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McPherson A, Tranter B, Phipps A, Laven R, House J, Zadoks RN, Rowe S. Etiology and epidemiology of digital dermatitis in Australian dairy herds. J Dairy Sci 2024; 107:5924-5941. [PMID: 38331178 DOI: 10.3168/jds.2023-24258] [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: 09/29/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
Bovine digital dermatitis (BDD) is an important cause of lameness in dairy cows worldwide. However, very little is known about this disease in Australian herds, which are predominantly managed on pasture. The primary objectives of this cross-sectional study were to describe the presence and prevalence of BDD in Australian dairy herds and to characterize the microbiota of healthy skin and M4 lesions of BDD-affected, pasture-managed cows. Cows from 71 dairy herds were examined at milking time to identify the presence of BDD lesions. True prevalence was estimated using Bayesian methods with informative priors for sensitivity and specificity. Biopsy samples (n = 60) were collected from cows with and without BDD lesions in 7 pasture-based herds. The microbiota in the superficial and deep strata of each tissue biopsy were characterized via sequencing of the V3-V4 region of the bacterial ribosomal RNA gene. Lesions were detected in 1,817 (11.5%) of 15,813 cows and in 68 of 71 (95.8%) herds. The median herd-level apparent and true prevalences of BDD were 8.5% and 18.1%, respectively, but prevalences varied considerably between farms. On farms with BDD, M4 lesions accounted for 70% to 100% of all lesions (interquartile range = 95.1%-100%, median = 100%); M2 lesions (i.e., large ulcerative lesions) were observed at low prevalence (<2.2%) in the few herds (7/71, 9.9%) where they were found. There was a significant difference in the composition of the microbiota between healthy skin and M4 lesions but not between superficial and deep tissue layers. Several gut- and effluent-associated bacterial taxa, including Lentimicrobium and Porphyromonas, which have previously been associated with BDD, were abundant in BDD lesions but not in control biopsies. Our study supports the idea that such taxa are involved in, although possibly not essential to, lesion development and persistence in pasture-managed cows in Australia. Our results also suggest that Dichelobacter may contribute to the disease process. We conclude that BDD is likely to occur in most Australian dairy farms, but that further studies are needed to identify its effect on cow welfare and productivity. Further investigation of the etiology of BDD in Australian dairy herds is also necessary to inform prevention and control strategies.
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Affiliation(s)
- Andrew McPherson
- Sydney School of Veterinary Science, University of Sydney, Camden, New South Wales, 2570, Australia
| | - Bill Tranter
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, 4810, Australia; Tableland Veterinary Service, Malanda, Queensland, 4885, Australia
| | - Ash Phipps
- Rochester Veterinary Practice, Rochester, Victoria, 3561, Australia
| | - Richard Laven
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North 4474, New Zealand
| | - John House
- Sydney School of Veterinary Science, University of Sydney, Camden, New South Wales, 2570, Australia
| | - Ruth N Zadoks
- Sydney School of Veterinary Science, University of Sydney, Camden, New South Wales, 2570, Australia
| | - Sam Rowe
- Sydney School of Veterinary Science, University of Sydney, Camden, New South Wales, 2570, Australia.
