Enlightening human gut microbial darkness with different carbon and nitrogen source. human gut metagenome

With the development of sequencing technology and computational biology, the understanding and identification of microbes are not only limited to traditional isolation and culture. In recent years, more and more studies have demonstrated the existence of unrecognized microbial darkness in the human gut. However, the exploration of them is often via expanding the intestinal environment of the population, which is difficult to study the metabolic potential and interactions between microbial darkness at the individual level. Therefore, we performed simulations of different nutrient sources in the intestine by setting up experiments with different single carbon and nitrogen sources in vitro as the specified material basis before metagenomics sequencing. The results suggested that microbial darkness can survive under different nutrient sources, and some of them did not directly metabolize basal substrates, implying that cross-feeding between gut microbes may serve as a material basis for gut microbial interactions. Through evolutionary analysis, we found that the microbial darkness in the gut had hundreds of SNP sites and some segmental duplication fragments under high selective pressures obtained in the intestine. In addition, the potential of producing secondary metabolites was observed. Overall, our study serves an important step toward understanding inter-species interactions in the intestine and ecological niche adaptation among the gut species.