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CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker

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Abstract

CrAss-like phages are a diverse group of bacteriophages genetically similar to the prototypical crAssphage (p-crAssphage), which was discovered in the human gut microbiome through a metagenomics approach. It was identified as a ubiquitous and highly abundant bacteriophage group in the gut microbiome. Initial co-occurrence analysis postulated Bacteroides spp. as the prospective bacterial host. Subsequent studies have confirmed multiple host species under Phylum Bacteroidetes and some Firmicutes. Detection of crAss-like phages in sewage-contaminated environmental water and robust correlation with enteric viruses and bacteria has culminated in their adoption as a microbial source tracking (MST) marker. Polymerase chain reaction (PCR) and real-time PCR assays have been developed utilizing the conserved genes in the p-crAssphage genome to detect human fecal contamination of different water sources, with high specificity. Numerous investigations have examined the implications of crAss-like phages in diverse disease conditions, including ulcerative colitis, obesity and metabolic syndrome, autism spectrum disorders, rheumatoid arthritis, atopic eczema, and other autoimmune disorders. These studies have unveiled associations between certain diseases and diminished abundance and diversity of crAss-like phages. This review offers insights into the diverse aspects of research on crAss-like phages, including their discovery, genomic characteristics, structure, taxonomy, isolation, molecular detection, application as an MST marker, and role as a gut microbiome modulator with consequential health implications.

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Acknowledgements

The authors would like to express their sincere gratitude to the members of the manuscript review committee and the Director of ICMR—National Institute of Virology, Pune, Maharashtra, India, for their guidance and support. We want to acknowledge Ms. Meera Prabhakar, Bacteriology Group, ICMR—National Institute of Virology, Pune, Maharashtra, India, for helping to prepare the image included in the manuscript.

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  1. Bacteriology Group, ICMR – National Institute of Virology, Pune, Maharashtra, India

    Arun Thachappully Remesh & Rajlakshmi Viswanathan

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  1. Arun Thachappully Remesh
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  2. Rajlakshmi Viswanathan
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Concept: RV, Review of literature: ATR and RV, first draft: ATR, Review and final draft: ATR and RV.

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Correspondence to Rajlakshmi Viswanathan.

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Remesh, A.T., Viswanathan, R. CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker. Food Environ Virol (2024). https://doi.org/10.1007/s12560-024-09584-5

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