Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle

Genome Biology

Nitin Kumar¹  Nicholas J. R. Dawson¹  Trevor D. Lawley¹  Elisa Viciani¹  Hilary P. Browne¹  Kevin Vervier¹  Samuel C. Forster²  Claire Cormie³  David Goulding³  Anne T. Adoum³  Alexandre Almeida⁴ 

[1] Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK;Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK;Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, 3168, Clayton, Victoria, Australia;Department of Molecular and Translational Sciences, Monash University, 3800, Clayton, Victoria, Australia;Wellcome Sanger Institute, Hinxton, UK;Wellcome Sanger Institute, Hinxton, UK;European Bioinformatics Institute, Hinxton, UK;

关键词: Sporulation;    Intestinal microbiota;    Microbiome;    Metagenomics;    Host adaptation;    Genome reduction;    Genome evolution;    Bacterial transmission;    Metabolic specialization;   

DOI  :  10.1186/s13059-021-02428-6

来源: Springer

【 摘 要 】

BackgroundHuman-to-human transmission of symbiotic, anaerobic bacteria is a fundamental evolutionary adaptation essential for membership of the human gut microbiota. However, despite its importance, the genomic and biological adaptations underpinning symbiont transmission remain poorly understood. The Firmicutes are a dominant phylum within the intestinal microbiota that are capable of producing resistant endospores that maintain viability within the environment and germinate within the intestine to facilitate transmission. However, the impact of host transmission on the evolutionary and adaptive processes within the intestinal microbiota remains unknown.ResultsWe analyze 1358 genomes of Firmicutes bacteria derived from host and environment-associated habitats. Characterization of genomes as spore-forming based on the presence of sporulation-predictive genes reveals multiple losses of sporulation in many distinct lineages. Loss of sporulation in gut Firmicutes is associated with features of host-adaptation such as genome reduction and specialized metabolic capabilities. Consistent with these data, analysis of 9966 gut metagenomes from adults around the world demonstrates that bacteria now incapable of sporulation are more abundant within individuals but less prevalent in the human population compared to spore-forming bacteria.ConclusionsOur results suggest host adaptation in gut Firmicutes is an evolutionary trade-off between transmission range and colonization abundance. We reveal host transmission as an underappreciated process that shapes the evolution, assembly, and functions of gut Firmicutes.

【 授权许可】

CC BY