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

Amornthep Kingkaw; Massalin Nakphaichit; Narissara Suratannon; Sunee Nitisinprasert; Chantha Wongoutong; Pantipa Chatchatee; Sucheewin Krobthong; Sawanya Charoenlappanit; Sittiruk Roytrakul; Wanwipa Vongsangnak

doi:10.7717/peerj.9988

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

PeerJ. 2020 Sep 25:8:e9988. doi: 10.7717/peerj.9988. eCollection 2020.

Affiliations

¹ Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand.
² Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand.
³ Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand.
⁴ Department of Statistics, Faculty of Science, Kasetsart University, Bangkok, Thailand.
⁵ Proteomics Research Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand.
⁶ Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand.
⁷ Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand.

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.

Keywords: Atopic dermatitis; Bioinformatics; Gut microbiome; Infants; Metabolic function; Metaproteomics.

Associated data

figshare/10.6084/m9.figshare.12154560.v2

Grants and funding

This work was supported by the National Science and Technology Development Agency (NSTDA), Thailand (Grant No. P-17-50648), Ratchadapisek Research Funds (Grant No. CU-GR(S)_61_38_30_03) Chulalongkorn University, Bangkok, Thailand and internal fund of Proteomics Research Laboratory, National Center for Genetic Engineering and Biotechnology, Department of Zoology, Faculty of Science, Kasetsart University, The Graduate Scholarship Program, Graduate School, Kasetsart University and Thrasher Research Fund. Wanwipa Vongsangnak received financial support from Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), International SciKU Branding (ISB), Faculty of Science, Kasetsart University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.