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Miller ML, Rota C, Welsh A. Transforming gastrointestinal helminth parasite identification in vertebrate hosts with metabarcoding: a systematic review. Parasit Vectors 2024; 17:311. [PMID: 39030625 PMCID: PMC11265005 DOI: 10.1186/s13071-024-06388-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 07/03/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Gastrointestinal helminths are a very widespread group of intestinal parasites that can cause major health issues in their hosts, including severe illness or death. Traditional methods of helminth parasite identification using microscopy are time-consuming and poor in terms of taxonomic resolution, and require skilled observers. DNA metabarcoding has emerged as a powerful alternative for assessing community composition in a variety of sample types over the last few decades. While metabarcoding approaches have been reviewed for use in other research areas, the use of metabarcoding for parasites has only recently become widespread. As such, there is a need to synthesize parasite metabarcoding methodology and highlight the considerations to be taken into account when developing a protocol. METHODS We reviewed published literature that utilized DNA metabarcoding to identify gastrointestinal helminth parasites in vertebrate hosts. We extracted information from 62 peer-reviewed papers published between 2014 and 2023 and created a stepwise guide to the metabarcoding process. RESULTS We found that studies in our review varied in technique and methodology, such as the sample type utilized, genetic marker regions targeted and bioinformatic databases used. The main limitations of metabarcoding are that parasite abundance data may not be reliably attained from sequence read numbers, metabarcoding data may not be representative of the species present in the host and the cost and bioinformatic expertise required to utilize this method may be prohibitive to some groups. CONCLUSIONS Overall, using metabarcoding to assess gastrointestinal parasite communities is preferable to traditional methods, yielding higher taxonomic resolution, higher throughput and increased versatility due to its utility in any geographical location, with a variety of sample types, and with virtually any vertebrate host species. Additionally, metabarcoding has the potential for exciting new discoveries regarding host and parasite evolution.
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Affiliation(s)
- Madison L Miller
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA.
| | - Christopher Rota
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
| | - Amy Welsh
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
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Dantas-Torres F, Bezerra-Santos MA, Mendoza-Roldan JA, Lia RP, Perles L, Barrera JP, Fagundes-Moreira R, Carbonara M, Varcasia A, Brianti E, Deak G, Rojas A, Miró G, Volf P, Baneth G, Otranto D. ParSCo: celebrating 10 years of a unique parasitology summer course. Parasit Vectors 2024; 17:89. [PMID: 38409043 PMCID: PMC10895767 DOI: 10.1186/s13071-024-06174-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 01/30/2024] [Indexed: 02/28/2024] Open
Abstract
ParSCo (Parasitology Summer Course) is an intense, 1-week-long summer course organized by the Parasitology Unit of the Department of Veterinary Medicine, University of Bari, Italy, with the support of the World Association for the Advancement of Veterinary Parasitology (WAAVP), the European Veterinary Parasitology College (EVPC) and Parasites and Vectors. The course, which is conducted in southern Italy, is planned for parasitologists and post-graduate students working in the field of parasitology. The course consists of theoretical and practical lessons, which include the collection, identification and diagnosis of parasites of pets, livestock and wildlife. The participants in ParSCo are afforded the opportunity to be involved in clinical examination and sample collection for the diagnosis of parasitic diseases (e.g. leishmaniosis, thelaziosis and many tick-borne diseases) present in the Mediterranean Basin. The course is conducted at Casa di Caccia, a hunting lodge situated in the Gallipoli Cognato Forest near the Basento River in the Basilicata region in southern Italy. In addition to the training purpose, ParSCo is a great opportunity for sharing knowledge and expertise while becoming part of the parasitology community in a pleasant environment. In this editorial, we share some information and celebrate 10 years of ParSCo, looking forward to forthcoming sessions of this unique parasitology summer course.
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Affiliation(s)
- Filipe Dantas-Torres
- Aggeu Magalhães Institute, Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil.
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Valenzano, Italy.
| | | | | | - Riccardo Paolo Lia
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Valenzano, Italy
| | - Livia Perles
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Valenzano, Italy
| | - Juan Pedro Barrera
- Animal Health Department, Veterinary Faculty, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Mariaelisa Carbonara
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Valenzano, Italy
| | - Antonio Varcasia
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Emanuele Brianti
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Georgiana Deak
- Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | - Alicia Rojas
- Laboratory of Helminthology, Faculty of Microbiology, University of Costa Rica, San Jose, Costa Rica
| | - Guadalupe Miró
- Animal Health Department, Veterinary Faculty, Universidad Complutense de Madrid, Madrid, Spain
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Gad Baneth
- Koret School of Veterinary Medicine, Hebrew University of Jerusalem, Rehovot, Israel
| | - Domenico Otranto
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Valenzano, Italy.
