1
|
Lu G, Wang Z, Zhang B, Zhou Z, Hu D, Zhang D. Detecting Forest Musk Deer Abscess Disease Pathogens Using 16S rRNA High-Throughput Sequencing Technology. Animals (Basel) 2023; 13:3142. [PMID: 37835748 PMCID: PMC10572063 DOI: 10.3390/ani13193142] [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: 08/06/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 10/15/2023] Open
Abstract
Currently, researchers use bacterial culture and targeted PCR methods to classify, culture, and identify the pathogens causing abscess diseases. However, this method is limited by factors such as the type of culture medium and culture conditions, making it challenging to screen and proliferate many bacteria effectively. Fortunately, with the development of high-throughput sequencing technology, pathogen identification at the genetic level has become possible. Not only can this approach overcome the limitations of bacterial culture, but it can also accurately identify the types and relative abundance of pathogens. In this study, we used high-throughput sequencing of 16S rRNA to identify the pathogens in purulent fluid samples. Our results not only confirmed the presence of the main pathogen reported by previous researchers, Trueperella pyogenes, but also other obligate anaerobes, Fusobacterium necrophorum and Bacteroides fragilis as the dominant pathogens causing abscess diseases for the first time. Therefore, our findings suggest that high-throughput sequencing technology has the potential to replace traditional bacterial culture and targeted PCR methods.
Collapse
Affiliation(s)
- Guanjie Lu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (G.L.); (Z.W.); (B.Z.); (Z.Z.); (D.H.)
| | - Zhe Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (G.L.); (Z.W.); (B.Z.); (Z.Z.); (D.H.)
| | - Baofeng Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (G.L.); (Z.W.); (B.Z.); (Z.Z.); (D.H.)
| | - Zhichao Zhou
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (G.L.); (Z.W.); (B.Z.); (Z.Z.); (D.H.)
| | - Defu Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (G.L.); (Z.W.); (B.Z.); (Z.Z.); (D.H.)
| | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (G.L.); (Z.W.); (B.Z.); (Z.Z.); (D.H.)
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China
| |
Collapse
|
2
|
Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V, Mrazek J. Dysbiosis of skin microbiome and gut microbiome in melanoma progression. BMC Microbiol 2022; 22:63. [PMID: 35216552 PMCID: PMC8881828 DOI: 10.1186/s12866-022-02458-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/29/2022] [Indexed: 12/11/2022] Open
Abstract
Background The microbiome alterations are associated with cancer growth and may influence the immune system and response to therapy. Particularly, the gut microbiome has been recently shown to modulate response to melanoma immunotherapy. However, the role of the skin microbiome has not been well explored in the skin tumour microenvironment and the link between the gut microbiome and skin microbiome has not been investigated in melanoma progression. Therefore, the aim of the present study was to examine associations between dysbiosis in the skin and gut microbiome and the melanoma growth using MeLiM porcine model of melanoma progression and spontaneous regression. Results Parallel analysis of cutaneous microbiota and faecal microbiota of the same individuals was performed in 8 to 12 weeks old MeLiM piglets. The bacterial composition of samples was analysed by high throughput sequencing of the V4-V5 region of the 16S rRNA gene. A significant difference in microbiome diversity and richness between melanoma tissue and healthy skin and between the faecal microbiome of MeLiM piglets and control piglets were observed. Both Principal Coordinate Analysis and Non-metric multidimensional scaling revealed dissimilarities between different bacterial communities. Linear discriminant analysis effect size at the genus level determined different potential biomarkers in multiple bacterial communities. Lactobacillus, Clostridium sensu stricto 1 and Corynebacterium 1 were the most discriminately higher genera in the healthy skin microbiome, while Fusobacterium, Trueperella, Staphylococcus, Streptococcus and Bacteroides were discriminately abundant in melanoma tissue microbiome. Bacteroides, Fusobacterium and Escherichia-Shigella were associated with the faecal microbiota of MeLiM piglets. Potential functional pathways analysis based on the KEGG database indicated significant differences in the predicted profile metabolisms between the healthy skin microbiome and melanoma tissue microbiome. The faecal microbiome of MeLiM piglets was enriched by genes related to membrane transports pathways allowing for the increase of intestinal permeability and alteration of the intestinal mucosal barrier. Conclusion The associations between melanoma progression and dysbiosis in the skin microbiome as well as dysbiosis in the gut microbiome were identified. Results provide promising information for further studies on the local skin and gut microbiome involvement in melanoma progression and may support the development of new therapeutic approaches. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02458-5.
