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

*Canonical URL: https://pri.pepkio.com/top-papers/bacteriophages-and-microbial-interactions/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.

## At a glance

| Fact | Value |
| --- | --- |
| 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

| Rank | Title | Authors | Corresponding authors | Affiliation | Journal | 18m citations | DOI |
| ---: | --- | --- | --- | --- | --- | ---: | --- |
| 1 | Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study | Jean-Paul Pirnay, Sarah Djebara, Griet Steurs, Johann Griselain, Christel Cochez, Steven De Soir, Tea Glonti, An Spiessens, Emily Vanden Berghe, Sabrina Green, Jeroen Wagemans, Cédric Lood, Eddie Schrevens, Nina Chanishvili, Mzia Kutateladze, Mathieu de Jode, Pieter-Jan Ceyssens, Jean-Pierre Draye, Gilbert Verbeken, Daniel De Vos, Thomas Rose, Jolien Onsea, Brieuc Van Nieuwenhuyse, Bacteriophage Therapy Providers, Bacteriophage Donors, Patrick Soentjens, Rob Lavigne, Maya Merabishvili | Jean‐Paul Pirnay | Queen Astrid Military Hospital, Belgium | Nature Microbiology | 262 | 10.1038/s41564-024-01705-x |
| 2 | Probiotic neoantigen delivery vectors for precision cancer immunotherapy | Andrew Redenti, Jongwon Im, Benjamin Redenti, Fangda Li, Mathieu Rouanne, Zeren Sheng, William Sun, Candice R Gurbatri, Shunyu Huang, Meghna Komaranchath, YoungUk Jang, Jaeseung Hahn, Edward R Ballister, Rosa L Vincent, Ana Vardoshivilli, Tal Danino, Nicholas Arpaia | Tal Danino, Nicholas Arpaia | Columbia University, United States | Nature | 128 | 10.1038/s41586-024-08033-4 |
| 3 | Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information | Baptiste Gaborieau, Hugo Vaysset, Florian Tesson, Inès Charachon, Nicolas Dib, Juliette Bernier, Tanguy Dequidt, Héloïse Georjon, Olivier Clermont, Pascal Hersen, Laurent Debarbieux, Jean-Damien Ricard, Erick Denamur, Aude Bernheim | Baptiste Gaborieau | Université Paris Cité, France | Nature Microbiology | 110 | 10.1038/s41564-024-01832-5 |
| 4 | A blueprint for broadly effective bacteriophage-antibiotic cocktails against bacterial infections | Minyoung Kevin Kim, Qingquan Chen, Arne Echterhof, Nina Pennetzdorfer, Robert C McBride, Niaz Banaei, Elizabeth B Burgener, Carlos E Milla, Paul L Bollyky | Minyoung Kevin Kim, Paul L. Bollyky | Stanford University, United States | Nature Communications | 97 | 10.1038/s41467-024-53994-9 |
| 5 | Prophage-encoded antibiotic resistance genes are enriched in human-impacted environments | Hanpeng Liao, Chen Liu, Shungui Zhou, Chunqin Liu, David J Eldridge, Chaofan Ai, Steven W Wilhelm, Brajesh K Singh, Xiaolong Liang, Mark Radosevich, Qiu-E Yang, Xiang Tang, Zhong Wei, Ville-Petri Friman, Michael Gillings, Manuel Delgado-Baquerizo, Yong-Guan Zhu | Shungui Zhou, Manuel Delgado‐Baquerizo, Yong‐Guan Zhu | Fujian Agriculture and Forestry University, China | Nature Communications | 80 | 10.1038/s41467-024-52450-y |
| 6 | LysSYL‐Loaded pH‐Switchable Self‐Assembling Peptide Hydrogels Promote Methicillin‐Resistant <i>Staphylococcus Aureus</i> Elimination and Wound Healing | He Liu, Xuemei Wei, Huagang Peng, Yi Yang, Zhen Hu, Yifan Rao, Zhefen Wang, Jianxiong Dou, Xiaonan Huang, Qiwen Hu, Li Tan, Yuting Wang, Juan Chen, Lu Liu, Yuhua Yang, Jianghong Wu, Xiaomei Hu, Shuguang Lu, Weilong Shang, Xiancai Rao | Shuguang Lu, Weilong Shang, Xiancai Rao | Army Medical University, China | Advanced Materials | 79 | 10.1002/adma.202412154 |
| 7 | In situ targeted base editing of bacteria in the mouse gut | Andreas K Brödel, Loïc H Charpenay, Matthieu Galtier, Fabien J Fuche, Rémi Terrasse, Chloé Poquet, Jan Havránek, Simone Pignotti, Antonina Krawczyk, Marion Arraou, Gautier Prevot, Dalila Spadoni, Matthew T N Yarnall, Edith M Hessel, Jesus Fernandez-Rodriguez, Xavier Duportet, David Bikard | Jesús Fernández-Rodríguez, Xavier Duportet, David Bikard | Eligo Bioscience, France | Nature | 77 | 10.1038/s41586-024-07681-w |
| 8 | Birth of protein folds and functions in the virome | Jason Nomburg, Erin E Doherty, Nathan Price, Daniel Bellieny-Rabelo, Yong K Zhu, Jennifer A Doudna | Jennifer A. Doudna | Gladstone-UCSF Institute of Data Science and Biotechnology, United States | Nature | 76 | 10.1038/s41586-024-07809-y |
| 9 | Rapid species-level metagenome profiling and containment estimation with sylph | Jim Shaw, Yun William Yu | Jim Shaw, Yun William Yu | University of Toronto, Canada | Nature Biotechnology | 74 | 10.1038/s41587-024-02412-y |
