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 microb...

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Autores principales:	Devin B. Holman, Brian W. Brunelle, Julian Trachsel, Heather K. Allen
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	16S rRNA gene bacteria gut microbiome gut microbiota livestock meta-analysis Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/2106ade9215b480b81a1b9392b3f901f
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spelling	oai:doaj.org-article:2106ade9215b480b81a1b9392b3f901f2021-12-02T19:45:29ZMeta-analysis To Define a Core Microbiota in the Swine Gut10.1128/mSystems.00004-172379-5077https://doaj.org/article/2106ade9215b480b81a1b9392b3f901f2017-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00004-17https://doaj.org/toc/2379-5077ABSTRACT 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.Devin B. HolmanBrian W. BrunelleJulian TrachselHeather K. AllenAmerican Society for Microbiologyarticle16S rRNA genebacteriagut microbiomegut microbiotalivestockmeta-analysisMicrobiologyQR1-502ENmSystems, Vol 2, Iss 3 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	16S rRNA gene bacteria gut microbiome gut microbiota livestock meta-analysis Microbiology QR1-502
spellingShingle	16S rRNA gene bacteria gut microbiome gut microbiota livestock meta-analysis Microbiology QR1-502 Devin B. Holman Brian W. Brunelle Julian Trachsel Heather K. Allen Meta-analysis To Define a Core Microbiota in the Swine Gut
description	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.
format	article
author	Devin B. Holman Brian W. Brunelle Julian Trachsel Heather K. Allen
author_facet	Devin B. Holman Brian W. Brunelle Julian Trachsel Heather K. Allen
author_sort	Devin B. Holman
title	Meta-analysis To Define a Core Microbiota in the Swine Gut
title_short	Meta-analysis To Define a Core Microbiota in the Swine Gut
title_full	Meta-analysis To Define a Core Microbiota in the Swine Gut
title_fullStr	Meta-analysis To Define a Core Microbiota in the Swine Gut
title_full_unstemmed	Meta-analysis To Define a Core Microbiota in the Swine Gut
title_sort	meta-analysis to define a core microbiota in the swine gut
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/2106ade9215b480b81a1b9392b3f901f
work_keys_str_mv	AT devinbholman metaanalysistodefineacoremicrobiotaintheswinegut AT brianwbrunelle metaanalysistodefineacoremicrobiotaintheswinegut AT juliantrachsel metaanalysistodefineacoremicrobiotaintheswinegut AT heatherkallen metaanalysistodefineacoremicrobiotaintheswinegut
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Meta-analysis To Define a Core Microbiota in the Swine Gut

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