1
|
Mady EA, Osuga H, Toyama H, El-Husseiny HM, Inoue R, Murase H, Yamamoto Y, Nagaoka K. Relationship between the components of mare breast milk and foal gut microbiome: shaping gut microbiome development after birth. Vet Q 2024; 44:1-9. [PMID: 38733121 PMCID: PMC11089936 DOI: 10.1080/01652176.2024.2349948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
The gut microbiota (GM) is essential for mammalian health. Although the association between infant GM and breast milk (BM) composition has been well established in humans, such a relationship has not been investigated in horses. Hence, this study was conducted to analyze the GM formation of foals during lactation and determine the presence of low-molecular-weight metabolites in mares' BM and their role in shaping foals' GM. The fecal and BM samples from six pairs of foals and mares were subjected to 16S ribosomal RNA metagenomic and metabolomic analyses, respectively. The composition of foal GM changed during lactation time; hierarchical cluster analysis divided the fetal GM into three groups corresponding to different time points in foal development. The level of most metabolites in milk decreased over time with increasing milk yield, while threonic acid and ascorbic acid increased. Further analyses revealed gut bacteria that correlated with changes in milk metabolites; for instance, there was a positive correlation between Bacteroidaceae in the foal's gut microbiota and serine/glycine in the mother's milk. These findings help improve the rearing environment of lactating horses and establish artificial feeding methods for foals.
Collapse
Affiliation(s)
- Eman A. Mady
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Department of Animal Hygiene, Behavior, and Management, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Elqaliobiya, Egypt
| | - Haruna Osuga
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Haruka Toyama
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hussein M. El-Husseiny
- Laboratory of Veterinary Surgery, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Ryo Inoue
- Laboratory of Animal Science, Department of Applied Biological Science, Setsunan University, Osaka, Japan
| | - Harutaka Murase
- Hidaka Training and Research Center, Japan Racing Association, Hokkaido, Japan
| | - Yuki Yamamoto
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Kentaro Nagaoka
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
| |
Collapse
|
2
|
Toomer OT, Redhead AK, Vu TC, Santos F, Malheiros R, Proszkowiec-Weglarz M. The effect of peanut skins as a natural antimicrobial feed additive on ileal and cecal microbiota in broiler chickens inoculated with Salmonella enterica Enteritidis. Poult Sci 2024; 103:104159. [PMID: 39153270 DOI: 10.1016/j.psj.2024.104159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/25/2024] [Accepted: 07/29/2024] [Indexed: 08/19/2024] Open
Abstract
The consumption of poultry products contaminated with Salmonella species is one of the most common causes of Salmonella infections. In vivo studies demonstrated the potential application of peanut skins (PS) as an antimicrobial poultry feed additive to help mitigate the proliferation of Salmonella in poultry environments. Tons of PS, a waste by-product of the peanut industry, are generated and disposed in U.S. landfills annually. Peanut skins and extracts have been shown to possess antimicrobial and antioxidant properties. Hence, we aimed to determine the effect of PS as a feed additive on the gut microbiota of broilers fed a control or PS supplemented (4% inclusion) diet and inoculated with or without Salmonella enterica Enteritidis (SE). At hatch 160 male broilers were randomly assigned to 4 treatments: 1) CON-control diet without SE, 2) PS-PS diet without SE, 3) CONSE-control diet with SE, 4) PSSE-PS diet with SE. On d 3, birds from CONSE and PSSE treatments were inoculated with 4.2 × 109 CFU/mL SE. At termination (4 wk), 10 birds/treatment were euthanized and ileal and cecal contents were collected for 16S rRNA analysis using standard methodologies. Sequencing data were analyzed using QIIME2. No effect of PS or SE was observed on ileal alpha and beta diversity, while evenness, richness, number of amplicon sequence variants (ASV) and Shannon, as well as beta diversity were significantly (P < 0.05) affected in ceca. Similarly, more differentially abundant taxa between treatment groups were identified in ceca than in ileum. However, more microbiota functional changes, based on the PICRUST2 prediction, were observed in ileum. Overall, relatively minor changes in microbiota were observed during SE infection and PS treatment, suggesting that PS addition may not attenuate the SE proliferation, as shown previously, through modulation of microbiota in gastrointestinal tract. However, while further studies are warranted, these results suggest that PS may potentially serve as a functional feed additive for poultry for improvement of animal health.
Collapse
Affiliation(s)
- Ondulla T Toomer
- Food Science & Market Quality and Handling Research Unit, ARS, USDA, Raleigh, NC 27695, USA.
| | - Adam K Redhead
- Math and Science Department, Andrew College, Cuthbert, GA 39840, USA
| | - Thien C Vu
- Food Science & Market Quality and Handling Research Unit, ARS, USDA, Raleigh, NC 27695, USA
| | - Fernanda Santos
- Food, Bioprocessing and Nutrition Sciences Dept., NC State University, Raleigh, NC 27695, USA
| | - Ramon Malheiros
- Prestage Department of Poultry Science, NC State University, Raleigh, NC 27695, USA
| | | |
Collapse
|
3
|
Raspa F, Chessa S, Bergero D, Sacchi P, Ferrocino I, Cocolin L, Corvaglia MR, Moretti R, Cavallini D, Valle E. Microbiota characterization throughout the digestive tract of horses fed a high-fiber vs. a high-starch diet. Front Vet Sci 2024; 11:1386135. [PMID: 38807937 PMCID: PMC11130486 DOI: 10.3389/fvets.2024.1386135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/29/2024] [Indexed: 05/30/2024] Open
Abstract
Introduction Diet is one of the main factors influencing the intestinal microbiota in horses, yet a systematic characterization of the microbiota along the length of the digestive tract in clinically healthy horses, homogenous for age and breed and receiving a specific diet is lacking. Methods The study used 16S rRNA amplicon sequencing to characterize the microbiota of the intestinal tracts of 19 healthy Bardigiano horses of 14.3 ± 0.7 months of age fed one of two diets. Nine horses received a high-starch diet (HS), and ten horses received a high-fiber diet (HF). After 129 days, the horses were slaughtered, and samples were collected from the different intestinal tract compartments. Results and discussion The microbiota alpha diversity indices were lower in the caecum, pelvic flexure and right dorsal colon of the horses fed the HS diet (False Discovery Rate, FDR < 0.05). The values of beta diversity indicated significant compositional differences between the studied intestinal tract compartments according to the diet received (FDR < 0.05). At the lower taxonomic level (genus or family), the HS diet was associated with a higher relative frequency of Enterobacteriaceae within the small intestine (jejunum and duodenum) (FDR < 0.05). Within the hindgut (caecum and sternal flexure), the HS diet was associated with lower relative frequencies (i.e., a smaller core community) of bacteria belonging to Fibrobacteraceae and Prevotellaceae (FDR < 0.05). Moreover, horses fed the HS diet displayed a higher relative abundance of Streptococcus in the caecum (FDR < 0.05) and Fusobacterium in the sternal flexure (FDR < 0.05), both of which are pathogenic bacteria responsible for inflammation diseases. Samples collected from the pelvic flexure and rectum of horses fed the HS diet showed significantly higher relative frequencies of Succinivibrionaceae (FDR < 0.05) - amylolytic bacteria associated with acidosis. The relative frequencies of the Lachnospiraceae and Ruminococcaceae were lower in the feces collected from the rectum of horses receiving the HS diet vs. HF diet, indicating smaller core communities of these bacteria (FDR < 0.05). Fibrous diets should be promoted to prevent dysbiosis of the microbiota associated with high-starch diet.
Collapse
Affiliation(s)
- Federica Raspa
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
| | - Stefania Chessa
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
| | - Domenico Bergero
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
| | - Paola Sacchi
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
| | - Ilario Ferrocino
- Department of Agricultural, Forestry and Food Science, University of Turin, Grugliasco, Italy
| | - Luca Cocolin
- Department of Agricultural, Forestry and Food Science, University of Turin, Grugliasco, Italy
| | - Maria Rita Corvaglia
- Department of Agricultural, Forestry and Food Science, University of Turin, Grugliasco, Italy
| | - Riccardo Moretti
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
| | - Damiano Cavallini
- Department of Veterinary Sciences, University of Bologna, Bologna, Italy
| | - Emanuela Valle
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
| |
Collapse
|
4
|
Niu H, Zhou M, Zogona D, Xing Z, Wu T, Chen R, Cui D, Liang F, Xu X. Akkermansia muciniphila: a potential candidate for ameliorating metabolic diseases. Front Immunol 2024; 15:1370658. [PMID: 38571945 PMCID: PMC10987721 DOI: 10.3389/fimmu.2024.1370658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024] Open
Abstract
Metabolic diseases are comprehensive disease based on obesity. Numerous cumulative studies have shown a certain correlation between the fluctuating abundance of Akkermansia muciniphila and the occurrence of metabolic diseases. A. muciniphila, a potential probiotic candidate colonized in the human intestinal mucus layer, and its derivatives have various physiological functions, including treating metabolic disorders and maintaining human health. This review systematically explicates the abundance change rules of A. muciniphila in metabolic diseases. It also details the high efficacy and specific molecules mechanism of A. muciniphila and its derivatives in treating obesity, type 2 diabetes mellitus, cardiovascular disease, and non-alcoholic fatty liver disease.
Collapse
Affiliation(s)
- Huifang Niu
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), Hubei Key Laboratory of Fruit Vegetable Processing Quality Control (Huazhong Agricultural University), School of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Minfeng Zhou
- Union Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Daniel Zogona
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), Hubei Key Laboratory of Fruit Vegetable Processing Quality Control (Huazhong Agricultural University), School of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zheng Xing
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), Hubei Key Laboratory of Fruit Vegetable Processing Quality Control (Huazhong Agricultural University), School of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ting Wu
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), Hubei Key Laboratory of Fruit Vegetable Processing Quality Control (Huazhong Agricultural University), School of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Rui Chen
- Union Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dandan Cui
- Union Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fengxia Liang
- School of Acupuncture and Bone Injury, Hubei University of Chinese Medicine, Wuhan, China
| | - Xiaoyun Xu
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), Hubei Key Laboratory of Fruit Vegetable Processing Quality Control (Huazhong Agricultural University), School of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| |
Collapse
|
5
|
Boucher L, Leduc L, Leclère M, Costa MC. Current Understanding of Equine Gut Dysbiosis and Microbiota Manipulation Techniques: Comparison with Current Knowledge in Other Species. Animals (Basel) 2024; 14:758. [PMID: 38473143 DOI: 10.3390/ani14050758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Understanding the importance of intestinal microbiota in horses and the factors influencing its composition have been the focus of many studies over the past few years. Factors such as age, diet, antibiotic administration, and geographic location can affect the gut microbiota. The intra- and inter-individual variability of fecal microbiota in horses complicates its interpretation and has hindered the establishment of a clear definition for dysbiosis. Although a definitive causal relationship between gut dysbiosis in horses and diseases has not been clearly identified, recent research suggests that dysbiosis may play a role in the pathogenesis of various conditions, such as colitis and asthma. Prebiotics, probiotics, and fecal microbiota transplantation to modulate the horse's gastrointestinal tract may eventually be considered a valuable tool for preventing or treating diseases, such as antibiotic-induced colitis. This article aims to summarize the current knowledge on the importance of intestinal microbiota in horses and factors influencing its composition, and also to review the published literature on methods for detecting dysbiosis while discussing the efficacy of gut microbiota manipulation in horses.
Collapse
Affiliation(s)
- Laurie Boucher
- Department of Veterinary Biomedical Sciences, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Laurence Leduc
- Department of Clinical Sciences, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Mathilde Leclère
- Department of Clinical Sciences, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Marcio Carvalho Costa
- Department of Veterinary Biomedical Sciences, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| |
Collapse
|
6
|
Rodriguez-Diaz C, Seyboldt C, Rupnik M. Non-human Clostridioides difficile Reservoirs and Sources: Animals, Food, Environment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:329-350. [PMID: 38175482 DOI: 10.1007/978-3-031-42108-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clostridioides difficile is ubiquitous and is found in humans, animals and in variety of environments. The substantial overlap of ribotypes between all three main reservoirs suggests the extensive transmissions. Here we give the overview of European studies investigating farm, companion and wild animals, food and environments including water, soil, sediment, wastewater treatment plants, biogas plants, air, and households. Studies in Europe are more numerous especially in last couple of years, but are still fragmented in terms of countries, animal species, or type of environment covered. Soil seem to be the habitat of divergent unusual lineages of C. difficile. But the most important aspect of animals and environment is their role in C. difficile transmissions and their potential as a source for human infection is discussed.
Collapse
Affiliation(s)
- Cristina Rodriguez-Diaz
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina-IBIMA Plataforma BIONAND, UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, Málaga, Spain
- Laboratory of Food Microbiology, Fundamental and Applied Research for Animals and Health (FARAH), Department of Food Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Jena, Germany
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food, NLZOH, Maribor, Slovenia
- University of Maribor, Faculty of Medicine, Maribor, Slovenia
| |
Collapse
|
7
|
Labens R, Raidal S, Borgen-Nielsen C, Pyecroft S, Pant SD, De Ridder T. Wound healing of experimental equine skin wounds and concurrent microbiota in wound dressings following topical propylene glycol gel treatment. Front Vet Sci 2023; 10:1294021. [PMID: 38155761 PMCID: PMC10752953 DOI: 10.3389/fvets.2023.1294021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/23/2023] [Indexed: 12/30/2023] Open
Abstract
Introduction Topical wound treatments rely on carrier formulations with little to no biological impact. The potential for a common vehicle, a propylene glycol (PG) gel, to affect wound healing measures including microbiota is not known. Microbiome characterization, based on next generation sequencing methods is typically performed on tissue or directly obtained wound fluid samples. The utility for primary wound dressings to characterize equine wound microbiota in the context of topical treatments is currently unknown. This investigation reports the topical effect of an 80% PG based gel on wound healing and microbiota in wound dressings. Methods Experiments were performed in six mature horses utilizing a surgical, distal limb wound model, histology of sequential wound biopsies, photographic wound measurements and microbiota profiling via 16s rRNA sequencing of wound dressing samples. Experimental wounds were surveyed for 42 days and either treated (Day 7, 14, 21 and 28; at 0.03 ml/cm2) or unexposed to the PG gel. Wound surface area, relative and absolute microbial abundances, diversity indices and histologic parameters were analyzed in the context of the experimental group (treatment; control) using qualitative or quantitative methods depending on data characteristics. Results Compared to controls, treatment slowed the wound healing rate (17.17 ± 4.27 vs. 18.56 ± 6.3 mm2/day), delayed the temporal decline of polymorphonucleated cells in wound beds and operational taxonomic units (OTU) in wound dressings and lowered alpha-diversity indices for microbiota in primary wound dressing. Relative abundances of OTUs were in line with those previously reported for equine wounds. Clinical outcomes 42 days post wounding were considered similar irrespective of PG gel exposure. Discussion Results highlight the potential for vehicle exposure to alter relevant wound outcome measures, imposing the need for stringent experimental control measures. Primary wound dressings may represent an alternate sample source for characterization of the wound microbiome alleviating the need for additional interventions. Further studies are warranted to contrast the microbiome in wound dressings against that present on wound surfaces to conclude on the validity of this approach.
