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Microbiomes in Canidae
Open accessAbstract
Because of their range expansion across North America, coyotes (Canis latrans) now occur sympatrically with numerous other predator species, including red foxes (Vulpes vulpes). This raises several interesting ecological questions, including if and how sympatry affects the diet and gut microbiomes of coyotes and red foxes. We examined the gut microbiomes of sympatric populations of coyotes and red foxes within two different National Parks in Virginia, USA, that differ in land use, vegetation, and anthropogenic disturbance: Prince William Forest Park (PRWI) and Manassas National Battlefield Park (MANA). From 2012 to 2017, scat samples from PRWI and MANA were collected and analyzed. Polymerase chain reaction (PCR) amplification of a region of the mitochondrial cytochrome‐b gene followed by restriction enzyme digestion of the PCR product was used to determine the origin of each scat sample. Next‐Generation DNA sequencing of a hypervariable 16S rRNA gene region was used to determine gut microbiome information about the scat samples. There was no evidence for a difference between the gut microbiomes of red foxes in either location, or for a difference between the gut microbiomes of red foxes at either location and coyotes at the location with lower human disturbance, PRWI. However, the gut microbiomes of coyotes at the location with higher anthropogenic disturbances, MANA, revealed a marked change from those found in red foxes at either location and from those in coyotes at the location with lower disturbances. The gut microbiomes of coyotes subjected to greater human impact may provide evidence of dysbiosis, indicative of increased physiological stress and reduced health. We discuss our observations in the context of understanding anthropogenic impacts on coyote and red fox interactions. Our results suggest that physiological stress in the form of human disturbance may play an important role in the composition of the gut microbiome of coyotes, which can affect their overall health.
Overview
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TL;DR
This study compared gut microbiomes of sympatric coyotes and red foxes in two Virginia national parks with different levels of human disturbance. Coyotes at the more human-disturbed site showed microbiome shifts consistent with dysbiosis, while red foxes did not differ between sites.
Key findings
- Coyote gut microbiomes differed significantly between Prince William Forest Park (PRWI) and Manassas National Battlefield Park (MANA) across all three distance measures (MRPP p = .002 for Euclidean, Jaccard, and Sorensen).
- Red fox microbiomes did not differ between parks (p = .956, .881, .871), and PRWI coyotes did not differ from PRWI red foxes (p = .147, .123, .178), but MANA coyotes did differ from MANA red foxes (p = .045, .031, .031).
- MANA coyotes had higher average Proteobacteria (55.47%) and lower Firmicutes (13.27%) than PRWI coyotes (37.01% Proteobacteria, 36.64% Firmicutes), a pattern the authors associate with dysbiosis.
- Microbial species richness differed significantly between sites (p = .001) but not hosts (p = .820); Shannon diversity did not differ significantly between hosts (p = .504) or sites (p = .125).
Methods
- Scat samples were collected from 2012 to 2017 at PRWI (low human disturbance) and MANA (high human disturbance): 264 samples were gathered, 198 underwent DNA isolation, and 161 were successfully PCR-amplified and sequenced, including 58 coyote and 67 red fox samples.
- Canid species were identified using mitochondrial cytochrome-b PCR followed by restriction enzyme digestion, confirmed with mitochondrial d-loop PCR product sizing; gut bacteria were assessed by 16S rRNA V3–V4 amplification and Illumina MiSeq sequencing.
- Sequencing data were analyzed with Illumina’s 16S Metagenomics application against Greengenes at phylum and family levels; MRPP in PC-ORD used Euclidean, Jaccard, and Sorensen distances, and Kruskal–Wallis tests compared Shannon diversity and microbial species richness.
Limitations
- Stated: the authors note it is difficult to know which factors in a complex, interconnected system are causal, resultant, or incidental, and they say their model is not meant to explain all results from wild animals forced into urban habitats.
- Evident: this is an observational scat-based study; 66 of 264 collected samples did not undergo DNA isolation, 37 of 198 failed PCR, and 23 of 161 analyzed samples had unidentified sources.
- Evident: sample sizes were uneven across host/site groups (e.g., 37 PRWI coyotes vs. 21 MANA coyotes; 27 PRWI red foxes vs. 40 MANA red foxes), and the study did not directly measure physiological stress, health, or diet.
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“With the PRWI coyote samples, the average percent reads identified to each major bacterial phylum were: 37.01% for Proteobacteria”
§ Microbiomes in Canidae > RESULTS > Coyote gut microbiome results
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“With the MANA coyote samples, the average percent reads were: 55.47% for Proteobacteria”
§ Microbiomes in Canidae > RESULTS > Coyote gut microbiome results
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Microbial species richness significantly different between sites | .001”
§ Microbiomes in Canidae > RESULTS > Coyote gut microbiome results
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The average Shannon diversity was 2.249, while the average number of microbial species in the PRWI red fox scat samples was 182.7.”
§ Microbiomes in Canidae > RESULTS > Red fox gut microbiome results
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The average Shannon diversity was 2.405, while the average number of microbial species in the PRWI coyote scat samples was 198.6.”
§ Microbiomes in Canidae > RESULTS > Coyote gut microbiome results
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
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Metadata
- Authors
- Biles, T. L., Beck, H., & Masters, B. S.
- Affiliations
- Towson University (US)
- Corresponding author
- Beck, Harald
- Venue
- Ecology and Evolution
- Publisher
- Wiley
- Published
- 2021-12
- Volume
- 11
- Issue
- 24
- Pages
- 18531-18539
- ISSN
- 2045-7758 (ISSN-L)
- PMC
- PMC8717330
- OpenAlex
- W4200396249
- Cited by
- 4
- References
- 33
- Citations by year
- 2026: 2 · 2023: 2
- FWCI
- 0.14
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Ecology and Evolution (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Park Service (P13AC00443)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Wildlife Ecology and Conservation
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- gut microbiota, coyote, red fox, Canidae, sympatry, human disturbance, anthropogenic impacts, physiological stress, dysbiosis, scat samples, diet, land use, wildlife health, species interactions
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