crAssphage

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crAssphage
Systematics
Classification : Viruses
Area : Duplodnaviria
Empire : Heunggongvirae
Phylum : Uroviricota
Class : Caudoviricetes
Order : Caudovirales
Family : Podoviridae ?
Genre : "CrAss-like phages"
Type : crAssphage
Taxonomic characteristics
Genome : dsDNA linear / circular
Baltimore : Group 1
Symmetry : icosahedral, tailed
Cover : no
Scientific name
crAssphage
Short name
ΦCrAss
Left
NCBI  Taxonomy: 2301731 (crAss001) ,
1211417 (uncultured)
ViralZone ( ExPASy , SIB): 8496

crAssphage ( English cross-assembly phage , more precisely crAss001 ) is a bacteriophage ( virus thatinfects bacteria ) that was discovered in 2014 through computer-aided analysis of publicly available scientific data on genomes in human stool . Be circular (lt SIB. Linear) DNA genome is about 97  kbp (kilo base pairs) in size and contains by Prediction 80 open reading frames ( English Open reading frames , ORFs). The sequence is often found in human stool samples. At the time of its discovery, the virus was predicted toinfectbacteria of the phylum (division) Bacteroidetes , which are common in the intestinal tract of many animals, including humans. Since then, the bacteriophage has beenisolated in vitro and confirmed toinfect Bacteroides intestinalis . Based on the analysis of metagenome data, crAssphage sequences were identifiedin around half of all examined people. The virus was named after the software crAss (cross-assembly), which was used to find the viral genome. This makes crAssphage possibly the first organism to be named after a computer program for advertising purposes.

As of March 2019, crAssphage had not yet been officially confirmed by the International Committee on Taxonomy of Viruses (ICTV).

Systematics

At the time of its discovery in 2014, crAssphage had no known relatives. However, a number of related viruses were discovered in 2017. Based on a screening of related sequences in public nucleotide databases and a phylogenetic analysis, it was concluded that crAssphage is part of the expansive bacteriophage family called Podoviridae (order Caudovirales ), representatives of which are found in different environments:

The NCBI names a number of (so far also unconfirmed ICTV) representatives of the crAss-like viruses , including:

  • Species: Bacteroides phage crAss001 (type - the crAssphage)
  • Species: Azobacteroides phage ProJPt-Bp1
  • Species Cellulophaga phage phi14: 2
  • Species IAS virus

clinic

There is no evidence that crAssphage is directly involved in human health or disease, but as bacteriophage it does, of course, affect the human intestinal flora. The virus can outperform indicator bacteria in its suitability as a biomarker for contamination of human stool .