Collapse
Affiliation(s)
- Raphael Labens
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, NSW, Australia
- QBiotics Group Ltd., Yungaburra, QLD, Australia
| | - Sharanne Raidal
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Cathrine Borgen-Nielsen
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Stephen Pyecroft
- School of Animal and Veterinary Sciences, Faculty of Sciences, Engineering and Technology, University of Adelaide, Roseworthy, SA, Australia
| | - Sameer D. Pant
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, NSW, Australia
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, Australia
| | | |
Collapse
|
8
|
Zeng SY, Liu YF, Liu JH, Zeng ZL, Xie H, Liu JH. Potential Effects of Akkermansia Muciniphila in Aging and Aging-Related Diseases: Current Evidence and Perspectives. Aging Dis 2023; 14:2015-2027. [PMID: 37199577 PMCID: PMC10676789 DOI: 10.14336/ad.2023.0325] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/25/2023] [Indexed: 05/19/2023] Open
Abstract
Akkermansia muciniphila (A. muciniphila) is an anaerobic bacterium that widely colonizes the mucus layer of the human and animal gut. The role of this symbiotic bacterium in host metabolism, inflammation, and cancer immunotherapy has been extensively investigated over the past 20 years. Recently, a growing number of studies have revealed a link between A. muciniphila, and aging and aging-related diseases (ARDs). Research in this area is gradually shifting from correlation analysis to exploration of causal relationships. Here, we systematically reviewed the association of A. muciniphila with aging and ARDs (including vascular degeneration, neurodegenerative diseases, osteoporosis, chronic kidney disease, and type 2 diabetes). Furthermore, we summarize the potential mechanisms of action of A. muciniphila and offer perspectives for future studies.
Collapse
Affiliation(s)
- Shi-Yu Zeng
- Department of Metabolism and Endocrinology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.
| | - Yi-Fu Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China.
| | - Jiang-Hua Liu
- Department of Orthopedics, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.
| | - Zhao-Lin Zeng
- Department of Metabolism and Endocrinology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.
| | - Hui Xie
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
- Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Jiang-Hua Liu
- Department of Metabolism and Endocrinology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.
| |
Collapse
|
9
|
Jabri H, Krings S, Fall PA, Baurain D, Daube G, Taminiau B. Microbiota Profiling on Veterinary Faculty Restroom Surfaces and Source Tracking. Microorganisms 2023; 11:2053. [PMID: 37630613 PMCID: PMC10459056 DOI: 10.3390/microorganisms11082053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/02/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
In this study, we aimed to develop a comprehensive microbial source amplicon database tailored for source tracking in veterinary settings. We rigorously tested our locally curated source tracking database by selecting a frequently accessed environment by veterinary students and veterinarians. By exploring the composition of resident microbiota and identifying potential sources of contamination, including animals, the environment, and human beings, we aimed to provide valuable insights into the dynamics of microbial transmission within veterinary facilities. The 16S rDNA amplicon sequencing was used to determine the bacterial taxonomic profiles of restroom surfaces. Bacterial sources were identified by linking our metadata-enriched local database to the microbiota profiling analysis using high-quality sequences. Microbiota profiling shows the dominance of four phyla: Actinobacteria, Bacteroidetes, Proteobacteria, and Firmicutes. If the restroom cleaning process did not appear to impact microbiota composition, significant differences regarding bacterial distribution were observed between male and female users in different sampling campaigns. Combining 16S rDNA profiling to our specific sources labeling pipeline, we found aquatic and human sources were the primary environment keywords in our campaigns. The probable presence of known animal sources (bovids, insects, equids, suids…) associated with bacterial genera such as Chryseobacterium, Bergeyella, Fibrobacter, and Syntrophococcus was also involved in restroom surfaces, emphasizing the proximity between these restrooms and the exchange of bacteria between people involved in animals handling. To summarize, we have demonstrated that DNA sequence-based source tracking may be integrated with high-throughput bacterial community analysis to enrich microbial investigation of potential bacterial contamination sources, especially for little known or poorly identified taxa. However, more research is needed to determine the tool's utility in other applications.
Collapse
Affiliation(s)
- Hiba Jabri
- Laboratory of Food Microbiology, Fundamental and Applied Research for Animals and Health Center (FARAH), Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, Quartier Vallée 2, B42, Avenue de Cureghem 10, 4000 Liège, Belgium; (H.J.); (G.D.)
| | - Simone Krings
- Department of Microbial Sciences, School of Biosciences, Faculty of Health and Medical Sciences, Univesity of Surrey, Guildford GU2 7XH, UK;
| | - Papa Abdoulaye Fall
- FoodChainID GENOMICS, Laboratory Manager NGS, Rue Hayeneux, 62, 4040 Herstal, Belgium;
| | - Denis Baurain
- Eukaryotic Phylogenomics, InBioS-PhytoSYSTEMS, University of Liège, 4000 Liège, Belgium;
| | - Georges Daube
- Laboratory of Food Microbiology, Fundamental and Applied Research for Animals and Health Center (FARAH), Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, Quartier Vallée 2, B42, Avenue de Cureghem 10, 4000 Liège, Belgium; (H.J.); (G.D.)
| | - Bernard Taminiau
- Laboratory of Food Microbiology, Fundamental and Applied Research for Animals and Health Center (FARAH), Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, Quartier Vallée 2, B42, Avenue de Cureghem 10, 4000 Liège, Belgium; (H.J.); (G.D.)
| |
Collapse
|
10
|
Chapuis RJJ, Becker AAMJ, Dowling PM, Weese JS. Characterisation of faecal microbiota in horses medicated with oral doxycycline hyclate. Equine Vet J 2023; 55:129-141. [PMID: 35202500 DOI: 10.1111/evj.13570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 01/19/2022] [Accepted: 02/17/2022] [Indexed: 12/16/2022]
Abstract
BACKGROUND Antimicrobial-associated diarrhoea is a common adverse effect of antimicrobial treatment in horses and has been reported following the administration of oral doxycycline. The administration of antimicrobials has also been associated with changes in the equine intestinal microbiota diversity yet has not been explored under doxycycline treatment. OBJECTIVES To describe the dynamics of the faecal microbial diversity following a 5-day oral administration of doxycycline in healthy horses with Streptococcus zooepidemicus infected tissue chambers. STUDY DESIGN Experimental prospective cohort study in a single horse group. METHODS Seven healthy adult horses with S. zooepidemicus infected tissue chambers received oral doxycycline at 10 mg/kg q 12 h for 5-days following the tissue chamber inoculation. Faeces were collected prior to the tissue chamber inoculation and until 28-days post inoculation. Faecal microbiota was characterised by high throughput sequencing of the V4 region of the 16S rRNA gene on the Illumina MiSeq sequencing platform. Bioinformatic analysis was performed with Mothur and statistical analysis were conducted on R Studio. RESULTS A significant decrease in alpha diversity, characterised by a decrease of richness and diversity, and a decrease in beta diversity, characterised by changes in relative abundance, occurred after initiation of and during the administration of doxycycline. A decrease in Verrucomicrobia and increase in Firmicutes:Bacteroidetes ratio occurred following the initiation of treatment, with a return to initial Firmicutes:Bacteroidetes ratio during the treatment. It took 23 days after discontinuing the treatment for the faecal microbiota to return close to the initial state. MAIN LIMITATIONS Lack of control population within the study. CONCLUSIONS Transitory intestinal dysbiosis occurs under oral administration of doxycycline in horses.
Collapse
Affiliation(s)
- Ronan J J Chapuis
- Clinical Sciences, Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis.,Large Animal Clinical Sciences, Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Anne A M J Becker
- Clinical Sciences, Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis.,Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Patricia M Dowling
- Large Animal Clinical Sciences, Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - J Scott Weese
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
11
|
Chaucheyras-Durand F, Sacy A, Karges K, Apper E. Gastro-Intestinal Microbiota in Equines and Its Role in Health and Disease: The Black Box Opens. Microorganisms 2022; 10:microorganisms10122517. [PMID: 36557769 PMCID: PMC9783266 DOI: 10.3390/microorganisms10122517] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/05/2022] [Accepted: 12/11/2022] [Indexed: 12/24/2022] Open
Abstract
Horses are large non-ruminant herbivores and rely on microbial fermentation for energy, with more than half of their maintenance energy requirement coming from microbial fermentation occurring in their enlarged caecum and colon. To achieve that, the gastro-intestinal tract (GIT) of horses harbors a broad range of various microorganisms, differing in each GIT segment, which are essential for efficient utilization of feed, especially to use nutrients that are not or little degraded by endogenous enzymes. In addition, like in other animal species, the GIT microbiota is in permanent interplay with the host's cells and is involved in a lot of functions among which inflammation, immune homeostasis, and energy metabolism. As for other animals and humans, the horse gut microbiome is sensitive to diet, especially consumption of starch, fiber, and fat. Age, breeds, stress during competitions, transportation, and exercise may also impact the microbiome. Because of its size and its complexity, the equine GIT microbiota is prone to perturbations caused by external or internal stressors that may result in digestive diseases like gastric ulcer, diarrhea, colic, or colitis, and that are thought to be linked with systemic diseases like laminitis, equine metabolic syndrome or obesity. Thus, in this review we aim at understanding the common core microbiome -in terms of structure and function- in each segment of the GIT, as well as identifying potential microbial biomarkers of health or disease which are crucial to anticipate putative perturbations, optimize global practices and develop adapted nutritional strategies and personalized nutrition.
Collapse
Affiliation(s)
- Frédérique Chaucheyras-Durand
- Lallemand SAS, 31702 Blagnac, France
- UMR MEDIS, INRAE, Université Clermont-Auvergne, 63122 Saint-Genès Champanelle, France
| | | | - Kip Karges
- Lallemand Specialities Inc., Milwaukee, WI 53218, USA
| | | |
Collapse
|
12
|
Li XB, Huang XX, Li Q, Li XY, Li JH, Li C, He LJ, Jing HX, Yang KL. Effects of different grains on bacterial diversity and enzyme activity associated with digestion of starch in the foal stomach. BMC Vet Res 2022; 18:407. [PMCID: PMC9670411 DOI: 10.1186/s12917-022-03510-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022] Open
Abstract
Abstract
Background
Compared with the stomach of ruminant cattle, the stomach of horse is small and mainly for chemical digestion, but the microorganisms in the stomach play an important role in maintaining the homeostasis of the internal environment. Due to the complexity of the microbes in the stomach, little is known about the diversity and structure of bacteria in the equine stomach. Grains are the main energy source for plant-eating livestock and energy is derived through enzymatic hydrolysis of grains into glucose or their microbial fermentation into Volatile fatty acids (VFA). However, the mechanism through which these ingested grains are chemically digested as well as the effect of these grains on the stomach remains elusive. This study explored the effects of feeding different grains (corn, oats, and barley) on bacterial diversity, structure, and composition in the foal’s stomach content. Furthermore, the effects of different grains on the vitality of starch digestion-related stomach enzymes were investigated.
Results
No significant differences were observed (P > 0.05) in the bacterial rarefaction curves of Operational Taxonomic Units (OTUs) and diversity of the stomach microbiota in all foals. This study also revealed the statistical differences for Firmicutes, Cyanobacteria, Actinobacteria, Fibrobacteres, Lactobacillaceae, Streptococcaceae, Unidentified_Clostridiales, Prevotellaceae, Lactobacillus, Streptococcus, Unidentified_Cyanobacteria, Unidentified_Clostridiales, Lactococcus, Sphingomonas, Lactobacillus_hayakitensis, Lactobacillus_equigenerosi, and Clostridium_perfringens. The linear discriminant analysis effect size analysis revealed 9 bacteria at each classification level. The functional analysis of species information by using FAPROTAX software was able to predict 35 functions, and the top 5 functions were chemoheterotrophy, fermentation, animal_parasites_or_symbionts, nitrate_reduction, and aerobic_chemoheterotrophy. The study also revealed statistical differences for pH, glucose concentration, β-amylase, maltase, and amylase.
Conclusions
The different grains had no significant effect on the microbial diversity of the stomach content of the foal. However, the relative bacterial abundances differed significantly in response to different diets. Particularly, oats fed to the foals significantly increased the relative abundance of Firmicutes, Lactobacillaceae, Lactobacillus, and Lactobacillus_hayakitensis. The grain had no significant effect on the pH of the stomach content, glucose concentration, and enzyme viability in the foal.
Collapse
|
13
|
Martinez E, Rodriguez C, Crèvecoeur S, Lebrun S, Delcenserie V, Taminiau B, Daube G. Impact of environmental conditions and gut microbiota on the in vitro germination and growth of Clostridioides difficile. FEMS Microbiol Lett 2022; 369:6692865. [PMID: 36066913 DOI: 10.1093/femsle/fnac087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/09/2022] [Accepted: 09/01/2022] [Indexed: 12/13/2022] Open
Abstract
Clostridioides difficile is a spore-forming anaerobic Gram-positive bacterium responsible for a broad spectrum of intestinal symptoms and healthcare-associated diarrhoea. The hypothesis of this work was that different in vitro conditions, notably pH and human faecal microbiota composition, impact the germination and/or the growth of C. difficile. This study aimed to correlate growth kinetics of the bacterium with these two physiochemical parameters by using a static in vitro model. To better understand the initial gut colonisation, several growth curve assays were carried out to monitor the behaviour of the spores and vegetative forms of C. difficile strain 078 under different conditions mimicking the gut environment. When the faeces were added, no spore germination or growth was observed, but C. difficile spores germinated in vitro when the pH was maintained between 6.6 and 6.9 for four different faeces donors. The evolution of microbiota studied by 16S rDNA profiling showed high proportions of Enterobacteriaceae and E. coli/Shigella when C. difficile grew, regardless of the inoculated faeces. This model helped us to understand that the germination and growth of C. difficile are strongly pH dependent, and further research is needed to evaluate the potential impact of the gut microbiota composition on C. difficile.
