Meta-analysis to define a core microbiota in the swine gut

Authors: HOLMAN, DEVIN - Orise Fellow; Brunelle, Brian; TRACHSEL, JULIAN - Iowa State University; Allen, Heather

Submitted to: mSystems
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/21/2017
Publication Date: 5/23/2017
Citation: Holman, D.B., Brunelle, B.W., Trachsel, J., Allen, H.K. 2017. Meta-analysis to define a core microbiota in the swine gut. mSystems. 2(3):e00004-17. doi: 10.1128/mSystems.00004-17.

Interpretive Summary: The swine industry in the United States is worth approximately $23.5 billion each year. Similar to humans, pigs have a rich and diverse microbial community in their gastrointestinal tract that plays a significant role in the health of the animal. A number of independent studies have now investigated the microbial community in the pig gastrointestinal tract, often in response to dietary additives, but a global overview is lacking. Therefore, we combined all of the available studies that examined the pig gastrointestinal tract and performed a meta-analysis to identify bacteria that are shared among commercial pigs and to determine what factors most influence the bacterial community in the gut. We confirmed that each anatomical region (e.g. colon, cecum, stomach) in the pig gut has a distinct microbial community. We also identified several types of bacteria that are found in nearly all commercial pigs around the world and thus could potentially serve as targets for dietary manipulation and improvement of pig health in the future.

Technical Abstract: Background 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, independent of study variables such as country of origin and experimental design. To answer these questions we performed a meta-analysis using 20 publically available datasets from high-throughput 16S rRNA gene sequence studies of the swine gut microbiota. Results The gastrointestinal (GI) tract section that was sampled had the greatest effect on the composition and structure of the swine gut microbiota (P less than 0.001). Certain genera were relatively more abundant in a specific GI location, including Lactobacillus in the gastric mucosa, Prevotella, Helicobacter, and Campylobacter in the colonic mucosa, Clostridium in the ileal mucosa, Bacteroides in the colon, and Treponema in fecal samples. Technical variation among studies, particularly the 16S rRNA gene hypervariable region sequenced, also significantly affected the composition of the swine gut microbiota (P less than 0.001). Despite this, numerous commonalities were discovered. Among fecal samples, the genera Prevotella, Clostridium, Alloprevotella, Ruminococcus, and the RC9 gut group were found in 99 percent of all fecal samples. Additionally, Clostridium, Blautia, Lactobacillus, Prevotella, Ruminococcus, Roseburia, the RC9 gut group, and Subdoligranulum, were shared by greater than 90 percent of all GI samples, suggesting a so-called “core” microbiota for commercial swine worldwide. Conclusions The results of this meta-analysis demonstrate that GI sample location is the most significant driver of the swine gut microbiota. However, when comparing results from different studies, some biological factors may be obscured by technical variation among studies. Nonetheless, there are bacterial taxa that are strongly associated with 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.