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Metataxonomic and histopathological study of rabbit epizootic enteropathy in Mexico.

Pu�n-Pel�ez, Xiao-Haitzi Daniel; McEwan, Neil Ross; G�mez-Soto, Jos� Guadalupe; �lvarez-Mart�nez, Roberto Carlos; Olvera-Ram�rez, Andrea Margarita


Xiao-Haitzi Daniel Pu�n-Pel�ez

Neil Ross McEwan

Jos� Guadalupe G�mez-Soto

Roberto Carlos �lvarez-Mart�nez

Andrea Margarita Olvera-Ram�rez


Epizootic rabbit enteropathy (ERE) affects young rabbits and represents 32% of the enteropathies in rabbit production farms in Mexico. The etiology of this syndrome has not been clarified yet. A metataxonomic and histopathology study of ERE was carried out to compare the gastrointestinal microbiota and histopathological lesions of healthy and positive-ERE rabbits. The metataxonomic study was done using an Illumina MiSeq (MiSeq® system, Illumina, San Diego California, USA) massive segmentation platform, and a Divisive Amplicon Denoising Algorithm 2 (DADA2 algorithm) was used to obtain Shannon and Simpson diversity indices as well as the relative abundance of the identified communities. For the histopathological study, paraffin sections of the cecum, ileo-cecal valve, and colon were stained with eosin and hematoxylin. AxioVision 4.9 software (Carl Zeiss MicroImaging GmbH, Jena, Germany) was used to measure the crypt depths. Statistical analysis was done using PERMANOVA analysis for the metataxonomic study and ANOVA for the histopathology study. Histopathologic analysis showed smaller sizes of crypts in the colon of ERE rabbits. Differences were observed in the diversity and abundance of the gastrointestinal microbiota between the analyzed groups. The genus Clostridium and the species Cloacibacillus porcorum and Akkermansia muciniphila were associated with ERE. The results obtained from this study can provide information for future clarification of the etiology and proposals of effective treatments.


PUÓN-PELÁEZ, X.-H.D., MCEWAN, N.R., GÓMEZ-SOTO, J.G., ÁLVAREZ-MARTÍNEZ, R.C., and OLVERA-RAMÍREZ, A.M. 2020. Metataxonomic and histopathological study of rabbit epizootic enteropathy in Mexico. Animals [online], 10(6), article ID 936. Available from:

Journal Article Type Article
Acceptance Date May 24, 2020
Online Publication Date May 28, 2020
Publication Date Jun 30, 2020
Deposit Date Jun 12, 2020
Publicly Available Date Jun 12, 2020
Journal Animals
Electronic ISSN 2076-2615
Publisher MDPI
Peer Reviewed Peer Reviewed
Volume 10
Issue 6
Article Number 936
Keywords Rabbits; ERE; Etiology
Public URL


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