A taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter
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Alauzet, 2007, Prevotella nanceiencis sp. nov., isolated from human clinical samples, Int J Syst Evol Microbiol, 57, 2216, 10.1099/ijs.0.65173-0
Altschul, 1990, Basic local alignment search tool, J Mole Biol, 215, 403, 10.1016/S0022-2836(05)80360-2
Asnicar, 2020, Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0, Nat Commun, 11, 1, 10.1038/s41467-020-16366-7
Avgustin, 2001, Systematics and evolution of ruminal species of the genus Prevotella, Folia Microbiol (Praha), 46, 40, 10.1007/BF02825882
Avguštin, 1997, Phenotypic diversity among ruminal isolates of Prevotella ruminicola: proposal of Prevotella brevis sp. nov., Prevotella bryantii sp. nov., and Prevotella albensis sp. nov. and redefinition of Prevotella ruminicola, Int J Syst Bacteriol, 47, 284, 10.1099/00207713-47-2-284
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
Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170
Bryant, 1958, Bacteroides ruminicola, sp. and succinimonas amylolytica the new genus and species, J Bacteriol, 15, 10.1128/jb.76.1.15-23.1958
Buchfink, 2014, Fast and sensitive protein alignment using DIAMOND, Nat Methods, 12, 59, 10.1038/nmeth.3176
Buhl, 2016, Prevotella colorans sp. Nov., isolated from a human wound, Int J Syst Evol Microbiol, 66, 3005, 10.1099/ijsem.0.001134
Cantarel, 2009, The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics, Nucleic Acids Res, 37, 233, 10.1093/nar/gkn663
Chaumeil, 2019, GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database, Bioinformatics, 36, 1925, 10.1093/bioinformatics/btz848
De Filippis, 2019, Distinct genetic and functional traits of human intestinal prevotella copri strains are associated with different habitual diets, Cell Host Microbe, 25, 444, 10.1016/j.chom.2019.01.004
Diop, 2018, Microbial culturomics broadens human vaginal flora diversity: genome sequence and description of Prevotella lascolaii sp. nov. isolated from a patient with bacterial vaginosis, Omi A J Integr Biol, 22, 210, 10.1089/omi.2017.0151
Diop, 2016, ‘Lascolabacter vaginalis’ strain KHD1, a new bacterial species cultivated from human female genital tract, New Microbes New Infect, 13, 22, 10.1016/j.nmni.2016.05.017
Downes, 2007, Prevotella maculosa sp. nov., isolated from the human oral cavity, Int J Syst Evol Microbiol, 57, 2936, 10.1099/ijs.0.65281-0
Downes, 2006, Prevotella bergensis sp. nov., isolated from human infections, Int J Syst Evol Microbiol, 56, 609, 10.1099/ijs.0.63888-0
Downes, 2005, Prevotella marshii sp. nov. and Prevotella baroniae sp. nov., isolated from the human oral cavity, Int J Syst Evol Microbiol, 55, 1551, 10.1099/ijs.0.63634-0
Downes, 2010, Prevotella saccharolytica sp. nov., isolated from the human oral cavity, Int J Syst Evol Microbiol, 60, 2458, 10.1099/ijs.0.014720-0
Efimov, 2018, Prevotella rara sp. nov., isolated from human faeces, Int J Syst Evol Microbiol, 68, 3818, 10.1099/ijsem.0.003066
El-Gebali, 2019, The Pfam protein families database in 2019, Nucleic Acids Res, 47, D427, 10.1093/nar/gky995
Eren, 2021, Community-led, integrated, reproducible multi-omics with anvi’o, Nat Microbiol, 6, 3, 10.1038/s41564-020-00834-3
Fehlner-Peach, 2019, Distinct polysaccharide utilization profiles of human intestinal Prevotella copri isolates, Cell Host Microbe, 26, 680, 10.1016/j.chom.2019.10.013
Finn, 2011, HMMER web server: Interactive sequence similarity searching, Nucleic Acids Res, 39, 29, 10.1093/nar/gkr367
