Codiversification of gut microbiota with humans

Abstract

The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia, and Africa, including mothers and their children. Between and within countries, a parallel evolutionary history was evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes.

HIV Tat Expression and Cocaine Exposure Lead to Sex- and Age-Specific Changes of the Microbiota Composition in the Gut

“…The dynamic crosstalk between these microbes and the host also affects the host’s health [ 1 , 10 ]. The balance of various microbial communities in the gut plays a fundamental role in normal physiological functions such as breakdown of food for absorption, protection against pathogens, elicitation of immunity, and maintenance of the barrier integrity of the gut and intestines [ 12 , 13 , 14 ]. Thus, disruption of the balance, also known as dysbiosis, is often associated with various disorders and diseases such as cancer, viral infection, and abnormal behaviors [ 2 , 15 , 16 , 17 , 18 , 19 ].…”

Targeted modulation of gut microbiota by traditional Chinese medicine and natural products for liver disease therapy

“…The gut microbiota is essential for maintaining body metabolism and health, while dysbiosis plays a vital role during the occurrence and progression of various diseases, including liver disease ( 94 , 95 ). Therefore, regulating the gut microbiota to maintain it in a relatively stable state, including gut microbiota diversity, distribution and metabolic stability, has great potential and clinical research value in the treatment of various types of liver diseases.…”

Limited codiversification of the gut microbiota with humans

“…Phylogenies and alignments from Ref. (1) were downloaded from the Dryad repository provided in that work; host and bacterial metadata were obtained from the Supplementary Materials. All analysis code used in this work is available on Github (https://github.com/bgoodlab/codiversification_microbiome).…”

“… A recent study by Suzuki & Fitzstevens et al (1) argued that dozens of species of gut bacteria have codiversified with modern human populations. Reanalysis of their data reveals that the correlations between human and microbial phylogenies are substantially weaker than unlinked human chromosomes, and that similar correlations can arise through geographic structure alone.…”