223b354f02301e7c40d763d4c2c21ae5 pmc_9913788.pdf 419a04709b6dbcdc28cd6fb46df0c3cd9febe75b pmc_9913788.pdf 92e740a4f3139fcae1ffa067537d7726eb9cea528a337ca4df044532ac82bd31 pmc_9913788.pdf Title: Characterization of the Fecal and Mucosa-Associated Microbiota in Dogs with Chronic Inflammatory Enteropathy Subject: Canine chronic inflammatory enteropathy implicates multifactorial pathogenesis where immunological dysregulation and gut microbiota changes have a central role. Most sequencing-based taxonomic studies have been focused on the fecal microbiota. However, the analysis of these samples does not provide complete information regarding the composition of the small intestine affected by this canine disease. Therefore, in this study, we aimed to characterize the intestinal bacterial microbiota in dogs with inflammatory bowel disease (IBD) (n = 34) by means of duodenal biopsies and fecal samples collected at the time of the diagnosis and to compare those to a group of healthy dogs (n = 12) using the 16S ribosomal RNA (16S rRNA) gene-targeted sequencing (Illumina MiSeq platform). Our study showed that IBD dogs presented differences in the fecal bacterial communities when compared with healthy dogs, with a lower relative abundance of Prevotellaceae (p = 0.005), Prevotella (p = 0.002), and Prevotellaceae Ga6A1 group (0.006); Erysipelotrichales (p = 0.019), Candidatus Stoquefichus (p < 0.001), Erysipelotrichaceae (p = 0.011), and Allobaculum (p = 0.003); Lachnospiraceae NK4A136 group (p = 0.015), Sellimonas (p = 0.042), Oscillospirales (p = 0.037), Oscillospiraceae UCG–005 (p < 0.001), Faecalibacterium (p = 0.028), and Fournierella (p = 0.034); Acidaminococcales, Acidaminococcaceae, and Phascolarctobacterium (p = 0.001); Aeromonadales (p = 0.026), Succinivibrionaceae (p = 0.037), and Succinivibrio (p = 0.031). On the other hand, a higher relative abundance of Enterococcaceae (Enterococcus; p = 0.003), Streptococcaceae (Streptococcus, p = 0.021), Enterobacterales (p = 0.027), Enterobacteriaceae (p = 0.008), and Escherichia–Shigella (p = 0.011) was detected. Moreover, when evaluating –diversity, the dogs with IBD showed lower diversity in terms of richness and abundance of species (observed species [p = 0.031] and Shannon index [p = 0.039]). Furthermore, fecal microbiota in dogs with IBD was significantly different from healthy dogs (p = 0.006). However, only a few taxa relative abundance shifts (lower Rubrobacteria, Rubrobacterales, Rubrobacteriaceae, and Rubrobacter [p = 0.002]; Cyanobacteria [p = 0.010], Vampirivibrionia, Obscuribacterales, and Obscuribacteraceae [p = 0.005]; Neisseriaceae [p = 0.004] and Conchiformibius [p = 0.003]) were observed when assessing duodenal-associated microbiota of dogs with IBD. Thus, even if the bowel inflammation mainly affects the small intestine in the IBD-affected dogs of the study, fecal specimens may constitute a better sample due not only to their easy availability but also in terms of searching for bacterial taxa as biomarkers for canine IBD. The use of different diets in the study can also have a partial influence on the microbiota composition. Future studies encompassing multi-omics approaches should evaluate the functionality in both levels to unravel the pathophysiology of canine IBD. Keywords: dog; IBD; chronic enteropathy; gut microbiota; bacterial diversity; bacterial composition; 16S rRNA Author: David Díaz-Regañón, Mercedes García-Sancho, Alejandra Villaescusa, Ángel Sainz, Beatriz Agulla, Mariana Reyes-Prieto, Antonio Rodríguez-Bertos and Fernando Rodríguez-Franco Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Sat Jan 28 14:35:50 2023 CET ModDate: Sat Jan 28 14:41:46 2023 CET Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 22 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 1472953 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- CMFVHJ+VnURWPalladioL Type 1 Custom yes yes no 10 0 VVSYYB+EURM10 Type 1 Builtin yes yes no 15 0 VMZCPY+URWPalladioL-Bold Type 1 Custom yes yes no 19 0 HCIDLG+URWPalladioL-Roma Type 1 Custom yes yes no 24 0 YWNVUB+URWPalladioL-Ital Type 1 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CID TrueType Identity-H yes yes yes 179 0 BCDEEE+PalatinoLinotype-Bold TrueType WinAnsi yes yes no 198 0 BCDFEE+PalatinoLinotype-Roman TrueType WinAnsi yes yes no 202 0 BCDGEE+PalatinoLinotype-Italic TrueType WinAnsi yes yes no 206 0 BCDHEE+PalatinoLinotype-Roman CID TrueType Identity-H yes yes yes 210 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2023-03-11 02:34:16 CET RepresentationInformation: pmc_9913788.