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Comparison of the red fox gut microbiota among different habitat types in southern Anatolia
Open accessPublished version of a preprint
Abstract
Environmental conditions, especially diet, affect the diversity of gut microbiota (GM). This diversity within and between populations may influence the host’s health and fitness and, therefore, play an important role in adaptation. Regarding this, we collected fecal samples from natural, rural, suburban, and urban habitats to reveal the interaction between diet and compositional diversity of GM of a generalist carnivore, the red fox. The prokaryotic diversity of fecal microbiota was investigated by sequencing the 16S rRNA gene V3-V4 regions. A total of 46 archaeal and bacterial phyla were identified, with Bacillota being the most common phylum in most samples. The dominant genera in the GM of the red fox were Collinsella , Fusobacterium , Faecalibacterium , Escherichia-Shigella , and Blautia . Fusobacterium showed higher relative abundance in suburban (16.0%), natural (11.0%), and rural habitats (10.8%) compared to urban habitats (2.0%), indicating dietary differences of the red foxes that feed close to human settlements. Despite the observed differences in specific taxa, the overall microbial diversity remained relatively stable across the habitats. Our study determined the compositional changes of the GM of a wild animal for the first time in the Anatolian peninsula and revealed the effects of dietary changes, especially urbanization, on the diversity of GM of red foxes.
Overview
CoChat Summary
TL;DR
This study used 16S rRNA sequencing of red fox fecal samples from natural, rural, suburban, and urban habitats in Adana, Türkiye, to test whether habitat-associated dietary differences alter gut microbiota composition. It found habitat-related shifts in specific taxa but no statistically significant differences in overall alpha diversity, with the paper stating that community composition remained relatively stable across habitats.
Key findings
- A total of 46 archaeal and bacterial phyla were identified, with Bacillota most common in most samples (13/24); Bacillota relative abundance was 37.6% in natural, 17.2% in rural, 58.4% in suburban, and 66.1% in urban samples. The dominant genera were *Collinsella*, *Fusobacterium*, *Faecalibacterium*, *Escherichia-Shigella*, and *Blautia*.
- *Fusobacterium* was higher in suburban (16.0%), natural (11.0%), and rural (10.8%) habitats than in urban habitats (2.0%). *Faecalibacterium* was higher in urban samples (19.5%) than in suburban (4.3%), rural (1.6%), or natural (8.9%) samples; *Catenibacterium* and *Peptoclostridium* were more abundant in suburban and urban samples.
- DESeq2 identified 23 genera significantly different between urban and natural samples (adj. P < 0.01). Alpha diversity (Observed, Shannon, Simpson) showed no statistically significant differences across habitats (Wilcoxon test, P.adj > 0.05), and the paper reports that fecal communities did not cluster separately by habitat in PCoA (PERMANOVA R² = 0.186, F = 1.52, P = 0.026 as reported).
Methods
- Cross-sectional fecal sampling across four habitat types in Adana province, southern Anatolia, Türkiye (natural, rural, suburban, urban) between June and September 2021. A total of 64 samples were collected (22 natural, 22 rural, 13 suburban, 7 urban); 41 amplified successfully, and 24 were randomly selected for sequencing (7 natural, 7 rural, 6 suburban, 4 urban).
- DNA was extracted, and the 16S rRNA gene V3–V4 region was amplified with 314F/806R primers and sequenced on an Illumina NovaSeq 6000 system (2 × 250 read length, minimum 100,000 reads per sample). Bioinformatics used cutadapt, DADA2, and the SILVA v138.1 reference database; analyses were performed in R with vegan, phyloseq, DESeq2, and ggplot2.
- Alpha diversity (Observed, Shannon, Simpson) was tested with Wilcoxon tests and FDR < 0.05; beta diversity used Bray-Curtis PCoA and PERMANOVA (1000 permutations); differential abundance used DESeq2 after excluding ASVs seen in fewer than 20% of samples (440 ASVs retained), with an FDR cutoff of 0.01.
Limitations
- Stated: The study did not directly measure diet; dietary differences were inferred from the habitat types where fecal samples were collected.
- Stated: The authors report no statistically significant differences in alpha diversity or overall community structure, despite observable differences in specific taxa.
- Evident from the text: the sequenced sample is small (24 total; urban n = 4), limiting statistical power and generalizability; the design is cross-sectional and relies on fecal samples assumed to belong to red foxes, with no longitudinal or direct dietary data.
