Abstract
The rat is an important model animal used frequently in biological researches exploring the correlations between gut microbiome and a wide array of diseases. In this study, we used an extended ancestral-state reconstruction algorithm to predict the functional capabilities of the rat gastrointestinal microbiome. Our results indicate an apparent tendency toward metabolic heterogeneity along the longitudinal and transverse axes of the rat gastrointestinal tract (GIT). This heterogeneity was suggested by the enriched small-molecule transport activity and amino acid metabolism in the upper GIT, the aerobic energy metabolism in the stomach and the mucolysis-related metabolism in the lower GIT mucus layer. In contrast to prior results, many functional overlaps were observed when the gastrointestinal microbiomes of different hosts were compared. These overlaps implied that although both the biogeographic location and host genotype were prominent driving forces in shaping the gastrointestinal microbiota, the microbiome functions were similar across hosts when observed under similar physicochemical conditions at identical anatomical sites. Our work effectively complements the rat microbial biogeography dataset we released in 2017 and, thus, contributes to a better understanding and prediction of disease-related alterations in microbial community function.
Highlights
Symbiotic microorganisms located inside and on the surface of the host body provide many biological functions that are not encoded in their host genome [1]
Based on a total of 6009 Kyoto Encyclopaedia of Genes and Genomes (KEGG) orthologue (KO) annotations, we observed an apparent tendency toward a metabolic heterogeneity along the longitudinal and transverse axes of the rat gastrointestinal tract (GIT)
This tendency was intuitively displayed on the principal component analysis (PCA) ordination plots (Figure 1A–C), where samples were grouped by different biogeographic factors such as the anatomic region, subsite and niche location
Summary
Symbiotic microorganisms located inside and on the surface of the host body provide many biological functions that are not encoded in their host genome [1]. In the past decade, encouraged by the progress in high-throughput sequencing technology and new developments in bioinformatics, the scientific community has continuously and gradually investigated the gut microbial communities underlying biological functions observed in human- [11,12] and host-associated [13,14] habitats. In 2010, the MetaHIT project released the first human gut microbial gene catalogue established by metagenomic sequencing [16]. In 2015, the Beijing Genomics Institute (BGI) released the first mouse gut microbial gene catalogue [17]. These catalogues have since served as valuable references for numerous studies. Most of these studies used functional gene sets derived from faecal samples, the appropriateness of using faeces as a proxy for the whole gastrointestinal tract (GIT) remains unconfirmed
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
