animals Case Report Faecal Microbiome Transplantation as a Solution to Chronic Enteropathies in Dogs: A Case Study of Beneficial Microbial Evolution Michele Berlanda 1 , Giada Innocente 2 , Barbara Simionati 2 , Barbara Di Camillo 2,3,4 , Sonia Facchin 2,5 , Maria Cecilia Giron 2,6 , Edoardo Savarino 2,5 , Federico Sebastiani 2 , Francesca Fiorio 7 and Ilaria Patuzzi 2, *   Citation: Berlanda, M.; Innocente, G.; Simionati, B.; Di Camillo, B.; Facchin, S.; Giron, M.C.; Savarino, E.; Sebastiani, F.; Fiorio, F.; Patuzzi, I. Faecal Microbiome Transplantation as a Solution to Chronic Enteropathies in Dogs: A Case Study of Beneficial Microbial Evolution. Animals 2021, 11, 1433. https://doi.org/10.3390/ ani11051433 Academic Editors: Robert Li and Stefania Silvi Received: 10 March 2021 Accepted: 13 May 2021 Published: 17 May 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). 1 Department of Animal Medicine, Production and Health, University of Padova, 35020 Padova, Italy 2 Research & Development Division, EuBiome S.r.l., 35129 Padova, Italy 3 Department of Information Engineering, University of Padova, 35131 Padova, Italy 4 Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy 5 Department of Surgery, Oncological and Gastrointestinal Science, University of Padova, 35121 Padova, Italy 6 Pharmacology Building, Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy 7 Clinica Veterinaria Airone, 36015 Vicenza, Italy * Correspondence: ilaria.patuzzi@eubiome.it Simple Summary: Chronic enteropathies are common gastrointestinal diseases in domestic dogs characterised by long-term duration, often impairing quality of life both for pets and owners. It has been demonstrated that the gut microbial community plays a central role in defining the host health status. Indeed, among a variety of biological functions, gut microbiota are involved in the metabolism of nutrients, in training the immune system and in preventing the gastrointestinal ecosystem from being colonised by pathogens. In chronic intestinal diseases, the equilibrium of the gut microbial population is largely impaired, as a consequence of both disease and therapy (e.g., antibiotic treatment). Faecal microbiota transplantation has the aim to restore a balanced microbial population in the patient by simply implanting a healthy gut microbiota derived from a healthy donor to a diseased animal. In doing so, the eubiotic community—and the extensive network of beneficial cross-feeding interactions—are transferred to the receiver’s gut as a whole, favouring the patient to renew a healthy intestinal ecosystem. In this work, we report the encouraging results of a faecal transplantation on a 9-year-old dog suffering from chronic enteropathy for the last 3 years. After the treatment, the dog’s appetite, body weight and vitality were restored, with complete disappearance of gastrointestinal and systemic symptoms. Abstract: Chronic enteropathies (CE) are gastrointestinal diseases that afflict about one in five dogs in Europe. Conventional therapeutic approaches include dietary intervention, pharmacological treat- ment and probiotic supplements. The patient response can be highly variable and the interventions are often not resolutive. Moreover, the therapeutic strategy is usually planned (and gradually cor- rected) based on the patient’s response to empirical treatment, with few indirect gut health indicators useful to drive clinicians’ decisions. The ever-diminishing cost of high-throughput sequencing (HTS) allows clinicians to directly follow and characterise the evolution of the whole gut microbial commu- nity in order to highlight possible weaknesses. In this framework, faecal microbiome transplantation (FMT) is emerging as a feasible solution to CE, based on the implant of a balanced, eubiotic microbial community from a healthy donor to a dysbiotic patient. In this study, we report the promising results of FMT carried out in a 9-year-old dog suffering from CE for the last 3 years. The patient underwent a two-cycle oral treatment of FMT and the microbiota evolution was monitored by 16S rRNA gene sequencing both prior to FMT and after the two administrations. We evaluated the variation of microbial composition by calculating three different alpha diversity indices and compared the patient and donor data to a healthy control population of 94 dogs. After FMT, the patient’s microbiome and clinical parameters gradually shifted to values similar to those observed in healthy dogs. Symptoms disappeared during a follow-up period of six months after the second FMT. We believe that this Animals 2021, 11, 1433. https://doi.org/10.3390/ani11051433 https://www.mdpi.com/journal/animals