Comparative Genomics of Host–Symbiont and Free-Living Oceanobacillus Species

Abstract

Survival in a given environment requires specific functions, so genomic variation is anticipated within in individual taxonomic groups that exhibit a large diversity in lifestyles. In this study, we sequence and assemble the genome of Oceanobacillus faecalis strain HM6, a resident of the human gut. Using the genus Oceanobacillus and the HM6 draft genome sequence, we explore the functional requirements for survival in a symbiotic arrangement within the human gut, in contrast to free living in the environment. Comparative genomics of seven available Oceanobacillus complete genomes highlight a genomically heterogeneous group. Our analysis did not find strict phylogenetic separation between free-living and host–symbiont Oceanobacillus members. By comparing functional gene content between host-associated and free-living species, we identified candidate genes that are potentially involved in symbiotic lifestyles, including phosphotransferase genes, transporters and two component response regulators. This study summarizes genomic and phylogenetic differences in the Oceanobacillus genus. Additionally, we highlight functions that may be key for survival in the human gut community.

Comparative Genomics Reveals Broad Genetic Diversity, Extensive Recombination and Nascent Ecological Adaptation in Micrococcus luteus

“…Functional annotation revealed a gene (OG_1965) coding for an ABC transporter permease protein (COG0577). Consistent with its distribution in HA strains in subclade III-b, it has been reported that it is associated with isolates from human gut compared with free-living environments in Oceanobacillus species [86]. However, the potential functions of most genes detected in the association with HA/NHA habitats remain unclear.…”

Metagenomic Profiling of Soil Microbes to Mine Salt Stress Tolerance Genes

“…These studies explain the abundance of Proteobacteria, Actinobacteria, Gemmatimonadetes , and Bacteroidetes in the studied ecosystem. Evolution of novel genetic features is a key to their successful survival in a changing environment (Gupta et al, 2017 ; Kumar Mondal et al, 2017 ). These saline microorganisms could have evolved salt stress tolerant genetic machinery to adapt and survive under salt induced osmotic stresses (Meena et al, 2017 ).…”

Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes

“…Microbial diversity within the human gut plays a significant role in human health, physiology and tissue development 16 . They do so by their ability to counter numerous environmental stresses such as low pH, bile acids, elevated osmolarity, iron limitation, insufficient nutrient availability and host immune factors 17 – 19 . These physiological mechanisms which cumulatively resist rapid changes in the gastrointestinal environment are crucial for their successful colonization 19 , 20 .…”

“…They do so by their ability to counter numerous environmental stresses such as low pH, bile acids, elevated osmolarity, iron limitation, insufficient nutrient availability and host immune factors 17 – 19 . These physiological mechanisms which cumulatively resist rapid changes in the gastrointestinal environment are crucial for their successful colonization 19 , 20 . Efforts were made to elucidate salt tolerance genes from human gut microbiome and following salt tolerance genes including brp/blh, galE, murB , mazG were identified 21 – 23 .…”