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However, on the <jats:italic>L. rhamnosus<\/jats:italic> 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 <jats:italic>L. rhamnosus<\/jats:italic> 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 <jats:italic>L. rhamnosus<\/jats:italic> 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 <jats:italic>L. rhamnosus<\/jats:italic> clinical isolates in comparison to probiotic <jats:italic>L. rhamnosus<\/jats:italic> strains.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>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 <jats:italic>L. rhamnosus<\/jats:italic> clinical isolates noted above and <jats:italic>Lactobacillus<\/jats:italic> spp. HMSC077C11, a clinical isolate from a neck abscess. The EPS cluster was shared with only two other strains, <jats:italic>L. rhamnosus<\/jats:italic> BPL5 and BPL15, which formed a distant clade on the <jats:italic>L. rhamnosus<\/jats:italic> phylogenetic tree, with a closest genome neighbour gapped identity of 97.51% with <jats:italic>L. rhamnosus<\/jats:italic> LRHMDP2 and LRHMDP3.<\/jats:p>\n                <jats:p>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 <jats:italic>L. rhamnosus<\/jats:italic> BPL5 and BPL15 when compared to the remaining <jats:italic>L. rhamnosus<\/jats:italic> strains. Comparative genome analysis between the clade of 5 clinical isolates and <jats:italic>L. rhamnosus<\/jats:italic> BPL5 and BPL15 showed a set of 58 potentially unique genes characteristic of the clade of 5.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>The potentially unique functional protein orthologs associated with the clade of 5 clinical isolates may provide understanding of fitness under selective pressure.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12864-020-07062-3","type":"journal-article","created":{"date-parts":[[2020,9,24]],"date-time":"2020-09-24T11:03:41Z","timestamp":1600945421000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Intra-species variation within Lactobacillus rhamnosus correlates to beneficial or harmful outcomes: lessons from the oral cavity"],"prefix":"10.1186","volume":"21","author":[{"given":"Mangala A.","family":"Nadkarni","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nandan P.","family":"Deshpande","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc R.","family":"Wilkins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neil","family":"Hunter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,9,24]]},"reference":[{"issue":"6","key":"7062_CR1","doi-asserted-by":"publisher","first-page":"1889","DOI":"10.1093\/gbe\/evw123","volume":"8","author":"C Ceapa","year":"2016","unstructured":"Ceapa C, Davids M, Ritari J, Lambert J, Wels M, Douillard FP, Smokvina T, de Vos WM, Knol J, Kleerebezem M. 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