1887

Abstract

Two strains (NLN63 and NLN82) of Gram-stain-negative, oxidase- and catalase-positive, bacilli-shaped organisms were isolated from the faecal samples of two separate in Baisha county of Hainan Province, Southern PR China. Phylogenetic analysis based on the near full-length 16S rRNA sequences revealed that strain NLN63 belongs to the genus , having maximum similarity to CCUG 64465 (97.1 %), CCUG 39967 (96.2 %) and DSM 27484 (96.2 %), respectively. The phylogenomic tree built on 553 core genes from genomes of 20 species in the genus and other adjacent genera further confirmed that strains NLN63 and NLN82 form a distinct subline and exhibit specific phylogenetic affinity with CCUG 39967. In digital DNA–DNA hybridization analyses, strain NLN63 showed low estimated DNA reassociation values (21.4–22.6 %) with the type strains of the species in the genus . The DNA G+C contents of strains NLN63 and NLN82 were 37.3 and 37.1 mol%, respectively. Strain NLN63 had a unique MALDI-TOF MS profile, contained Q-8 as the major quinone and C, summed feature 8 (C 7/C 6 or both) and summed feature 3 (C 7/C 6 or both) as the dominant fatty acids. Based upon these polyphasic characterization data obtained from the present study, a novel species of the genus , sp. nov., is proposed with NLN63 (=GDMCC 1.1697=JCM 33788) as the type strain.

Funding
This study was supported by the:
  • the Innovative research project for graduate students of Hainan Medical University (Award HYYS2020-18)
    • Principle Award Recipient: DuanduanXuan
  • Key R&D Programs of Hainan Province (Award ZDYF2018113)
    • Principle Award Recipient: XiaojunZhou
  • the Key Science and Technology Projects of Hainan Province (Award ZDYF2018140)
    • Principle Award Recipient: XiaojunZhou
  • the Finance science and technology project of Hainan Privince (Award ZDYF2018155)
    • Principle Award Recipient: XiaojunZhou
  • the National Natural Science Foundation of China (Award 82060377, 81760376)
    • Principle Award Recipient: LinaNiu
  • Education Department of Hainan Province (CN) (Award Hnky2019ZD-27)
    • Principle Award Recipient: LinaNiu
  • Hainan Provincial Natural Science Foundation of China (Award 820RC650)
    • Principle Award Recipient: LinaNiu
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004733
2021-03-10
2021-10-17
Loading full text...

Full text loading...

