Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities

Afrizal, 2022, Anaerobic single-cell dispensing facilitates the cultivation of human gut bacteria, Environ. Microbiol, 10.1111/1462-2920.15935 Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2 Aranda-Díaz, 2022, Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota, Cell Host Microbe, 30, 260, 10.1016/j.chom.2021.12.008 Asnicar, 2020, Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0, Nat. Commun., 11, 2500, 10.1038/s41467-020-16366-7 Bankevich, 2012, SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J. Comput. Biol., 19, 455, 10.1089/cmb.2012.0021 Basic, 2021, Monitoring and contamination incidence of gnotobiotic experiments performed in microisolator cages, Int. J. Med. Microbiol., 311, 151482, 10.1016/j.ijmm.2021.151482 Belcheva, 2014, Gut Microbial Metabolism Drives Transformation of Msh2-Deficient Colon Epithelial Cells, Cell, 158, 288, 10.1016/j.cell.2014.04.051 Beresford-Jones, 2022, The Mouse gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping, Cell Host Microbe, 30, 124, 10.1016/j.chom.2021.12.003 Bessis, 2016, "Emergencia timonensis," a new bacterium isolated from the stool of a healthy patient, New Microbes New Infect., 12, 73, 10.1016/j.nmni.2016.05.001 Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 Brugiroux, 2016, Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium, Nat. Microbiol., 2, 16215, 10.1038/nmicrobiol.2016.215 Buchfink, 2015, Fast and sensitive protein alignment using DIAMOND, Nat. Methods, 12, 59, 10.1038/nmeth.3176 Bushnell Campbell, 2020, Bacterial metabolism of bile acids promotes generation of peripheral regulatory T cells, Nature, 581, 475, 10.1038/s41586-020-2193-0 Cheng, 2022, Design, construction, and in vivo augmentation of a complex gut microbiome, Cell, 185, 3617, 10.1016/j.cell.2022.08.003 Clavel, 2009, Isolation of bacteria from the ileal mucosa of TNFdeltaARE mice and description of Enterorhabdus mucosicola gen. nov., sp. nov, Int. J. Syst. Evol. Microbiol., 59, 1805, 10.1099/ijs.0.003087-0 Darnaud, 2021, A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes, Nat. Commun., 12, 6686, 10.1038/s41467-021-26963-9 Dou, 2020, Sodium butyrate alleviates mouse colitis by regulating gut microbiota dysbiosis, 10, 1154 Eberl, 2019, Reproducible colonization of Germ-free mice With the oligo-mouse-microbiota in different animal facilities, Front. Microbiol., 10, 2999, 10.3389/fmicb.2019.02999 Edgar, 2013, Uparse: highly accurate OTU sequences from microbial amplicon reads, Nat. Methods, 10, 996, 10.1038/nmeth.2604 Mähler Convenor, 2014, FELASA recommendations for the health monitoring of mouse, rat, hamster, guinea pig and rabbit colonies in breeding and experimental units, Lab Anim., 48, 178, 10.1177/0023677213516312 Finn, 2011, HMMER web server: interactive sequence similarity searching, Nucleic Acids Res., 39, W29, 10.1093/nar/gkr367 Fleissner, 2010, Absence of intestinal microbiota does not protect mice from diet-induced obesity, Br. J. Nutr., 104, 919, 10.1017/S0007114510001303 Forster, 2022, Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis, Nat. Microbiol., 7, 590, 10.1038/s41564-022-01094-z Forster, 2019, A human gut bacterial genome and culture collection for improved metagenomic analyses, Nat. Biotechnol., 37, 186, 10.1038/s41587-018-0009-7 Frese, 2011, The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri, PLoS Genet., 7, e1001314, 10.1371/journal.pgen.1001314 Gálvez, 2020, Distinct polysaccharide utilization determines interspecies competition between intestinal Prevotella spp, Cell Host Microbe, 28, 838, 10.1016/j.chom.2020.09.012 Gehrig, 2019, Effects of microbiota-directed foods in gnotobiotic animals and undernourished children, Science, 365, eaau4732, 10.1126/science.aau4732 Geuking, 2020, Microbial modulation of intestinal T helper cell responses and implications for disease and therapy, Mucosal Immunol., 13, 855, 10.1038/s41385-020-00335-w Godon, 1997, Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis, Appl. Environ. Microbiol., 63, 2802, 