Abstract
BackgroundThe complex network of interactions occurring between gastrointestinal (GI) and extra-intestinal (EI) parasitic helminths of humans and animals and the resident gut microbial flora is attracting increasing attention from biomedical researchers, because of the likely implications for the pathophysiology of helminth infection and disease. Nevertheless, the vast heterogeneity of study designs and microbial community profiling strategies, and of bioinformatic and biostatistical approaches for analyses of metagenomic sequence datasets hinder the identification of bacterial targets for follow-up experimental investigations of helminth-microbiota cross-talk. Furthermore, comparative analyses of published datasets are made difficult by the unavailability of a unique repository for metagenomic sequence data and associated metadata linked to studies aimed to explore potential changes in the composition of the vertebrate gut microbiota in response to GI and/or EI helminth infections.ResultsHere, we undertake a meta-analysis of available metagenomic sequence data linked to published studies on helminth-microbiota cross-talk in humans and veterinary species using a single bioinformatic pipeline, and introduce the 'MICrobiome HELminth INteractions database' (MICHELINdb), an online resource for mining of published sequence datasets, and corresponding metadata, generated in these investigations.ConclusionsBy increasing data accessibility, we aim to provide the scientific community with a platform to identify gut microbial populations with potential roles in the pathophysiology of helminth disease and parasite-mediated suppression of host inflammatory responses, and facilitate the design of experiments aimed to disentangle the cause(s) and effect(s) of helminth-microbiota relationships.3-P6fXwiUKUizQ4bBEnJ8wVideo abstract.
Highlights
The complex network of interactions occurring between gastrointestinal (GI) and extra-intestinal (EI) parasitic helminths of humans and animals and the resident gut microbial flora is attracting increasing attention from biomedical researchers, because of the likely implications for the pathophysiology of helminth infection and disease
All sequence datasets retrieved using this method, as well as associated metadata, were included in MICHELINdb, together with study findings, whilst only studies that satisfied the following criteria were included in the metaanalysis: (a) Available paired-end high-throughput bacterial 16S rRNA sequence data in .fastq format deposited in publicly accessible databases
Sequence datasets linked to studies that required additional ethics committee approval or institutional authorization for data access were not included in the meta-analysis; these datasets and corresponding findings, as presented in the original publications, are available for mining in MICHELINdb
Summary
The complex network of interactions occurring between gastrointestinal (GI) and extra-intestinal (EI) parasitic helminths of humans and animals and the resident gut microbial flora is attracting increasing attention from biomedical researchers, because of the likely implications for the pathophysiology of helminth infection and disease. Whilst a small number of qualitative and/or quantitative changes in the composition of the host gut microbiota have been repeatedly observed in helminth-infected humans or animals and irrespective of infecting helminth species, the vast majority of published investigations are characterised by inconsistent and seldom contradictory findings [20, 29]. These apparent discrepancies may be linked to the fundamentally diverse biology of the parasites under investigation, that might result in microbiota alterations that are specific to the colonising helminth species. One possible explanation is technical and linked to the vast heterogeneity of experimental designs and metagenomic sequence analysis techniques that characterise currently available studies and that may have contributed to the observed differences between published datasets [29]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
