title: Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case.
abstract: Microbial colonization of the human gastrointestinal tract plays an important role in establishing health and homeostasis. However, the time-dependent functional signatures of microbial and human proteins during early colonization of the gut have yet to be determined. To this end, we employed shotgun proteomics to simultaneously monitor microbial and human proteins in fecal samples from a preterm infant during the first month of life. Microbial community complexity increased over time, with compositional changes that were consistent with previous metagenomic and rRNA gene data. More specifically, the function of the microbial community initially involved biomass growth, protein production, and lipid metabolism, and then switched to more complex metabolic functions, such as carbohydrate metabolism, once the community stabilized and matured. Human proteins detected included those responsible for epithelial barrier function and antimicrobial activity. Some neutrophil-derived proteins increased in abundance early in the study period, suggesting activation of the innate immune system. Likewise, abundances of cytoskeletal and mucin proteins increased later in the time course, suggestive of subsequent adjustment to the increased microbial load. This study provides the first snapshot of coordinated human and microbial protein expression in a preterm infant's gut during early development.
authors.affiliation: Genome Sciences and Technology Graduate School, University of Tennessee, Knoxville, TN, USA.|Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
authors.forename: Jacque C
authors.initials: JC
authors.lastname: Young
authors.affiliation: Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
authors.forename: Chongle
authors.initials: C
authors.lastname: Pan
authors.affiliation: Genome Sciences and Technology Graduate School, University of Tennessee, Knoxville, TN, USA.|Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
authors.forename: Rachel M
authors.initials: RM
authors.lastname: Adams
authors.affiliation: Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA.
authors.forename: Brandon
authors.initials: B
authors.lastname: Brooks
authors.affiliation: Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA.
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Banfield
authors.affiliation: Division of Pediatric General & Thoracic Surgery, University of Pittsburgh, Pittsburgh, PA, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Morowitz
authors.affiliation: Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Hettich
mesh_terms: D005243:Feces / Q000382:microbiology; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D007234:Infant, Premature; D056186:Metagenomics; D064307:Microbiota / Q000235:genetics*; D040901:Proteomics
keywords: Infant gut; Metaproteomics; Microbial colonization; Microbiome; Systems biology