Analysis of the infant gut microbiome reveals metabolic functional roles associated with healthy infants and infants with atopic dermatitis using metaproteomics

Abstract

The infant gut microbiome consists of a complex and diverse microbial community. Comprehensive taxonomic and metabolic functional knowledge about microbial communities supports medical and biological applications, such as fecal diagnostics. Among the omics approaches available for the investigation of microbial communities, metaproteomics-based analysis is a very powerful approach; under this method, the activity of microbial communities is explored by investigating protein expression within a sample. Through use of metaproteomics, this study aimed to investigate the microbial community composition of the infant gut to identify different key proteins playing metabolic functional roles in the microbiome of healthy infants and infants with atopic dermatitis in a Thai population-based birth cohort. Here, 18 fecal samples were analyzed by liquid chromatography-tandem mass spectrometry to conduct taxonomic, functional, and pathway-based protein annotation. Accordingly, 49,973 annotated proteins out of 68,232 total proteins were investigated in gut microbiome samples and compared between the healthy and atopic dermatitis groups. Through differentially expressed proteins (DEPs) analysis, 130 significant DEPs were identified between the healthy and atopic dermatitis groups. Among these DEPs, eight significant proteins were uniquely expressed in the atopic dermatitis group. For instance, triosephosphate isomerase (TPI) in Bifidobacteriaceae in the genus Alloscardovia and demethylmenaquinone methyltransferase (DMM) in Bacteroides were shown to potentially play metabolic functional roles related to disease. PPI network analysis revealed seven reporter proteins showing metabolic alterations between the healthy and disease groups associated with the biosynthesis of ubiquinone and other quinones as well as the energy supply. This study serves as a scaffold for microbial community-wide metabolic functional studies of the infant gut microbiome in relation to allergic disease.

ITS2 Sequencing and Targeted Meta-Proteomics of Infant Gut Mycobiome Reveal the Functional Role of Rhodotorula sp. during Atopic Dermatitis Manifestation

“…Moreover, metaproteomics-based analysis was further studied for the activity of microbial communities. Kingkaw et al [28] recently investigated the microbial community composition of the human gut to identify different key proteins playing metabolic functional roles in the microbiome of healthy infants and infants with atopic dermatitis. However, the existence of microorganisms does not always reflect similarly in vivo metabolic characteristics [29].…”

Potential Phosphorylation of Viral Nonstructural Protein 1 in Dengue Virus Infection

“…Sequencing-grade trypsin (Promega Corporation, Madison, WI, USA) was added to the gel fragments that were then incubated at 37 °C overnight for in-gel protein digestion. Peptide products were extracted from the gel fragments by incubation with 50% acetonitrile in 0.1% formic acid at RT for 10 min and dried at 45 °C for 4 h. Tryptic peptides were protonated with 0.1% formic acid and prepared for injection into an Ultimate 3000 Nano/Capillary LC System (Thermo Fisher Scientific, Waltham, MA, USA) coupled to a Hybrid Quadrupole Q-Tof Impact II (Bruker Daltonics, Billerica, MA, USA) with a nano-captive spray ion source, as previously described [ 60 ]. Briefly, peptides were enriched in an Acclaim PepMap100 C18 column (5 μm, 100 Å, 300 μm i.d.…”

The role of gut microbiome in inflammatory skin disorders: a systematic review

“…We found sixteen articles that correlated atopic dermatitis (AD) and the gut microbiome. Even though ten reports stated there were non-significant differences in the bacterial families between healthy and AD, [23][24][25][26][27][28][29][30][31][32] four articles support significant low abundance diversity in AD gut microbiome (Table 2). [33][34][35][36] The subjects of all the papers ranged from infants, toddlers, and children.…”