Host species and habitats shape the bacterial community of gut microbiota of three non-human primates: Siamangs, white-handed gibbons, and Bornean orangutans

High-Throughput DNA Metabarcoding for the Gut Microbiome Assessment of Captive White-Handed Gibbon and Siamang

BACKGROUND

The gut microbiota plays a vital role in primates' overall health and well-being, including small apes (Hylobatidae). The symbiotic relationships between bacteria and the gut aid food digestion, maintain host health, and help them adapt to their environment, including captive conditions. Despite being listed as endangered in the International Union for Conservation of Nature (IUCN) red list category, molecular studies on the small ape's gut microbiome are limited compared to other primates. This study aimed to characterize the gut microbiota of captive small apes at Zoo Taiping and Night Safari, Peninsular Malaysia, by evaluating their microbial communities.

METHODS

Seven fecal samples from Hylobatidae (white-handed gibbon and siamang) were collected, and the bacteria therein were successfully isolated and subjected to high-throughput sequencing of the 16S rRNA gene.

RESULTS

The acquired amplicon sequence variants (ASVs) were successfully classified into 17 phyla, 82 families, 164 genera, and 43 species of microbes. Each small ape exhibited a unique gut microbiota profile. The phyla Bacteroidota and Firmicutes were dominant in each individual. Environmental conditions and host genetics are among the factors that influence the small ape's gut microbiome composition.

CONCLUSIONS

These findings provide valuable insights into the gut microbiota composition of small apes at Zoo Taiping and Night Safari, thus contributing to the health management and welfare efforts of small apes in captivity.

Profiling the Gut Microbiome of Hylobatidae and Cercopithecinae: Insights Into the Health of Primates in Captivity

BACKGROUND

A healthy gut microbiome is essential for digestion in primates, for developing the gut immune system, and for defense against pathogen invasion. Next-generation sequencing allows for determining the microbiome composition and enables the continuous monitoring of primate health.

METHODS

To comprehensively analyze the gut microbiome diversity of three endangered primate species at Matang Wildlife Centre-Hylobates abbotti, Macaca fascicularis, and Macaca nemestrina, using high-throughput sequencing of the 16S rRNA gene.

RESULTS

A total of 18 phyla, 84 families, 188 genera, and 46 species were successfully classified. H. abbotti exhibited the highest microbial diversity with a distinct microbiome profile from the Macaca species. The presence of Treponema (nonpallidum), Bifidobacterium, and Faecalibacterium prausnitzii is critical for gut health, promoting digestion and maintaining the microbial balance.

CONCLUSION

This study highlights the importance of monitoring microbial diversity in captive primates to better understand their health and facilitate the early detection of potential pathogens. This also offers insights into microbiome-based strategies for improving overall animal welfare.

Analysis of the microbial diversity in the fecal material of the critically endangered orangutan

The orangutan ( Pongo spp.) is a critically endangered species. Today, populations of these animals are rapidly declining by up to 75%. They are found in the tropical rainforests of Borneo and Sumatra. In this study, using a next generation sequencing approach, the bacterial and fungal diversity in the fecal material of orangutans living in the Racine Zoo were investigated. The most predominant bacterial phyla were the Bacillota along with Bacteroidota. The most predominant fungal phylum was Ascomycota. Finally, the various functions of the bacterial communities present in the fecal material were predicted with PICRUSt2 using the KEGG database.

Social organization and physical environment shape the microbiome of harvester ants

All animals harbor microbiomes, which are obtained from the surrounding environment and are impacted by host behavior and life stage. To determine how two non-mutually exclusive drivers - physical environment and social organization - affect an organism's microbiome, we examined the bacterial communities within and around nests of harvester ants (Veromessor andrei). We collected soil and nest content samples from five different ant nests. We used 16S rRNA gene sequencing and calculated alpha and beta diversity to compare bacterial diversity and community composition across samples. To test the hypotheses that physical environment and/or social organization impact ant colonies' community of microbes we compared our samples across (i) sample types (ants, brood, seeds and reproductives (winged alates), and soil), (ii) soil inside and outside the nest, and (iii) soil from different chamber types. Interestingly, we found that both the environment and social organization impact the bacterial communities of the microbiome of V. andrei colonies. Soil from the five nests differed from one another in a way that mapped onto their geographical distance. Furthermore, soil from inside the nests resembled the surrounding soil, supporting the physical environment hypothesis. However, the bacterial communities associated with the contents within the nest chambers, i.e., ants, brood, seeds, and reproductives, differed from one another and from the surrounding soil, supporting the social organization hypotheses. This study highlights the importance of considering environmental and social factors in understanding microbiome dynamics.

