Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life

Abstract

BackgroundEstablishment of the human gut microbiota begins at birth. This early-life microbiota development can impact host physiology during infancy and even across an entire life span. However, the functional stability and population structure of the gut microbiota during initial colonization remain poorly understood. Metaproteomics is an emerging technology for the large-scale characterization of metabolic functions in complex microbial communities (gut microbiota).ResultsWe applied a metagenome-informed metaproteomic approach to study the temporal and inter-individual differences of metabolic functions during microbial colonization of preterm human infants’ gut. By analyzing 30 individual fecal samples, we identified up to 12,568 protein groups for each of four infants, including both human and microbial proteins. With genome-resolved matched metagenomics, proteins were confidently identified at the species/strain level. The maximum percentage of the proteome detected for the abundant organisms was ~45%. A time-dependent increase in the relative abundance of microbial versus human proteins suggested increasing microbial colonization during the first few weeks of early life. We observed remarkable variations and temporal shifts in the relative protein abundances of each organism in these preterm gut communities. Given the dissimilarity of the communities, only 81 microbial EggNOG orthologous groups and 57 human proteins were observed across all samples. These conserved microbial proteins were involved in carbohydrate, energy, amino acid and nucleotide metabolism while conserved human proteins were related to immune response and mucosal maturation. We identified seven proteome clusters for the communities and showed infant gut proteome profiles were unstable across time and not individual-specific. Applying a gut-specific metabolic module (GMM) analysis, we found that gut communities varied primarily in the contribution of nutrient (carbohydrates, lipids, and amino acids) utilization and short-chain fatty acid production.ConclusionsOverall, this study reports species-specific proteome profiles and metabolic functions of human gut microbiota during early colonization. In particular, our work contributes to reveal microbiota-associated shifts and variations in the metabolism of three major nutrient sources and short-chain fatty acid during colonization of preterm infant gut.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-017-0290-6) contains supplementary material, which is available to authorized users.

Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles

“…Metaproteomics sequencing was conducted on 0.3 g of stool as previously described (Xiong et al 2017). Each sample was suspended in 10 mL cold phosphate buffered saline.…”

“…However, it is still likely that microbial communities play an important role, with the context-dependent metabolism of specific strains potentially critical to infant health and disease. Recent studies have applied proteomics and metabolomics to premature infant gut microbiomes to measure functional profiles in healthy premature infants and those that went on to develop NEC (Xiong et al 2017;Stewart et al 2016). These studies reported temporal variation in the infant proteome and identified metabolites associated with NEC.…”

Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles

“…However, it is still likely that microbial communities play an important role, with the context-dependent metabolism of specific strains potentially critical to infant health and disease. Recent studies have applied proteomics and metabolomics to premature infant gut microbiomes to measure functional profiles in healthy premature infants and in those that went on to develop NEC ( 18 , 19 ). Those studies reported temporal variation in the infant proteome and identified metabolites associated with NEC.…”

Metaproteomics reveals potential signatures of disease-specific alterations in the gut microbial proteolytic events in inflammatory bowel disease

“…In a routine (meta)proteomics data analysis [12][13][14][15], to reliably quantify proteins, it is necessary to select the most representative peptides and usually semi-tryptic peptides are not considered, because the expended search space will increase database search time and detection of semi-tryptic peptides was less consistent than that of fully tryptic peptides. In general, semi-tryptic peptides are mainly derived from endogenous proteolysis while the impacts of other factors such as in-source fragmentation and sample degradation are negligible [16,17].…”