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Claims the paper makes
0 Valid · 1 Not valid · 16 Not checked · 24 Own results and interpretations
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
“While Bacillota was the most common phylum in most samples (13 out of 24), its proportion was different between the samples that were collected from different habitats (37.6% in natural, 17.2% in rural, 58.4% in suburban, and 66.1% in urban).”
plainstates an association- 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 dominant genera in the GM of the red fox were Collinsella , Fusobacterium , Faecalibacterium , Escherichia-Shigella , and Blautia”
- Also stated in: § Results · p. 4 · plain
“Collinsella , Fusobacterium , Faecaelibacterium , Escherichia-Shigella , and Blautia were the most common genera in all samples”
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.
- Also stated in: § Results · p. 4 · plain
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
“Faecalibacterium showed higher relative abundance in urban samples (19.5%) than in other samples (4.3% in suburban, 1.6% in rural, and 8.9% in natural)”
plainstates an association- 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 genera Catenibacterium and Peptoclostridium from the Bacillota phylum were more abundant in suburban, and urban samples than in natural and rural samples.”
plainstates an association- 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
“While Bacillota was the most common phylum in most samples (13 out of 24)”
- Also stated in: § Abstract · p. 1 · plain
“with Bacillota being the most common phylum in most samples”
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.
- Also stated in: § Abstract · p. 1 · plain
17 more claims
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Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Rated major: it would touch a result — a value a result rests on, reported and recomputed p-values on opposite sides of the significance level, two passages that conflict with no sign which is right, or a cited work retracted before this paper was published.
In the paper
§ Results · p. 4
“PERMANOVA test, R 2 = 0.186, F = 1.52, P = 0.026”
§ Discussion · p. 6
“we could not find statistically significant differences in alpha diversity (observed species richness, Shannon index, and Simpson evenness) or in the overall community structure (beta diversity) of the prokaryotic communities”
Citations
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
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DADA2: High–resolution sample inference from Illumina amplicon data
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Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
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phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
McMurdie, P. J., & Holmes, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061217 · Cited by 21,322
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2676 · Cited by 9,116
Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., & Glöckner, F. O. (2013) · Nucleic Acids Research · doi:10.1093/nar/gks808 · Cited by 8,850
Cited by
Berezina, Y. A., Bespyatykh, O. Y., Domsky, I., Syutkina, A. S., & Strelyaniy, S. F. (2025) · Agricultural science Euro-North-East · doi:10.30766/2072-9081.2025.26.3.671-679
Domínguez-Sánchez, C., Friesen, O. C., Breiter, C.-J. C., Florko, K. R. N., Gamblin, H. E. L., Nace, A., Petersen, S. D., Pisani-Konert, M., Shuert, C. R., Yurkowski, D. J., et al. (2026) · Royal Society Open Science · doi:10.1098/rsos.251653
Metadata
- Authors
- Akbaba, B., Kucukyildirim, S., & Ünal, H.
- Affiliations
- Hacettepe University (TR)
- Corresponding author
- Akbaba, Burak
- Venue
- Mammal Research
- Published
- 2025-02-07
- Volume
- 70
- Issue
- 2
- Pages
- 175-182
- ISSN
- 2199-241X (ISSN-L)
- 2199-2401
- OpenAlex
- W4407241066
- Semantic Scholar
- 90926edfecbeb56347c73ac8d797f7e19d56e4f7
- Cited by
- 2
- References
- 63
- Citations by year
- 2026: 1 · 2025: 1
- FWCI
- 0.44
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- creativecommons.org/licenses/by/4.0 (tdm)
- creativecommons.org/licenses/by/4.0 (vor)
- Locations
- Mammal Research (publishedVersion, cc-by)
- Research Square (submittedVersion, cc-by)
- Funders
- Hacettepe University
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Nutrition and Physiology
- Keywords
- red fox, gut microbiota, habitat type, urbanization, diet, microbial diversity, Fusobacterium, 16S rRNA gene, wild carnivores, southern Anatolia, human-wildlife interactions
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- CoChat. (2026). Citation check: Comparison of the red fox gut microbiota among different habitat types in southern Anatolia. https://app.cochat.ai/papers/10.1007/s13364-025-00783-4
- The paper
- Akbaba, B., Kucukyildirim, S., & Ünal, H. (2025). Comparison of the red fox gut microbiota among different habitat types in southern Anatolia. Mammal Research. https://doi.org/10.1007/s13364-025-00783-4
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