Gastrointestinal symbiont diversity in wild gorilla: a comparison of bacterial and strongylid communities across multiple localities

Cardiometabolic disease risk in gorillas is associated with altered gut microbial metabolism

Cardiometabolic disease is the leading cause of death in zoo apes; yet its etiology remains unknown. Here, we investigated compositional and functional microbial markers in fecal samples from 57 gorillas across U.S. zoos, 20 of which are diagnosed with cardiovascular disease, in contrast with 17 individuals from European zoos and 19 wild gorillas from Central Africa. Results show that zoo-housed gorillas in the U.S. exhibit the most diverse gut microbiomes and markers of increased protein and carbohydrate fermentation, at the expense of microbial metabolic traits associated with plant cell-wall degradation. Machine learning models identified unique microbial traits in U.S. gorillas with cardiometabolic distress; including reduced metabolism of sulfur-containing amino acids and hexoses, increased abundance of potential enteric pathogens, and low fecal butyrate and propionate production. These findings show that cardiometabolic disease in gorillas is potentially associated with altered gut microbial function, influenced by zoo-specific diets and environments.

Location Matters: Variations in Cloacal Microbiota Composition of Spatially Separated Freshwater Turtles

The gut microbiota of vertebrates is malleable and may be shaped by both intrinsic and extrinsic factors. Here, the effect that geography has on the cloacal microbiota of two species of Australian freshwater chelonians, eastern longneck turtle (Chelodina longicollis) and Macquarie River turtle (Emydura macquarii), captured from waterbodies with different levels of anthropogenic pressure was investigated. We analysed the microbiota composition, structure and diversity through 16S rRNA gene amplicon sequencing. It was hypothesised that animals from less disturbed environments would harbour a more diverse cloacal microbial population. The cloacal microbiotas from 93 turtles (C. longicollis n = 78; E. macquarii n = 15), from five locations, were analysed. For both species, the most predominant phylum was Proteobacteria. Cloacal microbiota alpha diversity varied significantly between the C. longicollis from all locations, but no differences were found for E. macquarii. In C. longicollis, turtles from wetlands within the centre of Melbourne had the lowest alpha diversity metrics, while the highest alpha diversity values were seen in turtles captured from an undisturbed rural waterbody. Beta diversity, obtained by weighted UniFrac distance, showed significant differences between locations of capture for both species of turtles in this investigation. For C. longicollis, 87 biomarkers were identified responsible for explaining differences between locations, and in E. macquarii, 42 biomarkers were found. This is the first study to explore the cloacal microbiota composition of the eastern longneck turtle and gives greater insight into microbial community structures in Macquarie River turtles. Our study demonstrated that cloacal microbiota composition of freshwater turtles was significantly influenced by locality and that disrupted environments may reduce microbial diversity in C. longicollis. Interestingly, we discovered that the effects of location contrasted significantly between species for alpha diversity with differences discovered for C. longicollis but not E. macquarii. However, for both species, beta diversity was notably influenced by habitat type. These results highlight the need to interpret chelonian microbiota data in the context of geography and human disturbance of the environment.

Leaf age structures phyllosphere microbial communities in the field and greenhouse

The structure of the leaf microbiome can alter host fitness and change in response to abiotic and biotic factors, like seasonality, climate, and leaf age. However, relatively few studies consider the influence of host age on microbial communities at a time scale of a few days, a short time scale relevant to microbes. To understand how host age modulates changes in the fungal and bacterial leaf microbiome on a short time scale, we ran independent field and greenhouse-based studies and characterized phyllosphere communities using next-generation sequencing approaches. Our field study characterized changes in the fungal and bacterial phyllosphere by examining leaves of different relative ages across individuals, whereas the greenhouse study examined changes in the fungal microbiome by absolute leaf age across individuals. Together, these results indicate that fungal communities are susceptible to change as a leaf ages as evidenced by shifts in the diversity of fungal taxa both in the field and the greenhouse. Similarly, there were increases in the diversity of fungal taxa by leaf age in the greenhouse. In bacterial communities in the field, we observed changes in the diversity, composition, and relative abundance of common taxa. These findings build upon previous literature characterizing host-associated communities at longer time scales and provide a foundation for targeted work examining how specific microbial taxa might interact with each other, such as fine-scale interactions between pathogenic and non-pathogenic species.

