crAssphage

crAssphage (cross-assembly phage) is a bacteriophage (virus that infects bacteria) that was discovered in 2014 by computational analysis of publicly accessible scientific data on human faecal metagenomes.[2] Its circular DNA genome is around 97 kbp in size and contains 80 predicted open reading frames, and the sequence is commonly found in human faecal samples.[2] At its time of discovery, the virus was predicted to infect bacteria of the phylum Bacteroidetes that are common in the intestinal tract of many animals including humans.[2] Since then, the bacteriophage has been isolated in vitro and confirmed to infect Bacteroides intestinalis.[3] Based on analysis of metagenomics data, crAssphage sequences have been identified in about half of all sampled humans.[2] The virus was named after the crAss (cross-assembly)[4][5] software that was used to find the viral genome. CrAssphage is possibly the first organism to be named after a computer program for promotional purposes.[6]

crAssphage
crAssphage (schematic drawing)
Virus classification
Group:
Group I (dsDNA)
Order:
Caudovirales?[1]
Family:
Podoviridae?[1]
Genus:
crAss-like phages[1]
Type Species

While crAssphage did not have any known relatives when it was discovered in 2014, a range of related viruses were discovered in 2017.[1] Based on a screen of related sequences in public nucleotide databases and phylogenetic analysis, it was concluded that crAssphage may be part of an expansive bacteriophage family (Podoviridae, order Caudovirales) that is found in a range of environments including human gut and feces, termite gut,[1][7][8] terrestrial/groundwater environments, soda lake (hypersaline brine), marine sediment, and plant root environments.[1]

There is no indication that crAssphage is involved in human health or disease.[9] The virus may outperform indicator bacteria as a marker for human faecal contamination.[10][11][12]

References
  1. Natalia Yutin; Kira S. Makarova; Ayal B. Gussow; Mart Krupovic; Anca Segall; Robert A. Edwards; Eugene V. Koonin (2017). "Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut". Nature Microbiology. 3 (1): 38–46. doi:10.1038/s41564-017-0053-y. PMC 5736458. PMID 29133882.; and Eugene V. Koonin: Behind the paper: The most abundant human-associated virus no longer an orphan, November 13th, 2017
  2. Bas E. Dutilh; Noriko Cassman; Katelyn McNair; Savannah E. Sanchez; Genivaldo G. Z. Silva; Lance Boling; Jeremy J. Barr; Daan R. Speth; Victor Seguritan; Ramy K. Aziz; Ben Felts; Elizabeth A. Dinsdale; John L. Mokili; Robert A. Edwards (2014). "A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes". Nature Communications. 5: 4498. Bibcode:2014NatCo...5.4498D. doi:10.1038/ncomms5498. PMC 4111155. PMID 25058116.
  3. Shkoporov AN, Khokhlova EV, Fitzgerald CB, Stockdale SR, Draper LA, Ross P, Hill C (2018). "ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis". Nature Communications. 9 (1): 4781. Bibcode:2018NatCo...9.4781S. doi:10.1038/s41467-018-07225-7. PMC 6235969. PMID 30429469.
  4. Cross-Assembly of Metagenomes
  5. Bas E. Dutilh; Robert Schimeder; Jim Nulton; Ben Felts; Peter Salamon; Robert A. Edwards; John L. Mokili (2012). "Reference-independent comparative metagenomics using cross-assembly: crAss". Bioinformatics. 28 (24): 3225–3231. doi:10.1093/bioinformatics/bts613. PMC 3519457. PMID 23074261.
  6. Chamary, J. V. "A Common Virus Is Eating Your Gut Bacteria". Forbes. Retrieved 2019-04-19.
  7. Tikhe, Chinmay V.; Husseneder, Claudia (2018). "Metavirome Sequencing of the Termite Gut Reveals the Presence of an Unexplored Bacteriophage Community". Frontiers in Microbiology. 8: 2548. doi:10.3389/fmicb.2017.02548. ISSN 1664-302X. PMC 5759034. PMID 29354098.
  8. Pramono, Ajeng K.; Kuwahara, Hirokazu; Itoh, Takehiko; Toyoda, Atsushi; Yamada, Akinori; Hongoh, Yuichi (2017). "Discovery and Complete Genome Sequence of a Bacteriophage from an Obligate Intracellular Symbiont of a Cellulolytic Protist in the Termite Gut". Microbes and Environments. 32 (2): 112–117. doi:10.1264/jsme2.ME16175. ISSN 1342-6311. PMC 5478533. PMID 28321010.
  9. Y.Y. LIANG; W. ZHANG; Y.G. TONG; S.P. CHEN (2016). "crAssphage is not associated with diarrhoea and has high genetic diversity". Epidemiology & Infection. 144 (16): 3549–3553. doi:10.1017/S095026881600176X. PMID 30489235.
  10. Ahmed W; Lobos A; Senkbeil J; Peraud J; Gallard J; Harwood VJ (2017). "Evaluation of the novel crAssphage marker for sewage pollution tracking in storm drain outfalls in Tampa, Florida". Water Research. 131: 142–150. doi:10.1016/j.watres.2017.12.011. PMID 29281808.
  11. García-Aljaro C; Ballesté E; Muniesa M; Jofre J (2017). "Determination of crAssphage in water samples and applicability for tracking human faecal pollution". Microbial Biotechnology. 10 (6): 1775–1780. doi:10.1111/1751-7915.12841. PMC 5658656. PMID 28925595.
  12. Stachler E; Kelty C; Sivaganesan M; Li X; Bibby K; Shanks OC (2017). "Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement". Environmental Science and Technology. 51 (16): 9146–9154. Bibcode:2017EnST...51.9146S. doi:10.1021/acs.est.7b02703. PMC 7350147. PMID 28700235.
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