The potential use of mitochondrial ribosomal genes (12S and 16S) in DNA barcoding and phylogenetic analysis of trematodes

Validating a web application's use of genetic distance to determine helminth species boundaries and aid in identification

BACKGROUND

Parasitic helminths exhibit significant diversity, complicating both morphological and molecular species identification. Moreover, no helminth-specific tool is currently available to aid in species identification of helminths using molecular data. To address this, we developed and validated a straightforward, user-friendly application named Applying Taxonomic Boundaries for Species Identification of Helminths (ABIapp) using R and the Shiny framework. Serving as a preliminary step in species identification, ABIapp is designed to assist in visualizing taxonomic boundaries for nematodes, trematodes, and cestodes. ABIapp employs a database of genetic distance cut-offs determined by the K-means algorithm to establish taxonomic boundaries for ten genetic markers. Validation of ABIapp was performed both in silico and with actual specimens to determine its classification accuracy. The in silico validation involved 591 genetic distances sourced from 117 publications, while the validation with actual specimens utilized ten specimens. ABIapp's accuracy was also compared with other online platforms to ensure its robustness to assist in helminth identification.

RESULTS

ABIapp achieved an overall classification accuracy of 76% for in silico validation and 75% for actual specimens. Additionally, compared to other platforms, the classification accuracy of ABIapp was superior, proving its effectiveness to determine helminth taxonomic boundaries. With its user-friendly interface, minimal data input requirements, and precise classification capabilities, ABIapp offers multiple benefits for helminth researchers and can aid in identification.

CONCLUSIONS

Built on a helminth-specific database, ABIapp serves as a pioneering tool for helminth researchers, offering an invaluable resource for determining species boundaries and aiding in species identification of helminths. The availability of ABIapp to the community of helminth researchers may further enhance research in the field of helminthology. To enhance ABIapp's accuracy and utility, the database will be updated annually.

Unveiling Tick Diversity in Cattle in Cameroon: Emergence of Rhipicephalus microplus, Replacing the Original Rhipicephalus spp

Ticks are well-known vectors of pathogens, posing considerable risks to livestock health and productivity. In Cameroon, where livestock production is vital, established tick species such as Amblyomma variegatum and Hyalomma truncatum are prevalent in key cattle-rearing areas. The recent introduction of the invasive, acaricide-resistant Rhipicephalus microplus further complicates control efforts. In this study, we deliver baseline data on the composition of tick species and their shifts within agroecological zone I (AEZ I) and agroecological zone III (AEZ III) of Cameroon, providing a foundation for targeted vector control strategies to ultimately reduce the risk of pathogen transmission. From 1100 ticks collected across two Cameroonian agroecological zones, H. truncatum (39.9%), A. variegatum (31%), and R. microplus (10.64%) were the most prevalent species, along with Rhipicephalus lunulatus (4.45%), Hyalomma rufipes (1.45%), Hyalomma marginatum (1.09%), Hyalomma dromedarii (0.45%), and Rhipicephalus sanguineus (0.9%). Molecular identification using cytochrome C oxidase subunit 1 (cox1) and 16s led to the identification of five additional species, Hyalomma nitidum (0.73%), Rhipicephalus simus (3.54%), Rhipicephalus sulcatus (2.64%), Rhipicephalus praetextatus (2.1%), and Rhipicephalus pusillus (1.1%). R. microplus emerged as the most dominant Rhipicephalus spp. in AEZ I, comprising 67.5% of the total Rhipicephalus ticks. In conclusion, we demonstrate the further spread of R. microplus, which represents a major source of vector-borne diseases, affecting both humans and animals.

Helminths infection of Schizothorax niger in Kashmir, India: morphological and molecular characterization

BACKGROUND

The identification of helminth parasites in Schizothorax spp. from Kashmir, including Schyzocotyle acheilognathi, Pomphorhynchus kashmirensis, and Adenoscolex oreini, is hindered by morphological limitations and high intraspecific variation. While previous studies have relied on morphological diagnosis, a comprehensive molecular characterization is lacking. To address these limitations and achieve more accurate species identification, this study employs molecular techniques such as DNA sequencing and phylogenetic analysis.

METHOD

Genomic DNA was extracted using standardized protocols. Partial amplification of 18S, ITS, and 28S rRNA was carried out using specific primer sets, followed by Sanger sequencing. Genetic characteristics were analyzed using bioinformatic approaches, focusing on Nucleotide divergence and Phylogenetic relationships.

