Biology subjects

Hunt, V. L.

Publications and source records attributed to Hunt, V. L..

4 recordsLinked to original sources

bioRxiv2026

Nematode species differ in susceptibility and response to the nematode-trapping fungus Arthrobotrys oligospora

Fungal predators of nematodes are widespread and represent promising candidates for biological control of parasitic nematodes. However, the behavioural and molecular mechanisms underlying nematode-fungus interactions remain poorly understood, especially for nematodes other than Caenorhabditis elegans. We investigated the interactions between the nematode-trapping fungus Arthrobotrys oligospora and three nematode species: (i) free-living C. elegans, (ii) fig-associated C. inopinata, and (iii) the free-living adult life cycle stage of the gastrointestinal parasite Strongyloides ratti. A. oligospora trapped S. ratti more efficiently than either C. elegans or C. inopinata. Behavioural analyses revealed species-specific differences in nematode locomotion. S. ratti moved slower, travelled shorter distances and showed lower displacement than Caenorhabditis spp. To test whether locomotion influences fungal trapping, we examined eight C. elegans mutants with hyper- or hypoactive locomotory phenotypes. Although both groups moved at similar speeds, hyperactive mutants showed greater displacement, which positively correlated with trap formation but did not explain trapping efficiency by A. oligospora. We investigated the fungal response during interaction with the three nematodes. Exposure to S. ratti, but not to Caenorhabditis spp, resulted in reduced sporulation and differential expression of sporulation-associated genes. In nematodes, myosin-related genes responded to A. oligospora in a species-specific manner, including upregulation in C. elegans and downregulation in S. ratti. These transcriptional changes may reflect alterations in muscle structure, including reduction in dense body and mitochondrial size in Caenorhabditis species but not S. ratti during A. oligospora exposure. Together, our findings demonstrate that both fungal and nematode responses are nematode species dependent. These results improve our understanding of nematode-fungus interactions and highlight the importance of nematode species when developing nematode-trapping fungi as a biological control agent.

evolutionary biology↗

bioRxiv2026

Hunting for Helminths: short- and long-read shotgun metagenomics for parasite detection in faecal samples

Soil-transmitted helminths (STHs) pose significant challenges to public health in endemic areas, necessitating reliable methods for their detection. Shotgun metagenomics enables simultaneous detection of STHs and microbes in a sample without prior knowledge of what is present. However, validation of shotgun metagenomics with known infection intensity or across different sequencing platforms has not been carried out for eukaryote parasites including STHs, and false positives remain a pervasive issue. We validated shotgun metagenomics as a method of STH detection in faecal samples. Using the Strongyloides ratti laboratory model of a STH infection we investigated how analytical methods (nucleotide-nucleotide matching, nucleotide-protein matching, marker gene detection, mitochondrial mapping), infection intensity and sequencing technology (short-read vs. long-read) affects sensitivity and specificity of detection. S. ratti was accurately detected at a standard laboratory dose, but low intensity infections were more difficult to detect. Only mitochondrial sequence mapping was 100% accurate at identifying S. ratti with no false positives. Overall, short-read outperformed long-read sequencing methods. We applied the same analytical methods to human faecal samples with confirmed infections for at least one of four STHs. Mitochondrial sequence mapping was also the most effective method for detecting STHs in human faecal samples, detecting 100% of Necator americanus and 92% of Ascaris spp. infections, but could not reliably detect STHs where DNA levels are expected to be low or variable. In conclusion, mitochondrial mapping was the most effective method of detection for sensitivity and specificity in both the laboratory system and human faecal samples. Our findings indicate that shotgun metagenomics should be approached cautiously using validated methods, particularly when infection intensity or DNA levels are expected to be low. Author SummarySoil-transmitted helminths (STH) such as the parasite Strongyloides, are important gastrointestinal parasites of humans and livestock. Accurate methods of detection for diagnostics and monitoring are important to implement suitable control and treatment strategies. Here we validate a shotgun metagenomics approach, where all DNA in a sample is sequenced, for detecting STH in faecal samples using a Strongyloides laboratory model for infection. Strongyloides was reliability detected in faecal samples at higher infection levels, but mitochondrial genome mapping of the sequences was the only analytical method that reliably detected Strongyloides at lower infections levels. These results were reflected in stool samples from humans infected with STH, where mitochondrial mapping was also the most reliable method. However, species that were associated with low levels of parasite material or DNA in the faeces including Strongyloides stercoralis, were more difficult to detect. We compared two sequencing methods: short-read Illumina and long-read Oxford Nanopore Technologies, but short-read outperformed long-read shotgun metagenomics. Contamination of bacteria sequences in parasite genome assemblies was problematic for analysis and contributed to false positive results. Future work should focus on specific targeting of eukaryote DNA either at the laboratory or bioinformatic stage to improve STH detection further.

molecular biology↗

bioRxiv2022

piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode

The small RNA (sRNA) pathways identified in the model organism Caenorhabditis elegans are not widely conserved across nematodes. For example, the PIWI pathway and PIWI-interacting RNAs (piRNAs) are involved in regulating and silencing transposable elements (TE) in most animals but have been lost in nematodes outside of the Caenorhabditis elegans group (Clade V), and little is known about how nematodes regulate TEs in the absence of the PIWI pathway. Here, we investigated the role of sRNAs in the Clade IV parasitic nematode Strongyloides ratti by comparing two genetically identical adult stages (the parasitic female and free-living female). We identified putative small-interfering RNAs, microRNAs and tRNA-derived sRNA fragments that are differentially expressed between the two adult stages. Two classes of sRNAs were predicted to regulate TE activity including (i) a parasite-associated class of 21-22 nt long sRNAs with a 5 uracil (21-22Us) and monophosphate modification, and (ii) 27 nt long sRNAs with a 5 guanine/adenine (27GAs) and polyphosphate modification. The 21-22Us show striking resemblance to the 21U PIWI-interacting RNAs found in C. elegans, including an AT rich upstream sequence, overlapping loci and physical clustering in the genome.

genomics↗

bioRxiv2020

Genome analysis of the fatal tapeworm Sparganum proliferum unravels the cryptic lifecycle and mechanisms underlying the aberrant larval proliferation

BackgroundThe cryptic parasite Sparganum proliferum proliferates in humans and invades tissues and organs. Only scattered cases have been reported, but S. proliferum infection is always fatal. However, the S. proliferum phylogeny and lifecycle are still an enigma. ResultsTo investigate the phylogenetic relationships between S. proliferum and other cestode species, and to examine the underlying mechanisms of pathogenicity, we sequenced the entire S. proliferum genome. Additionally, S. proliferum plerocercoid larvae transcriptome analyses were performed to identify genes involved in asexual reproduction in the host. The genome sequences confirmed that the S. proliferum genetic sequence is distinct from that of the closely related Spirometra erinaceieuropaei. Moreover, nonordinal extracellular matrix coordination allows for asexual reproduction in the host and loss of sexual maturity in S. proliferum is related to its fatal pathogenicity in humans. ConclusionsThe high-quality reference genome sequences generated should prove valuable for future studies of pseudophyllidean tapeworm biology and parasitism.

genomics↗