Gut bacteriophage
15th Jun, 2021



In a new study published in Cell, researchers identified 140,000 viral species living in the human gut, more than half of which have not been previously observed (1). The data provides opportunities for new research to expand our understanding of how viruses in the gut influence health and disease.

The human gut microbiome is a complex ecosystem comprising trillions of microorganisms. In addition to bacteria, a vast array of viruses inhabits the gut. More than 90% of these are bacteriophages (or phages) - viruses that infect and replicate in bacterial cells (2). Bacteriophages inject their genome into their host and alter bacteria function and composition through direct lysis of their hosts (lytic state) or by integrating with its genetic material (prophage state) (3). They play crucial roles in shaping microbial composition, driving bacterial diversity, and facilitating horizontal gene transfer  (3,4). In addition, bacteriophages can interact directly with the human immune system and have both pro- and anti-inflammatory action (5,6). However, despite being highly abundant in the gut (>1010 per gram of faeces) (7,8) and having considerable impacts on gut bacteria composition and function, they remain one of the least understood members of the gut microbiome.

Over the past decade, the advancement of high-throughput metagenomics  has improved our ability to identify viral genes and uncover the diversity of bacteriophages residing in the human gut. 


Gut Phage Database

In the current study, 142,809 non-redundant gut phage genomes were obtained from examining a dataset of 28,060 globally distributed human gut metagenomes  and 2,898 bacterial isolate genomes cultured from the human gut. These metagenomic datasets were sampled from 28 countries across the six major continents. The data were collated into a global database called the Gut Phage Database (1).

Viral diversity was highest in the Firmicutes phyla, and 36% of viral clusters were not restricted to a single bacterial species, indicating that specific bacteriophage can facilitate gene transfer between bacterial species. 

Gut bacteriophages exhibit significant diversity between individuals (9). However, several longitudinal studies demonstrate that there is a core of shared bacteriophages within a population that can be used to distinguish between other geographically distinct groups (10,11). The current study identified 280 globally distributed viral clusters across five continents. The global variation in the observed gut phageomes  was associated with human lifestyle (urban versus rural/hunter-gather), most likely mediated by differences in the host gut microbiome. 

Among the tens of thousands of viruses discovered, a new highly prevalent clade (a group of viruses believed to have a common ancestor) was identified. The clade, referred to as Gubaphage, infects several members of Bacteroidales. This new clade was found to be the second most prevalent virus clade in the human gut, after the crAssphage (Cross-Assembled phage), which was discovered in 2014, and is found in >50% of western human gut microbiomes (12,13). While both clades infect similar bacteria, further research is required to understand their functions within the human gut. 


Clinical significance and application 

Bacteriophages are clinically significant for several reasons. Bacteriophage-driven alterations of the gut microbiome have been linked to several disease states, including inflammatory bowel disease (IBD) (14,15,16), diabetes (17,18,19), malnutrition (20), and Parkinson’s disease (21). 

Furthermore, bacteriophages are vectors for horizontal gene transfer , including those that can enhance virulence, antibacterial resistance, and toxin production (22). Examples include the cholera toxin in Vibrio cholerae (23), diphtheria toxin in Corynebacterium diphtheriae (24), botulinum neurotoxin in Clostridium botulinum (25), and Shiga toxin of Shigella species (26). Without their phage-encoded toxins, these bacterial species are either much less pathogenic or not pathogenic at all. 

Currently, bacteriophages are being investigated for several clinical applications, including faecal microbiota transplantation (FMT). In individuals with Clostridium difficile (CDI) infection, more favourable treatment outcomes were observed when more bacteriophage taxa were transferred from donor to recipient, suggesting they may play a role in treatment success (27). 

A novel therapeutic intervention known as faecal virome transplantation (FVT) was recently developed, where only the viral component from FMT is transplanted. Several recent experimental studies have shown that FVT was effective for treating dysbiosis-related disorders, including diabetes (28) and small intestinal bacterial overgrowth (29). In a small clinical study, a sterilised faecal filtrate improved symptoms in patients with recurrent CDI for at least six months (30)

Another potential therapeutic application is the use of phage therapy to counteract the aggressive rise of antibiotic-resistant bacteria. Phage therapy utilises lytic bacteriophages for targeted elimination of a bacterial pathogen while leaving human cells intact and reducing the broader impact on commensal bacteria that often results from antibiotic use. Bacteriophages have been used to fight infectious diseases since the early 20th century; however, the arrival of antibiotics in the 1940s largely displaced their use (31). In the last decade, phage therapy has rapidly evolved and has resulted in cases of life-saving therapeutic use and multiple clinical trials for a range of antibiotic-resistant bacteria including, Pseudomonas aeruginosa, Staphyloccocus aureus and Escherichia coli (31,32,33).



