DOCSLIB.ORG

Towards a Better Understanding of Poultry Intestinal Microbiome Through Metagenomic and Microarray Studies

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Towards a Better Understanding of Poultry Intestinal Microbiome Through Metagenomic and Microarray Studies Towards a Better Understanding of Poultry Intestinal Microbiome through Metagenomic and Microarray Studies DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Shan Wei Graduate Program in Animal Sciences The Ohio State University 2013 Dissertation Committee: Dr. Zhongtang Yu, Advisor Dr. Hua Wang Dr. Michael Lilburn Dr. Macdonald Wick Copyrighted by Shan Wei 2013 Abstract The intestinal microbiome in poultry tracts functions as an interface between the host and the feed ingested and has important roles in nutrition and health of the host. This intestinal microbiome consisting of bacteria, archaea, fungi and few protozoa, with bacteria being the most abundant domain and greatly affecting the performance of the host. Modulation of the intestinal microbiome of poultry through dietary and managerial interventions has been used to improve poultry growth and health. However, the diversity and complexity of the intestinal microbiome hinders understanding of the mechanism of these interventions and achieving the intended modulations. Cultivation-based methods have been applied to intestinal microbiome studies, providing useful information. However, the fact that the majority of poultry intestinal microbiome are uncultivable limits the knowledge that can be learned about this microbiome. PCR-Denaturing Gradient Gel Electrophoresis (DGGE) and cloning and sequencing are primary cultivation-independent 16S rRNA gene-targeted molecular techniques commonly used in characterizing diversity and composition of poultry intestinal microbiome. However, they can only provide limited information because neither can provide detailed information on most of the bacteria present in the microbiome in a cost-effective manner. Recently, microarray and next-generation sequencing (NGS) technologies have been widely applied to investigation of microbiomes in various habitats, including guts of ii humans and animals, greatly advancing our knowledge on microbiomes. However, few metagenomics or microarray studies have been conducted to investigate the poultry intestinal microbiome. The objectives of my study were to i) achieve a comprehensive understanding of the intestinal microbiomes of broiler chickens and turkeys, ii) establish a global phylogenetic framework of bacterial diversity of this microbiome, iii) examine how litter conditions and bacitracin (as a model antimicrobial growth promoter) affect colonization and abundance of common enteric pathogens in broiler chickens, and iv) develop a habitat-specific phylochip that can support comprehensive studies on poultry intestinal microbiome. In the first study (chapter 3), a naїve-analysis of all the available 16S rRNA gene sequences of poultry gut origin archived in the public databases was performed. By analyzing high quality sequences of chicken and turkey gastrointestinal origin (3,184 and 1,345, respectively) collected from the GenBank, Ribosomal Database Project (RDP), and Silva database, I identified 915 and 464 species-equivalent operational taxonomic units (OTUs, defined at 0.03 phylogenetic distance) in the chicken and the turkey intestinal microbiomes, respectively. Firmicutes, Bacteroidetes, and Proteobacteria were the largest phyla in both chicken and turkey, accounting for > 90% of all the sequences. The estimated coverage of bacterial diversity of chicken and turkey reached 89% and 68% at species-equivalent level, respectively. More than 7,000 bacterial sequences from each bird species would be needed to reach 99% diversity coverage for either bird species. iii In the second study (chapter 4), we used 454 pyrosequencing in investigating the bacterial diversity of cecal content and ileal mucosa samples of chickens and turkeys with two technical replicates. The objectives of this study were to uncover the major bacterial composition of poultry intestinal microbiome and to investigate the variations of bacteria diversity as affected by different sequencing runs and data processing pipelines. The 338,177 sequences analyzed represented on average 3,401 and 125 OTUs in chicken cecal content and ileal mucosa as well as 1,687 and 16 OTUs in turkey cecal content and ileal mucosa, respectively. The sequences from each bird species reached > 95% bacterial diversity in the intestinal microbiomes, except for the turkey mucosa microbiome. When compared to the public