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Table S8. Detailed Information in the Water Microbial Community at Phylum, Family, and Genus Level

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Table S8. Detailed information in the water microbial community at phylum, family, and genus level (a) The annotation information of water microbial community at phylum level No. Phylum The number of contigs Abundance(%) 1 Proteobacteria 10948 54.43516309 2 Bacteroidetes 3601 17.90473349 3 Actinobacteria 3029 15.0606603 4 Cyanobacteria 1032 5.131264916 5 Firmicutes 535 2.660103421 6 Planctomycetes 306 1.521479714 7 Verrucomicrobia 295 1.466785998 8 Tenericutes 77 0.382856006 9 Deinococcus-Thermus 48 0.238663484 10 Chlorobi 36 0.178997613 11 Spirochaetes 35 0.174025457 12 Fusobacteria 29 0.144192522 13 Chloroflexi 27 0.13424821 14 Acidobacteria 21 0.104415274 15 Gemmatimonadetes 18 0.089498807 16 Chlamydiae 9 0.044749403 17 Nitrospirae 8 0.039777247 18 Armatimonadetes 7 0.034805091 19 Lentisphaerae 7 0.034805091 20 Kiritimatiellaeota 7 0.034805091 21 Aquificae 7 0.034805091 22 Synergistetes 5 0.02486078 23 Ignavibacteriae 4 0.019888624 24 Thermotogae 4 0.019888624 25 Candidatus Saccharibacteria 3 0.014916468 26 Calditrichaeota 3 0.014916468 27 Fibrobacteres 2 0.009944312 28 Candidatus Gracilibacteria 2 0.009944312 29 Deferribacteres 2 0.009944312 30 Chrysiogenetes 2 0.009944312 31 Dictyoglomi 1 0.004972156 32 Elusimicrobia 1 0.004972156 33 Thermodesulfobacteria 1 0.004972156 (b) The annotation information of Proteobacteria at family level No. Family of Proteobacteria The number of contigs Abundance(%) 1 Rhodobacteraceae 4661 42.57398612 2 Comamonadaceae 1616 14.76068688 3 Pseudomonadaceae 413 3.772378517 4 Burkholderiaceae 322 2.941176471 5 others 270 2.466203873 6 Alcaligenaceae 238 2.173913043 7 Rhizobiaceae 182 1.662404092 8 Sphingomonadaceae 159 1.452320058 9 Xanthomonadaceae 150 1.370113263 10 Bradyrhizobiaceae 143 1.306174644 11 Hyphomonadaceae 123 1.123492875 12 Methylophilaceae 114 1.04128608 13 Enterobacteriaceae 113 1.032151991 14 Phyllobacteriaceae 98 0.895140665 15 Rhodospirillaceae 97 0.886006577 16 Halomonadaceae 93 0.849470223 17 Erythrobacteraceae 88 0.803799781 18 Oxalobacteraceae 82 0.74899525 19 Alteromonadaceae 79 0.721592985 20 Zoogloeaceae 70 0.639386189 21 Methylobacteriaceae 68 0.621118012 22 Caulobacteraceae 67 0.611983924 23 Ectothiorhodospiraceae 63 0.57544757 24 Moraxellaceae 59 0.538911217 25 Yersiniaceae 56 0.511508951 26 Vibrionaceae 56 0.511508951 27 Chromobacteriaceae 53 0.484106686 28 Campylobacteraceae 50 0.456704421 29 Polyangiaceae 47 0.429302156 30 Acetobacteraceae 46 0.420168067 31 Desulfovibrionaceae 46 0.420168067 32 Chromatiaceae 45 0.411033979 33 Methylococcaceae 44 0.40189989 34 Aeromonadaceae 44 0.40189989 35 Geobacteraceae 40 0.365363537 36 Neisseriaceae 38 0.34709536 37 Shewanellaceae 38 0.34709536 38 Hyphomicrobiaceae 37 0.337961271 39 Erwiniaceae 37 0.337961271 40 Pasteurellaceae 37 0.337961271 41 Aurantimonadaceae 34 0.310559006 42 Desulfuromonadaceae 33 0.301424918 43 Halieaceae 32 0.292290829 44 Francisellaceae 30 0.274022653 45 Morganellaceae 26 0.237486299 46 Archangiaceae 26 0.237486299 47 Legionellaceae 25 0.22835221 48 Sandaracinaceae 24 0.219218122 49 Myxococcaceae 24 0.219218122 