Plasmids encode niche-specific traits in Lactobacillaceae

Abstract

The species of family Lactobacillaceae are found in highly diverse environments and play an important role in fermented foods and probiotic products. Many of these species have been individually reported to harbor plasmids that encode important genes. In this study, we performed comparative genomic analysis of the publically available data of 512 plasmids from 282 strains represented by 51 species of this family and correlated the genomic features of plasmids with the ecological niches in which these species are found. Two-third of the species had at least one plasmid-harboring strain. Plasmid abundance and GC content were significantly lower in the host-adapted species as compared to the nomadic and free-living species. Hierarchical clustering (HCL) highlighted the distinct nature of plasmids from the nomadic and free-living species than those from the host-adapted species. EggNOG assisted functional annotation revealed that genes associated with transposition, conjugation, DNA repair and recombination, exopolysaccharide production, metal ion transport, toxin-antitoxin system, and stress tolerance were significantly enriched on the plasmids of the nomadic and in some cases nomadic and free-living species. On the other hand, genes related to anaerobic metabolism, ABC transporters, and major facilitator superfamily were found to be overrepresented on the plasmids of the host-adapted species. These genomic signatures are correlated to the comparatively nutrient-depleted, stressful and dynamic environments of nomadic and free-living species and nutrient-rich and anaerobic environments of the host-adapted species. Thus, these results indicate the contribution of the plasmids in the adaptation of lactobacilli to the respective habitats. This study also underlines the potential application of these plasmids in improving the technological and probiotic properties of lactic acid bacteria.

Potentially Probiotic Lactiplantibacillus Plantarum Strains From Indian Foods: Isolation, Characterization and Comparative Genomics

“…Some of the notable plasmid-encoded proteins were glycine betaine transporter, glucansucrase, fructansucrase, major facilitator transporters, metal ion uptake proteins, and toxin-antitoxin. Previously, we reported the presence of some such genes at a higher frequency on the plasmids of L. plantarum than any other species 44 . Overall, these results indicate the contribution of plasmids to the stress resistance as well as potentially technical properties of DKL3 and JGR2.…”

Genome Sequencing of five Lacticaseibacillus Strains and Analysis of Type I and II Toxin-Antitoxin System Distribution

“…In the perspective of a nomadic lifestyle, plasmids can carry several genes important for the growth and adaptation of microorganisms to varying environmental conditions, as well as technological traits useful for the selection of strains for industrial applications [ 33 ]. Indeed, a comparative analysis of plasmids from the broad Lactobacillus genus corroborated the association between plasmids and functional traits involved in niche adaptation, highlighting the enrichment of genes associated with transposition, and defense systems such as restriction–modification enzymes and toxin–antitoxin systems [ 34 ].…”

Antimicrobial resistance determinants in silage

“…Neither ErmB, nor tetM have ever been described to derive from the genetic material of Lactiplantibacillus species. Genus-level identification of tetM in Lactobacillaceae has recently happened 91 , but species-level identification and association with Levilactobacillus brevis or with Lactiplantibacillus argentoratensis has been executed for first. Latilactobacillus sakei and Lactiplantibacillus plantarum have already been found to harbour tetM by other publications 92,93 .…”

“…The possible plasmid origin of Lacticaseibacillus manihotivorans deriving ANT(6)-Ia is supported by the CARD description 13 . The identification of plasmid-encoded tetM has happened in Lactobacillaceae 91 , but species level association to Levilactobacillus brevis, Lactiplantibacillus argentoratensis, Latilactobacillus sakei or Lactiplantibacillus plantarum has been executed for first. Moreover, in Levilactobacillus brevis, plasmid-mediated tetM appeared to be flanked by an iMGE.…”

“…The plasmid association of Lelliottia amnigena originated FosA2 is in line with other publications 122 . LnuA and tetM that were found in Leuconostoc kimchii and L. mesenteroides, respectively, both normally appear on plasmids 13,91 . The plasmid association of Pediococcus acidilactici deriving tetM is in line with the current literature 13,96 .…”