References

  1. Vandamme P, Segers P, Ryll M, Hommez J, Vancanneyt M et al. Pelistega europaea gen. nov., sp. nov., a bacterium associated with respiratory disease in pigeons: taxonomic structure and phylogenetic allocation. Int J Syst Bacteriol 1998; 48:431–440 [View Article][PubMed]
    [Google Scholar]
  2. Prakash O, Munot H, Nimonkar Y, Sharma M, Kumbhare S et al. Description of Pelistega indica sp. nov., isolated from human gut. Int J Syst Evol Microbiol 2014; 64:1389–1394 [View Article][PubMed]
    [Google Scholar]
  3. Vela AI, Perez Sancho M, Domínguez L, Busse H-J, Fernández-Garayzábal JF. Pelistega suis sp. nov., isolated from domestic and wild animals. Int J Syst Evol Microbiol 2015; 65:4909–4914 [View Article][PubMed]
    [Google Scholar]
  4. Prakash O, Green SJ, Jasrotia P, Overholt WA, Canion A et al. Rhodanobacter denitrificans sp. nov., isolated from nitrate-rich zones of a contaminated aquifer. Int J Syst Evol Microbiol 2012; 62:2457–2462 [View Article][PubMed]
    [Google Scholar]
  5. Niu L, Lu S, Hu S, Jin D, Lai X et al. Streptococcus halotolerans sp. nov. isolated from the respiratory tract of Marmota himalayana in Qinghai-Tibet Plateau of China. Int J Syst Evol Microbiol 2016; 66:4211–4217 [View Article][PubMed]
    [Google Scholar]
  6. Andriushchenko SV, Perunova NB, Ivanova EV, Bukharin OV. Application of multiplex-PCR for bifidobacteria and propionibacteria genus identification. Zh Mikrobiol Epidemiol Immunobiol 2014; 5:78–82[PubMed]
    [Google Scholar]
  7. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
    [Google Scholar]
  8. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  9. Rasmussen SW. SEQ tools, a software package for analysis of nucleotide and protein sequences; 2002
  10. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
    [Google Scholar]
  11. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary?. J Comput Biol 2010; 17:337–354 [View Article][PubMed]
    [Google Scholar]
  12. 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]
  13. Wayne LG. International Committee on systematic bacteriology: announcement of the report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Zentralbl Bakteriol Mikrobiol Hyg A 1988; 268:433–434 [View Article][PubMed]
    [Google Scholar]
  14. Goodfellow P. A lust for science. Curr Biol 1998; 8:R223–R224 [View Article][PubMed]
    [Google Scholar]
  15. Goebel BM, Stackebrandt E. Cultural and phylogenetic analysis of mixed microbial populations found in natural and commercial bioleaching environments. Appl Environ Microbiol 1994; 60:1614–1621 [View Article][PubMed]
    [Google Scholar]
  16. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
    [Google Scholar]
  17. 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]
  18. Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten JP et al. Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. mBio 2014; 5:e02136 [View Article][PubMed]
    [Google Scholar]
  19. Garrido-Sanz D, Meier-Kolthoff JP, Göker M, Martín M, Rivilla R et al. Genomic and genetic diversity within the Pseudomonas fluorescens complex. PLoS One 2016; 11:e0150183 [View Article][PubMed]
    [Google Scholar]
  20. Meier-Kolthoff JP, Göker M, Spröer C, Klenk H-P. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article][PubMed]
    [Google Scholar]
  21. 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]
  22. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article][PubMed]
    [Google Scholar]
  23. 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]
  24. Wittouck S, Wuyts S, Meehan CJ, van Noort V, Lebeer S. A genome-based species taxonomy of the Lactobacillus genus complex. mSystems 2019; 4:e00264–19 [View Article][PubMed]
    [Google Scholar]
  25. Crompton MJ, Dunstan RH. Evaluation of in-situ fatty acid extraction protocols for the analysis of staphylococcal cell membrane associated fatty acids by gas chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1084:80–88 [View Article][PubMed]
    [Google Scholar]
  26. Beaz-Hidalgo R, Hossain MJ, Liles MR, Figueras M-J. Strategies to avoid wrongly labelled genomes using as example the detected wrong taxonomic affiliation for aeromonas genomes in the GenBank database. PLoS One 2015; 10:e0115813 [View Article][PubMed]
    [Google Scholar]
  27. 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]
  28. Petit RA, Read TD, rd RTD. Bactopia: a flexible pipeline for complete analysis of bacterial genomes. mSystems 2020; 5:e00190–20 [View Article][PubMed]
    [Google Scholar]
