DOCSLIB.ORG

1,520 Reference Genomes from Cultivated Human Gut Bacteria Enable Functional Microbiome Analyses

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
1,520 Reference Genomes from Cultivated Human Gut Bacteria Enable Functional Microbiome Analyses RESOURCE https://doi.org/10.1038/s41587-018-0008-8 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses Yuanqiang Zou 1,2,3,13, Wenbin Xue1,2,13, Guangwen Luo1,2,4,13, Ziqing Deng 1,2,13, Panpan Qin 1,2,5,13, Ruijin Guo1,2, Haipeng Sun1,2, Yan Xia1,2,5, Suisha Liang1,2,6, Ying Dai1,2, Daiwei Wan1,2, Rongrong Jiang1,2, Lili Su1,2, Qiang Feng1,2, Zhuye Jie1,2, Tongkun Guo1,2, Zhongkui Xia1,2, Chuan Liu1,2,6, Jinghong Yu1,2, Yuxiang Lin1,2, Shanmei Tang1,2, Guicheng Huo4, Xun Xu1,2, Yong Hou 1,2, Xin Liu 1,2,7, Jian Wang1,8, Huanming Yang1,8, Karsten Kristiansen 1,2,3,9, Junhua Li 1,2,10*, Huijue Jia 1,2,11* and Liang Xiao 1,2,6,9,12* Reference genomes are essential for metagenomic analyses and functional characterization of the human gut microbiota. We present the Culturable Genome Reference (CGR), a collection of 1,520 nonredundant, high-quality draft genomes generated from >6,000 bacteria cultivated from fecal samples of healthy humans. Of the 1,520 genomes, which were chosen to cover all major bacterial phyla and genera in the human gut, 264 are not represented in existing reference genome catalogs. We show that this increase in the number of reference bacterial genomes improves the rate of mapping metagenomic sequencing reads from 50% to >70%, enabling higher-resolution descriptions of the human gut microbiome. We use the CGR genomes to annotate functions of 338 bacterial species, showing the utility of this resource for functional studies. We also carry out a pan-genome analysis of 38 important human gut species, which reveals the diversity and specificity of functional enrichment between their core and dispensable genomes. he human gut microbiota refers to the all the microorganisms database belong to the human gut microbiota. Rather, the focus that inhabit the human gastrointestinal tract. Diverse roles of has been on clinically relevant pathogenic bacteria, which are over- the gut microbiota in human health and disease have been rec- represented in the microbial databases. The first catalog of 178 ref- T 1,2 ognized . Metagenomic studies have transformed our understand- erence bacterial genomes for the human microbiota was reported ing of the taxonomic and functional diversity of human microbiota, by the Human Microbiome Project (HMP)14 in 2010. To date, the but more than half of the sequencing reads from a typical human HMP has sequenced >2,000 microbial genomes cultivated from fecal metagenome cannot be mapped to existing bacterial reference human body sites, 437 of which are gut microbiota (data accessed genomes3,4. The lack of high-quality reference genomes has become an 8 September 2017). However, the number of reference gut bacterial obstacle for high-resolution analyses of the human gut microbiome. genomes is still far from saturated. Although the previously reported Integrated Gene Catalog (IGC) We present a reference catalog of genomes of cultivated human has enabled metagenomic, metatranscriptomic and metaproteomic gut bacteria (named the CGR), established by culture-based isola- analyses3,5,6, the gap between compositional and functional analy- tion of > 6,000 bacterial isolates from fecal samples of healthy indi- ses can only be filled by individual bacterial genomes. Genes that viduals. The CGR comprises 1,520 nonredundant, high-quality co-vary among samples can be clustered into metagenomic linkage draft