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Usié A, Leão C, Gaspar D, Monteiro H, Tábuas L, Bettencourt E, Caetano P, Padre L, Carolino N, Ramos AM, de Matos C, Branco S. A metagenomics approach to characterize the footrot microbiome in Merino sheep. Vet Microbiol 2023; 281:109745. [PMID: 37080086 DOI: 10.1016/j.vetmic.2023.109745] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/17/2023] [Accepted: 04/14/2023] [Indexed: 04/22/2023]
Abstract
In the Portuguese Alentejo region, Merino sheep breed is the most common breed, reared for the production of meat, dairy, and wool. Footrot is responsible for lameness, decreased animal welfare, and higher production losses, generating a negative economic impact. The disease is caused by Dichelobacter nodosus that interacts with the sheep foot microbiome, to date largely uncharacterized. In fact, Dichelobacter nodosus is not able to induce footrot by itself being required the presence of a second pathogen known as Fusobacterium necrophorum. To understand and characterize the footrot microbiome dynamics of different footrot lesion scores, a whole metagenome sequencing (WMGS) approach was used. Foot tissue samples were collected from 212 animals with different degrees of footrot lesion scores, ranging from 0 to 5. Distinct bacterial communities were associated with feet with different footrot scores identifying a total of 63 phyla and 504 families. As the severity of footrot infection increases the microorganisms' diversity decreases triggering a shift in the composition of the microbiome from a dominant gram-positive in mild stages to a dominant gram-negative in the severe stages. Several species previously associated with footrot and other polymicrobial diseases affecting the epidermis and provoking inflammatory responses such as Treponema spp., Staphylococcus spp., Streptococcus spp. and Campylobacter spp. were identified proliferating along with the lesions' severity. Although these bacteria are not able to initiate footrot, several evidences have been described supporting their association with the severity and incidence increase of footrot lesions caused by Dichelobacter nodosus and Fusobacterium necrophorum. Further investigation is required to establish the roles of particular taxa and identify which of them play a role in the disease process and which are opportunistic pathogens.
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Affiliation(s)
- Ana Usié
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), 7801-908 Beja, Portugal; MED - Mediterranean Institute for Agriculture, Environment and Development & CHANGE - Global Change and Sustainability Institute, CEBAL - Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, 7801-908 Beja, Portugal.
| | - Célia Leão
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), 7801-908 Beja, Portugal; MED - Mediterranean Institute for Agriculture, Environment and Development & CHANGE - Global Change and Sustainability Institute, CEBAL - Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, 7801-908 Beja, Portugal; Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
| | - Daniel Gaspar
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), 7801-908 Beja, Portugal; BIOPOIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Portugal
| | - Helena Monteiro
- Associação de Agricultores do Sul (ACOS), Rua Cidade De São Paulo, Aptd. 294, Beja, Portugal
| | - Lino Tábuas
- Associação de Agricultores do Sul (ACOS), Rua Cidade De São Paulo, Aptd. 294, Beja, Portugal
| | - Elisa Bettencourt
- MED-Mediterranean Institute for Agriculture, Environment and Development & CHANGE - Global Change and Sustainability Institute, University of Évora, Polo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - Pedro Caetano
- MED-Mediterranean Institute for Agriculture, Environment and Development & CHANGE - Global Change and Sustainability Institute, University of Évora, Polo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - Ludovina Padre
- MED-Mediterranean Institute for Agriculture, Environment and Development & CHANGE - Global Change and Sustainability Institute, University of Évora, Polo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - Nuno Carolino
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
| | - António Marcos Ramos
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), 7801-908 Beja, Portugal; MED - Mediterranean Institute for Agriculture, Environment and Development & CHANGE - Global Change and Sustainability Institute, CEBAL - Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, 7801-908 Beja, Portugal
| | - Claudino de Matos
- Associação de Agricultores do Sul (ACOS), Rua Cidade De São Paulo, Aptd. 294, Beja, Portugal.
| | - Sandra Branco
- MED-Mediterranean Institute for Agriculture, Environment and Development & CHANGE - Global Change and Sustainability Institute, University of Évora, Polo da Mitra, Ap. 94, 7006-554 Évora, Portugal.
