Bivalves have ecological and economic importance but information regarding their associated microbiomes is lacking. As suspension feeders, bivalves capture and ingest a myriad of particles, and their digestive organs have a high throughput of particle-associated microbiota. To better understand the complement of transient and resident microbial communities, standard methods need to be developed. For example, fecal sampling could represent a convenient proxy for the gut microbiome and is simple, nondestructive, and allows for sampling of individuals through time. The goal of this study was to evaluate fecal sampling as a reliable proxy for gut microbiome assessment in the blue mussel (Mytilus edulis). Mussels were collected from the natural environment and placed into individual sterilized microcosms for 6 h to allow for fecal egestion. Feces and gut homogenates from the same individuals were sampled and subjected to 16S rRNA gene amplicon sequencing. Fecal communities of different mussels resembled each other but did not resemble gut communities. Fecal communities were significantly more diverse, in terms of amplicon sequence variant (ASV) richness and evenness, than gut communities. Results suggested a mostly transient nature for fecal microbiota. Nonetheless, mussels retained a distinct resident microbial community in their gut after fecal egestion that was dominated by ASVs belonging to Mycoplasma. The use of fecal sampling as a nondestructive substitute for direct sampling of the gut is strongly discouraged. Experiments that aim to study solely resident bivalve gut microbiota should employ an egestion period prior to gut sampling to allow time for voidance of transient microbes.

双壳类动物具有生态和经济重要性，但缺乏有关其相关微生物群落的信息。作为悬浮物进料器，双壳类动物捕获并摄取了无数的颗粒，它们的消化器官具有与颗粒相关的微生物群的高通量。为了更好地了解瞬时和居住微生物群落的互补性，需要开发标准方法。例如，粪便采样可以代表肠道微生物组的便捷代理，并且简单，无损，并且可以随时间进行个体采样。这项研究的目的是评估粪便采样，作为蓝贻贝（Mytilus edulis）肠道微生物组评估的可靠替代品。）。从自然环境中收集贻贝，并将其放入单独的灭菌缩影中6小时，以便排便。对来自同一个体的粪便和肠匀浆进行采样，并进行16S rRNA基因扩增子测序。不同贻贝的粪便群落彼此相似，但与肠道群落却不相似。就扩增子序列变异（ASV）的丰富性和均匀性而言，粪便群落比肠道群落明显多样化。结果表明粪便微生物群大部分是暂时性的。尽管如此，贻贝在粪便排泄后仍保留在肠道内独特的微生物群落，而支原体属于支原体。。强烈建议不要将粪便采样作为对肠道的直接采样的非破坏性替代。旨在仅研究驻留双壳类肠道菌群的实验应在肠道采样之前采用节食期，以留出时间使暂时性微生物无效。