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Peer-reviewedCC BY 4.0The Veterinary Quarterly

Fecal microbiome-based clustering identifies distinct disease subtypes with differing metabolomic profiles and treatment outcomes in canine chronic enteropathy

  • Junjie Li1
  • Takahiro Aoki2
  • Shiho Miyata1
  • Atsushi Fukaya3
  • Yuhei Hayashi3
  • Hidehiro Hirao3
  • Shin Yoshimoto2
  • Kentaro Nagaoka1
  1. 1Laboratory of Veterinary Physiology, Cooperative Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
  2. 2Biotics Research Institute, Morinaga Milk Industry Co., Ltd., Kanagawa, Japan
  3. 3Japan Animal Referral Medical Center Kawasaki, Kanagawa, Japan
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Abstract

Canine chronic enteropathy (CE) is a heterogeneous disorder with variable clinical outcomes. We aimed to identify fecal microbiome and metabolomic signatures associated with CE severity and treatment outcomes. Fecal samples from dogs with CE (n = 56), acute diarrhea (n = 8), and healthy controls (n = 126) were analyzed by 16S rRNA gene sequencing and GC-MS-based untargeted metabolomics. CE dogs exhibited significantly reduced microbial diversity compared with the other groups, and unsupervised Partitioning Around Medoids clustering identified two microbiome clusters within the CE cohort. Cluster 2 was characterized by dysbiosis, with enrichment of Streptococcus, Enterococcus, and Klebsiella, and depletion of short-chain fatty acid producers, including Fusobacterium and Blautia. Among dogs with baseline Canine Chronic Enteropathy Clinical Activity Index (CCECAI) > 3, 10 of 12 Cluster 1 dogs (83.3%) achieved remission (CCECAI ≤ 3) after treatment, compared with 7 of 18 Cluster 2 dogs (38.9%; p = 0.0256). CCECAI scores decreased significantly after treatment in Cluster 1 (p = 0.0005) but not in Cluster 2 (p = 0.077). Fecal propanoic acid and kynurenic acid levels also differed between clusters. These findings suggest that gut microbiota and associated metabolites may contribute to differences in CE severity and treatment outcomes.

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Cite

BibTeXRIS
BibTeX
@article{li2026fecal,
  title = {{Fecal microbiome-based clustering identifies distinct disease subtypes with differing metabolomic profiles and treatment outcomes in canine chronic enteropathy}},
  author = {Junjie Li and Takahiro Aoki and Shiho Miyata and Atsushi Fukaya and Yuhei Hayashi and Hidehiro Hirao and Shin Yoshimoto and Kentaro Nagaoka},
  journal = {The Veterinary Quarterly},
  year = {2026},
  month = oct,
  doi = {10.1080/01652176.2026.2744638},
  url = {https://doi.org/10.1080/01652176.2026.2744638},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Fecal microbiome-based clustering identifies distinct disease subtypes with differing metabolomic profiles and treatment outcomes in canine chronic enteropathy
AU  - Junjie Li
AU  - Takahiro Aoki
AU  - Shiho Miyata
AU  - Atsushi Fukaya
AU  - Yuhei Hayashi
AU  - Hidehiro Hirao
AU  - Shin Yoshimoto
AU  - Kentaro Nagaoka
PY  - 2026
DA  - 2026/10/29
JO  - The Veterinary Quarterly
DO  - 10.1080/01652176.2026.2744638
UR  - https://doi.org/10.1080/01652176.2026.2744638
AB  - Canine chronic enteropathy (CE) is a heterogeneous disorder with variable clinical outcomes. We aimed to identify fecal microbiome and metabolomic signatures associated with CE severity and treatment outcomes. Fecal samples from dogs with CE (n = 56), acute diarrhea (n = 8), and healthy controls (n = 126) were analyzed by 16S rRNA gene sequencing and GC-MS-based untargeted metabolomics. CE dogs exhibited significantly reduced microbial diversity compared with the other groups, and unsupervised Partitioning Around Medoids clustering identified two microbiome clusters within the CE cohort. Cluster 2 was characterized by dysbiosis, with enrichment of Streptococcus, Enterococcus, and Klebsiella, and depletion of short-chain fatty acid producers, including Fusobacterium and Blautia. Among dogs with baseline Canine Chronic Enteropathy Clinical Activity Index (CCECAI) > 3, 10 of 12 Cluster 1 dogs (83.3%) achieved remission (CCECAI ≤ 3) after treatment, compared with 7 of 18 Cluster 2 dogs (38.9%; p = 0.0256). CCECAI scores decreased significantly after treatment in Cluster 1 (p = 0.0005) but not in Cluster 2 (p = 0.077). Fecal propanoic acid and kynurenic acid levels also differed between clusters. These findings suggest that gut microbiota and associated metabolites may contribute to differences in CE severity and treatment outcomes.
SN  - 0165-2176
SN  - 1875-5941
ER  -