1
|
Álvarez Narváez S, Beaudry MS, Norris CG, Bartlett PB, Glenn TC, Sanchez S. Improved Equine Fecal Microbiome Characterization Using Target Enrichment by Hybridization Capture. Animals (Basel) 2024; 14:445. [PMID: 38338088 PMCID: PMC10854943 DOI: 10.3390/ani14030445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
GITDs are among the most common causes of death in adult and young horses in the United States (US). Previous studies have indicated a connection between GITDs and the equine gut microbiome. However, the low taxonomic resolution of the current microbiome sequencing methods has hampered the identification of specific bacterial changes associated with GITDs in horses. Here, we have compared TEHC, a new approach for 16S rRNA gene selection and sequencing, with conventional 16S rRNA gene amplicon sequencing for the characterization of the equine fecal microbiome. Both sequencing approaches were used to determine the fecal microbiome of four adult horses and one commercial mock microbiome. Our results show that TEHC yielded significantly more operational taxonomic units (OTUs) than conventional 16S amplicon sequencing when the same number of reads were used in the analysis. This translated into a deeper and more accurate characterization of the fecal microbiome when the samples were sequenced with TEHC according to the relative abundance analysis. Alpha and beta diversity metrics corroborated these findings and demonstrated that the microbiome of the fecal samples was significantly richer when sequenced with TEHC compared to 16S amplicon sequencing. Altogether, our study suggests that the TEHC strategy provides a more extensive characterization of the fecal microbiome of horses than the current alternative based on the PCR amplification of a portion of the 16S rRNA gene.
Collapse
Affiliation(s)
- Sonsiray Álvarez Narváez
- Department of Infectious Disease, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.G.N.); (P.B.B.)
| | - Megan S. Beaudry
- Department of Environmental Health Science, College of Public Health, The University of Georgia, Athens, GA 30602, USA; (M.S.B.); (T.C.G.)
| | - Connor G. Norris
- Department of Infectious Disease, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.G.N.); (P.B.B.)
| | - Paula B. Bartlett
- Department of Infectious Disease, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.G.N.); (P.B.B.)
| | - Travis C. Glenn
- Department of Environmental Health Science, College of Public Health, The University of Georgia, Athens, GA 30602, USA; (M.S.B.); (T.C.G.)
| | - Susan Sanchez
- Department of Infectious Disease, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.G.N.); (P.B.B.)
| |
Collapse
|
2
|
Scilimati N, Cerullo A, Nannarone S, Gialletti R, Giusto G, Bertoletti A. Small Colon Faecalith with Large Colon Displacement in Ten Cases (2015-2023): A Detailed Case Description and Literature Review. Animals (Basel) 2024; 14:262. [PMID: 38254431 PMCID: PMC10812404 DOI: 10.3390/ani14020262] [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: 11/08/2023] [Revised: 01/07/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
Small colon impaction can result in accumulation of ingesta, gas, and fluid orally to the impaction site in horses. Large colon tympany, which is caused by ingesta fermentation, can be a predisposing factor for intestinal displacement. The aim of this study is to report the history, clinical, and surgical findings of horses and ponies referred for abdominal pain not responsive to drugs where a right dorsal displacement (RDD) or large colon volvulus (LCV), together with a small colon faecalith (SCF), were diagnosed during surgery. This study included a total of five horses and five ponies. Based on clinical features, ultrasonographic examination, and rectal palpation, an initial suspected diagnosis of RDD, LCV or severe large colon and caecum distension was made in all clinical cases. Due to the lack of response to medical treatment or worsening of colic symptoms, surgery was performed in all horses: diagnosis of RDD or LCV was made and a SCF was incidentally detected in all cases. While exploratory laparotomy was carried out in all the patients for the presence of a large colon issue, it was probably subsequent to an obstruction of the small colon caused by the presence of an SCF, which is generally difficult to diagnose. This study reported the presence of SCF as a possible cause of secondary RDD or LCV in horses and ponies that, to the authors' knowledge, has never been reported.