Collapse
Affiliation(s)
- Chahrazed Mekadim
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Helena Kupcova Skalnikova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburska 89, 277 21, Libechov, Czech Republic
| | - Jana Cizkova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburska 89, 277 21, Libechov, Czech Republic.,Department of Radiobiology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic
| | - Veronika Cizkova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburska 89, 277 21, Libechov, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University, Vinicna 7, 128 00, Prague, Czech Republic
| | - Anna Palanova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburska 89, 277 21, Libechov, Czech Republic
| | - Vratislav Horak
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburska 89, 277 21, Libechov, Czech Republic
| | - Jakub Mrazek
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic.
| |
Collapse
|
3
|
Laryngeal chondritis as a differential for upper airway diseases in German sheep. Acta Vet Scand 2020; 62:12. [PMID: 32131871 PMCID: PMC7057637 DOI: 10.1186/s13028-020-0510-0] [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: 10/04/2019] [Accepted: 02/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ovine laryngeal chondritis is a rare entity of sheep in the USA, Great Britain, New Zealand and Iceland, but has not been reported in Germany so far. Here, two German cases are reported. CASE PRESENTATION Two rams showed severe and progressive signs of dyspnea. Endoscopically, a severe bilateral swelling of the larynx was identified in both rams. Due to poor prognosis and progression of clinical signs one ram was euthanized, while the other ram died overnight. In both cases, a necrosuppurative laryngitis and chondritis of arytenoid cartilages was found at necropsy. Fusobacterium necrophorum and Streptococcus ovis were isolated from the laryngeal lesion in one animal. CONCLUSIONS This is the first report of ovine laryngeal chondritis in continental Europe. This entity should be considered a differential diagnosis for upper airway disease in sheep.
Collapse
|
4
|
Carvallo FR, Uzal FA, Flores C, Diab SS, Giannitti F, Crossley B, Wünschmann A. Alimentary necrobacillosis in alpacas. J Vet Diagn Invest 2020; 32:339-343. [PMID: 32070228 DOI: 10.1177/1040638720906409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Ulcers of the oral cavity, esophagus, and gastric compartments of South American camelids are uncommon. Multifocal-to-coalescing ulcers were identified in the oral cavity, esophagus, and/or gastric compartments of 5 alpacas submitted for postmortem examination. Fusobacterium necrophorum was isolated from the lesions in all alpacas, in combination with other aerobic and anaerobic bacteria. In 4 of these cases, F. necrophorum-associated lesions were considered secondary to neoplasia or other chronic debilitating conditions; in 1 case, the alimentary ulcers were considered the most significant autopsy finding. It is not known if this agent acted as a primary or opportunistic agent in mucosal membranes previously damaged by a traumatic event, chemical insult, immunodeficiency, or any other debilitating condition of the host.
Collapse
Affiliation(s)
- Francisco R Carvallo
- California Animal Health and Food Safety Laboratory System, San Bernardino (Carvallo, Uzal) branches, University of California-Davis, Davis, CA.,Davis (Diab, Crossley) branches, University of California-Davis, Davis, CA.,Universidad Mayor, Santiago, Chile (Flores).,Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), La Estanzuela, Colonia, Uruguay (Giannitti).,University of Minnesota Veterinary Diagnostic Laboratory, St. Paul, MN (Wünschmann)
| | - Francisco A Uzal
- California Animal Health and Food Safety Laboratory System, San Bernardino (Carvallo, Uzal) branches, University of California-Davis, Davis, CA.,Davis (Diab, Crossley) branches, University of California-Davis, Davis, CA.,Universidad Mayor, Santiago, Chile (Flores).,Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), La Estanzuela, Colonia, Uruguay (Giannitti).,University of Minnesota Veterinary Diagnostic Laboratory, St. Paul, MN (Wünschmann)
| | - Carlos Flores
- California Animal Health and Food Safety Laboratory System, San Bernardino (Carvallo, Uzal) branches, University of California-Davis, Davis, CA.,Davis (Diab, Crossley) branches, University of California-Davis, Davis, CA.,Universidad Mayor, Santiago, Chile (Flores).,Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), La Estanzuela, Colonia, Uruguay (Giannitti).,University of Minnesota Veterinary Diagnostic Laboratory, St. Paul, MN (Wünschmann)
| | - Santiago S Diab
