R Graphics Output

Total Page：16

File Type：pdf, Size：1020Kb

Woesearchaeota Archaea A Thaumarchaeota Archaea Euryarchaeota Diapherotrites CP Verstraetaerchaeota CP Parvarchaeota CP Pacearchaeota CP Bathyarchaeota CP Altiarchaeota CP Aenigmarchaeota Verrucomicrobia V6 Verrucomicrobia V4 Verrucomicrobia V3 Verrucomicrobia V2 Verrucomicrobia V1 Planctomycetes Phycisphaerae Nitrospirae Lentisphaerae Kirimatiellacea Ignavibacteria Gs Gemmatimonadetes A Gammaproteobacteria Firmicutes Fibrobacteres acidobacteria Deltaproteobacteria Cyanobacteria CP Zixibacteria CP Ziwabacteria CP WWE3 CP WWE1 y of 523 M CP WOR−3 n CP WOR−2 Omnitrophica CP Urhbacteria CP TM6 Bacte Bacte CP Tectomicrobia CP Tanganyikabacteria axono CP Staskawiczbacteria T CP Shapirobacteria r r CP Saccharibacteria ia ia CP Rokubacteria ual CP Poribacteria n CP Perigrinibacteria CP Peribacteria Ma CP Nealsonbacteria CP Moranbacteria CP Liptonbacteria CP Kaiserbacteria CP Hydrogenedentes CP Harrisonbacteria CP Handelsmanbacteria CP Gribaldobacteria CP Gottesmanbacteria CP Eisenbacteria CP BRC1 CP Aminicemantes (OP8) Chloroflexi Chlorobi Chlamydiae Calditrichaeota Betaproteobacteria Bacteroidetes Armatimonadetes Alphaproteobacteria non LD12 Alphaproteobacteria LD12 Actinobacteria Acidobacteria 0 50 60 70 80 90 20 40 60 100 Count Genome completeness (CheckM) (%) B Not a match, Thaumarchaeota are named Crenarchaeota Not a match, only classified to Bacteria in GTDB Not a match, Lentisphaerae are lumped with Kiritimatiellae in GTDB−tk Not a match - renamed y (RP16) Not a match, Deltaproteobacteria are renamed into Desulfobacterota in GTDB m Not a match, Deltaproteobacteria are broken down into UBP10 in GTDB−tk y (GTDB−tk) m Not a match, Deltaproteobacteria are broken down into Myxococcota phylum Not a match, but in Patescibacteria ual taxono n Not a match, but in Cyanobacteria Not a match, Archaea classified as Bacteria in GTDB Not a match ison of ma r Match, but Nitrospirae are renamed Nitrospirota Match, but Kirimatiellae are within Verrucomicrobia in GTDB−tk and automated taxono Compa Match, but here GTDB puts Chlamydia within Verrucomicrobia Match but here GTDB puts Chlorobi within Bacteroidetes Match 50 60 70 80 90 100 Genome Completeness (%) Supplementary Figure 6. A. Comparison of manual RP16 taxonomy versus the GTDB-tk automated taxonomy, and distribution of completeness levels on for each taxonomy group. B. Distribution of completeness values among categories. The colors in panel B is the legend for the colors in the bar plot of panel A. There were matches across the range of completeness values (“Match”). However, when there is a mismatch, it is not always because the genome is less complete..

Copy Link

Recommended publications

Ninety-Nine De Novo Assembled Genomes from the Moose (Alces Alces) Rumen Microbiome Provide New Insights Into Microbial Plant Biomass Degradation
The ISME Journal (2017) 11, 2538–2551 © 2017 International Society for Microbial Ecology All rights reserved 1751-7362/17 www.nature.com/ismej ORIGINAL ARTICLE Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation Olov Svartström1, Johannes Alneberg2, Nicolas Terrapon3,4, Vincent Lombard3,4, Ino de Bruijn2, Jonas Malmsten5,6, Ann-Marie Dalin6, Emilie EL Muller7, Pranjul Shah7, Paul Wilmes7, Bernard Henrissat3,4,8, Henrik Aspeborg1 and Anders F Andersson2 1School of Biotechnology, Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden; 2School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden; 3CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France; 4INRA, USC 1408 AFMB, 13288 Marseille, France; 5Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden; 6Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden; 7Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg and 8Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes.
