Topics and Trends in Most Cited Bacteriophages and microbial interactions Papers, Class of 2026

What topics and trends defined most-cited Bacteriophages and microbial interactions research in the Class of 2026?

The Class of 2026 highlights the critical role of bacteriophages in microbial interactions, emphasizing phage therapy, anti-phage defense systems, and the intricate dynamics of the virome. Key developments show increased research on phage cocktails for combating multidrug resistance and the complex evolutionary arms race between phages and bacterial defense mechanisms.

See details ↓

Updated July 17, 2026

At a glance

Field: Bacteriophages and microbial interactions
Cohort label: Class of 2026 (2024 publications)
Papers analyzed: 7,418
Papers ranked: 20
Top topics in ranked papers: Phage therapy, Anti-phage defense systems, Phage cocktails, Phage immune evasion
Publication window: Jan 1, 2024 – Dec 31, 2024
Eligibility: Research articles; reviews excluded
Citation window: 18 months post-publication
18m citation range: 61–262
Data source: OpenAlex · Retrieved Jul 2026
License: CC BY 4.0

Rankings

20 papers ranked by 18-month citation count

#1 of 7,418

26218m citations

Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study

Jean-Paul Pirnay, Sarah Djebara et al.Nature Microbiology202410.1038/s41564-024-01705-x

Jean‐Paul PirnayQueen Astrid Military Hospital, Belgium

Phage therapydifficult-to-treat infectionsPhage-antibiotic synergyin vivo bacteriophage resistance selectionantibiotic re-sensitizationPhage neutralizationlower respiratory tract infectionsskin and soft tissue infectionsbone infectionsbacterial pathogen eradicationconcomitant antibiotic usePhage cocktailspre-adapted bacteriophagesreduced virulence in phage-resistant isolatesclinical improvement assessmentadverse drug reactionsretrospective observational studyBelgian consortiumreal-world bacteriophage therapy outcomes

Badge

#2 of 7,418

12818m citations

Probiotic neoantigen delivery vectors for precision cancer immunotherapy

Andrew Redenti, Jongwon Im et al.Nature202410.1038/s41586-024-08033-4

Tal Danino, Nicholas ArpaiaColumbia University, United States

Escherichia coli Nissle 1917probiotic cancer vaccineneoepitope peptide arrayscytosolic deliveryTumor-colonizing bacteriaengineered probiotic vectorsneoantigen-specific CD8+ T cellsneoantigen-specific CD4+ T cellsdendritic cell activationnatural killer cell activationtumor-infiltrating regulatory T cellsimmunosuppressive myeloid cellsmetastatic solid tumorsblood clearance susceptibilityphagocytosis enhancementantitumor T cell immunityliving medicine platformsynthetic bacterial engineeringtumor microenvironment modulation

Badge

#3 of 7,418

11018m citations

Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information

Baptiste Gaborieau, Hugo Vaysset, Florian Tesson et al.Nature Microbiology202410.1038/s41564-024-01832-5

Baptiste GaborieauUniversité Paris Cité, France

Phage-host interactionsStrain-level predictionEscherichia coliGenomic featuresBacteriophagesHost rangecomputational prediction modelphage receptor binding proteinsBacterial surface receptorsmachine learningphage infectivityPhage genomeshost genome sequencescross-strain prediction

Badge

#4 of 7,418

9718m citations

A blueprint for broadly effective bacteriophage-antibiotic cocktails against bacterial infections

Minyoung Kevin Kim et al.Nature Communications202410.1038/s41467-024-53994-9

Minyoung Kevin Kim, Paul L. BollykyStanford University, United States

Phage therapyPhage cocktailscomplementarity groupsnon-redundant receptorsPhage-antibiotic synergyphage-phage interactionsPseudomonas aeruginosaStaphylococcus aureusMultidrug resistancebacterial resistance emergenceBiofilmwound infection modelpolymicrobial culturesHost rangebroad-spectrum therapeuticsreceptor diversity

Badge

#5 of 7,418

8018m citations

Prophage-encoded antibiotic resistance genes are enriched in human-impacted environments

Hanpeng Liao, Chen Liu et al.Nature Communications202410.1038/s41467-024-52450-y

Shungui Zhou, Manuel Delgado‐Baquerizo, Yong‐Guan ZhuFujian Agriculture and Forestry University, China