10.1128/aem.63.7.2802-2813.1997 Graham, 2018, Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes, Nat. Med., 24, 1762, 10.1038/s41591-018-0203-7 Gremse, 2016, Imalytics preclinical: interactive analysis of biomedical volume data, Theranostics, 6, 328, 10.7150/thno.13624 Greuter, 2016, probeBase--an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016, Nucleic Acids Res., 44, D586, 10.1093/nar/gkv1232 Groussin, 2021, Elevated rates of horizontal gene transfer in the industrialized human microbiome, Cell, 184, 2053, 10.1016/j.cell.2021.02.052 Gundogdu, 2016, In vitro effectiveness of commercial bacteriophage cocktails on diverse extended-spectrum beta-lactamase producing Escherichia coli Strains., Front. Microbiol., 7, 1761, 10.3389/fmicb.2016.01761 Gurevich, 2013, QUAST: quality assessment tool for genome assemblies, Bioinformatics, 29, 1072, 10.1093/bioinformatics/btt086 Hang, 2019, Bile acid metabolites control TH17 and Treg cell differentiation, Nature, 576, 143, 10.1038/s41586-019-1785-z Herp, 2019, Mucispirillum schaedleri antagonizes salmonella virulence to protect mice against colitis, Cell Host Microbe, 25, 681, 10.1016/j.chom.2019.03.004 Herp, 2021, The human symbiont Mucispirillum schaedleri: causality in health and disease, Med. Microbiol. Immunol., 210, 173, 10.1007/s00430-021-00702-9 Hitch, 2021, Recent advances in culture-based gut microbiome research, Int. J. Med. Microbiol., 311, 151485, 10.1016/j.ijmm.2021.151485 Hitch, 2022, A taxonomic note on the genus Prevotella: description of four novel genera and emended description of the genera Hallella and Xylanibacter, Syst. Appl. Microbiol., 45, 126354, 10.1016/j.syapm.2022.126354 Hitch, 2021, Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria, ISME Commun., 1, 16, 10.1038/s43705-021-00017-z Hitch, 2021, Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria, ISME Commun, 1, 16, 10.1038/s43705-021-00017-z Hyatt, 2010, Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinformatics, 11, 119, 10.1186/1471-2105-11-119 Irrazabal, 2020, Limiting oxidative DNA damage reduces microbe-induced colitis-associated colorectal cancer, Nat Commun, 11, 1802, 10.1038/s41467-020-15549-6 Ivanov, 2009, Induction of intestinal Th17 cells by segmented filamentous bacteria, Cell, 139, 485, 10.1016/j.cell.2009.09.033 Jain, 2018, High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries, Nat. Commun., 9, 5114, 10.1038/s41467-018-07641-9 Kabbert, 2020, High microbiota reactivity of adult human intestinal IgA requires somatic mutations, J. Exp. Med., 217, e20200275, 10.1084/jem.20200275 Kumar, 2021, MiMiC: a bioinformatic approach for generation of synthetic communities from metagenomes, Microb. Biotechnol., 14, 1757, 10.1111/1751-7915.13845 Kumar, 2016, MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets, Mol Biol Evol, 33, 1870, 10.1093/molbev/msw054 Lagier, 2018, Culturing the human microbiota and culturomics, Nat. Rev. Microbiol., 16, 540, 10.1038/s41579-018-0041-0 Lagkouvardos, 2016, IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies, Sci. Rep., 6, 33721, 10.1038/srep33721 Lagkouvardos, 2016, The mouse intestinal bacterial collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota, Nat. Microbiol., 1, 16131, 10.1038/nmicrobiol.2016.131 Lagkouvardos, 2016, IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies, Sci Rep, 6, 33721, 10.1038/srep33721 Lagkouvardos, 2019, Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family, Microbiome, 7, 28, 10.1186/s40168-019-0637-2 Lécuyer, 2014, Segmented filamentous bacterium uses secondary and tertiary lymphoid tissues to induce gut IgA and specific T helper 17 cell responses, Immunity, 40, 608, 10.1016/j.immuni.2014.03.009 Lesker, 2020, An integrated metagenome catalog reveals new insights into the murine gut microbiome, Cell Rep., 30, 2909, 10.1016/j.celrep.2020.02.036 Letunic, 2021, Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation, Nucleic Acids Res., 49, W293, 10.1093/nar/gkab301 Li, 2015, MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph, Bioinformatics, 31, 1674, 