1887

Abstract

Four strictly anaerobic, Gram-stain-positive, urease-, oxidase- and catalase-negative, rod-shaped strains (zg-886/zg-887 and zg-1050/zg-1084) were isolated from . Comparison analysis of 16S rRNA genes showed that the two strain pairs belong to the family : zg-1050 and zg-1084 were most closely related to 68-1-3 (97.2 %), while zg-886/zg-887 had the highest similarity to YIT 12062 (91.6 %), followed by DSM 16106 (91.4 %) and DSM 27213 (91.4 %). Phylogenetic analyses based on 16S rRNA genes and genomes showed that the two strain pairs represent two different lineages within the family . The genomic G+C contents of strains zg-886 and zg-1050 were 63.0 and 66.3 mol%, respectively. The values of digital DNA–DNA hybridization, average nucleotide identity, average amino acid identity and the percentage of conserved proteins between the two new type strains and members of the family were lower than the respective thresholds for delineation of a species or genus. In contrast to the absence of any known quinones in strain zg-1050, strain zg-886 contained MK-6 (42.5 %), MMK-6 (25.0 %) and DMMK-6 (32.5 %). The four strains grew optimally at pH 7.0, 37 ºC and 0.5 % NaCl (w/v). According to these polyphasic analyses, two new members within the family are proposed, gen. nov., sp. nov. (zg-886=JCM 34097=GDMCC 1.1710) and sp. nov. (zg-1050=GDMCC 1.2426=JCM 34748).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005509
2022-09-20
2024-05-02
Loading full text...

Full text loading...

