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Volume 72, Issue 11

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

Abstract

A lactic acid bacteria isolated from pig faeces was characterized using a polyphasic approach. Cells of the strain were Gram-stain-positive, rod-shaped and facultative anaerobic. Phylogenetic analysis of 16S rRNA gene sequence indicated that the isolate belonged to the genus ; however, the similarity to other homologues within the genus was <98 %. Analysis of housekeeping gene sequences ( and ) revealed that the strain formed a sub-cluster adjacent to and . The main fatty acids of the strain is the Cω9 and C. The G+C content of the genomic DNA was 62.8 mol %. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, aminophospholipids and phospholipids. The cell-wall peptidoglycan did not contain -diaminopimelic acid. Thus, YH-lac21 (=KCTC 21185=JCM 34953) represents a novel species. The name sp. nov. is proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): feaces , Lacticaseibacillus , Lacticaseibacillus kribbianus 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
© 2022 The Authors
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2022-11-30
2024-05-04
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References

  1. Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B et al. Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci 2006; 103:15611–15616 [View Article]
     [Google Scholar]
  2. 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]
  3. 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]
     [Google Scholar]
  4. Nguyen DTL, Cnockaert M, Van Hoorde K, De Brandt E, Snauwaert I et al. Lactobacillus porcinae sp. nov., isolated from traditional Vietnamese nem chua. Int J Syst Evol Microbiol 2013; 63:1754–1759 [View Article] [PubMed]
     [Google Scholar]
  5. Bai L, Paek J, Shin Y, Park HY, 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]
  6. Bianchi F, Rossi EA, Sakamoto IK, Adorno MAT, Van de Wiele T et al. Beneficial effects of fermented vegetal beverages on human gastrointestinal microbial ecosystem in a simulator. Food Res Int 2014; 64:43–52 [View Article] [PubMed]
     [Google Scholar]
  7. Kechagia M, Basoulis D, Konstantopoulou S, Dimitriadi D, Gyftopoulou K et al. Health benefits of probiotics: a review. ISRN Nutr 2013; 2013:481651 [View Article] [PubMed]
     [Google Scholar]
  8. Huang J, Zhang W, Hu Z, Liu Z, Du T et al. Isolation, characterization and selection of potential probiotic lactic acid bacteria from feces of wild boar, native pig and commercial pig. Livestock Science 2020; 237:104036 [View Article]
     [Google Scholar]
  9. 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]
  10. 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]
  11. 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]
  12. Hansen PA, Lessel EF. Lactobacillus casei (Orla Jensen) comb. nov. Int J Syst Bacteriol 1971; 21:69–71
     [Google Scholar]
  13. 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]
  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. 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. Zentralblatt für Bakteriologie Mikrobiologie und Hygiene: I Abt Originale C: Allgemeine, angewandte und ökologische Mikrobiologie 1981; 2:242–253 [View Article]
     [Google Scholar]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. Jung MY, Kim JS, Paek WK, Styrak I, Park IS et al. Description of Lysinibacillus sinduriensis sp. nov., and transfer of Bacillus massiliensis and Bacillus odysseyi to the genus Lysinibacillus as Lysinibacillus massiliensis comb nov and Lysinibacillus odysseyi comb nov with emended description of the genus Lysinibacillus. Int J Syst Evol Microbiol 2012; 62:2347–2355
     [Google Scholar]
  21. Paek J, Shin Y, Kook J-K, Chang YH. Blautia argi sp. nov., a new anaerobic bacterium isolated from dog faeces. Int J Syst Evol Microbiol 2019; 69:33–38 [View Article] [PubMed]
     [Google Scholar]
  22. 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]
  23. Chang YH, Jung MY, Park IS, Oh HM. 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]
  24. Chun J, Goodfellow M. A phylogenetic analysis of the genus nocardia with 16S rRNA gene sequences. Int J Syst Evol 1995; 45:240–245
     [Google Scholar]
  25. Felis GE, Dellaglio F, Mizzi L, Torriani S. Comparative sequence analysis of a recA gene fragment brings new evidence for a change in the taxonomy of the Lactobacillus casei group. Int J Syst Evol Microbiol 2001; 51:2113–2117 [View Article] [PubMed]
     [Google Scholar]
  26. Rocha J, Botelho J, Ksiezarek M, Perovic SU, Machado M et al. Lactobacillus mulieris sp. nov., a new species of Lactobacillus delbrueckii group. Int J Syst Evol Microbiol 2022; 70:1522–1527 [View Article]
     [Google Scholar]
  27. 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]
  28. Madeira F, Pearce M, Tivey ARN, Basutkar P, Lee J et al. Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res 2022; 50:W276–W279 [View Article]
     [Google Scholar]
  29. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 2022 [View Article]
     [Google Scholar]
  30. Felsenstein J. PHYLIP (Phylogeny Inference Package). Version 3.6. Department340 of Genetics, University of Washington, Seattle USA: Washington; 2005
     [Google Scholar]
  31. Jeon Y-S, Chung H, Park S, Hur I, Lee J-H et al. jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences. Bioinformatics 2005; 21:3171–3173 [View Article] [PubMed]
     [Google Scholar]
  32. 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]
  33. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  34. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967
     [Google Scholar]
  35. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  36. 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]
  37. 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]
  38. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  39. 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]
  40. 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]
  41. 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]
  42. 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]
  43. 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]
  44. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101 Newark, DE: Midi Inc; 1990
     [Google Scholar]
  45. Schumann P. Peptidoglycan structure. Methods Microbiol 2011; 38:101–129
     [Google Scholar]
  46. 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]
  47. Naser SM, Dawyndt P, Hoste B, Gevers D, Vandemeulebroecke K et al. Identification of lactobacilli by pheS and rpoA gene sequence analyses. Int J Syst Evol Microbiol 2007; 57:2777–2789 [View Article] [PubMed]
     [Google Scholar]
  48. Silvaraju S, Menon N, Fan H, Lim K, Kittelmann S. Phylotype-level characterization of complex communities of Lactobacilli using a high-throughput, high-resolution phenylalanyl-tRNA synthetase (pheS) gene amplicon sequencing approach. Appl Environ Microbiol 2020; 87:e02191-20 [View Article]
     [Google Scholar]
  49. Torriani S, Felis GE, Dellaglio F. Differentiation of Lactobacillus plantarum, L. pentosus, and L. paraplantarum by recA gene sequence analysis and multiplex PCR assay with recA gene-derived primers. Appl Environ Microbiol 2001; 67:3450–3454 [View Article]
     [Google Scholar]
  50. 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]
  51. 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]
  52. Brady A, Salzberg SL. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated markov models. Nat Methods 2009; 6:673–676 [View Article]
     [Google Scholar]
  53. Parks DH, MacDonald NJ, Beiko RG. Classifying short genomic fragments from novel lineages using composition and homology. BMC Bioinformatics 2011; 12:328 [View Article] [PubMed]
     [Google Scholar]
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Lacticaseibacillus kribbianus sp. nov., isolated from pig farm faeces dump
Int J Syst Evol Microbiol 72, 005617 (2022); https://doi.org/10.1099/ijsem.0.005617
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