[Show full text]
Distribution and Diversity of Members of the Bacterial Phylum Fibrobacteres in Environments Where Cellulose Degradation Occurs
Aberystwyth University Distribution and diversity of members of the bacterial phylum Fibrobacteres in environments where cellulose degradation occurs. Ransom-Jones, Emma; Jones, Davey L.; Edwards, Arwyn; McDonald, J. E. Published in: Systematic and Applied Microbiology DOI: 10.1016/j.syapm.2014.06.001 Publication date: 2014 Citation for published version (APA): Ransom-Jones, E., Jones, D. L., Edwards, A., & McDonald, J. E. (2014). Distribution and diversity of members of the bacterial phylum Fibrobacteres in environments where cellulose degradation occurs. Systematic and Applied Microbiology, 37(7), 502-509. https://doi.org/10.1016/j.syapm.2014.06.001 General rights Copyright and moral rights for the publications made accessible in the Aberystwyth Research Portal (the Institutional Repository) are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the Aberystwyth Research Portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the Aberystwyth Research Portal Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. tel: +44 1970 62 2400 email: [email protected] Download date: 28. Sep. 2021 G Model SYAPM-25635; No. of Pages 8 ARTICLE IN PRESS Systematic and Applied Microbiology xxx (2014) xxx–xxx Contents lists available at ScienceDirect Systematic and Applied Microbiology j ournal homepage: www.elsevier.de/syapm Distribution and diversity of members of the bacterial phylum Fibrobacteres in environments where cellulose degradation occurs a b c a, Emma Ransom-Jones , David L.
[Show full text]
Expanding the Chlamydiae Tree
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2040 Expanding the Chlamydiae tree Insights into genome diversity and evolution JENNAH E. DHARAMSHI ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-513-1203-3 UPPSALA urn:nbn:se:uu:diva-439996 2021 Dissertation presented at Uppsala University to be publicly examined in A1:111a, Biomedical Centre (BMC), Husargatan 3, Uppsala, Tuesday, 8 June 2021 at 13:15 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Prof. Dr. Alexander Probst (Faculty of Chemistry, University of Duisburg-Essen). Abstract Dharamshi, J. E. 2021. Expanding the Chlamydiae tree. Insights into genome diversity and evolution. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2040. 87 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-1203-3. Chlamydiae is a phylum of obligate intracellular bacteria. They have a conserved lifecycle and infect eukaryotic hosts, ranging from animals to amoeba. Chlamydiae includes pathogens, and is well-studied from a medical perspective. However, the vast majority of chlamydiae diversity exists in environmental samples as part of the uncultivated microbial majority. Exploration of microbial diversity in anoxic deep marine sediments revealed diverse chlamydiae with high relative abundances. Using genome-resolved metagenomics various marine sediment chlamydiae genomes were obtained, which significantly expanded genomic sampling of Chlamydiae diversity. These genomes formed several new clades in phylogenomic analyses, and included Chlamydiaceae relatives. Despite endosymbiosis-associated genomic features, hosts were not identified, suggesting chlamydiae with alternate lifestyles. Genomic investigation of Anoxychlamydiales, newly described here, uncovered genes for hydrogen metabolism and anaerobiosis, suggesting they engage in syntrophic interactions.