RESULTS

Phylogenetic analysis confirmed the monophyly of S. acheilognathi, revealing close relationships with S. nayarensis. Interspecific variation ranged from 2.0 - 4.1% for 18S and 0.8 - 2.2% for 28S rDNA, while P. kashmirensis showed high genetic similarity to P. tereticollis and P. laevis with variations ranging from 0.1 - 1.5% for 18S and 2.3-6.0% for ITS rDNA. A. oreini forms a monophyletic lineage separate from Caryophyllaeides and Caryophyllaeus species.

CONCLUSION

Our study resolved persistent taxonomic ambiguities within the order Bothriocephalidea, resulting in the reassignment of Schyzocotyle acheilognathi (previously Bothriocephalus acheilognathi) to the reinstated genus Schyzocotyle. This study underscores the utility of ribosomal gene sequencing in characterizing fish parasites and highlights the need for taxonomic re-evaluation of A. oreini within the Capingentidae family.

Genetic differentiation of Oncomelania hupensis robertsoni in hilly regions of China: Using the complete mitochondrial genome

OBJECTIVE

Oncomelania hupensis robertsoni is the only intermediate host of Schistosoma japonicum in hilly regions of south-west China, which plays a key role during the transmission of Schistosomiasis. This study aimed to sequence the complete mitochondrial genome of Oncomelania hupensis robertsoni and analyze genetic differentiation of Oncomelania hupensis robertsoni.

METHODS

Samples were from 13 villages in Yunnan Province of China, with 30 Oncomelania hupensis snails per village, and the complete mitochondrial genome was sequenced. A comprehensive analysis of the genetic differentiation of Oncomelania hupensis robertsoni was conducted by constructing phylogenetic trees, calculating genetic distances, and analyzing identity.

RESULTS

A total of 26 complete mitochondrial sequences were determined. The length of genome ranged from 15,181 to 15,187 bp, and the base composition of the genome was A+T (67.5%) and G+C content (32.5%). This genome encoded 37 genes, including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. The phylogenetic trees and identity analysis confirmed that Oncomelania hupensis robertsoni was subdivided into Oncomelania hupensis robertsoni Yunnan strain and Sichuan strain, with a genetic distance of 0.0834. Oncomelania hupensis robertsoni Yunnan strain was further subdivided into two sub-branches, corresponding to "Yunnan North" and "Yunnan South", with a genetic distance of 0.0216, and the samples exhibited over 97% identity.

CONCLUSION

Oncomelania hupensis robertsoni is subdivided into Oncomelania hupensis robertsoni Yunnan strain and Sichuan strain. Oncomelania hupensis robertsoni Yunnan strain exhibits a higher level of genetic identity and clear north-south differentiation. This work reported the first mitochondrial genome of Oncomelania hupensis robertsoni Yunnan strain, which could be used as an important reference genome for Oncomelania hupensis, and also provide the important information for explaining the distribution pattern of Oncomelania hupensis robertsoni and control of Schistosoma japonicum.

Mitochondrial DNA as a target for analyzing the biodistribution of cell therapy products

Biodistribution tests are crucial for evaluating the safety of cell therapy (CT) products in order to prevent unwanted organ homing of these products in patients. Quantitative polymerase chain reaction (qPCR) using intronic Alu is a popular method for biodistribution testing owing to its ability to detect donor cells without modifying CT products and low detection limit. However, Alu-qPCR may generate inaccurate information owing to background signals caused by the mixing of human genomic DNA with that of experimental animals. The aim of this study was to develop a test method that is more specific and sensitive than Alu-qPCR, targeting the mitochondrial DNA (mtDNA) sequence that varies substantially between humans and experimental animals. We designed primers for 12S, 16S, and cytochrome B in mtDNA regions, assessed their specificity and sensitivity, and selected primers and probes for the 12S region. Human adipose-derived stem cells, used as CT products, were injected into the tail vein of athymic NCr-nu/nu mice and detected, 7 d after administration, in their lungs at an average concentration of 2.22 ± 0.69 pg/μg mouse DNA, whereas Alu was not detected. Therefore, mtDNA is more specific and sensitive than Alu and is a useful target for evaluating CT product biodistribution.