bacterial genomes, contributing at least 264 new reference groups7, metagenomic clusters8 and metagenomic species9,10, whose genomes to the gut microbiome. After inclusion of CGR genomes, annotation depends on alignment to the limited number of exist- the mapping rate of selected metagenomic datasets improved from ing reference genomes. Other metagenomics-based analyses of the around 50% to over 70%. In addition to improving metagenomic gut microbiome—for example, single nucleotide polymorphisms analyses, the CGR will improve functional characterization and (SNPs), indels and copy number variations—rely on the coverage pan-genomic analyses of the gut microbiota at high resolution. and quality of reference genomes11–13. Despite the rapid increase in the number of sequenced bacte- Results rial and archaeal genomes, reference genomes for gut bacteria are Expanded catalog of gut bacterial genomes. We obtained underrepresented. It is estimated that < 4% of the bacterial genomes 6,487 bacterial isolates from fresh fecal samples donated by 155 in the US National Center for Biotechnology Information (NCBI) healthy volunteers by using 11 different media under anaerobic 1BGI-Shenzhen, Shenzhen, China. 2China National Genebank, BGI-Shenzhen, Shenzhen, China. 3Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark. 4Key Laboratory of Dairy Science, College of Food Sciences, Northeast Agricultural University, Harbin, Heilongjiang, China. 5BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China. 6Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China. 7BGI-Qingdao, BGI-Shenzhen, Qingdao, China. 8James D. Watson Institute of Genome Sciences, Hangzhou, China. 9Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China. 10School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China. 11Macau University of Science and Technology, Taipa, Macau, China. 12Department of Digestive Diseases, Huashan Hospital of Fudan University, Shanghai, China. 13These authors contributed equally: Yuanqiang Zou, Wenbin Xue, Guangwen Luo, Ziqing Deng, Panpan Qin. *e-mail: [email protected]; [email protected]; [email protected] NATURE BIOTECHNOLOgy | VOL 37 | FEBRUARY 2019 | 179–185 | www.nature.com/naturebiotechnology 179 RESOURCE NATURE BIOTECHNOLOGY Clu 243 Clu 107 Clu 197 Phylum annotation Clu 149 Clu 126 Clu 292 Clu 14 Clu 17 9 Clu 20 Clu 65 1 Clu 73 127 u 28 Clu 184 Clu 1 u 262 7 9 Clu 28 6 Clu 248 Clu 46 2 CluC 9 u 78 CluC Clu 262 7 Clu 128 5 CluC 101 Clu 81 CluC 7 3 Clu 78 0 Clu 1 CluC 153 2 Clu 18 Clu 23 4 Clu 199 CluC 246 Clu Clu 307 Clu 222 Clu 319 62 44 CluC 60 Clu 283 4 CluC 320 92 6 Clu Clu 47 Clu 279 CluC 124 2 Clu CluC 64 3 CluC 162 Clu 75 Clu 198 Clu 32 268 Bacteroidetes CluC 84 Clu 2 8 61 7 CluC 10 Clu 133 5 CluC 77 9 9 Clu 121 02 CluC 1 Clu 27 Clu 155 94 Clu 256 CluC 25 Clu Clu 0 138 Clu 109 138 147 Clu 17 CluC Clu 103 CluC 33 Clu 45 7 Clu 220 3 Clu 115 Clu 52 Actinobacteria Clu 5 Clu 142 13 2 CluC 53 Clu Clu 331 4 CluC 131 54 4 CluC 66 Clu 22 CluC 337 Clu 249 4 CluC 51 Clu 48 9 CluC 176 Clu 223 CluC 216 Clu 26 3 CluC 50 9 Clu 0 CluC 3 Firmicutes 49 4 Clu 6 CluC 285 Clu 9 CluC 21 125 Clu CluC 42 Clu 338 6 CluC 173 Clu 8 Clu 150 24 Clu 1 4 CluC 130 Clu 2 233 CluC 135 21 Proteobacteria Clu 95 CluC 299 Clu 116 5 CluC 309 Clu 6 CluC 239 102 CluC 291 Clu 61 2 Clu 105 CluC 191 CluC 287 Clu 205 CluC 247 Clu 229 5 CluC 89 Fusobacteria 9 1 CluC 30 CluC 163 293 CluC CluC 278 3 CluC 27 Clu 57 2 15 Clu CluC 271 CluC 297 288 CluC Clu 91 Clu 83 Clu 26 26 7 CluC 2 Clu 234 4 CluC 328 Clu 16 4 CluC 323 Clu 140 86 Clu 1 Clu 196 CluC 175 Clu 3 06 Clu 257 Clu 251 1 CluC 136 Clu 252 CluC 266 Clu 21 3 CluC 201 Clu 228 8 