16S Phyloseq R object accompanying the paper: Effects of storage methods on total bacterial count and microbial composition of bovine colostrum

This ready to load <strong>phyloseq</strong> R S4 object contains the ASV table, taxonomy table and sample metadata (16S V3-V4). This data was build using the DaDa2 (version 1.12.1) and phyloseq (version 1.32) R packages using our raw Illumina MiSeq PE300 sequencing data deposited at NCBI-SRA under BioProject: PRJNA872909. The accompanying (peer-reviewed) scientific article can be found here: https://www.todo DOI: todo <strong>Study/draft abstract:</strong> Lisa Robbers, Hannes Bijkerk, Lars Ravesloot, Alex Bossers, Mirjam Nielen, Ruurd Jorritsma, Ad Koets, Lindert Benedictus Neonatal calves need to acquire passive immunity through maternal colostrum, as they are immunologically naïve and the structure of the bovine placenta does not allow passage of maternal antibodies during pregnancy. Milked colostrum is not initially sterile and may even contain high bacterial counts. Minimizing total bacterial counts in colostrum is generally advised, however bacterial quality of colostrum comprises more than just bacterial quantities, but also depends on the specific bacteria present. While duration and temperature of colostrum storage are known to affect total plate counts (TPC), less is known about the effects of storage on the actual bacterial composition of the TPC. We speculated that, depending on the storage conditions, colostrum is a substrate in which certain bacterial species can thrive affecting the quality of colostrum. We therefore aimed to characterize the effects of different colostrum storage methods on the composition of the viable, aerobic, microbial community. Colostrum samples were stored at different temperatures and for different durations. Next, bacterial growth was assessed using the aerobe plate count culture method, followed by 16S rRNA gene amplicon sequencing. Differences in the TPC bacterial compositions of the stored colostrum samples, as determined by 16S rRNA gene amplicon sequencing, were mostly explained by the variation in bacterial composition of the colostrum sample directly after milking. In line with earlier studies, the results from our study show that the TPC increased when colostrum was stored for 24 hours at room temperature, but not when stored in a refrigerator for the same duration. Community structure of the TPC of colostrum stored at room temperature for 24 hours and stored in a refrigerator for a week was significantly different from the baseline samples. The 16S rRNA sequencing results indicate this is because of increased numbers of <em>Enterobacteriaceae.</em> <em>Enterobacteriaceae</em> abundance in refrigerated samples seemed to remain stable for the first 24 hours, but increased drastically after one week. The results indicate that microbial composition of stored colostrum is mostly influenced by the composition of the colostrum sample directly after milking, which is most probably the result of contamination or other environmental influences during the milking process. This study provides a deeper insight in the changes in the microbial composition of colostrum TPC during practical storage conditions and provides a primer for more detailed research into the determinants of bacterial composition of colostrum and the linked health effects.本可直接加载的<strong>phyloseq</strong> R S4 对象包含扩增子序列变异（amplicon sequence variant, ASV）表、分类学表以及样本元数据（16S V3-V4）。本数据集基于我们上传至NCBI-SRA（美国国家生物技术信息中心序列读取档案）BioProject编号为PRJNA872909的原始Illumina MiSeq PE300测序数据，使用DaDa2（版本1.12.1）与phyloseq（版本1.32）R包构建而成。配套的经同行评议学术论文可查阅于此：https://www.todo DOI: todo <strong>研究/稿件摘要：</strong> Lisa Robbers、Hannes Bijkerk、Lars Ravesloot、Alex Bossers、Mirjam Nielen、Ruurd Jorritsma、Ad Koets、Lindert Benedictus 新生犊牛因免疫尚未成熟，且牛胎盘结构无法在孕期转运母体抗体，需通过母体初乳获得被动免疫。初乳在挤出之初并非无菌状态，甚至可能携带高浓度细菌。当前学界普遍建议尽量降低初乳中的总细菌数，但初乳的细菌质量不仅取决于总平板计数 (total plate count, TPC)，还与所存在的特定菌种密切相关。已知初乳储存的时长与温度会影响总平板计数，但目前针对储存条件如何影响初乳总菌实际菌群组成的研究仍较为匮乏。我们推测，根据储存条件的不同，初乳可作为特定细菌的增殖基质，进而影响初乳品质。因此本研究旨在表征不同初乳储存方式对活菌需氧微生物群落组成的影响。 我们将初乳样本在不同温度下储存不同时长，随后通过需氧平板计数培养法评估细菌生长，并开展16S核糖体RNA (16S ribosomal RNA, 16S rRNA) 基因扩增子测序。经16S rRNA基因扩增子测序分析发现，储存后初乳样本的总菌菌群组成差异，主要可归因于挤奶后即刻采集的初乳样本本身的菌群组成变异。与既往研究结果一致，本研究结果显示：初乳在室温下储存24小时后总平板计数会升高，但冷藏储存相同时长则无此变化。室温储存24小时与冷藏储存一周的初乳总菌群落结构，均与基线样本存在显著差异。16S rRNA测序结果表明，这一现象源于<em>肠杆菌科 (Enterobacteriaceae)</em> 的丰度升高。<em>肠杆菌科</em>在冷藏样本中的丰度在最初24小时内保持稳定，但在储存一周后会急剧增加。 本研究结果提示，储存后初乳的菌群组成主要受挤奶后即刻采集的初乳样本菌群组成影响，这大概率源于挤奶过程中的污染或其他环境因素。本研究深入阐明了实际储存条件下初乳总菌菌群组成的变化规律，可为后续深入研究初乳菌群组成的决定因素及其相关健康效应提供基础。