Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome. Issue 3 (7th February 2020)

• Record Type: Journal Article
• Authors: Fenske, Gavin J; Ghimire, Sudeep; Antony, Linto; Christopher-Hennings, Jane; Scaria, Joy
• Is Part Of: FEMS microbiology ecology. Volume 96:Issue 3(2020)
• Publication Date: 2020-02-07
• Subjects: metagenomics -- pig -- microbiome -- culturomics -- antibiotic resistance -- ecology; Microbial ecology -- Periodicals; Microbiology -- Periodicals; 579.17
• DOI: 10.1093/femsec/fiaa022
• Languages: English
• ISSNs: 0168-6496

Abstract

ABSTRACT: Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models. Abstract : We report the gut microbiome composition of feral and Tamworth pigs using metagenomics, culturomics, the development of a pure culture library of isolates from these breeds and the characterization of the strains using whole genome sequencing.