DNA barcoding for the identification and authentication of medicinal deer (Cervus sp.) products in China

Deer products from sika deer (Cervus nippon) and red deer (C. elaphus) are considered genuine and used for Traditional Chinese Medicine (TCM) materials in China. Deer has a very high economic and ornamental value, resulting in the formation of a characteristic deer industry in the prescription preparation of traditional Chinese medicine, health food, cosmetics, and other areas of development and utilization. Due to the high demand for deer products, the products are expensive and have limited production, but the legal use of deer is limited to only two species of sika deer and red deer; other wild deer are prohibited from hunting, so there are numerous cases of mixing and adulteration of counterfeit products and so on. There have been many reports that other animal (pig, cow, sheep, etc.) tissues or organs are often used for adulteration and confusion, resulting in poor efficacy of deer traditional medicine and trade fraud in deer products. To authenticate the deer products in a rapid and effective manner, the analysis used 22 deer products (antler, meat, bone, fetus, penis, tail, skin, and wool) that were in the form of blind samples. Total DNA extraction using a modified protocol successfully yielded DNA from the blind samples that was useful for PCR. Three candidate DNA barcoding loci, cox1, Cyt b, and rrn12, were evaluated for their discrimination strength through BLAST and phylogenetic clustering analyses. For the BLAST analysis, the 22 blind samples obtained 100% match identity across the three gene loci tested. It was revealed that 12 blind samples were correctly labeled for their species of origin, while three blind samples that were thought to originate from red deer were identified as C. nippon, and seven blind samples that were thought to originate from sika deer were identified as C. elaphus, Dama dama, and Rangifer tarandus. DNA barcoding analysis showed that all three gene loci were able to distinguish the two Cervus species and to identify the presence of adulterant species. The DNA barcoding technique was able to provide a useful and sensitive approach in identifying the species of origin in deer products.

Discovery of Encyclometra bungara (Digenea: Encyclometridae) in a new host (Enhydris enhydris) from Thailand and Cambodia through morphological and molecular identification

The genus Encyclometra is one of the two genera in family Encyclometridae, known for parasitising the oesophagus, stomach and intestine of snakes. Among Encyclometra, the species present are: Encyclometra colubrimurorum, Encyclometra japonica, Encyclometra asymmetrica and Encyclometra bungara. Species discrimination within Encyclometra has predominantly relied on morphological differences, such as the length of the caeca and the position of the testes. Morphological overlaps exist among these species making species discrimination challenging. Additionally, the use of molecular information has been limited for Encyclometra. To determine the Encyclometra species infecting Enhydris enhydris from Thailand and Cambodia, morphological and molecular identification was conducted. Morphological characters and measurements were obtained from 30 Encyclometra adults, and they were compared with previous studies of other Encyclometra species. Novel sequences of E. bungara were generated using the nuclear 18S and 28S ribosomal RNA genes, and the mitochondrial cytochrome c oxidase subunit 1 gene. Our results revealed that the specimens could be morphologically identified as E. bungara, with support from molecular information obtained from the phylogenies of the 3 genetic markers employed. Molecular analysis showed that the Encyclometra specimens were distinct from E. colubrimurorum and E. japonica. Through morphological and molecular identification of the Encyclometra specimens found in E. enhydris from Thailand and Cambodia, we describe and provide a record of E. bungara in a new host and new locality. Additionally, novel molecular sequences were generated, revealing the phylogenetic position of E. bungara within the superfamily Gorgoderoidea.

Morphological constraint obscures richness: a mitochondrial exploration of cryptic richness in Transversotrema (Trematoda: Transversotrematidae)

Species of Transversotrema Witenberg, 1944 (Transversotrematidae) occupy a unique ecological niche for the Trematoda, living externally under the scales of their teleost hosts. Previous studies of the genus have been impeded partly by limited variation in ribosomal DNA sequence data between closely related species and partly by a lack of morphometrically informative characters. Here, we assess richness of the tropical Indo-west Pacific species through parallel phylogenetic and morphometric analyses, generating cytochrome c oxidase subunit 1 mitochondrial sequence data and morphometric data for hologenophore specimens from Australia, French Polynesia, Japan and Palau. These analyses demonstrate that molecular data provide the only reliable basis for species identification; host distribution, and to a lesser extent morphology, are useful for identifying just a few species of Transversotrema. We infer that a combination of morphological simplicity and infection site constraint has led to the group displaying exceptionally low morphological diversification. Phylogenetic analyses of the mitochondrial data broadly support previous systematic interpretations based on ribosomal data, but also demonstrate the presence of several morphologically and ecologically cryptic species. Ten new species are described, eight from the Great Barrier Reef, Australia (Transversotrema chrysallis n. sp., Transversotrema daphnidis n. sp., Transversotrema enceladi n. sp., Transversotrema hyperionis n. sp., Transversotrema iapeti n. sp., Transversotrema rheae n. sp., Transversotrema tethyos n. sp., and Transversotrema titanis n. sp.) and two from off Japan (Transversotrema methones n. sp. and Transversotrema panos n. sp.). There are now 26 Transversotrema species known from Australian marine fishes, making it the richest trematode genus for the fauna.

