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Rapid evolution and strain turnover in the infant gut microbiome - Easy Microbial Genomics

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Rapid evolution and strain turnover in the infant gut microbiome

Posted May 7, 2022

The infant's gut flora is a rapidly changing ecosystem that plays an important role in infant health. This includes digestion of infants, development of the immune system, and prevention of pathogen colonization. Given its importance, many studies have focused on the ecological and functional maturation of the intestinal microflora of infants and the extent to which delivery mode, feeding and exposure to antibiotics affect their development.

Strain tracking using single nucleotide variants (SNVs) suggests that mothers, whole families, and hospitals play an important role in seeding the infant microbiome. In contrast, it remains unclear how these strains evolved after the infant formed a colony. Although the ecological dynamics of the infant's gut microbiota have been intensively studied, little is known about the evolutionary dynamics of the infant's gut microbiota.

A research group of Dr. Nandita R Garud, from University of California, analyzed longitudinal fecal metagenomic data from more than 700 infants in the first year of life and their mothers, and found that the evolutionary dynamics of the intestinal flora of infants differed from those of adults. There is evidence that the rate of intestinal evolution and turnover of strains in infants is increased almost 100-fold compared to healthy adults, and maternal-to-child transfer during childbirth is a particularly dynamic period in which gene loss is dominant. is. During the first few months of life, these dynamics are stable and gene acquisition becomes more frequent as the microbial flora matures. In addition, we found that evolutionary changes in infants exhibit seeded traits due to a mixture of de novo mutations and the spread of pre-evolved strains from a wider family. Some of these evolutionary changes have highlighted candidate genes that occur simultaneously in multiple infants and may play an important role in the development of the infant's gut flora. Our findings show an unstable state of the intestinal flora of infants, characterized by rapid evolution and ecological changes early in life.


Comparison in rates of evolutionary change and replacement decay with life stage

image source: Genome Res

Reference

Chen DW, Garud NR. Rapid evolution and strain turnover in the infant gut microbiome. Genome Res. 2022 May 11:gr.276306.121. doi: 10.1101/gr.276306.121. Epub ahead of print. PMID: 35545448.