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. 2018 Oct 1;9(10):477.
doi: 10.3390/genes9100477.

Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics

Vikas Sharma  1 , Fauzul Mobeen  2 , Tulika Prakash  3
Affiliations

Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics

Vikas Sharma et al. Genes (Basel). .

Abstract

Members of the genus Bifidobacterium are found in a wide-range of habitats and are used as important probiotics. Thus, exploration of their functional traits at the genus level is of utmost significance. Besides, this genus has been demonstrated to exhibit an open pan-genome based on the limited number of genomes used in earlier studies. However, the number of genomes is a crucial factor for pan-genome calculations. We have analyzed the pan-genome of a comparatively larger dataset of 215 members of the genus Bifidobacterium belonging to different habitats, which revealed an open nature. The pan-genome for the 56 probiotic and human-gut strains of this genus, was also found to be open. The accessory- and unique-components of this pan-genome were found to be under the operation of Darwinian selection pressure. Further, their genome-size variation was predicted to be attributed to the abundance of certain functions carried by genomic islands, which are facilitated by insertion elements and prophages. In silico functional and host-microbe interaction analyses of their core-genome revealed significant genomic factors for niche-specific adaptations and probiotic traits. The core survival traits include stress tolerance, biofilm formation, nutrient transport, and Sec-secretion system, whereas the core probiotic traits are imparted by the factors involved in carbohydrate- and protein-metabolism and host-immunomodulations.

Keywords: Bifidobacterium; comparative genomics; host-microbe interaction; human-gut; immunomodulations; niche-specific adaptations; pan-genome; probiotic.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Plot of pan- and core-genomes of the genus Bifidobacterium (n = 215 members). Pan-genome estimate is shown after using 30 random samples of the 215 genomes. The plot represents a stabilized core structure but an open pan-genome.
Figure 2
Figure 2
The relative entropy of chromosome versus core-genome for the 56 PHBifs. The relative entropy depicts the magnitude of the selection pressure. The core part has a higher selection pressure than that of the chromosome. Significant differences between the two groups were tested with the Welch’s t-test (p-value < 0.001).
Figure 3
Figure 3
A plot of Ka versus Ks of the 613 gene groups of the orthologous genes from the 56 PHBifs. Straight line represents Ka = Ks. Each symbol (+) represents a gene group of 56 orthologous nucleotide sequences from the 56 bifidobacterial genomes. The figure implies that the rates of synonymous substitutions for 613 core genes is higher than that of the non-synonymous substitutions. The resulting core proteins will not be altered and remain conserved during evolution.
Figure 4
Figure 4
An abundance heat map of the different COGs classes present in the genomes of the 56 PHBifs. The strains are sorted (top to bottom) according to increasing genome sizes. D: Cell cycle control, cell division, chromosome partitioning; M: Cell motility; N: Cell wall/membrane/envelope biogenesis; O: Posttranslational modification, protein turnover, chaperones; T: Signal transduction mechanisms; U: Intracellular trafficking, secretion, and vesicular transport; V: Defense mechanisms; A: RNA processing and modification; J: Translation, ribosomal structure and biogenesis; K: Transcription; L: Replication, recombination and repair; C: Energy production and conversion; E: Amino acid transport and metabolism; F: Nucleotide transport and metabolism; G: Carbohydrate transport and metabolism; H: Coenzyme transport and metabolism; I: Lipid transport and metabolism; P: Inorganic ion transport and metabolism; Q: Secondary metabolites biosynthesis, transport and catabolism; R: General function prediction only; S: Function unknown; MC: Multiple classes. The Spearman’s R statistic (p-value < 0.001) was used to estimate the significant correlation between the two groups, including COGs class and genome-size, star represents the status of correlation; for details refer to Table S9.
Figure 5
Figure 5
A bar plot of the KEGG pathways of the human innate immunity-related proteins, which are interacting with the core proteins of the 56 PHBifs. The pathway legends corresponding to the bars (from bottom to top) are given on the right panel.
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