Metaproteomic and 16S rDNA sequencing analysis of the infant fecal microbiome

A metaproteomic analysis was conducted on the infant fecal microbiota to characterize global protein expression in 8 samples obtained from infants with a range of early-life experiences. Samples were analyzed from infants with different feeding modes (breast-fed, formula- or mixed-fed), birth modes (normal and C-section delivery), one set of monozygotic twins, as well as one antibiotic treated infant. Although label-free mass spectrometry-based proteomics is routinely used for the identification and quantification of thousands of proteins in complex samples, the metaproteomic analysis of the gut microbiome presents particular technical challenges. Among them is the extreme complexity and dynamic range of member taxa, the need for matched, well-annotated metagenomic databases, and the high inter-protein sequence redundancy and similarity between related micro-organisms. In this study, a metaproteomic approach was developed for assessment of biological phenotype and metabolic status, and as a complement to 16S ribosomal DNA-gene sequencing analysis to identify constituent taxa.