A metagenomic approach to characterize temperate bacteriophage populations from Cystic Fibrosis and non-Cystic Fibrosis bronchiectasis patients

Tariq, Mohammad; Everest, Francesca; Cowley, Lauren A.; Soyza, Anthony De; Holt, Giles; Bridge, Simon; Perry, Audrey; Perry, John D.; Bourke, Stephen; Cummings, Stephen; Lanyon, Clare; Barr, Jeremy J.; Smith, Darren

doi:10.3389/fmicb.2015.00097

Cited by 16 publications

(15 citation statements)

References 34 publications

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“…Similar protein domains are encoded by ∼25% of the known members of the predominant order of phages (Caudovirales) (47). Given the enormous diversity of phages associated with mucosal surfaces, we expect many will be found to use Ig-like proteins or other carbohydrate-adherent surface proteins to increase their replicative success via subdiffusive motion (48)(49)(50). Furthermore, we speculate that their mucin-binding is finely tuned to position the phage particles in the optimal mucus zone where their bacterial hosts reside, further increasing encounter rates.…”

Section: Discussionmentioning

confidence: 99%

Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters

Barr

Auro

Sam-Soon

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Bacteriophages (phages) defend mucosal surfaces against bacterial infections. However, their complex interactions with their bacterial hosts and with the mucus-covered epithelium remain mostly unexplored. Our previous work demonstrated that T4 phage with Hoc proteins exposed on their capsid adhered to mucin glycoproteins and protected mucus-producing tissue culture cells in vitro. On this basis, we proposed our bacteriophage adherence to mucus (BAM) model of immunity. Here, to test this model, we developed a microfluidic device (chip) that emulates a mucosal surface experiencing constant fluid flow and mucin secretion dynamics. Using mucus-producing human cells and Escherichia coli in the chip, we observed similar accumulation and persistence of mucus-adherent T4 phage and nonadherent T4Δhoc phage in the mucus. Nevertheless, T4 phage reduced bacterial colonization of the epithelium >4,000-fold compared with T4Δhoc phage. This suggests that phage adherence to mucus increases encounters with bacterial hosts by some other mechanism. Phages are traditionally thought to be completely dependent on normal diffusion, driven by random Brownian motion, for host contact. We demonstrated that T4 phage particles displayed subdiffusive motion in mucus, whereas T4Δhoc particles displayed normal diffusion. Experiments and modeling indicate that subdiffusive motion increases phage-host encounters when bacterial concentration is low. By concentrating phages in an optimal mucus zone, subdiffusion increases their host encounters and antimicrobial action. Our revised BAM model proposes that the fundamental mechanism of mucosal immunity is subdiffusion resulting from adherence to mucus. These findings suggest intriguing possibilities for engineering phages to manipulate and personalize the mucosal microbiome.BAM | virus | mucus | subdiffusion | search strategy I n all animals, mucosal surfaces provide critical immunological services by both protecting against invading bacterial pathogens and supporting large communities of commensal microorganisms (1, 2). Being exposed to the environment, mucosal surfaces are also the infection sites for many important bacterial diseases, including acute diarrhea and cystic fibrosis in humans. This, combined with their accessibility, make mucosal surfaces attractive venues for phage therapy; that is, the use of bacteriophages (phages) to treat and clear bacterial infections (3,4). Clinical success so far has been erratic (5). The complexities and dynamics of the mucus layer are rarely considered, and the activity of phages therein is mostly unknown. Not surprisingly, phages effective in vitro do not consistently reduce mucosal bacterial host levels in vivo (6, 7). An understanding of the interactions between phages and their bacterial hosts within the relevant physiological environment is critical for consistent success of phage therapy applications.The multilayered mucus is composed primarily of gel-forming mucin glycoproteins that are continually secreted by the underlying epithelium (8). The mucin...