Antimicrobial resistance genesProphagesTransductionBacterial genomesMetagenomesMetatranscriptomicshuman-impacted environmentsprophage-encoded ARGscargo ARGsheterologous E. coli hostPhage-host interactionsARG mobilizationantibiotic exposureARG abundanceARG diversityprophage activityhabitat comparisonhorizontal gene transfer

Badge

#6 of 7,418

7918m citations

LysSYL‐Loaded pH‐Switchable Self‐Assembling Peptide Hydrogels Promote Methicillin‐Resistant <i>Staphylococcus Aureus</i> Elimination and Wound Healing

He Liu et al.Advanced Materials202410.1002/adma.202412154

Shuguang Lu, Weilong Shang, Xiancai RaoArmy Medical University, China

LysSYL endolysinMethicillin-resistant Staphylococcus aureusself-assembling peptide hydrogelspH-switchable antimicrobial effectpeptide L5acidic wound microenvironmentphage SYLbacterial membrane disruptioncell separation inhibitionslow-release deliverythermal stability enhancementmouse wound infection modelvessel formation factorscytokine modulationpH-sensitive wound dressingbioavailability in acidic pHL5@LysSYL hydrogels

Badge

#7 of 7,418

7718m citations

In situ targeted base editing of bacteria in the mouse gut

Andreas K Brödel, Loïc H Charpenay et al.Nature202410.1038/s41586-024-07681-w

Jesús Fernández-Rodríguez, Xavier Duportet, David BikardEligo Bioscience, France

in situ base editingGut microbiomephage-derived particlebase editor deliveryEscherichia coliβ-lactamase genenon-replicative DNA vectorKlebsiellacurli productionBacterial colonizationediting efficiencystable bacterial maintenancemicrobiome-targeted therapiesCRISPR-derived tools

Badge

#8 of 7,418

7618m citations

Birth of protein folds and functions in the virome

Jason Nomburg et al.Nature202410.1038/s41586-024-07809-y

Jennifer A. DoudnaGladstone-UCSF Institute of Data Science and Biotechnology, United States

Viral proteinseukaryotic viral speciesAlphaFold Protein Structure DatabaseStructural similarityPhage immune evasionRNA ligase T-like phosphodiesterasesCyclic dinucleotidecGAMPavian poxvirusesBacteriophagescGAMP hydrolysisPhage-host interactionsprotein fold evolutionsequence divergencestructural analogue predictionimmune-activating moleculesPhage proteinsvirome structural database

Badge

#9 of 7,418

7418m citations

Rapid species-level metagenome profiling and containment estimation with sylph

Jim Shaw et al.Nature Biotechnology202410.1038/s41587-024-02412-y

Jim Shaw, Yun William YuUniversity of Toronto, Canada

sylphMetagenomicsgenome-to-metagenome containmentaverage nucleotide identity (ANI)zero-inflated Poisson k-mer statisticsspecies-level detectionCAMI2 Marine datasetKraken2multisample profilingANI-based metagenome-wide association studyParkinson diseasebutyrate-PD associationsstrain-level analysisBacterial genomesPhage genomesGut microbiomeRefSeqlow-coverage genomescontainment ANI estimation

Badge

#10 of 7,418

7318m citations

Soil viral–host interactions regulate microplastic-dependent carbon storage

Lu Wang et al.Proceedings of the National Academy of Sciences202410.1073/pnas.2413245121

Dong Zhu, Yong‐Guan ZhuInstitute of Urban Environment, China

Microplasticsbiodegradable microplasticsnondegradable microplasticsSoil carbon storagevirus-bacteria coadaptationsviral lysisauxiliary metabolic genesPiggyback-the-winner strategyMicrobial carbon use efficiencycomplex carbohydrate metabolismAmino acid metabolism pathwaysglycolysisDissolved organic matteroligotrophscopiotrophssoil plastisphereMultiomicssoil chemodiversityexploitation competitionPhage-host interactions

Badge

#11 of 7,418

7118m citations

A Klebsiella-phage cocktail to broaden the host range and delay bacteriophage resistance both in vitro and in vivo

Huanchang Chen et al.npj Biofilms and Microbiomes202410.1038/s41522-024-00603-8

Trevor Lithgow, Tieli ZhouThe First Affiliated Hospital of Wenzhou Medical University, China

