The porphyran degradation system of the human gut microbiota is complete, phylogenetically diverse and geographically structured across Asian populations

Abstract

The human gut microbiota can acquire new catabolic functions by integrating genetic material coming from the environment, for example from food-associated bacteria. The most illustrative example is the acquisition by the human gut microbiota of Asian populations of genes coming from marine bacteria living on the surface of red algae that are incorporated into their diet when eating maki-sushi. To better understand the function and evolution of this set of algal genes corresponding to a polysaccharide utilization locus (PUL) dedicated to the degradation of porphyran, the main polysaccharide of the red algae Porphyra sp., we characterized it biochemically, assessed its genetic diversity and investigated its geographical distribution in large public worldwide datasets. We first demonstrated that both methylated and unmethylated fractions are catabolized without the help of external enzymes. By scanning the genomic data of more than 10,000 cultivated isolates, we then found that the porphyran PUL organization is conserved in 22 different Bacteroides strains coming from at least 8 species, highlighting multiple lateral transfers within the gut microbiota. We then analyzed the metagenomic data of more than 14,000 individuals coming from 32 countries worldwide and showed that the porphyran PUL exists only in East Asia (Japan, China, Korea), but not anywhere else. Finally, we identified three major PUL haplotypes which frequency differ between countries. This geographic structure is likely the reflect of the rate of bacterial horizontal transmission between individuals. BackgroundThe human gut microbiota can acquire new catabolic functions by integrating genetic material coming from the environment, for example from food-associated bacteria. The most illustrative example is the acquisition by the gut microbiota of Asian populations of genes coming from marine bacteria living on the surface of red algae that are incorporated into their diet when eating maki-sushi. To better understand the function and evolution of this set of algal genes corresponding to a polysaccharide utilization locus (PUL) dedicated to the degradation of porphyran, the main polysaccharide of the red algae Porphyra sp., we characterized it biochemically, assessed its genetic diversity and investigated its geographical distribution in large public worldwide datasets. ResultsWe first demonstrated that both methylated and unmethylated fractions of porphyran are catabolized by the porphyran PUL without the help of external enzymes. By scanning the genomic data of more than 10,000 cultivated isolates, we then found that the porphyran PUL organization is conserved in 22 different Bacteroides strains coming from at least 8 species, highlighting multiple lateral transfers within the gut microbiota. We then analyzed the metagenomic data of more than 14,000 individuals coming from 32 countries worldwide and confirmed that the porphyran PUL exists only in East Asia (Japan, China, Korea). We identified three major porphyran PUL haplotypes which frequency differ between countries. ConclusionThe encoded genes of the PUL porphyran can autonomously catabolized all the complex porphyran structure. The PUL is further encoded by a variety of bacterial species, and its genetic diversity is geographically structured, likely reflecting the rate of bacterial horizontal transmission between individuals.