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Wong NST, Malmuthge N, Gellatly D, Nordi WM, Alexander TW, Ortega Polo R, Janzen E, Schwartzkopf-Genswein K, Jelinski M. Characterization of the hoof bacterial communities in feedlot cattle affected with digital dermatitis, foot rot or both using a surface swab technique. Anim Microbiome 2024; 6:2. [PMID: 38254160 PMCID: PMC10804539 DOI: 10.1186/s42523-023-00277-1] [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: 05/17/2023] [Accepted: 10/20/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Lameness is defined as altered or abnormal gait due to dysfunction of the locomotor system, and is a health issue of feedlot cattle, having major economic, labour, and welfare implications. Digital dermatitis (DD-a lesion of the plantar surface of the foot) and foot rot (FR-affects the interdigital cleft) are common infectious causes of lameness in feedlots. These hoof lesions can occur alone or in combination (DD + FR) in the same hoof. A total of 208 hoof swabs were collected from three commercial feedlots located in southern Alberta. Every lesion sample was matched with a corresponding control skin sample taken from a healthy contralateral foot. Control skin samples were also collected from cattle with no lesion on any feet. Bacterial communities of three types of hoof lesions (DD, DD + FR, FR) and healthy skin were profiled using 16S amplicon sequencing. RESULTS Alpha diversity analysis revealed a lower bacterial diversity on DD and FR lesions compared to control skin. Beta diversity analysis showed that bacterial communities of DD, FR, and DD + FR lesions were distinct from those of the control skin. While the impact of feedlot was minimal, lesion type contributed to 22% of the variation observed among bacterial communities (PERMANOVA-R = 0.22, P < 0.01). Compared to the corresponding control skin, there were 11, 12, and 3 differentially abundant (DA) bacterial genera in DD, DD + FR, and FR lesions, respectively. CONCLUSIONS The bacterial community description of a DD + FR lesion is a novel finding. Not only did lesions lead to altered bacterial communities when compared to healthy skin, but the composition of those communities also differed depending on the hoof lesion. The 16S amplicon sequencing of surface swabs has significant value as a research tool in separating different hoof lesions and can provide additional insights to the polybacterial etiology of DD and FR in feedlot cattle.
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Affiliation(s)
- Nicholas S T Wong
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Nilusha Malmuthge
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Désirée Gellatly
- Technology Access Centre for Livestock, Olds College of Agriculture and Technology, Olds, Canada
| | - Wiolene M Nordi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Trevor W Alexander
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Rodrigo Ortega Polo
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Eugene Janzen
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Karen Schwartzkopf-Genswein
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada.
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada.
| | - Murray Jelinski
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
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Wu R, Yu T, Liu S, Shi R, Jiang G, Ren Y, van der Mei HC, Busscher HJ, Liu J. A Heterocatalytic Metal-Organic Framework to Stimulate Dispersal and Macrophage Combat with Infectious Biofilms. ACS NANO 2023; 17:2328-2340. [PMID: 36692081 PMCID: PMC9933606 DOI: 10.1021/acsnano.2c09008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
Eradication of infectious biofilms is becoming increasingly difficult due to the growing number of antibiotic-resistant strains. This necessitates development of nonantibiotic-based, antimicrobial approaches. To this end, we designed a heterocatalytic metal-organic framework composed of zirconium 1,4-dicarboxybenzene (UiO-66) with immobilized Pt nanoparticles (Pt-NP/UiO-66). Pt-NP/UiO-66 enhanced singlet-oxygen generation compared with Pt nanoparticles or UiO-66, particularly in an acidic environment. Singlet-oxygen generation degraded phosphodiester bonds present in eDNA gluing biofilms together and therewith dispersed biofilms. Remaining biofilms possessed a more open structure. Concurrently, Pt-NP/UiO-66 stimulated macrophages to adapt a more M1-like, "fighting" phenotype, moving faster toward their target bacteria and showing increased bacterial killing. As a combined effect of biofilm dispersal and macrophage polarization, a subcutaneous Staphylococcus aureus biofilm in mice was more readily eradicated by Pt-NP/UiO-66 than by Pt nanoparticles or UiO-66. Therewith, heterocatalytic Pt-NP/UiO-66 metal-organic frameworks constitute a nonantibiotic-based strategy to weaken protective matrices and disperse infectious biofilms, while strengthening macrophages in bacterial killing.