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Dong H, Chen X, Zhao X, Zhao C, Mehmood K, Kulyar MFEA, Bhutta ZA, Zeng J, Nawaz S, Wu Q, Li K. Intestine microbiota and SCFAs response in naturally Cryptosporidium-infected plateau yaks. Front Cell Infect Microbiol 2023; 13:1105126. [PMID: 36936759 PMCID: PMC10014559 DOI: 10.3389/fcimb.2023.1105126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/16/2023] [Indexed: 03/06/2023] Open
Abstract
Diarrhea is a severe bovine disease, globally prevalent in farm animals with a decrease in milk production and a low fertility rate. Cryptosporidium spp. are important zoonotic agents of bovine diarrhea. However, little is known about microbiota and short-chain fatty acids (SCFAs) changes in yaks infected with Cryptosporidium spp. Therefore, we performed 16S rRNA sequencing and detected the concentrations of SCFAs in Cryptosporidium-infected yaks. Results showed that over 80,000 raw and 70,000 filtered sequences were prevalent in yak samples. Shannon (p<0.01) and Simpson (p<0.01) were both significantly higher in Cryptosporidium-infected yaks. A total of 1072 amplicon sequence variants were shared in healthy and infected yaks. There were 11 phyla and 58 genera that differ significantly between the two yak groups. A total of 235 enzymes with a significant difference in abundance (p<0.001) were found between healthy and infected yaks. KEGG L3 analysis discovered that the abundance of 43 pathways was significantly higher, while 49 pathways were significantly lower in Cryptosporidium-infected yaks. The concentration of acetic acid (p<0.05), propionic acid (p<0.05), isobutyric acid (p<0.05), butyric acid (p<0.05), and isovaleric acid was noticeably lower in infected yaks, respectively. The findings of the study revealed that Cryptosporidium infection causes gut dysbiosis and results in a significant drop in the SCFAs concentrations in yaks with severe diarrhea, which may give new insights regarding the prevention and treatment of diarrhea in livestock.
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Affiliation(s)
- Hailong Dong
- Key Laboratory of Clinical Veterinary Medicine in Tibet, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
| | - Xiushuang Chen
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiaoxiao Zhao
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Chenxi Zhao
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Khalid Mehmood
- Department of Clinical Medicine and Surgery, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | | | - Zeeshan Ahmad Bhutta
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Jiangyong Zeng
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Shah Nawaz
- Department of Anatomy, Faculty of Veterinary Science, University of Agriculture, Faisalabad, Pakistan
| | - Qingxia Wu
- Key Laboratory of Clinical Veterinary Medicine in Tibet, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- *Correspondence: Qingxia Wu, ; Kun Li,
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Qingxia Wu, ; Kun Li,
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Canales N, Bustamante H, Wilson-Welder J, Thomas C, Ramirez E, Salgado M. First Molecular Confirmation of Treponema spp. in Lesions Consistent with Digital Dermatitis in Chilean Dairy Cattle. Pathogens 2022; 11:pathogens11050510. [PMID: 35631031 PMCID: PMC9145681 DOI: 10.3390/pathogens11050510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/17/2022] [Accepted: 04/20/2022] [Indexed: 12/10/2022] Open
Abstract
Digital dermatitis (DD) is a highly contagious and infectious disease in cattle which has a considerable negative economic impact worldwide, and adversely affects animal welfare. Members of the genus Treponema are the only bacterial agents for which there is consistent evidence of participation in DD lesions. In Chile, DD has been described since the 1990s, but only under a clinical approach. To date, the presence of the pathogenic agent has not been confirmed in Chile by any type of confirmatory microbiological diagnosis. The aim of the present study was to detect the presence of Treponema spp. DNA in lesions consistent with DD, in Chilean dairy cattle for the first time. We provide PCR confirmation of Treponema spp. in Chilean dairy cattle affected by DD. The high rate of positive results, as well as the proportion of the main Treponema species involved, is in line with what have been described in published studies elsewhere. Future herd control plans should benefit from the molecular detection of these pathogenic bacteria associated with DD.
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Affiliation(s)
- Nivia Canales
- Laboratorio de Enfermedades Infecciosas, Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Casilla, P.O. Box 567, Valdivia 5090000, Chile; (N.C.); (C.T.); (E.R.)
- Escuela de Graduados, P.O. Box 567, Valdivia 5090000, Chile
| | - Hedie Bustamante
- Institute de Ciencias Clínicas Veterinarias, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Casilla, P.O. Box 567, Valdivia 5090000, Chile;
| | - Jennifer Wilson-Welder
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA;
| | - Cristian Thomas
- Laboratorio de Enfermedades Infecciosas, Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Casilla, P.O. Box 567, Valdivia 5090000, Chile; (N.C.); (C.T.); (E.R.)
| | - Emilio Ramirez
- Laboratorio de Enfermedades Infecciosas, Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Casilla, P.O. Box 567, Valdivia 5090000, Chile; (N.C.); (C.T.); (E.R.)
| | - Miguel Salgado
- Laboratorio de Enfermedades Infecciosas, Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Casilla, P.O. Box 567, Valdivia 5090000, Chile; (N.C.); (C.T.); (E.R.)