Collapse
Affiliation(s)
- Elisa Martinez
- Fundamental and Applied Research for Animals & Health (FARAH), Faculté de Médecine Vétérinaire, Département des Sciences des Denrées alimentaires, Université de Liège, Avenue de Cureghem 10, 4000 Liège, Belgique
| | - Cristina Rodriguez
- Instituto de Investigación Biomédica de Málaga-IBIMA. Málaga, Spain. Unidad de Gestión Clínica de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, Málaga, 29590, Spain
| | - Sébastien Crèvecoeur
- Fundamental and Applied Research for Animals & Health (FARAH), Faculté de Médecine Vétérinaire, Département des Sciences des Denrées alimentaires, Université de Liège, Avenue de Cureghem 10, 4000 Liège, Belgique
| | - Sarah Lebrun
- Fundamental and Applied Research for Animals & Health (FARAH), Faculté de Médecine Vétérinaire, Département des Sciences des Denrées alimentaires, Université de Liège, Avenue de Cureghem 10, 4000 Liège, Belgique
| | - Véronique Delcenserie
- Fundamental and Applied Research for Animals & Health (FARAH), Faculté de Médecine Vétérinaire, Département des Sciences des Denrées alimentaires, Université de Liège, Avenue de Cureghem 10, 4000 Liège, Belgique
| | - Bernard Taminiau
- Fundamental and Applied Research for Animals & Health (FARAH), Faculté de Médecine Vétérinaire, Département des Sciences des Denrées alimentaires, Université de Liège, Avenue de Cureghem 10, 4000 Liège, Belgique
| | - Georges Daube
- Fundamental and Applied Research for Animals & Health (FARAH), Faculté de Médecine Vétérinaire, Département des Sciences des Denrées alimentaires, Université de Liège, Avenue de Cureghem 10, 4000 Liège, Belgique
| |
Collapse
|
14
|
Ayoub C, Arroyo LG, MacNicol JL, Renaud D, Weese JS, Gomez DE. Fecal microbiota of horses with colitis and its association with laminitis and survival during hospitalization. J Vet Intern Med 2022; 36:2213-2223. [PMID: 36271677 DOI: 10.1111/jvim.16562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/21/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The association of microbiota with clinical outcomes and the taxa associated with colitis in horses remains generally unknown. OBJECTIVES Describe the fecal microbiota of horses with colitis and investigate the association of the fecal microbiota with the development of laminitis and survival. ANIMALS Thirty-six healthy and 55 colitis horses subdivided into laminitis (n = 15) and non-laminitis (n = 39, 1 horse with chronic laminitis was removed from this comparison) and survivors (n = 27) and nonsurvivors (n = 28). METHODS Unmatched case-control study. The Illumina MiSeq platform targeting the V4 region of the 16S ribosomal RNA gene was used to assess the microbiota. RESULTS The community membership (Jaccard index) and structure (Yue and Clayton index) were different (analysis of molecular variance [AMOVA]; P < .001) between healthy and colitis horses. The linear discriminant analysis effect size (LEfSe; linear discriminant analysis [LDA] >3; P < .05) and random forest analyses found Enterobacteriaceae, Lactobacillus, Streptococcus, and Enterococcus enriched in colitis horses, whereas Treponema, Faecalibacterium, Ruminococcaceae, and Lachnospiraceae were enriched in healthy horses. The community membership and structure of colitis horses with or without laminitis was (AMOVA; P > .05). Enterobacteriaceae, Streptococcus, and Lactobacillus were enriched in horses with laminitis (LDA > 3; P < .05). The community membership (AMOVA; P = .008) of surviving and nonsurviving horses was different. Nonsurviving horses had an enrichment of Enterobacteriaceae, Pseudomonas, Streptococcus, and Enterococcus (LDA >3; P < .05). CONCLUSION AND CLINICAL IMPORTANCE Differences in the microbiota of horses with colitis that survive or do not survive are minor and, similarly, the microbiota differences in horses with colitis that do or do not develop laminitis are minor.
Collapse
Affiliation(s)
- Cosette Ayoub
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Luis G Arroyo
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Jennifer L MacNicol
- Department of Animal Biosciences, Ontario Agricultural College, University of Guelph, Guelph, Ontario, Canada
| | - David Renaud
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - J Scott Weese
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Diego E Gomez
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
15
|
Collinet A, Grimm P, Jacotot E, Julliand V. Biomarkers for monitoring the equine large intestinal inflammatory response to stress-induced dysbiosis and probiotic supplementation. J Anim Sci 2022; 100:skac268. [PMID: 35980768 PMCID: PMC9576022 DOI: 10.1093/jas/skac268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/16/2022] [Indexed: 11/14/2022] Open
Abstract
Large intestine barrier disturbances can have serious consequences for the health of horses. The loss of mucosal integrity that leads to increased intestinal permeability may result from a local inflammatory immune response following alterations of the microbiota, known as dysbiosis. Therefore, our research aimed to identify noninvasive biomarkers for studying the intestinal permeability and the local inflammatory immune response in horses. Regarding the biomarkers used in other mammalian species, we measured the concentrations of lipopolysaccharides (LPS), reflected by 3-OH C14, C16, and C18 fatty acids, in blood, and fecal secretory immunoglobulin-A (SIgA). These biomarkers were evaluated in two trials including 9 and 12 healthy horses, which developed large intestinal dysbiosis experimentally induced by 5 d of antibiotic administration (trimethoprim sulfadiazine [TMS]) or 5 d of abrupt introduction of high starch levels (barley) into the diet. Horses were either control or supplemented with Lactobacillus acidophilus, Ligilactobacillus salivarius, and Bifidobacterium lactis. Correlations were performed between biomarkers and fecal bacterial diversity, composition, and function. No significant interaction between day and supplementation, or supplementation effect were observed for each biomarker. However, with the dietary stressor, a significant increase in blood concentrations of 3-OH C16 (P = 0.0125) and C14 (P = 0.0252) fatty acids was measured 2 d after the cessation of barley administration. Furthermore, with the antibiotic stressor, blood levels of 3-OH C16 progressively increased (P = 0.0114) from the first day to 2 d after the end of TMS administration. No significant day effect was observed for fecal SIgA concentrations for both stressors. These results indicate that both antibiotic- and diet-induced dysbiosis resulted in a local translocation of LPS 2 d after the cessation of the stressor treatments, suggesting an impairment of intestinal permeability, without detectable local inflammation. Blood LPS and fecal SIgA concentrations were significantly correlated with several bacterial variations in the large intestine, which are features of antibiotic- and diet-induced dysbiosis. These findings support the hypothesis that a relationship exists between dysbiosis and the loss of mucosal integrity in the large intestine of horses.
Collapse
Affiliation(s)
- Axelle Collinet
- Lab To Field, 21000 Dijon, France
- Univ. Bourgogne Franche–Comté, L’Institut Agro Dijon, PAM UMR A 02.102, 21000 Dijon, France
| | | | - Emmanuel Jacotot
- Univ. Bourgogne Franche–Comté, L’Institut Agro Dijon, PAM UMR A 02.102, 21000 Dijon, France
| | - Véronique Julliand
- Univ. Bourgogne Franche–Comté, L’Institut Agro Dijon, PAM UMR A 02.102, 21000 Dijon, France
| |
Collapse
|
16
|
Fecal Microbiota Comparison between Healthy Teaching Horses and Client-Owned Horses. J Equine Vet Sci 2022; 118:104105. [PMID: 36058504 DOI: 10.1016/j.jevs.2022.104105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/07/2022] [Accepted: 08/08/2022] [Indexed: 11/20/2022]
Abstract
The objective of this study was to compare the fecal microbiota of 2 healthy teaching horse herds with that of client-owned horses from the same geographic areas. The fecal microbiota of client-owned horses from Ontario Canada (n = 15) and Florida, USA (n = 11) was compared with that teaching horses from the University of Guelph, Ontario, Canada (n = 10) and the University of Florida, Florida, USA (n = 15). The fecal microbiota was characterized by sequencing of bacterial DNA using the V4 hypervariable region of the 16S rRNA gene. The diversity (inverse Simpson index) of the fecal microbiota was significantly higher in teaching than client owned horses from the same geographical area (P < 0.05). The community membership (Jaccard Index) and structure (Yue and Clayton index) of teaching horses was also significantly different from that of client owned horses from the same geographical area (AMOVA P < 0.001). The bacterial membership and structure of the fecal microbiota of Ontario and Florida teaching horses were significantly different, while the bacterial membership, but not the structure of Ontario and Florida client owned horses was significantly different (AMOVA P < 0.001). In all 4 groups of healthy horses, Lachnospiraceae, Ruminococcaceae, Bacteroidales, Clostridiales, and Treponema were detected in high relative abundance. The fecal microbiota of healthy horses from teaching herds kept in the same environment with identical management practices differs significantly from that of horses housed in different facilities with dissimilar management practices. Our results suggest an effect of the environment and management practices on the gastrointestinal microbiota. Researchers should attempt to include healthy horses from the same farm with similar management as control groups when comparing with diseased horses.
Collapse
|
17
|
Rodriguez-Diaz C, Taminiau B, García-García A, Cueto A, Robles-Díaz M, Ortega-Alonso A, Martín-Reyes F, Daube G, Sanabria-Cabrera J, Jimenez-Perez M, Isabel Lucena M, Andrade RJ, García-Fuentes E, García-Cortes M. Microbiota diversity in nonalcoholic fatty liver disease and in drug-induced liver injury. Pharmacol Res 2022; 182:106348. [PMID: 35817360 DOI: 10.1016/j.phrs.2022.106348] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/06/2022] [Accepted: 07/06/2022] [Indexed: 10/17/2022]
Abstract
The gut microbiota could play a significant role in the progression of nonalcoholic fatty liver disease (NAFLD); however, its relevance in drug-induced liver injury (DILI) remains unexplored. Since the two hepatic disorders may share damage pathways, we analysed the metagenomic profile of the gut microbiota in NAFLD, with or without significant liver fibrosis, and in DILI, and we identified the main associated bacterial metabolic pathways. In the NAFLD group, we found a decrease in Alistipes, Barnesiella, Eisenbergiella, Flavonifractor, Fusicatenibacter, Gemminger, Intestinimonas, Oscillibacter, Parasutterella, Saccharoferementans and Subdoligranulum abundances compared with those in both the DILI and control groups. Additionally, we detected an increase in Enterobacter, Klebsiella, Sarcina and Turicibacter abundances in NAFLD, with significant liver fibrosis, compared with those in NAFLD with no/mild liver fibrosis. The DILI group exhibited a lower microbial bacterial richness than the control group, and lower abundances of Acetobacteroides, Blautia, Caloramator, Coprococcus, Flavobacterium, Lachnospira, Natronincola, Oscillospira, Pseudobutyrivibrio, Shuttleworthia, Themicanus and Turicibacter compared with those in the NAFLD and control groups. We found seven bacterial metabolic pathways that were impaired only in DILI, most of which were associated with metabolic biosynthesis. In the NAFLD group, most of the differences in the bacterial metabolic pathways found in relation to those in the DILI and control groups were related to fatty acid and lipid biosynthesis. In conclusion, we identified a distinct bacterial profile with specific bacterial metabolic pathways for each type of liver disorder studied. These differences can provide further insight into the physiopathology and development of NAFLD and DILI.
Collapse
Affiliation(s)
- Cristina Rodriguez-Diaz
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
| | - Bernard Taminiau
- Fundamental and Applied Research for Animals & Health (FARAH), Department of Food Microbiology, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Alberto García-García
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
| | - Alejandro Cueto
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; Servicio de Farmacologia Clinica, Hospital Universitario Virgen de la Victoria, Departamento de Farmacología, Facultad de Medicina, Universidad de Málaga, 29010 Málaga, Spain
| | - Mercedes Robles-Díaz
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; Departamento de Medicina, Facultad de Medicina, Universidad de Málaga, 29010 Málaga, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 29010 Málaga, Spain
| | - Aida Ortega-Alonso
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
| | - Flores Martín-Reyes
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
| | - Georges Daube
- Fundamental and Applied Research for Animals & Health (FARAH), Department of Food Microbiology, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Judith Sanabria-Cabrera
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; Servicio de Farmacologia Clinica, Hospital Universitario Virgen de la Victoria, Departamento de Farmacología, Facultad de Medicina, Universidad de Málaga, 29010 Málaga, Spain; UICEC IBIMA, Plataforma SCReN (Spanish Clinical Research Network), Servicio de Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, 29010 Málaga, Spain
| | - Miguel Jimenez-Perez
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; UGC de Enfermedades Digestivas, Hospital Regional Universitario, 29010 Málaga, Spain
| | - M Isabel Lucena
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; Servicio de Farmacologia Clinica, Hospital Universitario Virgen de la Victoria, Departamento de Farmacología, Facultad de Medicina, Universidad de Málaga, 29010 Málaga, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 29010 Málaga, Spain; UICEC IBIMA, Plataforma SCReN (Spanish Clinical Research Network), Servicio de Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, 29010 Málaga, Spain.
| | - Raúl J Andrade
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain; Departamento de Medicina, Facultad de Medicina, Universidad de Málaga, 29010 Málaga, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 29010 Málaga, Spain
| | - Eduardo García-Fuentes
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 29010 Málaga, Spain.
| | - Miren García-Cortes
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 29010 Málaga, Spain
| |
Collapse
|
18
|
Weinert-Nelson JR, Biddle AS, Williams CA. Fecal microbiome of horses transitioning between warm-season and cool-season grass pasture within integrated rotational grazing systems. Anim Microbiome 2022; 4:41. [PMID: 35729677 PMCID: PMC9210719 DOI: 10.1186/s42523-022-00192-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/10/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Diet is a key driver of equine hindgut microbial community structure and composition. The aim of this study was to characterize shifts in the fecal microbiota of grazing horses during transitions between forage types within integrated warm- (WSG) and cool-season grass (CSG) rotational grazing systems (IRS). Eight mares were randomly assigned to two IRS containing mixed cool-season grass and one of two warm-season grasses: bermudagrass [Cynodon dactylon (L.) Pers.] or crabgrass [Digitaria sanguinalis (L.) Scop.]. Fecal samples were collected during transitions from CSG to WSG pasture sections (C-W) and WSG to CSG (W-C) on days 0, 2, 4, and 6 following pasture rotation and compared using 16S rRNA gene sequencing. RESULTS Regardless of IRS or transition (C-W vs. W-C), species richness was greater on day 4 and 6 in comparison to day 0 (P < 0.05). Evenness, however, did not differ by day. Weighted UniFrac also did not differ by day, and the most influential factor impacting β-diversity was the individual horse (R2 ≥ 0.24; P = 0.0001). Random forest modeling was unable to accurately predict days within C-W and W-C, but could predict the individual horse based on microbial composition (accuracy: 0.92 ± 0.05). Only three differentially abundant bacterial co-abundance groups (BCG) were identified across days within all C-W and W-C for both IRS (W ≥ 126). The BCG differing by day for all transitions included amplicon sequence variants (ASV) assigned to bacterial groups with known fibrolytic and butyrate-producing functions including members of Lachnospiraceae, Clostridium sensu stricto 1, Anaerovorax the NK4A214 group of Oscillospiraceae, and Sarcina maxima. In comparison, 38 BCG were identified as differentially abundant by horse (W ≥ 704). The ASV in these groups were most commonly assigned to genera associated with degradation of structural carbohydrates included Rikenellaceae RC9 gut group, Treponema, Christensenellaceae R-7 group, and the NK4A214 group of Oscillospiraceae. Fecal pH also did not differ by day. CONCLUSIONS Overall, these results demonstrated a strong influence of individual horse on the fecal microbial community, particularly on the specific composition of fiber-degraders. The equine fecal microbiota were largely stable across transitions between forages within IRS suggesting that the equine gut microbiota adjusted at the individual level to the subtle dietary changes imposed by these transitions. This adaptive capacity indicates that horses can be managed in IRS without inducing gastrointestinal dysfunction.