- Department of Veterinary Clinical Sciences, City University of Hong Kong, Kowloon, Hong Kong.
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Festa M, Abbruscato P, Manachini B. Use of PCR-DGGE-Based Molecular Methods to Analyze Nematode Community Diversity. Methods Mol Biol 2024; 2756:247-255. [PMID: 38427297 DOI: 10.1007/978-1-0716-3638-1_6] [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] [Indexed: 03/02/2024]
Abstract
DGGE (denaturing gradient gel electrophoresis) is a nucleic acid separation technique applied to the evaluation of microbial biodiversity. This technique is quite rapid and cheap compared to other types of analysis. Here we describe the comparison of nematode communities inhabiting different ecosystems. After an ecologically representative sampling collection and the nematode extraction from soil, nematodes are centrifuged in Eppendorf tubes to facilitate DNA extraction. DNA from the whole community of each type of soil is extracted, amplified with primers for 18 S rDNA and used in DGGE analysis. The profiles of DGGE can be analyzed with appropriate software, and biodiversity indices can be estimated.
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Affiliation(s)
| | | | - Barbara Manachini
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy.
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Zapałowska A, Skwiercz A, Tereba A, Puchalski C, Malewski T. Next-Generation Sequencing for Evaluating the Soil Nematode Diversity and Its Role in Composting Processes. Int J Mol Sci 2023; 24:15749. [PMID: 37958731 PMCID: PMC10650539 DOI: 10.3390/ijms242115749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023] Open
Abstract
Biodiversity within composting systems involves a variety of microorganisms including nematodes. In the research, nematode populations were monitored within six simultaneously operating composting processes. These processes involved varying proportions of feedstock materials. The primary objective was to evaluate the consistency of nematode community succession patterns across the composting processes over a time of 3 months. During the study, samples were taken every month to isolate nematodes, determine the population density of the five trophic groups (per genus) and determine the dominant nematode species. It was shown that the bacterial-feeding community maintained dominance, while the fungus-feeding nematodes gradually increased in dominance as the maturation process progressed. The presence of predatory nematodes Mononchoides which were initially absent, along with the total absence of parasitic nematodes in the late stages of waste stabilization, serves as strong evidence for the reliable evaluation of the biodegradable waste processing level. Based on the obtained results, it is evident that the succession of nematode communities holds promise as a reliable method for evaluating compost maturity.
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Affiliation(s)
- Anita Zapałowska
- Department of Agriculture and Waste Management, Collegium of Natural Sciences, University of Rzeszów, St. Ćwiklinskiej 1a, 35-601 Rzeszów, Poland
| | - Andrzej Skwiercz
- National Institute of Horticultural Research, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland;
| | - Anna Tereba
- Department of Forest Ecology, Forest Research Institute, Braci Leśnej 3, Sękocin Stary, 05-090 Raszyn, Poland;
| | - Czesław Puchalski
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, Collegium of Natural Sciences, University of Rzeszów, St. Ćwiklińskiej 2D, 35-601 Rzeszów, Poland;
| | - Tadeusz Malewski
- Department of Molecular and Biometric Techniques, Museum and Institute of Zoology, Polish Academy of Sciences, 00-679 Warsaw, Poland;
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Fatemi E, Melzer S, Jung C. DNA-based assessment of root lesion nematode infections in cereal roots. Sci Rep 2023; 13:12602. [PMID: 37537261 PMCID: PMC10400682 DOI: 10.1038/s41598-023-39559-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023] Open
Abstract
Root lesion nematodes (RLN) of the genus Pratylenchus are causing significant damage in cereal production worldwide. Due to climate change and without efficient and environment-friendly treatments, the damages through RLNs are predicted to increase. Microscopic assessments of RLNs in the field and the greenhouses are time-consuming and laborious. As a result, cereal breeders have mostly ignored this pest. We present a method measuring RLN in infected cereal roots using a standardized PCR approach. Publicly available Pratylenchus neglectus primer combinations were evaluated. An optimal primer combination for RT-qPCR assay was identified to detect and quantify P. neglectus within infected cereal roots. Using the RT-qPCR detection assay, P. neglectus could be clearly distinguished from other plant parasitic nematodes. We could identify P. neglectus DNA in barley and wheat roots as low as 0.863 and 0.916 ng/µl of total DNA, respectively. A single P. neglectus individual was detected in water suspension and within barley and wheat roots. The RT-qPCR detection assay provides a robust and accurate alternative to microscopic nematode identification and quantification. It could be of interest for resistance breeding, where large populations must be screened to detect and quantify P. neglectus in farmer's fields.