- Correspondence: ; Tel.: +56-63-2-444358
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Mo K, Li J, Liu F, Xu Y, Huang X, Ni H. Superiority of Microencapsulated Essential Oils Compared With Common Essential Oils and Antibiotics: Effects on the Intestinal Health and Gut Microbiota of Weaning Piglet. Front Nutr 2022; 8:808106. [PMID: 35096948 PMCID: PMC8790512 DOI: 10.3389/fnut.2021.808106] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022] Open
Abstract
Essential oils (EOs) have long been considered an alternative to antibiotics in the breeding industry. However, they are unstable and often present unpleasant odors, which hampers their application. Microencapsulation can protect the active gradients from oxidation and allow them to diffuse slowly in the gastrointestinal tract. The purpose of this study was to investigate the effect of microencapsulation technology on the biological function of EOs and the possibility of using microencapsulate EOs (MEEOs) as an alternative to antibiotics in weaning piglets. First, we prepared MEEOs and common EOs both containing 2% thymol, 5% carvacrol and 3% cinnamaldehyde (w/w/w). Then, a total of 48 weaning piglets were randomly allotted to six dietary treatments: (1) basal diet; (2) 75 mg/kg chlortetracycline; (3) 100 mg/kg common EOs; (4) 500 mg/kg common EOs; (5) 100 mg/kg MEEOs; and (6) 500 mg/kg MEEO. The trial lasted 28 days. The results showed that piglets in the 100 mg/kg MEEOs group had the lowest diarrhea index during days 15–28 (P < 0.05). In addition, 100 mg/kg MEEOs significantly alleviated intestinal oxidative stress and inflammation (P < 0.05), whereas 500 mg/kg common EOs caused intestinal oxidative stress (P < 0.05) and may lead to intestinal damage through activation of inflammatory cytokine response. MEEOs (100 mg/kg) significantly reduced the ratio of the relative abundance of potential pathogenic and beneficial bacteria in the cecum and colon (P < 0.05), thus contributing to the maintenance of intestinal health. On the other hand, chlortetracycline caused an increase in the ratio of the relative abundance of potential pathogenic and beneficial bacteria in the colon (P < 0.05), which could potentially have adverse effects on the intestine. The addition of a high dose of MEEOs may have adverse effects on the intestine and may lead to diarrhea by increasing the level of colonic acetic acid (P < 0.05). Collectively, the results suggest that microencapsulation technology significantly promotes the positive effect of EOs on the intestinal health of weaning piglets and reduces the adverse effect of EOs, and 100 mg/kg MEEOs are recommended as a health promoter in piglets during the weaning period.
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Affiliation(s)
- Kaibin Mo
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jing Li
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Province Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Fenfen Liu
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Province Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Ying Xu
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xianhui Huang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hengjia Ni
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Province Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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Marčeková P, Mad’ar M, Styková E, Kačírová J, Sondorová M, Mudroň P, Žert Z. The Presence of Treponema spp. in Equine Hoof Canker Biopsies and Skin Samples from Bovine Digital Dermatitis Lesions. Microorganisms 2021; 9:microorganisms9112190. [PMID: 34835315 PMCID: PMC8625648 DOI: 10.3390/microorganisms9112190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/05/2021] [Accepted: 10/18/2021] [Indexed: 11/16/2022] Open
Abstract
Equine hoof canker and bovine digital dermatitis are infectious inflammatory diseases of the hooves with an unknown etiology. However, anaerobic spirochetes of the genus Treponema are considered to be potential etiological agents. The aim of this study was to find a suitable way to isolate DNA and to detect the presence of treponemal DNA in samples of equine hoof canker and bovine digital dermatitis. DNAzol®® Direct and column kits were used to isolate DNA from samples of equine hoof canker and bovine digital dermatitis. The presence of Treponema spp. was detected using PCR and Sanger sequencing. DNAzol®® Direct is suitable for isolating DNA from these types of samples. Treponemal DNA was detected in equine hoof samples as well as in bovine digital dermatitis skin samples. In equine hoof biopsies, the most frequently detected was Treponema pedis (8/13). Treponema brennaborense (2/13) and Treponema denticola (2/13) were also found. In the case of bovine digital dermatitis, Treponema medium ssp. bovis was confirmed in 14 of 36 skin samples. Treponema pedis (9/36), Treponema vincentii (1/36), Treponema phagedenis (1/36), and Treponema brennaborense (1/36) were detected as well. DNAzol®® Direct was more appropriate for isolation of treponemal DNA because the columns isolation method was more equipment and time-consuming. The presence of several Treponema spp. was determined in the samples. In horses, the most commonly detected species was a T. pedis, while in cattle it was T. medium ssp. bovis.