databases, this study identified 39 and 50 new genera in the chicken and turkey cecal microbiome, respectively. Noticeable variations were observed from the number of OTUs revealed by different sequencing runs and data processing pipelines. This study provided comprehensive perspectives on the chicken and turkey intestinal microbiota. In the third study (chapter 5), a habitat-specific phylochip microarray (referred to as PITChip) was developed based on the sequences collected in the first and the second studies. The PITChip enables simultaneous detection and semi-quantification of 1,848 different bacterial OTUs and 105 genera of bacteria. After careful validation, the PITChip was used to analyze microbiomes of ileal mucosa and cecal content of broiler chicken reared on fresh and reused litters to assess how litter conditions affected the intestinal microbiome. More than 85 groups of bacteria were found to be influenced by litter status iv in each sampling location. This study indicated that litter management can modulate the intestinal microbiome of broiler chickens and may have a profound effect on bird health and performance. This is the first phylochip developed for comprehensive studies of the intestinal microbiome of poultry. The PITChip may be used in future integrated studies to investigate interrelations between intestinal microbiomes, diets, feed additives, and managerial factors to promote flock health and performance. In the last study (chapter 6), we further investigated the effects of supplemental bacitracin and litter management (fresh vs. reused) on the abundance of Campylobacter, Clostridium perfringens, and Salmonella in broiler chickens using specific quantitative PCR (qPCR) assays. This is the first study that has examined the effect of dietary bacitracin and litter conditions on the prevalence of these three common enteric pathogens. Bacitracin was shown to be effective to reduce abundance of C. perfringens, but it had no effect on Campylobacter or Salmonella. A somewhat negative correlation was noted between the abundance of C. perfringens and Salmonella. Unless contaminated by pathogens from a previous flock, litter reuse did not appear to increase the risk of necrotic enteritis caused by C. perfringens or Salmonella infection in subsequent flocks. Taken together, the findings of the series of studies on poultry intestinal microbiome advanced our knowledge on the bacterial communities of poultry, provided new insight into the effects of litter management and bacitracin on the intestinal microbiome of v broiler chickens, and established a new microarray that can be used to support comprehensive analysis of the intestinal microbiome of chickens and turkeys that are often needed in studies of poultry nutrition and host health. vi Acknowledgments I first would like to thank my advisor, Dr. Zhongtang Yu, for his support and guidance during my graduate study. Dr. Zhongtang Yu’s strong support and thoughtful discussions during individual meetings were critical for this research project to move forwards smoothly. I would like to thank Drs. Hua Wang, Michael Lilburn, and Macdonald Wick for their service on my dissertation committee and great efforts in making every committee meeting possible. The constructive suggestions from my committee were of great value to my research. I wish to thank Dr. Mark Morrison for his service on my candidacy committee and his enlightening suggestion for my research project. I wish to thank Dr. Norman St-Pierre for his help with my statistical analysis. I wish to acknowledge all former and present colleagues for their friendship and helps in the Yu lab: Jill Stiverson, Lingling Wang, Yueh-Fen Li, Mike Nelson, Mike Cressman, Minseok Kim, Wen Lv, Deng Pan, Katie Shaw, Yan Zhang, Amanda Gutek, Amlan Patra, Phongthorn Kongmun, Gunilla Bech-Nielsen, Zhenming Zhou, Mohd Saufi Bastami, Dr. Paul, Jackie Gano, and anyone else I may have missed. I am especially grateful to Jill Stiverson for her help and technical support throughout my research. I especially thank Lingling Wang and Yueh-Fen Li for their helps in troubleshooting and discussion. I would like to thank all my fellow graduate students working in the Department of Animal vii Sciences for their friendship. I would like to thank Danni Ye and Josie Plank for being supportive friends. Last but not least, I wish to acknowledge all my family members for their support, love and encouragement. viii Vita Feb 1985.........................................................Qingyuan, China 2003................................................................B.S. Biology Sciences, Nankai Univeristy 2003 to present Graduate Research Associate, Department of Animal Sciences, The Ohio State University Publications Wang CY, Ding DF, Yu XJ, Wei S, Wei AM, Du SL, Li MG, 2008. Preliminary transformation research of cucumber with a floral dip method. Bulletin of Biology (in Chinese), 43 (2). Wei S., Morrison M, and Yu Z., 2013. Bacterial census of poultry intestinal microbiome. Poultry Science (in press). Fields of Study Major Field: Animal Sciences Focus: Poultry