There are significant gaps in our understanding of bacteriophage-host interactions in the gut. However, recent data demonstrating the diversity of gut bacteriophages opens up new opportunities for future research into the actual significance of these viruses. Such studies hold the promise of yielding insights into the complex interactions between human physiology and bacteriophages and provide the basis for devising new therapeutic strategies for improving human health.

1Camarillo-Guerrero LF, Almeida A, Rangel-Pineros G, Finn RD, Lawley TD. Massive expansion of human gut bacteriophage diversity. Cell. 2021 Feb 18;184(4):1098-109.
2Reyes A, Semenkovich NP, Whiteson K, Rohwer F, Gordon JI. Going viral: next-generation sequencing applied to phage populations in the human gut. Nature Reviews Microbiology. 2012 Sep;10(9):607-17.
3Sutton TD, Hill C. Gut bacteriophage: current understanding and challenges. Frontiers in endocrinology. 2019 Nov 29;10:784.
4Mirzaei MK, Maurice CF. Ménage à trois in the human gut: interactions between host, bacteria and phages. Nature Reviews Microbiology. 2017 Jul;15(7):397.
5Focà A, Liberto MC, Quirino A, Marascio N, Zicca E, Pavia G. Gut inflammation and immunity: what is the role of the human gut virome?. Mediators of inflammation. 2015 Apr 7;2015.
6Popescu M, Van Belleghem JD, Khosravi A, Bollyky PL. Bacteriophages and the Immune System. Annual Review of Virology. 2021 May 20;8.
7Hoyles L, McCartney AL, Neve H, Gibson GR, Sanderson JD, Heller KJ, van Sinderen D. Characterization of virus-like particles associated with the human faecal and caecal microbiota. Research in microbiology. 2014 Dec 1;165(10):803-12.
8Shkoporov AN, Ryan FJ, Draper LA, Forde A, Stockdale SR, Daly KM, McDonnell SA, Nolan JA, Sutton TD, Dalmasso M, McCann A. Reproducible protocols for metagenomic analysis of human faecal phageomes. Microbiome. 2018 Dec 1;6(1):68.
9Shkoporov AN, Clooney AG, Sutton TD, Ryan FJ, Daly KM, Nolan JA, McDonnell SA, Khokhlova EV, Draper LA, Forde A, Guerin E. The human gut virome is highly diverse, stable, and individual specific. Cell host & microbe. 2019 Oct 9;26(4):527-41.
10Rampelli S, Turroni S, Schnorr SL, Soverini M, Quercia S, Barone M, Castagnetti A, Biagi E, Gallinella G, Brigidi P, Candela M. Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin. Environmental microbiology. 2017 Nov;19(11):4728-35.
11Zuo T, Sun Y, Wan Y, Yeoh YK, Zhang F, Cheung CP, Chen N, Luo J, Wang W, Sung JJ, Chan PK. Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization. Cell Host & Microbe. 2020 Nov 11;28(5):741-51.
12Dutilh, B. E., N. Cassman, K. McNair, S. E. Sanchez, G. G. Silva, L. Boling, J. J. Barr, D. R. Speth, V. Seguritan, R. K. Aziz, et al. 2014. A highly abundant bacteriophage discovered in the unknown sequences of human faecal meta- genomes. Nat. Commun. 5: 4498.
13Yutin, N., K. S. Makarova, A. B. Gussow, M. Krupovic, A. Segall, R. A. Edwards, and E. V. Koonin. 2018. Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut. Nat. Microbiol. 3: 38–46.
14Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, Kambal A, Monaco CL, Zhao G, Fleshner P, Stappenbeck TS. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell. 2015 Jan 29;160(3):447-60.
15Zuo T, Lu XJ, Zhang Y, Cheung CP, Lam S, Zhang F, Tang W, Ching JY, Zhao R, Chan PK, Sung JJ. Gut mucosal virome alterations in ulcerative colitis. Gut. 2019 Jul 1;68(7):1169-79.
16Ungaro F, Massimino L, Furfaro F, Rimoldi V, Peyrin-Biroulet L, D’alessio S, Danese S. Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease. Gut Microbes. 2019 Mar 4;10(2):149-58.
