A recent study published in Science noted that the set of children’s intestinal microbiome varies according to lifestyles. A complex process of assembling the intestinal microbiome begins shortly after human birth. The new microbial species that colonize the gut depend on the niches established by previous colonizing species. Therefore, the composition of the intestinal microbiome in adults may depend on the microbes acquired in early life.
Study: solid variation in the whole intestinal microbiome of children through a spectrum of lifestyles. Image credit: Design_Cells / Shutterstock
Fund
The process of assembling the microbiome is well characterized for the babies of the industrialized nations and leads to a gut microbiome of low diversity, characteristic of the adults of these places. However, the process of assembling the microbiome in infants from non-industrialized regions, which gives rise to diverse characteristic microbiomes in adults, is poorly defined.
The Hadza tribe is a group of Tanzanian indigenous hunter-gatherers who inhabit semi-nomadic camps with a moderate level of community rearing. Babies are breastfed early in life and then weaned on a diet that includes baobab powder and pre-chewed meat at age two.
The study and conclusions
In the present study, researchers performed metagenome sequencing on fecal samples from babies of the Hadza ethnic group. The research team cured a data set of 1 million 900 ribosomal ribonucleic acid (rRNA) 16S sequences in fecal samples from healthy babies from 18 populations, including 62 Hadza baby samples. Deep metagenomic sequencing was performed on 39 Hadza infant samples and corresponding maternal samples for 23 children.
When comparing populations with different lifestyles within the same nation, the authors noted that shared lifestyles strongly affected the composition of the microbiome rather than geographical proximity. The microbiome of children living industrialized lifestyles showed a divergence from others at six months of age. In contrast, for infants living a transitional lifestyle, the microbiome diverged from the others at approximately 30 months of age.
Five groups of microbial co-abundance (CAG) were identified, which, on average, make up more than 93% of the microbiota composition in each sample. At the beginning of life, that is, up to six months, Bifidobacterium-Streptococcus CAG was predominant in all infants regardless of lifestyle. Over time, Bacteroides-Ruminococcus CAG was observed in industrialized infants and Prevotella-Fecalibacterium CAG in transitional or non-industrialized infants.
Then, from the in-depth analysis of metagenome sequencing, the authors found wide differences associated with age and lifestyle in the functional capacity of microbiomes in infants. Childhood Hadza metagenomes were grouped into metagenome-assembled genomes (MAG) spanning 745 species. In particular, more than 23% represented new species in relation to the unified human gastrointestinal genome collection.
A complete dataset was created that includes 5,755 representative genomes of species integrating MAG with Hadza adult genomes and publicly available human intestinal genomes. About 23.4% of the genomes of Hadza babies belonged to new species, which admits that there is a great diversity of uncharacterized species in the Hadza gut, similar to Hadza adults. In addition, with industrialized lifestyles, more microbial species were lost than were gained.
Bifidobacterium was the most prevalent taxon early in life, and B. infantis was the predominant species in non-industrialized infants during its first six months, depleting in industrialized infants or remaining at intermediate levels in babies with transitional lifestyles during this time period. In contrast, B. breve is the abundant species of Bifidobacterium in industrialized infants.
Assessment of strain level differences between the genomic sequences of B. infantis from infants aged 0 to 1 years revealed that the enzyme, the family of glycoside hydrolase 163 (GH163), was enriched in non-industrialized infants. in relation to industrialized babies. In addition, 20 strains of B. infantis were isolated from fecal samples from Hadza infants and subjected to sequencing. GH163 enrichment in B. Hadza infant infant isolates was also observed compared to public reference sequences.
In addition, a strong lifestyle-specific phylogenetic clustering was evident among B. infantis isolate and MAG sequences. This could indicate the emergence of long-term vertical transmission over several generations. The researchers then examined the degree of vertical transmission of Hadza babies by in-depth sequencing of fecal samples from 23 corresponding mothers (Hadza days).
On average, day-old couples had much more common / shared strains than non-day-old couples. People who did not live in the same camps in Hadza also shared more strains than those living in different camps. Vertical transmission of the strain was highest among members of Bacteroidetes and Cyanobacteria, but lower among Firmicutes in Hadza.
The stress monitoring analysis was repeated in a Swedish data set containing 100 days. Bacteroides and Prevotella strains were most frequently transmitted vertically on the Swedish and Hadza days, respectively. Species that were abundant in mothers were more likely to be transmitted vertically.
Conclusions
Overall, the results showed that the child microbiome is the dominant bifidobacterium during the first years of life, regardless of lifestyle. In particular, the taxa that differentiate lifestyles in the six months of life exhibited the most frequent vertical transmission. These observations also raised the intriguing question of whether differences in the development of the gut microbiome based on lifestyles predispose people to diseases prevalent in industrialized countries.