Load more

Recommended publications
  • Phylogenetic Analysis of the Gut Bacterial Microflora of the Fungus-Growing Termite Macrotermes Barneyi
    African Journal of Microbiology Research Vol. 6(9), pp. 2071-2078, 9 March, 2012 Available online at http://www.academicjournals.org/AJMR DOI: 10.5897/AJMR11.1345 ISSN 1996-0808 ©2012 Academic Journals Full Length Research Paper Phylogenetic analysis of the gut bacterial microflora of the fungus-growing termite Macrotermes barneyi Yunhua Zhu1,2,3, Jian Li1,2, Huhu Liu1,2, Hui Yang1,2, Sheng Xin1,2, Fei Zhao1,2, Xuejia Zhang1,2, Yun Tian1,2* and Xiangyang Lu1,2* 1College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China. 2Hunan Agricultural Bioengineering Research Institute, Changsha 410128, China. 3College of Pharmacy and Life Science, Nanhua University, Hengyang 421001, China. Accepted 29 December, 2011 Termites are an extremely successful group of wood-degrading organisms and are therefore important both for their roles in carbon turnover in the environment and as potential sources of biochemical catalysts for efforts aimed at converting wood into biofuels. To contribute to the evolutional study of termite digestive symbiosis, a bacterial 16S rRNA gene clone library from the gut microbial community of the fungus-growing termite Macrotermes barneyi was constructed. After screening by restriction fragment length polymorphism (RFLP) analysis, 25 out of 105 clones with unique RFLP patters were sequenced and phylogenetically analyzed. Many of the clones (95%) were derived from three phyla within the domain bacteria: Bacteroidetes, Firmicutes and Proteobacteria. In addition, a few clones derived from Deferribacteres, Actinobacteria and Planctomycetes were also found. No one clone affiliated with the phylum Spirochaetes was identified, in contrast to the case of wood-feeding termites. The phylogenetic analysis revealed that nearly half of the representative clones (11 phylotypes) formed monophyletic clusters with clones obtained from other termite species, especially with the sequences retrieved from fungus-growing termites.
    [Show full text]
  • Geomicrobiological Processes in Extreme Environments: a Review
    202 Articles by Hailiang Dong1, 2 and Bingsong Yu1,3 Geomicrobiological processes in extreme environments: A review 1 Geomicrobiology Laboratory, China University of Geosciences, Beijing, 100083, China. 2 Department of Geology, Miami University, Oxford, OH, 45056, USA. Email: [email protected] 3 School of Earth Sciences, China University of Geosciences, Beijing, 100083, China. The last decade has seen an extraordinary growth of and Mancinelli, 2001). These unique conditions have selected Geomicrobiology. Microorganisms have been studied in unique microorganisms and novel metabolic functions. Readers are directed to recent review papers (Kieft and Phelps, 1997; Pedersen, numerous extreme environments on Earth, ranging from 1997; Krumholz, 2000; Pedersen, 2000; Rothschild and crystalline rocks from the deep subsurface, ancient Mancinelli, 2001; Amend and Teske, 2005; Fredrickson and Balk- sedimentary rocks and hypersaline lakes, to dry deserts will, 2006). A recent study suggests the importance of pressure in the origination of life and biomolecules (Sharma et al., 2002). In and deep-ocean hydrothermal vent systems. In light of this short review and in light of some most recent developments, this recent progress, we review several currently active we focus on two specific aspects: novel metabolic functions and research frontiers: deep continental subsurface micro- energy sources. biology, microbial ecology in saline lakes, microbial Some metabolic functions of continental subsurface formation of dolomite, geomicrobiology in dry deserts, microorganisms fossil DNA and its use in recovery of paleoenviron- Because of the unique geochemical, hydrological, and geological mental conditions, and geomicrobiology of oceans. conditions of the deep subsurface, microorganisms from these envi- Throughout this article we emphasize geomicrobiological ronments are different from surface organisms in their metabolic processes in these extreme environments.