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Affiliation(s)
- Paulína Marčeková
- Clinic of Ruminants, University Veterinary Hospital, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Košice, Slovakia; (P.M.); (P.M.)
| | - Marián Mad’ar
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Košice, Slovakia; (J.K.); (M.S.)
- Correspondence:
| | - Eva Styková
- Clinic of Horses, University Veterinary Hospital, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Košice, Slovakia; (E.S.); (Z.Ž.)
| | - Jana Kačírová
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Košice, Slovakia; (J.K.); (M.S.)
| | - Miriam Sondorová
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Košice, Slovakia; (J.K.); (M.S.)
| | - Pavol Mudroň
- Clinic of Ruminants, University Veterinary Hospital, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Košice, Slovakia; (P.M.); (P.M.)
| | - Zdeněk Žert
- Clinic of Horses, University Veterinary Hospital, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Košice, Slovakia; (E.S.); (Z.Ž.)
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Ijoma GN, Nkuna R, Mutungwazi A, Rashama C, Matambo TS. Applying PICRUSt and 16S rRNA functional characterisation to predicting co-digestion strategies of various animal manures for biogas production. Sci Rep 2021; 11:19913. [PMID: 34620937 PMCID: PMC8497515 DOI: 10.1038/s41598-021-99389-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/24/2021] [Indexed: 02/08/2023] Open
Abstract
An estimated 25 million tons of animal manure is produced globally every year, causing considerable impact to the environment. These impacts can be managed through the use of anaerobic digestion (AD) This process achieves waste degradation through enzymatic activity, the efficiency of the AD process is directly related to microorganisms that produce these enzymes. Biomethane potential (BMP) assays remain the standard theoretical framework to pre-determine biogas yield and have been used to determine the feasibility of substrates or their combination for biogas production. However, an integrated approach that combines substrate choice and co-digestion would provide an improvement to the current predictive models. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) addresses the limitations of assays in this regard. In this paper, the biochemical functions of horse, cow, and pig manures are predicted. A total of 135 predicted KEGG Orthologies (KOs) showed amino acids, carbohydrate, energy, lipid, and xenobiotic metabolisms in all the samples. Linear discriminant analysis (LDA) combined with the effect size measurements (LEfSe), showed that fructose, mannose, amino acid and nucleotide sugar, phosphotransferase (PST) as well as starch and sucrose metabolisms were significantly higher in horse manure samples. 36 of the KOs were related to the acidogenesis and/or acetogenesis AD stages. Extended bar plots showed that 11 significant predictions were observed for horse-cow, while 5 were predicted for horse-pig and for cow-pig manures. Based on these predictions, the AD process can be enhanced through co-digestion strategies that takes into account the predicted metabolic contributions of the manure samples. The results supported the BMP calculations for the samples in this study. Biogas yields can be improved if this combined approach is employed in routine analysis before co-digesting different substrates.
