Meta-analysis To Define a Core Microbiota in the Swine Gut.
Meta-analysis To Define a Core Microbiota in the Swine Gut.
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DOI：
10.1128/msystems.00004-17
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发表时间：
2017-05
期刊：
影响因子：
6.4
通讯作者：
Allen HK
中科院分区：
文献类型：
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作者：
Holman DB;Brunelle BW;Trachsel J;Allen HK
这项荟萃分析的结果表明，“研究”和GI样本位置是形成猪肠道微生物群的最重要因素。然而，在比较不同研究的结果时，一些生物学因素可能会被研究之间的技术差异所掩盖。尽管如此，仍有一些细菌分类群似乎在猪胃肠道内形成核心微生物群，无论原产国、饮食、年龄或品种如何。因此，这些结果为未来的研究提供了框架，以操纵猪肠道微生物群以获得潜在的健康益处。猪肠道微生物群包含大量不同的细菌群体，这些细菌在猪的健康中发挥着重要作用。因此，最近的一些研究利用16S rRNA基因的高通量测序来表征猪肠微生物群的组成和结构，通常是响应于膳食饲料添加剂。重要的是要确定哪些因素在多项研究中塑造肠道微生物群的组成，以及某些细菌是否总是存在于猪的肠道微生物群中，而与原产国和实验设计等研究变量无关。因此，我们使用来自猪肠道微生物群的高通量16S rRNA基因序列研究的20个实验可用数据集进行了荟萃分析。除了“研究”本身，取样的胃肠道（GI）部分对猪肠道微生物群的组成和结构影响最大（P = 0.0001）。研究中的技术差异，特别是16S rRNA基因高变区测序，也显著影响了猪肠道菌群的组成（P = 0.0001）。尽管如此，还是发现了许多共同点。在粪便样品中，普雷沃氏菌属、梭菌属、别普雷沃氏菌属和瘤胃球菌属以及RC 9肠道群在所有粪便样品的99%中被发现。此外，梭菌属、布劳特氏菌属、乳杆菌属、普雷沃氏菌属、瘤胃球菌属、罗斯拜瑞氏菌属、RC 9肠道菌群和亚长粒菌属在所有GI样品中的比例>90%，这表明全球商业猪的所谓“核心”微生物群。重要性该荟萃分析的结果表明，“研究”和GI样本位置是形成猪肠道微生物群的最重要因素。然而，在比较不同研究的结果时，一些生物学因素可能会被研究之间的技术差异所掩盖。尽管如此，仍有一些细菌分类群似乎在猪胃肠道内形成核心微生物群，无论原产国、饮食、年龄或品种如何。因此，这些结果为未来的研究提供了框架，以操纵猪肠道微生物群以获得潜在的健康益处。
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. 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.