Clu 114 Clu 32 2 CluC 110 Clu 76 CluC 275 Clu 334 Clu 36 Clu 211 Clu 141 Clu 2500 CluC 59 Clu 255 CluC 8 Clu 210 CluC 167 Clu 2988 Clu 277 Clu 87 Clu 258 Clu 588 CluC 305 Clu 2644 ClC u 300 Clu 2322 CluC 67 Clu 1466 CluC 139 Clu 1299 CluC 219 6 Clu 206 Clu 276 Clu 231 CluC 55 Clu 3188 Clu 104 Clu 156 ClC u 37 6 CluC 2 Clu 336 08 6 Clu 166 Clu 159 5 CluC 118 Clu 325 8 Clu 1 Clu 178 82 3 Clu 237 Clu 203 600 CluC 2 Clu 1 42 Clu 30 Clu 261 8 6 CluC 241 Clu 106 0 ClC u 314 Clu 170 6 Clu 96 Clu 26 5 Clu 137 Clu 19 4 CluC 100 Clu 174 CluC 111 Clu 311 Clu 233 171 Clu 2 CluC 28 Clu 312 4 CluC 3 Clu 40 30 0 Clu 190 Clu 230 9 CluC 316 179 Clu 5 CluC 2 Clu 15 74 4 Clu Clu 4 281 0 CluC 215 Clu 20 CluC Clu 3 11 7 Clu 20 9 Clu 327 8 CluC 18 4 Clu 148 3 Clu 9 217 Clu 183 5 CluC 2 09 Clu 335 4 CluC 72 Clu 254 2 Clu 80 Clu 12 Clu 212 8 CluC 99 Clu 238 2 2 Clu 22 6 CluC CluC 74 Clu 56 7 263 3 Clu Clu 207 169 6 CluC 333 Clu 113 p Clu 85 Clu 296 3 Clu 9 CluC 25 Outgroup 8 3 Clu 303 CluC 157 Clu 108 Clu Clu 11 8 CluC 18 4 324 Clu 158 2 Clu Clu 44 5 5 CluC 68 Clu 2 225 CluC 315 0 Clu 35 CluC 16 2 CluC 2 Clu 310 8 CluC 86 8 Clu 112 5 82 Clu 38 8 Clu 8 Clu Clu 295 Clu 98 Clu 18 8 63 CluC 18 9 Clu 290 CluC 265 7 Clu 321 Clu 2 Clu 79 CluC 1 1 Clu 16 CluC 31 180 4 Clu 82 Clu 14 9 Clu 32 Clu 17 Clu 34 Clu 21 7 CluC 33 Clu 29 3 3 Clu 2 Clu 28 2 Clu 145 72 Clu 41 CluC 2 4 CluC 240 151 Clu 13 2 0 CluC 43 1 Clu 280 Clu 2 Clu 3 27 6 Clu Clu 313 3 Clu 71 Clu 154 Clu 21 Clu 70 0 Clu 11 7 CluC 253 Clu 3 0 CluC CluC 188 3 120 Clu 2 04 4 Clu 165 CluC 132 Clu 19 Clu 1 Clu 24 Clu 326 4 2 9 5 Clu 193 9 44 Clu 3 5 Clu 97 8 Clu 90 7 Clu 23 7 Clu 194 2 Clu 294 5 Clu 2 Clu 302 Clu 269 Clu 235 Clu 28 Fig.
Load more

Recommended publications
  • A Taxonomic Note on the Genus Lactobacillus
    Taxonomic Description template 1 A taxonomic note on the genus Lactobacillus: 2 Description of 23 novel genera, emended description 3 of the genus Lactobacillus Beijerinck 1901, and union 4 of Lactobacillaceae and Leuconostocaceae 5 Jinshui Zheng1, $, Stijn Wittouck2, $, Elisa Salvetti3, $, Charles M.A.P. Franz4, Hugh M.B. Harris5, Paola 6 Mattarelli6, Paul W. O’Toole5, Bruno Pot7, Peter Vandamme8, Jens Walter9, 10, Koichi Watanabe11, 12, 7 Sander Wuyts2, Giovanna E. Felis3, #*, Michael G. Gänzle9, 13#*, Sarah Lebeer2 # 8 '© [Jinshui Zheng, Stijn Wittouck, Elisa Salvetti, Charles M.A.P. Franz, Hugh M.B. Harris, Paola 9 Mattarelli, Paul W. O’Toole, Bruno Pot, Peter Vandamme, Jens Walter, Koichi Watanabe, Sander 10 Wuyts, Giovanna E. Felis, Michael G. Gänzle, Sarah Lebeer]. 11 The definitive peer reviewed, edited version of this article is published in International Journal of 12 Systematic and Evolutionary Microbiology, https://doi.org/10.1099/ijsem.0.004107 13 1Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Hubei Key 14 Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, P.R. China. 15 2Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience 16 Engineering, University of Antwerp, Antwerp, Belgium 17 3 Dept. of Biotechnology, University of Verona, Verona, Italy 18 4 Max Rubner‐Institut, Department of Microbiology and Biotechnology, Kiel, Germany 19 5 School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland 20 6 University of Bologna, Dept. of Agricultural and Food Sciences, Bologna, Italy 21 7 Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit 22 Brussel, Brussels, Belgium 23 8 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, 24 Belgium 25 9 Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada 26 10 Department of Biological Sciences, University of Alberta, Edmonton, Canada 27 11 National Taiwan University, Dept.