Individual evidence

  1. ↑ a b c d ICTV: ICTV Taxonomy history: Enterobacteria phage T4 , EC 51, Berlin, Germany, July 2019; Email ratification March 2020 (MSL # 35)
  2. ↑ a b c d e f Natalia Yutin, Kira S. Makarova, Ayal B. Gussow, Mart Krupovic, Anca Segall, Robert A. Edwards, Eugene V. Koonin: Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human good . In: Nature Microbiology . 3, No. 1, 2018, pp. 38–46. doi : 10.1038 / s41564-017-0053-y . PMID 29133882 . PMC 5736458 (free full text). ; and Eugene V. Koonin: Behind the paper: The most abundant human-associated virus no longer an orphan , November 13, 2017
  3. ↑ a b SIB : Double Strand DNA Viruses , on: ViralZone
  4. ↑ NCBI : Page no longer available , search in web archives: crAss-like viruses@1@ 2Template: Dead Link / www.ncbi.nlm.nih.gov
  5. ↑ a b SIB: crAssphage , on: ViralZone
  6. ↑ a b c d e Bas E. Dutilh, Noriko Cassman, Katelyn McNair, Savannah E. Sanchez, Genivaldo GZ 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: A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes . In: Nature Communications . 5, 2014, p. 4498. bibcode : 2014NatCo ... 5.4498D . doi : 10.1038 / ncomms5498 . PMID 25058116 . PMC 4111155 (free full text).
  7. ↑ Shkoporov AN, Khokhlova EV, Fitzgerald CB, Stockdale SR, Draper LA, Ross P, Hill C: ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis . In: Nature Communications . 9, No. 1, 2018, p. 4781. bibcode : 2018NatCo ... 9.4781S . doi : 10.1038 / s41467-018-07225-7 . PMID 30429469 . PMC 6235969 (free full text).
  8. ^ Bas E. Dutilh, Robert Schmieder, Jim Nulton, Ben Felts, Peter Salamon, Robert A. Edwards, John L. Mokili: Cr oss- Ass embly of Metagenomes , in: Bioinformatics 2012. PMID 23074261
  9. ^ Bas E. Dutilh, Robert Schmieder, Jim Nulton, Ben Felts, Peter Salamon, Robert A. Edwards, John L. Mokili: Reference-independent comparative metagenomics using cross-assembly: crAss . In: Bioinformatics . 28, No. 24, 2012, pp. 3225-3231. doi : 10.1093 / bioinformatics / bts613 . PMID 23074261 . PMC 3519457 (free full text).
  10. ↑ JV Chamary: A Common Virus Is Eating Your Gut Bacteria ( en )
  11. ↑ ICTV: Master Species List 2018b.v2 , MSL # 34v, March 2019
  12. ↑ Chinmay V. Tikhe, Claudia Husseneder: Metavirome Sequencing of the Termite Gut Reveals the Presence of an Unexplored Bacteriophage Community . In: Frontiers in Microbiology . 8, 2018, ISSN  1664-302X , p. 2548. doi : 10.3389 / fmicb.2017.02548 . PMID 29354098 . PMC 5759034 (free full text).
  13. ↑ Ajeng K. Pramono, Hirokazu Kuwahara, Takehiko Itoh, Atsushi Toyoda, Akinori Yamada, Yuichi Hongoh: Discovery and Complete Genome Sequence of a Bacteriophage from an Obligate Intracellular Symbiont of a Cellulolytic Protist in the Termite Gut . In: Microbes and Environments . 32, No. 2, 2017, ISSN  1342-6311 , pp. 112-117. doi : 10.1264 / jsme2.ME16175 . PMID 28321010 . PMC 5478533 (free full text).
  14. ↑ NCBI: Bacteroides phage crAss001 (species)
  15. ↑ NCBI: Azobacteroides phage ProJPt-Bp1 (species)
  16. ↑ NCBI: Cellulophaga phage phi14: 2 (species)
  17. ↑ NCBI: IAS virus (species)
  18. ↑ YY Liang, author2 = W. Zhang, author3 = YG Tong, SP Chen: crAssphage is not associated with diarrhea and has high genetic diversity . In: Epidemiology & Infection . 144, No. 16, 2016, pp. 3549-3553. doi : 10.1017 / S095026881600176X . PMID 30489235 .
  19. ↑ Ahmed W, Lobos A, Senkbeil J, Peraud J, Gallard J, Harwood VJ: Evaluation of the novel crAssphage marker for sewage pollution tracking in storm drain outfalls in Tampa, Florida . In: Water Research . 131, 2017, pp. 142-150. doi : 10.1016 / j.watres.2017.12.011 . PMID 29281808 .
  20. ↑ García-Aljaro C, Ballesté E, Muniesa M, Jofre J: Determination of crAssphage in water samples and applicability for tracking human faecal pollution . In: Microbial Biotechnology . 10, No. 6, 2017, pp. 1775–1780. doi : 10.1111 / 1751-7915.12841 . PMID 28925595 . PMC 5658656 (free full text).
  21. ↑ Stachler E, Kelty C, Sivaganesan M, Li X, Bibby K, Shanks OC: Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement . In: Environmental Science and Technology . 51, No. 16, 2017, pp. 9146–9154. bibcode : 2017EnST ... 51.9146S . doi : 10.1021 / acs.est.7b02703 . PMID 28700235 .

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