- In humans, the presence of bifidobacteria in the gut has been correlated with health-promoting benefits. - Here, we compared the genome sequences of a subset of the over 400 Bifidobacterium strains publicly available to investigate the adaptation of bifidobacteria diversity. - We analyzed Bifidobacterium genomes available in the PATRIC and NCBI repositories and identified the hosts and/or environment from which they were isolated. - Results: We found that bifidobacteria diversity appears to have evolved with their hosts as strains isolated from the same host were non-randomly associated with their phylogenetic relatedness. - Moreover, bifidobacteria isolated from different sources displayed differences in genomic traits such as genome size and accessory gene composition and on particular traits related to amino acid production and degradation of carbohydrates. - 2020 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - Bifidobacteria are gram- positive, anaerobic, saccharolytic bacteria, members of the genus Bifidobacterium of the phylum Actinobacteria [7]. - Bifidobacteria are ubiquitous inhabitants of the gastrointestinal tract, va- gina, and mouth of mammals, including humans and are also present in guts of insects such as bees [16,17]. - We analyzed a subset of the over 400 bifidobacteria genomes publicly available to answer two questions: 1) Do bifidobacteria show a phylogenetic signal with their. - Genome size is broadly associ- ated with different bacterial lifestyles [29–31], and accessory gene composition can capture horizontally transferred regions of the genome, which are thought to allow for rapid adaptation to a specific environment [32]. - To investigate the phylogenetic relationships between bifidobacteria strains isolated from different environ- ments and hosts, two phylogenetic trees were con- structed based on 107 concatenated core genes. - In both trees, members of the same taxonomic species clustered closely, and the phylogenetic structure of the trees was similar to previ- ous reports based on 16S rRNA sequences and based on various core genes . - asteroides phylogroup has been previously shown to be positioned in the deepest branches of the bifidobacteria lineage [16,24,40]. - branch corresponded to a member of the B. - perhaps, this is due to the fact that we did not have a representative of the B. - in the human-derived tree. - In the larger tree, the deepest branches corresponded to strains from the B. - The strains isolated from a variety of human stages and body locations showed no phylogenetic signal (ANOSIM: R = 0.022, p >. - Similarly, strains isolated from the blood were not more genetically similar to one another than those found in milk or in the urogenital tract.. - These broader evolutionary patterns seem particularly robust for strains isolated from the orders Artiodactyla (pig and cattle-derived strains), Hymenoptera (bee-derived strains), and Primates (human and non-human primate- derived strains) as they clustered mostly within the same branches (Fig. - Furthermore, the range of genome sizes for bifidobacteria isolated from diverse animal hosts and environments (e.g. - 0.001), and the phylogeny of the bifidobacteria strains (based on 107 core genes. - Strains isolated from the other host categories carried between 86 and 90 genes (Fig. - Bifidobacteria strains isolated from the same host or environment were non-randomly associated with their phylogenetic relatedness. - For example, Lamendella et al.. - [19] found that bifidobacteria strains from the same host, including those isolated from birds and pigs, tended to cluster by clade. - pseudolongum strains were isolated from pigs as previously noted [43]. - branches of the genus. - Sun et al. - More specifically, bifidobacteria strains isolated from different hosts differed in the abundance and diversity of amino acid biosynthesis genes. - Given that previous studies have shown evidence that species isolated from bees, like B. - 2A|The pan-genome of the 129 bifidobacteria strains is summarized in a pie chart showing the core genes (438), the soft genes (115), the shell genes (1802), and the cloud genes (24,550). - 2B|Pan- genome alignment of 129 bifidobacteria strains is depicted by combining the phylogenetic tree inferred by RAxML 8.2.10 and the pan-genome heatmap showing gene presence (royal blue) or absence (white) in each of the strains obtained with Roary 3.11.2. - and there was genomic evidence of carbohydrate specialization by bifidobacteria isolated from different hosts. - In particular, strains isolated from primates (in- cluding humans) carried relatively high abundances of CAZyme encoding genes. - 4 Amino acid biosynthesis gene A) abundances and B) diversity among different hosts and environments. - longum, isolated from the vagina and gut of humans were indistinguishable based on phylogenetic and genomic trait analyses [22]. - 5 CAZyme abundances for strains isolated from A) humans and B) multiple hosts and environments. - In particular, we expected high numbers of CAZymes from infant strains as some bifidobacteria can degrade HMOs in the babies’ gut allowing the modulation of the im- mune system and succession of the microbiome in the infants [10,35,47]. - Related to this, we had to exclude many human-derived genomes that were not accompanied by information about the specific isolation site and age stage of the host.. - Lastly, it is unclear whether some of the observed pat- terns might have been influenced by different isolation methods, which likely varied across different studies.. - This adaptation is reflected in the evolutionary history of the shared core genome as well as their accessory gene composition and specific gene sets. - We iden- tified the hosts for each of the strains by searching the PATRIC and NCBI databases or associated publications (n = 446) (Additional file 1). - The vast ma- jority of the strains in the databases were derived from human hosts followed by primates, cattle, pigs and bees.. - For strains isolated from humans (n = 271), we assigned each strain to the most specific category possible, ac- knowledging that some categories are subsets of other categories: infant (n = 117), adult (n = 20), human blood (n = 13), human milk (n = 10), urogenital (n = 9), elderly (n = 5), child (n = 4), probiotic (n = 3), oral (n = 2), hu- man unspecified (n = 88). - These strains included the majority of the non-human bifidobacteria, in addition to a subset of human strains from adult and in- fant feces (n = 13), blood (n = 1), vagina (n = 1), and mouth (n = 1). - Each of the genome sequences was searched for 107 conserved single-copy genes defined by Dupont et al. - We next tested whether some of the variation in the traits encoded by bifidobacteria genomes could be ex- plained by the host or environment from which they were isolated. - For human-derived strains we used the same 60 sequences used in the phylogenetic analysis since they were carefully chosen to encompass variable human environments and tried to keep similar sample sizes when possible between categories. - however, for the comparison among multiple hosts and environments we used a subset of the 129 strains to keep sample sizes the same for each category (n = 6). - The pan-genome and gene ontology of the 129 se- lected bifidobacteria strains were established with Roary v using the annotated genome assemblies ob- tained from Prokka v1.13 (.gff files). - 100% of the strains), soft core genes (present in 95–99%. - of the strains), shell genes (present in 15–95% of the strains), and cloud genes (present in 0–15. - We used ANOSIM in PRIMER-6 Software [64] to test whether the isolation source categories were associated with phylogenetic relatedness and accessory genes of the bifidobacteria strains. - To construct heatmaps and boxplots, RStudio version 1.1.453 (http://www.rstu- dio.com/) was implemented and to help with the optimization of the images created, Adobe® Acrobat® Pro 2017 was used.. - List of the 60 bifidobacteria human-derived strains in- cluded in the analysis.. - List of the 129 bifidobacteria strains across all environments included in the analysis.. - We would like to thank and acknowledge Katrine Whiteson, Brandon Gaut, and the members of the Martiny lab for their feedback while working on the manuscript.. - McFall-Ngai M, Hadfield MG, Bosch TCG, Carey HV, Domazet-Lo š o T, Douglas AE, et al. - David LA, Materna AC, Friedman J, Campos-Baptista MI, Blackburn MC, Perrotta A, et al. - 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