Hookworm genomics: dusk or dawn?

Hookworms are parasites, closely related to the model nematode Caenorhabditis elegans, that are a major economic and health burden worldwide. Primarily three hookworm species (Necator americanus, Ancylostoma duodenale, and Ancylostoma ceylanicum) infect humans. Another 100 hookworm species from 19 genera infect primates, ruminants, and carnivores. Genetic data exist for only seven of these species. Genome sequences are available from only four of these species in two genera, leaving 96 others (particularly those parasitizing wildlife) without any genomic data. The most recent hookworm genomes were published 5 years ago, leaving the field in a dusk. However, assembling genomes from single hookworms may bring a new dawn. Here we summarize advances, challenges, and opportunities for studying these neglected but important parasitic nematodes.

Novel insight into the genetic diversity of strongylid nematodes infecting South-East and East Asian primates

With many non-human primates (NHPs) showing continued population decline, there is an ongoing need to better understand their ecology and conservation threats. One such threat is the risk of disease, with various bacterial, viral and parasitic infections previously reported to have damaging consequences for NHP hosts. Strongylid nematodes are one of the most commonly reported parasitic infections in NHPs. Current knowledge of NHP strongylid infections is restricted by their typical occurrence as mixed infections of multiple genera, which are indistinguishable through traditional microscopic approaches. Here, modern metagenomics approaches were applied for insight into the genetic diversity of strongylid infections in South-East and East Asian NHPs. We hypothesized that strongylid nematodes occur in mixed communities of multiple taxa, dominated by Oesophagostomum, matching previous findings using single-specimen genetics. Utilizing the Illumina MiSeq platform, ITS-2 strongylid metabarcoding was applied to 90 samples from various wild NHPs occurring in Malaysian Borneo and Japan. A clear dominance of Oesophagostomum aculeatum was found, with almost all sequences assigned to this species. This study suggests that strongylid communities of Asian NHPs may be less species-rich than those in African NHPs, where multi-genera communities are reported. Such knowledge contributes baseline data, assisting with ongoing monitoring of health threats to NHPs.

High diversity and sharing of strongylid nematodes in humans and great apes co-habiting an unprotected area in Cameroon

Rapid increases in human populations and environmental changes of past decades have led to changes in rates of contact and spatial overlap with wildlife. Together with other historical, social and environmental processes, this has significantly contributed to pathogen transmission in both directions, especially between humans and non-human primates, whose close phylogenetic relationship facilitates cross-infections. Using high-throughput amplicon sequencing, we studied strongylid communities in sympatric western lowland gorillas, central chimpanzees and humans co-occurring in an unprotected area in the northern periphery of the Dja Faunal Reserve, Cameroon. At the genus level, we classified 65 strongylid ITS-2 amplicon sequencing variants (ASVs) in humans and great apes. Great apes exhibited higher strongylid diversity than humans. Necator and Oesophagostomum were the most prevalent genera, and we commonly observed mixed infections of more than one strongylid species. Human strongylid communities were dominated by the human hookworm N. americanus, while great apes were mainly infected with N. gorillae, O. stephanostomum and trichostrongylids. We were also able to detect rare strongylid taxa (such as Ancylostoma and Ternidens). We detected eight ASVs shared between humans and great apes (four N. americanus variants, two N. gorillae variants, one O. stephanostomum type I and one Trichostrongylus sp. type II variant). Our results show that knowledge of strongylid communities in primates, including humans, is still limited. Sharing the same habitat, especially outside protected areas (where access to the forest is not restricted), can enable mutual parasite exchange and can even override host phylogeny or conserved patterns. Such studies are critical for assessing the threats posed to all hosts by increasing human-wildlife spatial overlap. In this study, the term "contact" refers to physical contact, while "spatial overlap" refers to environmental contact.