50 Rhodanobacteraceae 23 0.210084034 51 Oceanospirillaceae 23 0.210084034 52 Xanthobacteraceae 22 0.200949945 53 Pseudoalteromonadaceae 22 0.200949945 54 Cellvibrionaceae 22 0.200949945 55 Nitrosomonadaceae 20 0.182681768 56 Microbulbiferaceae 18 0.164413592 57 Anaeromyxobacteraceae 18 0.164413592 58 Desulfobacteraceae 18 0.164413592 59 Helicobacteraceae 18 0.164413592 60 Gallionellaceae 17 0.155279503 61 Pectobacteriaceae 17 0.155279503 62 Alcanivoracaceae 17 0.155279503 63 Wenzhouxiangellaceae 17 0.155279503 64 Sterolibacteriaceae 16 0.146145415 65 Rhodocyclaceae 14 0.127877238 66 Cohaesibacteraceae 13 0.118743149 67 Kofleriaceae 13 0.118743149 68 Piscirickettsiaceae 12 0.109609061 69 Azonexaceae 11 0.100474973 70 Acidithiobacillaceae 11 0.100474973 71 Rhodobiaceae 10 0.091340884 72 Methylocystaceae 10 0.091340884 73 Thiotrichaceae 10 0.091340884 74 Sinobacteraceae 9 0.082206796 75 Desulfobulbaceae 9 0.082206796 76 Beijerinckiaceae 8 0.073072707 77 Rickettsiaceae 8 0.073072707 78 Colwelliaceae 8 0.073072707 79 Woeseiaceae 8 0.073072707 80 Brucellaceae 7 0.063938619 81 Idiomarinaceae 7 0.063938619 82 Orbaceae 7 0.063938619 83 Desulfomicrobiaceae 7 0.063938619 84 Chelatococcaceae 6 0.054804531 85 Caedimonadaceae 6 0.054804531 86 Magnetococcaceae 6 0.054804531 87 Thiobacillaceae 6 0.054804531 88 Saccharospirillaceae 6 0.054804531 89 Spongiibacteraceae 6 0.054804531 90 Acidiferrobacteraceae 6 0.054804531 91 Halobacteriovoraceae 6 0.054804531 92 Bartonellaceae 5 0.045670442 93 Psychromonadaceae 5 0.045670442 94 Immundisolibacteraceae 5 0.045670442 95 Syntrophaceae 5 0.045670442 96 Bacteriovoracaceae 5 0.045670442 97 Anaplasmataceae 4 0.036536354 98 Pelagibacteraceae 4 0.036536354 99 Hafniaceae 4 0.036536354 100 Granulosicoccaceae 4 0.036536354 101 Halothiobacillaceae 4 0.036536354 102 Bradymonadaceae 4 0.036536354 103 Mariprofundaceae 4 0.036536354 104 Parvularculaceae 3 0.027402265 105 Ferrimonadaceae 3 0.027402265 106 Moritellaceae 3 0.027402265 107 Kangiellaceae 3 0.027402265 108 Vulgatibacteraceae 3 0.027402265 109 Desulfohalobiaceae 3 0.027402265 110 Candidatus Paracaedibacteraceae 2 0.018268177 111 Oleiphilaceae 2 0.018268177 112 Coxiellaceae 2 0.018268177 113 Cardiobacteriaceae 2 0.018268177 114 Candidatus Desulfofervidaceae 2 0.018268177 115 Desulfarculaceae 2 0.018268177 116 Hydrogenophilaceae 2 0.018268177 117 Sutterellaceae 1 0.009134088 118 Budviciaceae 1 0.009134088 119 Endozoicomonadaceae 1 0.009134088 120 Hahellaceae 1 0.009134088 121 Salinisphaeraceae 1 0.009134088 122 Syntrophobacteraceae 1 0.009134088 123 Desulfurellaceae 1 0.009134088 124 Nautiliaceae 1 0.009134088 125 Bdellovibrionaceae 1 0.009134088 (c) The annotation information of Proteobacteria at genus level No. Genus of Proteobacteria The number of contigs Abundance(%) 1 Yoonia 2453 22.40591889 2 Limnohabitans 740 6.759225429 3 Pseudomonas 403 3.681037632 4 Rhodobacter 343 3.132992327 5 Paracoccus 333 3.041651443 6 Hydrogenophaga 238 2.173913043 7 Sulfitobacter 212 1.936426745 8 others 208 1.899890391 9 Acidovorax 142 1.297040555 10 Celeribacter 140 1.278772379 11 Burkholderia 129 1.178297406 12 Bordetella 128 1.169163318 13 Hyphomonas 106 0.968213372 14 Rhodoferax 100 0.913408842 15 Octadecabacter 98 0.895140665 16 Rhodobaca 92 0.840336134 17 Rhodovulum 88 0.803799781 