Meta-analysis To Define a Core Microbiota in the Swine Gut

• Published in: mSystems Vol. 2; no. 3
• Main Authors: Holman, Devin B, Brunelle, Brian W, Trachsel, Julian, Allen, Heather K
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 01.05.2017
• Subjects: 16S rRNA gene; bacteria; Digestive system; Gastrointestinal tract; gut microbiome; gut microbiota; Intestinal microflora; livestock; Meta-analysis; Microbiota; Next-generation sequencing; swine; gut microbiome; bacteria; livestock; meta-analysis; microbial ecology; gut microbiota; 16S rRNA gene
• ISSN: 2379-5077; 2379-5077
• DOI: 10.1128/msystems.00004-17

The swine gut microbiota encompasses a large and diverse population of bacteria that play a significant role in pig health. As such, a number of recent studies have utilized high-throughput sequencing of the 16S rRNA gene to characterize the composition and structure of the swine gut microbiota, often in response to dietary feed additives. It is important to determine which factors shape the composition of the gut microbiota among multiple studies and if certain bacteria are always present in the gut microbiota of swine, independently of study variables such as country of origin and experimental design. Therefore, we performed a meta-analysis using 20 publically available data sets from high-throughput 16S rRNA gene sequence studies of the swine gut microbiota. Next to the "study" itself, the gastrointestinal (GI) tract section that was sampled had the greatest effect on the composition and structure of the swine gut microbiota ( = 0.0001). Technical variation among studies, particularly the 16S rRNA gene hypervariable region sequenced, also significantly affected the composition of the swine gut microbiota ( = 0.0001). Despite this, numerous commonalities were discovered. Among fecal samples, the genera , , , and and the RC9 gut group were found in 99% of all fecal samples. Additionally, , , , , , , the RC9 gut group, and were shared by >90% of all GI samples, suggesting a so-called "core" microbiota for commercial swine worldwide. The results of this meta-analysis demonstrate that "study" and GI sample location are the most significant factors in shaping the swine gut microbiota. However, in comparisons of results from different studies, some biological factors may be obscured by technical variation among studies. Nonetheless, there are some bacterial taxa that appear to form a core microbiota within the swine GI tract regardless of country of origin, diet, age, or breed. Thus, these results provide the framework for future studies to manipulate the swine gut microbiota for potential health benefits.