Characterizing the gastrointestinal microbiome diversity in endangered Malayan Siamang (Symphalangus syndactylus): Insights into group composition, age variability and sex-related patterns

BACKGROUND

The gut morphology of Symphalangus syndactylus exhibits an intermediate structure that aligns with its consumption of fruit and ability to supplement its diet with leaves. The Siamang relies on its gut microbiome for energy extraction, immune system development, and the synthesis of micronutrients. Gut microbiome composition may be structured based on several factors such as age, sex, and habitat. No study has yet been carried out on the gut microbiota of the Hylobatidae members in Malaysia especially S. syndactylus.

METHODS

This study aims to resolve the gut microbiome composition of S. syndactylus by using a fecal sample as DNA source, adapting high-throughput sequencing, and 16S rRNA as the targeted region.

RESULTS

A total of 1 272 903 operational taxonomic units (OTUs) reads were assigned to 22 phyla, 139 families, and 210 genera of microbes. The {Unknown Phylum} Bacteria-2 is the dominant phyla found across all samples. Meanwhile, {Unknown Phylum} Bacteria-2 and Firmicutes are genera that have the highest relative abundance found in the Siamang gut.

CONCLUSIONS

This study yields nonsignificance relationship between Siamang gut microbiome composition with these three factors: group, sex, and age.

Gut microbial assessment among Hylobatidae at the National Wildlife Rescue Centre, Peninsular Malaysia

IMPORTANCE

Recent developments in genetic analytical techniques have enabled the comprehensive analysis of gastrointestinal symbiotic bacteria as a screening tool for animal health conditions, especially the endangered gibbons at the National Wildlife Rescue Centre (NWRC).

OBJECTIVE

High-throughput sequencing based on 16S ribosomal RNA genes was used to determine the baseline gut bacterial composition and identify potential pathogenic bacteria among three endangered gibbons housed in the NWRC.

METHODS

Feces were collected from 14 individuals (Hylobates lar, n = 9; Hylobates agilis, n = 4; and Symphalangus syndactylus, n = 1) from March to November 2022. Amplicon sequencing were conducted by targeting V3-V4 region.

RESULTS

The fecal microbial community of the study gibbons was dominated by Bacteroidetes and Firmicutes (phylum level), Prevotellaceae and Lachnospiraceae/Muribaculaceae (family level), and Prevotella (and its subgroups) (genera level). This trend suggests that the microbial community composition of the study gibbons differed insignificantly from previously reported conspecific or closely related gibbon species.

CONCLUSIONS AND RELEVANCE

This study showed no serious health problems that require immediate attention. However, relatively low alpha diversity and few potential bacteria related to gastrointestinal diseases and streptococcal infections were detected. Information on microbial composition is essential as a guideline to sustain a healthy gut condition of captive gibbons in NWRC, especially before releasing this primate back into the wild or semi-wild environment. Further enhanced husbandry environments in the NWRC are expected through continuous health monitoring and increase diversity of the gut microbiota through diet diversification.

Distribution and roles of Ligilactobacillus murinus in hosts

Ligilactobacillus murinus, a member of the Ligilactobacillus genus, holds significant potential as a probiotic. While research on Ligilactobacillus murinus has been relatively limited compared to well-studied probiotic lactic acid bacteria such as Limosilactobacillus reuteri and Lactobacillus gasseri, a mounting body of evidence highlights its extensive involvement in host intestinal metabolism and immune activities. Moreover, its abundance exhibits a close correlation with intestinal health. Notably, beyond the intestinal context, Ligilactobacillus murinus is gaining recognition for its contributions to metabolism and regulation in the oral cavity, lungs, and vagina. As such, Ligilactobacillus murinus emerges as a potential probiotic candidate with a pivotal role in supporting host well-being. This review delves into studies elucidating the multifaceted roles of Ligilactobacillus murinus. It also examines its medicinal potential and associated challenges, underscoring the imperative to delve deeper into unraveling the mechanisms of its actions and exploring its health applications.