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Affiliation(s)
- Grace N Ijoma
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort, 1709, South Africa.
| | - Rosina Nkuna
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort, 1709, South Africa
| | - Asheal Mutungwazi
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort, 1709, South Africa
| | - Charles Rashama
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort, 1709, South Africa
| | - Tonderayi S Matambo
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort, 1709, South Africa
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8
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Yang J, Yu Z, Wang B, Ndayisenga F. Gut region induces gastrointestinal microbiota community shift in Ujimqin sheep (Ovis aries): from a multi-domain perspective. Environ Microbiol 2021; 23:7603-7616. [PMID: 34545655 DOI: 10.1111/1462-2920.15782] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/16/2021] [Accepted: 09/17/2021] [Indexed: 12/24/2022]
Abstract
Gastrointestinal (GI) microbiota is one of the most complicated microbial ecosystems and is vital in regulating biological processes associated with nutrient absorption and homeostatic maintenance. Although several efforts have been achieved in characterizing bacterial communities across gut regions, the variation of non-bacterial communities across GI tracts is still largely unexplored. To address this, we investigated microbial biogeography throughout the whole GI tracts of Ujimqin sheep (Ovis aries) by amplicon sequencing which targeted bacteria, fungi, and archaea. The results indicated that the community structures of all three domains were significantly distinguished according to GI tracts (stomach, small intestine, and large intestine), and a more strong and efficient species interaction was detected in small intestine based on cross-domain network analysis. Moreover, a between-domain difference in microbial assembly mechanism of among-GI regions was revealed here, wherein bacterial community is dominantly governed by variable selection (explaining ~62% of taxa turnover), while fungal and archaeal communities mainly governed by homogenizing dispersal (explaining ~49% and 60% of the turnover, respectively). Overall, these data highlight the GI section- and domain-dependence of GI microbial structure and assembly mechanism, suggesting that multi-domain should be explicitly considered when evaluating the influences of GI selection on gut microbial communities.
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Affiliation(s)
- Jie Yang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Forest & Nature Lab, Department of Environment, Faculty of Biosciences Engineering, Ghent University, Gontrode-Melle, Belgium
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China
| | - Bobo Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Fabrice Ndayisenga
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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9
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Zou Y, Liang N, Zhang X, Han C, Nan X. Functional differentiation related to decomposing complex carbohydrates of intestinal microbes between two wild zokor species based on 16SrRNA sequences. BMC Vet Res 2021; 17:216. [PMID: 34116670 PMCID: PMC8196462 DOI: 10.1186/s12917-021-02911-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/20/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The intestinal microbes in mammals play a key role in host metabolism and adaptation. As a subterranean rodent, zokor digs tunnels for foraging and mating. These digging activities of zokors increase the energy expenditure relative to their aboveground counterparts. However, relatively little is known regarding intestinal microbes of zokor and how they make full use of limited food resources underground for high energy requirements. RESULTS Eospalax cansus and Eospalax rothschildi had distinct intestinal microbes. Although the composition of intestinal microbes is similar in two species, the proportion of bacterium are distinctly different between them. At phylum level, 11 phyla were shared between two species. Firmicutes and Bacteroidota were two dominant microbes in both of two species, while Eospalax cansus have a significantly high proportion of Firmicutes/Bacteroidota than that of Eospalax rothschildi. At genus level, norank_f_Muribaculaceae were dominant microbes in both of two zokor species. The relative abundance of 12 genera were significantly different between two species. Some bacterium including unclassified_f__Lachnospiraceae, Lachnospiraceae_NK4A136_group, Ruminococcus and Eubacterium_siraeum_group associated with cellulose degradation were significantly enriched in Eospalax cansus. Although alpha diversity was with no significant differences between Eospalax cansus and Eospalax rothschildi, the intestinal microbes between them are significant distinct in PCoA analysis. We have found that trapping location affected the alpha diversity values, while sex and body measurements had no effect on alpha diversity values. PICRUSt metagenome predictions revealed significant enrichment of microbial genes involved in carbohydrate metabolism in Eospalax cansus rather than Eospalax rothschildi. CONCLUSIONS Our results demonstrate that Eospalax cansus harbor a stronger ability of fermentation for dietary plants than Eospalax rothschildi. The stronger ability of fermentation and degradation of cellulose of intestinal microbes of Eospalax cansus may be a long-time adaptation to limited food resources underground.
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Affiliation(s)
- Yao Zou
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, Northwest Agriculture and Forestry University, Yangling, 712100, China
| | - Nannan Liang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, Northwest Agriculture and Forestry University, Yangling, 712100, China
| | - Xuxin Zhang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, Northwest Agriculture and Forestry University, Yangling, 712100, China
| | - Chongxuan Han
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, Northwest Agriculture and Forestry University, Yangling, 712100, China.
| | - Xiaoning Nan
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, Northwest Agriculture and Forestry University, Yangling, 712100, China.
