the young ruminants. The objectives of this thesis were to: (i) evaluate the impact of early weaning on rumen development and function in artificially-reared lambs; (ii) characterize the impact of early weaning in lambs on the rumen microbiota in the first 16 weeks of life and examine the relationships between rumen microbiota composition and rumen fermentation profiles, rumen development and blood metabolites; (iii) assess whether contrasting feeding regimes in the first 7 months of life lead to an imprint in the rumen microbial community structure, fermentation profiles and methane emissions in the rumen of calves; (iv) and evaluate the effect of methane inhibitors on the rumen microbial community composition, fermentation pathways, and gas emissions in calves.
  • Determining the Culturability of the Rumen Bacterial Microbiome

    Determining the Culturability of the Rumen Bacterial Microbiome

    bs_bs_banner Determining the culturability of the rumen bacterial microbiome Christopher J. Creevey,1,2 William J. Kelly,3,4* list of cultured rumen isolates that are representative Gemma Henderson3,4 and Sinead C. Leahy3,4 of abundant, novel and core bacterial species in the 1Animal and Bioscience Research Department, Animal rumen. In addition, we have identified taxa, particu- and Grassland Research and Innovation Centre, larly within the phylum Bacteroidetes, where further Teagasc, Grange, Dunsany, Co. Meath, Ireland. cultivation efforts are clearly required. 2Institute of Biological, Environmental and Rural This information is being used to guide the isola- Sciences, Aberystwyth University, Aberystwyth, tion efforts and selection of bacteria from the rumen Ceredigion, UK. microbiota for sequencing through the Hungate1000. 3Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand. Introduction 4New Zealand Agricultural Greenhouse Gas Research Ruminants have evolved a symbiotic relationship with a Centre, Palmerston North, New Zealand. complex microbiome consisting of bacteria, archaea, fungi, protozoa, and viruses located in their fore-stomach Summary (reticulorumen) that allows these animals to utilize the lignocellulose component of plant material as their main The goal of the Hungate1000 project is to generate a energy source. The microbial degradation of lignocellu- reference set of rumen microbial genome sequences. lose, and fermentation of the released soluble sugars, Toward this goal we have carried out a meta-analysis produces short-chain fatty acids that are absorbed across using information from culture collections, scientific the rumen epithelium and utilized by the ruminant for literature, and the NCBI and RDP databases and growth, while the microbial cells pass from the rumen to linked this with a comparative study of several rumen the digestive tract where they become the main source of 16S rRNA gene-based surveys.
  • Computational Genomics of Lactobacilli

    Computational Genomics of Lactobacilli

    Department of Biosciences Faculty of Biological and Environmental Sciences University of Helsinki Finland Computational genomics of lactobacilli Matti Kankainen ACADEMIC DISSERTATION To be presented, with the permission of the Faculty of Biological and Environmental Sciences of the University of Helsinki, for public examination in the lecture room 228 at Koetilantie 5, Viikki, on 24 April 2015, at 12 o’clock noon. Finland 2015 Supervisor Professor Liisa Holm Department of Biological and Environmental Sciences, Faculty of Biosciences University of Helsinki Helsinki, Finland Reviewers Professor Mauno Vihinen Department of Experimental Medical Science Lund University Lund, Sweden Docent David Fewer Department of Food and Environmental Sciences University of Helsinki Helsinki, Finland Opponent Adjunct Professor Laura Elo Department of Mathematics and Statistics University of Turku Turku, Finland Custos Professor Liisa Holm Department of Biological and Environmental Sciences, Faculty of Biosciences University of Helsinki Helsinki, Finland Published in Dissertationes Scholae Doctoralis Ad Sanitatem Investigandam Universitatis Helsinkiensis ISBN 978-951-51-0886-9 (pbk.) ISBN 978-951-51-0887-6 (PDF) ISSN 2342-3161 (print) ISSN 2342-317X (online) Hansaprint Vantaa 2015 “If you wish to make an apple pie from scratch, you must first invent the universe.” - Carl Sagan Contents Abstract 1! List of original publications 3! Abbreviations 4! 1 Review of the literature 1! 1.1 Bacterial whole-genome sequencing 1! 1.1.1 DNA sequencing technologies 3! 1.1.2
  • Supplemental Material

