Age-associated variation in the gut microbiota of chinstrap penguins (Pygoscelis antarctica) reveals differences in food metabolism

Body site microbiota of Magellanic and king penguins inhabiting the Strait of Magellan follow species-specific patterns

Animal hosts live in continuous interaction with bacterial partners, yet we still lack a clear understanding of the ecological drivers of animal-associated bacteria, particularly in seabirds. Here, we investigated the effect of body site in the structure and diversity of bacterial communities of two seabirds in the Strait of Magellan: the Magellanic penguin (Spheniscus magellanicus) and the king penguin (Aptenodytes patagonicus). We used 16S rRNA gene sequencing to profile bacterial communities associated with body sites (chest, back, foot) of both penguins and the nest soil of Magellanic penguin. Taxonomic composition showed that Moraxellaceae family (specifically Psychrobacter) had the highest relative abundance across body sites in both penguin species, whereas Micrococacceae had the highest relative abundance in nest soil. We were able to detect a bacterial core among 90% of all samples, which consisted of Clostridium sensu stricto and Micrococcacea taxa. Further, the king penguin had its own bacterial core across its body sites, where Psychrobacter and Corynebacterium were the most prevalent taxa. Microbial alpha diversity across penguin body sites was similar in most comparisons, yet we found subtle differences between foot and chest body sites of king penguins. Body site microbiota composition differed across king penguin body sites, whereas it remained similar across Magellanic penguin body sites. Interestingly, all Magellanic penguin body site microbiota composition differed from nest soil microbiota. Finally, bacterial abundance in penguin body sites fit well under a neutral community model, particularly in the king penguin, highlighting the role of stochastic process and ecological drift in microbiota assembly of penguin body sites. Our results represent the first report of body site bacterial communities in seabirds specialized in subaquatic foraging. Thus, we believe it represents useful baseline information that could serve for long-term comparisons that use marine host microbiota to survey ocean health.

Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project

Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.

Composition, Diversity and Sex-Related Differences in Intestinal Microbiota in Captive African Penguins (Spheniscus demersus)

An understanding of the microbial communities in African penguins (Spheniscus demersus) could provide valuable information for saving this endangered species. The objective of this study was to investigate the composition, diversity and sex-related differences in the intestinal microbiota of captive African penguins. Fecal samples were collected from 21 captive adult African penguins reared in the same conditions at Shanghai Zoo. The results show that Proteobacteria, Actinobacteria and Firmicutes were the predominant bacteria in the intestinal microbiota of the captive African penguins. No difference was found in microbial diversity between female and male African penguins, as shown by their similar alpha and beta diversities. However, a notable sex-related difference was found between their microbial compositions. Female African penguins have a higher abundance of Pseudomonas and a lower abundance of Kocuria than males. A functional prediction indicates that the "mRNA surveillance pathway", "Polyketide sugar unit biosynthesis", "Wnt signaling pathway", "Lysosome" and "Cell cycle" pathways were significantly enriched in the microbiota of female African penguins. In conclusion, the present study indicates that the compositions and predicted functions of the intestinal microbiota are significantly different between the sexes. Our data suggest that the intestinal microbiota of female African penguins are more unstable than the intestinal microbiota of males in captivity.

Spotted seals (Phoca largha) harbor unique gut microbiota shaped by their host habitat

Assessing the structure and composition of gut microbiota of sentinel species such as spotted seals (Phoca largha) is a potential tool for assessing the health of the marine mammals and their habitats. However, the link between the host microbiome and their habitat is poorly understood. In this study, microbial communities in the habitat (sea ice and water) and marine mammalian host (fecal matter from P. largha) were evaluated in samples obtained from the Liaodong Bay, China during population aggregation period. Results from high-throughput sequencing showed that the bacterial communities in P. largha fecal matter were less rich and diverse compared to those from the water and ice samples. Significant differences in the composition and function of bacterial communities were also found among the water, ice, and fecal samples, in which sample type and sampling site had the greatest impact on composition and function variations, respectively. Several potential pathogenic bacteria and bacteria with functions associated with human disease were significantly enhanced in the communities of P. largha feces compared to those of surrounding environments. The ratios of environmental microorganisms sourced from the P. largha fecal matter were estimated. The results showed that certain bacteria in P. largha-inhabited fecal matter were associated with sea ice and had specific antibiotic resistance and infectious capacity. These findings provide critical data for monitoring the health of marine mammals and their habitats, which is essential for predicting the impact of anthropogenic disturbances on marine ecosystems.

Comparative Study of the Gut Microbiota Among Four Different Marine Mammals in an Aquarium

Despite an increasing appreciation in the importance of host–microbe interactions in ecological and evolutionary processes, information on the gut microbial communities of some marine mammals is still lacking. Moreover, whether diet, environment, or host phylogeny has the greatest impact on microbial community structure is still unknown. To fill part of this knowledge gap, we exploited a natural experiment provided by an aquarium with belugas (Delphinapterus leucas) affiliated with family Monodontidae, Pacific white-sided dolphins (Lagenorhynchus obliquidens) and common bottlenose dolphin (Tursiops truncatus) affiliated with family Delphinidae, and Cape fur seals (Arctocephalus pusillus pusillus) affiliated with family Otariidae. Results show significant differences in microbial community composition of whales, dolphins, and fur seals and indicate that host phylogeny (family level) plays the most important role in shaping the microbial communities, rather than food and environment. In general, the gut microbial communities of dolphins had significantly lower diversity compared to that of whales and fur seals. Overall, the gut microbial communities were mainly composed of Firmicutes and Gammaproteobacteria, together with some from Bacteroidetes, Fusobacteria, and Epsilonbacteraeota. However, specific bacterial lineages were differentially distributed among the marine mammal groups. For instance, Lachnospiraceae, Ruminococcaceae, and Peptostreptococcaceae were the dominant bacterial lineages in the gut of belugas, while for Cape fur seals, Moraxellaceae and Bacteroidaceae were the main bacterial lineages. Moreover, gut microbial communities in both Pacific white-sided dolphins and common bottlenose dolphins were dominated by a number of pathogenic bacteria, including Clostridium perfringens, Vibrio fluvialis, and Morganella morganii, reflecting the poor health condition of these animals. Although there is a growing recognition of the role microorganisms play in the gut of marine mammals, current knowledge about these microbial communities is still severely lacking. Large-scale research studies should be undertaken to reveal the roles played by the gut microbiota of different marine mammal species.