Characterization of faecal and caecal microbiota of free-ranging black-tailed prairie dogs (<i>Cynomys ludovicianus</i>) using high-throughput sequencing of the V4 region of the 16S rRNA gene

Rooney, Tess; Eshar, David; Lee, Charles; Weese, J. Scott

doi:10.1093/conphys/coab042

Cited by 7 publications

(5 citation statements)

References 34 publications

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“…Overall, Bacteroidetes was the most dominant phylum in this study, with Rikenellaceae representing the most dominant group within it. These results are similar to studies on other rodents [85, 86] but not consistent with studies on the fecal and caecal microbiota of black-tailed prairie dogs in Kansas, USA [45] and fecal microbiota of Cynomys ludovicianus in Chihuahua, Mexico [44]. In particular, the proportion of Bacteroidetes accounted for less than 10% of the microbiota in previous studies of black-tailed prairie dogs (Supplementary Information: Table S3), versus 57.3% in this study.…”

Section: Fecal Microbiota Compositionsupporting

confidence: 88%

“…The fecal microbial diversity and abundance have been determined attributed to 10 samples in Janos Biosphere Reserve in Mexico [44]. Recent studies have examined the fecal and cecal microbiota of black-tailed prairie dogs in Kansas focused on 58 samples and compared sex and geographic variation between groups [45]. However, the response of fecal microbiota to habitat and environmental parameters has been rarely reported.…”

Section: Introductionmentioning

confidence: 99%

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Fine-scale spatial variation shape fecal microbiome diversity and composition in black- tailed prairie dogs (Cynomys ludovicianus)

Neha

Salazar‐Bravo

2022

Preprint

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BackgroundHost associated gut microbiota are important in understanding the coevolution of host-microbe, it’s causes and consequences that may help wildlife population to adapt to its rapid climatic changes. Mammalian gut microbiota composition and diversity may be affected by a variety of factors including geographic variation, seasonal variation in diet, habitat disturbance, environmental conditions, age, and sex. However, there have been few studies that have examined how ecological and environmental factors influence gut microbiota composition in animals' natural environments. In this study, we explore how host habitat, geographical location and environmental factors affect the fecal microbiota of Cynomys ludovicianus at a small spatial scale. We collected fecal samples from five geographically distinct locations in Texas Panhandle occupying habitat classified as urban and rural areas using high throughput 16S rRNA gene amplicon sequencing. ResultsThe results showed that microbiota of fecal samples was largely dominated by phylum Bacteroidetes. Fecal microbiome diversity and composition differed significantly across sampling sites and habitats. Prairie dogs inhabiting urban areas showed reduced fecal diversity due to more homogenous environment and anthropogenic disturbance. Urban prairie dog colonies displayed greater phylogenetic variation than those in rural habitats. Differentially abundant analysis revealed that bacterial species pathogenic to humans and animals were highly abundant in urban areas which indicates that host health and fitness might be negatively affected. Random forest model identified Alistipes shahii as the important species driving the changes in fecal microbiome composition. Despite the effects of habitat and geographic location of host, we found a strong correlation with environmental factors- average maximum temperature was the best predictor of prairie dog fecal microbial diversity. ConclusionsOur findings suggest that reduction in alpha diversity in conjunction with greater dispersion in beta diversity could be indicative of declining host health in urban areas which could help determine in future conservation efforts. Moreover, several bacterial species pathogenic to humans and other animals were highly abundant in prairie dog colonies near urban areas, which may in turn adversely affect host phenotype and fitness.

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Section: Fecal Microbiota Compositionsupporting

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Fine-scale spatial variation shape fecal microbiome diversity and composition in black- tailed prairie dogs (Cynomys ludovicianus)

Neha

Salazar‐Bravo

2022

Preprint

View full text Add to dashboard Cite

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“…Overall, Bacteroidetes was the most dominant phylum in this study, with Rikenellaceae representing the most dominant group within it. These results are similar to studies on other rodents [49,50] but not consistent with studies on the fecal and caecal microbiota of black-tailed prairie dogs in Kansas, USA [45] and fecal microbiota of Cynomys ludovicianus in Chihuahua, Mexico [44]. In particular, the proportion of Bacteroidetes accounted for less than 10% of the microbiota in previous studies of black-tailed prairie dogs (Table S4), versus 57.3% in this study.…”

Section: Fecal Microbiota Compositionsupporting

confidence: 87%

“…Previous work in the fecal microbial diversity and abundance of the species only analyzed a small sample (n = 10) in the Janos Biosphere Reserve in Mexico [44]. Recent study examined the fecal and cecal microbiota of black-tailed prairie dogs in Kansas focused on 58 samples and compared sex and geographic variation between groups [45]. However, the response of fecal microbiota to habitat and environmental parameters has yet to be analyzed in detail.…”

