Department of Biology, University of Puget Sound, Tacoma, Washington, USA.
Mol Ecol Resour. 2022 Jul;22(5):1693-1705. doi: 10.1111/1755-0998.13573. Epub 2021 Dec 20.
Microbial diversity and community function are related, and can be highly specialized in different gut regions. The cloacal microbiome of Sceloporus virgatus females provides antifungal protection to eggshells, a specialized function that suggests a specialized microbiome. Here, we describe the cloacal, intestinal, and oviductal microbiome from S. virgatus gravid females, adding to growing evidence of microbiome localization in reptiles and other taxa. We further assessed whether common methods for sampling gastrointestinal (GI) microbes - cloacal swabs and faeces - provide accurate representations of these microbial communities. We found that different regions of the gut had unique microbial communities. The cloacal microbiome showed extreme specialization averaging 99% Proteobacteria (Phylum) and 83% Enterobacteriacaea (Family). Enterobacteriacaea decreased up the GI and reproductive tracts. Cloacal swabs recovered communities similar to that of lower intestine and cloacal tissues. In contrast, faecal samples had much higher diversity and a distinct composition (common Phyla: 62% Firmicutes, 18% Bacteroidetes, 10% Proteobacteria; common families: 39% Lachnospiraceae, 11% Ruminococcaceae, 11% Bacteroidaceae) relative to all gut regions. The common families in faecal samples made up <1% of cloacal tissue samples, increasing to 43% at the upper intestine. Similarly, the common families in gut tissue (Enterobacteriaceae and Helicobacteraceae) made up <1% of the faecal microbiome. Further, we found that cloacal swabs taken shortly after defaecation may be contaminated with faecal matter. Our results serve as a caution against using faeces as a proxy for GI microbes, and may help explain high between-sample variation seen in some studies using cloacal swabs.
微生物多样性和群落功能是相关的，并且在不同的肠道区域可以高度专业化。Sceloporus virgatus 雌性的泄殖腔微生物组为蛋壳提供抗真菌保护，这是一种专门的功能，表明存在专门的微生物组。在这里，我们描述了 Sceloporus virgatus 怀孕雌性的泄殖腔、肠道和输卵管微生物组，这增加了越来越多的关于爬行动物和其他分类群中微生物组定位的证据。我们进一步评估了用于采样胃肠道（GI）微生物的常用方法 - 泄殖腔拭子和粪便 - 是否能准确代表这些微生物群落。我们发现，肠道的不同区域具有独特的微生物群落。泄殖腔微生物组表现出极端的专业化，平均 99%为变形菌门（门）和 83%肠杆菌科（科）。肠杆菌科在上消化道和生殖道中减少。泄殖腔拭子回收的群落与下消化道和泄殖腔组织相似。相比之下，粪便样本具有更高的多样性和明显不同的组成（常见门：62%厚壁菌门，18%拟杆菌门，10%变形菌门；常见科：39%lachnospiraceae，11%瘤胃球菌科，11%拟杆菌科），与所有肠道区域相比。粪便样本中的常见科占泄殖腔组织样本的比例<1%，在上消化道增加到 43%。同样，肠道组织中的常见科（肠杆菌科和螺旋杆菌科）占粪便微生物组的比例<1%。此外，我们发现，在排便后不久采集的泄殖腔拭子可能会受到粪便的污染。我们的研究结果提醒人们不要将粪便作为 GI 微生物的替代物，并可能有助于解释某些使用泄殖腔拭子的研究中看到的高样本间变异。
