Sellimonas intestinalis is a Gram-positive and anaerobic bacterial species previously considered as uncultivable. Although little is known about this Lachnospiraceae family member, its increased abundance has been reported in patients who have recovered from intestinal homeostasis after dysbiosis events. In this context, the aim of the present study was to take advantage of a massive in vitro culture protocol that allowed the recovery of extremely oxygen-sensitive species from faecal samples, which led to isolation of S. intestinalis . Whole genome analyses of 11 S . intestinalis genomes revealed that this species has a highly conserved genome with 99.7 % 16S rRNA gene sequence similarity, average nucleotide polymorphism results >95, and 50.1 % of its coding potential being part of the core genome. Despite this, the variable portion of its genome was informative enough to reveal the existence of three lineages (lineage-I including isolates from Chile and France, lineage-II from South Korea and Finland, and lineage-III from China and one isolate from the USA) and evidence of some recombination signals. The identification of a cluster of orthologous groups revealed a high number of genes involved in metabolism, including amino acid and carbohydrate transport as well as energy production and conversion, which matches with the metabolic profile previously reported for microbiota from healthy individuals. Additionally, virulence factors and antimicrobial resistance genes were found (mainly in lineage-III), which could favour their survival during antibiotic-induced dysbiosis. These findings provide the basis of knowledge about the potential of S. intestinalis as a bioindicator of intestinal homeostasis recovery and contribute to advancing the characterization of gut microbiota members with beneficial potential.
Comprehensive genome analyses of Sellimonas intestinalis, a potential 19 biomarker of homeostasis gut recovery 20 Sellimonas intestinalis is a Gram positive and anaerobic bacterial species 21 previously considered as uncultivable. Although little is known about this 22 Lachnospiraceae family member, its increased abundance has been reported in 23 patients who recovered intestinal homeostasis after dysbiosis events. In this 24 context, the aim of this work was taken advantage of a culturomics protocol that 25 allowed the recovery species extremely oxygen-sensitive from faecal samples, 26 which led to the establishment of an S. intestinalis isolate. Whole genome 27 sequencing and taxonomic allocation confirmation were the base to develop 28 comparative analyses including 11 public genomes closely related. 29 Phylogeographic analysis revealed the existence of three lineages (linage-I 30 including isolates from Chile and France, linage-II from South Korea and Finland, 31 and linage-III from China and one isolate from USA). Pangenome analysis on the 32 established dataset revealed that although S. intestinalis seems to have a highly 33 conserved genome (with 50.1% of its coding potential being part of the 34 coregenome), some recombination signals were evidenced. The identification of 35 cluster of orthologous groups revealed a high number of genes involved in 36 metabolism, including amino acid and carbohydrate transport as well as energy 37 production and conversion, which matches with the metabolic profile previously 38 reported for healthy microbiota. Additionally, virulence factors and antimicrobial 39 resistance genes were found (mainly in linage-III), which could favour their 40 survival during antibiotic-induced dysbiosis. These findings provide the basis of 41 knowledge about this species with potential as a bioindicator of intestinal 42 homeostasis recovery and contribute to advance in the characterization of gut 43 microbiota members with beneficial potential.44
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