    [Show full text]
  • Macellibacteroides Fermentans Gen. Nov., Sp. Nov., a Member of the Family Porphyromonadaceae Isolated from an Upflow Anaerobic Filter Treating Abattoir Wastewaters
    International Journal of Systematic and Evolutionary Microbiology (2012), 62, 2522–2527 DOI 10.1099/ijs.0.032508-0 Macellibacteroides fermentans gen. nov., sp. nov., a member of the family Porphyromonadaceae isolated from an upflow anaerobic filter treating abattoir wastewaters Linda Jabari,1,2 Hana Gannoun,2 Jean-Luc Cayol,1 Abdeljabbar Hedi,1 Mitsuo Sakamoto,3 Enevold Falsen,4 Moriya Ohkuma,3 Moktar Hamdi,2 Guy Fauque,1 Bernard Ollivier1 and Marie-Laure Fardeau1 Correspondence 1Aix-Marseille Universite´ du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, Case 925, Marie-Laure Fardeau 163 Avenue de Luminy, 13288 Marseille Cedex 9, France [email protected] 2Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Applique´es et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis Cedex, Tunisia 3Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center 2-1 Hirosawa, Wako, Saitama 351-0198, Japan 4CCUG, Culture Collection, Department of Clinical Bacteriology, University of Go¨teborg, 41346 Go¨teborg, Sweden A novel obligately anaerobic, non-spore-forming, rod-shaped mesophilic bacterium, which stained Gram-positive but showed the typical cell wall structure of Gram-negative bacteria, was isolated from an upflow anaerobic filter treating abattoir wastewaters in Tunisia. The strain, designated LIND7HT, grew at 20–45 6C (optimum 35–40 6C) and at pH 5.0–8.5 (optimum pH 6.5–7.5). It did not require NaCl for growth, but was able to grow in the presence of up to 2 % NaCl. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors.
    [Show full text]
  • Robust Taxonomic Classification of Uncharted Microbial Sequences and Bins with CAT and BAT
    bioRxiv preprint doi: https://doi.org/10.1101/530188; this version posted January 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT F.A. Bastiaan von Meijenfeldt1,†, Ksenia Arkhipova1,†, Diego D. Cambuy1, Felipe H. Coutinho2,3, Bas E. Dutilh1,2,* 1 Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, The Netherlands. 2 Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands. 3 Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. * To whom correspondence should be addressed. Tel: +31 30 253 4212; Email: [email protected]. † These authors contributed equally to this work. Present Address: [Felipe H. Couthinho], Evolutionary Genomics Group, Departamento de Produccíon y Microbiología, Universidad Miguel Hernández, Campus San Juan, San Juan, Alicante 03550, Spain. ABSTRACT Current-day metagenomics increasingly requires taxonomic classification of long DNA sequences and metagenome-assembled genomes (MAGs) of unknown microorganisms. We show that the standard best-hit approach often leads to classifications that are too specific. We present tools to classify high- quality metagenomic contigs (Contig Annotation Tool, CAT) and MAGs (Bin Annotation Tool, BAT) and thoroughly benchmark them with simulated metagenomic sequences that are classified against a reference database where related sequences are increasingly removed, thereby simulating increasingly unknown queries. We find that the query sequences are correctly classified at low taxonomic ranks if closely related organisms are present in the reference database, while classifications are made higher in the taxonomy when closely related organisms are absent, thus avoiding spurious classification specificity.