Section: Introductionmentioning

confidence: 99%

Fine-scale spatial variation shape fecal microbiome diversity and composition in black-tailed prairie dogs (Cynomys ludovicianus)

Neha

Salazar‐Bravo

2023

BMC Microbiol

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Background Host associated gut microbiota are important in understanding the coevolution of host-microbe, and how they may help wildlife populations to adapt to rapid environmental changes. Mammalian gut microbiota composition and diversity may be affected by a variety of factors including geographic variation, seasonal variation in diet, habitat disturbance, environmental conditions, age, and sex. However, there have been few studies that examined how ecological and environmental factors influence gut microbiota composition in animals' natural environments. In this study, we explore how host habitat, geographical location and environmental factors affect the fecal microbiota of Cynomys ludovicianus at a small spatial scale. We collected fecal samples from five geographically distinct locations in the Texas Panhandle classified as urban and rural areas and analyzed them using high throughput 16S rRNA gene amplicon sequencing. Results The results showed that microbiota of these fecal samples was largely dominated by the phylum Bacteroidetes. Fecal microbiome diversity and composition differed significantly across sampling sites and habitats. Prairie dogs inhabiting urban areas showed reduced fecal diversity due to more homogenous environment and, likely, anthropogenic disturbance. Urban prairie dog colonies displayed greater phylogenetic variation among replicates than those in rural habitats. Differentially abundant analysis revealed that bacterial species pathogenic to humans and animals were highly abundant in urban areas which indicates that host health and fitness might be negatively affected. Random forest models identified Alistipes shahii as the important species driving the changes in fecal microbiome composition. Despite the effects of habitat and geographic location of host, we found a strong correlation with environmental factors and that- average maximum temperature was the best predictor of prairie dog fecal microbial diversity. Conclusions Our findings suggest that reduction in alpha diversity in conjunction with greater dispersion in beta diversity could be indicative of declining host health in urban areas; this information may, in turn, help determine future conservation efforts. Moreover, several bacterial species pathogenic to humans and other animals were enriched in prairie dog colonies near urban areas, which may in turn adversely affect host phenotype and fitness.

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“…Previous studies have shown that age, sex, and physiological state are important factors affecting the intestinal ora of dogs [33]. For instance, among captive Beagle and Cocker Spaniel breeds, the abundance of Pseudomonas adaceae and Escherichia is signi cantly higher, while the abundance of Actinobacteria is signi cantly lower in the aged group (> 7 years) than in the adult group (2-7 years) [34].…”

Section: Discussionmentioning

confidence: 98%

Comparative analysis of the gut microbiota of the Chinese Kunming dog, German Shepherd, and Belgian Malinois

Hu,

Cheng,

Cao

et al. 2024

Preprint

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The composition of the gut microbiota is essential for the host’s health and adaptation to the environment. Due to bacterial functional redundancy in microbial communities, different bacteria can produce the same important metabolites beneficial to health, and studying the gut flora composition of dogs of different breeds under the same domestication conditions can help improve microbial diversity and normalize metabolite production in diseased dogs. In this study, noninvasive sampling and 16S rRNA high-throughput sequencing were used to compare and analyze the structure and function of the gut microbiota of three dog breeds, namely the Chinese Kunming dog (CKD), German Shepherd dog (GSD) and Belgian Malinois dog (BMD). The results showed that the gut microbiota of the three dog breeds consisted of 257 species across 146 genera, 60 families, 35 orders, 15 classes, and 10 phyla. The dominant bacterial phyla across the three breeds were Firmicutes (57.44%), Fusobacteriota (28.86%), and Bacteroidota (7.63%), while the dominant bacterial genera across the three breeds were Peptostreptococcus (21.08%), Fusobacterium (18.50%), Lactobacillus (12.37%), and Cetobacter (10.29%). Further analysis also revealed significant differences in the intestinal flora of the three breeds, at both the phylum and genus levels. The richness of intestinal flora of BMD was significantly higher than that of CKD and GSD. The results of this study provide novel insights into the intestinal flora of intervention dogs and suggest novel methods to improve their health status.

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Characterization of faecal and caecal microbiota of free-ranging black-tailed prairie dogs (Cynomys ludovicianus) using high-throughput sequencing of the V4 region of the 16S rRNA gene

Cited by 7 publications

References 34 publications

Fine-scale spatial variation shape fecal microbiome diversity and composition in black- tailed prairie dogs (Cynomys ludovicianus)

Fine-scale spatial variation shape fecal microbiome diversity and composition in black- tailed prairie dogs (Cynomys ludovicianus)

Fine-scale spatial variation shape fecal microbiome diversity and composition in black-tailed prairie dogs (Cynomys ludovicianus)

Comparative analysis of the gut microbiota of the Chinese Kunming dog, German Shepherd, and Belgian Malinois

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