18 Phaeobacter 85 0.776397516 19 Methylotenera 77 0.703324808 20 Bradyrhizobium 75 0.685056631 21 Ruegeria 74 0.675922543 22 Variovorax 73 0.666788455 23 Pseudohongiella 73 0.666788455 24 Rhizobium 71 0.648520278 25 Halomonas 69 0.630252101 26 Comamonas 61 0.557179393 27 Cupriavidus 53 0.484106686 28 Gemmobacter 52 0.474972598 29 Sphingomonas 49 0.447570332 30 Stenotrophomonas 49 0.447570332 31 Defluviimonas 47 0.429302156 32 Achromobacter 47 0.429302156 33 Sinorhizobium 46 0.420168067 34 Mesorhizobium 46 0.420168067 35 Methylobacterium 46 0.420168067 36 Sphingobium 46 0.420168067 37 Polaromonas 46 0.420168067 38 Marinobacter 46 0.420168067 39 Paraburkholderia 43 0.392765802 40 Vibrio 42 0.383631714 41 Azoarcus 41 0.374497625 42 Sagittula 40 0.365363537 43 Xanthomonas 40 0.365363537 44 Confluentimicrobium 39 0.356229448 45 Antarctobacter 39 0.356229448 46 Azospirillum 39 0.356229448 47 Dinoroseobacter 38 0.34709536 48 Acinetobacter 38 0.34709536 49 Shewanella 38 0.34709536 50 Desulfovibrio 37 0.337961271 51 Thalassococcus 36 0.328827183 52 Sorangium 34 0.310559006 53 Yangia 33 0.301424918 54 Roseovarius 33 0.301424918 55 Rhodopseudomonas 33 0.301424918 56 Altererythrobacter 33 0.301424918 57 Polynucleobacter 33 0.301424918 58 Lysobacter 32 0.292290829 59 Roseibacterium 31 0.283156741 60 Leisingera 31 0.283156741 61 Pandoraea 31 0.283156741 62 Caulobacter 30 0.274022653 63 Geobacter 30 0.274022653 64 Martelella 29 0.264888564 65 Ralstonia 29 0.264888564 66 Herbaspirillum 29 0.264888564 67 Campylobacter 29 0.264888564 68 Marinovum 28 0.255754476 69 Candidatus Methylopumilus 28 0.255754476 70 Thioalkalivibrio 28 0.255754476 71 Francisella 28 0.255754476 72 Ottowia 27 0.246620387 73 Ramlibacter 27 0.246620387 74 Thauera 27 0.246620387 75 Serratia 27 0.246620387 76 Brevirhabdus 26 0.237486299 77 Roseobacter 26 0.237486299 78 Massilia 26 0.237486299 79 Sphingopyxis 25 0.22835221 80 Halioglobus 25 0.22835221 81 Jannaschia 24 0.219218122 82 Ketogulonicigenium 24 0.219218122 83 Sandaracinus 24 0.219218122 84 Agrobacterium 23 0.210084034 85 Bosea 23 0.210084034 86 Erythrobacter 23 0.210084034 87 Brevundimonas 23 0.210084034 88 Melaminivora 23 0.210084034 89 Thiomonas 23 0.210084034 90 Aeromonas 23 0.210084034 91 Desulfuromonas 23 0.210084034 92 Pseudoalteromonas 22 0.200949945 93 Myxococcus 22 0.200949945 94 Thioclava 21 0.191815857 95 Legionella 21 0.191815857 96 Pelagibaca 20 0.182681768 97 Yersinia 20 0.182681768 98 Ensifer 19 0.17354768 99 Novosphingobium 19 0.17354768 100 Porphyrobacter 19 0.17354768 101 Magnetospirillum 19 0.17354768 102 Chromobacterium 19 0.17354768 103 Neisseria 19 0.17354768 104 Salipiger 18 0.164413592 105 Pantoea 18 0.164413592 106 Microbulbifer 18 0.164413592 107 Anaeromyxobacter 18 0.164413592 108 Tateyamaria 17 0.155279503 109 Maricaulis 17 0.155279503 110 Microvirga 17 0.155279503 111 Curvibacter 17 0.155279503 112 Pusillimonas 17 0.155279503 113 Wenzhouxiangella 17 0.155279503 114 Enterobacter 16 0.146145415 115 Klebsiella 16 0.146145415 116 Methylomicrobium 16 0.146145415 117 Nitratireductor 15 0.137011326 118 Aminobacter 15 0.137011326 119 Nitrosomonas 15 0.137011326 120 Alteromonas 15 0.137011326 121 Pannonibacter 14 0.127877238
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  • WO 2018/064165 A2 (.Pdf)