Collapse
Affiliation(s)
- Nicola Scilimati
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy; (N.S.); (S.N.); (A.B.)
| | - Anna Cerullo
- Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, Italy; (A.C.); (G.G.)
| | - Sara Nannarone
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy; (N.S.); (S.N.); (A.B.)
| | - Rodolfo Gialletti
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy; (N.S.); (S.N.); (A.B.)
| | - Gessica Giusto
- Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, Italy; (A.C.); (G.G.)
| | - Alice Bertoletti
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy; (N.S.); (S.N.); (A.B.)
| |
Collapse
|
3
|
Bull K, Davies G, Jenkins TP, Peachey L. The faecal microbiome of Exmoor ponies shows step-wise compositional changes with increasing levels of management by humans. Equine Vet J 2024; 56:159-170. [PMID: 37264698 DOI: 10.1111/evj.13961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 05/05/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Horses can suffer from gastrointestinal (GI) disease in domestic environments, often precipitated by human-led changes in management. Understanding the consequences of these changes on equine gut microbiota is key to the prevention of such disease episodes. OBJECTIVE Profile the faecal microbiota of adult female Exmoor ponies under three management conditions, representing increasing levels of management by humans, encompassing different diets; whilst controlling for age, breed and sex. STUDY DESIGN Cross-sectional descriptive. METHODS Faecal samples were collected from three populations of Exmoor ponies kept under contrasting management conditions: 29 adult female ponies in groups with low management (LM) (n = 10), medium management (MM) (n = 10) and high management (HM) (n = 9) levels, based on diet, drug use, handling and exercise. Faecal microbial composition was profiled via high-throughput sequencing of the bacterial 16S rRNA gene, and functional metagenome predictions. RESULTS We observed profound step-wise changes in microbiome structure in the transition from LM to MM to HM. A relatively high abundance of Proteobacteria and Tenericutes was associated with the HM group; higher abundance of Methanobacteria was observed in the LM group. The MM group had intermediate levels of these taxa and exhibited high 'within group' variation in alpha diversity. Functional predictions revealed increased amino acid and lipid metabolism in HM; energy metabolism in LM and carbohydrate metabolism and immune/metabolic disease pathways in MM. MAIN LIMITATIONS Low group sizes, incomplete knowledge of bacterial genomes in equine gut microbiota and it was not possible to assess the relative impact of diet, drug use, handling and exercise on the microbiome as variables were confounded. CONCLUSIONS Human-led management factors had profound step-wise effects on faecal microbial composition. Based on functional metagenome predictions, we hypothesise that dietary differences between groups were the major driver of observed differences.
Collapse
Affiliation(s)
- Katie Bull
- School of Veterinary Sciences, University of Bristol, Bristol, UK
| | - Gareth Davies
- School of Veterinary Sciences, University of Bristol, Bristol, UK
| | - Timothy P Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Laura Peachey
- School of Veterinary Sciences, University of Bristol, Bristol, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| |
Collapse
|
4
|
Li C, Li X, Guo R, Ni W, Liu K, Liu Z, Dai J, Xu Y, Abduriyim S, Wu Z, Zeng Y, Lei B, Zhang Y, Wang Y, Zeng W, Zhang Q, Chen C, Qiao J, Liu C, Hu S. Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse. MICROBIOME 2023; 11:7. [PMID: 36631912 PMCID: PMC9835274 DOI: 10.1186/s40168-022-01448-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/14/2022] [Indexed: 06/12/2023]
Abstract
BACKGROUND As a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food production, and transportation. The gut microbiota plays an important role in the health, diseases, athletic performance, and behaviour of horses. RESULTS Here, using approximately 2.2 Tb of metagenomic sequencing data from gut samples from 242 horses, including 110 samples from the caecum and 132 samples from the rectum (faeces), we assembled 4142 microbial metagenome-assembled genomes (MAG), 4015 (96.93%) of which appear to correspond to new species. From long-read data, we successfully assembled 13 circular whole-chromosome bacterial genomes representing novel species. The MAG contained over 313,568 predicted carbohydrate-active enzymes (CAZy), over 59.77% of which had low similarity match in CAZy public databases. High abundance and diversity of antibiotic resistance genes (ARG) were identified in the MAG, likely showing the wide use of antibiotics in the management of horse. The abundances of at least 36 MAG (e.g. MAG belonging to Lachnospiraceae, Oscillospiraceae, and Ruminococcus) were higher in racehorses than in nonracehorses. These MAG enriched in racehorses contained every gene in a major pathway for producing acetate and butyrate by fibre fermentation, presenting potential for greater amount of short-chain fatty acids available to fuel athletic performance. CONCLUSION Overall, we assembled 4142 MAG from short- and long-read sequence data in the horse gut. Our dataset represents an exhaustive microbial genome catalogue for the horse gut microbiome and provides a valuable resource for discovery of performance-enhancing microbes and studies of horse gut microbiome. Video Abstract.