Collapse
Affiliation(s)
- Jennifer R. Weinert-Nelson
- grid.430387.b0000 0004 1936 8796Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
| | - Amy S. Biddle
- grid.33489.350000 0001 0454 4791Department of Animal and Food Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark, DE 19711 USA
| | - Carey A. Williams
- grid.430387.b0000 0004 1936 8796Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
| |
Collapse
|
19
|
Ang L, Vinderola G, Endo A, Kantanen J, Jingfeng C, Binetti A, Burns P, Qingmiao S, Suying D, Zujiang Y, Rios-Covian D, Mantziari A, Beasley S, Gomez-Gallego C, Gueimonde M, Salminen S. Gut Microbiome Characteristics in feral and domesticated horses from different geographic locations. Commun Biol 2022; 5:172. [PMID: 35217713 PMCID: PMC8881449 DOI: 10.1038/s42003-022-03116-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/01/2022] [Indexed: 12/12/2022] Open
Abstract
Domesticated horses live under different conditions compared with their extinct wild ancestors. While housed, medicated and kept on a restricted source of feed, the microbiota of domesticated horses is hypothesized to be altered. We assessed the fecal microbiome of 57 domestic and feral horses from different locations on three continents, observing geographical differences. A higher abundance of eukaryota (p < 0.05) and viruses (p < 0.05) and lower of archaea (p < 0.05) were found in feral animals when compared with domestic ones. The abundance of genes coding for microbe-produced enzymes involved in the metabolism of carbohydrates was significantly higher (p < 0.05) in feral animals regardless of the geographic origin. Differences in the fecal resistomes between both groups of animals were also noted. The domestic/captive horse microbiomes were enriched in genes conferring resistance to tetracycline, likely reflecting the use of this antibiotic in the management of these animals. Our data showed an impoverishment of the fecal microbiome in domestic horses with diet, antibiotic exposure and hygiene being likely drivers. The results offer a view of the intestinal microbiome of horses and the impact of domestication or captivity, which may uncover novel targets for modulating the microbiome of horses to enhance animal health and well-being. Li Ang et al. present an investigation of feral and domesticated horse gut microbiomes across three continents. Their results provide new insight into how changes in horse lifestyle are reflected in the resident gut microbiome.
Collapse
Affiliation(s)
- Li Ang
- Health Management Centre, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Henan Gene Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Infection Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Gabriel Vinderola
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland, Jokioinen, Finland
| | - Chen Jingfeng
- Health Management Centre, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ana Binetti
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Patricia Burns
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Shi Qingmiao
- Department of Henan Gene Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Infection Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ding Suying
- Health Management Centre, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Zujiang
- Department of Henan Gene Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Infection Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - David Rios-Covian
- Department and Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Asturias, Spain
| | - Anastasia Mantziari
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| | - Shea Beasley
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| | - Carlos Gomez-Gallego
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland.,Institute of Public Health and Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Miguel Gueimonde
- Department and Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Asturias, Spain.
| | - Seppo Salminen
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland.
| |
Collapse
|
20
|
Karamzin AM, Ropot AV, Sergeyev OV, Khalturina EO. Akkermansia muciniphila and host interaction within the intestinal tract. Anaerobe 2021; 72:102472. [PMID: 34743983 DOI: 10.1016/j.anaerobe.2021.102472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 02/07/2023]
Abstract
In the modern world, metabolic syndrome is one of the major health problems. Heredity, overeating, and a sedentary lifestyle are believed to be the main predisposing factors for its development. However, recent data indicate that gut microbiota plays a significant role in metabolic profile formation. In 2004, Derrien et al. isolated and characterized the bacterium Akkermansia muciniphila, which lives mainly in the human intestine and has the ability to utilize intestinal mucin. It proved to be a good candidate for the role of a new-generation probiotic due to its ability to improve the laboratory and physical indicators associated with metabolic syndrome and type 2 diabetes in mice and humans. In this review, we describe the basic microbiological characteristics of this bacterium, its main habitats, clinical effects after oral administration, and different ways of influencing the digestive tract. All these data allow us to understand the mechanism of its beneficial effects, which is important for its future introduction into the treatment of the metabolic syndrome.
Collapse
Affiliation(s)
- Andrei M Karamzin
- Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya Street, 8, Moscow, Russian Federation.
| | - Anastasiia V Ropot
- Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya Street, 8, Moscow, Russian Federation.
| | - Oleg V Sergeyev
- Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya Street, 8, Moscow, Russian Federation.
| | - Evgenia O Khalturina
- Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya Street, 8, Moscow, Russian Federation.
| |
Collapse
|
21
|
Costa M, Di Pietro R, Bessegatto JA, Pereira PFV, Stievani FC, Gomes RG, Lisbôa JAN, Weese JS. Evaluation of changes in microbiota after fecal microbiota transplantation in 6 diarrheic horses. THE CANADIAN VETERINARY JOURNAL = LA REVUE VETERINAIRE CANADIENNE 2021; 62:1123-1130. [PMID: 34602643 PMCID: PMC8439339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The purpose of this study was to characterize the fecal microbiota of horses with acute and chronic diarrhea before and after fecal microbiota transplantation (FMT). Six client-owned horses with acute and chronic diarrhea received FMT from 2 healthy donor horses. Microbiota analysis using next-generation sequencing was performed on fecal samples collected before and 2 and 7 d after FMT. Signs of diarrhea improved in 4 horses, whereas the remaining 2 horses did not survive. There was a significant difference in the number of bacterial species between donors and recipients (P < 0.05). The Order Lactobacillales and the genera Lactobacillus, Intestinimonas, and Streptococcus were increased in the microbiota of diarrheic horses, and Saccharofermentans genus increased in healthy donors. The results suggest that FMT from the healthy donors was not effective over a 7-day period as it did not change the fecal microbiota of the diarrheic horses. Further research to improve the efficacy of FMT in horses is needed.
Collapse
Affiliation(s)
- Marcio Costa
- Department of Biomedical Sciences, Université de Montréal, Montreal, Quebec (Costa, Di Pietro); Department of Clinical Studies, Universidade Estadual de Londrina, Londrina, Paraná, Brazil (Bessegatto, Pereira, Stievani, Gomes, Lisbôa); Department of Clinical Studies, Universidade Filadelfia, Londrina, Paraná, Brazil (Stievani); Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario (Weese)
| | - Rebecca Di Pietro
- Department of Biomedical Sciences, Université de Montréal, Montreal, Quebec (Costa, Di Pietro); Department of Clinical Studies, Universidade Estadual de Londrina, Londrina, Paraná, Brazil (Bessegatto, Pereira, Stievani, Gomes, Lisbôa); Department of Clinical Studies, Universidade Filadelfia, Londrina, Paraná, Brazil (Stievani); Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario (Weese)
| | - José Antonio Bessegatto
- Department of Biomedical Sciences, Université de Montréal, Montreal, Quebec (Costa, Di Pietro); Department of Clinical Studies, Universidade Estadual de Londrina, Londrina, Paraná, Brazil (Bessegatto, Pereira, Stievani, Gomes, Lisbôa); Department of Clinical Studies, Universidade Filadelfia, Londrina, Paraná, Brazil (Stievani); Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario (Weese)
| | - Priscilla Fajardo Valente Pereira
- Department of Biomedical Sciences, Université de Montréal, Montreal, Quebec (Costa, Di Pietro); Department of Clinical Studies, Universidade Estadual de Londrina, Londrina, Paraná, Brazil (Bessegatto, Pereira, Stievani, Gomes, Lisbôa); Department of Clinical Studies, Universidade Filadelfia, Londrina, Paraná, Brazil (Stievani); Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario (Weese)
| | - Fernanda C Stievani
- Department of Biomedical Sciences, Université de Montréal, Montreal, Quebec (Costa, Di Pietro); Department of Clinical Studies, Universidade Estadual de Londrina, Londrina, Paraná, Brazil (Bessegatto, Pereira, Stievani, Gomes, Lisbôa); Department of Clinical Studies, Universidade Filadelfia, Londrina, Paraná, Brazil (Stievani); Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario (Weese)
| | - Roberta Gaberlini Gomes
- Department of Biomedical Sciences, Université de Montréal, Montreal, Quebec (Costa, Di Pietro); Department of Clinical Studies, Universidade Estadual de Londrina, Londrina, Paraná, Brazil (Bessegatto, Pereira, Stievani, Gomes, Lisbôa); Department of Clinical Studies, Universidade Filadelfia, Londrina, Paraná, Brazil (Stievani); Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario (Weese)
| | - Júlio A N Lisbôa
- Department of Biomedical Sciences, Université de Montréal, Montreal, Quebec (Costa, Di Pietro); Department of Clinical Studies, Universidade Estadual de Londrina, Londrina, Paraná, Brazil (Bessegatto, Pereira, Stievani, Gomes, Lisbôa); Department of Clinical Studies, Universidade Filadelfia, Londrina, Paraná, Brazil (Stievani); Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario (Weese)
| | - J Scott Weese
- Department of Biomedical Sciences, Université de Montréal, Montreal, Quebec (Costa, Di Pietro); Department of Clinical Studies, Universidade Estadual de Londrina, Londrina, Paraná, Brazil (Bessegatto, Pereira, Stievani, Gomes, Lisbôa); Department of Clinical Studies, Universidade Filadelfia, Londrina, Paraná, Brazil (Stievani); Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario (Weese)
| |
Collapse
|
22
|
Free Faecal Water: Analysis of Horse Faecal Microbiota and the Impact of Faecal Microbial Transplantation on Symptom Severity. Animals (Basel) 2021; 11:ani11102776. [PMID: 34679798 PMCID: PMC8533009 DOI: 10.3390/ani11102776] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Free faecal water (FFW) in equines causes soiling of the hindquarters and tail and may also include additional symptoms. The cause of FFW is unknown. In this study it was investigated whether the microbes present in the last part of the gut (i.e., the hindgut microbiota) may be involved. From the analysis of faecal samples, it was found that horses suffering from FFW had no differences in their hindgut microbiota compared to healthy horses stabled at the same location. However, subsequent treatment of the FFW horses with a faecal microbiota transplantation (FMT) from a healthy donor animal resulted in a decrease in FFW symptom severity. Nevertheless, animals did not respond uniformly to this treatment, with some only having temporary decreases in FFW symptom severity. No lasting changes in the hindgut microbiota of the FFW horses occurred as a result of the faecal transplant. The practical implication of these findings is that FMT can potentially be used to temporarily alleviate FFW symptom severity in horses, although future studies using controls are needed to confirm the effectiveness of FMT to treat FFW. Abstract Free faecal water (FFW) in equines results in pollution of the hindquarters and tail and can also involve clinical signs. Though the cause of FFW is unknown, it was hypothesized that it may involve the gut microbiota. This hypothesis was addressed as follows. First, the faecal prokaryotic community composition of horses suffering from FFW relative to healthy controls (n = 10) was compared. Second, FFW horses were treated with a standardised faecal microbiota transplantation (FMT) protocol (n = 10), followed by assessment of FFW symptom severity and faecal prokaryotic community composition over a follow-up period of 168 days. No significant differences were found in the faecal microbiota composition of FFW horses compared to healthy controls (p > 0.05). Relative to before FMT, FFW symptom severity decreased in affected horses 14 days after FMT (p = 0.02) and remained decreased for the remainder of the study (p < 0.02). However, individual animal responses to FMT varied. FMT had no effect on FFW horse faecal prokaryotic community composition in terms of alpha or beta diversity. Alpha diversity of the donor inocula used in the FMT was always lower than that of the faecal microbiota of the FFW treated horses (p < 0.001). In conclusion, whilst findings indicate FFW horses do not have an altered hindgut microbiota, some horses that received FMT had a temporary alleviation of FFW symptom severity without causing changes in the faecal microbiota. Future studies using controls are now needed to confirm the effectiveness of FMT to treat FFW.
Collapse
|
23
|
Jiang G, Zhang X, Gao W, Ji C, Wang Y, Feng P, Feng Y, Zhang Z, Li L, Zhao F. Transport stress affects the fecal microbiota in healthy donkeys. J Vet Intern Med 2021; 35:2449-2457. [PMID: 34331476 PMCID: PMC8478045 DOI: 10.1111/jvim.16235] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/28/2022] Open
Abstract
Background With the development of large‐scale donkey farming in China, long‐distance transportation has become common practice, and the incidence of intestinal diseases after transportation has increased. The intestinal microbiota is important in health and disease, and whether or not transportation disturbs the intestinal microbiota in donkeys has not been investigated. Objectives To determine the effects of transportation on the fecal microbiota of healthy donkeys using 16S rRNA sequencing. Animals Fecal and blood samples were collected from 12 Dezhou donkeys before and after transportation. Methods Prospective controlled study. Cortisol, ACTH, and heat‐shock protein 90 (HSP90) concentrations were measured. Sequencing of 16S rRNA was used to assess the microbial composition. Alpha diversity and beta diversity were assessed. Results Results showed significant (P < .05) increases in cortisol (58.1 ± 14.6 to 71.1 ± 9.60 ng/mL), ACTH (163.8 ± 31.9 to 315.8 ± 27.9 pg/mL), and HSP90 (10.8 ± 1.67 to 14.6 ± 1.75 ng/mL) on the day of arrival. A significantly lower (P = .04) level of bacterial richness was found in fecal samples after transportation, compared with that before transportation without distinct changes in diversity. Most notably, donkeys had significant decreases in Atopostipes, Eubacterium, Streptococcus, and Coriobacteriaceae. Conclusions and Clinical Importance Transportation can induce stress in healthy donkeys and have some effect on the composition of the in fecal microbiota. Additional studies are required to understand the potential effect of these microbiota changes, especially significantly decreased bacteria, on the development intestinal diseases in donkeys during recovery from transportation.
Collapse
Affiliation(s)
- Guimiao Jiang
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.,National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd, Liaocheng, Shandong Province, China
| | - Xinhao Zhang
- National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd, Liaocheng, Shandong Province, China.,College of Animal Science and Technology, Shangdong Agricultural University, Taian, China
| | - Weiping Gao
- National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd, Liaocheng, Shandong Province, China
| | - Chuanliang Ji
- National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd, Liaocheng, Shandong Province, China
| | - Yantao Wang
- National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd, Liaocheng, Shandong Province, China
| | - Peixiang Feng
- National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd, Liaocheng, Shandong Province, China
| | - Yulong Feng
- National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd, Liaocheng, Shandong Province, China
| | - Zhiping Zhang
- The College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Lin Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Fuwei Zhao
- National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd, Liaocheng, Shandong Province, China.,College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| |
Collapse
|
24
|
Alterations in the Fecal Microbiome and Metabolome of Horses with Antimicrobial-Associated Diarrhea Compared to Antibiotic-Treated and Non-Treated Healthy Case Controls. Animals (Basel) 2021; 11:ani11061807. [PMID: 34204371 PMCID: PMC8235368 DOI: 10.3390/ani11061807] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/30/2021] [Indexed: 12/16/2022] Open
Abstract
Diarrhea is an adverse effect of antimicrobial therapy in horses. This matched, case-controlled study compared the fecal microbiome and metabolome of horses on antibiotics that developed diarrhea (AAD, n = 17) to those that did not develop diarrhea (ABX, n = 15) and to a control population not exposed to antibiotics (CON, n = 31). Fecal samples were collected from horses that were matched for diet and antimicrobial agent (including dose, route, and duration of therapy). Illumina sequencing of 16S rRNA genes was performed, and QIIME 2.0 was used to generate alpha and beta diversity metrics. Untargeted metabolomics using GC-MS platforms was performed and analyzed using Metaboanalyst 5.0. Microbiome composition was significantly different in AAD compared to CON (ANOSIM, R = 0.568, p = 0.001) but not to ABX (ANOSIM, R = 0.121, p = 0.0012). AAD and ABX horses had significantly decreased richness and evenness compared to CON horses (p < 0.05). Horses on antimicrobials (AAD and ABX) had significant changes in 14 phyla compared to CON horses. Only Verrucomicrobia distinguished AAD from ABX and CON horses (q = 0.0005). Metabolite profiles of horses with AAD clustered separately from ABX and CON horses. Seven metabolites were found to be significantly different between groups (p < 0.05): L-tyrosine, kynurenic acid, xanthurenic acid, 5-hydroxyindole-3-acetic acid, docosahexaenoic acid ethyl ester, daidzein, and N-acetyltyramine. Metabolite profiles of horses on antimicrobials, especially those with AAD, are altered compared to CON horses.