    Supplemental Material

    Online Supporting Material SUPPLEMENTAL MATERIAL A taxonomic signature of obesity in a large study of American adults Brandilyn A. Peters,1 Jean A. Shapiro,2 Timothy R. Church,3 George Miller,4,5,6 Chau Trinh-Shevrin,1,6 Elizabeth Yuen,7 Charles Friedlander,7 Richard B. Hayes,1,6 Jiyoung Ahn1,6 1Department of Population Health, New York University School of Medicine, New York, NY, USA 2Division of Cancer Prevention and Control, Centers for Disease Control and Prevention, Atlanta, GA, USA 3Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN, USA 4Departments of Surgery and 5Cell Biology, New York University School of Medicine, New York, NY, USA 6NYU Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA 7Kips Bay Endoscopy Center, New York, NY, USA Online Supporting Material Supplemental Figure 1. (a, b, c) Richness, Shannon diversity index, and Evenness rarefaction curves in healthy-weight, overweight, obese class I, and obese class II-III participants. Rarefaction curves were estimated by taking the mean of the α-diversity indices averaged for each participant over 100 iterations at each rarefaction sequencing depth. (d) Principal coordinate analysis of the weighted UniFrac distances. Shapes outlined in black represent centroids for healthy-weight, overweight, and obese participants. (e) Partial constrained analysis of principal coordinates (CAP) based on the weighted UniFrac distance. BMI category was the constraining variable, and sex, age, polyp status, and study were conditioning variables. Online Supporting Material Supplemental Figure 2. (a) Boxplots of richness (number of OTUs) in relation to BMI in subgroups by study, polyp status, and sex.
  • Gut Microbiota Composition in Relation to Intake of Added Sugar, Sugar‑Sweetened Beverages and Artifcially Sweetened Beverages in the Malmö Ofspring Study

    Gut Microbiota Composition in Relation to Intake of Added Sugar, Sugar‑Sweetened Beverages and Artifcially Sweetened Beverages in the Malmö Ofspring Study

    European Journal of Nutrition https://doi.org/10.1007/s00394-020-02392-0 ORIGINAL CONTRIBUTION Gut microbiota composition in relation to intake of added sugar, sugar‑sweetened beverages and artifcially sweetened beverages in the Malmö Ofspring Study Stina Ramne1 · Louise Brunkwall1 · Ulrika Ericson1 · Nicola Gray2 · Gunter G. C. Kuhnle3 · Peter M. Nilsson1 · Marju Orho‑Melander1 · Emily Sonestedt1 Received: 22 April 2020 / Accepted: 21 September 2020 © The Author(s) 2020 Abstract Purpose It has been suggested that a high intake of sugar or sweeteners may result in an unfavorable microbiota composition; however, evidence is lacking. Hence, in this exploratory epidemiological study, we aim to examine if intake of added sugar, sugar-sweetened beverages (SSBs) or artifcially sweetened beverages (ASBs) associate with the gut microbiota composition. Methods Participants (18–70 years) in the Malmö Ofspring Study have provided blood, urine, and fecal samples and com- pleted both web-based 4 day food records and short food frequency questionnaires. The gut microbiota was assessed by 16S rRNA sequencing, processed in QIIME and matched to Greengenes (v.13.8), giving 64 included genera after fltering. Intake of added sugar (n = 1371) (also supported by the overnight urinary sugar biomarker in a subgroup n = 577), SSBs (n = 1086) and ASBs (n = 1085) were examined as exposures in negative binomial regressions. Results Various genera nominally associated with intake of added sugar, SSBs, and ASBs. Only the negative association between SSB intake and Lachnobacterium remained signifcant after multiple testing correction. A positive association between SSB intake and the Firmicutes:Bacteroidetes ratio was also observed. Conclusion In this wide population, the cross-sectional associations between added sugar and sweet beverage intake and the gut microbiota are modest, but the results suggest that SSB intake is associated negatively with the genus Lachnobacterium and positively with the Firmicutes:Bacteroidetes ratio.
  • Fmicb-10-02207.Pdf

