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

BMC Genomics

Neil Hunter¹  Mangala A. Nadkarni²  Nandan P. Deshpande³  Marc R. Wilkins⁴ 

[1] Institute of Dental Research, Westmead Centre for Oral Health, Westmead Hospital, Sydney, New South Wales, Australia;Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia;Institute of Dental Research, Westmead Centre for Oral Health, Westmead Hospital, Sydney, New South Wales, Australia;Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia;The School of Dentistry, the Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia;Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia;Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia;School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia;Ramaciotti Centre for Genomics, The University of New South Wales, Sydney, New South Wales, Australia;

关键词: Lactobacillus rhamnosus;    Dental caries;    Infection;    Genome;    Defense;    Toxin-antitoxin;    Extracellular polysaccharide;   

DOI  :  10.1186/s12864-020-07062-3

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsIn 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.ConclusionThe potentially unique functional protein orthologs associated with the clade of 5 clinical isolates may provide understanding of fitness under selective pressure.

【 授权许可】

CC BY