Intra-species variation within Lactobacillus rhamnosus correlates to beneficial or harmful outcomes: lessons from the oral cavity

Abstract

Background The origin of most of the Lactobacillus rhamnosus genome sequences lodged in NCBI can be traced to food and faecal isolates followed by blood and tissue sites but with minimal representation from oral and vaginal isolates. However, on the L. rhamnosus phylogenetic tree no apparent clade is linked to the origin of isolation or to the relevant clinical source, except for a distinct clade exclusively shared by L. rhamnosus isolates from early stages of dental pulp infection (LRHMDP2 and LRHMDP3) and from bronchoalveolar lavage (699_LRHA and 708_LRHA) from a critical care patient. These L. rhamnosus strains, LRHMDP2, LRHMDP3, 699_LRHA and 708_LRHA isolated from different continents, display closest genome neighbour gapped identity of 99.95%. The aim of this study was to define a potentially unique complement of genes of clinical relevance shared between these L. rhamnosus clinical isolates in comparison to probiotic L. rhamnosus strains. Results In this analysis we used orthologous protein identification tools such as ProteinOrtho followed by tblastn alignments to identify a novel tyrosine protein phosphatase (wzb)-tyrosine-protein kinase modulator EpsC (wzd)- synteny exopolysaccharide (EPS) cluster. This EPS cluster was specifically conserved in a clade of 5 clinical isolates containing the four L. rhamnosus clinical isolates noted above and Lactobacillus spp. HMSC077C11, a clinical isolate from a neck abscess. The EPS cluster was shared with only two other strains, L. rhamnosus BPL5 and BPL15, which formed a distant clade on the L. rhamnosus phylogenetic tree, with a closest genome neighbour gapped identity of 97.51% with L. rhamnosus LRHMDP2 and LRHMDP3. Exclusivity of this EPS cluster (from those identified before) was defined by five EPS genes, which were specifically conserved between the clade of 5 clinical isolates and L. rhamnosus BPL5 and BPL15 when compared to the remaining L. rhamnosus strains. Comparative genome analysis between the clade of 5 clinical isolates and L. rhamnosus BPL5 and BPL15 showed a set of 58 potentially unique genes characteristic of the clade of 5. Conclusion The potentially unique functional protein orthologs associated with the clade of 5 clinical isolates may provide understanding of fitness under selective pressure.

Ethnic Specificity of Species and Strain Composition of Lactobacillus Populations From Mother–Infant Pairs, Uncovered by Multilocus Sequence Typing

“…According to published literature, there are more Lactobacillus species reported in human gut than Bifidobacterium spp. Although Lactobacillus species were scarcely reported in human skin specimens using either classical plating techniques and/or DNA sequencing-based approaches, human-associated Lactobacillus species exist not only in the human breast milk and gut tract but also in the oral cavity and vagina of healthy mothers ( Martín et al, 2007 ; Nadkarni et al, 2020 ; Wang et al, 2021 ). Given lifestyle transitions of some Lactobacillus species from free living to host adapted, the migration of some exogenously free-living Lactobacillus species to the infant’s gut cannot be ruled out.…”

Lactobacilli and human dental caries: more than mechanical retention

“…Different from dairy isolates, clinical and oral L. rhamnosus were found to possess l -fucisidase, which enables them to utilize various fucosyl-glycoconjugates on epithelia cell surface and intestinal mucin [22]. Lactobacilli possess rich and redundant transport systems for a variety of mono- and disaccharides, and to a less degree, trisaccharides, which include the high-affinity, sugar-specific phosphotransferase transporter systems (PTSs).…”

“…To name a few, they include glucosidases, fructosidases, galactosidases, glucansucrase, levansucrases and fructansucrases for oligosaccharides and the α-and β-amylases and amyloglucosidases for starches [13,[22][23][24][25][26][27]. Different from dairy isolates, clinical and oral L. rhamnosus were found to possess l-fucisidase, which enables them to utilize various fucosyl-glycoconjugates on epithelia cell surface and intestinal mucin [22]. Lactobacilli possess rich and redundant transport systems for a variety of mono-and disaccharides, and to a less degree, trisaccharides, which include the high-affinity, sugarspecific phosphotransferase transporter systems (PTSs).…”

“…Lactobacillus sp. are diverse, and major differences also exist within the different species (Table S1), as revealed by 16S rRNA and whole-genome sequence analyses [13,14,22,23]. However, they all possess a broad repertoire of enzymes that enable them to utilize various carbohydrates, which are rich in oligosaccharides and starches in the oral cavity.…”

“…However, they all possess a broad repertoire of enzymes that enable them to utilize various carbohydrates, which are rich in oligosaccharides and starches in the oral cavity. To name a few, they include glucosidases, fructosidases, galactosidases, glucansucrase, levansucrases and fructansucrases for oligosaccharides and the α-and β-amylases and amyloglucosidases for starches [13,[22][23][24][25][26][27]. Different from dairy isolates, clinical and oral L. rhamnosus were found to possess l-fucisidase, which enables them to utilize various fucosyl-glycoconjugates on epithelia cell surface and intestinal mucin [22].…”