Collapse
|
25
|
Park T, Cheong H, Yoon J, Kim A, Yun Y, Unno T. Comparison of the Fecal Microbiota of Horses with Intestinal Disease and Their Healthy Counterparts. Vet Sci 2021; 8:vetsci8060113. [PMID: 34204317 PMCID: PMC8234941 DOI: 10.3390/vetsci8060113] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022] Open
Abstract
(1) Background: The intestinal microbiota plays an essential role in maintaining the host's health. Dysbiosis of the equine hindgut microbiota can alter the fermentation patterns and cause metabolic disorders. (2) Methods: This study compared the fecal microbiota composition of horses with intestinal disease and their healthy counterparts living in Korea using 16S rRNA sequencing from fecal samples. A total of 52 fecal samples were collected and divided into three groups: horses with large intestinal disease (n = 20), horses with small intestinal disease (n = 8), and healthy horses (n = 24). (3) Results: Horses with intestinal diseases had fewer species and a less diverse bacterial population than healthy horses. Lactic acid bacteria, Lachnospiraceae, and Lactobacillaceae were overgrown in horses with large intestinal colic. The Firmicutes to Bacteroidetes ratio (F/B), which is a relevant marker of gut dysbiosis, was 1.94, 2.37, and 1.74 for horses with large intestinal colic, small intestinal colic, and healthy horses, respectively. (4) Conclusions: The overgrowth of two lactic acid bacteria families, Lachnospiraceae and Lactobacillaceae, led to a decrease in hindgut pH that interfered with normal fermentation, which might cause large intestinal colic. The overgrowth of Streptococcus also led to a decrease in pH in the hindgut, which suppressed the proliferation of the methanogen and reduced methanogenesis in horses with small intestinal colic.
Collapse
Affiliation(s)
- Taemook Park
- Equine Clinic, Jeju Stud Farm, Korea Racing Authority, Jeju 63346, Korea; (T.P.); (J.Y.); (A.K.)
- College of Veterinary Medicine and Veterinary Medical Research Institute, Jeju National University, Jeju 63243, Korea
| | - Heetae Cheong
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Korea;
| | - Jungho Yoon
- Equine Clinic, Jeju Stud Farm, Korea Racing Authority, Jeju 63346, Korea; (T.P.); (J.Y.); (A.K.)
| | - Ahram Kim
- Equine Clinic, Jeju Stud Farm, Korea Racing Authority, Jeju 63346, Korea; (T.P.); (J.Y.); (A.K.)
| | - Youngmin Yun
- College of Veterinary Medicine and Veterinary Medical Research Institute, Jeju National University, Jeju 63243, Korea
- Correspondence: (Y.Y.); (T.U.); Tel.: +82-64-754-3376 (Y.Y.); +82-64-754-3354 (T.U.)
| | - Tatsuya Unno
- Faculty of Biotechnology, School of Life Sciences, SARI, Jeju 63243, Korea
- Subtropical/Tropical Organism Gene Bank, Jeju National University, Jeju 63243, Korea
- Correspondence: (Y.Y.); (T.U.); Tel.: +82-64-754-3376 (Y.Y.); +82-64-754-3354 (T.U.)
| |
Collapse
|
26
|
Pedroso AA, Lee MD, Maurer JJ. Strength Lies in Diversity: How Community Diversity Limits Salmonella Abundance in the Chicken Intestine. Front Microbiol 2021; 12:694215. [PMID: 34211451 PMCID: PMC8239400 DOI: 10.3389/fmicb.2021.694215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022] Open
Abstract
The transfer of the intestinal microbiota from adult to juvenile animals reduces Salmonella prevalence and abundance. The mechanism behind this exclusion is unknown, however, certain member species may exclude or promote pathogen colonization and Salmonella abundance in chickens correlates with intestinal community composition. In this study, newly hatched chicks were colonized with Salmonella Typhimurium and 16S rRNA libraries were generated from the cecal bacterial community at 21, 28, 35, and 42 days of age. Salmonella was quantified by real-time PCR. Operational taxonomic units (OTUs) were assigned, and taxonomic assignments were made, using the Ribosomal Database Project. Bacterial diversity was inversely proportional to the Salmonella abundance in the chicken cecum (p < 0.01). In addition, cecal communities with no detectable Salmonella (exclusive community) displayed an increase in the abundance of OTUs related to specific clostridial families (Ruminococcaceae, Eubacteriaceae, and Oscillospiraceae), genera (Faecalibacterium and Turicibacter) and member species (Ethanoligenens harbinense, Oscillibacter ruminantium, and Faecalibacterium prausnitzii). For cecal communities with high Salmonella abundance (permissive community), there was a positive correlation with the presence of unclassified Lachnospiraceae, clostridial genera Blautia and clostridial species Roseburia hominis, Eubacterium biforme, and Robinsoniella peoriensis. These findings strongly support the link between the intestinal bacterial species diversity and the presence of specific member species with Salmonella abundance in the chicken ceca. Exclusive bacterial species could prove effective as direct-fed microbials for reducing Salmonella in poultry while permissive species could be used to predict which birds will be super-shedders.
Collapse
Affiliation(s)
- Adriana A Pedroso
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Margie D Lee
- Department of Population Health, University of Georgia, Athens, GA, United States.,Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - John J Maurer
- Department of Population Health, University of Georgia, Athens, GA, United States.,Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| |
Collapse
|
27
|
The Equine Faecal Microbiota of Healthy Horses and Ponies in The Netherlands: Impact of Host and Environmental Factors. Animals (Basel) 2021; 11:ani11061762. [PMID: 34204691 PMCID: PMC8231505 DOI: 10.3390/ani11061762] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Several studies have described the bacterial composition in the intestines of horses, and several factors of influence have been detected. Variation in the results between studies, however, is substantial. Therefore, the current study aimed to study the bacterial composition in the faeces of healthy horses and ponies kept under standard housing and management condition in The Netherlands. Seventy-nine horses and ponies originating from two farms were included. Several factors, such as location, age, the season of sampling, horse type (horses vs. ponies) and pasture access significantly affected the bacterial composition. The current study provides important baseline information on variation in the bacterial composition in healthy horses and ponies under standard housing and management conditions. The aforementioned factors identified in this study to affect the bacterial population of the gut should be considered in future studies regarding the bacterial population of the equine gut. Abstract Several studies have described the faecal microbiota of horses and the factors that influence its composition, but the variation in results is substantial. This study aimed to investigate the microbiota composition in healthy equids in The Netherlands under standard housing and management conditions and to evaluate the effect of age, gender, horse type, diet, pasture access, the season of sampling and location on it. Spontaneously produced faecal samples were collected from the stall floor of 79 healthy horses and ponies at two farms. The validity of this sampling technique was evaluated in a small pilot study including five ponies showing that the microbiota composition of faecal samples collected up to 6 h after spontaneous defaecation was similar to that of the samples collected rectally. After DNA extraction, Illumina Miseq 16S rRNA sequencing was performed to determine microbiota composition. The effect of host and environmental factors on microbiota composition were determined using several techniques (NMDS, PERMANOVA, DESeq2). Bacteroidetes was the largest phylum found in the faecal microbiota (50.1%), followed by Firmicutes (28.4%). Alpha-diversity and richness decreased significantly with increasing age. Location, age, season, horse type and pasture access had a significant effect on beta-diversity. The current study provides important baseline information on variation in faecal microbiota in healthy horses and ponies under standard housing and management conditions. These results indicate that faecal microbiota composition is affected by several horse-related and environment-related factors, and these factors should be considered in future studies of the equine faecal microbiota.
Collapse
|
28
|
Mitchell S, Bull M, Muscatello G, Chapman B, Coleman NV. The equine hindgut as a reservoir of mobile genetic elements and antimicrobial resistance genes. Crit Rev Microbiol 2021; 47:543-561. [PMID: 33899656 DOI: 10.1080/1040841x.2021.1907301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Antibiotic resistance in bacterial pathogens is a growing problem for both human and veterinary medicine. Mobile genetic elements (MGEs) such as plasmids, transposons, and integrons enable the spread of antibiotic resistance genes (ARGs) among bacteria, and the overuse of antibiotics drives this process by providing the selection pressure for resistance genes to establish and persist in bacterial populations. Because bacteria, MGEs, and resistance genes can readily spread between different ecological compartments (e.g. soil, plants, animals, humans, wastewater), a "One Health" approach is needed to combat this problem. The equine hindgut is an understudied but potentially significant reservoir of ARGs and MGEs, since horses have close contact with humans, their manure is used in agriculture, they have a dense microbiome of both bacteria and fungi, and many antimicrobials used for equine treatment are also used in human medicine. Here, we collate information to date about resistance genes, plasmids, and class 1 integrons from equine-derived bacteria, we discuss why the equine hindgut deserves increased attention as a potential reservoir of ARGs, and we suggest ways to minimize the selection for ARGs in horses, in order to prevent their spread to the wider community.
Collapse
Affiliation(s)
- Scott Mitchell
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | | | - Gary Muscatello
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | | | - Nicholas V Coleman
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| |
Collapse
|
29
|
Faecal bacterial composition in horses with and without free faecal liquid: a case control study. Sci Rep 2021; 11:4745. [PMID: 33637818 PMCID: PMC7910430 DOI: 10.1038/s41598-021-83897-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/09/2021] [Indexed: 12/31/2022] Open
Abstract
Free faecal liquid (FFL) is a condition in horses which manifests as differential defecation of solid and liquid phases of faeces. The etiology of FFL is currently unknown, but deviances in the hindgut microbiota has been suggested to be of importance. The present study aimed to compare the faecal bacterial composition of farm-matched horses with (case, n = 50) and without (control, n = 50) FFL. Samples were collected at three different occasions. The V3 and V4 regions of the 16S rRNA gene were amplified and sequenced using Illumina sequencing. Also, samples were cultivated for detection of Clostridioides difficile and Clostridium perfringens. Analysis revealed similar faecal bacterial composition between case and control horses, but an effect of sampling period (p = 0.0001). Within sampling periods, 14 genera were present in higher or lower proportions in case compared to control horses in at least one sampling period. Compared to controls, case horses had higher relative abundance of Alloprevotella (adjusted p < 0.04) and lower relative abundance of Bacillus spp. (adjusted p < 0.03) in at least two sampling periods. All horses tested negative for C. difficile and C. perfringens by culture of faeces. Further studies are required to establish the clinical relevance of specific bacterial taxa in FFL.
Collapse
|
30
|
Wimmer-Scherr C, Taminiau B, Renaud B, van Loon G, Palmers K, Votion D, Amory H, Daube G, Cesarini C. Comparison of Fecal Microbiota of Horses Suffering from Atypical Myopathy and Healthy Co-Grazers. Animals (Basel) 2021; 11:ani11020506. [PMID: 33672034 PMCID: PMC7919468 DOI: 10.3390/ani11020506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 12/21/2022] Open
Abstract
Equine atypical myopathy (AM) is caused by hypoglycin A (HGA) and methylenecyclopropylglycine (MCPG) intoxication resulting from the ingestion of seeds or seedlings of some Acer tree species. Interestingly, not all horses pasturing in the same toxic environment develop signs of the disease. In other species, it has been shown that the intestinal microbiota has an impact on digestion, metabolism, immune stimulation and protection from disease. The objective of this study was to characterize and compare fecal microbiota of horses suffering from AM and healthy co-grazers. Furthermore, potential differences in fecal microbiota regarding the outcome of diseased animals were assessed. This prospective observational study included 59 horses with AM (29 survivors and 30 non-survivors) referred to three Belgian equine hospitals and 26 clinically healthy co-grazers simultaneously sharing contaminated pastures during spring and autumn outbreak periods. Fresh fecal samples (rectal or within 30 min of defecation) were obtained from all horses and bacterial taxonomy profiling obtained by 16S amplicon sequencing was used to identify differentially distributed bacterial taxa between AM-affected horses and healthy co-grazers. Fecal microbial diversity and evenness were significantly (p < 0.001) higher in AM-affected horses as compared with their non-affected co-grazers. The relative abundance of families Ruminococcaceae, Christensenellaceae and Akkermansiaceae were higher (p ≤ 0.001) whereas those of the Lachnospiraceae (p = 0.0053), Bacteroidales (p < 0.0001) and Clostridiales (p = 0.0402) were lower in horses with AM, especially in those with a poor prognosis. While significant shifts were observed, it is still unclear whether they result from the disease or might be involved in the onset of disease pathogenesis.
Collapse
Affiliation(s)
- Christina Wimmer-Scherr
- Equine Clinical Department, Faculty of Veterinary Medicine, Bât. B41, Sart Tilman, University of Liège, 4000 Liège, Belgium; (C.W.-S.); (H.A.)
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, Sart Tilman, University of Liège, 4000 Liège, Belgium; (B.T.); (B.R.); (D.V.); (G.D.)
| | - Bernard Taminiau
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, Sart Tilman, University of Liège, 4000 Liège, Belgium; (B.T.); (B.R.); (D.V.); (G.D.)
- Department of Food Sciences–Microbiology, Faculty of Veterinary Medicine, University of Liège, Avenue de Cureghem 10, Bât. B43b, 4000 Liège, Belgium
| | - Benoît Renaud
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, Sart Tilman, University of Liège, 4000 Liège, Belgium; (B.T.); (B.R.); (D.V.); (G.D.)
- Department of Functional Sciences, Pharmacology and Toxicology, Faculty of Veterinary Medicine, Bât. B41, Sart Tilman, University of Liège, 4000 Liège, Belgium
| | - Gunther van Loon
- Large Animal Internal Medicine, Gent University, 9820 Gent, Belgium;
| | | | - Dominique Votion
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, Sart Tilman, University of Liège, 4000 Liège, Belgium; (B.T.); (B.R.); (D.V.); (G.D.)
| | - Hélène Amory
- Equine Clinical Department, Faculty of Veterinary Medicine, Bât. B41, Sart Tilman, University of Liège, 4000 Liège, Belgium; (C.W.-S.); (H.A.)
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, Sart Tilman, University of Liège, 4000 Liège, Belgium; (B.T.); (B.R.); (D.V.); (G.D.)
| | - Georges Daube
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, Sart Tilman, University of Liège, 4000 Liège, Belgium; (B.T.); (B.R.); (D.V.); (G.D.)
- Department of Food Sciences–Microbiology, Faculty of Veterinary Medicine, University of Liège, Avenue de Cureghem 10, Bât. B43b, 4000 Liège, Belgium
| | - Carla Cesarini
- Equine Clinical Department, Faculty of Veterinary Medicine, Bât. B41, Sart Tilman, University of Liège, 4000 Liège, Belgium; (C.W.-S.); (H.A.)
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, Sart Tilman, University of Liège, 4000 Liège, Belgium; (B.T.); (B.R.); (D.V.); (G.D.)