    [Show full text]
  • Gut Microbiota and Inflammation
    Nutrients 2011, 3, 637-682; doi:10.3390/nu3060637 OPEN ACCESS nutrients ISSN 2072-6643 www.mdpi.com/journal/nutrients Review Gut Microbiota and Inflammation Asa Hakansson and Goran Molin * Food Hygiene, Division of Applied Nutrition, Department of Food Technology, Engineering and Nutrition, Lund University, PO Box 124, SE-22100 Lund, Sweden; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +46-46-222-8327; Fax: +46-46-222-4532. Received: 15 April 2011; in revised form: 19 May 2011 / Accepted: 24 May 2011 / Published: 3 June 2011 Abstract: Systemic and local inflammation in relation to the resident microbiota of the human gastro-intestinal (GI) tract and administration of probiotics are the main themes of the present review. The dominating taxa of the human GI tract and their potential for aggravating or suppressing inflammation are described. The review focuses on human trials with probiotics and does not include in vitro studies and animal experimental models. The applications of probiotics considered are systemic immune-modulation, the metabolic syndrome, liver injury, inflammatory bowel disease, colorectal cancer and radiation-induced enteritis. When the major genomic differences between different types of probiotics are taken into account, it is to be expected that the human body can respond differently to the different species and strains of probiotics. This fact is often neglected in discussions of the outcome of clinical trials with probiotics. Keywords: probiotics; inflammation; gut microbiota 1. Inflammation Inflammation is a defence reaction of the body against injury. The word inflammation originates from the Latin word ―inflammatio‖ which means fire, and traditionally inflammation is characterised by redness, swelling, pain, heat and impaired body functions.
    [Show full text]
  • Integrative Annotation of 21,037 Human Genes Validated by Full-Length Cdna Clones
    PLoS BIOLOGY Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones Tadashi Imanishi1, Takeshi Itoh1,2, Yutaka Suzuki3,68, Claire O’Donovan4, Satoshi Fukuchi5, Kanako O. Koyanagi6, Roberto A. Barrero5, Takuro Tamura7,8, Yumi Yamaguchi-Kabata1, Motohiko Tanino1,7, Kei Yura9, Satoru Miyazaki5, Kazuho Ikeo5, Keiichi Homma5, Arek Kasprzyk4, Tetsuo Nishikawa10,11, Mika Hirakawa12, Jean Thierry-Mieg13,14, Danielle Thierry-Mieg13,14, Jennifer Ashurst15, Libin Jia16, Mitsuteru Nakao3, Michael A. Thomas17, Nicola Mulder4, Youla Karavidopoulou4, Lihua Jin5, Sangsoo Kim18, Tomohiro Yasuda11, Boris Lenhard19, Eric Eveno20,21, Yoshiyuki Suzuki5, Chisato Yamasaki1, Jun-ichi Takeda1, Craig Gough1,7, Phillip Hilton1,7, Yasuyuki Fujii1,7, Hiroaki Sakai1,7,22, Susumu Tanaka1,7, Clara Amid23, Matthew Bellgard24, Maria de Fatima Bonaldo25, Hidemasa Bono26, Susan K. Bromberg27, Anthony J. Brookes19, Elspeth Bruford28, Piero Carninci29, Claude Chelala20, Christine Couillault20,21, Sandro J. de Souza30, Marie-Anne Debily20, Marie-Dominique Devignes31, Inna Dubchak32, Toshinori Endo33, Anne Estreicher34, Eduardo Eyras15, Kaoru Fukami-Kobayashi35, Gopal R. Gopinath36, Esther Graudens20,21, Yoonsoo Hahn18, Michael Han23, Ze-Guang Han21,37, Kousuke Hanada5, Hideki Hanaoka1, Erimi Harada1,7, Katsuyuki Hashimoto38, Ursula Hinz34, Momoki Hirai39, Teruyoshi Hishiki40, Ian Hopkinson41,42, Sandrine Imbeaud20,21, Hidetoshi Inoko1,7,43, Alexander Kanapin4, Yayoi Kaneko1,7, Takeya Kasukawa26, Janet Kelso44, Paul Kersey4, Reiko Kikuno45, Kouichi
    [Show full text]
  • Gut Microbiota Features Associated with Clostridioides Difficile Colonization in Dairy Calves
    bioRxiv preprint doi: https://doi.org/10.1101/2021.05.11.443551; this version posted May 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 4.0 International license. 1 Gut microbiota features associated with Clostridioides 2 difficile colonization in dairy calves 3 4 Laurel E. Redding1, Alexander S. Berry2,3, Nagaraju Indugu1, Elizabeth Huang1, Daniel P. Beiting3, Dipti 5 Pitta1 6 7 8 1Department of Clinical Sciences, University of Pennsylvania, School of Veterinary Medicine, Kennett 9 Square, PA, USA 10 11 2Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, 12 PA, USA 13 14 3Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 15 USA 16 17 18 Corresponding author: Laurel Redding, [email protected] 19 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.05.11.443551; this version posted May 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 4.0 International license. 20 Abstract 21 Diarrheal disease, a major cause of morbidity and mortality in dairy calves, is strongly associated with the 22 health and composition of the gut microbiome. Clostridioides difficile is an opportunistic pathogen that 23 proliferates and can produce enterotoxins when the host experiences gut dysbiosis.