10.1093/bioinformatics/btv033 Liu, 2021, Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank, Microbiome, 9, 119, 10.1186/s40168-021-01064-3 Liu, 2020, The Mouse Gut Microbial biobank expands the coverage of cultured bacteria, Nat. Commun., 11, 79, 10.1038/s41467-019-13836-5 Lloyd-Price, 2019, Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases, Nature, 569, 655, 10.1038/s41586-019-1237-9 Lourenço, 2020, The spatial heterogeneity of the gut limits predation and fosters coexistence of bacteria and bacteriophages, Cell Host Microbe, 28, 390, 10.1016/j.chom.2020.06.002 Loy, 2017, Lifestyle and horizontal gene transfer-mediated evolution of Mucispirillum schaedleri, a core member of the murine gut microbiota, mSystems, 2, 10.1128/mSystems.00171-16 Lu, 2013, Escherichia coli-based cell free production of flagellin and ordered flagellin display on virus-like particles, Biotechnol. Bioeng., 110, 2073, 10.1002/bit.24903 Lund, 2015, Draft genome sequence of "terrisporobacter othiniensis" isolated from a blood culture from a human patient, Genome Announc., 3, 10.1128/genomeA.00042-15 Mandić, 2019, Clostridium ramosum regulates enterochromaffin cell development and serotonin release, Sci. Rep., 9, 1177, 10.1038/s41598-018-38018-z Marion, 2020, Biogeography of microbial bile acid transformations along the murine gut, J. Lipid Res., 61, 1450, 10.1194/jlr.RA120001021 Matthies, 2008, Conversion of daidzein and genistein by an anaerobic bacterium newly isolated from the mouse intestine, Appl. Environ. Microbiol., 74, 4847, 10.1128/AEM.00555-08 Meier-Kolthoff, 2022, TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes, Nucleic Acids Res., 50, D801, 10.1093/nar/gkab902 Meier-Kolthoff, 2014, Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age, Int. J. Syst. Evol. Microbiol., 64, 352, 10.1099/ijs.0.056994-0 Mistry, 2021, Pfam: The protein families database in 2021, Nucl. Acids Res., 49, D412, 10.1093/nar/gkaa913 Nowosad, 2020, Tunable dynamics of B cell selection in gut germinal centres, Nature, 588, 321, 10.1038/s41586-020-2865-9 Pabst, 2016, Secretory IgA in the coordination of establishment and maintenance of the microbiota, Trends Immunol., 37, 287, 10.1016/j.it.2016.03.002 Parks, 2020, A complete domain-to-species taxonomy for Bacteria and Archaea, Nat. Biotechnol., 38, 1079, 10.1038/s41587-020-0501-8 Parks, 2015, CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes, Genome Res., 25, 1043, 10.1101/gr.186072.114 Parte, 2020, List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ, Int. J. Syst. Evol. Microbiol., 70, 5607, 10.1099/ijsem.0.004332 Pruesse, 2012, SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes, Bioinformatics, 28, 1823, 10.1093/bioinformatics/bts252 Pryor, 2019, Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy, Cell, 178, 1299, 10.1016/j.cell.2019.08.003 Qin, 2014, A proposed genus boundary for the prokaryotes based on genomic insights, J. Bacteriol., 196, 2210, 10.1128/JB.01688-14 Quince, 2017, Shotgun metagenomics, from sampling to analysis, Nat. Biotechnol., 35, 833, 10.1038/nbt.3935 Ramanan, 2020, An immunologic mode of multigenerational transmission governs a gut Treg setpoint, Cell, 181, 1276, 10.1016/j.cell.2020.04.030 Rautio, 2003, Reclassification of Bacteroides putredinis (Weinberg et al., 1937) in a new genus Alistipes gen. nov., as Alistipes putredinis comb. nov., and description of Alistipes finegoldii sp. nov., from human sources, Syst. Appl. Microbiol., 26, 182, 10.1078/072320203322346029 Reitmeier, 2021, Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling, ISME Commun., 1, 31, 10.1038/s43705-021-00033-z Rhee, 2011, Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1, Stand. Genom. Sci., 5, 331, 10.4056/sigs.2365342 Robertson, 2005, Mucispirillum schaedleri gen. nov., sp. nov., a spiral-shaped bacterium colonizing the mucus layer of the gastrointestinal tract of laboratory rodents, Int. J. Syst. Evol. Microbiol., 55, 1199, 10.1099/ijs.0.63472-0 Rosshart, 2019, Laboratory mice born to wild mice have natural microbiota and model human immune