    Fmicb-10-02207.Pdf

    UCC Library and UCC researchers have made this item openly available. Please let us know how this has helped you. Thanks! Title Use of lactic acid bacteria to reduce methane production in ruminants, a critical review Author(s) Doyle, Natasha; Mbandlwa, Philiswa; Kelly, William J.; Attwood, Graeme; Li, Yang; Ross, R. Paul; Stanton, Catherine; Leahy, Sinead Publication date 2019-09-09 Original citation Doyle, N., Mbandlwa, P., Kelly, W. J., Attwood, G., Li, Y., Ross, R. P., Stanton, C. and Leahy, S. (2019) 'Use of Lactic Acid Bacteria to Reduce Methane Production in Ruminants, a Critical Review', Frontiers in Microbiology, 10, 2207 (13pp.) DOI: 10.3389/fmicb.2019.02207 Type of publication Article (peer-reviewed) Link to publisher's https://www.frontiersin.org/articles/10.3389/fmicb.2019.02207/full version http://dx.doi.org/10.3389/fmicb.2019.02207 Access to the full text of the published version may require a subscription. Rights ©2019 Doyle, Mbandlwa, Kelly, Attwood, Li, Ross, Stanton and Leahy. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. http://creativecommons.org/licenses/by/4.0/ Item downloaded http://hdl.handle.net/10468/8748 from Downloaded on 2021-09-30T19:28:23Z fmicb-10-02207 October 1, 2019 Time: 13:9 # 1 MINI REVIEW published: 01 October 2019 doi: 10.3389/fmicb.2019.02207 Use of Lactic Acid Bacteria to Reduce Methane Production in Ruminants, a Critical Review Natasha Doyle1,2†, Philiswa Mbandlwa2†, William J.
  • Rumen Metagenome and Metatranscriptome Analyses of Low

    Rumen Metagenome and Metatranscriptome Analyses of Low

    Lawrence Berkeley National Laboratory Recent Work Title Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation. Permalink https://escholarship.org/uc/item/80d9t5qg Journal Microbiome, 4(1) ISSN 2049-2618 Authors Kamke, Janine Kittelmann, Sandra Soni, Priya et al. Publication Date 2016-10-19 DOI 10.1186/s40168-016-0201-2 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Kamke et al. Microbiome (2016) 4:56 DOI 10.1186/s40168-016-0201-2 RESEARCH Open Access Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea- enriched microbiome characterised by lactic acid formation and utilisation Janine Kamke1, Sandra Kittelmann1, Priya Soni1, Yang Li1, Michael Tavendale1, Siva Ganesh1, Peter H. Janssen1, Weibing Shi2,3, Jeff Froula2,3, Edward M. Rubin2,3 and Graeme T. Attwood1* Abstract Background: Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and is a heritable trait that can be used to select animals that yield less methane per unit of feed eaten. We previously demonstrated elevated expression of hydrogenotrophic methanogenesis pathway genes of methanogenic archaea in the rumens of high methane yield (HMY) sheep compared to their low methane yield (LMY) counterparts. Methane production in the rumen is strongly connected to microbial hydrogen production through fermentation processes. In this study, we investigate the contribution that rumen bacteria make to methane yield phenotypes in sheep.
  • The Interplay Between Host Genetics and the Gut Microbiome Reveals Common

    The Interplay Between Host Genetics and the Gut Microbiome Reveals Common

    bioRxiv preprint doi: https://doi.org/10.1101/2019.12.26.888313; this version posted January 6, 2020. 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 1 The interplay between host genetics and the gut microbiome reveals common 2 and distinct microbiome features for human complex diseases 3 Fengzhe Xu1#, Yuanqing Fu1#, Ting-yu Sun2, Zengliang Jiang1,3, Zelei Miao1, Menglei 4 Shuai1, Wanglong Gou1, Chu-wen Ling2, Jian Yang4,5, Jun Wang6*, Yu-ming Chen2*, 5 Ju-Sheng Zheng1,3,7* 6 #These authors contributed equally to the work 7 1 School of Life Sciences, Westlake University, Hangzhou, China. 8 2 Guangdong Provincial Key Laboratory of Food, Nutrition and Health; Department 9 of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, 10 China. 11 3 Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 12 Hangzhou, China. 13 4 Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 14 Australia. 15 5 Institute for Advanced Research, Wenzhou Medical University, Wenzhou, Zhejiang 16 325027, China 17 6 CAS Key Laboratory for Pathogenic Microbiology and Immunology, Institute of 18 Microbiology, Chinese Academy of Sciences, Beijing, China. 19 7 MRC Epidemiology Unit, University of Cambridge, Cambridge, UK. 20 21 Short title: Interplay between and host genetics and gut microbiome 22 1 bioRxiv preprint doi: https://doi.org/10.1101/2019.12.26.888313; this version posted January 6, 2020.