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Affiliation(s)
- Renfei Wu
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Joint International
Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren’ai Rd., Suzhou, Jiangsu215123, P. R. China
- University
of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713 AVGroningen, The Netherlands
| | - Tianrong Yu
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Joint International
Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren’ai Rd., Suzhou, Jiangsu215123, P. R. China
- University
of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713 AVGroningen, The Netherlands
| | - Sidi Liu
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Joint International
Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren’ai Rd., Suzhou, Jiangsu215123, P. R. China
- University
of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713 AVGroningen, The Netherlands
| | - Rui Shi
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Joint International
Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren’ai Rd., Suzhou, Jiangsu215123, P. R. China
- University
of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713 AVGroningen, The Netherlands
| | - Guimei Jiang
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Joint International
Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren’ai Rd., Suzhou, Jiangsu215123, P. R. China
- University
of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713 AVGroningen, The Netherlands
| | - Yijin Ren
- University
of Groningen and University Medical Center of Groningen, Department of Orthodontics, Hanzeplein 1, 9700
RBGroningen, The
Netherlands
| | - Henny C. van der Mei
- University
of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713 AVGroningen, The Netherlands
| | - Henk J. Busscher
- University
of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713 AVGroningen, The Netherlands
| | - Jian Liu
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Joint International
Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren’ai Rd., Suzhou, Jiangsu215123, P. R. China
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3
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Protoporphyrin IX derived from dual-species anaerobic biofilms of Fusobacterium necrophorum and Porphyromonas levii attenuates bovine neutrophil function. Biofilm 2022; 4:100095. [DOI: 10.1016/j.bioflm.2022.100095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022] Open
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Identification and Quantification of Bovine Digital Dermatitis-Associated Microbiota across Lesion Stages in Feedlot Beef Cattle. mSystems 2021; 6:e0070821. [PMID: 34313462 PMCID: PMC8409723 DOI: 10.1128/msystems.00708-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Bovine digital dermatitis (DD) is a skin disorder that is a significant cause of infectious lameness in cattle around the world. However, very little is known about the etiopathogenesis of the disease and the microbiota associated with DD in beef cattle. In this study, we provide a comprehensive characterization of DD and healthy skin microbiota of feedlot beef cattle. We also developed and validated a novel multiplex quantitative PCR (qPCR) assay to quantify the distribution of DD-associated bacterial species across DD lesion stages. We determined the DD-associated microbiota with deep amplicon sequencing of the V3-V4 hypervariable region of the 16S rRNA gene, followed by the application of novel and existing qPCR assays to quantify species distributions of Treponema, Porphyromonas, Fusobacterium, and Bacteroides across lesion stages. Deep amplicon sequencing revealed that Treponema, Mycoplasma, Porphyromonas, and Fusobacterium were associated with DD lesions. Culturing of DD biopsy specimens identified Porphyromonas levii, Bacteroides pyogenes, and two Fusobacterium spp. within DD lesions. Using species-specific qPCR on DD lesion DNA, we identified P. levii in 100% of active lesion stages. Early-stage lesions were particularly associated with Treponema medium, T. phagedenis, and P. levii. This study suggests a core DD microbial group consisting of species of Treponema, Fusobacterium, Porphyromonas, and Bacteroides, which may be closely tied with the etiopathogenesis of DD. Further characterizations of these species and Mycoplasma spp. are necessary to understand the microbial factors involved in DD pathogenesis, which will help elucidate DD etiology and facilitate more targeted and effective mitigation and treatment strategies. IMPORTANCE Previous work, primarily in dairy cattle, has identified various taxa associated with digital dermatitis (DD) lesions. However, there is a significant gap in our knowledge of DD microbiology in beef cattle. In addition, characterization of bacteria at the species level in DD lesions is limited. In this study, we provide a framework for the accurate and reproducible quantification of major DD-associated bacterial species from DNA samples. Our findings support DD as a polymicrobial infection, and we identified a variety of bacterial species spanning multiple genera that are consistently associated with DD lesions. The DD-associated microbiota identified in this study may be capable of inducing the formation and progression of DD lesions and thus should be primary targets in future DD pathogenesis studies.
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Caddey B, De Buck J. Meta-Analysis of Bovine Digital Dermatitis Microbiota Reveals Distinct Microbial Community Structures Associated With Lesions. Front Cell Infect Microbiol 2021; 11:685861. [PMID: 34336713 PMCID: PMC8322762 DOI: 10.3389/fcimb.2021.685861] [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: 03/27/2021] [Accepted: 06/16/2021] [Indexed: 01/04/2023] Open
Abstract
Bovine digital dermatitis (DD) is a significant cause of infectious lameness and economic losses in cattle production across the world. There is a lack of a consensus across different 16S metagenomic studies on DD-associated bacteria that may be potential pathogens of the disease. The goal of this meta-analysis was to identify a consistent group of DD-associated bacteria in individual DD lesions across studies, regardless of experimental design choices including sample collection and preparation, hypervariable region sequenced, and sequencing platform. A total of 6 studies were included in this meta-analysis. Raw sequences and metadata were identified on the NCBI sequence read archive and European nucleotide archive. Bacterial community structures were investigated between normal skin and DD skin samples. Random forest models were generated to classify DD status based on microbial composition, and to identify taxa that best differentiate DD status. Among all samples, members of Treponema, Mycoplasma, Porphyromonas, and Fusobacterium were consistently identified in the majority of DD lesions, and were the best genera at differentiating DD lesions from normal skin. Individual study and 16S hypervariable region sequenced had significant influence on final DD lesion microbial composition (P < 0.05). These findings indicate that members of Treponema, Mycoplasma, Porphyromonas, and/or Fusobacterium may have significant roles in DD pathogenesis, and should be studied further in respect to elucidating DD etiopathogenic mechanisms and developing more effective treatment and mitigation strategies.
