README
----- GENERAL INFORMATION -----
DATA TITLE: Glucocorticoid effects on mucosal microbiota in healthy dogs and dogs with IBD

PROJECT TITLE: Glucocorticoid and dietary effects on mucosal microbiota in canine 
inflammatory bowel disease

DATA ABSTRACT: The mucosal microbiota from endoscopic biopsies of inflammatory bowel disease (IBD) dogs and healthy controls (HC; n=15 dogs) was evaluated by fluorescence in situ hybridization (FISH) targeting the 16S rRNA genes of total bacteria and bacterial species using a seven probe array. We also used immunohistochemical (IHC) techniques to evaluate the impact of steroid therapy on mucosal apical junction protein (AJP) expression in dogs with IBD.

AUTHORS: 
	Author: Todd Atherly
	Institution: Iowa State University

	Author: Giacomo Rossi
	Institution: University of Camerino

	Author: Robin White
	Institution: Iowa State University

	Author: Yeon-Jung Seo
	Institution: Iowa State University

	Author: Chong Wang
	Institution: Iowa State University

	Author: Mark Ackermann
	Institution: Oregon State University

	Author: Mary Breuer
	Institution: Iowa State University

	Author: Karin Allenspach
	Institution: Iowa State University

	Author: Jonathan P. Mochel
	Institution: Iowa State University

	Corresponding author: Albert E. Jergens
	ORCID: 0000-0003-2375-8685
	Institution: Iowa State University
	Email:	ajergens@iastate.edu

----- ASSOCIATED PUBLICATIONS -----
Relationship of the mucosal microbiota to gastrointestinal inflammation and small cell intestinal lymphoma in cats.
	Garraway K, Johannes CM, Bryan A, Peauroi J, Rossi G, Zhang M, Wang C, Allenspach K, Jergens AE. 
	J Vet Intern Med. 2018 Sep;32(5):1692-1702. doi: 10.1111/jvim.15291. Epub 2018 Aug 7. PMID: 30084202. https://www.ncbi.nlm.nih.gov/pubmed/30084202 

Randomized, controlled trial evaluating the effect of multi-strain probiotic on the mucosal microbiota in canine idiopathic inflammatory bowel disease.
	White R, Atherly T, Guard B, Rossi G, Wang C, Mosher C, Webb C, Hill S, Ackermann M, Sciabarra P, Allenspach K, Suchodolski J, Jergens AE. 
	Gut Microbes. 2017 Sep 3;8(5):451-466. 
	doi: 10.1080/19490976.2017.1334754. Epub 2017 Jul 5. PMID: 28678609. https://www.ncbi.nlm.nih.gov/pubmed/28678609

Alterations of the Ileal and Colonic Mucosal Microbiota in Canine Chronic Enteropathies.
	Cassmann E, White R, Atherly T, Wang C, Sun Y, Khoda S, Mosher C, Ackermann M, Jergens A. 
	PLoS One. 2016 Feb 3;11(2):e0147321. doi: 10.1371/journal.pone.0147321. 
	eCollection 2016. PMID: 26840462. https://www.ncbi.nlm.nih.gov/pubmed/26840462 

Fluorescence in situ hybridization confirms clearance of visible Helicobacter spp. associated with gastritis in dogs and cats.
	Jergens AE, Pressel M, Crandell J, Morrison JA, Sorden SD, Haynes J, Craven M, Baumgart M, Simpson KW.
	J Vet Intern Med. 2009 Jan-Feb;23(1):16-23. doi: 10.1111/j.1939-1676.2008.0211.x. 
	Erratum in: J Vet Intern Med. 2009 Mar-Apr;23(2):443.
	PMID:19175715. https://www.ncbi.nlm.nih.gov/pubmed/19175715

----- COLLECTION INFORMATION:----- 
Time period(s):  2015-2016
Location(s): Iowa State University, Small Animal Teaching Hospital
	
----- FILE DIRECTORY -----
There are 4 files containing the raw data for FISH bacterial counts in ileal/colonic mucosa of 
healthy dogs and dogs with IBD (2 files); there is raw data for the number of mucosal cells in 
healthy dogs and dogs with IBD expressing apical junction proteins (2 files).

----- DATA FILE LIST----- 
File_1_Control_ dogs_FISH_steroid_trial.csv = FISH counts in healthy dogs by individual probe
File_2_IBD_dogs_FISH_steroid_trial.csv = FISH counts in dogs with IBD by individual probe.csv.	
File_3_Apical _junction_proteins_healthy_dogs.csv = Apical junction proteins in healthy dogs
File_4_Apical _junction_proteins_IBD dogs_ pre_versus_post_steroids.csv = Apical junction proteins in dogs with IBD pre- vs. post-treatment

----- CODEBOOK -----  
See file: Codebook_Jergens_FISH_steroid_effects.csv

----- DATA COLLECTION METHODS ----- 
Endoscopic biopsies of the ileum and colon were obtained and evaluated by FISH for their content of mucosal bacteria. Seven bacterial groups were identified using this technique and standard assays. Images of fluorescing bacteria were captured using a fluorescent microscope. The number of cells expressing apical junction proteins E-cadherin, occludin, claudin-2 and zonulin were identified using IHC and enumerated in standardized mucosal areas.

----- DATA PROCESSING METHODS ----- 
Showing raw data for FISH and AJP expression.

------- SOFTWARE -------
Metamorph software was used to enumerate mucosal bacteria identified by FISH with images 
captured using fluorescence microscopy.

------- EQUIPMENT -------
FISH analysis performed using fluorescent microscopy.

------- Licensing -------
This work is licensed under a Creative Commons Attribution 4.0 International License. 
http://creativecommons.org/licenses/by/4.0/