    [Show full text]
  • Originally Published As
    Originally published as: Westphal, A., Lerm, S., Miethling-Graff, R., Seibt, A., Wolfgramm, M., Würdemann, H. (2016): Effects of plant downtime on the microbial community composition in the highly saline brine of a geothermal plant in the North German Basin. - Applied Microbiology and Biotechnology, 100, 7, pp. 3277—3290. DOI: http://doi.org/10.1007/s00253-015-7181-1 1 Effects of plant downtime on the microbial community composition in the highly saline brine 2 of a geothermal plant in the North German Basin 3 4 Anke Westphala, Stephanie Lerma, Rona Miethling-Graffa, Andrea Seibtb, Markus 5 Wolfgrammc, Hilke Würdemannad# 6 7 a GFZ German Research Centre for Geosciences, Section 4.5 Geomicrobiology, 14473 Pots- 8 dam, Germany 9 b BWG Geochemische Beratung GmbH, 17041 Neubrandenburg, Germany 10 c Geothermie Neubrandenburg (GTN), 17041 Neubrandenburg, Germany 11 d Environmental Technology, Water- and Recycling Technology, Department of Engineering 12 and Natural Sciences, University of Applied Sciences Merseburg, 06217 Merseburg, Germa- 13 ny 14 15 16 17 18 19 20 21 22 23 24 # Address correspondence to Hilke Würdemann 25 [email protected] 26 Phone: +49 331 288 1516 27 Fax: ++49 331 2300662 1 28 Abstract 29 The microbial biocenosis in highly saline fluids produced from the cold well of a deep geo- 30 thermal heat store located in the North German Basin was characterized during regular plant 31 operation and immediately after plant downtime phases. Genetic fingerprinting revealed the 32 dominance of sulfate-reducing bacteria (SRB) and fermentative Halanaerobiaceae during 33 regular plant operation, whereas after shut-down phases, sequences of sulfur-oxidizing bacte- 34 ria (SOB) were also detected.
    [Show full text]
  • Inhibition of Tumor Growth by Dietary Indole-3-Carbinol in a Prostate Cancer Xenograft Model May Be Associated with Disrupted Gut Microbial Interactions
    nutrients Article Inhibition of Tumor Growth by Dietary Indole-3-Carbinol in a Prostate Cancer Xenograft Model May Be Associated with Disrupted Gut Microbial Interactions Yanbei Wu 1,2,3, Robert W. Li 4, Haiqiu Huang 3 , Arnetta Fletcher 2,5, Lu Yu 2, Quynhchi Pham 3, Liangli Yu 2, Qiang He 1,* and Thomas T. Y. Wang 3,* 1 College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu 610065, China; [email protected] 2 Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; afl[email protected] (A.F.); [email protected] (L.Y.); [email protected] (L.Y.) 3 Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, USDA-ARS, Beltsville, MD 20705, USA; [email protected] (H.H.); [email protected] (Q.P.) 4 Animal Parasitic Diseases Laboratory, USDA-ARS, Beltsville, MD 20705, USA; [email protected] 5 Department of Family and Consumer Sciences, Shepherd University, Shepherdstown, WV 25443, USA * Correspondence: [email protected] (Q.H.); [email protected] (T.T.Y.W.); Tel.: +86-28-85468323 (Q.H.); +(301)-504-8459 (T.T.Y.W.) Received: 2 January 2019; Accepted: 19 February 2019; Published: 22 February 2019 Abstract: Accumulated evidence suggests that the cruciferous vegetables-derived compound indole-3-carbinol (I3C) may protect against prostate cancer, but the precise mechanisms underlying its action remain unclear. This study aimed to verify the hypothesis that the beneficial effect of dietary I3C may be due to its modulatory effect on the gut microbiome of mice. Athymic nude mice (5–7 weeks old, male, Balb c/c nu/nu) with established tumor xenografts were fed a basal diet (AIN-93) with or without 1 µmoles I3C/g for 9 weeks.
    [Show full text]
  • Exploring the Role of Mucispirillum Schaedleri in Enteric Salmonella Enterica Serovar Typhimurium Infection
    Aus dem Max von Pettenkofer-Institut Lehrstuhl für Medizinische Mikrobiologie und Krankenhaushygiene der Ludwig-Maximilians-Universität München Vorstand: Prof. Dr. med. Sebastian Suerbaum Exploring the role of Mucispirillum schaedleri in enteric Salmonella enterica serovar Typhimurium infection Dissertation zum Erwerb des Doktorgrades der Naturwissenschaften an der Medizinischen Fakultät der Ludwig-Maximilians-Universität München vorgelegt von Simone Herp aus Offenburg 2018 Gedruckt mit Genehmigung der Medizinischen Fakultät der Ludwig-Maximilians-Universität München Betreuerin: Prof. Dr. Barbara Stecher-Letsch Zweitgutachterin: Prof. Dr. Gabriele Rieder Dekan: Prof. Dr. med. dent. Reinhard Hickel Tag der mündlichen Prüfung: 19.02.2019 i Eidesstattliche Erklärung Ich, Simone Herp, erkläre hiermit an Eides statt, dass ich die vorliegende Dissertation mit dem Thema: Exploring the role of Mucispirillum schaedleri in enteric Salmonella enterica serovar Typhimurium infection selbständig verfasst, mich außer der angegebenen keiner weiteren Hilfsmittel bedient und alle Erkenntnisse, die aus dem Schrifttum ganz oder annähernd übernommen sind, als solche kenntlich gemacht und nach ihrer Herkunft unter Bezeichnung der Fundstelle einzeln nachgewiesen habe. Ich erkläre des Weiteren, dass die hier vorgelegte Dissertation nicht in gleicher oder in ähnlicher Form bei einer anderen Stelle zur Erlangung eines akademischen Grades eingereicht wurde. München, den 07.03.2019 Simone Herp ii Table of Contents Table of Contents Table of Contents .......................................................................................................................
