Strains, isolated from the same children in different time points.

<p>Horizontal axis represent the age of the subject, rows represent the children, labels in the cells correspond to the isolated strains. Dotted lines connect similar strains.</p

Total numbers of IS elements of different families in the complete <i>B</i>. <i>longum</i> genome sequences.

<p>Total numbers of IS elements of different families in the complete <i>B</i>. <i>longum</i> genome sequences.</p

Distribution of ortholog groups by the number of strains in which they are present.

<p>Ortholog groups were divided into three categories based on their prevalence.</p

Intraspecies Genomic Diversity and Long-Term Persistence of <i>Bifidobacterium longum</i>

<div><p>Members of genus <i>Bifidobacterium</i> are Gram-positive bacteria, representing a large part of the human infant microbiota and moderately common in adults. However, our knowledge about their diversity, intraspecific phylogeny and long-term persistence in humans is still limited. <i>Bifidobacterium longum</i> is generally considered to be the most common and prevalent species in the intestinal microbiota. In this work we studied whole genome sequences of 28 strains of <i>B</i>. <i>longum</i>, including 8 sequences described in this paper. Part of these strains were isolated from healthy children during a long observation period (up to 10 years between isolation from the same patient). The three known subspecies (<i>longum</i>, <i>infantis</i> and <i>suis</i>) could be clearly divided using sequence-based phylogenetic methods, gene content and the average nucleotide identity. The profiles of glycoside hydrolase genes reflected the different ecological specializations of these three subspecies. The high impact of horizontal gene transfer on genomic diversity was observed, which is possibly due to a large number of prophages and rapidly spreading plasmids. The pan-genome characteristics of the subspecies <i>longum</i> corresponded to the open pan-genome model. While the major part of the strain-specific genetic loci represented transposons and phage-derived regions, a large number of cell envelope synthesis genes were also observed within this category, representing high variability of cell surface molecules. We observed the cases of isolation of high genetically similar strains of <i>B</i>. <i>longum</i> from the same patients after long periods of time, however, we didn’t succeed in the isolation of genetically identical bacteria: a fact, reflecting the high plasticity of microbiota in children.</p></div

Small cryptic plasmids from <i>B</i>. <i>longum</i> strains sequenced for this study.

<p>Small cryptic plasmids from <i>B</i>. <i>longum</i> strains sequenced for this study.</p

Structure of CRISPR-Cas systems in <i>B</i>. <i>longum</i>.

<p>Each scheme represents a typical locus from one of the studied strains.</p

Pairwise comparison of ortholog groups content in <i>B</i>. <i>longum</i> strains.

<p>Heatmap represents the number of shared orthologs between strains, the tree was inferred by complete linkage hierarchical clustering.</p

Sizes of pan-genome and core genome of <i>B</i>. <i>longum</i> subsp. <i>longum</i> as functions of the number of strains sequentially added.

<p>Each dot represents distribution of data obtained from 10000 random permutations of strain order. Central horizontal lines, medians; lower and upper border of boxes, 25 and 75 quartiles, respectively; ends of the whiskers, minimal and maximal values; black dots, mean values.</p

CRISPR-Cas systems found in the <i>B</i>. <i>longum</i> genome sequences.

<p>CRISPR-Cas systems found in the <i>B</i>. <i>longum</i> genome sequences.</p

Neighbor-joining phylogenetic tree of <i>B</i>. <i>longum</i> based on concatenated sequences of 43 housekeeping genes.

<p><i>Bifidobacterium breve</i> strain UCC2003 was used as an outgroup (branch length is given out of scale). Clades confirmed by ClonalFrame analysis are marked with asterisk (*), numbers in nodes represent bootstrap confidence levels.</p