17Tetz G, Brown SM, Hao Y, Tetz V. Type 1 diabetes: an association between autoimmunity, the dynamics of gut amyloid-producing E. coli and their phages. Scientific reports. 2019 Jul 4;9(1):1-1.
18Ma Y, You X, Mai G, Tokuyasu T, Liu C. A human gut phage catalog correlates the gut phageome with type 2 diabetes. Microbiome. 2018 Dec;6(1):1-2.
19Zhao G, Vatanen T, Droit L, Park A, Kostic AD, Poon TW, Vlamakis H, Siljander H, Härkönen T, Hämäläinen AM, Peet A. Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children. Proceedings of the National Academy of Sciences. 2017 Jul 25;114(30):E6166-75.
20Reyes A, Blanton LV, Cao S, Zhao G, Manary M, Trehan I, Smith MI, Wang D, Virgin HW, Rohwer F, Gordon JI. Gut DNA viromes of Malawian twins discordant for severe acute malnutrition. Proceedings of the National Academy of Sciences. 2015 Sep 22;112(38):11941-6.
21Tetz G, Brown SM, Hao Y, Tetz V. Parkinson’s disease and bacteriophages as its overlooked contributors. Scientific reports. 2018 Jul 17;8(1):1-1.
22Abedon ST, Lejeune JT. Why bacteriophage encode exotoxins and other virulence factors. Evol Bioinform Online. 2007 Feb 28;1:97-110.
23Pham TD, Nguyen TH, Iwashita H, Takemura T, Morita K, Yamashiro T. Comparative analyses of CTX prophage region of Vibrio cholerae seventh pandemic wave 1 strains isolated in Asia. Microbiology and immunology. 2018 Oct;62(10):635-50.
24Holmes RK. Biology and molecular epidemiology of diphtheria toxin and the tox gene. Journal of Infectious Diseases. 2000 Feb 1;181(Supplement_1):S156-67.
25Fortier LC. The contribution of bacteriophages to the biology and virulence of pathogenic clostridia. Advances in applied microbiology. 2017 Jan 1;101:169-200.
26Yara DA, Greig DR, Gally DL, Dallman TJ, Jenkins C. Comparison of Shiga toxin-encoding bacteriophages in highly pathogenic strains of Shiga toxin-producing Escherichia coli O157: H7 in the UK. Microbial genomics. 2020 Mar;6(3).
27Zuo T, Wong SH, Lam K, Lui R, Cheung K, Tang W, Ching JY, Chan PK, Chan MC, Wu JC, Chan FK. Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome. Gut. 2018 Apr 1;67(4):634-43.
28Rasmussen TS, Mentzel CM, Kot W, Castro-Mejía JL, Zuffa S, Swann JR, Hansen LH, Vogensen FK, Hansen AK, Nielsen DS. Faecal virome transplantation decreases symptoms of type 2 diabetes and obesity in a murine model. Gut. 2020 Dec 1;69(12):2122-30.
29Lin DM, Koskella B, Ritz NL, Lin D, Carroll-Portillo A, Lin HC. Transplanting fecal virus-like particles reduces high-fat diet-induced small intestinal bacterial overgrowth in mice. Frontiers in cellular and infection microbiology. 2019 Oct 15;9:348.
30Ott SJ, Waetzig GH, Rehman A, Moltzau-Anderson J, Bharti R, Grasis JA, Cassidy L, Tholey A, Fickenscher H, Seegert D, Rosenstiel P. Efficacy of sterile fecal filtrate transfer for treating patients with Clostridium difficile infection. Gastroenterology. 2017 Mar 1;152(4):799-811.
31Álvarez A, Fernández L, Gutiérrez D, Iglesias B, Rodríguez A, García P. Methicillin-Resistant Staphylococcus aureus in Hospitals: Latest Trends and Treatments Based on Bacteriophages. J Clin Microbiol. 2019 Nov 22;57(12):e01006-19.
32Lin DM, Koskella B, Lin HC. Phage therapy: An alternative to antibiotics in the age of multi-drug resistance. World J Gastrointest Pharmacol Ther. 2017 Aug 6;8(3):162-173 .
33Furfaro LL, Payne MS, Chang BJ. Bacteriophage therapy: clinical trials and regulatory hurdles. Frontiers in cellular and infection microbiology. 2018 Oct 23;8:376.