    [Show full text]
  • Desulfohalobium Retbaense Gen. Nov. Sp. Nov. a Halophilic Sulfate-Reducing Bacterium from Sediments of a Hypersaline Lake in Senegal
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1991, p. 74-81 Vol. 41, No. 1 0020-7713/91/010074-08$02.OO/O Copyright 0 1991, International Union of Microbiological Societies Desulfohalobium retbaense gen. nov. sp. nov. a Halophilic Sulfate-Reducing Bacterium from Sediments of a Hypersaline Lake in Senegal B. OLLIVIER,, C. E. HATCHIKIAN,, G. PRENSIER,3 J. GUEZENNEC,, AND J.-L. GARCIA1* Laboratoire de Microbiologie ORSTOM, Universite' de Provence, 13331 Marseille Ce'dex 3, Laboratoire de Chimie Bacte'rienne, Centre National de la Recherche Scientifique, 13277 Marseille Ce'dex 9,, Laboratoire de Microbiologie, Universite' Blaise Pascal, 63177 A~biPre,~and Departement DEROIEP IFREMER, 29280 Plou~ane,~France Sulfate-reducingbacterial strain HR,, was isolated from sediments of Retba Lake, a pink hypersaline lake in Senegal. The cells were motile, nonsporulating, and rod shaped with polar flagella and incompletely oxidized a limited range of substrates to acetate and CO,. Acetate and vitamins were required for growth and could be replaced by Biotrypcase or yeast extract. Sulfate, sulfite, thiosulfate, and elemental sulfur were used as electron acceptors and were reduced to H,S. Growth occurred at pH values ranging from 5.5 to 8.0. The optimum temperature for growth was 37 to 4OOC. NaCl and MgCI, were required for growth; the optimum NaCl concentration was near 10%.The guanine-plus-cytosinecontent of the DNA was 57.1 f 0.2 mol%. On the basis of the morphological and physiological properties of this strain, we propose that it should be classified in a new genus, Desulfohalobium, which includes a single species, Desulfohalobium retbaense. The type strain is strain DSM 5692.
    [Show full text]
  • 1 Characterization of Sulfur Metabolizing Microbes in a Cold Saline Microbial Mat of the Canadian High Arctic Raven Comery Mast
    Characterization of sulfur metabolizing microbes in a cold saline microbial mat of the Canadian High Arctic Raven Comery Master of Science Department of Natural Resource Sciences Unit: Microbiology McGill University, Montreal July 2015 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Master in Science © Raven Comery 2015 1 Abstract/Résumé The Gypsum Hill (GH) spring system is located on Axel Heiberg Island of the High Arctic, perennially discharging cold hypersaline water rich in sulfur compounds. Microbial mats are found adjacent to channels of the GH springs. This thesis is the first detailed analysis of the Gypsum Hill spring microbial mats and their microbial diversity. Physicochemical analyses of the water saturating the GH spring microbial mat show that in summer it is cold (9°C), hypersaline (5.6%), and contains sulfide (0-10 ppm) and thiosulfate (>50 ppm). Pyrosequencing analyses were carried out on both 16S rRNA transcripts (i.e. cDNA) and genes (i.e. DNA) to investigate the mat’s community composition, diversity, and putatively active members. In order to investigate the sulfate reducing community in detail, the sulfite reductase gene and its transcript were also sequenced. Finally, enrichment cultures for sulfate/sulfur reducing bacteria were set up and monitored for sulfide production at cold temperatures. Overall, sulfur metabolism was found to be an important component of the GH microbial mat system, particularly the active fraction, as 49% of DNA and 77% of cDNA from bacterial 16S rRNA gene libraries were classified as taxa capable of the reduction or oxidation of sulfur compounds.