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2023-03-03 02:15:53 CET Size: 1472953 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 515 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@44c8afef Item: Title: Materials and Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7b69c6ba Children: Item: Title: Dogs Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@46daef40 Children: Item: Title: Healthy Control (HC) Dogs Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@12f41634 Item: Title: IBD Dogs Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@13c27452 Item: Title: Sample Collection, Upper GI Endoscopy, and Histopathological Evaluation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@262b2c86 Item: Title: DNA Extraction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@371a67ec Item: Title: Library Preparation and Sequencing Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5ed828d Item: Title: Bioinformatic Analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@50d0686 Item: Title: Statistical Analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a3d45bd Item: Title: Results Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1e7c7811 Children: Item: Title: Dogs Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77ec78b9 Item: Title: Endoscopic and Histopathological Evaluation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1a3869f4 Item: Title: 16S-rRNA Sequencing Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@a38d7a3 Children: Item: Title: Duodenal Biopsy Specimens Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77f99a05 Item: Title: Fecal Microbiota Communities Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@63440df3 Item: Title: Duodenal Biopsies vs. Fecal Samples Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3aeaafa6 Item: Title: Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@76a3e297 Item: Title: Conclusions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4d3167f4 Item: Title: References Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@ed9d034 Info: Title: Characterization of the Fecal and Mucosa-Associated Microbiota in Dogs with Chronic Inflammatory Enteropathy Author: David Díaz-Regañón, Mercedes García-Sancho, Alejandra Villaescusa, Ángel Sainz, Beatriz Agulla, Mariana Reyes-Prieto, Antonio Rodríguez-Bertos and Fernando Rodríguez-Franco Subject: Canine chronic inflammatory enteropathy implicates multifactorial pathogenesis where immunological dysregulation and gut microbiota changes have a central role. Most sequencing-based taxonomic studies have been focused on the fecal microbiota. However, the analysis of these samples does not provide complete information regarding the composition of the small intestine affected by this canine disease. Therefore, in this study, we aimed to characterize the intestinal bacterial microbiota in dogs with inflammatory bowel disease (IBD) (n = 34) by means of duodenal biopsies and fecal samples collected at the time of the diagnosis and to compare those to a group of healthy dogs (n = 12) using the 16S ribosomal RNA (16S rRNA) gene-targeted sequencing (Illumina MiSeq platform). Our study showed that IBD dogs presented differences in the fecal bacterial communities when compared with healthy dogs, with a lower relative abundance of Prevotellaceae (p = 0.005), Prevotella (p = 0.002), and Prevotellaceae Ga6A1 group (0.006); Erysipelotrichales (p = 0.019), Candidatus Stoquefichus (p < 0.001), Erysipelotrichaceae (p = 0.011), and Allobaculum (p = 0.003); Lachnospiraceae NK4A136 group (p = 0.015), Sellimonas (p = 0.042), Oscillospirales (p = 0.037), Oscillospiraceae UCG 005 (p < 0.001), Faecalibacterium (p = 0.028), and Fournierella (p = 0.034); Acidaminococcales, Acidaminococcaceae, and Phascolarctobacterium (p = 0.001); Aeromonadales (p = 0.026), Succinivibrionaceae (p = 0.037), and Succinivibrio (p = 0.031). On the other hand, a higher relative abundance of Enterococcaceae (Enterococcus; p = 0.003), Streptococcaceae (Streptococcus, p = 0.021), Enterobacterales (p = 0.027), Enterobacteriaceae (p = 0.008), and Escherichia Shigella (p = 0.011) was detected. Moreover, when evaluating  diversity, the dogs with IBD showed lower diversity in terms of richness and abundance of species (observed species [p = 0.031] and Shannon index [p = 0.039]). Furthermore, fecal microbiota in dogs with IBD was significantly different from healthy dogs (p = 0.006). However, only a few taxa relative abundance shifts (lower Rubrobacteria, Rubrobacterales, Rubrobacteriaceae, and Rubrobacter [p = 0.002]; Cyanobacteria [p = 0.010], Vampirivibrionia, Obscuribacterales, and Obscuribacteraceae [p = 0.005]; Neisseriaceae [p = 0.004] and Conchiformibius [p = 0.003]) were observed when assessing duodenal-associated microbiota of dogs with IBD. Thus, even if the bowel inflammation mainly affects the small intestine in the IBD-affected dogs of the study, fecal specimens may constitute a better sample due not only to their easy availability but also in terms of searching for bacterial taxa as biomarkers for canine IBD. The use of different diets in the study can also have a partial influence on the microbiota composition. Future studies encompassing multi-omics approaches should evaluate the functionality in both levels to unravel the pathophysiology of canine IBD. 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