    [Show full text]
  • Genus Contributing to the Top 70% of Significant Dissimilarity of Bacteria Between Day 7 and 18 Age Groups As Determined by SIMPER
    Table S1: Genus contributing to the top 70% of significant dissimilarity of bacteria between day 7 and 18 age groups as determined by SIMPER. Overall average dissimilarity between ages is 51%. Day 7 Day 18 Average Average Phyla Class Order Family Genus % Abundance Abundance Actinobacteria Actinobacteria Actinomycetales Actinomycetaceae Actinomyces 0.57 0.24 0.74 Coriobacteriia Coriobacteriales Coriobacteriaceae Collinsella 0.51 0.61 0.57 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides 2.1 1.63 1.03 Marinifilaceae Butyricimonas 0.82 0.81 0.9 Sanguibacteroides 0.08 0.42 0.59 CAG-873 0.01 1.1 1.68 Marinifilaceae 0.38 0.78 0.91 Marinifilaceae 0.78 1.04 0.97 p-2534-18B5 gut group 0.06 0.7 1.04 Prevotellaceae Alloprevotella 0.46 0.83 0.89 Prevotella 2 0.95 1.11 1.3 Prevotella 7 0.22 0.42 0.56 Prevotellaceae NK3B31 group 0.62 0.68 0.77 Prevotellaceae UCG-003 0.26 0.64 0.89 Prevotellaceae UCG-004 0.11 0.48 0.68 Prevotellaceae 0.64 0.52 0.89 Prevotellaceae 0.27 0.42 0.55 Rikenellaceae Alistipes 0.39 0.62 0.77 dgA-11 gut group 0.04 0.38 0.56 RC9 gut group 0.79 1.17 0.95 Epsilonbacteraeota Campylobacteria Campylobacterales Campylobacteraceae Campylobacter 0.58 0.83 0.97 Helicobacteraceae Helicobacter 0.12 0.41 0.6 Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus 0.36 0.31 0.64 Lactobacillaceae Lactobacillus 1.4 1.24 1 Streptococcaceae Streptococcus 0.82 0.58 0.53 Firmicutes Clostridia Clostridiales Christensenellaceae Christensenellaceae R-7 group 0.38 1.36 1.56 Clostridiaceae Clostridium sensu stricto 1 1.16 0.58
    [Show full text]
  • Acidaminococcus Provencensis Sp. Nov., a New Bacterium Isolated from a Fresh Human Stool Specimen
    NEW SPECIES Acidaminococcus provencensis sp. nov., a new bacterium isolated from a fresh human stool specimen T. Takakura1,2, H. Anani3, A. Fadlane2, A. Fontanini2, D. Raoult2,3 and J. Y. Bou Khalil2 1) Hitachi High-Technologies Corporation, Analytical & Medical Solution Business Group, Ibaraki-ken, Japan, 2) Institut Hospitalo-Universitaire Méditerranée- Infection, Marseille, France and 3) Aix-Marseille Université, Institut de Recherche pour le Developpement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France Abstract Acidaminococcus provencensis strain Marseille-P4266T (= CSURP4266T) is a new species isolated from a fresh human stool specimen. © 2019 The Author(s). Published by Elsevier Ltd. Keywords: Acidaminococcus provencensis, Culturomics, Microbiota, New species, Taxonogenomics, TM4000, Stool Original Submission: 17 May 2019; Accepted: 5 June 2019 Article published online: 14 June 2019 imported into MALDI BIOTYPER 3.0 software (Bruker Dal- Corresponding author: J.Y. Bou Khalil, MEPHI, Institut Hospitalo- tonics) and analysed against the main spectra of the bacteria Universitaire Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France. included in two databases (Bruker and the constantly updated E-mail: [email protected] MEPHI databases: https://www.mediterranee-infection.com/ urms-data-base/). The study was validated by the ethics com- mittee of the Institut Fédératif de Recherche IFR48 under number 09-022. Initial growth was obtained after 72 h of Introduction culture in Colombia agar enriched with 5% sheep’s blood (bioMérieux, Marcy l’Etoile, France) in strict anaerobic con- ditions at 37°C. Culturomics is a concept that involves the development of different culture conditions to enlarge our knowledge of the human microbiota through the discovery of previously uncul- Phenotypic characteristics tured bacteria [1–4].
