Microbial community structure and composition is associated with host species and sex in Sigmodon cotton rats

Animal Microbiome

Shibu Yooseph¹  Meghan H. Shilts²  Christian Rosas-Salazar²  Arash Kamali²  Helen H. Boone²  Seesandra V. Rajagopala²  Britton A. Strickland³  Suman R. Das⁴  Daniel Stylos⁵  Wei Zhang⁵  Marina S. Boukhvalova⁵  Jorge C. G. Blanco⁵  Mira C. Patel⁶ 

[1] Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, USA;Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA;Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA;Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA;Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA;Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA;Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN, USA;Division of Infectious Diseases, Vanderbilt University Medical Center, 1211 21st Avenue South, S2108 Medical Center North, 37232, Nashville, TN, USA;Sigmovir Biosystems Inc., 9610 Medical Center Drive, Suite 100, 20850, Rockville, MD, USA;Sigmovir Biosystems Inc., 9610 Medical Center Drive, Suite 100, 20850, Rockville, MD, USA;Present Address: Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA;

关键词: Microbiome;    Metagenomics;    Cotton rat;    Sigmodon;    16S rRNA gene;    Gut;    Skin;    Respiratory;   

DOI  :  10.1186/s42523-021-00090-8

来源: Springer

【 摘 要 】

BackgroundThe cotton rat (genus Sigmodon) is an essential small animal model for the study of human infectious disease and viral therapeutic development. However, the impact of the host microbiome on infection outcomes has not been explored in this model, partly due to the lack of a comprehensive characterization of microbial communities across different cotton rat species. Understanding the dynamics of their microbiome could significantly help to better understand its role when modeling viral infections in this animal model.ResultsWe examined the bacterial communities of the gut and three external sites (skin, ear, and nose) of two inbred species of cotton rats commonly used in research (S. hispidus and S. fulviventer) by using 16S rRNA gene sequencing, constituting the first comprehensive characterization of the cotton rat microbiome. We showed that S. fulviventer maintained higher alpha diversity and richness than S. hispidus at external sites (skin, ear, nose), but there were no differentially abundant genera. However, S. fulviventer and S. hispidus had distinct fecal microbiomes composed of several significantly differentially abundant genera. Whole metagenomic shotgun sequencing of fecal samples identified species-level differences between S. hispidus and S. fulviventer, as well as different metabolic pathway functions as a result of differential host microbiome contributions. Furthermore, the microbiome composition of the external sites showed significant sex-based differences while fecal communities were not largely different.ConclusionsOur study shows that host genetic background potentially exerts homeostatic pressures, resulting in distinct microbiomes for two different inbred cotton rat species. Because of the numerous studies that have uncovered strong relationships between host microbiome, viral infection outcomes, and immune responses, our findings represent a strong contribution for understanding the impact of different microbial communities on viral pathogenesis. Furthermore, we provide novel cotton rat microbiome data as a springboard to uncover the full therapeutic potential of the microbiome against viral infections.

【 授权许可】

CC BY