Article

Decoding the Intestinal Microbiota Repertoire of Sow and Weaned Pigs using Culturomic and Metagenomic Approaches

Daye Mun1, Hayoung Kim1, Minhye Shin2, Sangdon Ryu1, Minho Song3, Sangnam Oh4, Younghoon Kim1,*
Author Information & Copyright
1Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea.
2Department of Microbiology, Inha University School of Medicine, Incheon 22212, Korea.
3Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea.
4Department of Functional Food and Biotechnology, Jeonju University, Jeonju 55069, Korea.
*Corresponding Author: Younghoon Kim, Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea, Republic of. Phone: +82-2-880-4808. E-mail: ykeys2584@snu.ac.kr.

© Copyright 2021 Korean Society of Animal Science and Technology. This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Received: Sep 09, 2021; Revised: Oct 24, 2021; Accepted: Nov 05, 2021

Published Online: Nov 23, 2021

Abstract

The intestinal microbiota greatly affects not only the intestinal health of the host but also the immune system and diseases. When controlling animal health and preventing, diagnosing, and treating diseases, a complete understanding of the intestinal microbiota is necessary. Although there are considerable reports on culture-independent analysis in the gut microbiota of porcine, information regarding the mechanisms and specific roles of the microorganisms remain insufficient due to the inability to secure a culturable microbiota. To elucidate the role and mechanism of microbes, we combined culture-dependent and culture-independent approaches to investigate differences in gut bacterial composition between sows and weaned pigs. Under anaerobic conditions, several nonselective and selective media were used for isolation from fecal samples. All isolated bacteria were identified and classified through 16S rRNA sequencing, and the microbiota composition of the fecal samples was analyzed by metagenomics using next generation sequencing (NGS) technology. A total of 278 and 149 colonies were acquired from the sow and weaned pig fecal samples, respectively. Culturomics analysis revealed that diverse bacterial genus and species belonged to Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were isolated from sow and weaned pigs. When comparing culture-dependent and culture-independent analyses, 191 bacterial species and 2 archaeal bacterial species were detected through culture-independent analysis, and a total of 23 bacteria were isolated through a culture-dependent approach, of which 65% were not detected by metagenomics. In conclusion, culturomics and metagenomics should be properly combined to fully understand the intestinal microbiota, and livestock-derived microbial resources should be informed by culturomic approaches to understand and utilize the mechanism of host-microbe interactions.

Keywords: Culturomics; Metagenomics; Intestinal microbiota; Sow; Weaned pig