Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
PLoS One. 2019 Nov 7;14(11):e0224950. doi: 10.1371/journal.pone.0224950. eCollection 2019.
The common marmoset (Callithrix jacchus) is increasingly used as an animal model for biomedical research; however, gastrointestinal diseases causing significant morbidity are endemic in many captive marmoset colonies. Establishing gut microbiome patterns in a marmoset colony may aid in clinical decision-making and model reproducibility. A standardized method of sample collection and storage is essential for proper interpretation of microbiome data. While microbiome studies commonly utilize fecal samples, the goal of this study was to determine whether the microbiome profile from a rectal swab performed on a sedated animal was comparable to the microbiome profile from a fecal sample. During routine physical exams, paired fecal and rectal swab samples were collected from each of 23 marmosets. DNA was extracted from all fecal and rectal swab samples and 16S ribosomal RNA gene sequences were amplified and analyzed. Initial comparison of the relative abundance of bacterial phyla between paired samples had a r2 value of 0.70 with S of 0.08 with no significant differences in α and β diversity metrics between fecal and rectal samples. Initial analysis however, revealed 5 discordant fecal-rectal pairs which corresponded only with the 5 rectal swabs that were classified as free of visible fecal matter during collection. Exclusion of these 5 pairs resulted in an optimized fit of the data as evidenced by a r2 value of 0.91 with S of 0.05. These results demonstrate that rectal swabs are a reliable method for profiling the fecal microbiome in the marmoset since the bacterial composition from a rectal swab with visible fecal contents correlated well with the bacterial composition from a fecal sample from the same marmoset. This study highlights the importance of standardized sample collection methods and exclusion of inappropriate samples.
普通狨猴（Callithrix jacchus）越来越多地被用作生物医学研究的动物模型；然而，许多圈养狨猴群体中存在导致发病率显著升高的胃肠道疾病。在狨猴群体中建立肠道微生物组模式可能有助于临床决策和模型重现性。标准化的样本采集和储存方法对于正确解释微生物组数据至关重要。虽然微生物组研究通常使用粪便样本，但本研究的目的是确定在镇静动物上进行的直肠拭子的微生物组谱是否与粪便样本的微生物组谱相媲美。在常规体检期间，从 23 只狨猴中分别采集配对的粪便和直肠拭子样本。从所有粪便和直肠拭子样本中提取 DNA，并扩增和分析 16S 核糖体 RNA 基因序列。初始比较配对样本中细菌门的相对丰度的 r2 值为 0.70，S 值为 0.08，粪便和直肠样本之间的 α 和 β 多样性指标无显著差异。然而，初步分析显示 5 对粪便 - 直肠不一致，这仅与在采集过程中被归类为无可见粪便的 5 个直肠拭子相对应。排除这 5 对样本后，数据的优化拟合效果明显，r2 值为 0.91，S 值为 0.05。这些结果表明，直肠拭子是分析狨猴粪便微生物组的可靠方法，因为带有可见粪便内容物的直肠拭子的细菌组成与来自同一狨猴的粪便样本的细菌组成相关性良好。本研究强调了标准化样本采集方法的重要性和排除不适当样本的重要性。
