Meta-analysis To Define a Core Microbiota in the Swine Gut
- PMID: 28567446
- PMCID: PMC5443231
- DOI: 10.1128/mSystems.00004-17
Meta-analysis To Define a Core Microbiota in the Swine Gut
Abstract
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 (P = 0.0001). Technical variation among studies, particularly the 16S rRNA gene hypervariable region sequenced, also significantly affected the composition of the swine gut microbiota (P = 0.0001). Despite this, numerous commonalities were discovered. Among fecal samples, the genera Prevotella, Clostridium, Alloprevotella, and Ruminococcus and the RC9 gut group were found in 99% of all fecal samples. Additionally, Clostridium, Blautia, Lactobacillus, Prevotella, Ruminococcus, Roseburia, the RC9 gut group, and Subdoligranulum were shared by >90% of all GI samples, suggesting a so-called "core" microbiota for commercial swine worldwide. IMPORTANCE 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.
Keywords: 16S rRNA gene; bacteria; gut microbiome; gut microbiota; livestock; meta-analysis; microbial ecology; swine.
Figures
![FIG 1](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/5443231/bin/sys0031721030001.gif)
![FIG 2](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/5443231/bin/sys0031721030002.gif)
![FIG 3](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/5443231/bin/sys0031721030003.gif)
![FIG 4](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/5443231/bin/sys0031721030004.gif)
![FIG 5](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/5443231/bin/sys0031721030005.gif)
Similar articles
-
A meta-analysis of the bovine gastrointestinal tract microbiota.FEMS Microbiol Ecol. 2019 Jun 1;95(6):fiz072. doi: 10.1093/femsec/fiz072. FEMS Microbiol Ecol. 2019. PMID: 31116403
-
Core gut microbiota in Jinhua pigs and its correlation with strain, farm and weaning age.J Microbiol. 2018 May;56(5):346-355. doi: 10.1007/s12275-018-7486-8. Epub 2018 May 2. J Microbiol. 2018. PMID: 29721832
-
The pig gut microbial diversity: Understanding the pig gut microbial ecology through the next generation high throughput sequencing.Vet Microbiol. 2015 Jun 12;177(3-4):242-51. doi: 10.1016/j.vetmic.2015.03.014. Epub 2015 Mar 23. Vet Microbiol. 2015. PMID: 25843944 Review.
-
Characterization of the fecal microbiome in different swine groups by high-throughput sequencing.Anaerobe. 2014 Aug;28:157-62. doi: 10.1016/j.anaerobe.2014.06.002. Epub 2014 Jun 19. Anaerobe. 2014. PMID: 24954845
-
Diet, gut enterotypes and health: is there a link?Nestle Nutr Inst Workshop Ser. 2013;77:65-73. doi: 10.1159/000351385. Epub 2013 Aug 29. Nestle Nutr Inst Workshop Ser. 2013. PMID: 24107497 Review.
Cited by
-
Diversity and host interaction of the gut microbiota in specific pathogen-free pigs.Front Microbiol. 2024 May 10;15:1402807. doi: 10.3389/fmicb.2024.1402807. eCollection 2024. Front Microbiol. 2024. PMID: 38800748 Free PMC article.
-
Progression of swine fecal microbiota during early stages of life and its association with performance: a longitudinal study.BMC Microbiol. 2024 May 25;24(1):182. doi: 10.1186/s12866-024-03336-y. BMC Microbiol. 2024. PMID: 38789948 Free PMC article.
-
Increased Dietary Trp, Thr, and Met Supplementation Improves Performance, Health, and Protein Metabolism of Weaned Piglets under Mixed Management and Poor Housing Conditions.Animals (Basel). 2024 Apr 9;14(8):1143. doi: 10.3390/ani14081143. Animals (Basel). 2024. PMID: 38672291 Free PMC article.
-
Effects of supplemental bacteriophage on the gut microbiota and nutrient digestibility of ileal-cannulated pigs.J Anim Sci Technol. 2024 Mar;66(2):340-352. doi: 10.5187/jast.2023.e96. Epub 2024 Mar 31. J Anim Sci Technol. 2024. PMID: 38628684 Free PMC article.
-
Effect of a probiotic and an antibiotic on the mobilome of the porcine microbiota.Front Genet. 2024 Mar 28;15:1355134. doi: 10.3389/fgene.2024.1355134. eCollection 2024. Front Genet. 2024. PMID: 38606356 Free PMC article.
References
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials