Desulfovibrio falkowii sp. nov., Porphyromonas miyakawae sp. nov., Mediterraneibacter flintii sp. nov. and Owariibacterium komagatae gen. nov., sp. nov., isolated from human faeces

References

1. de Vos WM, Tilg H, Van Hul M, Cani PD. Gut microbiome and health: mechanistic insights. Gut 2022; 71:1020–1032 [View Article] [PubMed]
   [Google Scholar]
2. Murros KE, Huynh VA, Takala TM, Saris PEJ. Desulfovibrio bacteria are associated with Parkinson’s disease. Front Cell Infect Microbiol 2021; 11:652617 [View Article] [PubMed]
   [Google Scholar]
3. Hertel J, Harms AC, Heinken A, Baldini F, Thinnes CC et al. Integrated analyses of microbiome and longitudinal metabolome data reveal microbial-host interactions on sulfur metabolism in Parkinson’s disease. Cell Rep 2019; 29:1767–1777 [View Article] [PubMed]
   [Google Scholar]
4. Huang B, Chau SWH, Liu Y, Chan JWY, Wang J et al. Gut microbiome dysbiosis across early Parkinson’s disease, REM sleep behavior disorder and their first-degree relatives. Nat Commun 2023; 14:2501 [View Article]
   [Google Scholar]
5. Huynh VA, Takala TM, Murros KE, Diwedi B, Saris PEJ. Desulfovibrio bacteria enhance alpha-synuclein aggregation in a Caenorhabditis elegans model of Parkinson’s disease. Front Cell Infect Microbiol 2023; 13:1181315 [View Article] [PubMed]
   [Google Scholar]
6. Wallen ZD, Appah M, Dean MN, Sesler CL, Factor SA et al. Characterizing dysbiosis of gut microbiome in PD: evidence for overabundance of opportunistic pathogens. NPJ Parkinsons Dis 2020; 6:11 [View Article] [PubMed]
   [Google Scholar]
7. Adams B, Nunes JM, Page MJ, Roberts T, Carr J et al. Parkinson’s disease: a systemic inflammatory disease accompanied by bacterial inflammagens. Front Aging Neurosci 2019; 11:210 [View Article] [PubMed]
   [Google Scholar]
8. Feng Y-K, Wu Q-L, Peng Y-W, Liang F-Y, You H-J et al. Oral P. gingivalis impairs gut permeability and mediates immune responses associated with neurodegeneration in LRRK2 R1441G mice. J Neuroinflammation 2020; 17:347 [View Article] [PubMed]
   [Google Scholar]
9. Togo AH, Diop A, Bittar F, Maraninchi M, Valero R et al. Description of Mediterraneibacter massiliensis, gen. nov., sp. nov., a new genus isolated from the gut microbiota of an obese patient and reclassification of Ruminococcus faecis, Ruminococcus lactaris, Ruminococcus torques, Ruminococcus gnavus and Clostridium glycyrrhizinilyticum as Mediterraneibacter faecis comb. nov., Mediterraneibacter lactaris comb. nov., Mediterraneibacter torques comb. nov., Mediterraneibacter gnavus comb. nov. and Mediterraneibacter glycyrrhizinilyticus comb. nov. Antonie van Leeuwenhoek 2018; 111:2107–2128 [View Article] [PubMed]
   [Google Scholar]
10. Shkoporov AN, Chaplin AV, Shcherbakova VA, Suzina NE, Kafarskaia LI et al. Ruthenibacterium lactatiformans gen. nov., sp. nov., an anaerobic, lactate-producing member of the family Ruminococcaceae isolated from human faeces. Int J Syst Evol Microbiol 2016; 66:3041–3049 [View Article] [PubMed]
    [Google Scholar]
11. Wallen ZD, Demirkan A, Twa G, Cohen G, Dean MN et al. Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms. Nat Commun 2022; 13:6958 [View Article] [PubMed]
    [Google Scholar]
12. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
13. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
    [Google Scholar]
14. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
    [Google Scholar]
15. Nishiwaki H, Ito M, Ishida T, Hamaguchi T, Maeda T et al. Meta-analysis of gut dysbiosis in Parkinson’s disease. Mov Disord 2020; 35:1626–1635 [View Article] [PubMed]
    [Google Scholar]
16. Wilkins TD, Chalgren S. Medium for use in antibiotic susceptibility testing of anaerobic bacteria. Antimicrob Agents Chemother 1976; 10:926–928 [View Article] [PubMed]
    [Google Scholar]
17. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
    [Google Scholar]
18. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
    [Google Scholar]
19. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
    [Google Scholar]
20. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
22. Stecher G, Tamura K, Kumar S. Molecular Evolutionary Genetics Analysis (MEGA) for macOS. Mol Biol Evol 2020; 37:1237–1239 [View Article] [PubMed]
    [Google Scholar]
23. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article] [PubMed]
    [Google Scholar]
24. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
25. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
    [Google Scholar]
26. Hisatomi A, Ohkuma M, Sakamoto M. Sellimonas catena sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2023; 73: [View Article] [PubMed]
    [Google Scholar]
27. Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil P-A et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res 2022; 50:D785–D794 [View Article] [PubMed]
    [Google Scholar]
28. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 2019; 36:1925–1927 [View Article] [PubMed]
    [Google Scholar]
29. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article] [PubMed]
    [Google Scholar]
30. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article] [PubMed]
    [Google Scholar]
31. Sakamoto M, Iino T, Ohkuma M. Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov. Int J Syst Evol Microbiol 2017; 67:1219–1227 [View Article] [PubMed]
    [Google Scholar]
32. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article] [PubMed]
    [Google Scholar]
33. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
34. Ueyama J, Oda M, Hirayama M, Sugitate K, Sakui N et al. Freeze-drying enables homogeneous and stable sample preparation for determination of fecal short-chain fatty acids. Anal Biochem 2020; 589:113508 [View Article] [PubMed]
    [Google Scholar]
35. Chen S. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. Imeta 2023; 2:e107 [View Article] [PubMed]
    [Google Scholar]
36. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421 [View Article] [PubMed]
    [Google Scholar]
37. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
38. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
    [Google Scholar]
39. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
40. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
41. Fournier D, Mouton C, Lapierre P, Kato T, Okuda K et al. Porphyromonas gulae sp. nov., an anaerobic, gram-negative coccobacillus from the gingival sulcus of various animal hosts. Int J Syst Evol Microbiol 2001; 51:1179–1189 [View Article] [PubMed]
    [Google Scholar]
42. Fröhlich J, Sass H, Babenzien HD, Kuhnigk T, Varma A et al. Isolation of Desulfovibrio intestinalis sp. nov. from the hindgut’ of the lower termite Mastotermes darwiniensis. Can J Microbiol 1999; 45:145–152 [View Article] [PubMed]
    [Google Scholar]
43. Moore WEC, Johnson JL, Holdeman LV. Emendation of Bacteroidaceae and Butyrivibrio and descriptions of Desulfomonas gen. nov. and ten new species in the genera Desulfomonas, Butyrivibrio, Eubacterium, Clostridium, and Ruminococcus. Int J Syst Bacteriol 1976; 26:238–252 [View Article]
    [Google Scholar]
44. Thabet OBD, Wafa T, Eltaief K, Cayol J-L, Hamdi M et al. Desulfovibrio legallis sp. nov.: a moderately halophilic, sulfate-reducing bacterium isolated from a wastewater digestor in Tunisia. Curr Microbiol 2011; 62:486–491 [View Article] [PubMed]
    [Google Scholar]
45. Shah HN, Collins MD. Proposal for reclassification of Bacteroides asaccharolyticus, Bacteroides gingivalis, and Bacteroides endodontalis in a new genus, Porphyromonas. Int J Syst Bacteriol 1988; 38:128–131 [View Article]
    [Google Scholar]
46. Finegold SM, Vaisanen M-L, Rautio M, Eerola E, Summanen P et al. Porphyromonas uenonis sp. nov., a pathogen for humans distinct from P. asaccharolytica and P. endodontalis. J Clin Microbiol 2004; 42:5298–5301 [View Article] [PubMed]
    [Google Scholar]
47. Holdeman LV, Moore WEC. New genus, Coprococcus, twelve new species, and emended descriptions of four previously described species of bacteria from human feces. Int J Syst Bacteriol 1974; 24:260–277 [View Article]
    [Google Scholar]
48. Kim J-S, Lee KC, Suh MK, Han K-I, Eom MK et al. Mediterraneibacter butyricigenes sp. nov., a butyrate-producing bacterium isolated from human faeces. J Microbiol 2019; 57:38–44 [View Article] [PubMed]
    [Google Scholar]
49. Togo AH, Durand G, Khelaifia S, Armstrong N, Robert C et al. Fournierella massiliensis gen. nov., sp. nov., a new human-associated member of the family Ruminococcaceae. Int J Syst Evol Microbiol 2017; 67:1393–1399 [View Article] [PubMed]
    [Google Scholar]