Collapse
Affiliation(s)
- Cunyuan Li
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
- Key Laboratory of Ecological Corps for Oasis City and Mountain Basin System, Shihezi University, Shihezi, 832003 Xinjiang China
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Xiaoyue Li
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
- Key Laboratory of Ecological Corps for Oasis City and Mountain Basin System, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Rongjun Guo
- Novogene Bioinformatics Institute, Beijing, 100000 China
| | - Wei Ni
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
- Key Laboratory of Ecological Corps for Oasis City and Mountain Basin System, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Kaiping Liu
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 830003 Xinjiang China
| | - Zhuang Liu
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Jihong Dai
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Yueren Xu
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
| | | | - Zhuangyuan Wu
- Xinjiang Altay Animal Husbandry and Veterinary Station, Altay, 836501 Xinjiang China
| | - Yaqi Zeng
- College of Animal Science, Xinjiang Agricultural University, Urumqi, 830000 Xinjiang China
| | - Bingbing Lei
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Yunfeng Zhang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 830003 Xinjiang China
| | - Yue Wang
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Weibin Zeng
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Qiang Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Chuangfu Chen
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Jun Qiao
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003 Xinjiang China
| | - Chen Liu
- Novogene Bioinformatics Institute, Beijing, 100000 China
| | - Shengwei Hu
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China
- Key Laboratory of Ecological Corps for Oasis City and Mountain Basin System, Shihezi University, Shihezi, 832003 Xinjiang China
| |
Collapse
|
5
|
Quiñones-Pérez C, Hidalgo M, Ortiz I, Crespo F, Vega-Pla JL. Characterization of the seminal bacterial microbiome of healthy, fertile stallions using next-generation sequencing. Anim Reprod 2021; 18:e20200052. [PMID: 34394753 PMCID: PMC8356074 DOI: 10.1590/1984-3143-ar2020-0052] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/22/2021] [Indexed: 11/22/2022] Open
Abstract
High-throughput sequencing studies have shown the important role microbial communities play in the male reproductive tract, indicating differences in the semen microbial composition between fertile and infertile males. Most of these studies were made on human beings but little is known regarding domestic animals. Seminal bacteria studies made in stallions mostly focus on pathogenic bacteria and on their impact on reproductive technology. However, little is known about stallion commensal seminal microflora. That ultimately hinders our capacity to associate specific bacteria to conditions or seminal quality. Therefore, the aim of this study was to characterize the seminal microbial composition of 12 healthy, fertile stallion using next-generation sequencing. Hypervariable region V3 was chosen for bacterial identification. A total of nine phyla was detected. The most abundant ones were Bacteroidetes (46.50%), Firmicutes (29.92%) and Actinobacteria (13.58%). At family level, we found 69 bacterial families, but only nine are common in all samples. Porphyromonadaceae (33.18%), Peptoniphilaceae (14.09%), Corynebacteriaceae (11.32%) and Prevotellaceae (9.05%) were the most representative ones, while the Firmicutes phylum displayed the highest number of families (23, a third of the total). Samples showed high inter-subject variability. Findings previously described in other species notably differ from our findings. Families found in human such as Lactobacillaceae, Staphylococcaceae and Streptococcaceae only represented a 0.00%, 0.17% and 0.22% abundance in our samples, respectively. In conclusion, Porphyromonadaceae, Prevotellaceae, Peptoniphilaceae and Corynebacteriaceae families are highly represented in the seminal microbiome of healthy, fertile stallions. A high variation among individuals is also observed.
