An official website of the United States government
Microbial diversity and community function are related, and can be highly specialized in different gut regions. The cloacal microbiome of Sceloporus virgatus females provides antifungal protection to eggshells, a specialized function that suggests a specialized microbiome. Here, we describe the cloacal, intestinal, and oviductal microbiome from S. virgatus gravid females, adding to growing evidence of microbiome localization in reptiles and other taxa. We further assessed whether common methods for sampling gastrointestinal (GI) microbes – cloacal swabs and feces – provide accurate representations of these microbial communities. We found that different regions of the gut had unique microbial communities. The cloacal microbiome showed extreme specialization averaging 99% Proteobacteria (Phylum) and 83% Enterobacteriacaea (Family). Enterobacteriacaea decreased up the GI and reproductive tracts. Cloacal swabs recovered communities similar to that of lower intestine and cloacal tissues. In contrast, fecal samples had much higher diversity and a distinct composition (common Phyla: 62% Firmicutes, 18% Bacteroidetes, 10% Proteobacteria; common Families: 39% Lachnospiraceae, 11% Ruminococcaceae, 11% Bacteroidaceae) relative to all gut regions. The common families in fecal samples made up < 1% of cloacal tissue samples, increasing to 43% at the upper intestine. Similarly, the common families in gut tissue (Enterobacteriaceae and Helicobacteraceae) made up < 1% of the fecal microbiome. Further, we found that cloacal swabs taken shortly after defecation may be contaminated with fecal matter. Our results serve as a caution against using feces as a proxy for GI microbes, and may help explain high between-sample variation seen in some studies using cloacal swabs.
more »
« less
Fecal and cloacal microbiomes of cold-stunned loggerhead Caretta caretta, Kemp’s ridley Lepidochelys kempii, and green sea turtles Chelonia mydas
Investigating animal gut microbiomes can lead to a better understanding of their foraging preferences and their overall health. In this study, the fecal and cloacal microbiomes of 4 cold-stunned, frozen loggerhead Caretta caretta, 9 Kemp’s ridley Lepidochelys kempi , and 5 green sea turtles Chelonia mydas that stranded on beaches in Massachusetts, USA, were surveyed. Cloacal swabs and in situ fecal samples were collected from each turtle. From the extracted DNA, the hypervariable V1-V3 regions of the 16S rRNA gene were amplified with PCR, then sequenced using next generation Illumina MiSeq technology. Fecal and cloacal microbiomes were primarily composed of the phyla Proteobacteria , Bacteroidetes , and Firmicutes . Microbial communities varied significantly based on location of the gut sampled. Cloacal samples were largely dominated by Proteobacteria , while fecal samples appeared to have a greater distribution of taxa and higher alpha diversity. Green turtles had a higher abundance of Firmicutes and Bacteroidetes than Kemp’s ridley and loggerhead turtles, but a lower abundance of Proteobacteria . The information gained from this study contributes to knowledge of cold-stunned sea turtle gut microbiomes and may eventually be applied to rehabilitation efforts.
more »
« less
- Award ID(s):
- 1655221
- PAR ID:
- 10437652
- Date Published:
- Journal Name:
- Endangered Species Research
- Volume:
- 50
- ISSN:
- 1863-5407
- Page Range / eLocation ID:
- 93 to 105
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Insects that undergo metamorphosis from juveniles to adults provide an intriguing opportunity to examine the effects of life stage, species, and the environment on their gut microbiome. In this study, we surveyed the gut microbiomes of 13 species of dragonfly collected from five different locations subject to different levels of human impact. Juveniles were collected as nymphs from aquatic habitats while airborne adults were caught at the same locations. The gut microbiome was characterized by next generation sequencing of the bacterial 16S rRNA gene. Life stage was an important factor, with the gut microbiomes of dragonfly nymphs differing from those of adult dragonflies. Gut microbiomes of nymphs were influenced by sample site and, to a lesser extent, host species. Neither sample location nor host species had a strong effect on the gut microbiome of dragonfly adults. Regardless of life stage, gut microbiomes were dominated by members of the Proteobacteria, with members of the Bacteroidetes (especially in adults), Firmicutes, and Acidobacteria (especially in nymphs) also being proportionally abundant. These results demonstrate that different life stages of metamorphosing insects can harbor very different gut microbiomes and differ in how this microbiome is influenced by the surrounding environment.more » « less
-