responses, Science, 365, 10.1126/science.aaw4361 Roy, 2017, Distinct microbial communities trigger colitis development upon intestinal barrier damage via innate or adaptive immune cells, Cell Rep., 21, 994, 10.1016/j.celrep.2017.09.097 Sakamoto, 2018, Lawsonibacter asaccharolyticus gen. nov., sp. nov., a butyrate-producing bacterium isolated from human faeces, Int. J. Syst. Evol. Microbiol., 68, 2074, 10.1099/ijsem.0.002800 Schwarzer, 2016, Lactobacillus plantarum strain maintains growth of infant mice during chronic undernutrition, Science, 351, 854, 10.1126/science.aad8588 Seedorf, 2014, Bacteria from diverse habitats colonize and compete in the mouse gut, Cell, 159, 253, 10.1016/j.cell.2014.09.008 Selmer, 2002, Propionate CoA-transferase from Clostridium propionicum. Cloning of gene and identification of glutamate 324 at the active site, Eur. J. Biochem., 269, 372, 10.1046/j.0014-2956.2001.02659.x Song, 2020, Microbial bile acid metabolites modulate gut RORgamma(+) regulatory T cell homeostasis, Nature, 577, 410, 10.1038/s41586-019-1865-0 Stackebrandt, 2022, Authors need to be prudent when assigning names to microbial isolates, Antonie Leeuwenhoek, 115, 1, 10.1007/s10482-021-01675-8 Stamatakis, 2014, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 30, 1312, 10.1093/bioinformatics/btu033 Stecher, 2012, Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae, Proc. Natl. Acad. Sci. USA, 109, 1269, 10.1073/pnas.1113246109 Streidl, 2021, The gut bacterium Extibacter muris produces secondary bile acids and influences liver physiology in gnotobiotic mice, Gut Microbes, 13, 1, 10.1080/19490976.2020.1854008 Thomas, 2019, Multiple levels of the unknown in microbiome research, BMC Biol., 17, 48, 10.1186/s12915-019-0667-z Tong, 2016, Propionate ameliorates dextran sodium sulfate-induced colitis by improving intestinal barrier function and reducing inflammation and oxidative stress, Front. Pharmacol., 7, 253, 10.3389/fphar.2016.00253 Waters, 2019, The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health, BMC Biol., 17, 83, 10.1186/s12915-019-0699-4 Wegner, 2017, Rapid analysis of bile acids in different biological matrices using LC-ESI-MS/MS for the investigation of bile acid transformation by mammalian gut bacteria, Anal. Bioanal. Chem., 409, 1231, 10.1007/s00216-016-0048-1 Wilson, 2019, The human gut bacterial genotoxin colibactin alkylates DNA, Science, 363, eaar7785, 10.1126/science.aar7785 Wong, 2022, The CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine Gut, MBio, 13, 10.1128/mbio.02949-21 Woting, 2014, Clostridium ramosum promotes high-fat diet-induced obesity in gnotobiotic mouse models, mBio, 5, 10.1128/mBio.01530-14 Wymore Brand, 2015, The altered Schaedler Flora: continued applications of a defined murine microbial community, ILAR J., 56, 169, 10.1093/ilar/ilv012 Yarza, 2014, Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences, Nat. Rev. Microbiol., 12, 635, 10.1038/nrmicro3330 Yilmaz, 2021, Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice, Cell Host Microbe, 29, 650, 10.1016/j.chom.2021.02.001 Yoo, 2021, High-fat diet-induced colonocyte dysfunction escalates microbiota-derived trimethylamine N-oxide, Science, 373, 813, 10.1126/science.aba3683 Yoon, 2017, Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies, Int. J. Syst. Evol. Microbiol., 67, 1613, 10.1099/ijsem.0.001755 Youngblut, 2021, Vertebrate host phylogeny influences gut archaeal diversity, Nat. Microbiol., 6, 1443, 10.1038/s41564-021-00980-2 Zheng, 2020, A taxonomic note on the genus Lactobacillus: description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae, Int. J. Syst. Evol. Microbiol., 70, 2782, 10.1099/ijsem.0.004107 Zhu, 2018, Precision editing of the gut microbiota ameliorates colitis, Nature, 553, 208, 10.1038/nature25172 Zou, 2019, 1,520 Reference genomes from cultivated human gut bacteria enable functional microbiome analyses, Nat. Biotechnol., 37, 179, 10.1038/s41587-018-0008-8 Zünd, 2021, High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains, Microbiome, 9, 77, 10.1186/s40168-021-01033-w