Metaproteogenomics Reveals Taxonomic and Functional Changes between Cecal and Fecal Microbiota in Mouse.

Alessandro Tanca,Cristina Fraumene,Antonio Palomba,Marcello Abbondio,Massimo Deligios,Michael Silverman,Valeria Manghina,Sergio Uzzau

doi:10.3389/fmicb.2017.00391

Abstract

Previous studies on mouse models report that cecal and fecal microbial communities may differ in the taxonomic structure, but little is known about their respective functional activities. Here, we employed a metaproteogenomic approach, including 16S rRNA gene sequencing, shotgun metagenomics and shotgun metaproteomics, to analyze the microbiota of paired mouse cecal contents (CCs) and feces, with the aim of identifying changes in taxon-specific functions. As a result, Gram-positive anaerobes were observed as considerably higher in CCs, while several key enzymes, involved in oxalate degradation, glutamate/glutamine metabolism, and redox homeostasis, and most actively expressed by Bacteroidetes, were clearly more represented in feces. On the whole, taxon and function abundance appeared to vary consistently with environmental changes expected to occur throughout the transit from the cecum to outside the intestine, especially when considering metaproteomic data. The results of this study indicate that functional and metabolic differences exist between CC and stool samples, paving the way to further metaproteogenomic investigations aimed at elucidating the functional dynamics of the intestinal microbiota.

Highlights

Compelling evidence has emerged in the last years supporting the gut microbiota as a key factor in mammalian physiology and disease (Marchesi et al, 2016)
The levels of overlap among OTUs, genera and functions identified with the three omic approaches in cecal contents (CCs) and F samples are illustrated in the Venn diagrams of Supplementary Figures S1–S7
No univocal and significant differences could be observed between CC and F, apart from a significantly higher taxonomic diversity in CC according to MP data

Summary

Introduction

Compelling evidence has emerged in the last years supporting the gut microbiota as a key factor in mammalian physiology and disease (Marchesi et al, 2016). Mouse and human gastrointestinal tracts share many anatomical and functional features, mouse cecum is relatively larger and able to ferment indigestible food components, while the human cecum is smaller and vestigial (Nguyen et al, 2015). For both human and mouse studies, an essential question regards what kind of sample ought to be collected for achieving the best information on structure and functions of the gut microbiota. Fecal samples are typically used as a proxy for the gut microbiota, as they are accessible; the collection of luminal or mucosa-associated material directly from the intestine is often unfeasible. Stool is always preferred as sample in time-course studies, because it can be collected from the same mouse throughout the entire duration of the experiment, while cecal samples are collected post mortem, often together with other organs to be analyzed

Objectives

Methods

Results

Discussion

Conclusion