Impact of specimen type on findings for bacterial composition within the intestinal tract of dogs and cats with and without chronic enteropathy

Stacie C. Summers From the Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523. Dr. Summers' present address is the College of Veterinary Medicine, Oregon State University, Corvallis, OR 97330.

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Allysa Galloni From the Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523. Dr. Summers' present address is the College of Veterinary Medicine, Oregon State University, Corvallis, OR 97330.

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Craig B. Webb From the Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523. Dr. Summers' present address is the College of Veterinary Medicine, Oregon State University, Corvallis, OR 97330.

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DOI:
https://doi.org/10.2460/ajvr.82.6.494
Volume/Issue:
Volume 82: Issue 6
Online Publication Date:
Jun 2021
Restricted access
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Abstract

OBJECTIVE

To compare bacterial diversity and community composition among fecal, rectal swab, and colonic mucosal biopsy specimens from dogs and cats with and without chronic enteropathy (CE).

ANIMALS

9 healthy dogs, 8 dogs with CE, 8 healthy cats, and 9 cats with CE.

PROCEDURES

In a cross-sectional study design, fecal, rectal swab, and colonic mucosal biopsy specimens were obtained by colonoscopy from healthy dogs and dogs and cats with CE. Fecal and rectal swab specimens were collected from healthy cats. Genomic DNA was extracted, the 16S rRNA V4 gene region was amplified, and sequencing was performed by use of primers 515F to 806R on a paired-end platform.

RESULTS

For healthy dogs and dogs and cats with CE, bacterial diversity based on the Chao1 estimate of total species richness was higher for colonic mucosal biopsy specimens than for fecal specimens. Analysis of similarities by use of the Bray-Curtis dissimilarity index revealed that the bacterial communities captured in rectal swab specimens were similar to those captured in fecal specimens for healthy dogs and dogs with CE and similar to those captured in colonic mucosal biopsy specimens for both dog groups and cats with CE.

CONCLUSIONS AND CLINICAL RELEVANCE

Rectal swab and colonic biopsy specimens were successfully used to characterize the bacteriome of the intestinal tract in dogs and cats by 16S rRNA gene sequencing. Although the specimen types evaluated in this study were not interchangeable in results, rectal swab specimens were practical to collect from dogs and cats to study bacterial composition within the intestinal tract and may provide an alternative to colonic mucosal biopsy and fecal specimens.

Abstract

OBJECTIVE

To compare bacterial diversity and community composition among fecal, rectal swab, and colonic mucosal biopsy specimens from dogs and cats with and without chronic enteropathy (CE).

ANIMALS

9 healthy dogs, 8 dogs with CE, 8 healthy cats, and 9 cats with CE.

PROCEDURES

In a cross-sectional study design, fecal, rectal swab, and colonic mucosal biopsy specimens were obtained by colonoscopy from healthy dogs and dogs and cats with CE. Fecal and rectal swab specimens were collected from healthy cats. Genomic DNA was extracted, the 16S rRNA V4 gene region was amplified, and sequencing was performed by use of primers 515F to 806R on a paired-end platform.

RESULTS

For healthy dogs and dogs and cats with CE, bacterial diversity based on the Chao1 estimate of total species richness was higher for colonic mucosal biopsy specimens than for fecal specimens. Analysis of similarities by use of the Bray-Curtis dissimilarity index revealed that the bacterial communities captured in rectal swab specimens were similar to those captured in fecal specimens for healthy dogs and dogs with CE and similar to those captured in colonic mucosal biopsy specimens for both dog groups and cats with CE.

CONCLUSIONS AND CLINICAL RELEVANCE

Rectal swab and colonic biopsy specimens were successfully used to characterize the bacteriome of the intestinal tract in dogs and cats by 16S rRNA gene sequencing. Although the specimen types evaluated in this study were not interchangeable in results, rectal swab specimens were practical to collect from dogs and cats to study bacterial composition within the intestinal tract and may provide an alternative to colonic mucosal biopsy and fecal specimens.

Supplementary Materials

    • Supplementary Figure S1 (PDF 154 kb)
    • Supplementary Figure S2 (PDF 534 kb)
    • Supplementary Table S1 (PDF 622 kb)

Contributor Notes

Address correspondence to Dr. Summers (stacie.summers@oregonstate.edu).
Cover American Journal of Veterinary Research
American Journal of Veterinary Research
Publication Date:
01 Jun 2021
  • 1.

    Suchodolski JS. Diagnosis and interpretation of intestinal dysbiosis in dogs and cats. Vet J 2016;215:30–37.

  • 2.

    Bassis CM, Moore NM, Lolans K, et al. Comparison of stool versus rectal swab samples and storage conditions on bacterial community profiles. BMC Microbiol 2017;17:78.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 3.

    Budding AE, Grasman ME, Eck A, et al. Rectal swabs for analysis of the intestinal microbiota. PLoS One 2014;9:e101344.

  • 4.

    Jones RB, Zhu X, Moan E, et al. Inter-niche and inter-individual variation in gut bacterial community assessment using stool, rectal swab, and mucosal samples. Sci Rep 2018;8:4139.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 5.

    Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010;7:335–336.

  • 6.

    Edgar RC, Haas BJ, Clemente JC, et al. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011;27:2194–2200.

  • 7.

    Haas BJ, Gevers D, Earl AM, et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 2011;21:494–504.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 8.

    Edgar RC. UPARSE: highly accurate OTU sequences from bacterial amplicon reads. Nat Methods 2013;10:996–998.

  • 9.

    Schloss PD, Westcott SL, Ryabin T, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009;75:7537–7541.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 10.

    Wang Q, Garrity GM, Tiedje JM, et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007;73:5261–5267.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 11.

    Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013;41:D590–D596.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 12.

    Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792–1797.

  • 13.

    Biehl LM, Garzetti D, Farowski F, et al. Usability of rectal swabs for bacteriome sampling in a cohort study of hematological and oncological patients. PLoS One 2019;14:e0215428.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 14.

    Fair K, Dunlap DG, Fitch A, et al. Rectal swabs from critically ill patients provide discordant representations of the gut bacteriome compared to stool samples. MSphere 2019;4:e00358-e19.

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 15.

    Durbán A, Abellan JJ, Jimenez-Hernandez N, et al. Assessing gut bacterial diversity from feces and rectal mucosa. Microb Ecol 2011;61:123–133.

  • 16.

    Zoetendal EG, von Wright A, Vilpponen-Salmela T, et al. Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol 2002;68:3401–3407.

    • Crossref
    • Search Google Scholar
    • Export Citation

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