    [Show full text]
  • Comparison of Gut Microbiota of 96 Healthy Dogs by Individual Traits: Breed, Age, and Body Condition Score
    animals Article Comparison of Gut Microbiota of 96 Healthy Dogs by Individual Traits: Breed, Age, and Body Condition Score Inhwan You 1,2 and Min Jung Kim 1,2,* 1 Department of Research and Development, Mjbiogen Corp., 144 Gwangnaru-ro, Seongdong-gu, Seoul 14788, Korea; [email protected] 2 College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea * Correspondence: [email protected] Simple Summary: The gut microbial ecosystem is affected by various factors such as lifestyle, environment, and disease. Although gut microbiota is closely related to host health, an understanding of the gut microbiota of dogs is still lacking. Therefore, we investigated gut microbial composition in healthy dogs and divided them into groups according to their breed, age, or body condition score. From our results, age is the most crucial factor driving the gut microbial community of dogs compared to breed and body condition score (especially Fusobacterium perfoetens, which was much more abundant in the older group). We have revealed that even in healthy dogs without any diseases, there are differences in gut microbiota depending on individual traits. These results can be used as a basis for improving the quality of life by managing dogs’ gut microbiota. Abstract: Since dogs are part of many peoples’ lives, research and industry related to their health and longevity are becoming a rising topic. Although gut microbiota (GM) is a key contributor to Citation: You, I.; Kim, M.J. host health, limited information is available for canines. Therefore, this study characterized GM Comparison of Gut Microbiota of 96 according to individual signatures (e.g., breed, age, and body condition score—BCS) of dogs living Healthy Dogs by Individual Traits: in the same environment.
    [Show full text]
  • Dietary Energy Level Affects the Composition of Cecal Microbiota of Starter Pekin Ducklings
    Original Paper Czech J. Anim. Sci., 63, 2018 (1): 24–31 doi: 10.17221/53/2017-CJAS Dietary Energy Level Affects the Composition of Cecal Microbiota of Starter Pekin Ducklings Jun-Qiang Liu1, Yan-Hong Wang1, Xing-Tang Fang1, Ming Xie3, Yun-Sheng Zhang3, Shui-Sheng Hou3, Hong Chen1, Guo-Hong Chen2, Chun-Lei Zhang1,2* 1Institute of Cellular and Molecular Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, P.R. China 2College of Animal Science and Technology, Yangzhou University, Yangzhou, P.R. China 3Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China *Corresponding author: [email protected] ABSTRACT Liu J.-Q., Wang Y.-H., Fang X.-T., Xie M., Zhang Y.-S., Hou S.-S., Chen H., Chen G.-H., Zhang C.-L. (2018): Dietary energy level affects the composition of cecal microbiota of starter Pekin ducklings. Czech J. Anim. Sci., 63, 24–31. In this study, we evaluated the phylogenetic diversity of the cecal microbiota of 3-week-old ducklings fed three diets differing in metabolizable energy. The contents of the ceca were collected from ducklings of different groups. The ceca bacterial DNA was isolated and the V3 to V4 regions of 16S rRNA genes were amplified. The amplicons were subjected to high-throughput sequencing to analyze the bacterial diversity of different groups. The predominant bacterial phyla were Bacteroidetes (~65.67%), Firmicutes (~17.46%), and Proteobacteria (~10.73%). The abundance of Bacteroidetes increased and that of Firmicutes decreased with increasing dietary energy level. The diversity decreased (Simpson diversity index and Shannon diversity index) with the increase in dietary energy level, but the richness remained constant.
    [Show full text]
  • Distinct Microbial Communities in the Murine Gut Are Revealed by Taxonomy- 2 Independent Phylogenetic Random Forests 3 Gurdeep Singh1, Andrew Brass2, Sheena M
    bioRxiv preprint doi: https://doi.org/10.1101/790923; this version posted October 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Distinct microbial communities in the murine gut are revealed by taxonomy- 2 independent phylogenetic random forests 3 Gurdeep Singh1, Andrew Brass2, Sheena M. Cruickshank1, and Christopher G. Knight3. 4 5 1 Faculty of Biology, Medicine and Health, Lydia Becker Institute of Immunology and 6 Inflammation, Manchester Academic Health Science Centre, A.V. Hill Building, The 7 University of Manchester, Oxford Road, Manchester, M13 9PT, United Kingdom. 8 [email protected], [email protected] 9 10 2 Faculty of Biology, Medicine and Health, Division of Informatics, Imaging and Data 11 Sciences, Stopford Building, The University of Manchester, Oxford Road, Manchester, M13 12 9PT, United Kingdom. [email protected] 13 14 3 Faculty of Science and Engineering, School of Earth and Environmental Sciences, Michael 15 Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, United 16 Kingdom. [email protected] 17 Corresponding author: Sheena M. Cruickshank A.V. Hill Building The University of Manchester Oxford Road Manchester M13 9PT [email protected] Phone +44 (0) 161 275 1582 18 19 Running title: Phylogenetic mouse gut microbiomes 20 21 1 bioRxiv preprint doi: https://doi.org/10.1101/790923; this version posted October 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.