KlebsiellaPhage cocktailsΦK2044ΦKR1ΦKR8NTUH-K2044Anti-phage defense systemsKL1 capsule-typeCapsular typesBiofilmGalleria mellonella modelMurine modelcatheter biofilm modelhospital sewageHost rangePhage therapyMultidrug resistance

Badge

#12 of 7,418

6718m citations

Safety, pharmacokinetics, and pharmacodynamics of LBP-EC01, a CRISPR-Cas3-enhanced bacteriophage cocktail, in uncomplicated urinary tract infections due to Escherichia coli (ELIMINATE): the randomised, open-label, first part of a two-part phase 2 trial

Paul Kim et al.The Lancet Infectious Diseases202410.1016/s1473-3099(24)00424-9

Paul KimLocus Biosciences, United States

LBP-EC01CRISPR-Cas3Phage cocktailsuncomplicated urinary tract infectionsEscherichia coliELIMINATE trialphase 2 trialpharmacokineticspharmacodynamicsEngineered phagesPhage therapyAntimicrobial resistancebacteriophage safetyUTI treatment

Badge

#13 of 7,418

6618m citations

A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases

Florian Tesson et al.Peer Community Journal202410.24072/pcjournal.470

Florian TessonInstitut Pasteur, France

Anti-phage defense systemsDefenseFinderbioinformatic identificationdefense system mechanismsRefSeq genomesAlphaFold Protein Structure Databasecommunity-curated repositoryweb-service search functionprecomputed databasesProtein structure predictiondefense system annotations152 antiphage systemssystematic detectionPhage-host interactionsdefense system evolution

Badge

#14 of 7,418

6618m citations

BFVD—a large repository of predicted viral protein structures

Rachel Seongeun Kim et al.Nucleic Acids Research202410.1093/nar/gkae1119

Martin SteineggerSeoul National University, South Korea

Big Fantastic Virus DatabaseAlphaFold Protein Structure DatabaseColabFoldViral proteinsUniRef30 clustershomology searchesassembled sequencing dataPhage proteinsFoldseekStructural similarityProtein structure predictionPhage genomesunannotated proteinsvirus-specific repository

Badge

#15 of 7,418

6318m citations

High-quality metagenome assembly from long accurate reads with metaMDBG

Gaëtan Benoit et al.Nature Biotechnology202410.1038/s41587-023-01983-6

Christopher QuinceEarlham Institute, United Kingdom

metaMDBGmetagenome assemblyPacBio HiFi readslong accurate readsde Bruijn graphMinimizer spaceiterative assemblyabundance-based filteringstrain complexityBacterial genomesmetagenome-assembled genomesMAGsvirus recoveryPlasmidsMicrobial communitiesgenome coverage depth variation

Badge

#16 of 7,418

6318m citations

A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts

Emily B Graham et al.Nature Microbiology202410.1038/s41564-024-01686-x

Emily GrahamPacific Northwest National Laboratory, United States

ViromeGlobal Soil Virus Atlassoil metagenomesUncultivated virusesviral operational taxonomic unitsrarefaction curvesspatial turnoverBiogeochemical cyclingcarbon cyclingnutrient cyclingMicrobial communitiesViral diversityauxiliary metabolic genes

Badge

#17 of 7,418

6218m citations

A virally encoded tRNA neutralizes the PARIS antiviral defence system

Nathaniel Burman, Svetlana Belukhina, Florence Depardieu et al.Nature202410.1038/s41586-024-07874-3

David Bikard, Blake WiedenheftMontana State University, United States

Phage-encoded tRNAsPARIS defence systemPhage immune evasiontRNA anticodon targetinghost-pathogen interactionantiviral immunity

Badge

#18 of 7,418

6218m citations

Diverse anti-defence systems are encoded in the leading region of plasmids

Bruria Samuel et al.Nature202410.1038/s41586-024-07994-w

David BursteinTel-Aviv University, Israel

plasmid leading regionAnti-defense systemsAnti-CRISPR proteinsanti-restriction proteinsanti-SOS proteinshorizontal gene transferconjugationCRISPR-CasRestriction-modification systemsSOS-response genessingle-stranded DNA promotersantimicrobial resistance disseminationplasmid establishmentconjugative delivery systemsPhage immune evasionmobile genetic elements

