Table_5_Rumen Epithelial Communities Share a Core Bacterial Microbiota: A Meta-Analysis of 16S rRNA Gene Illumina MiSeq Sequencing Datasets.pdf

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.

本荟萃分析共纳入17份瘤胃上皮16S核糖体RNA基因（16S rRNA gene）Illumina MiSeq扩增子测序数据集，旨在鉴定纳入的不同研究间共有的核心瘤胃上皮微生物群与核心瘤胃上皮操作分类单元（Operational Taxonomic Unit，OTU）。在进行封闭参考97% OTU聚类与从头（de novo）97% OTU聚类前，先对序列开展质量过滤并筛选嵌合序列。其中，封闭参考OTU聚类用于鉴定核心瘤胃上皮OTU，其定义为在≥80%的样本中均存在的OTU；同时将从头聚类得到的数据按每个样本随机抽平至10000条读段（reads），以生成门水平与属水平的物种分布及β多样性（beta diversity）指标。本次分析共鉴定出57个核心瘤胃上皮OTU，其中包含代谢功能重要的类群，如瘤胃球菌属（Ruminococcus）、丁酸弧菌属（Butyrivibrio）及其他毛螺菌科（Lachnospiraceae）成员，同时还包括硫酸盐还原菌脱硫球菌属（Desulfobulbus）与脱硫弧菌属（Desulfovibrio）。有2个隶属于β变形菌纲（Betaproteobacteria）的OTU分别属于奈瑟菌科（Neisseriaceae）与伯克霍尔德菌科（Burkholderiaceae），被鉴定为核心瘤胃上皮OTU；而此前研究显示，这两类类群在瘤胃内容物中极少被检出。另有2个核心OTU为产甲烷古菌（methanogenic archaea），分别隶属于甲烷短杆菌属（Methanobrevibacter）与甲基嗜甲基菌科（Methanomethylophilaceae）。无论纳入研究间存在宿主物种、地理区域、日粮、年龄、牧场管理模式、采样季节、测序高变区等诸多差异，这些核心OTU均能稳定检出。若仅分析牛源样本，核心瘤胃上皮OTU的数量增至147个，这表明即便存在地理位置与其他变量差异，同一宿主物种内的瘤胃上皮微生物群落相似性仍显著提升。从头OTU聚类结果显示，瘤胃上皮微生物群落结构高度相似，在门水平上以厚壁菌门（Firmicutes）、拟杆菌门（Bacteroidetes）和变形菌门（Proteobacteria）为主，这三类菌占抽平后序列总量的79.7%。丰度排名前15的菌属平均占每项研究中序列总量的54.5%。这些高丰度类群与核心瘤胃上皮OTU大体重合，但普雷沃氏菌科（Prevotellaceae）例外——该类群丰度较高，但并未被纳入核心OTU。本研究明确了瘤胃上皮微环境中的核心与高丰度细菌类群，可为后续深入解析瘤胃上皮微生物群落的组成与功能提供研究基础。