References

  1. Lu L, Ren Z, Yue Y, Yu X, Lu S et al. Niche modeling predictions of the potential distribution of Marmota himalayana, the host animal of plague in Yushu County of Qinghai. BMC Public Health 2016; 16:183 [View Article] [PubMed]
    [Google Scholar]
  2. Zhang G, Yang J, Lai XH, Jin D, Lu S et al. Corynebacterium zhongnanshanii sp. nov. isolated from trachea of Marmota himalayana, Corynebacterium lujinxingii sp. nov. and Corynebacterium wankanglinii sp. nov. from human feces. Int J Syst Evol Microbiol 2021; 71: [View Article]
    [Google Scholar]
  3. Liu S, Jin D, Lan R, Wang Y, Meng Q et al. Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana. Int J Syst Evol Microbiol 2015; 65:2130–2134 [View Article] [PubMed]
    [Google Scholar]
  4. Hu S, Jin D, Lu S, Liu S, Zhang J et al. Helicobacter himalayensis sp. nov. isolated from gastric mucosa of Marmota himalayana. Int J Syst Evol Microbiol 2015; 65:1719–1725 [View Article] [PubMed]
    [Google Scholar]
  5. Niu L, Lu S, Lai X-H, Hu S, Chen C et al. Streptococcus himalayensis sp. nov., isolated from the respiratory tract of Marmota himalayana. Int J Syst Evol Microbiol 2017; 67:256–261 [View Article] [PubMed]
    [Google Scholar]
  6. Wylensek D, Hitch TCA, Riedel T, Afrizal A, Kumar N et al. A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. Nat Commun 2020; 11:6389 [View Article] [PubMed]
    [Google Scholar]
  7. Beltrán D, Romo-Vaquero M, Espín JC, Tomás-Barberán FA, Selma MV. Ellagibacter isourolithinifaciens gen. nov., sp. nov., a new member of the family Eggerthellaceae, isolated from human gut. Int J Syst Evol Microbiol 2018; 68:1707–1712 [View Article] [PubMed]
    [Google Scholar]
  8. Danylec N, Göbl A, Stoll DA, Hetzer B, Kulling SE et al. Rubneribacter badeniensis gen. nov., sp. nov. and Enteroscipio rubneri gen. nov., sp. nov., new members of the Eggerthellaceae isolated from human faeces. Int J Syst Evol Microbiol 2018; 68:1533–1540 [View Article]
    [Google Scholar]
  9. Traore SI, Bilen M, Beye M, Diop A, Mbogning Fonkou MD et al. Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut. Microbiologyopen 2019; 8:e00758 [View Article]
    [Google Scholar]
  10. Nakazawa F, Poco SE, Ikeda T, Sato M, Kalfas S et al. Cryptobacterium curtum gen. nov., sp. nov., a new genus of gram-positive anaerobic rod isolated from human oral cavities. Int J Syst Bacteriol 1999; 49 Pt 3:1193–1200 [View Article]
    [Google Scholar]
  11. Anderson RC, Rasmussen MA, Jensen NS, Allison MJ. Denitrobacterium detoxificans gen. nov., sp. nov., a ruminal bacterium that respires on nitrocompounds. Int J Syst Evol Microbiol 2000; 50 Pt 2:633–638 [View Article]
    [Google Scholar]
  12. Zhang G, Yang J, Lai X-H, Jin D, Pu J et al. Neisseria weixii sp. nov., isolated from rectal contents of Tibetan Plateau pika (Ochotona curzoniae). Int J Syst Evol Microbiol 2019; 69:2305–2311 [View Article] [PubMed]
    [Google Scholar]
  13. 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]
  14. Rosselló-Móra R, Amann R. Past and future species definitions for bacteria and archaea. Syst Appl Microbiol 2015; 38:209–216 [View Article] [PubMed]
    [Google Scholar]
  15. Thompson JD, Gibson TJ, Higgins DG. Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics 2002; Chapter 2:Unit [View Article]
    [Google Scholar]
  16. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
  17. 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]
  18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  19. Zhang G, Lai X-H, Yang J, Jin D, Pu J et al. Luteimonas chenhongjianii, a novel species isolated from rectal contents of Tibetan Plateau pika (Ochotona curzoniae). Int J Syst Evol Microbiol 2020; 70:3186–3193 [View Article] [PubMed]
    [Google Scholar]
  20. Bilen M, Fonkou MDM, Caputo A, Nguyen T-T, Di Pinto F et al. Phoenicibacter congonensis gen. nov., sp. nov., a new genus isolated from the human gut and its description using a taxonogenomic approach. Antonie Van Leeuwenhoek 2019; 112:775–784 [View Article]
    [Google Scholar]
  21. Gupta RS, Chen WJ, Adeolu M, Chai Y. Molecular signatures for the class Coriobacteriia and its different clades; proposal for division of the class Coriobacteriia into the emended order Coriobacteriales, containing the emended family Coriobacteriaceae and Atopobiaceae fam. nov., and Eggerthellales ord. nov., containing the family Eggerthellaceae fam. nov. Int J Syst Evol Microbiol 2013; 63:3379–3397 [View Article] [PubMed]
    [Google Scholar]