    WO 2018/064165 A2 (.Pdf)

    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/064165 A2 05 April 2018 (05.04.2018) W !P O PCT (51) International Patent Classification: Published: A61K 35/74 (20 15.0 1) C12N 1/21 (2006 .01) — without international search report and to be republished (21) International Application Number: upon receipt of that report (Rule 48.2(g)) PCT/US2017/053717 — with sequence listing part of description (Rule 5.2(a)) (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 62/400,372 27 September 2016 (27.09.2016) US 62/508,885 19 May 2017 (19.05.2017) US 62/557,566 12 September 2017 (12.09.2017) US (71) Applicant: BOARD OF REGENTS, THE UNIVERSI¬ TY OF TEXAS SYSTEM [US/US]; 210 West 7th St., Austin, TX 78701 (US). (72) Inventors: WARGO, Jennifer; 1814 Bissonnet St., Hous ton, TX 77005 (US). GOPALAKRISHNAN, Vanch- eswaran; 7900 Cambridge, Apt. 10-lb, Houston, TX 77054 (US). (74) Agent: BYRD, Marshall, P.; Parker Highlander PLLC, 1120 S. Capital Of Texas Highway, Bldg. One, Suite 200, Austin, TX 78746 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
  • Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X

    Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X

    Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae
  • Extensive Microbial Diversity Within the Chicken Gut Microbiome Revealed by Metagenomics and Culture

    Extensive Microbial Diversity Within the Chicken Gut Microbiome Revealed by Metagenomics and Culture

    Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture Rachel Gilroy1, Anuradha Ravi1, Maria Getino2, Isabella Pursley2, Daniel L. Horton2, Nabil-Fareed Alikhan1, Dave Baker1, Karim Gharbi3, Neil Hall3,4, Mick Watson5, Evelien M. Adriaenssens1, Ebenezer Foster-Nyarko1, Sheikh Jarju6, Arss Secka7, Martin Antonio6, Aharon Oren8, Roy R. Chaudhuri9, Roberto La Ragione2, Falk Hildebrand1,3 and Mark J. Pallen1,2,4 1 Quadram Institute Bioscience, Norwich, UK 2 School of Veterinary Medicine, University of Surrey, Guildford, UK 3 Earlham Institute, Norwich Research Park, Norwich, UK 4 University of East Anglia, Norwich, UK 5 Roslin Institute, University of Edinburgh, Edinburgh, UK 6 Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia 7 West Africa Livestock Innovation Centre, Banjul, The Gambia 8 Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem, Israel 9 Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK ABSTRACT Background: The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. Results: We performed metagenomic sequencing of fifty chicken faecal samples from Submitted 4 December 2020 two breeds and analysed these, alongside all (n = 582) relevant publicly available Accepted 22 January 2021 chicken metagenomes, to cluster over 20 million non-redundant genes and to Published 6 April 2021 construct over 5,500 metagenome-assembled bacterial genomes.
  • Pathogen Challenge and Dietary Shift Alter Microbiota Composition And

    Pathogen Challenge and Dietary Shift Alter Microbiota Composition And

    fmicb-12-703421 July 19, 2021 Time: 11:40 # 1 ORIGINAL RESEARCH published: 19 July 2021 doi: 10.3389/fmicb.2021.703421 Pathogen Challenge and Dietary Shift Alter Microbiota Composition and Activity in a Mucin-Associated in vitro Model of the Piglet Colon (MPigut-IVM) Simulating Weaning Transition Raphaële Gresse1,2, Frédérique Chaucheyras-Durand1,2, Juan J. Garrido3, Sylvain Denis1, Angeles Jiménez-Marín3, Martin Beaumont4, Tom Van de Wiele5, Evelyne Forano1 and Stéphanie Blanquet-Diot1* 1 INRAE, UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France, 2 Lallemand SAS, Blagnac, France, 3 Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain, 4 GenPhySE, INRAE, ENVT, Université de Toulouse, Castanet-Tolosan, France, 5 Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium Edited by: Wakako Ikeda-Ohtsubo, Tohoku University, Japan Enterotoxigenic Escherichia coli (ETEC) is the principal pathogen responsible for post- Reviewed by: weaning diarrhea in newly weaned piglets. Expansion of ETEC at weaning is thought to Katie Lynn Summers, be the consequence of various stress factors such as transient anorexia, dietary change United States Department or increase in intestinal inflammation and permeability, but the exact mechanisms remain of Agriculture (USDA), United States Åsa Sjöling, to be elucidated. As the use of animal experiments raise more and more ethical Karolinska Institutet (KI), Sweden concerns, we used a recently developed in vitro model of piglet colonic microbiome *Correspondence: and mucobiome, the MPigut-IVM, to evaluate the effects of a simulated weaning Stéphanie Blanquet-Diot [email protected] transition and pathogen challenge at weaning.