1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 3

sp. nov., isolated from a pig farm faeces dump No Access

Abstract

A lactic acid bacterium isolated from pig faeces was characterized using a polyphasic approach. The strain was Gram-stain-positive, rod-shaped, and facultative anaerobic. Phylogenetic analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the genus . The multi-locus sequence tree revealed that the strain formed a sub-cluster adjacent to . The main fatty acids were C and Cω9. The average nucleotide identity value, average amino acid identity, and genome-to-genome distance for YH-lacS6 and its most closely related strain, , were 85.4, 85.2 and 29.2 %, respectively. The G+C content of the genomic DNA was 61.6 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, aminophospholipids and phospholipids. The cell-wall peptidoglycan did not contain -diaminopimelic acid. Thus, YH-lacS6 (=KCTC 21186=JCM 34954) represents a novel species. The name sp. nov. is proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): faeces , Lacticaseibacillus , Lacticaseibacillus parakribbianus and new species
Funding
This study was supported by the:
  • Korea Research Institute of Bioscience and Biotechnology (Award KGS2222221)
    • Principle Award Recipient: YoungHyo Chang
  • National Research Foundation of Korea (Award 2021R1A2C2009051)
    • Principle Award Recipient: Joong-KiKook
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005758
2023-03-21
2024-05-11
Loading full text...

Full text loading...

