Positive Selection in Bifidobacterium Genes Drives Species-Specific Host-Bacteria Communication.

Valery N Danilenko,Marina S Dyachkova,Evgeny V Chekalin

doi:10.3389/fmicb.2019.02374

Valery N Danilenko, Marina S Dyachkova + Show 1 more

Open Access

https://doi.org/10.3389/fmicb.2019.02374

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Abstract

Bifidobacteria are commensal microorganisms that inhabit a wide range of hosts, including insects, birds and mammals. The mechanisms responsible for the adaptation of bifidobacteria to various hosts during the evolutionary process remain poorly understood. Previously, we reported that the species-specific PFNA gene cluster is present in the genomes of various species of the Bifidobacterium genus. The cluster contains signal transduction and adhesion genes that are presumably involved in the communication between bifidobacteria and their hosts. The genes in the PFNA cluster show high sequence divergence between bifidobacterial species, which may be indicative of rapid evolution that drives species-specific adaptation to the host organism. We used the maximum likelihood approach to detect positive selection in the PFNA genes. We tested for both pervasive and episodic positive selection to identify codons that experienced adaptive evolution in all and individual branches of the Bifidobacterium phylogenetic tree, respectively. Our results provide evidence that episodic positive selection has played an important role in the divergence process and molecular evolution of sequences of the species-specific PFNA genes in most bifidobacterial species. Moreover, we found the signatures of pervasive positive selection in the molecular evolution of the tgm gene in all branches of the Bifidobacterium phylogenetic tree. These results are consistent with the suggested role of PFNA gene cluster in the process of specific adaptation of bifidobacterial species to various hosts.

Highlights

Bifidobacteria are anaerobic bacteria, some of the most ancient representatives of the phylum Actinobacteria (Gao et al, 2006), which existed in the times when the Earth’s atmosphere contained little oxygen
We calculated the pairwise Pearson correlation coefficients between the evolutionary distance matrices of phylogenetic trees based on multiple sequence alignments of the orthologous genes pkb2, fn3, aaa-atp, duf58, and tgm belonging to various bifidobacterial species
We constructed an unrooted Bifidobacterium phylogenetic tree based on the concatenated coding regions of the pkb2, fn3, aaa-atp, duf58, and tgm genes (Figure 1)

Summary

Introduction

Bifidobacteria are anaerobic bacteria, some of the most ancient representatives of the phylum Actinobacteria (Gao et al, 2006), which existed in the times when the Earth’s atmosphere contained little oxygen. Bifidobacteria are commensal microorganisms that inhabit a wide range of hosts, including insects, birds and mammals. The overview of bifidobacteria ecology suggests a strict association between bifidobacterial species and the animal niches that they occupy (Mattarelli et al, 2017). One possible explanation is that species-specific adaptation and long-term coevolution led to the formation of this association. The mechanisms responsible for the adaptation of bifidobacteria to various hosts during the evolutionary process remain poorly understood. Host colonization is accompanied by bidirectional host-commensal microbiota communication. Studies in the field of microbial endocrinology show that microorganisms, through their long

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