[Show full text]
Global Metagenomic Survey Reveals a New Bacterial Candidate Phylum in Geothermal Springs
ARTICLE Received 13 Aug 2015 | Accepted 7 Dec 2015 | Published 27 Jan 2016 DOI: 10.1038/ncomms10476 OPEN Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs Emiley A. Eloe-Fadrosh1, David Paez-Espino1, Jessica Jarett1, Peter F. Dunfield2, Brian P. Hedlund3, Anne E. Dekas4, Stephen E. Grasby5, Allyson L. Brady6, Hailiang Dong7, Brandon R. Briggs8, Wen-Jun Li9, Danielle Goudeau1, Rex Malmstrom1, Amrita Pati1, Jennifer Pett-Ridge4, Edward M. Rubin1,10, Tanja Woyke1, Nikos C. Kyrpides1 & Natalia N. Ivanova1 Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia’) found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot’ because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery. 1 Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA. 2 Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
[Show full text]
Fiber-Associated Spirochetes Are Major Agents of Hemicellulose Degradation in the Hindgut of Wood-Feeding Higher Termites
Fiber-associated spirochetes are major agents of hemicellulose degradation in the hindgut of wood-feeding higher termites Gaku Tokudaa,b,1, Aram Mikaelyanc,d, Chiho Fukuia, Yu Matsuuraa, Hirofumi Watanabee, Masahiro Fujishimaf, and Andreas Brunec aTropical Biosphere Research Center, Center of Molecular Biosciences, University of the Ryukyus, Nishihara, 903-0213 Okinawa, Japan; bGraduate School of Engineering and Science, University of the Ryukyus, Nishihara, 903-0213 Okinawa, Japan; cResearch Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; dDepartment of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27607; eBiomolecular Mimetics Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8634 Ibaraki, Japan; and fDepartment of Sciences, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yoshida 1677-1, 753-8512 Yamaguchi, Japan Edited by Nancy A. Moran, University of Texas at Austin, Austin, TX, and approved November 5, 2018 (received for review June 25, 2018) Symbiotic digestion of lignocellulose in wood-feeding higher digestion in the hindgut of higher termites must be attributed to termites (family Termitidae) is a two-step process that involves their entirely prokaryotic microbial community (5). endogenous host cellulases secreted in the midgut and a dense The gut microbiota of higher termites comprises more than bacterial community in the hindgut compartment. The genomes of 1,000 bacterial phylotypes, which are organized into distinc- the bacterial gut microbiota encode diverse cellulolytic and hemi- tive communities colonizing the microhabitats provided by the cellulolytic enzymes, but the contributions of host and bacterial compartmentalized intestine, including the highly differentiated symbionts to lignocellulose degradation remain ambiguous.
[Show full text]
Systema Naturae 2000 (Phylum, 6 Nov 2017)
The Taxonomicon Systema Naturae 2000 Classification of Domain Bacteria (prokaryotes) down to Phylum Compiled by Drs. S.J. Brands Universal Taxonomic Services 6 Nov 2017 Systema Naturae 2000 - Domain Bacteria - Domain Bacteria Woese et al. 1990 1 Genus †Eoleptonema Schopf 1983, incertae sedis 2 Genus †Primaevifilum Schopf 1983, incertae sedis 3 Genus †Archaeotrichion Schopf 1968, incertae sedis 4 Genus †Siphonophycus Schopf 1968, incertae sedis 5 Genus Bactoderma Tepper and Korshunova 1973 (Approved Lists 1980), incertae sedis 6 Genus Stibiobacter Lyalikova 1974 (Approved Lists 1980), incertae sedis 7.1.1.1.1.1 Superphylum "Proteobacteria" Craig et al. 2010 1.1 Phylum "Alphaproteobacteria" 1.2.1 Phylum "Acidithiobacillia" 1.2.2.1 Phylum "Gammaproteobacteria" 1.2.2.2.1 Candidate phylum Muproteobacteria (RIF23) Anantharaman et al. 2016 1.2.2.2.2 Phylum "Betaproteobacteria" 2 Phylum "Zetaproteobacteria" 7.1.1.1.1.2 Phylum "Deltaproteobacteria_1" 7.1.1.1.2.1.1.1 Phylum "Deltaproteobacteria" [polyphyletic] 7.1.1.1.2.1.1.2.1 Phylum "Deltaproteobacteria_2" 7.1.1.1.2.1.1.2.2 Phylum "Deltaproteobacteria_3" 7.1.1.1.2.1.2 Candidate phylum Dadabacteria (CSP1-2) Hug et al. 2015 7.1.1.1.2.2.1 Candidate phylum "MBNT15" 7.1.1.1.2.2.2 Candidate phylum "Uncultured Bacterial Phylum 10 (UBP10)" Parks et al. 2017 7.1.1.2.1 Phylum "Nitrospirae_1" 7.1.1.2.2 Phylum Chrysiogenetes Garrity and Holt 2001 7.1.2.1.1 Phylum "Nitrospirae" Garrity and Holt 2001 [polyphyletic] 7.1.2.1.2.1.1 Candidate phylum Rokubacteria (CSP1-6) Hug et al.