Collapse
Affiliation(s)
- Carlota Quiñones-Pérez
- Laboratorio de Investigación Aplicada, Cría Caballar de las Fuerzas Armadas, Córdoba, España
| | - Manuel Hidalgo
- Veterinary Reproduction Group Department of Animal Medicine and Surgery, Universidad de Córdoba, Córdoba, España
| | - Isabel Ortiz
- Veterinary Reproduction Group Department of Animal Medicine and Surgery, Universidad de Córdoba, Córdoba, España
| | - Francisco Crespo
- Centro Militar de Cría Caballar de Ávila, Cría Caballar de las Fuerzas Armadas, Ávila, España
| | - José Luis Vega-Pla
- Laboratorio de Investigación Aplicada, Cría Caballar de las Fuerzas Armadas, Córdoba, España
| |
Collapse
|
6
|
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
|
7
|
Hesta M, Costa M. How Can Nutrition Help with Gastrointestinal Tract-Based Issues? Vet Clin North Am Equine Pract 2021; 37:63-87. [PMID: 33820610 DOI: 10.1016/j.cveq.2020.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Many horses are fed differently than their wild ancestors. They often have limited access to pasture and are fed conserved forage and concentrates rich in starch and sugars, in only 2 meals per day. Feeding practices in contrast to natural feeding behavior can lead to gastrointestinal issues. Standard nutritional evaluation is warranted because of its important role in prevention and in treatment and management of diseases. When medical and nutritional treatments are combined, success rates are higher. New techniques to characterize equine microbiota have been used, allowing for microbiota manipulation to prevent and treat intestinal diseases.
Collapse
Affiliation(s)
- Myriam Hesta
- Department of Veterinary Medical Imaging and Small Animal Orthopedics, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke B9820, Belgium.
| | - Marcio Costa
- Department of Veterinary Biomedical Sciences, University of Montreal, Saint-Hyacinthe, Canada
| |
Collapse
|
8
|
Willette JA, Pitta D, Indugu N, Vecchiarelli B, Hennessy ML, Dobbie T, Southwood LL. Experimental crossover study on the effects of withholding feed for 24 h on the equine faecal bacterial microbiota in healthy mares. BMC Vet Res 2021; 17:3. [PMID: 33402190 PMCID: PMC7786913 DOI: 10.1186/s12917-020-02706-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/02/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND An association between equine gastrointestinal disease causing colic signs and changes in faecal bacterial microbiota has been identified. The reasons for these changes and their clinical relevance has not been investigated. Withholding feed, which is an integral part of managing horses with colic, may contribute to the observed changes in the microbiota and impact interpretation of findings in horses with colic. Study objectives were, therefore, to determine the effect of withholding feed for 24 h on equine faecal bacterial microbiota in healthy mares to differentiate the effects of withholding feed from the changes potentially associated with the disease. RESULTS Species richness and Shannon diversity (alpha diversity) were significantly lower at the late withheld (10-24 h post withholding feed) and early refed (2-12 h post re-feeding) time points compared to samples from fed horses (P < 0.01). Restoration of species richness and diversity began to occur at the late refed (18-24 h post re-feeding) time points. Horses having feed withheld had a distinct bacterial population compared to fed horses (beta diversity). Bacteroidetes BS11 and Firmicutes Christensenellaceae, Christensenella, and Dehalobacteriaceae were significantly increased in horses withheld from feed primarily during the late withheld and early refed time points. Bacteroidetes Marinilabiaceae and Prevotellaceae, Firmicutes Veillonellaceae, Anaerovibrio, and Bulleidia, and Proteobacteria GMD14H09 were significantly decreased in horses with feed withheld at late withheld, early refed, and late refed time periods (P < 0.01). Changes in commensal gut microbiota were not significant between groups. CONCLUSIONS Withholding feed has a significant effect on faecal bacterial microbiota diversity and composition particularly following at least 10 h of withholding feed and should be taken into consideration when interpreting data on the equine faecal bacterial microbiota in horses.