Badge

#19 of 7,418

6118m citations

Bacterial defense systems exhibit synergistic anti-phage activity

Yi Wu et al.Cell Host & Microbe202410.1016/j.chom.2024.01.015

Franklin L. NóbregaUniversity of Southampton, United Kingdom

Anti-phage defense systemsAnti-phage activitysynergistic defense mechanismsZorya IIDruantia IIIietAStmnGabija complexSeptu IPrrCATPase domainnon-random co-occurrencenegative associationEscherichia coliphage predationimmune repertoireshost-specific phagesnegative epistasisdefense system compatibility

Badge

#20 of 7,418

6118m citations

Targeting Pseudomonas aeruginosa biofilm with an evolutionary trained bacteriophage cocktail exploiting phage resistance trade-offs

Fabian Kunisch et al.Nature Communications202410.1038/s41467-024-52595-w

Andrej TrampužUniversität Münster, Germany

Pseudomonas aeruginosaBiofilmPhage cocktailsin vitro-directed evolutionphage resistance trade-offsMultidrug resistanceLytic phagesHost rangeisothermal microcalorimetryquantitative polymerase chain reactiondual-phage-resistancePhage therapybiofilm evolution assayantimicrobial efficacy

Badge

Topic trends

Dominant research themes and year-over-year shifts in Bacteriophages and microbial interactions

What Topics Define the Class of 2026?

In the Class of 2026, research on bacteriophages and microbial interactions is dominated by topics central to understanding and exploiting phage-host dynamics. Phage therapy emerges as the leading theme, driven by the pressing need for alternatives to conventional antibiotics in the face of widespread multidrug resistance. Closely tied to this is the intense study of anti-phage defense systems and phage immune evasion, highlighting the evolutionary arms race between bacteria and viruses. Additionally, there is a strong focus on the broader virome and horizontal gene transfer, underscoring the vital role phages play in driving microbial evolution, ecosystem functioning, and the dissemination of antimicrobial resistance genes. These dominant topics collectively define a field deeply invested in both the foundational biology of phages and their transformative therapeutic potential.

How Did Topics Shift from the Class of 2025 to the Class of 2026?

The transition to the Class of 2026 reveals notable shifts in research priorities within bacteriophage studies. There is a marked surge in the exploration of phage cocktails, likely reflecting a strategic shift toward more robust and resilient therapeutic approaches designed to overcome bacterial resistance. Conversely, some foundational topics like basic host range analysis have seen a relative decline, suggesting the field is moving beyond simple characterizations toward more complex functional and therapeutic applications. Furthermore, the rising prominence of topics such as protein structure prediction underscores a growing integration of advanced computational tools into phage research. This evolution highlights a discipline that is rapidly maturing, leveraging both deeper mechanistic insights and cutting-edge technologies to tackle complex clinical and ecological challenges.

Methodology

PRI identifies high-impact research using a transparent, topic-agnostic framework applied consistently across scientific domains. Bibliographic records are drawn from OpenAlex, including publication dates, citation relationships, and document types.

This ranking covers the Class of 2026 cohort: journal articles published in 2024. Reviews and other non-article document types are excluded to ensure comparability.

Research impact is quantified with an 18-month post-publication citation window—the number of citing works published within 18 months of each paper's publication date. This metric captures early impact while controlling for publication age.

An LLM-based relevance classifier then reviews each candidate's title and abstract to confirm substantive alignment with the target domain. Only papers classified as relevant appear in the final ranking.

Zheng Su, Tinsley Li, Thematic Shifts in Early-High-Impact Cancer Genomics and Diagnostics Research: A Bibliometric and Semantic Analysis. bioRxiv 2026.07.04.736459; doi: https://doi.org/10.64898/2026.07.04.736459

Full methodology GitHub bioRxiv preprint

Cite this ranking

Pepkio Research Index (PRI). Topics and Trends in Most Cited Bacteriophages and microbial interactions Papers, Class of 2026. https://pri.pepkio.com/top-papers/bacteriophages-and-microbial-interactions/2026. Accessed 2026-07-17.

Zheng Su, Tinsley Li, Thematic Shifts in Early-High-Impact Cancer Genomics and Diagnostics Research: A Bibliometric and Semantic Analysis. bioRxiv 2026.07.04.736459; doi: https://doi.org/10.64898/2026.07.04.736459