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Affiliation(s)
- Ben Caddey
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Jeroen De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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6
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Motta JP, Wallace JL, Buret AG, Deraison C, Vergnolle N. Gastrointestinal biofilms in health and disease. Nat Rev Gastroenterol Hepatol 2021; 18:314-334. [PMID: 33510461 DOI: 10.1038/s41575-020-00397-y] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/25/2020] [Indexed: 01/30/2023]
Abstract
Microorganisms colonize various ecological niches in the human habitat, as they do in nature. Predominant forms of multicellular communities called biofilms colonize human tissue surfaces. The gastrointestinal tract is home to a profusion of microorganisms with intertwined, but not identical, lifestyles: as isolated planktonic cells, as biofilms and in biofilm-dispersed form. It is therefore of major importance in understanding homeostatic and altered host-microorganism interactions to consider not only the planktonic lifestyle, but also biofilms and biofilm-dispersed forms. In this Review, we discuss the natural organization of microorganisms at gastrointestinal surfaces, stratification of microbiota taxonomy, biogeographical localization and trans-kingdom interactions occurring within the biofilm habitat. We also discuss existing models used to study biofilms. We assess the contribution of the host-mucosa biofilm relationship to gut homeostasis and to diseases. In addition, we describe how host factors can shape the organization, structure and composition of mucosal biofilms, and how biofilms themselves are implicated in a variety of homeostatic and pathological processes in the gut. Future studies characterizing biofilm nature, physical properties, composition and intrinsic communication could shed new light on gut physiology and lead to potential novel therapeutic options for gastrointestinal diseases.
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Affiliation(s)
- Jean-Paul Motta
- Institute of Digestive Health Research, IRSD, INSERM U1220, Toulouse, France.
| | - John L Wallace
- Department of Physiology & Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Antibe Therapeutics Inc., Toronto, ON, Canada
| | - André G Buret
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Céline Deraison
- Institute of Digestive Health Research, IRSD, INSERM U1220, Toulouse, France
| | - Nathalie Vergnolle
- Institute of Digestive Health Research, IRSD, INSERM U1220, Toulouse, France. .,Department of Physiology & Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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Ekman L, Bagge E, Nyman A, Persson Waller K, Pringle M, Segerman B. A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows. PLoS One 2020; 15:e0242880. [PMID: 33264351 PMCID: PMC7710049 DOI: 10.1371/journal.pone.0242880] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/10/2020] [Indexed: 01/03/2023] Open
Abstract
Udder cleft dermatitis (UCD) is a skin condition affecting the fore udder attachment of dairy cows. UCD may be defined as mild (eczematous skin changes) or severe (open wounds, large skin changes). Our aims were to compare the microbiota of mild and severe UCD lesions with the microbiota of healthy skin from the fore udder attachment of control cows, and to investigate whether mastitis-causing pathogens are present in UCD lesions. Samples were obtained from cows in six dairy herds. In total, 36 UCD samples categorized as mild (n = 17) or severe (n = 19) and 13 control samples were sequenced using a shotgun metagenomic approach and the reads were taxonomically classified based on their k-mer content. The Wilcoxon rank sum test was used to compare the abundance of different taxa between different sample types, as well as to compare the bacterial diversity between samples. A high proportion of bacteria was seen in all samples. Control samples had a higher proportion of archaeal reads, whereas most samples had low proportions of fungi, protozoa and viruses. The bacterial microbiota differed between controls and mild and severe UCD samples in both composition and diversity. Subgroups of UCD samples were visible, characterized by increased proportion of one or a few bacterial genera or species, e.g. Corynebacterium, Staphylococcus, Brevibacterium luteolum, Trueperella pyogenes and Fusobacterium necrophorum. Bifidobacterium spp. were more common in controls compared to UCD samples. The bacterial diversity was higher in controls compared to UCD samples. Bacteria commonly associated with mastitis were uncommon. In conclusion, a dysbiosis of the microbiota of mild and severe UCD samples was seen, characterized by decreased diversity and an increased proportion of certain bacteria. There was no evidence of a specific pathogen causing UCD or that UCD lesions are important reservoirs for mastitis-causing bacteria.
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Affiliation(s)
- Lisa Ekman
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute, Uppsala, Sweden
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Elisabeth Bagge
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute, Uppsala, Sweden
| | - Ann Nyman
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Växa Sverige, Stockholm, Sweden
| | - Karin Persson Waller
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute, Uppsala, Sweden
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Märit Pringle
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute, Uppsala, Sweden
| | - Bo Segerman
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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