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10
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Espiritu HM, Mamuad LL, Jin SJ, Kim SH, Lee SS, Cho YI. High quality genome sequence of Treponema phagedenis KS1 isolated from bovine digital dermatitis. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2021; 62:948-951. [PMID: 33987574 PMCID: PMC7721586 DOI: 10.5187/jast.2020.62.6.948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/24/2020] [Accepted: 09/17/2020] [Indexed: 11/20/2022]
Abstract
Treponema phagedenis KS1, a fastidious anaerobe, was isolated from a bovine digital dermatitis (BDD)-infected dairy cattle in Chungnam, Korea. Initial data indicated that T. phagedenis KS1 exhibited putative virulent phenotypic characteristics. This study reports the whole genome assembly and annotation of T. phagedenis KS1 (KCTC14157BP) to assist in the identification of putative pathogenicity related factors. The whole genome of T. phagedenis KS1 was sequenced using PacBio RSII and Illumina HiSeqXTen platforms. The assembled T. phagedenis KS1 genome comprises 16 contigs with a total size of 3,769,422 bp and an overall guanine-cytosine (GC) content of 40.03%. Annotation revealed 3,460 protein-coding genes, as well as 49 transfer RNA- and 6 ribosomal RNA-coding genes. The results of this study provide insight into the pathogenicity of T. phagedenis KS1.
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Affiliation(s)
- Hector M Espiritu
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea
| | - Lovelia L Mamuad
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea
| | - Su-Jeong Jin
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea
| | - Seon-Ho Kim
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea
| | - Sang-Suk Lee
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea
| | - Yong-Il Cho
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea
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11
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Tracking Reservoirs of Antimicrobial Resistance Genes in a Complex Microbial Community Using Metagenomic Hi-C: The Case of Bovine Digital Dermatitis. Antibiotics (Basel) 2021; 10:antibiotics10020221. [PMID: 33672258 PMCID: PMC7926801 DOI: 10.3390/antibiotics10020221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 02/08/2023] Open
Abstract
Bovine digital dermatitis (DD) is a contagious infectious cause of lameness in cattle with unknown definitive etiologies. Many of the bacterial species detected in metagenomic analyses of DD lesions are difficult to culture, and their antimicrobial resistance status is largely unknown. Recently, a novel proximity ligation-guided metagenomic approach (Hi-C ProxiMeta) has been used to identify bacterial reservoirs of antimicrobial resistance genes (ARGs) directly from microbial communities, without the need to culture individual bacteria. The objective of this study was to track tetracycline resistance determinants in bacteria involved in DD pathogenesis using Hi-C. A pooled sample of macerated tissues from clinical DD lesions was used for this purpose. Metagenome deconvolution using ProxiMeta resulted in the creation of 40 metagenome-assembled genomes with ≥80% complete genomes, classified into five phyla. Further, 1959 tetracycline resistance genes and ARGs conferring resistance to aminoglycoside, beta-lactams, sulfonamide, phenicol, lincosamide, and erythromycin were identified along with their bacterial hosts. In conclusion, the widespread distribution of genes conferring resistance against tetracycline and other antimicrobials in bacteria of DD lesions is reported for the first time. Use of proximity ligation to identify microorganisms hosting specific ARGs holds promise for tracking ARGs transmission in complex microbial communities.