- Correspondence:
| |
Collapse
|
31
|
McKinney CA, Bedenice D, Pacheco AP, Oliveira BCM, Paradis MR, Mazan M, Widmer G. Assessment of clinical and microbiota responses to fecal microbial transplantation in adult horses with diarrhea. PLoS One 2021; 16:e0244381. [PMID: 33444319 PMCID: PMC7808643 DOI: 10.1371/journal.pone.0244381] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/08/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND AND AIMS Fecal microbial transplantation (FMT) is empirically implemented in horses with colitis to facilitate resolution of diarrhea. The purpose of this study was to assess FMT as a clinical treatment and modulator of fecal microbiota in hospitalized horses with colitis. METHODS A total of 22 horses with moderate to severe diarrhea, consistent with a diagnosis of colitis, were enrolled at two referral hospitals (L1: n = 12; L2: n = 10). FMT was performed in all 12 patients on 3 consecutive days at L1, while treatment at L2 consisted of standard care without FMT. Manure was collected once daily for 4 days from the rectum in all colitis horses, prior to FMT for horses at L1, and from each manure sample used for FMT. Fecal samples from 10 clinically healthy control horses housed at L2, and 30 healthy horses located at 5 barns in regional proximity to L1 were also obtained to characterize the regional healthy equine microbiome. All fecal microbiota were analyzed using 16S amplicon sequencing. RESULTS AND CONCLUSIONS As expected, healthy horses at both locations showed a greater α-diversity and lower β-diversity compared to horses with colitis. The fecal microbiome of healthy horses clustered by location, with L1 horses showing a higher prevalence of Kiritimatiellaeota. Improved manure consistency (lower diarrhea score) was associated with a greater α-diversity in horses with colitis at both locations (L1: r = -0.385, P = 0.006; L2: r = -0.479, P = 0.002). Fecal transplant recipients demonstrated a greater overall reduction in diarrhea score (median: 4±3 grades), compared to untreated horses (median: 1.5±3 grades, P = 0.021), with a higher incidence in day-over-day improvement in diarrhea (22/36 (61%) vs. 10/28 (36%) instances, P = 0.011). When comparing microbiota of diseased horses at study conclusion to that of healthy controls, FMT-treated horses showed a lower mean UniFrac distance (0.53±0.27) than untreated horses (0.62±0.26, P<0.001), indicating greater normalization of the microbiome in FMT-treated patients.
Collapse
Affiliation(s)
- Caroline A. McKinney
- Department of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, United States of America
| | - Daniela Bedenice
- Department of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, United States of America
| | - Ana P. Pacheco
- Department of Clinical Sciences, Carlson College of Veterinary Medicine at Oregon State University, Corvallis, Oregon, United States of America
| | - Bruno C. M. Oliveira
- Faculdade de Medicina Veterinária, Universidade Estadual Paulista (UNESP), Araçatuba, Brazil
- Department of Infectious Diseases and Global Health, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, United States of America
| | - Mary-Rose Paradis
- Department of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, United States of America
| | - Melissa Mazan
- Department of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, United States of America
| | - Giovanni Widmer
- Department of Infectious Diseases and Global Health, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, United States of America
| |
Collapse
|
32
|
Sun Y, Li L, Song J, Mao W, Xiao K, Jiang C. Intrauterine Hypoxia Changed the Colonization of the Gut Microbiota in Newborn Rats. Front Pediatr 2021; 9:675022. [PMID: 33981656 PMCID: PMC8107277 DOI: 10.3389/fped.2021.675022] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 03/26/2021] [Indexed: 12/28/2022] Open
Abstract
Background: Accumulating evidence suggests a connection between the gut microbiota and neonatal diseases. Hypoxia may play an important role in the intestinal lesions in neonates. Objective: This study aims to determine whether the gut microbiota differs between intrauterine hypoxic rats and healthy controls and to identify the factors that influence the changes in the gut microbiota. Methods: We constructed an intrauterine hypoxia model in rats and collected the intestinal contents of intrauterine hypoxic newborn rats and normal newborn rats within 4 h and on the seventh day after birth. They were divided them into the intrauterine hypoxia first-day group (INH1), intrauterine hypoxia seventh-day group (INH7), normal first-day group (NOR1), and normal seventh-day group (NOR7). The contents of the intestines were sequenced with 16S rRNA sequencing, the sequencing results were analyzed for biological information, and the differences in the diversity, richness, and individual taxa among the groups were analyzed. Results: The abundance of the gut microbiota of neonatal rats with intrauterine hypoxia was higher than that of the control group rats. Intrauterine hypoxia altered the structural composition of the gut microbiota in neonatal rats. The INH1 group showed increased species richness, phylogenetic diversity, and β-diversity, and altered relative abundance in several taxa compared to those in the control group. The differences in the microbiota among the four groups were significantly higher than those within the group, and the differences in the abundance and diversity of the INH7 and NOR7 groups decreased after 7 days of suckling. Functional analysis based on the Cluster of Orthologous Groups (COG) suggested that 23 functional COG categories. There was no significant difference in the functional categories between the hypoxia group and the normal group. Conclusion: Intrauterine hypoxia changed the initial colonization of the gut microbiota in neonatal rats. It could increase the species richness and β-diversity of the gut microbiota, and altered relative abundances of several taxa.
Collapse
Affiliation(s)
- Yan Sun
- Department of Neonatology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lei Li
- Department of Neonatology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiayu Song
- Department of Neonatology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wei Mao
- Department of Neonatology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Kaihao Xiao
- Department of Neonatology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chunming Jiang
- Department of Neonatology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| |
Collapse
|
33
|
Thanissery R, McLaren MR, Rivera A, Reed AD, Betrapally NS, Burdette T, Winston JA, Jacob M, Callahan BJ, Theriot CM. Clostridioides difficile carriage in animals and the associated changes in the host fecal microbiota. Anaerobe 2020; 66:102279. [PMID: 33022384 PMCID: PMC10760528 DOI: 10.1016/j.anaerobe.2020.102279] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/31/2020] [Accepted: 09/27/2020] [Indexed: 02/08/2023]
Abstract
The relationship between the gut microbiota and Clostridioides difficile, and its role in the severity of C. difficile infection in humans is an area of active research. Intestinal carriage of toxigenic and non-toxigenic C. difficile strains, with and without clinical signs, is reported in animals, however few studies have looked at the risk factors associated with C. difficile carriage and the role of the host gut microbiota. Here, we isolated and characterized C. difficile strains from different animal species (predominantly canines (dogs), felines (cats), and equines (horses)) that were brought in for tertiary care at North Carolina State University Veterinary Hospital. C. difficile strains were characterized by toxin gene profiling, fluorescent PCR ribotyping, and antimicrobial susceptibility testing. 16S rRNA gene sequencing was done on animal feces to investigate the relationship between the presence of C. difficile and the gut microbiota in different hosts. Here, we show that C. difficile was recovered from 20.9% of samples (42/201), which included 33 canines, 2 felines, and 7 equines. Over 69% (29/42) of the isolates were toxigenic and belonged to 14 different ribotypes including ones known to cause CDI in humans. The presence of C. difficile results in a shift in the fecal microbial community structure in both canines and equines. Commensal Clostridium hiranonis was negatively associated with C. difficile in canines. Further experimentation showed a clear antagonistic relationship between the two strains in vitro, suggesting that commensal Clostridia might play a role in colonization resistance against C. difficile in different hosts.
Collapse
Affiliation(s)
- R Thanissery
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - M R McLaren
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - A Rivera
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - A D Reed
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - N S Betrapally
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - T Burdette
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - J A Winston
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - M Jacob
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - B J Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - C M Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA.
| |
Collapse
|
34
|
Zhao F, Jiang G, Ji C, Zhang Z, Gao W, Feng P, Li H, Li M, Liu H, Liu G, Magalhaes HB, Li J. Effects of long-distance transportation on blood constituents and composition of the nasal microbiota in healthy donkeys. BMC Vet Res 2020; 16:338. [PMID: 32933535 PMCID: PMC7493398 DOI: 10.1186/s12917-020-02563-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/08/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND This study aims to determine the effects of transportation on the nasal microbiota of healthy donkeys using 16S rRNA sequencing. RESULTS Deep nasal swabs and blood were sampled from 14 donkeys before and after 21 hours' long-distance transportation. The values of the plasma hormone (cortisol (Cor), adrenocorticotrophic hormone (ACTH)), biochemical indicators (total protein (TP), albumin (ALB), creatinine (CREA), lactic dehydrogenase (LDH), aspartate transaminase (AST), creatine kinase (CK), blood urea (UREA), plasma glucose (GLU)) and blood routine indices (white blood cell (WBC), lymphocyte (LYM), neutrophil (NEU), red blood cell (RBC), hemoglobin (HGB)) were measured. 16S rRNA sequencing was used to assess the nasal microbiota, including alpha diversity, beta diversity, and phylogenetic structures. Results showed that levels of Cor, ACTH, and heat-shock protein 90 (HSP90) were significantly increased (p < 0.05) after long-distance transportation. Several biochemical indicators (AST, CK) and blood routine indices (Neu, RBC, and HGB) increased markedly (p < 0.05), but the LYM decreased significantly (p < 0.05). Nine families and eight genera had a mean relative abundance over 1%. The predominant phyla in nasal microbiota after and before transportation were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Transportation stress induced significant changes in terms of nasal microbiota structure compared with those before transportation based on principal coordinate analysis (PCoA) coupled with analysis of similarities (ANOSIM) (p < 0.05). Among these changes, a notably gain in Proteobacteria and loss in Firmicutes at the phylum level was observed. CONCLUSIONS These results suggest transportation can cause stress to donkeys and change the richness and diversity of nasal microbiota. Further studies are required to understand the potential effect of these microbiota changes on the development of donkey respiratory diseases.
Collapse
Affiliation(s)
- Fuwei Zhao
- College of Veterinary Medicine, Yangzhou University, 225009, Yangzhou, P.R. China. .,National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd, 78 E-Jiao Street Donge County, Liaocheng, 252201, Shandong Province, China.
| | - Guimiao Jiang
- National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd, 78 E-Jiao Street Donge County, Liaocheng, 252201, Shandong Province, China.,Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, 110866, Shenyang, China
| | - Chuanliang Ji
- National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd, 78 E-Jiao Street Donge County, Liaocheng, 252201, Shandong Province, China
| | - Zhiping Zhang
- The College of Animal Science and Veterinary Medicine, Henan Agricultural University, 450002, Zhengzhou, China
| | - Weiping Gao
- National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd, 78 E-Jiao Street Donge County, Liaocheng, 252201, Shandong Province, China
| | - Peixiang Feng
- National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd, 78 E-Jiao Street Donge County, Liaocheng, 252201, Shandong Province, China
| | - Haijing Li
- National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd, 78 E-Jiao Street Donge County, Liaocheng, 252201, Shandong Province, China
| | - Min Li
- National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd, 78 E-Jiao Street Donge County, Liaocheng, 252201, Shandong Province, China
| | - Haibing Liu
- National Engineering Research Center for Gelatin-based TCM, Dong-E E-Jiao Co., Ltd, 78 E-Jiao Street Donge County, Liaocheng, 252201, Shandong Province, China
| | - Guiqin Liu
- College of Agronomy, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of Black Donkey, Liaocheng University, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng, China
| | - Humberto B Magalhaes
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Sp, 18618-681, Botucatu, Brazil
| | - Jianji Li
- College of Veterinary Medicine, Yangzhou University, 225009, Yangzhou, P.R. China.
| |
Collapse
|
35
|
Luminal and Mucosal Microbiota of the Cecum and Large Colon of Healthy and Diarrheic Horses. Animals (Basel) 2020; 10:ani10081403. [PMID: 32806591 PMCID: PMC7460328 DOI: 10.3390/ani10081403] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Acute diarrhea (colitis) is a major problem in adult horses and the role of the intestinal bacteria (microbiota) is still poorly understood in this species. The aim of this study was to compare the mucosal and luminal content microbiota of the cecum and colon of healthy and diarrheic horses. We concluded that microbial dysbiosis (changes in the normal microbiota composition) occurs in horses with colitis at different levels of the intestinal tract and microbiota composition is different between the mucosa and luminal content of diarrheic horses. Changes in species associated with dysbiosis could be used in the future for disease diagnosis, prognosis and treatment of equine colitis. Abstract The aim of this study was to compare the mucosal and luminal content microbiota of the cecum and colon of healthy and diarrheic horses. Marked differences in the richness and in the community composition between the mucosal and luminal microbiota of the cecum and large colon of horses with colitis were observed. Microbial dysbiosis occurs in horses with colitis at different levels of the intestinal tract, and microbiota composition is different between the mucosa and luminal content of diarrheic horses. The changes in some key taxa associated with dysbiosis in the equine intestinal microbiota, such as Escherichia, Fusobacterium and Lactobacillus, deserve further inquiry in order to determine their utility for disease diagnosis and treatment.
Collapse
|
36
|
Abstract
There is a need to develop feeding strategies to prevent the adverse effect of concentrate feeding in high-performance horses fed energy-dense diets aiming to maintain their health and welfare. The objective of this study is to determine the effect of a VistaEQ product containing 4% live yeast Saccharomyces cerevisiae (S. cerevisiae), with activity 5 × 108 colony-forming unit/g and fed 2 g/pony per day, on faecal microbial populations when supplemented with high-starch and high-fibre diets using Illumina next generation sequencing of the V3-V4 region of the 16S ribosomal RNA gene. The four treatments were allocated to eight mature Welsh section A pony geldings enrolled in a 4-period × 8 animal crossover design. Each 19-day experimental period consisted of an 18-day adaptation phase and a single collection day, followed by a 7-day wash out period. After DNA extraction from faeces and library preparation, α-diversity and linear discriminant analysis effect size were performed using 16S metagenomics pipeline in Quantitative Insights Into Microbial Ecology (QIIME™) and Galaxy/Hutlab. Differences between the groups were considered significant when linear discriminant analysis score was >2 corresponding to P < 0.05. The present study showed that S. cerevisiae used was able to induce positive changes in the equine microbiota when supplemented to a high-fibre diet: it increased relative abundance (RA) of Lachnospiraceae and Dehalobacteriaceae family members associated with a healthy core microbiome. Yeast supplementation also increased the RA of fibrolytic bacteria (Ruminococcus) when fed with a high-fibre diet and reduced the RA of lactate producing bacteria (Streptococcus) when a high-starch diet was fed. In addition, yeast increased the RA of acetic, succinic acid producing bacterial family (Succinivibrionaceae) and butyrate producing bacterial genus (Roseburia) when fed with high-starch and high-fibre diets, respectively. VistaEQ supplementation to equine diets can be potentially used to prevent acidosis and increase fibre digestibility. It may help to meet the energy requirements of performance horses while maintaining gut health.