  29. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  30. Randazzo A, Simon M, Goffinet P, Classen J-F, Hougardy N et al. Optimal turnaround time for direct identification of microorganisms by mass spectrometry in blood culture. J Microbiol Methods 2016; 130:1–5 [View Article][PubMed]
    [Google Scholar]
  31. Jo SJ, Park KG, Han K, Park DJ, Park Y-J. Direct identification and antimicrobial susceptibility testing of bacteria from positive blood culture bottles by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and the Vitek 2 system. Ann Lab Med 2016; 36:117–123 [View Article][PubMed]
    [Google Scholar]
  32. Mesureur J, Arend S, Cellière B, Courault P, Cotte-Pattat P-J et al. A MALDI-TOF MS database with broad genus coverage for species-level identification of Brucella . PLoS Negl Trop Dis 2018; 12:e0006874 [View Article][PubMed]
    [Google Scholar]
  33. Centonze AR, Bertoncelli A, Savio C, Orza P, Bedenić B et al. Evaluation of rapid KPC carbapenemase detection method based on MALDI-TOF Vitek MS spectra analysis. J Med Microbiol 2018; 67:1474–1479 [View Article][PubMed]
    [Google Scholar]
  34. Facklam R, Elliott J, Pigott N, Franklin AR. Identification of Streptococcus porcinus from human sources. J Clin Microbiol 1995; 33:385–388 [View Article][PubMed]
    [Google Scholar]
  35. Meng X, Wang Y, Lu S, Lai X-H, Jin D et al. Actinomyces gaoshouyii sp. nov., isolated from plateau pika (Ochotona curzoniae). Int J Syst Evol Microbiol 2017; 67:3363–3368 [View Article][PubMed]
    [Google Scholar]
  36. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids 101, MIDI Technical Note. 1990 pp 1–7
    [Google Scholar]
  37. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London, FL: Academic Press; 1985 pp 267–287
    [Google Scholar]
  38. Hiraishi A, Masamune K, Kitamura H. Characterization of the bacterial population structure in an anaerobic-aerobic activated sludge system on the basis of respiratory quinone profiles. Appl Environ Microbiol 1989; 55:897–901 [View Article][PubMed]
    [Google Scholar]
  39. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  40. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  41. Jang SS, Donahue JM, Arata AB, Goris J, Hansen LM et al. Taylorella asinigenitalis sp. nov., a bacterium isolated from the genital tract of male donkeys (Equus asinus). Int J Syst Evol Microbiol 2001; 51:971–976 [View Article][PubMed]
    [Google Scholar]
  42. Wübbeler JH, Lütke-Eversloh T, Van Trappen S, Vandamme P, Steinbüchel A. Tetrathiobacter mimigardefordensis sp. nov., isolated from compost, a betaproteobacterium capable of utilizing the organic disulfide 3,3'-dithiodipropionic acid. Int J Syst Evol Microbiol 2006; 56:1305–1310 [View Article][PubMed]
    [Google Scholar]
  43. Kämpfer P, Denger K, Cook AM, Lee S-T, Jäckel U et al. Castellaniella gen. nov., to accommodate the phylogenetic lineage of Alcaligenes defragrans, and proposal of Castellaniella defragrans gen. nov., comb. nov. and Castellaniella denitrificans sp. nov. Int J Syst Evol Microbiol 2006; 56:815–819 [View Article][PubMed]
    [Google Scholar]
  44. Blümel S, Mark B, Busse HJ, Kämpfer P, Stolz A. Pigmentiphaga kullae gen. nov., sp. nov., a novel member of the family Alcaligenaceae with the ability to decolorize azo dyes aerobically. Int J Syst Evol Microbiol 2001; 51:1867–1871 [View Article][PubMed]
    [Google Scholar]
  45. Busse HJ, el-Banna T, Oyaizu H, Auling G. Identification of xenobiotic-degrading isolates from the beta subclass of the Proteobacteria by a polyphasic approach including 16S rRNA partial sequencing. Int J Syst Bacteriol 1992; 42:19–26 [View Article][PubMed]
    [Google Scholar]
  46. Stolz A, Bürger S, Kuhm A, Kämpfer P, Busse H-J. Pusillimonas noertemannii gen. nov., sp. nov., a new member of the family Alcaligenaceae that degrades substituted salicylates. Int J Syst Evol Microbiol 2005; 55:1077–1081 [View Article][PubMed]
    [Google Scholar]
  47. Zhang DC, Busse HJ, Wieser C, Liu HC, Zhou YG. Candidimonas bauzanensis sp. nov., isolated from soil, and emended description of the genus Candidimonas VazMoreira, et al. 2011. Int J Syst Evol Microbiol 2012:2084–2089
    [Google Scholar]
  48. Póntigo F, Moraga M, Flores SV. Molecular phylogeny and a taxonomic proposal for the genus Streptococcus . Genet Mol Res 2015; 14:10905–10918 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004733
Loading
/content/journal/ijsem/10.1099/ijsem.0.004733
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

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