  22. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  23. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009; 26:1641–1650 [View Article] [PubMed]
    [Google Scholar]
  24. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 2012; 28:3150–3152 [View Article] [PubMed]
    [Google Scholar]
  25. Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 2012; 61:1061–1067 [View Article] [PubMed]
    [Google Scholar]
  26. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
    [Google Scholar]
  27. Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002; 30:1575–1584 [View Article] [PubMed]
    [Google Scholar]
  28. Chaumeil PA, 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. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
    [Google Scholar]
  30. 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]
  31. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article] [PubMed]
    [Google Scholar]
  32. 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]
  33. Elsawi Z, Togo AH, Beye M, Dubourg G, Andrieu C et al. Hugonella massiliensis gen. nov., sp. nov., genome sequence, and description of a new strictly anaerobic bacterium isolated from the human gut. Microbiologyopen 2017; 6:e004580 [View Article]
    [Google Scholar]
  34. Maruo T, Sakamoto M, Ito C, Toda T, Benno Y. Adlercreutzia equolifaciens gen. nov., sp. nov., an equol-producing bacterium isolated from human faeces, and emended description of the genus Eggerthella. Int J Syst Evol Microbiol 2008; 58:1221–1227 [View Article]
    [Google Scholar]
  35. Lo CI, Traore SI, Diop A, Bilen M, Azhar EI et al. Arabiibacter massiliensis gen. nov. sp. nov., new anaerobic bacterium isolated from the human gut. Curr Microbiol 2022; 79:47 [View Article]
    [Google Scholar]
  36. Würdemann D, Tindall BJ, Pukall R, Lünsdorf H, Strömpl C et al. Gordonibacter pamelaeae gen. nov., sp. nov., a new member of the Coriobacteriaceae isolated from a patient with Crohn’s disease, and reclassification of Eggerthella hongkongensis Lau et al. 2006 as Paraeggerthella hongkongensis gen. nov., comb. nov. Int J Syst Evol Microbiol 2009; 59:1405–1415 [View Article]
    [Google Scholar]
  37. Lau SKP, Woo PCY, Woo GKS, Fung AMY, Wong MKM et al. Eggerthella hongkongensis sp. nov. and Eggerthella sinensis sp. nov., two novel Eggerthella species, account for half of the cases of Eggerthella bacteremia. Diagn Microbiol Infect Dis 2004; 49:255–263 [View Article]
    [Google Scholar]
  38. Lagier J-C, Elkarkouri K, Rivet R, Couderc C, Raoult D et al. Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov. Stand Genomic Sci 2013; 7:343–356 [View Article] [PubMed]
    [Google Scholar]
  39. Wade WG, Downes J, Dymock D, Hiom SJ, Weightman AJ et al. The family Coriobacteriaceae: reclassification of Eubacterium exiguum (Poco et al. 1996) and Peptostreptococcus heliotrinreducens (Lanigan 1976) as Slackia exigua gen. nov., comb. nov. and Slackia heliotrinireducens gen. nov., comb. nov., and Eubacterium lentum (Prevot 1938) as Eggerthella lenta gen. nov., comb. nov. Int J Syst Bacteriol 1999; 49 Pt 2:595–600 [View Article]
    [Google Scholar]
  40. Nagai F, Watanabe Y, Morotomi M. Slackia piriformis sp. nov. and Collinsella tanakaei sp. nov., new members of the family Coriobacteriaceae, isolated from human faeces. Int J Syst Evol Microbiol 2010; 60:2639–2646 [View Article]
    [Google Scholar]
  41. Poco SE, Nakazawa F, Ikeda T, Sato M, Sato T et al. Eubacterium exiguum sp. nov., isolated from human oral lesions. Int J Syst Bacteriol 1996; 46:1120–1124 [View Article] [PubMed]
    [Google Scholar]
  42. Stoll DA, Danylec N, Soukup ST, Hetzer B, Kulling SE et al. Adlercreutzia rubneri sp. nov., a resveratrol-metabolizing bacterium isolated from human faeces and emended description of the genus Adlercreutzia. Int J Syst Evol Microbiol 2021; 71:004987 [View Article] [PubMed]
    [Google Scholar]
  43. Ge Y, Yang J, Lai X-H, Jin D, Lu S et al. Enorma shizhengliae sp. nov. and Eggerthella guodeyinii sp. nov., two new members of the family Coriobacteriaceae. Int J Syst Evol Microbiol 2021; 71:10 [View Article] [PubMed]
    [Google Scholar]
  44. Jin JS, Kitahara M, Sakamoto M, Hattori M, Benno Y. Slackia equolifaciens sp. nov., a human intestinal bacterium capable of producing equol. Int J Syst Evol Microbiol 2010; 60:1721–1724 [View Article] [PubMed]
    [Google Scholar]
  45. Lechevalier MP. The chemotaxonomy of actinomycetes. In Actinomycete Taxonomy 1980 pp 227–291
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005509
Loading
/content/journal/ijsem/10.1099/ijsem.0.005509
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error