Collapse
|
37
|
Paßlack N, Vahjen W, Zentek J. Impact of Dietary Cellobiose on the Fecal Microbiota of Horses. J Equine Vet Sci 2020; 91:103106. [PMID: 32684251 DOI: 10.1016/j.jevs.2020.103106] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 11/24/2022]
Abstract
Cellobiose is a disaccharide with potential prebiotic effects, as demonstrated in different animal species, but not yet in horses. It was, therefore, the aim of the present study to evaluate the impact of dietary cellobiose on the fecal microbiota of horses. Eight healthy adult horses and two ponies were included in this study. The animals received a diet without or with 10 g and 20 g cellobiose per day for 14 days each. At the end of the feeding periods, fresh fecal samples were collected to measure bacterial metabolites and the microbial composition. For the microbiota analysis, 16S rRNA gene sequencing was used. Cellobiose was well accepted and tolerated by the animals. The lowest fecal concentrations of D-lactate, propionic acid, i-valeric acid, and total short-chain fatty acids were measured at the dose 10 g cellobiose per horse per day (quadratic effect: P < .05). A dose-dependent increase of the relative abundance of Firmicutes (P = .049), Coriobacteriales (P < .001), and Clostridium (P = .031) could be detected. In addition, a dose-dependent decrease of the relative abundance of Bacteroidetes (P = .035) was observed. In conclusion, the increase of Coriobacteriales and Clostridium indicates a bacterial fermentation of cellobiose in the equine intestine, as members of both groups exert saccharolytic activity. As clostridia have previously been assumed to be a key component of the intestinal microbiota in horses, the observed increase of Clostridium in the feces might indicate beneficial and potentially prebiotic effects of cellobiose in horses. However, this finding requires further investigation, particularly with regard to the Clostridium species that have been promoted by dietary cellobiose.
Collapse
Affiliation(s)
- Nadine Paßlack
- Department of Veterinary Medicine, Institute of Animal Nutrition, Freie Universität Berlin, Berlin, Germany.
| | - Wilfried Vahjen
- Department of Veterinary Medicine, Institute of Animal Nutrition, Freie Universität Berlin, Berlin, Germany
| | - Jürgen Zentek
- Department of Veterinary Medicine, Institute of Animal Nutrition, Freie Universität Berlin, Berlin, Germany
| |
Collapse
|
38
|
Edwards JE, Schennink A, Burden F, Long S, van Doorn DA, Pellikaan WF, Dijkstra J, Saccenti E, Smidt H. Domesticated equine species and their derived hybrids differ in their fecal microbiota. Anim Microbiome 2020; 2:8. [PMID: 33499942 PMCID: PMC7807894 DOI: 10.1186/s42523-020-00027-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 03/02/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Compared to horses and ponies, donkeys have increased degradation of dietary fiber. The longer total mean retention time of feed in the donkey gut has been proposed to be the basis of this, because of the increased time available for feed to be acted upon by enzymes and the gut microbiota. However, differences in terms of microbial concentrations and/or community composition in the hindgut may also underpin the increased degradation of fiber in donkeys. Therefore, a study was conducted to assess if differences existed between the fecal microbiota of pony, donkey and hybrids derived from them (i.e. pony × donkey) when fed the same forage diet. RESULTS Fecal community composition of prokaryotes and anaerobic fungi significantly differed between equine types. The relative abundance of two bacterial genera was significantly higher in donkey compared to both pony and pony x donkey: Lachnoclostridium 10 and 'probable genus 10' from the Lachnospiraceae family. The relative abundance of Piromyces was significantly lower in donkey compared to pony × donkey, with pony not significantly differing from either of the other equine types. In contrast, the uncultivated genus SK3 was only found in donkey (4 of the 8 animals). The number of anaerobic fungal OTUs was also significantly higher in donkey than in the other two equine types, with no significant differences found between pony and pony × donkey. Equine types did not significantly differ with respect to prokaryotic alpha diversity, fecal dry matter content or fecal concentrations of bacteria, archaea and anaerobic fungi. CONCLUSIONS Donkey fecal microbiota differed from that of both pony and pony × donkey. These differences related to a higher relative abundance and diversity of taxa with known, or speculated, roles in plant material degradation. These findings are consistent with the previously reported increased fiber degradation in donkeys compared to ponies, and suggest that the hindgut microbiota plays a role. This offers novel opportunities for pony and pony × donkey to extract more energy from dietary fiber via microbial mediated strategies. This could potentially decrease the need for energy dense feeds which are a risk factor for gut-mediated disease.
Collapse
Affiliation(s)
- J. E. Edwards
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, Netherlands
| | - A. Schennink
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, Netherlands
- Present address: Micreos Human Health B.V, Bilthoven, Netherlands
| | - F. Burden
- The Donkey Sanctuary, Sidmouth, Devon EX10 ONU UK
| | - S. Long
- The Donkey Sanctuary, Sidmouth, Devon EX10 ONU UK
| | - D. A. van Doorn
- Division of Nutrition, Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, Netherlands
- Department of Equine Health, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, Netherlands
| | - W. F. Pellikaan
- Animal Nutrition Group, Wageningen University & Research, 6708 WD Wageningen, Netherlands
| | - J. Dijkstra
- Animal Nutrition Group, Wageningen University & Research, 6708 WD Wageningen, Netherlands
| | - E. Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - H. Smidt
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, Netherlands
| |
Collapse
|
39
|
McKinney CA, Oliveira BCM, Bedenice D, Paradis MR, Mazan M, Sage S, Sanchez A, Widmer G. The fecal microbiota of healthy donor horses and geriatric recipients undergoing fecal microbial transplantation for the treatment of diarrhea. PLoS One 2020; 15:e0230148. [PMID: 32155205 PMCID: PMC7064224 DOI: 10.1371/journal.pone.0230148] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 02/21/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND AND AIMS Fecal microbial transplantation (FMT), a treatment for certain gastrointestinal conditions associated with dysbiosis in people, is also empirically employed in horses with colitis. This study used microbiota high-throughput sequencing to compare the fecal microbial profile of healthy horses to that of geriatric microbial transplant recipients experiencing diarrhea and tested whether FMT restores microbiota diversity. METHODS To evaluate the effect of environment and donor characteristics on the intestinal microbiota, fecal samples were collected per rectum from 15 healthy young-adult (2-12 years) and 15 geriatric (≥20 years) horses. Additionally, FMT was performed for 3 consecutive days in 5 geriatric horses with diarrhea using feces from the same healthy donor. Fecal samples were collected from both donor and recipient prior to each FMT and from recipients 24 hours following the last FMT. The profile of the fecal bacterial microbiota was compared using 16S amplicon sequencing. RESULTS AND CONCLUSIONS In contrast to diet and farm location, age did not significantly affect the healthy equine fecal microbiota, indicating that both healthy geriatric and young-adult horses may serve as FMT donors. The fecal microbiota of horses with diarrhea was significantly more variable in terms of β-diversity than that of healthy horses. An inverse correlation between diarrhea score and relative abundance of Verrucomicrobia was identified in surviving FMT recipients. At study completion, the fecal microbiota of horses which responded to FMT had a higher α-diversity than prior to treatment and was phylogenetically more similar to that of the donor.
Collapse
Affiliation(s)
- Caroline A. McKinney
- Department of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA, United States of America
| | - Bruno C. M. Oliveira
- Department of Infectious Diseases and Global Health, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA, United States of America
- Faculdade de Medicina Veterinária, Universidade Estadual Paulista (Unesp), Araçatuba, Brazil
| | - Daniela Bedenice
- Department of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA, United States of America
| | - Mary-Rose Paradis
- Department of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA, United States of America
| | - Melissa Mazan
- Department of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA, United States of America
| | - Sophie Sage
- Department of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA, United States of America
| | - Alfredo Sanchez
- Department of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA, United States of America
| | - Giovanni Widmer
- Department of Infectious Diseases and Global Health, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA, United States of America
| |
Collapse
|
40
|
Su S, Zhao Y, Liu Z, Liu G, Du M, Wu J, Bai D, Li B, Bou G, Zhang X, Dugarjaviin M. Characterization and comparison of the bacterial microbiota in different gastrointestinal tract compartments of Mongolian horses. Microbiologyopen 2020; 9:1085-1101. [PMID: 32153142 PMCID: PMC7294312 DOI: 10.1002/mbo3.1020] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/12/2022] Open
Abstract
The intestinal microbiota plays an important role in the health and metabolism of the host. Next‐generation sequencing technology has enabled the characterization of the gut microbiota of several animal species. We analyzed the intestinal microbiota in six different parts of the gastrointestinal tracts (GITs) of five Mongolian horses by sequencing the 16S rRNA gene V3‐V4 hypervariable region. All horses were kept in the natural habitat of the Inner Mongolia grassland. Significant differences were observed among the microbiota compositions of the distinct GIT regions. In addition, while the microbial community structures of the small and large intestine were significantly different, those of the cecum and colon were similar. In the foregut, Firmicutes (65%) and Proteobacteria (23%) were the most abundant, while Firmicutes (45%) and Bacteroidetes (42%) were the most common in the hindgut. At the level of family, Ruminococcaceae (p = .203), Lachnospiraceae (p = .157), Rikenellaceae (p = .122), and Prevotellaceae (p = .068) were predominant in the hindgut, while the relative abundance of the Akkermansia genus (5.7%, p = .039) was higher in the ventral colon. In terms of the putative functions, the ratio of microbial abundance in the different parts of the GIT was similar, the result can help characterize the gut microbial structure of different animals.
Collapse
Affiliation(s)
- Shaofeng Su
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, China.,Biotechnology Research Centre, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Yiping Zhao
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, China
| | - Zongzheng Liu
- Animal Husbandry and Veterinary Research Institute of Qingdao, Qingdao, China
| | - Guiqin Liu
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, China.,Agricultural College, Liaocheng University, Liaocheng, China
| | - Ming Du
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, China
| | - Jing Wu
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, China
| | - Dongyi Bai
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, China
| | - Bei Li
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, China
| | - Gerelchimeg Bou
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, China
| | - Xinzhuang Zhang
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, China
| | - Manglai Dugarjaviin
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, China
| |
Collapse
|
41
|
Edwards JE, Shetty SA, van den Berg P, Burden F, van Doorn DA, Pellikaan WF, Dijkstra J, Smidt H. Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species. Anim Microbiome 2020; 2:6. [PMID: 33499982 PMCID: PMC7807809 DOI: 10.1186/s42523-020-0023-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 01/29/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Equine gut microbiology studies to date have primarily focused on horses and ponies, which represent only one of the eight extant equine species. This is despite asses and mules comprising almost half of the world's domesticated equines, and donkeys being superior to horses/ponies in their ability to degrade dietary fiber. Limited attention has also been given to commensal anaerobic fungi and archaea even though anaerobic fungi are potent fiber degrading organisms, the activity of which is enhanced by methanogenic archaea. Therefore, the objective of this study was to broaden the current knowledge of bacterial, anaerobic fungal and archaeal diversity of the equine fecal microbiota to multiple species of equines. Core taxa shared by all the equine fecal samples (n = 70) were determined and an overview given of the microbiota across different equine types (horse, donkey, horse × donkey and zebra). RESULTS Equine type was associated with differences in both fecal microbial concentrations and community composition. Donkey was generally most distinct from the other equine types, with horse and zebra not differing. Despite this, a common bacterial core of eight OTUs (out of 2070) and 16 genus level groupings (out of 231) was found in all the fecal samples. This bacterial core represented a much larger proportion of the equine fecal microbiota than previously reported, primarily due to the detection of predominant core taxa belonging to the phyla Kiritimatiellaeota (formerly Verrucomicrobia subdivision 5) and Spirochaetes. The majority of the core bacterial taxa lack cultured representation. Archaea and anaerobic fungi were present in all animals, however, no core taxon was detected for either despite several taxa being prevalent and predominant. CONCLUSIONS Whilst differences were observed between equine types, a core fecal microbiota existed across all the equines. This core was composed primarily of a few predominant bacterial taxa, the majority of which are novel and lack cultured representation. The lack of microbial cultures representing the predominant taxa needs to be addressed, as their availability is essential to gain fundamental knowledge of the microbial functions that underpin the equine hindgut ecosystem.
Collapse
Affiliation(s)
- J. E. Edwards
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE Netherlands
| | - S. A. Shetty
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE Netherlands
| | - P. van den Berg
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE Netherlands
| | - F. Burden
- The Donkey Sanctuary, Sidmouth, Devon EX10 ONU UK
| | - D. A. van Doorn
- Division of Nutrition, Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CM Netherlands
- Department of Equine Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL Netherlands
| | - W. F. Pellikaan
- Animal Nutrition Group, Wageningen University & Research, Wageningen, 6708 WD Netherlands
| | - J. Dijkstra
- Animal Nutrition Group, Wageningen University & Research, Wageningen, 6708 WD Netherlands
| | - H. Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE Netherlands
| |
Collapse
|
42
|
Garber A, Hastie P, Murray JA. Factors Influencing Equine Gut Microbiota: Current Knowledge. J Equine Vet Sci 2020; 88:102943. [PMID: 32303307 DOI: 10.1016/j.jevs.2020.102943] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 01/23/2020] [Accepted: 01/23/2020] [Indexed: 12/21/2022]
Abstract
Gastrointestinal microbiota play a crucial role in nutrient digestion, maintaining animal health and welfare. Various factors may affect microbial balance often leading to disturbances that may result in debilitating conditions such as colic and laminitis. The invention of next-generation sequencing technologies and bioinformatics has provided valuable information on the effects of factors influencing equine gut microbiota. Among those factors are nutrition and management (e.g., diet, supplements, exercise), medical substances (e.g., antimicrobials, anthelmintics, anesthetics), animal-related factors (breed and age), various pathological conditions (colitis, diarrhea, colic, laminitis, equine gastric ulcer syndrome), as well as stress-related factors (transportation and weaning). The aim of this review is to assimilate current knowledge on equine microbiome studies, focusing on the effect of factors influencing equine gastrointestinal microbiota. Decrease in microbial diversity and richness leading to decrease in stability; decrease in Lachnospiraceae and Ruminococcaceae family members, which contribute to gut homeostasis; increase in Lactobacillus and Streptococcus; decrease in lactic acid utilizing bacteria; decrease in butyrate-producing bacteria that have anti-inflammatory properties may all be considered as a negative change in equine gut microbiota. Shifts in Firmicutes and Bacteroidetes have often been observed in the literature in response to certain treatments or when describing healthy and unhealthy animals; however, these shifts are inconsistent. It is time to move forward and use the knowledge now acquired to start manipulating the microbiota of horses.
Collapse
Affiliation(s)
- Anna Garber
- School of Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK.
| | - Peter Hastie
- School of Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Jo-Anne Murray
- School of Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| |
Collapse
|
43
|
Kauter A, Epping L, Semmler T, Antao EM, Kannapin D, Stoeckle SD, Gehlen H, Lübke-Becker A, Günther S, Wieler LH, Walther B. The gut microbiome of horses: current research on equine enteral microbiota and future perspectives. Anim Microbiome 2019; 1:14. [PMID: 33499951 PMCID: PMC7807895 DOI: 10.1186/s42523-019-0013-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/09/2019] [Indexed: 12/26/2022] Open
Abstract
Understanding the complex interactions of microbial communities including bacteria, archaea, parasites, viruses and fungi of the gastrointestinal tract (GIT) associated with states of either health or disease is still an expanding research field in both, human and veterinary medicine. GIT disorders and their consequences are among the most important diseases of domesticated Equidae, but current gaps of knowledge hinder adequate progress with respect to disease prevention and microbiome-based interventions. Current literature on enteral microbiomes mirrors a vast data and knowledge imbalance, with only few studies tackling archaea, viruses and eukaryotes compared with those addressing the bacterial components.Until recently, culture-dependent methods were used for the identification and description of compositional changes of enteral microorganisms, limiting the outcome to cultivatable bacteria only. Today, next generation sequencing technologies provide access to the entirety of genes (microbiome) associated with the microorganisms of the equine GIT including the mass of uncultured microbiota, or "microbial dark matter".This review illustrates methods commonly used for enteral microbiome analysis in horses and summarizes key findings reached for bacteria, viruses and fungi so far. Moreover, reasonable possibilities to combine different explorative techniques are described. As a future perspective, knowledge expansion concerning beneficial compositions of microorganisms within the equine GIT creates novel possibilities for early disorder diagnostics as well as innovative therapeutic approaches. In addition, analysis of shotgun metagenomic data enables tracking of certain microorganisms beyond species barriers: transmission events of bacteria including pathogens and opportunists harboring antibiotic resistance factors between different horses but also between humans and horses will reach new levels of depth concerning strain-level distinctions.
