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Gemmellaro MD, Lorusso NS, Domke R, Kovalska KM, Hashim A, Arevalo Mojica M, O’Connor AJ, Patel U, Pate O, Raise G, Shumskaya M. Assessment of Fungal Succession in Decomposing Swine Carcasses ( Sus scrofa L.) Using DNA Metabarcoding. J Fungi (Basel) 2023; 9:866. [PMID: 37754974 PMCID: PMC10532525 DOI: 10.3390/jof9090866] [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: 07/17/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 09/28/2023] Open
Abstract
The decomposition of animal bodies is a process defined by specific stages, described by the state of the body and participation of certain guilds of invertebrates and microorganisms. While the participation of invertebrates in decomposing is well-studied and actively used in crime scene investigations, information on bacteria and fungi from the scene is rarely collected or used in the identification of important factors such as estimated time of death. Modern molecular techniques such as DNA metabarcoding allow the identification and quantification of the composition of microbial communities. In this study, we used DNA metabarcoding to monitor fungal succession during the decomposition of juvenile pigs in grasslands of New Jersey, USA. Our findings show that decomposition stages differ in a diversity of fungal communities. In particular, we noted increased fungal species richness in the more advanced stages of decomposition (e.g., bloat and decay stages), with unique fungal taxa becoming active with the progression of decay. Overall, our findings improve knowledge of how fungi contribute to forensically relevant decomposition and could help with the assessment of crime scenes.
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Affiliation(s)
| | | | - Rachel Domke
- Department of Biology, Kean University, Union, NJ 07083, USA
| | | | - Ayesha Hashim
- Department of Biology, Kean University, Union, NJ 07083, USA
| | | | | | - Urvi Patel
- Department of Biology, Kean University, Union, NJ 07083, USA
| | - Olivia Pate
- Department of Biology, Kean University, Union, NJ 07083, USA
| | - Gloria Raise
- Department of Biology, Kean University, Union, NJ 07083, USA
| | - Maria Shumskaya
- Department of Biology, Kean University, Union, NJ 07083, USA
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Díaz L, Castellá G, Bragulat MR, Paytuví-Gallart A, Sanseverino W, Cabañes FJ. Study of the variation of the Malassezia load in the interdigital fold of dogs with pododermatitis. Vet Res Commun 2022; 47:385-396. [PMID: 35704160 DOI: 10.1007/s11259-022-09951-2] [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: 11/17/2021] [Accepted: 06/04/2022] [Indexed: 11/25/2022]
Abstract
The yeast Malassezia pachydermatis is a common inhabitant of the skin and mucosae of dogs. However, under certain circumstances this yeast can overgrow and act as an opportunistic pathogen causing otitis and dermatitis in dogs. Canine pododermatitis is a common disorder in dogs in which M. pachydermatis acts as an opportunistic pathogen. In the present study, the presence of Malassezia yeasts was assessed and quantified in samples collected from the interdigital space of dogs with pododermatitis before and after treatment, and from healthy dogs. The samples were subjected to two different cytological examinations, culture on Sabouraud glucose agar and modified Dixon's agar and a quantitative PCR targeting the internal transcribed spacer (ITS) genomic region. A selection of samples was analyzed by next generation sequencing (NGS) using the D1D2 domain of the large subunit of the ribosomal DNA as target. The pododermatitis samples before treatment showed higher cell counts, colony-forming units and ITS copies than the rest of samples. The NGS analysis revealed that Ascomycota was the main phylum in the healthy and post-treatment samples. However, Basidiomycota and M. pachydermatis was more abundant in the pododermatitis samples before treatment. These results support M. pachydermatis as an opportunistic agent in canine pododermatitis by a variety of methods, and demonstrate the correlation between cytologic and molecular methods for quantification.
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Affiliation(s)
- Leyna Díaz
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Gemma Castellá
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain.
| | - M Rosa Bragulat
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | | | | | - F Javier Cabañes
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
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Díaz L, Castellá G, Bragulat MR, Martorell J, Paytuví-Gallart A, Sanseverino W, Cabañes FJ. External ear canal mycobiome of some rabbit breeds. Med Mycol 2020; 59:683-693. [PMID: 33369664 DOI: 10.1093/mmy/myaa097] [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] [Received: 07/31/2020] [Revised: 09/28/2020] [Accepted: 11/13/2020] [Indexed: 12/17/2022] Open
Abstract
The genus Malassezia is part of the normal skin mycobiota of a wide range of warm-blooded animals. In this genus, M. cuniculi is the only species described from rabbits. However, Malassezia species are rarely studied in lagomorphs. In the present study, the presence of Malassezia was assessed in samples from the external ear canal of healthy rabbits of different breeds. Cytological and culture techniques, Sanger sequencing, and Next-generation sequencing (NGS) were used to describe the ear mycobiota in the samples. Although no growth was observed in the cultured plates, cytological examination revealed the presence of round cells similar to those of Malassezia yeasts. For metagenomics analysis, the D1/D2 domain of the large subunit of the ribosomal DNA (LSU rDNA) was PCR amplified and the resulting reads were mapped against a custom-made cured database of 26S fungal sequences. NGS analysis revealed that Basidiomycota was the most abundant phylum in all the samples followed by Ascomycota. Malassezia was the most common genus presenting the highest abundance in the external ear canal. Malassezia phylotype 131 and M. cuniculi were the main sequences detected in the external auditory canal of rabbits. The study included both lop-eared and erect-eared rabbits and no differences were observed in the results when comparing both groups. This is the first attempt to study the external ear canal mycobiome of rabbits of different breeds using NGS. LAY SUMMARY In the present study, the presence of Malassezia was assessed in samples from the external ear canal of healthy rabbits of different breeds. Cytological and culture techniques, Sanger sequencing, and Next-generation sequencing (NGS) were used to describe the ear mycobiota in the samples.
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Affiliation(s)
- Leyna Díaz
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Gemma Castellá
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - M Rosa Bragulat
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Jaume Martorell
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | | | | | - F Javier Cabañes
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
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