[Show full text]
Distribution and Diversity of Members of the Bacterial Phylum Fibrobacteres in Environments Where Cellulose Degradation Occurs
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Aberystwyth Research Portal Aberystwyth University Distribution and diversity of members of the bacterial phylum Fibrobacteres in environments where cellulose degradation occurs. Ransom-Jones, Emma; Jones, Davey L.; Edwards, Arwyn; McDonald, J. E. Published in: Systematic and Applied Microbiology DOI: 10.1016/j.syapm.2014.06.001 Publication date: 2014 Citation for published version (APA): Ransom-Jones, E., Jones, D. L., Edwards, A., & McDonald, J. E. (2014). Distribution and diversity of members of the bacterial phylum Fibrobacteres in environments where cellulose degradation occurs. Systematic and Applied Microbiology, 37(7), 502-509. https://doi.org/10.1016/j.syapm.2014.06.001 General rights Copyright and moral rights for the publications made accessible in the Aberystwyth Research Portal (the Institutional Repository) are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the Aberystwyth Research Portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the Aberystwyth Research Portal Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. tel: +44 1970 62 2400 email: [email protected] Download date: 03.
[Show full text]
Characterization of Ruminal Bacteria in Grazing Nellore Steers
248 Characterization of ruminal bacteria in grazing Nellore steers Caracterización de bacterias ruminales en novillos Nelore en pastoreo Caraterização bacteriana ruminal em novilhos Nelore em pastejo Raphael B de Jesus1 ; Yury T Granja-Salcedo1* ; Juliana D Messana1 ; Luciano T Kishi2 ; Eliana G M Lemos3 ; Jackson Antonio M de Souza3 ; Telma T Berchielli1. 1Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Câmpus Jaboticabal, Jaboticabal SP, Brazil . 2Departamento de Tecnologia, Faculdade de Ciências Agrarias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Câmpus Jaboticabal, Jaboticabal, SP, Brazil . 3Departamento de Biologia, Faculdade de Ciências Agrarias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Câmpus Jaboticabal, Jaboticabal, SP, Brazil . Received: November 7, 2017; accepted: March 5, 2019 To cite this article: De Jesus RB, Granja-Salcedo YT, Messana JD, Kishi LT, Lemos EGM, De Souza JAM, Barchielli TT. Characterization of ruminal bacteria in grazing Nellore steers. Rev Colomb Cienc Pecu 2019; 32(4): 248-260. DOI: https://doi.org/10.17533/udea.rccp.v32n4a01 This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. eISSN: 2256-2958 Rev Colomb Cienc Pecu 2019; 32(4):248-260 Ruminal bacteria in grazing steers 249 Abstract Background: Rumen microorganisms have developed a series of complex interactions, representing one of the best examples of symbiosis between microorganisms in nature. Conventional taxonomic methods based on culture techniques are being replaced by molecular techniques that are faster and more accurate. Objective: To characterize rumen bacterial diversity of Nellore steers grazing on tropical pastures by sequencing the 16S rRNA gene using Illumina sequencing.