Collapse
Affiliation(s)
- Anne Kauter
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Lennard Epping
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | | | - Dania Kannapin
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Sabita D Stoeckle
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Heidrun Gehlen
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Antina Lübke-Becker
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany
| | - Sebastian Günther
- Pharmaceutical Biology Institute of Pharmacy, Universität Greifswald, Greifswald, Germany
| | | | - Birgit Walther
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
| |
Collapse
|
44
|
Schoster A, Kunz T, Lauper M, Graubner C, Schmitt S, Weese JS. Prevalence of Clostridium difficile and Clostridium perfringens in Swiss horses with and without gastrointestinal disease and microbiota composition in relation to Clostridium difficile shedding. Vet Microbiol 2019; 239:108433. [PMID: 31767096 DOI: 10.1016/j.vetmic.2019.108433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 11/27/2022]
Abstract
Overgrowth of enteric clostridia in dysbiosis in horses with colic is presumed but scarcely investigated. The objective was to provide prevalence data of Clostridium difficile and Clostridium perfringens in horses with and without gastrointestinal disease in Switzerland, and investigate microbiota differences between C. difficile shedders and non-shedders. Fecal samples were taken from healthy horses (n = 103), horses with colic (n = 98) and horses with diarrhea (n = 151). Colic horses were sampled on three days. Selective enrichment culture and molecular typing for C. difficile and C. perfringens was performed. Microbiota differences between horses with colic shedding (n = 7) and not shedding (n = 7) C. difficile were assessed using metagenomic sequencing. The cumulative prevalence (19% C. difficile; 16% C. perfringens) was higher compared to single day samples (1-10% C. difficile; 3-8% C. perfringens, all p < 0.003). Horses with colic shed significantly more C. difficile (p < 0.001) but not C. perfringens (p = 0.09) compared to healthy horses. Prevalence in horses with diarrhea was 8% for both Clostridium species. There were no significant microbiota differences between C. difficile shedders and non-shedders with regards to relative abundance on any phylogenetic level, and alpha diversity. Limited differences were seen on LEfSE analysis and in beta diversity indices. Multiple fecal samples should be taken when investigating shedding of enteric clostridia. As horses with colic shed more enteric clostridia compared to healthy horses special biosecurity protocols for horses with colic should be considered in hospitals. Differences in microbiota composition between C. difficile shedders and non-shedders were limited. Further studies on the role of dysbiosis in C. difficile are needed.
Collapse
Affiliation(s)
- A Schoster
- University of Zurich, Vetsuisse Faculty, Equine Department, Winterthurerstrasse 260, 8057 Zurich, Switzerland.
| | - T Kunz
- University of Zurich, Vetsuisse Faculty, Equine Department, Winterthurerstrasse 260, 8057 Zurich, Switzerland.
| | - M Lauper
- University of Berne, Vetsuisse Faculty, Institut Suisse de Médicine Equine, Länggassstrasse 124, 3012 Bern, Switzerland.
| | - C Graubner
- University of Berne, Vetsuisse Faculty, Institut Suisse de Médicine Equine, Länggassstrasse 124, 3012 Bern, Switzerland.
| | - S Schmitt
- University of Zurich, Vetsuisse Faculty, Section of Veterinary Bacteriology, Winterthurerstrasse 270, 8057 Zurich, Switzerland.
| | - J S Weese
- University of Guelph, Ontario Veterinary College, Department of Pathobiology, N1G2W1 Guelph, Canada.
| |
Collapse
|
45
|
Berry ASF, Kelly BJ, Barnhart D, Kelly DJ, Beiting DP, Baldassano RN, Redding LE. Gut microbiota features associated with Clostridioides difficile colonization in puppies. PLoS One 2019; 14:e0215497. [PMID: 31469837 PMCID: PMC6716646 DOI: 10.1371/journal.pone.0215497] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/05/2019] [Indexed: 02/06/2023] Open
Abstract
In people, colonization with Clostridioides difficile, the leading cause of antibiotic-associated diarrhea, has been shown to be associated with distinct gut microbial features, including reduced bacterial community diversity and depletion of key taxa. In dogs, the gut microbiota features that define C. difficile colonization are less well understood. We sought to define the gut microbiota features associated with C. difficile colonization in puppies, a population where the prevalence of C. difficile has been shown to be elevated, and to define the effect of puppy age and litter upon these features and C. difficile risk. We collected fecal samples from weaned (n = 27) and unweaned (n = 74) puppies from 13 litters and analyzed the effects of colonization status, age and litter on microbial diversity using linear mixed effects models. Colonization with C. difficile was significantly associated with younger age, and colonized puppies had significantly decreased bacterial community diversity and differentially abundant taxa compared to non-colonized puppies, even when adjusting for age. C. difficile colonization remained associated with decreased bacterial community diversity, but the association did not reach statistical significance in a mixed effects model incorporating litter as a random effect. Even though litter explained a greater proportion (67%) of the variability in microbial diversity than colonization status, we nevertheless observed heterogeneity in gut microbial community diversity and colonization status within more than half of the litters, suggesting that the gut microbiota contributes to colonization resistance against C. difficile. The colonization of puppies with C. difficile has important implications for the potential zoonotic transfer of this organism to people. The identified associations point to mechanisms by which C. difficile colonization may be reduced.
Collapse
Affiliation(s)
- Alexander S. F. Berry
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Brendan J. Kelly
- Divisions of Infectious Diseases and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Denise Barnhart
- Department of Pathobiology, University of Pennsylvania, School of Veterinary Medicine, Kennett Square, Pennsylvania, United States of America
| | - Donna J. Kelly
- Department of Pathobiology, University of Pennsylvania, School of Veterinary Medicine, Kennett Square, Pennsylvania, United States of America
| | - Daniel P. Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Robert N. Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Laurel E. Redding
- Department of Clinical Sciences, University of Pennsylvania, School of Veterinary Medicine, Kennett Square, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
46
|
Li Y, Zhang K, Liu Y, Li K, Hu D, Wronski T. Community Composition and Diversity of Intestinal Microbiota in Captive and Reintroduced Przewalski's Horse ( Equus ferus przewalskii). Front Microbiol 2019; 10:1821. [PMID: 31440229 PMCID: PMC6693443 DOI: 10.3389/fmicb.2019.01821] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 07/23/2019] [Indexed: 01/11/2023] Open
Abstract
Large and complex intestinal microbiota communities in hosts have profound effects on digestion and metabolism. To better understand the community structure of intestinal microbiota in Przewalski’s horse (Equus ferus przewalskii) under different feeding regimes, we compared bacterial diversity and composition between captive and reintroduced Przewalski’s horses, using high-throughput 16S-rRNA gene sequencing for identification. Reintroduced Przewalski’s horses were sampled in two Chinese nature reserves, i.e., Dunhuang Xihu Nature Reserve (DXNR; n = 8) in Gansu Province and Kalamaili Nature Reserve (KNR; n = 12) in Xinjiang Province, and compared to a captive population at the Przewalski’s Horse Breeding Center in Xinjiang (PHBC; n = 11). The composition of intestinal microbiota in Przewalski’s horses was significantly different at the three study sites. Observed species was lowest in DXNR, but highest in KNR. Lowest Shannon diversity was observed in DXNR, while in KNR and PHBC had a moderately high diversity; Simpson diversity showed an opposite trend compared with the Shannon index. Linear Discriminant Analysis effect size was used to determine differentially distributed bacterial taxa at each study site. The most dominant phyla of intestinal microbiota were similar in all feeding regimes, including mainly Firmicutes, Bacteroidetes, Verrucomicrobia, and Spirochaetes. Differing abundances of intestinal microbiota in Przewalski’s horses may be related to different food types at each study site, differences in diversity may be attributed to low quality food in DXNR. Results indicated that diet is one of the important factors that can influence the structure of intestinal microbiota communities in Przewalski’s horse. These findings combined with a detailed knowledge of the available and consumed food plant species could provide guidelines for the selection of potential future reintroduction sites.
Collapse
Affiliation(s)
- Yimeng Li
- College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Ke Zhang
- College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yang Liu
- College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Kai Li
- College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Defu Hu
- College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Torsten Wronski
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, United Kingdom
| |
Collapse
|
47
|
De Witte C, Demeyere K, De Bruyckere S, Taminiau B, Daube G, Ducatelle R, Meyer E, Haesebrouck F. Characterization of the non-glandular gastric region microbiota in Helicobacter suis-infected versus non-infected pigs identifies a potential role for Fusobacterium gastrosuis in gastric ulceration. Vet Res 2019; 50:39. [PMID: 31126330 PMCID: PMC6534906 DOI: 10.1186/s13567-019-0656-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/08/2019] [Indexed: 02/08/2023] Open
Abstract
Helicobacter suis has been associated with development of gastric ulcers in the non-glandular part of the porcine stomach, possibly by affecting gastric acid secretion and altering the gastric microbiota. Fusobacterium gastrosuis is highly abundant in the gastric microbiota of H. suis-infected pigs and it was hypothesized that this micro-organism could play a role in the development of gastric ulceration. The aim of this study was to obtain further insights in the influence of a naturally acquired H. suis infection on the microbiota of the non-glandular part of the porcine stomach and in the pathogenic potential of F. gastrosuis. Infection with H. suis influenced the relative abundance of several taxa at phylum, family, genus and species level. H. suis-infected pigs showed a significantly higher colonization rate of F. gastrosuis in the non-glandular gastric region compared to non-infected pigs. In vitro, viable F. gastrosuis strains as well as their lysate induced death of both gastric and oesophageal epithelial cell lines. These gastric cell death inducing bacterial components were heat-labile. Genomic analysis revealed that genes are present in the F. gastrosuis genome with sequence similarity to genes described in other Fusobacterium spp. that encode factors involved in adhesion, invasion and induction of cell death as well as in immune evasion. We hypothesize that, in a gastric environment altered by H. suis, colonization and invasion of the non-glandular porcine stomach region and production of epithelial cell death inducing metabolites by F. gastrosuis, play a role in gastric ulceration.
Collapse
Affiliation(s)
- Chloë De Witte
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
| | - Kristel Demeyere
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Sofie De Bruyckere
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Bernard Taminiau
- Department of Food Sciences, FARAH, University of Liège, Liège, Belgium
| | - Georges Daube
- Department of Food Sciences, FARAH, University of Liège, Liège, Belgium
| | - Richard Ducatelle
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Evelyne Meyer
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| |
Collapse
|
48
|
Abstract
Akkermansia muciniphila, a symbiotic bacterium of the mucus layer, can utilize mucin as its sole carbon, nitrogen, and energy source. As an abundant resident in the intestinal tract of humans and animals, the probiotic effects of A. muciniphila including metabolic modulation, immune regulation and gut health protection, have been widely investigated. Various diseases such as metabolic syndromes and auto-immnue diseases have been reported to be associated with the disturbance of the abundance of A. muciniphila. In this review, we describe the biological characterization of A. muciniphia, the factors that influence its colonization of the intestinal tract; and discuss the current state of our knowledge on its role in host health and disease.
Collapse
Affiliation(s)
- Qixiao Zhai
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
| | - Saisai Feng
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Narbad Arjan
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China.,Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China.,Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, P.R. China.,(Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
| |
Collapse
|
49
|
Costa MC, Weese JS. Understanding the Intestinal Microbiome in Health and Disease. Vet Clin North Am Equine Pract 2018; 34:1-12. [PMID: 29402480 DOI: 10.1016/j.cveq.2017.11.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
This article provides readers with the basic concepts necessary to understand studies using recent molecular methods performed in intestinal microbiome assessment, with special emphasis on the high throughput sequencing. This review also summarizes the current knowledge on this topic and discusses future insights on the interaction between the intestinal microbiome and equine health.
Collapse
Affiliation(s)
- Marcio Carvalho Costa
- Department of Veterinary Biomedicine, University of Montreal, 3200 Rue Sicotte, Saint-Hyacinthe, Quebec J2S 2M2, Canada.
| | - Jeffrey Scott Weese
- Department of Pathobiology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| |
Collapse
|
50
|
De Witte C, Taminiau B, Flahou B, Hautekiet V, Daube G, Ducatelle R, Haesebrouck F. In-feed bambermycin medication induces anti-inflammatory effects and prevents parietal cell loss without influencing Helicobacter suis colonization in the stomach of mice. Vet Res 2018; 49:35. [PMID: 29636083 PMCID: PMC5894178 DOI: 10.1186/s13567-018-0530-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/21/2018] [Indexed: 12/18/2022] Open
Abstract
The minimum inhibitory concentration of bambermycin on three porcine Helicobacter suis strains was shown to be 8 μg/mL. The effect of in-feed medication with this antibiotic on the course of a gastric infection with one of these strains, the host response and the gastric microbiota was determined in mice, as all of these parameters may be involved in gastric pathology. In H. suis infected mice which were not treated with bambermycin, an increased number of infiltrating B-cells, T-cells and macrophages in combination with a Th2 response was demonstrated, as well as a decreased parietal cell mass. Compared to this non-treated, infected group, in H. suis infected mice medicated with bambermycin, gastric H. suis colonization was not altered, but a decreased number of infiltrating T-cells, B-cells and macrophages as well as downregulated expressions of IL-1β, IL-8M, IL-10 and IFN-γ were demonstrated and the parietal cell mass was not affected. In bambermycin treated mice that were not infected with H. suis, the number of infiltrating T-cells and expression of IL-1β were lower than in non-infected mice that did not receive bambermycin. Gastric microbiota analysis indicated that the relative abundance of bacteria that might exert unfavorable effects on the host was decreased during bambermycin supplementation. In conclusion, bambermycin did not affect H. suis colonization, but decreased gastric inflammation and inhibited the effects of a H. suis infection on parietal cell loss. Not only direct interaction of H. suis with parietal cells, but also inflammation may play a role in death of these gastric acid producing cells.
Collapse
Affiliation(s)
- Chloë De Witte
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
| | - Bernard Taminiau
- Department of Food Sciences, FARAH, Université de Liège, Avenue de Cureghem 10, 4000, Liège, Belgium
| | - Bram Flahou
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | | | - Georges Daube
- Department of Food Sciences, FARAH, Université de Liège, Avenue de Cureghem 10, 4000, Liège, Belgium
| | - Richard Ducatelle
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
| |
Collapse
|