Abstract Among closely related species, host phylogenetic relationships are typically a stronger predictor of gut microbiome composition than environmental variation. However, the relative impact of genetic admixture caused by hybridization versus environmental variation on gut microbiome communities is poorly understood. To explore this knowledge gap, we used fecal metabarcoding to characterize chickadee gut microbiomes along a hybrid zone transect in natural environments and after transfer to a common, controlled environment. We collected fecal samples from nestling black‐capped (Poecile atricapillus), Carolina (Poecile carolinensis), and hybrid chickadees immediately after removal from their nests and twice after entering captivity and experiencing common diet and environmental conditions. To characterize gut microbiome communities, we extracted fecal DNA and sequenced the V3–V4 region of the 16S rRNA gene using Illumina MiSeq. Overall,FirmicutesandProteobacteriawere the major microbial phyla present across host species groups. Our analysis of alpha diversity showed that the transition to common environmental conditions significantly impacted host gut microbiome richness. In contrast, the change in host environment did not impact the community composition (i.e., beta diversity) of the gut microbiomes. Although not statistically significant, host ancestry may influence the microbiome composition more than host environment. Additional analyses suggest chloroplast 16S rRNA sequences accurately characterized host diets in captivity. In certain cases, 16S rRNA sequences can provide reliable characterization of habitat and dietary variation in wild birds. Although environment more strongly shapes microbiome richness and evenness, host ancestry may have a greater influence on the specific microbes present in the microbiome.more » « less
-
Abstract Small populations of imperiled species are susceptible to the negative consequences of skewed sex‐ratios. In imperiled species with environmental sex determination such as sea turtles, examining sex ratios across a range of environments and population abundance levels can provide insight into factors that influence population resilience, which can then be the foci of management plans for these species. Breeding sex ratios (the ratio of actively breeding males to females during a reproductive season; BSRs) extrapolated from genetic parentage analyses are a common approach for enumerating sex ratios in sea turtles. Such analyses also allow for the characterization of multiple paternity within sea turtle clutches, which should reflect BSRs and breeding behaviors. We characterized the first BSR for a breeding assemblage of loggerhead sea turtles (Caretta caretta) belonging to the temperate, low‐abundance Northern Gulf of Mexico Recovery Unit using genotypes of 16 microsatellite loci from nesting females and hatchlings. Unlike prior studies at both more‐tropical and more‐temperate, and higher‐abundance, Recovery Units in this region, we found a balanced BSR of 1.3:1 males:female and a low incidence (~17%) of multiple paternity. This suggests that there are relatively few males breeding at this assemblage and within this Recovery Unit. Beaches in this region are expected to produce substantial numbers of male hatchlings based on sand temperature data. The relative dearth of mature males may then be due to hydrologic disturbances that disproportionately affect the fitness and survival of male hatchlings, or due to demographic stochasticity. More work is needed to study the factors that might influence male hatchling production and fitness in this region, particularly as climate change is predicted to lead to feminization in global sea turtle populations. Our work demonstrates the broad utility of characterizing BSRs and other sex ratios across a range of populations in imperiled, environmentally sensitive species.more » « less
-
Gut microbiomes can affect host health, fitness, and evolution. A large majority of gut microbiome research focuses on inferring microbial taxonomic diversity with the 16S rRNA gene, while shotgun metagenomic approaches can quantify both taxonomic and functional diversity of microbes. This level of detail is critical for understanding relationships between taxonomic, functional, and strain-level diversity of the microbial community and its interactions with host ecology, life history, and behavior. During 2023-2024, we collected fecal samples and behavioral data from a group of habituated Kinda baboons (Papio kindae) in Kasanka National Park, Zambia. We characterized taxonomic and functional microbiome diversity in more than 90 fecal samples using a shotgun metagenomics approach with the Watchmaker DNA Library Prep Kit and the HUMAnN3 bioinformatics pipeline. We found that Firmicutes was the most abundantly representative phylum, comprising more than 75% of our dataset, followed by Proteobacteria, Bacteroidota, and Candidatus Melainabacteria, each comprising less than 5% in all of our samples. Multidimensional scaling analysis of Bray-Curtis dissimilarity indices did not reveal any differences between the gut microbiome community of adult male and female baboons. These results may be due to a limited sample size but could also indicate that the relatively close social connections between males and females may facilitate the transmission of microbes among individuals and reduce sex differences. Future research will discuss these possibilities, and test hypotheses related to individual personality traits and social network characteristics.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript
- Journal Article:
- https://doi.org/10.3354/esr01220