Collapse
Affiliation(s)
- Jaclyn A Willette
- Departments of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, 382 West Street Rd, Kennett Square, PA, 19348, USA
- Present address: Department of Clinical Sciences, Michigan State University, East Lansing, MI, USA
| | - Dipti Pitta
- Departments of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, 382 West Street Rd, Kennett Square, PA, 19348, USA
| | - Nagaraju Indugu
- Departments of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, 382 West Street Rd, Kennett Square, PA, 19348, USA
| | - Bonnie Vecchiarelli
- Departments of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, 382 West Street Rd, Kennett Square, PA, 19348, USA
| | - Meagan L Hennessy
- Departments of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, 382 West Street Rd, Kennett Square, PA, 19348, USA
| | - Tamara Dobbie
- Departments of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, 382 West Street Rd, Kennett Square, PA, 19348, USA
| | - Louise L Southwood
- Departments of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, 382 West Street Rd, Kennett Square, PA, 19348, USA.
| |
Collapse
|
9
|
Stewart HL, Pitta D, Indugu N, Vecchiarelli B, Hennessy ML, Engiles JB, Southwood LL. Changes in the faecal bacterial microbiota during hospitalisation of horses with colic and the effect of different causes of colic. Equine Vet J 2020; 53:1119-1131. [PMID: 33222287 DOI: 10.1111/evj.13389] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 10/08/2020] [Accepted: 11/12/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Previous studies have identified alterations in the faecal microbiota of horses with colic; however, further work is needed to interpret these findings. OBJECTIVES To compare the faecal microbiota of horses presenting for colic at hospital admission, day 1 and day 3/discharge and with different colic duration and lesion locations. STUDY DESIGN Prospective observational clinical study. METHODS Faecal samples were collected from 17 colic cases at hospital admission, on day 1 and on day 3 post-admission or at the time of hospital discharge if prior to 72 hours. Faecal samples were extracted for genomic DNA, PCR-amplified, sequenced and analysed using QIIME. Species richness and Shannon diversity (alpha diversity) were estimated. The extent of the relationship between bacterial communities (beta diversity) was quantified using pairwise UniFrac distances, visualised using principal coordinate analysis (PCoA) and statistically analysed using permutational multivariate analysis of variance (PERMANOVA). The relative abundance of bacterial populations at the different time points and in different types of colic was compared using ANCOM. RESULTS There was a decrease in species richness from admission to day 3/hospital discharge (P < .05), and a lower species richness (P = .005) and Shannon diversity (P = .02) in horses with colic ≥60 h compared to <60 h. Based on PCoA and PERMANOVA, there was a significant difference in bacterial community composition for horses with different colic duration (P = .001) and lesion location (P = .006). Several differences in bacterial phyla and genera were observed at different time points and with different types of colic. MAIN LIMITATIONS Relatively low numbers and a diverse population of horses. CONCLUSIONS The microbiota change from hospital admission to day 3/discharge in horses with colic and horses with colic ≥60 h and large colon lesions have a distinct bacterial population compared to horses with colic <60 h and small intestinal lesions.
Collapse
Affiliation(s)
- Holly L Stewart
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, Kennett Square, PA, USA
| | - Dipti Pitta
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, Kennett Square, PA, USA
| | - Nagaraju Indugu
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, Kennett Square, PA, USA
| | - Bonnie Vecchiarelli
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, Kennett Square, PA, USA
| | - Meagan L Hennessy
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, Kennett Square, PA, USA
| | - Julie B Engiles
- Department of Pathobiology, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, Kennett Square, PA, USA
| | - Louise L Southwood
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, Kennett Square, PA, USA
| |
Collapse
|
10
|
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
|