References

  1. Zheng J, Wittouck S, Salvetti E, Franz CMAP, Harris HMB et al. 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 2020; 70:2782–2858 [View Article]
     [Google Scholar]
  2. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
     [Google Scholar]
  3. Gänzle MG. Fermented foods. In Doyle MP, DiezGonzalez F, Hill C. eds Food Microbiology: Fundamentals and Frontiers, 5th edn. ASM Press; 2019 pp 855–900
     [Google Scholar]
  4. Hutkins RW. Microbiology and Technology of Fermented Foods, 2nd Chigaco, IL: IFT Press; 2019
     [Google Scholar]
  5. Oki K, Kudo Y, Watanabe K. Lactobacillus saniviri sp. nov. and Lactobacillus senioris sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2012; 62:601–607 [View Article] [PubMed]
     [Google Scholar]
  6. Volokhov DV, Amselle M, Beck BJ, Popham DL, Whittaker P et al. Lactobacillus brantae sp. nov., isolated from faeces of Canada geese (Branta canadensis). Int J Syst Evol Microbiol 2012; 62:2068–2076 [View Article] [PubMed]
     [Google Scholar]
  7. Bai L, Paek J, Shin Y, Park H-Y, Chang YH. Lacticaseibacillus absianus sp. nov., isolated from the cecum of a mini-pig. Int J Syst Evol Microbiol 2019; 71: [View Article] [PubMed]
     [Google Scholar]
  8. Hansen PA, Lessel EF. Lactobacillus casei (Orla-Jensen) comb. nov. Int J Syst Bacteriol 1971; 21:69–71 [View Article]
     [Google Scholar]
  9. Tanasupawat S, Pakdeeto A, Thawai C, Yukphan P, Okada S. Identification of lactic acid bacteria from fermented tea leaves (miang) in Thailand and proposals of Lactobacillus thailandensis sp. nov., Lactobacillus camelliae sp. nov., and Pediococcus siamensis sp. nov. J Gen Appl Microbiol 2007; 53:7–15 [View Article]
     [Google Scholar]
  10. Morlon-Guyot J, Guyot JP, Pot B, Jacobe de Haut I, Raimbault M. Lactobacillus manihotivorans sp. nov., a new starch-hydrolysing lactic acid bacterium isolated during cassava sour starch fermentation. Int J Syst Bacteriol 1998; 48 Pt 4:1101–1109 [View Article] [PubMed]
     [Google Scholar]
  11. Collins MD, Phillips BA, Zanoni P. Deoxyribonucleic acid homology studies of Lactobacillus casei, Lactobacillus paracasei sp. nov., subsp. paracasei and subsp. tolerans, and lactobacillus rhamnosus sp. nov., comb. nov. Int J Syst Bacteriol 1989; 39:105–108 [View Article]
     [Google Scholar]
  12. Long GY, Gu CT. Lactobacillus jixianensis sp. nov., Lactobacillus baoqingensis sp. nov., Lactobacillus jiayinensis sp. nov., Lactobacillus zhaoyuanensis sp. nov., Lactobacillus lindianensis sp. nov., Lactobacillus huananensis sp. nov., Lactobacillus tangyuanensis sp. nov., Lactobacillus fuyuanensis sp. nov., Lactobacillus tongjiangensis sp. nov., Lactobacillus fujinensis sp. nov. and Lactobacillus mulengensis sp. nov., isolated from Chinese traditional pickle. Int J Syst Evol Microbiol 2019; 69:2340–2353 [View Article]
     [Google Scholar]
  13. Weiss N, Schillinger U, Laternser M, Kandler O. Lactobacillus sharpeae sp.nov. and Lactobacillus agilis sp.nov., two new species of homofermentative, meso-diaminopimelic acid-containing lactobacilli isolated from sewage. Zentralbl Mikrobiol Parasitenkd Infektionskr Hyg Abt 1 Orig 1981; 2:242–253 [View Article]
     [Google Scholar]
  14. Cai Y, Pang H, Kitahara M, Ohkuma M. Lactobacillus nasuensis sp. nov., a lactic acid bacterium isolated from silage, and emended description of the genus Lactobacillus. Int J Syst Evol Microbiol 2012; 62:1140–1144 [View Article] [PubMed]
     [Google Scholar]
  15. Huang C-H, Liou J-S, Lee A-Y, Tseng M, Miyashita M et al. Polyphasic characterization of a novel species in the Lactobacillus casei group from cow manure of Taiwan: description of L. chiayiensis sp. nov. Syst Appl Microbiol 2018; 41:270–278 [View Article]
     [Google Scholar]
  16. Paek J, Bai L, Shin Y, Kim H, Kook J-K et al. Lacticaseibacillus kribbianus sp. nov., isolated from pig farm faeces dump. Int J Syst Evol Microbiol 2022; 72: [View Article]
     [Google Scholar]
  17. Liu B, Dong X. Lactobacillus pantheris sp. nov., isolated from faeces of a jaguar. Int J Syst Evol Microbiol 2002; 52:1745–1748 [View Article] [PubMed]
     [Google Scholar]
  18. Long GY, Wei YX, Tu W, Gu CT. Lactobacillus hegangensis sp. nov., Lactobacillus suibinensis sp. nov., Lactobacillus daqingensis sp. nov., Lactobacillus yichunensis sp. nov., Lactobacillus mulanensis sp. nov., Lactobacillus achengensis sp. nov., Lactobacillus wuchangensis sp. nov., Lactobacillus gannanensis sp. nov., Lactobacillus binensis sp. nov. and Lactobacillus angrenensis sp. nov., isolated from Chinese traditional pickle and yogurt. Int J Syst Evol Microbiol 2020; 70:2467–2484 [View Article]
     [Google Scholar]
  19. Chang Y-H, Jung MY, Park I-S, Oh H-M. Sporolactobacillus vineae sp. nov., a spore-forming lactic acid bacterium isolated from vineyard soil. Int J Syst Evol Microbiol 2008; 58:2316–2320 [View Article] [PubMed]
     [Google Scholar]
  20. Chun J, Goodfellow M. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 1995; 45:240–245 [View Article] [PubMed]
     [Google Scholar]
  21. Shin Y, Paek J, Kim H, Kook J-K, Kim J-S et al. Absicoccus porci gen. nov., sp. nov., a member of the family Erysipelotrichaceae isolated from pig faeces. Int J Syst Evol Microbiol 2020; 70:732–737 [View Article]
     [Google Scholar]
  22. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article] [PubMed]
     [Google Scholar]
  23. 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]
  24. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016 [View Article]
     [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]
     [Google Scholar]
  26. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article]
     [Google Scholar]
  27. Paek J, Shin Y, Kim J-S, Kim H, Kook J-K et al. Description of Absiella argi gen. nov., sp. nov., and transfer of Eubacterium dolichum and Eubacterium tortuosum to the genus Absiella as Absiella dolichum comb. nov. and Absiella tortuosum comb. nov. Anaerobe 2017; 48:70–75 [View Article]
     [Google Scholar]
  28. Schumann P. Peptidoglycan structure. Methods Microbiol 2011; 38:101–129
     [Google Scholar]
  29. 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]
  30. 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]
  31. Kim M, Oh HS, Park SC, 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]
  32. Brady A, Salzberg SL. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods 2009; 6:673–676 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005758
Loading
Lacticaseibacillus parakribbianus sp. nov., isolated from a pig farm faeces dump
Int J Syst Evol Microbiol 73, 005758 (2023); https://doi.org/10.1099/ijsem.0.005758
/content/journal/ijsem/10.1099/ijsem.0.005758
/content/journal/ijsem/10.1099/ijsem.0.005758
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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