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Section: Discussionmentioning

confidence: 99%

Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters

Barr

Auro

Sam-Soon

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

182

186

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“…Lysogen mediated differences encoded by ϕ24 B also supports these numerous studies as metabolomics profiling identifies increased pyrimidine catabolism as 5-methyluridine intensity decreases in the lysogen sample. It has also been previously shown through metagenomic analysis that well adapted phages of Pseudomonas aeruginosa in the lung carry genes that are involved with purine, pyrimidine and different phosphate utilisation57. This is further supported by Chevallereau, et al 58.…”

Section: Discussionmentioning

confidence: 68%

Shigatoxin encoding Bacteriophage ϕ24B modulates bacterial metabolism to raise antimicrobial tolerance

Holt

Lodge

McCarthy

et al. 2017

Sci Rep

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How temperate bacteriophages play a role in microbial infection and disease progression is not fully understood. They do this in part by carrying genes that promote positive evolutionary selection for the lysogen. Using Biolog phenotype microarrays and comparative metabolite profiling we demonstrate the impact of the well-characterised Shiga toxin-prophage φ24 B on its Escherichia coli host MC1061. As a lysogen, the prophage alters the bacterial physiology by increasing the rates of respiration and cell proliferation. This is the first reported study detailing phage-mediated control of the E. coli biotin and fatty acid synthesis that is rate limiting to cell growth. Through φ24 B conversion the lysogen also gains increased antimicrobial tolerance to chloroxylenol and 8-hydroxyquinoline. Distinct metabolite profiles discriminate between MC1061 and the φ24 B lysogen in standard culture, and when treated with 2 antimicrobials. This is also the first reported use of metabolite profiling to characterise the physiological impact of lysogeny under antimicrobial pressure. We propose that temperate phages do not need to carry antimicrobial resistance genes to play a significant role in tolerance to antimicrobials.Colonisation by Shiga toxin-encoding Escherichia coli (STEC) causes a potentially fatal gastrointestinal infection in humans. There are currently > 500 different characterised STEC serogroups that cause disease including O157:H7 and more recently O104:H4 1,2 . Symptoms of STEC infection can vary from bloody diarrhoea through to haemorrhagic colitis, thrombotic thrombocytopaenic purpura (TTP) and haemolytic-uraemic syndrome (HUS), the latter can be fatal 3,4 . STEC is a zoonotic infection transmitted from an animal reservoir via contaminated food or water 5 . Shiga toxins are responsible for the severe downstream sequelae due to high cytotoxicity to human renal microvascular endothelial cells 4,6 . Importantly, the genes encoding Shiga toxin (Stx) are disseminated by temperate bacteriophages.Stx-phages enter one of two replication pathways: a productive lytic life cycle or a more passive lysogenic cycle where the prophage is replicated by the bacterium as any other genetic loci. The lytic-lysogen decision of lambdoid-like bacteriophages is regulated by early gene expression and sequential binding of proteins to a well characterised genetic switch 7-9 .The co-evolutionary interaction between a phage and its bacterial host is dynamic, with interplay linked to rounds of inhibition, selection and evolution, often referred to as an 'arms race' 10 . Smith et al. 11 used a multi-loci PCR typing approach to demonstrate that no two Stx phage isolates had the same genotype 11 . This heterogeneity is further supported by Bonanno et al. 12 who identified multiple Stx-phage morphologies not previously reported 12 . Stx-phages are closely related to bacteriophage lambda, with a comparable genome organisation. In comparison to lambda, Stx-phages carry significantly larger amounts of DNA (~20-25 Kbp), with up to 73% of the geno...

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“…Phages populate biotic aspects of environments as well. Perhaps best studied is the human microbiome, where phages have been observed in the mouth, gastrointestinal tract, bladder, skin, and lungs (Edlund et al 2015;Hannigan et al 2015;Tariq et al 2015;Manrique et al 2016;Barr 2017;Miller-Ensminger et al 2018). Phage numbers in organismal microbiomes likely reflect those of their hosts, with highly populated regions like the gut containing the highest numbers of phages.…”

Section: Phage Prevalence Within Environmentsmentioning

confidence: 99%

Bacteriophage Ecology

Dennehy

Abedon

2020

Bacteriophages

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A metagenomic approach to characterize temperate bacteriophage populations from Cystic Fibrosis and non-Cystic Fibrosis bronchiectasis patients

Cited by 16 publications

References 34 publications

Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters

Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters

Shigatoxin encoding Bacteriophage ϕ24B modulates bacterial metabolism to raise antimicrobial tolerance

Bacteriophage Ecology

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