Godino Sanchez Alisson, Serghine Joëlle, Le Mennec Cécile, Noël Cyril, Schaeffer Julien, Goraguer Herlé, Vincent Cécile, Vitré Thomas, Le Guyader Françoise S, Gourmelon Michèle
IFREMER, ODE-DYNECO-PELAGOS, Plouzané, France.
IFREMER, U. Microbiologie Aliment Santé et Environnement, LSEM, Nantes, France.
Front Microbiol. 2024 Dec 4;15:1484094. doi: 10.3389/fmicb.2024.1484094. eCollection 2024.
Seals, protected wild marine mammals, are widely found in waters around the world. However, rising concerns about their increasing numbers in some areas have led to potential worries regarding microbiological contamination of coastal areas by their feces, which could impact bathing and shellfish-harvesting activities. To the best of our knowledge, no study has been conducted on the bacterial and RNA viral communities present in the feces of both grey and harbor seals, which are the two main seal species observed in mainland France and overseas.
Fecal bacterial ( = 132) and RNA viral ( = 40) communities of seals were analyzed using 16S rRNA gene amplicon high-throughput sequencing and viral RNA sequencing methods, respectively. In addition, to identify the specific characteristics of seal fecal microbial communities compared to other animal fecal microbial communities that may also contaminate coastal areas, the bacterial communities of seals were compared to those of wild waterbirds and breeding animals (i.e., cattle and pigs) which could be present in upstream catchments of coastal areas. Finally, ANCOM was used to identify unique and seal-associated Amplicon Sequence Variants (ASVs), aiming to develop a Microbial Source Tracking (MST) bacterial qPCR marker associated with seals.
The bacterial communities of grey and harbor seals were not found to be significantly different and were characterized by a predominance of Firmicutes, including the genera 1 and , followed by Fusobacteriota with the genus , and Bacteroidota with the genus . However, variations in bacterial communities between sites and individuals were observed. Similar observations were made for the RNA viral communities being characterized by a predominance of (44% of total reads) and (15%). This study successfully developed a sensitive (89.8%) and specific (97.1%) MST qPCR marker targeting grey seal-associated bacteria belonging to the Bifidobacteriaceae family. This marker can be used to identify potential fecal contamination of coastal areas by seals and complements the MST toolboxes of markers already developed for humans, wild birds and livestock.
海豹是受保护的野生海洋哺乳动物，在世界各地的水域广泛分布。然而，人们越来越担心某些地区海豹数量的增加会导致其粪便对沿海地区造成微生物污染，进而影响游泳和贝类捕捞活动。据我们所知，尚未对灰海豹和港海豹（这是在法国本土和海外观察到的两种主要海豹物种）粪便中的细菌和RNA病毒群落进行研究。
分别使用16S rRNA基因扩增子高通量测序和病毒RNA测序方法分析海豹的粪便细菌群落（n = 132）和RNA病毒群落（n = 40）。此外，为了确定海豹粪便微生物群落与其他可能也会污染沿海地区的动物粪便微生物群落相比的特定特征，将海豹的细菌群落与可能存在于沿海地区上游集水区的野生水鸟和养殖动物（即牛和猪）的细菌群落进行了比较。最后，使用ANCOM来识别独特的、与海豹相关的扩增子序列变体（ASV），旨在开发一种与海豹相关的微生物源追踪（MST）细菌qPCR标记。
未发现灰海豹和港海豹的细菌群落存在显著差异，其特征是厚壁菌门占优势，包括1属和属，其次是梭杆菌门的属，以及拟杆菌门的属。然而，观察到不同地点和个体之间细菌群落存在差异。对于RNA病毒群落也有类似的观察结果，其特征是占优势（占总读数的44%）和（占15%）。本研究成功开发了一种针对属于双歧杆菌科的与灰海豹相关细菌的敏感（89.8%）且特异（97.1%）的MST qPCR标记。该标记可用于识别海豹对沿海地区可能的粪便污染，并补充已为人类、野生鸟类和牲畜开发的MST标记工具箱。