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Affiliation(s)
- Ehsan Fatemi
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098, Kiel, Germany
| | - Siegbert Melzer
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098, Kiel, Germany
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098, Kiel, Germany.
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Sikandar A, Jia L, Wu H, Yang S. Meloidogyne enterolobii risk to agriculture, its present status and future prospective for management. FRONTIERS IN PLANT SCIENCE 2023; 13:1093657. [PMID: 36762171 PMCID: PMC9902769 DOI: 10.3389/fpls.2022.1093657] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/05/2022] [Indexed: 06/18/2023]
Abstract
Meloidogyne enterolobii, commonly known as guava root-knot nematode, poses risk due to its widespread distribution and extensive host range. This species is recognized as the most virulent root-knot nematode (RKN) species because it can emerge and breed in plants that have resistance to other tropical RKNs. They cause chlorosis, stunting, and yield reductions in host plants by producing many root galls. It is extremely challenging for farmers to diagnose due to the symptoms' resemblance to nutritional inadequacies. This pathogen has recently been considered a significant worldwide threat to agricultural production. It is particularly challenging to diagnose a M. enterolobii due to the similarities between this species and other RKN species. Identified using traditional morphological and molecular techniques, which is a crucial first in integrated management. Chemical control, biological control, the adoption of resistant cultivars, and cultural control have all been developed and effectively utilized to combat root-knot nematodes in the past. The object of this study was to get about the geographical distribution, host plants, symptoms, identification, and control techniques of M. enterolobii and recommend future initiatives to progress its management.
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Deng YP, Suleman, Zhang XL, Li R, Li LY, Fu YT, Liu GH, Yao C. Aonchotheca (Nematoda: Capillariidae) is validated as a separated genus from Capillaria by both mitochondrial and nuclear ribosomal DNA. Parasit Vectors 2022; 15:493. [PMID: 36585724 PMCID: PMC9805247 DOI: 10.1186/s13071-022-05609-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 12/03/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The family Capillariidae is a group of thread-like nematodes of 27 genera and over 300 species that infect a great variety of hosts including humans. Among these, some taxa such as the genus Aonchotheca have remained controversial regarding their systematic status for decades. The aim of the current study was to verify Aonchotheca's systemic status and to further determine whether it is a distinct genus from Capillaria using molecular and phylogenetic analyses. RESULTS We sequenced the mitochondrial (mt) genome and nuclear small subunit (18S) rRNA gene of Aonchotheca putorii, a representative species of the genus, and investigated its systematic status in Trichinellida using maximum likelihood and Bayesian inference. The differences in amino acid sequences of 13 protein-coding genes were 12.69-67.35% among Aonchotheca, Capillaria, Eucoleus, and Pseudocapillaria with cox1 (12.69%) and atp8 (67.35%) as the most and the least conserved gene, respectively, and the difference of two mt rRNAs was 18.61-34.15%. Phylogenetic analyses of the complete mt genome and 18S rRNAs unequivocally showed that Aonchotheca was a distinct genus from Capillaria. CONCLUSIONS Large difference exists among Aonchotheca, Capillaria, Eucoleus, and Pseudocapillarias. Aonchotheca putorii is the first species in the genus Aonchotheca for which a complete mitogenome has been sequenced. These data are useful for phylogenetics, systematics and the evolution of Capillariidae.
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Affiliation(s)
- Yuan-Ping Deng
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Suleman
- grid.502337.00000 0004 4657 4747Department of Zoology, University of Swabi, Swabi, 23561 Khyber Pakhtunkhwa Pakistan
| | - Xue-Ling Zhang
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Rong Li
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Le-Yan Li
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Yi-Tian Fu
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Guo-Hua Liu
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Chaoqun Yao
- grid.412247.60000 0004 1776 0209Department of Biomedical Sciences and One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
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