García-López, 2019, Analysis of 1,000 type-strain genomes improves taxonomic classification of bacteroidetes, Front Microbiol, 10, 10.3389/fmicb.2019.02083
Glazunova, 2007, Prevotella timonensis sp. nov., isolated from a human breast abscess, Int J Syst Evol Microbiol, 57, 883, 10.1099/ijs.0.64609-0
Hahnke, 2016, Genome-based taxonomic classification of Bacteroidetes, Front Microbiol, 7, 10.3389/fmicb.2016.02003
Hayashi, 2007, Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces, Int J Syst Evol Microbiol, 57, 941, 10.1099/ijs.0.64778-0
Henderson, 2019, Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework, PeerJ, 2019, 1
Hitch, 2021, Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria, ISME Commun, 1, 10.1038/s43705-021-00017-z
Holdeman, 1982, Description of Bacteroides loescheii sp. nov. and emendation of the descriptions of Bacteroides melaninogenicus (Oliver and Wherry) Roy and Kelly 1939 and Bacteroides denticola Shah and Collins 1981, Int J Syst Bacteriol, 32, 399, 10.1099/00207713-32-4-399
Holdeman, 1982, Bacteroides oris and bacteroides buccae new species from human periodontitis and other human infections, Int J Syst Bacteriol, 32, 125, 10.1099/00207713-32-1-125
Hyatt, 2010, Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinformatics, 11, 119, 10.1186/1471-2105-11-119
Iljazovic, 2020, Perturbation of the gut microbiome by Prevotella spp. enhances host susceptibility to mucosal inflammation, Mucosal Immunol
Konstantinidis, 2017, Uncultivated microbes in need of their own taxonomy, ISME J, 11, 2399, 10.1038/ismej.2017.113
Kumar, 2021, MiMiC : a bioinformatic approach for generation of synthetic communities from metagenomes, Microb Biotechnol, 10.1111/1751-7915.13845
Lagkouvardos, 2016, IMNGS: a comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies, Sci Rep, 6, 1, 10.1038/srep33721
Liou, 2020, Prevotella hominis sp. Nov., isolated from human faeces, Int J Syst Evol Microbiol, 70, 4767, 10.1099/ijsem.0.004342
Loesche, 1964, Bacteroides oralis, proposed new species isolated from the oral cavity of man, J Bacteriol, 88, 1329, 10.1128/jb.88.5.1329-1337.1964
Lombard, 2014, The carbohydrate-active enzymes database (CAZy) in 2013, Nucleic Acids Res, 42, 490, 10.1093/nar/gkt1178
Moore, 1994, Descriptions of Prevotella tannerae sp. nov. and Prevotella enoeca sp. nov. from the human gingival crevice and emendation of the description of Prevotella zoogleoformans, Int J Syst Bacteriol, 44, 599, 10.1099/00207713-44-4-599
Moore, 1994, Oribaculum catoniae gen. nov., sp. nov.; Catonella morbi gen. nov., sp. nov.; Hallella seregens gen. nov., sp. nov.; Johnsonella ignava gen. nov., sp. nov.; and Dialister pneumosintes gen. nov., comb. nov., nom. rev., Anaerobic gram-negative bacilli from, Int J Syst Bacteriol, 44, 187, 10.1099/00207713-44-2-187
Moss, 1989, Identification of monounsaturated fatty acids of Aerococcus viridans with dimethyl disulfide derivatives and combined gas chromatography-mass spectrometry, J Clin Microbiol, 27, 2130, 10.1128/jcm.27.9.2130-2132.1989
Nakata, 2019, Prevotella cerevisiae sp. Nov., beer-spoilage obligate anaerobic bacteria isolated from brewery wastewater, Int J Syst Evol Microbiol, 69, 1789, 10.1099/ijsem.0.003393
Okuda, 1985, Bacteroides heparinolyticus sp. nov. isolated from humans with periodontitis, Int J Syst Bacteriol, 35, 438, 10.1099/00207713-35-4-438
Oren, 2021, Valid publication of new names and new combinations effectively published outside the IJSEM, Int J Syst Evol Microbiol, 71, 1, 10.1099/ijsem.0.005096
Pareek, 2019, Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi, 5