[Show full text]
Bacterial Community in Soils Following Century-Long Application of Organic Or Inorganic Fertilizers Under Continuous Winter Wheat Cultivation
agronomy Article Bacterial Community in Soils Following Century-Long Application of Organic or Inorganic Fertilizers under Continuous Winter Wheat Cultivation Xiufen Li 1,2 , Shiping Deng 1,*, William R. Raun 1, Yan Wang 1 and Ying Teng 3 1 Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078, USA; [email protected] (X.L.); [email protected] (W.R.R.); [email protected] (Y.W.) 2 Texas A&M AgriLife Research Center at Beaumont, Texas A&M University System, Beaumont, TX 77713, USA 3 Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; [email protected] * Correspondence: [email protected]; Tel.: +1-405-744-9591 Received: 30 July 2020; Accepted: 29 September 2020; Published: 1 October 2020 Abstract: Fertilization is one of the most common agricultural practices to achieve high yield. Although microbes play a critical role in nutrient cycling and organic matter decomposition, knowledge of the long-term responses of the soil bacterial community to organic and inorganic fertilizers is still limited. This study was conducted to evaluate the effects of century-long organic (manure), inorganic (NPK), and no fertilization (control) treatments on soil bacterial community structure under continuous winter wheat (Triticum aestivum L.) cultivation. Fertilization treatments altered the richness, diversity and composition of the soil bacterial community. Compared with the control, manure significantly increased the operational taxonomic units (OTUs), Chao 1 and Shannon indices, and taxonomic groups, while NPK significantly decreased these parameters. Fertilization treatments did not alter the types of dominant phyla but did significantly affect their relative abundances.
[Show full text]
Community Structure and Influencing Factors of Airborne Microbial
atmosphere Article Community Structure and Inﬂuencing Factors of Airborne Microbial Aerosols over Three Chinese Cities with Contrasting Social-Economic Levels 1,2,3, , 2,4, , 5 1,6,7, 1 1 Ying Rao * y , Heyang Li * y, Mingxia Chen , Kan Huang *, Jia Chen , Jian Xu and Guoshun Zhuang 1,* 1 Center for Atmospheric Chemistry Study, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China; [email protected] (J.C.); [email protected] (J.X.) 2 Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China 3 Education and Research oﬃce of Health Centre, Minnan Normal University, Zhangzhou 363000, China 4 Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen 361005, China 5 Department of Biological Technology and Engineering, HuaQiao University, Xiamen 361021, China; [email protected] 6 Institute of Eco-Chongming (IEC), Shanghai 202162, China 7 Institute of Atmospheric Sciences, Fudan University, Shanghai 200433, China * Correspondence: [email protected] (Y.R.); [email protected] (H.L.); [email protected] (K.H.); [email protected] (G.Z.) Ying Rao and Heyang Li contributed equally to this work. y Received: 6 February 2020; Accepted: 11 March 2020; Published: 25 March 2020 Abstract: As an important part of atmospheric aerosol, airborne bacteria have major impacts on human health. However, variations of airborne community structure due to human-induced activities and their possible impact on human health have not been well understood. In this study, we sampled atmospheric microbial aerosols in three Chinese cities (Shanghai, Xiamen, and Zhangzhou) with contrasting social-economic levels and analyzed the bacterial composition using high-throughput sequencing methods.
