Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life

Abstract

Summary The human gut microbiome matures toward the adult composition during the first years of life and is implicated in early immune development. Here, we investigate the effects of microbial genomic diversity on gut microbiome development using integrated early childhood datasets collected in the DIABIMMUNE study in Finland, Estonia and Russian Karelia. We show that gut microbial diversity is associated with household location and linear growth of children. Single nucleotide polymorphism (SNP)- and metagenomic assembly-based strain tracking revealed large and highly dynamic microbial pangenomes, especially in the genus Bacteroides , in which we identified evidence of variability deriving from Bacteroides -targeting bacteriophages. Our analyses revealed functional consequences of strain diversity; only 10% of Finnish infants harbored Bifidobacterium longum subsp. infantis , a subspecies specialized in human milk metabolism, whereas Russian infants commonly maintained a probiotic Bifidobacterium bifidum strain in infancy. Groups of bacteria contributing to diverse, characterized metabolic pathways converged to highly subject-specific configurations over the first two years of life. This longitudinal study extends the current view of early gut microbial community assembly based on strain-level genomic variation.

Bifidobacterium bifidum and the infant gut microbiota: an intriguing case of microbe‐host co‐evolution

“…Bifidobacterium bifidum, Bifidobacterium breve and Bifidobacterium longum, possess genetic adaptations to facilitate colonization of the infant gut (Matamoros et al, 2013;Milani et al, 2017b). Recently, a number of studies have presented comprehensive data showing that these three species can be maternally inherited by vertical transmission (Milani et al, 2015a;Duranti et al, 2017b;Vatanen et al, 2018;Moossavi et al, 2019). Further evidence has found that horizontal transfer of bifidobacterial DNA from mother to foetus may occur also via placenta (Satokari et al, 2009).…”

InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strains

“…Because it uses sample-assembled genomes and full paired-read information there is greatly increased confidence that reads are aligned correctly, which improves the high resolution comparisons being made based on entire genomes. Many of these capabilities have been successfully implemented individually in previous studies 15,19,[30][31][32][33] . However, their simultaneous integration into a well-documented and easy to use pipeline allows substantially more rigorous detection of near-identical strains than the existing commonly used pipelines ( Figure 2 ) used in recent high-profile publications to quantify the ecologically critical process of microbiome transmission 14,34 .…”

When Cultures Meet: The Landscape of “Social” Interactions between the Host and Its Indigenous Microbes

“…[5,[22][23][24] Likewise, in adults, Firmicutes and Bacteroidetes are prominent in the gut, and metabolize dietary plant polysaccharides, which are otherwise indigestible by the mammalian host. Indeed, a mammalian host is unable to complete digestion of the entirety of food or to de novo produce all food-related vitamins that are critically important for a healthy living.…”