Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico.
Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico.
PLoS One. 2019 Aug 29;14(8):e0221770. doi: 10.1371/journal.pone.0221770. eCollection 2019.
Diet is a primary driver of the composition of gut microbiota and is considered one of the main routes of microbial colonization. Prey identification is fundamental for correlating the diet with the presence of particular microbial groups. The present study examined how diet influenced the composition and function of the gut microbiota of the Pacific harbor seal (Phoca vitulina richardii) in order to better understand the role of prey consumption in shaping its microbiota. This species is a good indicator of the quality of the local environment due to both its foraging and haul-out site fidelity. DNA was extracted from 20 fecal samples collected from five harbor seal colonies located in Baja California, Mexico. The V4 region of 16S rRNA gene was amplified and sequenced using the Illumina technology. Results showed that the gut microbiota of the harbor seals was dominated by the phyla Firmicutes (37%), Bacteroidetes (26%) and Fusobacteria (26%) and revealed significant differences in its composition among the colonies. Funtional analysis using the PICRUSt software suggests a high number of pathways involved in the basal metabolism, such as those for carbohydrates (22%) and amino acids (20%), and those related to the degradation of persistent environmental pollutants. In addition, a DNA metabarcoding analysis of the same samples, via the amplification and sequencing of the mtRNA 16S and rRNA 18S genes, was used to identify the prey consumed by harbor seals revealing the consumption of prey with mainly demersal habits. Functional redundancy in the seal gut microbiota was observed, irrespective of diet or location. Our results indicate that the frequency of occurrence of specific prey in the harbor seal diet plays an important role in shaping the composition of the gut microbiota of harbor seals by influencing the relative abundance of specific groups of gut microorganisms. A significant relationship was found among diet, gut microbiota composition and OTUs assigned to a particular metabolic pathway.
饮食是肠道微生物群落组成的主要驱动因素，被认为是微生物定植的主要途径之一。猎物识别对于将饮食与特定微生物群的存在相关联至关重要。本研究检查了饮食如何影响太平洋港海豹（Phoca vitulina richardii）肠道微生物群落的组成和功能，以便更好地了解猎物消耗在塑造其微生物群中的作用。由于觅食和上岸地点的忠诚度，该物种是当地环境质量的良好指标。从位于墨西哥下加利福尼亚州的五个港海豹聚居地采集的 20 个粪便样本中提取了 DNA。使用 Illumina 技术扩增和测序了 16S rRNA 基因的 V4 区。结果表明，港海豹的肠道微生物群主要由厚壁菌门（Firmicutes）（37%）、拟杆菌门（Bacteroidetes）（26%）和梭杆菌门（Fusobacteria）（26%）主导，并且在聚居地之间存在明显的组成差异。使用 PICRUSt 软件进行的功能分析表明，涉及基础代谢的途径数量众多，例如碳水化合物（22%）和氨基酸（20%），以及与持久性环境污染物降解相关的途径。此外，还通过扩增和测序 mtRNA 16S 和 rRNA 18S 基因对相同样本进行了 DNA 代谢组学分析，以鉴定港海豹消耗的猎物，发现消耗的猎物主要是底栖习性。无论饮食或位置如何，海豹肠道微生物群都存在功能冗余。我们的结果表明，港海豹饮食中特定猎物的出现频率在塑造港海豹肠道微生物群落组成方面起着重要作用，这影响了特定肠道微生物群体的相对丰度。饮食、肠道微生物群落组成和特定代谢途径分配的 OTUs 之间存在显著关系。
