Worms and bugs of the gut: the search for diagnostic signatures using barcoding, and metagenomics–metabolomics

Abstract

Gastrointestinal (GI) helminth infections cause significant morbidity in both humans and animals worldwide. Specific and sensitive diagnosis is central to the surveillance of such infections and to determine the effectiveness of treatment strategies used to control them. In this article, we: (i) assess the strengths and limitations of existing methods applied to the diagnosis of GI helminth infections of humans and livestock; (ii) examine high-throughput sequencing approaches, such as targeted molecular barcoding and shotgun sequencing, as tools to define the taxonomic composition of helminth infections; and (iii) discuss the current understanding of the interactions between helminths and microbiota in the host gut. Stool-based diagnostics are likely to serve as an important tool well into the future; improved diagnostics of helminths and their environment in the gut may assist the identification of biomarkers with the potential to define the health/disease status of individuals and populations, and to identify existing or emerging anthelmintic resistance. Graphical Abstract

Evaluation of genome skimming to detect and characterise human and livestock helminths

“…Scale bar indicates the number of substitutions per site. approach for diagnosing mixed helminth infections of human and livestock importance (Papaiakovou et al, 2022). Using 20 wellcharacterised faecal DNA extracts, we found that genome skimming is specific, but not as sensitive as qPCR-based diagnostics.…”

“…Whole metagenome sequencing of DNA isolated from faecal samples represents a powerful alternative. Deep amplicon sequencing and shotgun metagenomics are increasingly being applied to the field of parasitology (Papaiakovou et al, 2022). For example, application of untargeted shotgun metagenomics to detect conserved 18S rDNA has enabled broad taxonomic detection of eukaryotic parasites (Cannon et al, 2018;Wylezich et al, 2020).…”

Species interactions, stability, and resilience of the gut microbiota - Helminth assemblage in horses

“…Fourth, whole metabarcoding approaches have significantly improved the depth at which the gut microbiota and nemabiome structure and function can be described. Nonetheless, future studies incorporating deeper functional resolution of the host-gut microbiome-nemabiome system (e.g., shotgun metagenomics, metatranscriptomics and metabolomics) will provide additional value, 106 including the role that ciliate protozoa and fungi play in cyathostomin success in the equine intestines. 17 Last, although whole blood RNAseq analysis was ideal for obtaining a broad overview of host gene expression within a specific environment, it curtailed our ability to detect differences between cell type populations or specific biological processes.…”

Gastrointestinal worms and bacteria: From association to intervention

“…78 Nevertheless, in order for this technology to be fully exploited, two key technical barriers must be overcome; first, specific molecules acting as unequivocal indicators of infection must be identified; second, these indicators must be detectable through bacterial biosensors. Once these live biosensors are developed, their use could be extended to diagnostic purposes, 78,79 coupling the detection system with a response mechanism that outputs a detectable (and measurable) signal. 80 Lastly, microbial bioengineering approaches might also be applied to fine-tuning of host-parasite interactions to achieve a beneficial effect for the host.…”