Unraveling the gut microbiota of Mexican pinnipeds: the dominance of life histories over phylogeny

The First Report of Mycoplasmas in Antarctic Pinnipeds: The Results of a Survey

The aim of this study was to investigate the presence of Mycoplasma spp. and their identification in seals from Antarctica. During January and February 2010, 59 Antarctic fur seals (Arctocephalus gazella), 17 Weddell seals (Leptonychotes weddellii), and 5 Southern elephant seals (Mirounga leonina) were captured in three Antarctic islands. Oral and genital samples were collected, cultured, and cloned. The Intergenic Spacer Region 16S-23S rDNA (ISR) PCR products were sent for sequencing. Seventy-four (91.4%) out of the eighty-one seals sampled were PCR positive. From those, 57 isolates were cultured. Mycoplasmas were more prevalent in the mouth in comparison to the reproductive tract. The percentage of isolates were 76.3%, 58.8%, and 40.0% for Antarctic fur seals, Weddell seals, and Southern elephant seals, respectively. The ISR sequences divided the isolates into six clusters. Four clusters presented a very high similarity percentage with mycoplasma sequences obtained from seals. However, none of these mycoplasmas have been described to date. Cluster 1 is also close to M. miroungigenitalium. This study represents the first report of Mycoplasma species adapted to Antarctic pinnipeds. The findings contribute to the understanding of the ecology of mycoplasmas in Antarctic pinnipeds.

Grey and harbor seals in France (mainland and Saint-Pierre et Miquelon): microbial communities and identification of a microbial source tracking seal marker

Introduction

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.

Methods

Fecal bacterial (n = 132) and RNA viral (n = 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.

Results and discussion

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 Clostridium sensu stricto 1 and Peptoclostridium, followed by Fusobacteriota with the genus Fusobacterium, and Bacteroidota with the genus Bacteroides. 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 Picobirnaviridae (44% of total reads) and Astroviridae (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.

Long-Read Sequencing Revealing the Effectiveness of Captive Breeding Strategy for Improving the Gut Microbiota of Spotted Seal (Phoca largha)

The spotted seal (Phoca largha) is the sole pinniped species that can reproduce in China and has been classified as the First-Grade State Protection animal. The conventional method for the protection and maintenance of the spotted seal population is the captive maintenance of the species in artificially controlled environments. Nevertheless, the efficacy of the captive strategy remains uncertain, with the potential to impact the health of spotted seals through alterations in gut microbiota. In this study, PacBio sequencing based on the full-length of the bacterial 16S rRNA gene was applied to faeces from captive and wild spotted seals, thereby providing a first reference for the gut microbiota profile of spotted seals at the species scale. The gut microbiota of captive spotted seals was found to be more diverse than that of the wild population. The gut microbiota of spotted seals exhibited notable variation due to captive breeding, with an enrichment of Firmicutes and a reduction in Proteobacteria. The results of the co-occurrence network analysis indicated that the gut microbiota of captive spotted seals exhibited a greater degree of complexity and stability in comparison to that observed in their wild counterparts. The analysis of community assembly mechanisms revealed an increased determinism for the gut microbiota of captive individuals, with a concomitant decrease in the contribution of drift. Furthermore, the results of the predicted functions indicated a reduction in stress responses and an enhanced ability to metabolise sugars in the gut microbiota of captive spotted seals. In conclusion, the results of this study provide evidence that the current captive breeding strategy is an effective approach for improving the gut microbiota of spotted seals. Furthermore, this study demonstrates the potential of monitoring the gut microbiota to assess the health of marine mammals and inform conservation strategies for endangered species.