High-throughput DNA metabarcoding for determining the gut microbiome of captive critically endangered Malayan tiger (Pantheratigrisjacksoni) during fasting

The Malayan tiger (Pantheratigrisjacksoni) is a critically endangered species native to the Malaysian Peninsula. To imitate wild conditions where tigers do not hunt every day, numerous wildlife sanctuaries do not feed their tigers daily. However, the effects of fasting on the gut microbiota of captive Malayan tigers remains unknown. This study aimed to characterise the gut microbiota of captive Malayan tigers by comparing their microbial communities during fasting versus normal feeding conditions. This study was conducted at the Melaka Zoo, Malaysian Peninsula and involved Malayan tigers fasted every Monday. In total, ten faecal samples of Malayan tiger, two of Bengal tiger (outgroup) and four of lion (outgroup) were collected and analysed for metabarcoding targeting the 16S rRNA V3-V4 region. In total, we determined 14 phyla, 87 families, 167 genera and 53 species of gut microbiome across Malayan tiger samples. The potentially harmful bacterial genera found in this study included Fusobacterium, Bacteroides, Clostridium sensu stricto 1, Solobacterium, Echerichiashigella, Ignatzschineria and Negativibacillus. The microbiome in the fasting phase had a higher composition and was more diverse than in the feeding phase. The present findings indicate a balanced ratio in the dominant phyla, reflecting a resetting of the imbalanced gut microbiota due to fasting. These findings can help authorities in how to best maintain and improve the husbandry and health of Malayan tigers in captivity and be used for monitoring in ex-situ veterinary care unit.

Sensitive and accurate DNA metabarcoding of parasitic helminth mock communities using the mitochondrial rRNA genes

Next-generation sequencing technologies have accelerated the pace of helminth DNA metabarcoding research, enabling species detection in bulk community samples. However, finding suitable genetic markers with robust species-level resolution and primers targeting a broad species range among parasitic helminths are some of the challenges faced. This study aimed to demonstrate the potential use of the mitochondrial 12S and 16S rRNA genes for parasitic helminth (nematodes, trematodes, cestodes) DNA metabarcoding. To demonstrate the robustness of the 12S and 16S rRNA genes for DNA metabarcoding, we determined the proportion of species successfully recovered using mock helminth communities without environment matrix and mock helminth communities artificially spiked with environmental matrices. The environmental matrices are human fecal material, garden soil, tissue, and pond water. Our results revealed the robustness of the mitochondrial rRNA genes, through the high sensitivity of the 12S rRNA gene, and the effectiveness of the 12S and 16S primers targeting platyhelminths. With the mitochondrial rRNA genes, a broad range of parasitc helminths were successfully detected to the species level. The potential of the mitochondrial rRNA genes for helminth DNA metabarcoding was demonstrated, providing a valuable gateway for future helminth DNA metabarcoding applications like helminth detection and biodiversity studies.

What lies behind the curtain: Cryptic diversity in helminth parasites of human and veterinary importance

Parasite cryptic species are morphologically indistinguishable but genetically distinct organisms, leading to taxa with unclear species boundaries. Speciation mechanisms such as cospeciation, host colonization, taxon pulse, and oscillation may lead to the emergence of cryptic species, influencing host-parasite interactions, parasite ecology, distribution, and biodiversity. The study of cryptic species diversity in helminth parasites of human and veterinary importance has gained relevance, since their distribution may affect clinical and epidemiological features such as pathogenicity, virulence, drug resistance and susceptibility, mortality, and morbidity, ultimately affecting patient management, course, and outcome of treatment. At the same time, the need for recognition of cryptic species diversity has implied a transition from morphological to molecular diagnostic methods, which are becoming more available and accessible in parasitology. Here, we discuss the general approaches for cryptic species delineation and summarize some examples found in nematodes, trematodes and cestodes of medical and veterinary importance, along with the clinical implications of their taxonomic status. Lastly, we highlight the need for the correct interpretation of molecular information, and the correct use of definitions when reporting or describing new cryptic species in parasitology, since molecular and morphological data should be integrated whenever possible.