    [Show full text]
  • Download Or Browsing at Phylomedb [118]
    Gerdol et al. Genome Biology (2020) 21:275 https://doi.org/10.1186/s13059-020-02180-3 RESEARCH Open Access Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel Marco Gerdol1, Rebeca Moreira2, Fernando Cruz3, Jessica Gómez-Garrido3, Anna Vlasova4, Umberto Rosani5, Paola Venier5, Miguel A. Naranjo-Ortiz4,6, Maria Murgarella7, Samuele Greco1, Pablo Balseiro2,8, André Corvelo3,9, Leonor Frias3, Marta Gut3, Toni Gabaldón4,6,10,11, Alberto Pallavicini1,12, Carlos Canchaya7,13,14, Beatriz Novoa2, Tyler S. Alioto3,6, David Posada7,13,14* and Antonio Figueras2* * Correspondence: dposada@uvigo. es; [email protected] Abstract 7Department of Biochemistry, Genetics and Immunology, Background: The Mediterranean mussel Mytilus galloprovincialis is an ecologically University of Vigo, 36310 Vigo, and economically relevant edible marine bivalve, highly invasive and resilient to Spain biotic and abiotic stressors causing recurrent massive mortalities in other bivalves. 2Instituto de Investigaciones Marinas (IIM - CSIC), Eduardo Although these traits have been recently linked with the maintenance of a high Cabello, 6, 36208 Vigo, Spain genetic variation within natural populations, the factors underlying the evolutionary Full list of author information is success of this species remain unclear. available at the end of the article Results: Here, after the assembly of a 1.28-Gb reference genome and the resequencing of 14 individuals from two independent populations, we reveal a complex pan-genomic architecture in M. galloprovincialis, with a core set of 45,000 genes plus a strikingly high number of dispensable genes (20,000) subject to presence-absence variation, which may be entirely missing in several individuals.
    [Show full text]
  • Description of Gabonibacter Massiliensis Gen. Nov., Sp. Nov., a New Member of the Family Porphyromonadaceae Isolated from the Human Gut Microbiota
    Curr Microbiol DOI 10.1007/s00284-016-1137-2 Description of Gabonibacter massiliensis gen. nov., sp. nov., a New Member of the Family Porphyromonadaceae Isolated from the Human Gut Microbiota 1,2 1 3,4 Gae¨l Mourembou • Jaishriram Rathored • Jean Bernard Lekana-Douki • 5 1 1 Ange´lique Ndjoyi-Mbiguino • Saber Khelaifia • Catherine Robert • 1 1,6 1 Nicholas Armstrong • Didier Raoult • Pierre-Edouard Fournier Received: 9 June 2016 / Accepted: 8 September 2016 Ó Springer Science+Business Media New York 2016 Abstract The identification of human-associated bacteria Gabonibacter gen. nov. and the new species G. mas- is very important to control infectious diseases. In recent siliensis gen. nov., sp. nov. years, we diversified culture conditions in a strategy named culturomics, and isolated more than 100 new bacterial Keywords Gabonibacter massiliensis Á Taxonogenomics Á species and/or genera. Using this strategy, strain GM7, a Culturomics Á Gabon Á Gut microbiota strictly anaerobic gram-negative bacterium was recently isolated from a stool specimen of a healthy Gabonese Abbreviations patient. It is a motile coccobacillus without catalase and CSUR Collection de Souches de l’Unite´ des oxidase activities. The genome of Gabonibacter mas- Rickettsies siliensis is 3,397,022 bp long with 2880 ORFs and a G?C DSM Deutsche Sammlung von content of 42.09 %. Of the predicted genes, 2,819 are Mikroorganismen protein-coding genes, and 61 are RNAs. Strain GM7 differs MALDI-TOF Matrix-assisted laser desorption/ from the closest genera within the family Porphyromon- MS ionization time-of-flight mass adaceae both genotypically and in shape and motility.