[Show full text]
Mean and SD Archaea Bacteria Genome Size (Mb)
Distributions for kingdom level Primer score mean and SD Genomic GC (%) mean and SD 60 3 2 50 1 Primer score 40 0 Genomic GC (%) Bacteria Bacteria Archaea Archaea kingdom kingdom 16S GC (%) mean and SD Genome size (Mb) mean and SD 65 5 60 4 55 3 16S GC (%) 2 Genome size (Mb) Genome size 50 Bacteria Bacteria Archaea Archaea kingdom kingdom 16S GC (%) Primer score 45 50 55 60 65 0 1 2 3 4 Acidobacteria Acidobacteria Actinobacteria Actinobacteria Aquificae Aquificae Bacteroidetes Bacteroidetes Caldiserica Caldiserica Chlamydiae Chlamydiae Chlorobi Primer scoremeanandSD Chlorobi 16S GC(%)meanandSD Chloroflexi Chloroflexi Chrysiogenetes Chrysiogenetes Crenarchaeota Crenarchaeota Cyanobacteria Cyanobacteria Deferribacteres Deferribacteres Deinococcus−Thermus Deinococcus−Thermus Dictyoglomi Dictyoglomi Elusimicrobia Elusimicrobia phylum phylum Euryarchaeota Euryarchaeota Fibrobacteres Fibrobacteres Firmicutes Firmicutes Fusobacteria Fusobacteria Gemmatimonadetes Gemmatimonadetes Ignavibacteria Ignavibacteria Ignavibacteriae Ignavibacteriae Korarchaeota Korarchaeota Lentisphaerae Lentisphaerae Nanoarchaeota Nanoarchaeota Nitrospirae Nitrospirae Planctomycetes Planctomycetes level phylum for Distributions Proteobacteria Proteobacteria Spirochaetes Spirochaetes Synergistetes Synergistetes Tenericutes Tenericutes Thaumarchaeota Thaumarchaeota Thermodesulfobacteria Thermodesulfobacteria Thermotogae Thermotogae unclassified unclassified Verrucomicrobia Verrucomicrobia Genome size (Mb) Genomic GC (%) 10.0 30 40 50 60 70 2.5 5.0 7.5 Acidobacteria Acidobacteria
[Show full text]
Changes in Digestive Microbiota, Rumen Fermentations and Oxidative Stress Around Parturition Are Alleviated by Live Yeast Feed Supplementation to Gestating Ewes
Journal of Fungi Article Changes in Digestive Microbiota, Rumen Fermentations and Oxidative Stress around Parturition Are Alleviated by Live Yeast Feed Supplementation to Gestating Ewes Lysiane Dunière 1,2 , Damien Esparteiro 1,2,†, Yacine Lebbaoui 1,2, Philippe Ruiz 2 , Mickael Bernard 3, Agnès Thomas 4, Denys Durand 4 , Evelyne Forano 2 and Frédérique Chaucheyras-Durand 1,2,* 1 Lallemand SAS, 19 rue des Briquetiers, BP 59, CEDEX, 31702 Blagnac, France; [email protected] (L.D.); [email protected] (D.E.); [email protected] (Y.L.) 2 UMR (Unité Mixte de Recherches) 454 MEDIS (Microbiologie Environnement Digestif et Santé), INRAE, Université Clermont Auvergne, 63122 Saint-Genès Champanelle, France; [email protected] (P.R.); [email protected] (E.F.) 3 UE (Unité Expérimentale) 1414 Herbipôle, INRAE (Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement), Université Clermont Auvergne, 63122 Saint-Genès Champanelle, France; [email protected] 4 UMR (Unité Mixte de Recherches) 1213 Herbivores, INRAE (Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement), Université Clermont Auvergne, 63122 Saint-Genès Champanelle, France; [email protected] (A.T.); [email protected] (D.D.) * Correspondence: [email protected] † Present address: Faculté des Sciences et Techniques, Université de Brest, 29200 Brest, France. Citation: Dunière, L.; Esparteiro, D.; Lebbaoui, Y.; Ruiz, P.; Bernard, M.; Abstract: Background: In ruminants, physiological and nutritional changes occur peripartum. We Thomas, A.; Durand, D.; Forano, E.; investigated if gastro-intestinal microbiota, rumen metabolism and antioxidant status were affected Chaucheyras-Durand, F. Changes in around parturition and what could be the impact of a daily supplementation of a live yeast additive Digestive Microbiota, Rumen in late gestating ewes.
[Show full text]