Rumen Epithelial Communities Share a Core Bacterial Microbiota: A Meta-Analysis of 16S rRNA Gene Illumina MiSeq Sequencing Datasets.
Rumen Epithelial Communities Share a Core Bacterial Microbiota: A Meta-Analysis of 16S rRNA Gene Illumina MiSeq Sequencing Datasets.
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瘤胃上皮群落共享核心细菌菌群：16S rRNA基因Illumina Miseq测序数据集的荟萃分析。
DOI：
10.3389/fmicb.2021.625400
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发表时间：
2021
影响因子：
5.2
通讯作者：
Schmitz-Esser S
中科院分区：
文献类型：
--
作者：
Anderson CJ;Koester LR;Schmitz-Esser S
在该荟萃分析中，分析了17个瘤胃上皮16S rRNA基因Illumina MiSeq扩增子测序数据集，以鉴定所包括的不同研究之间共享的核心瘤胃上皮微生物群和核心瘤胃上皮OTU。对序列进行质量过滤并筛选嵌合序列，然后进行封闭参考97%OTU聚类和从头97%OTU聚类。封闭参考OTU聚类鉴定了核心瘤胃上皮OTU，其定义为存在于≥ 80%的样品中的任何OTU，而从头数据被随机二次采样至每个样品10，000个读数，以生成门和属水平分布和β多样性度量。鉴定了57个核心瘤胃上皮OTU，包括代谢上重要的分类群，如瘤胃球菌属、丁酸弧菌属和其他毛螺菌科，以及硫酸盐还原菌脱硫弧菌属和脱硫弧菌属。两种Betroproteobacteria OTU（Neisseriaceae和Burkholderiaceae）是瘤胃上皮细胞的核心OTU，与以往文献中很少发现的瘤胃内容物不同，两种核心OTU被鉴定为产甲烷古菌Methanobrevibacter和Methanomethylophilaceae。这些核心OTU在研究之间的许多变量中始终存在，包括不同的宿主物种、地理区域、饮食、年龄、农场管理实践、一年中的时间、高变区测序等。当仅考虑牛样品时，核心瘤胃上皮OTU的数量扩展到147个，突出了宿主物种内增加的相似性，尽管地理位置和其他变量。从头OTU聚类显示高度相似的瘤胃上皮细胞群落，占主导地位的厚壁菌门，拟杆菌门，变形菌门在门的水平，其中包括79.7%的子采样序列。15个最丰富的属平均占每项研究序列的54.5%。这些丰富的分类群与核心瘤胃上皮OTU广泛重叠，除了普雷沃氏菌科（Prevotellaceae），其丰富但未在核心OTU内鉴定。我们的研究结果描述了在瘤胃上皮环境中发现的核心和丰富的细菌，并将作为更好地了解瘤胃上皮群落的组成和功能的基础。
In this meta-analysis, 17 rumen epithelial 16S rRNA gene Illumina MiSeq amplicon sequencing data sets were analyzed to identify a core rumen epithelial microbiota and core rumen epithelial OTUs shared between the different studies included. Sequences were quality-filtered and screened for chimeric sequences before performing closed-reference 97% OTU clustering, and de novo 97% OTU clustering. Closed-reference OTU clustering identified the core rumen epithelial OTUs, defined as any OTU present in ≥ 80% of the samples, while the de novo data was randomly subsampled to 10,000 reads per sample to generate phylum- and genus-level distributions and beta diversity metrics. 57 core rumen epithelial OTUs were identified including metabolically important taxa such as Ruminococcus, Butyrivibrio, and other Lachnospiraceae, as well as sulfate-reducing bacteria Desulfobulbus and Desulfovibrio. Two Betaproteobacteria OTUs (Neisseriaceae and Burkholderiaceae) were core rumen epithelial OTUs, in contrast to rumen content where previous literature indicates they are rarely found. Two core OTUs were identified as the methanogenic archaea Methanobrevibacter and Methanomethylophilaceae. These core OTUs are consistently present across the many variables between studies which include different host species, geographic region, diet, age, farm management practice, time of year, hypervariable region sequenced, and more. When considering only cattle samples, the number of core rumen epithelial OTUs expands to 147, highlighting the increased similarity within host species despite geographical location and other variables. De novo OTU clustering revealed highly similar rumen epithelial communities, predominated by Firmicutes, Bacteroidetes, and Proteobacteria at the phylum level which comprised 79.7% of subsampled sequences. The 15 most abundant genera represented an average of 54.5% of sequences in each individual study. These abundant taxa broadly overlap with the core rumen epithelial OTUs, with the exception of Prevotellaceae which were abundant, but not identified within the core OTUs. Our results describe the core and abundant bacteria found in the rumen epithelial environment and will serve as a basis to better understand the composition and function of rumen epithelial communities.
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影响因子：
3.7
作者：
Kasparovska, Jitka;Pecinkova, Martina;Kasparovsky, Tomas
通讯作者：
Kasparovsky, Tomas
影响因子：
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作者：
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DOI：
10.1099/ijs.0.048371-0
发表时间：
2013-09-01
影响因子：
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影响因子：
7.1
作者：
CHENG, KJ;MCCOWAN, RP;COSTERTON, JW
通讯作者：
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影响因子：
5.2
作者：
Jin D;Zhao S;Zheng N;Bu D;Beckers Y;Denman SE;McSweeney CS;Wang J
通讯作者：
Wang J