“Omic” investigations of protozoa and worms for a deeper understanding of the human gut “parasitome”

Abstract

The human gut has been continuously exposed to a broad spectrum of intestinal organisms, including viruses, bacteria, fungi, and parasites (protozoa and worms), over millions of years of coevolution, and plays a central role in human health. The modern lifestyles of Western countries, such as the adoption of highly hygienic habits, the extensive use of antimicrobial drugs, and increasing globalisation, have dramatically altered the composition of the gut milieu, especially in terms of its eukaryotic “citizens.” In the past few decades, numerous studies have highlighted the composition and role of human intestinal bacteria in physiological and pathological conditions, while few investigations exist on gut parasites and particularly on their coexistence and interaction with the intestinal microbiota. Studies of the gut “parasitome” through “omic” technologies, such as (meta)genomics, transcriptomics, proteomics, and metabolomics, are herein reviewed to better understand their role in the relationships between intestinal parasites, host, and resident prokaryotes, whether pathogens or commensals. Systems biology–based profiles of the gut “parasitome” under physiological and severe disease conditions can indeed contribute to the control of infectious diseases and offer a new perspective of omics-assisted tropical medicine.

Autism Spectrum Disorders and the Gut Microbiota

“…The microbiota, a microbial community of trillions of microorganisms and at least 1000 different bacterial species, few eucaryotic fungi and viruses, that covers every surface of the human body, plays a contributory role in many infections, immune-mediated disorders, rheumatologic diseases and disorders of the nervous system [10,11,12]. The microbiome, instead, is the collection of the whole genome sequences of those microorganisms, consisting of more than 5,000,000 genes [13,14]. Gut microbiota is strictly linked to the chronological age of each individual and modulates host physiology and metabolism through different mechanisms.…”

Untargeted metagenomics shows a reliable performance for synchronous detection of parasites

“…Indeed, the very large number of ribosomal reference sequences present in public databases allows the extraction and taxonomic assignments of ribosomal sequences from metagenomics datasets. In contrast, fully sequenced and well-annotated reference genomes are still lacking for many parasites, limiting the use of DNA-based sequencing and reference mapping approaches (e.g., Marzano et al 2017 ; Stensvold and van der Giezen 2018 ). Another benefit of the untargeted metagenomics approach is that no prior decision is necessary for which pathogen to screen, i.e., which specific test system needs to be applied, since sequences derived from all potential pathogens will be present in the metagenomics dataset.…”

Intestinal parasitic infection alters bacterial gut microbiota in children

“…Besides IBD, extra-intestinal autoimmune disorders like multiple sclerosis and rheumatoid arthritis have also been linked with intestinal dysbiosis, suggesting that BGM may play a role in the development and progression of inflammatory diseases (Belkaid & Hand, 2014). Other conditions that can be associated with the alterations of GM are obesity, type 2 diabetes, and autism (Marzano et al, 2017).…”