    [Show full text]
  • Desulfonatronovibrio Halophilus Sp. Nov., a Novel Moderately Halophilic Sulfate-Reducing Bacterium from Hypersaline Chloride–Sulfate Lakes in Central Asia
    Extremophiles (2012) 16:411–417 DOI 10.1007/s00792-012-0440-5 ORIGINAL PAPER Desulfonatronovibrio halophilus sp. nov., a novel moderately halophilic sulfate-reducing bacterium from hypersaline chloride–sulfate lakes in Central Asia D. Y. Sorokin • T. P. Tourova • B. Abbas • M. V. Suhacheva • G. Muyzer Received: 10 February 2012 / Accepted: 22 March 2012 / Published online: 10 April 2012 Ó The Author(s) 2012. This article is published with open access at Springerlink.com Abstract Four strains of lithotrophic sulfate-reducing soda lakes. The isolates utilized formate, H2 and pyruvate as bacteria (SRB) have been enriched and isolated from electron donors and sulfate, sulfite and thiosulfate as electron anoxic sediments of hypersaline chloride–sulfate lakes in acceptors. In contrast to the described species of the genus the Kulunda Steppe (Altai, Russia) at 2 M NaCl and pH Desulfonatronovibrio, the salt lake isolates could only tolerate 7.5. According to the 16S rRNA gene sequence analysis, high pH (up to pH 9.4), while they grow optimally at a neutral the isolates were closely related to each other and belonged pH. They belonged to the moderate halophiles growing to the genus Desulfonatronovibrio, which, so far, included between 0.2 and 2 M NaCl with an optimum at 0.5 M. On the only obligately alkaliphilic members found exclusively in basis of their distinct phenotype and phylogeny, the described halophilic SRB are proposed to form a novel species within the genus Desulfonatronovibrio, D. halophilus (type strain T T T Communicated by A. Oren. HTR1 = DSM24312 = UNIQEM U802 ). The GenBank/EMBL accession numbers of the 16S rRNA gene Keywords Sulfate-reducing bacteria (SRB) Á sequences of the HTR strains are GQ922847, HQ157562, HQ157563 and JN408678; the dsrAB gene sequences of (halo)alkaliphilic SRB Desulfonatronovibrio Á Hypersaline lakes Á Halophilic obtained in this study are JQ519392-JQ519396.
    [Show full text]
  • Longitudinal Analysis of the Faecal Microbiome in Pigs Fed Cyberlindnera Jadinii Yeast As a Protein Source During the Weanling P
    bioRxiv preprint doi: https://doi.org/10.1101/2021.02.11.430725; this version posted February 11, 2021. 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. Longitudinal analysis of the faecal microbiome in pigs fed Cyberlindnera jadinii yeast as a protein source during the weanling period followed by a rapeseed- and faba bean-based grower-finisher diet Iakhno, S.1,*, Delogu, F.2, Umu, O.C.O.¨ 1, Kjos, N.P.3, H˚aken˚asen,I.M.3, Mydland, L.T.3, Øverland, M.3 and Sørum, H.1 1 Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway 2 Luxembourg Centre for Systems Biomedicine, Universit´edu Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg 3 Faculty of Biosciences, Norwegian University of Life Sciences, As,˚ Norway * [email protected] Abstract The porcine gut microbiome is closely connected to diet and is central to animal health and growth. The gut microbiota composition in relation to Cyberlindnera jadinii yeast as a protein source in a weanling diet was studied previously. Also, there is a mounting body of knowledge regarding the porcine gut microbiome composition in response to the use of rapeseed (Brassica napus subsp. napus) meal, and faba beans (Vicia faba) as protein sources during the growing/finishing period. However, there is limited data on how the porcine gut microbiome respond to a combination of C.
    [Show full text]