Pinpoint ecological niches and metabolic essentiality of microbial communities using both metagenomics and metaproteomics

Microbes rely on various proteins to carry out functions, which are crucial for their metabolism and competitiveness in the community. In a given environment, a microbe usually expresses a fraction of its genomic capabilities as protein functions. It is not clear yet how microbial genomic capabilities map to their protein functions. In addition, how the role of one protein in the metabolic network and ecological competition shapes the mapping remains to be revealed either experimentally or through modeling. Here, we propose to compare the network degree and redundancy of each protein between the genomic content network obtained from metagenome and the protein content network obtained from metaproteome. We find that the difference in network degree and redundancy of each protein can characterize the ecological niches and metabolic essentiality. Furthermore, we develop an ecological model with the mapping from the genomic capabilities to protein functions that can reproduce the pattern of difference in network degree and redundancy. These results provide better insights into the metabolic and ecological functions of proteins and shed light on the impact of community competition on the selective expression of functions.