- California Animal Health and Food Safety Laboratory System, San Bernardino (Carvallo, Uzal) branches, University of California-Davis, Davis, CA.,Davis (Diab, Crossley) branches, University of California-Davis, Davis, CA.,Universidad Mayor, Santiago, Chile (Flores).,Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), La Estanzuela, Colonia, Uruguay (Giannitti).,University of Minnesota Veterinary Diagnostic Laboratory, St. Paul, MN (Wünschmann)
| | - Federico Giannitti
- California Animal Health and Food Safety Laboratory System, San Bernardino (Carvallo, Uzal) branches, University of California-Davis, Davis, CA.,Davis (Diab, Crossley) branches, University of California-Davis, Davis, CA.,Universidad Mayor, Santiago, Chile (Flores).,Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), La Estanzuela, Colonia, Uruguay (Giannitti).,University of Minnesota Veterinary Diagnostic Laboratory, St. Paul, MN (Wünschmann)
| | - Beate Crossley
- California Animal Health and Food Safety Laboratory System, San Bernardino (Carvallo, Uzal) branches, University of California-Davis, Davis, CA.,Davis (Diab, Crossley) branches, University of California-Davis, Davis, CA.,Universidad Mayor, Santiago, Chile (Flores).,Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), La Estanzuela, Colonia, Uruguay (Giannitti).,University of Minnesota Veterinary Diagnostic Laboratory, St. Paul, MN (Wünschmann)
| | - Arno Wünschmann
- California Animal Health and Food Safety Laboratory System, San Bernardino (Carvallo, Uzal) branches, University of California-Davis, Davis, CA.,Davis (Diab, Crossley) branches, University of California-Davis, Davis, CA.,Universidad Mayor, Santiago, Chile (Flores).,Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), La Estanzuela, Colonia, Uruguay (Giannitti).,University of Minnesota Veterinary Diagnostic Laboratory, St. Paul, MN (Wünschmann)
| |
Collapse
|
5
|
Brooks JW, Kumar A, Narayanan S, Myers S, Brown K, Nagaraja TG, Jayarao BM. Characterization of Fusobacterium isolates from the respiratory tract of white-tailed deer (Odocoileus virginianus). J Vet Diagn Invest 2014; 26:213-20. [DOI: 10.1177/1040638714523613] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A total of 23 clinical isolates of Fusobacterium spp. were recovered at necropsy over a 2-year period from the respiratory tract of white-tailed deer ( Odocoileus virginianus). Isolates were identified as Fusobacterium varium (18/23), Fusobacterium necrophorum subsp. funduliforme (3/23), and Fusobacterium necrophorum subsp. necrophorum (2/23). Using polymerase chain reaction–based detection of virulence genes, all F. necrophorum isolates were positive for the promoter region of the leukotoxin operon and the hemagglutinin-related protein gene, while all F. varium isolates were negative. The presence of the leukotoxin gene in F. necrophorum isolates and the absence of this gene in F. varium isolates were confirmed by Southern hybridization using 2 separate probes. Toxicity to bovine polymorphonuclear leukocytes was observed with all F. necrophorum isolates, but was not observed in any F. varium isolates. Susceptibility to antimicrobials was markedly different for F. varium as compared to F. necrophorum. In summary, no evidence of leukotoxin production was detected in any of the 23 F. varium isolates used in the current study. The data suggests that F. varium, the most common species isolated, may be a significant pathogen in deer with a different virulence mechanism than F. necrophorum.
Collapse
Affiliation(s)
- Jason W. Brooks
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA (Brooks, Myers, Brown, Jayarao)
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS (Kumar, Narayanan, Nagaraja)
| | - Amit Kumar
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA (Brooks, Myers, Brown, Jayarao)
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS (Kumar, Narayanan, Nagaraja)
| | - Sanjeev Narayanan
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA (Brooks, Myers, Brown, Jayarao)
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS (Kumar, Narayanan, Nagaraja)
| | - Suzanne Myers
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA (Brooks, Myers, Brown, Jayarao)
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS (Kumar, Narayanan, Nagaraja)
| | - Kayla Brown
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA (Brooks, Myers, Brown, Jayarao)
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS (Kumar, Narayanan, Nagaraja)
| | - T. G. Nagaraja
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA (Brooks, Myers, Brown, Jayarao)
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS (Kumar, Narayanan, Nagaraja)
| | - Bhushan M. Jayarao
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA (Brooks, Myers, Brown, Jayarao)
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS (Kumar, Narayanan, Nagaraja)
| |
Collapse
|