Parks, 2015, CheckM: assessing the quality of microbial genomes recovered from, Cold Spring Harb Lab Press Method, 1, 1
Parks, 2017, Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life, Nat Microbiol, 903, 1
Parte, 2020, List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ, Int J Syst Evol Microbiol, 10.1099/ijsem.0.004332
Price, 2009, Fasttree: Computing large minimum evolution trees with profiles instead of a distance matrix, Mol Biol Evol, 26, 1641, 10.1093/molbev/msp077
Qin, 2014, A proposed genus boundary for the prokaryotes based on genomic insights, J Bacteriol, 196, 2210, 10.1128/JB.01688-14
Sakamoto, 2012, Reclassification of Xylanibacter oryzae Ueki et al. 2006 as Prevotella oryzae comb. nov., with an emended description of the genus Prevotella, Int J Syst Evol Microbiol, 62, 2637, 10.1099/ijs.0.038638-0
Sakamoto, 2007, Prevotella pleuritidis sp. nov., isolated from pleural fluid, Int J Syst Evol Microbiol, 57, 1725, 10.1099/ijs.0.64885-0
Sakamoto, 2004, Prevotella shahii sp. nov. and Prevotella salivae sp. nov., isolated from the human oral cavity, Int J Syst Evol Microbiol, 54, 877, 10.1099/ijs.0.02876-0
Sakamoto, 2005, Prevotella multisaccharivorax sp. nov., isolated from human subgingival plaque, Int J Syst Evol Microbiol, 55, 1839, 10.1099/ijs.0.63739-0
Segata, 2013, PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes, Nat Commun, 4, 1, 10.1038/ncomms3304
Shah, 2015, Prevotella, Bergey’s Man Syst Archaea Bact, 1
Shah, 1990, Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides, Int J Syst Bacteriol, 40, 205, 10.1099/00207713-40-2-205
Shah, 1981, Bacteroides buccalis, sp. nov., Bacteroides denticola, sp. nov., and Bacteroides pentosaceus, sp. nov., new species of the genus Bacteroides from the oral cavity, Zentralblatt für Bakteriol Mikrobiol und Hyg I Abt Orig C Allg Angew und ökologische Mikrobiol, 2, 235
Shah, 1985, Bacteroides oulorum sp. nov., a nonpigmented saccharolytic species from the oral activity, Int J Syst Bacteriol, 35, 193, 10.1099/00207713-35-2-193
Spitzer, 1996, Structure analysis of fatty acids by gas chromatography - Low resolution electron impact mass spectrometry of their 4,4-dimethyloxazoline derivatives – a review, Prog Lipid Res, 35, 387, 10.1016/S0163-7827(96)00011-2
Tett, 2021, Prevotella diversity, niches and interactions with the human host, Nat Rev Microbiol, 10.1038/s41579-021-00559-y
Ueki, 2007, Prevotella paludivivens sp. nov., a novel strictly anaerobic, Gram-negative, hemicellulose-decomposing bacterium isolated from plant residue and rice roots in irrigated rice-field soil, Int J Syst Evol Microbiol, 57, 1803, 10.1099/ijs.0.64914-0
Ueki, 2006, Xylanibacter oryzae gen. nov., sp. nov., a novel strictly anaerobic, Gram-negative, xylanolytic bacterium isolated from rice-plant residue in flooded rice-field soil in Japan, Int J Syst Evol Microbiol, 56, 2215, 10.1099/ijs.0.64364-0
Vieira, 2021, Usitatibacter rugosus gen. nov., sp. nov. and Usitatibacter palustris sp. nov., novel members of Usitatibacteraceae fam. nov. within the order Nitrosomonadales isolated from soil, Int J Syst Evol Microbiol, 10.1099/ijsem.0.004631
Willems, 1995, 16S rRNA gene similarities indicate that Hallella seregens (Moore and Moore) and Mitsuokella dentalis (Haapasalo et al.) are genealogically highly related and are members of the genus Prevotella: emended description of the genus Prevotella (Shah and Colli), Int J Syst Bacteriol, 45, 832, 10.1099/00207713-45-4-832
Wylensek, 2020, A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity, Nat Commun, 11, 1