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12
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Espiritu HM, Mamuad LL, Kim SH, Jin SJ, Lee SS, Kwon SW, Cho YI. Microbiome Shift, Diversity, and Overabundance of Opportunistic Pathogens in Bovine Digital Dermatitis Revealed by 16S rRNA Amplicon Sequencing. Animals (Basel) 2020; 10:ani10101798. [PMID: 33022998 PMCID: PMC7599724 DOI: 10.3390/ani10101798] [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: 08/27/2020] [Revised: 09/22/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Bovine digital dermatitis (BDD) is a foot infection known as the primary cause of lameness in cattle due to painful lesions, posing serious impacts on the productivity and welfare of affected animals. Members of the bacterial group Treponema have long been considered as the main causative agents because previous investigations by bacterial isolation, tissue analyses, and high molecular sequencing have persistently identified this group in BDD. However, other studies indicated that the presence of several bacteria on the lesion due to the slurry environment the cattle foot are exposed to, suggests an interdependent polybacterial nature which could also play a role in disease development and progression. Therefore, we analyzed the diversity and relationship of the diverse microbiome in BDD lesions compared to normal skin from cattle foot by using next-generation high throughput sequencing. Based on the results obtained, we concluded that the shift in microbial composition which leads to richer diversity in BDD, and the overabundance of opportunistic bacterial pathogens could be associated with BDD pathogenesis. Abstract This study analyzed the diversity and phylogenetic relationship of the microbiome of bovine digital dermatitis (BDD) lesions and normal skin from cattle foot by using 16S rRNA amplicon sequencing. Three BDD samples and a normal skin sample were pre-assessed for analysis. The Illumina Miseq platform was used for sequencing and sequences were assembled and were categorized to operational taxonomic units (OTUs) based on similarity, then the core microbiome was visualized. The phylogeny was inferred using MEGA7 (Molecular evolutionary genetics analysis version 7.0). A total of 129 and 185 OTUs were uniquely observed in normal and in BDD samples, respectively. Of the 47 shared OTUs, 15 species presented increased abundance in BDD. In BDD and normal samples, Spirochetes and Proteobacteria showed the most abundant phyla, respectively, suggesting the close association of observed species in each sample group. The phylogeny revealed the evolutionary relationship of OTUs and the Euclidean distance suggested a high sequence divergence between OTUs. We concluded that a shift in the microbiome leads to richer diversity in BDD lesions, and the overabundance of opportunistic pathogens and its synergistic relationship with commensal bacteria could serve as factors in disease development. The influence of these factors should be thoroughly investigated in future studies to provide deeper insights on the pathogenesis of BDD.
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Affiliation(s)
- Hector M. Espiritu
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
| | - Lovelia L. Mamuad
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
| | - Seon-ho Kim
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
| | - Su-jeong Jin
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
| | - Sang-suk Lee
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
| | - Seok-won Kwon
- Woosarang Animal Hospital, Yongin, Gyeonggi 17026, Korea;
| | - Yong-il Cho
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
- Correspondence: ; Tel.: +82-61-750-3234
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13
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Genotypic and Phenotypic Characterization of Treponema phagedenis from Bovine Digital Dermatitis. Microorganisms 2020; 8:microorganisms8101520. [PMID: 33023205 PMCID: PMC7600072 DOI: 10.3390/microorganisms8101520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/17/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022] Open
Abstract
This study aimed to isolate and characterize Treponema spp. from bovine digital dermatitis (BDD)-infected dairy cattle. Seven isolates were characterized in this study. Isolates exhibited slow growth, and colonies penetrated the agar and exhibited weak β-hemolysis. Round bodies were observed in old and antibiotic-treated cultures. Cells ranged from 9–12 µm in length, 0.2–2.5 µm in width, and were moderately spiraled. The 16S rRNA analysis revealed the isolates as Treponema phagedenis with >99% sequence homology. Isolates had alkaline phosphatase, acid phosphatase, β-galactosidase, N-acetyl-β-glucosaminidase, esterase (C4), esterase lipase (C8), naphthol-AS-BI-phosphohydrolase, and β-glucuronidase activities. Low concentrations of ampicillin, erythromycin, and tetracycline were required to inhibit the growth of isolates. Formic, acetic, and butyric acids were produced, while propionic acid was significantly utilized, indicating its essentiality for treponemal growth. The isolates shared the same characteristics and, therefore, were considered as a single strain. Isolate HNL4 was deposited as a representative isolate (Treponema phagedenis KS1). The average nucleotide identity of strain KS1 showed a small difference with the human strain (99.14%) compared with bovine strain (99.72%). This study was the first to isolate and characterize Treponema phagedenis from BDD in Korea and, hence, it delivered pathogenicity-related insights and provided valuable information that can be used for the management of BDD.
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