    [Show full text]
  • Alterations in the Gut Bacterial Microbiome in Fungal Keratitis Patients
    RESEARCH ARTICLE Alterations in the gut bacterial microbiome in fungal Keratitis patients Sama Kalyana Chakravarthy1☯, Rajagopalaboopathi Jayasudha1☯, Konduri Ranjith1, Anirban Dutta2, Nishal Kumar Pinna2, Sharmila S. Mande2, Savitri Sharma1, Prashant Garg3, Somasheila I. Murthy3, Sisinthy Shivaji1* 1 Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, India, 2 Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India, 3 Tej Kohli Cornea Institute, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, India a1111111111 a1111111111 ☯ These authors contributed equally to this work. a1111111111 * [email protected] a1111111111 a1111111111 Abstract Dysbiosis in the gut microbiome has been implicated in several diseases including auto- immune diseases, inflammatory diseases, cancers and mental disorders. Keratitis is an OPEN ACCESS inflammatory disease of the eye significantly contributing to corneal blindness in the devel- Citation: Kalyana Chakravarthy S, Jayasudha R, oping world. It would be worthwhile to investigate the possibility of dysbiosis in the gut micro- Ranjith K, Dutta A, Pinna NK, Mande SS, et al. (2018) Alterations in the gut bacterial microbiome biome being associated with Keratitis. Here, we have analyzed fungal and bacterial in fungal Keratitis patients. PLoS ONE 13(6): populations in stool samples through high-throughput sequencing of the ITS2 region for e0199640. https://doi.org/10.1371/journal. fungi and V3-V4 region of 16S rRNA gene for bacteria in healthy controls (HC, n = 31) and pone.0199640 patients with fungal keratitis (FK, n = 32). Candida albicans (2 OTUs), Aspergillus (1 OTU) Editor: Suresh Yenugu, University of Hyderabad, and 3 other denovo-OTUs were enriched in FK samples and an unclassified denovo-OTU INDIA was enriched in HC samples.
    [Show full text]
  • Fecal Microbiota Alterations and Small Intestinal Bacterial Overgrowth in Functional Abdominal Bloating/Distention
    J Neurogastroenterol Motil, Vol. 26 No. 4 October, 2020 pISSN: 2093-0879 eISSN: 2093-0887 https://doi.org/10.5056/jnm20080 JNM Journal of Neurogastroenterology and Motility Original Article Fecal Microbiota Alterations and Small Intestinal Bacterial Overgrowth in Functional Abdominal Bloating/Distention Choong-Kyun Noh and Kwang Jae Lee* Department of Gastroenterology, Ajou University School of Medicine, Suwon, Gyeonggi-do, Korea Background/Aims The pathophysiology of functional abdominal bloating and distention (FABD) is unclear yet. Our aim is to compare the diversity and composition of fecal microbiota in patients with FABD and healthy individuals, and to evaluate the relationship between small intestinal bacterial overgrowth (SIBO) and dysbiosis. Methods The microbiota of fecal samples was analyzed from 33 subjects, including 12 healthy controls and 21 patients with FABD diagnosed by the Rome IV criteria. FABD patients underwent a hydrogen breath test. Fecal microbiota composition was determined by 16S ribosomal RNA amplification and sequencing. Results Overall fecal microbiota composition of the FABD group differed from that of the control group. Microbial diversity was significantly lower in the FABD group than in the control group. Significantly higher proportion of Proteobacteria and significantly lower proportion of Actinobacteria were observed in FABD patients, compared with healthy controls. Compared with healthy controls, significantly higher proportion of Faecalibacterium in FABD patients and significantly higher proportion of Prevotella and Faecalibacterium in SIBO (+) patients with FABD were found. Faecalibacterium prausnitzii, was significantly more abundant, but Bacteroides uniformis and Bifidobacterium adolescentis were significantly less abundant in patients with FABD, compared with healthy controls. Significantly more abundant Prevotella copri and F.
    [Show full text]