Bacteriophage (phage) analysis

Recent studies underscore the significant influence of bacteriophages on human health and disease, despite their historical underrepresentation in microbiome studies. Around 5% of the sequencing reads in a shotgun metagenomic sample from feces corresponds to bacteriophages. Powered by the CHAMP™ profiler, microbiome analysis is now expanding to include the entire viral community, beyond just prokaryotic organisms. This broadened scope allows for a more comprehensive understanding of the microbiome’s impact on health.

Comprehensive Virus Database, including bacteriophages

Central to this is the extensive virus database built from curated genomes from previously isolated and sequenced viruses as well as de novo-identified phages from more than 30,000 human microbiome samples. Over 64,000 virus species (vOTUs) can be profiled, making it the largest commercial database in the human virome field.

Beyond identification, the CHAMP™ profiling platform enables phage lifestyle annotation to distinguish between lysogenic and lytic phases. This allows us to track over 14,000 virulent phage species that are candidates for targeting bacteria of interest such as pathobionts and pathogens. Simultaneously, we can track over 12,700 temperate phage species, which are capable of lysing bacteria but also integrating into their genomes, and therefore would require downstream genetic engineering for phage therapy applications. Additionally, phage-host mapping provides insights into phage relationships with their bacterial hosts for comprehensive viral analysis. The CHAMP™ profiler can determine the host affiliation down to genus level for >55% of all tailed bacteriophages in our database.

Increased Profiling Fidelity with CHAMP™

Paired with the industry-leading precision of the CHAMP Human Microbiome Profiler, benchmarking analyses show that the incidence of false positives is minimized while more viral species are detected, thereby exceeding metrics compared to competing tools [1]

Advanced Insights across Applications

In probiotic or LBP development, mapping phage-host relationships can explain different engraftment outcomes among patient populations.

 

For example, in figure A below, a lean phenotype is not only driven by the presence of certain gut bacteria in the mouse. A fecal viral transplant (FVT) from a lean mouse to an obese mouse shows the different phenotype outcomes after FVT based on the presence of possible phages (either red or orange) in the lean donor. If the orange phages are transferred, it has no effect on the obese phenotype. In this scenario, there is no matched host for the orange phages, or endogenous bacteria in the obese mouse are resistant to phage attack. A lean phenotype results from the transfer of red phages who find and lyse their bacterial host, thus shaping the bacterial structure toward the lean phenotype.

Figure B shows a similar concept where the blue phages recognize an LBP intervention and lyse it, preventing engraftment in the gut. The orange phages recognize the LBP, but some of the bacterial strains have endogenous phage resistance resulting in some engraftment. In the red scenario, phages either do not find a suitable bacterial host or the bacteria hosts are present but are resistant to the phages. The red LBP shows strong engraftment.

Profiling and identification of such mechanisms can be used to engineer next-generation microbiome-based therapeutics with phage resistance and enhanced efficacy. This approach can also be used to enhance discovery pipelines by linking phage characteristics directly to specific phenotypes or health outcomes.

Created with BioRender.com

For the phage therapeutic developer, phage profiling offers a discovery tool for phages capable of remodelling bacteriome structures to reverse disease phenotypes and target pathobionts [2, 3]. Additionally, it can be used as a precision tool to identify a range of phage candidate(s) with specific host range that target only the intended bacteria. This focused strategy enhances the safety and efficacy of phage therapies and provides a funnel approach for enabling the development of highly specialized treatments that address bacterial infections without disrupting the beneficial microbiota.

Recently, phage analysis has been used to understand novel metabolic interactions in populations that are more resistant to aging due to enhanced mucosal integrity and resistance to pathobionts. [4] Bacteriophage are at the forefront of the fight against antimicrobial resistance (AMR) due to their ability to effectively disrupt AMR motifs and kill bacterial hosts [5]. These functions have unveiled a new toolbox for controlling infection [6].

Phage and viral analysis are an important component in microbiome science, enabling insights across applications including gut microbiome evolution, women’s health, infant microbiome studies, and the creation of live biotherapeutic products and probiotics. Recognizing phages as a significant modulator, the CHAMP™ profiler enables a deeper understanding of microbial ecosystems, highlighting their role in shaping health outcomes and therapeutic strategies. Get in touch to learn more about our phage services and whether phage analysis can add value to your study.

References:

[1] Pinto Y, Chakraborty M, Jain N, Bhatt AS. Phage-inclusive profiling of human gut microbiomes with Phanta. Nat Biotechnol. 2023 May 25. doi: 10.1038/s41587-023-01799-4. PMID: 37231259.

[2] Rasmussen TS, Mentzel CMJ, 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;69(12):2122-2130. doi: 10.1136/gutjnl-2019-320005. Epub 2020 Mar 12. PMID: 32165408.

[3] Ritz NL, Draper LA, Bastiaanssen TFS, Turkington CJR, Peterson VL, van de Wouw M, Vlckova K, Fülling C, Guzzetta KE, Burokas A, Harris H, Dalmasso M, Crispie F, Cotter PD, Shkoporov AN, Moloney GM, Dinan TG, Hill C, Cryan JF. The gut virome is associated with stress-induced changes in behaviour and immune responses in mice. Nat Microbiol. 2024 Feb;9(2):359-376. doi: 10.1038/s41564-023-01564-y. Epub 2024 Feb 5. PMID: 38316929; PMCID: PMC10847049.

[4] Johansen J, Atarashi K, Arai Y, Hirose N, Sørensen SJ, Vatanen T, Knip M, Honda K, Xavier RJ, Rasmussen S, Plichta DR. Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan. Nat Microbiol. 2023 Jun;8(6):1064-1078. doi: 10.1038/s41564-023-01370-6. Epub 2023 May 15. PMID: 37188814.

[5] UK Parliment. The antimicrobial potential of bacteriophages. 3 January 2024. https://publications.parliament.uk/pa/cm5804/cmselect/cmsctech/328/report.html

[6] Strathdee SA, Hatfull GF, Mutalik VK, Schooley RT. Phage therapy: From biological mechanisms to future directions. Cell. 2023 Jan 5;186(1):17-31. doi: 10.1016/j.cell.2022.11.017. PMID: 36608652; PMCID: PMC9827498.

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