1887

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Volume 8, Issue 7

Genomic diversity of genus Open Access

Abstract

The genus (formerly ) contains multiple species considered to be adapted to vertebrates, yet their genomic diversity has not been explored. In this study, we performed comparative genomic analysis of (22 species; 332 genomes) isolated from different niches, further focusing on human strains (11 species; 74 genomes) and their adaptation features to specific body sites. Phylogenomic analysis of showed misidentification of some strains deposited in public databases and existence of putative novel species. The pangenome analysis revealed a remarkable genomic diversity (only 1.3 % of gene clusters are shared), and we did not observe a strong association of the accessory genome with different niches. The pangenome of and was open, suggesting that acquisition of genes is still occurring. Although most were predicted as antibiotic susceptible (83%), acquired antibiotic-resistance genes were common in from food-producing animals. Genes related to lactic acid isoform production (>95 %) and putative bacteriocins (70.2%) were identified in most strains, while prophages (55.4%) and CRISPR-Cas systems (32.0%) were less prevalent. Among strains from human sources, several metabolic pathways were predicted as conserved and completed. Their accessory genome was highly variable and did not cluster according to different human body sites, with some exceptions (urogenital , , and or gastrointestinal ). Moreover, we identified 12 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologues that were significantly enriched in strains from particular body sites. We concluded that evolution of the highly diverse is complex and not always related to niche or human body site origin.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): animals , antimicrobial resistance , comparative genomics , human microbiome , Lactobacillaceae and pangenome
Funding
This study was supported by the:
  • Unidade de Ciências Biomoleculares Aplicada (Award UIDP/QUI/04378/2020)
    • Principle Award Recipient: TeresaMaria Pinto Gonçalves Ribeiro
  • Fundação para a Ciência e a Tecnologia (Award DL57/2016/CP1346/CT0034)
    • Principle Award Recipient: FilipaGrosso
  • Fundação para a Ciência e a Tecnologia (Award SFRH/BD/132497/2017)
    • Principle Award Recipient: MagdalenaKsiezarek
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2022-07-15
2024-04-29
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Genomic diversity of genus Limosilactobacillus
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