| 10 | Soil viral–host interactions regulate microplastic-dependent carbon storage | Lu Wang, Da Lin, Ke-Qing Xiao, Li-Juan Ma, Yan-Mei Fu, Yu-Xin Huo, Yanjie Liu, Mao Ye, Ming-Ming Sun, Dong Zhu, Matthias C Rillig, Yong-Guan Zhu | Dong Zhu, Yong‐Guan Zhu | Institute of Urban Environment, China | Proceedings of the National Academy of Sciences | 73 | 10.1073/pnas.2413245121 |
| 11 | A Klebsiella-phage cocktail to broaden the host range and delay bacteriophage resistance both in vitro and in vivo | Huanchang Chen, Haifeng Liu, Yanchun Gong, Rhys A Dunstan, Zhexiao Ma, Cui Zhou, Deyi Zhao, Miran Tang, Trevor Lithgow, Tieli Zhou | Trevor Lithgow, Tieli Zhou | The First Affiliated Hospital of Wenzhou Medical University, China | npj Biofilms and Microbiomes | 71 | 10.1038/s41522-024-00603-8 |
| 12 | 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, Ana M Sanchez, Taylor J R Penke, Hannah H Tuson, James C Kime, Robert W McKee, William L Slone, Nicholas R Conley, Lana J McMillan, Cameron J Prybol, Paul M Garofolo | Paul Kim | Locus Biosciences, United States | The Lancet Infectious Diseases | 67 | 10.1016/s1473-3099(24)00424-9 |
| 13 | A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases | Florian Tesson, Rémi Planel, Artyom A. Egorov, Héloïse Georjon, Hugo Vaysset, Bryan Brancotte, Bertrand Néron, Ernest Mordret, Gemma C. Atkinson, Aude Bernheim, Jean Cury | Florian Tesson | Institut Pasteur, France | Peer Community Journal | 66 | 10.24072/pcjournal.470 |
| 14 | BFVD—a large repository of predicted viral protein structures | Rachel Seongeun Kim, Eli Levy Karin, Milot Mirdita, Rayan Chikhi, Martin Steinegger | Martin Steinegger | Seoul National University, South Korea | Nucleic Acids Research | 66 | 10.1093/nar/gkae1119 |
| 15 | High-quality metagenome assembly from long accurate reads with metaMDBG | Gaëtan Benoit, Sébastien Raguideau, Robert James, Adam M Phillippy, Rayan Chikhi, Christopher Quince | Christopher Quince | Earlham Institute, United Kingdom | Nature Biotechnology | 63 | 10.1038/s41587-023-01983-6 |
| 16 | A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts | Emily B Graham, Antonio Pedro Camargo, Ruonan Wu, Russell Y Neches, Matt Nolan, David Paez-Espino, Nikos C Kyrpides, Janet K Jansson, Jason E McDermott, Kirsten S Hofmockel, Soil Virosphere Consortium | Emily Graham | Pacific Northwest National Laboratory, United States | Nature Microbiology | 63 | 10.1038/s41564-024-01686-x |
| 17 | A virally encoded tRNA neutralizes the PARIS antiviral defence system | Nathaniel Burman, Svetlana Belukhina, Florence Depardieu, Royce A Wilkinson, Mikhail Skutel, Andrew Santiago-Frangos, Ava B Graham, Alexei Livenskyi, Anna Chechenina, Natalia Morozova, Trevor Zahl, William S Henriques, Murat Buyukyoruk, Christophe Rouillon, Baptiste Saudemont, Lena Shyrokova, Tatsuaki Kurata, Vasili Hauryliuk, Konstantin Severinov, Justine Groseille, Agnès Thierry, Romain Koszul, Florian Tesson, Aude Bernheim, David Bikard, Blake Wiedenheft, Artem Isaev | David Bikard, Blake Wiedenheft | Montana State University, United States | Nature | 62 | 10.1038/s41586-024-07874-3 |
| 18 | Diverse anti-defence systems are encoded in the leading region of plasmids | Bruria Samuel, Karin Mittelman, Shirly Ynbal Croitoru, Maya Ben Haim, David Burstein | David Burstein | Tel-Aviv University, Israel | Nature | 62 | 10.1038/s41586-024-07994-w |
| 19 | Bacterial defense systems exhibit synergistic anti-phage activity | Yi Wu, Sofya K Garushyants, Anne van den Hurk, Cristian Aparicio-Maldonado, Simran Krishnakant Kushwaha, Claire M King, Yaqing Ou, Thomas C Todeschini, Martha R J Clokie, Andrew D Millard, Yilmaz Emre Gençay, Eugene V Koonin, Franklin L Nobrega | Franklin L. Nóbrega | University of Southampton, United Kingdom | Cell Host & Microbe | 61 | 10.1016/j.chom.2024.01.015 |
| 20 | Targeting Pseudomonas aeruginosa biofilm with an evolutionary trained bacteriophage cocktail exploiting phage resistance trade-offs | Fabian Kunisch, Claudia Campobasso, Jeroen Wagemans, Selma Yildirim, Benjamin K Chan, Christoph Schaudinn, Rob Lavigne, Paul E Turner, Michael J Raschke, Andrej Trampuz, Mercedes Gonzalez Moreno | Andrej Trampuž | Universität Münster, Germany | Nature Communications | 61 | 10.1038/s41467-024-52595-w |

## Topic trends

### 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.

*Leading research themes*

### 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.

*How topics shifted year over year*

## 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
```