# Topics and Trends in Most Cited Bacterial Genetics and Biotechnology Papers, Class of 2026

*Canonical URL: https://pri.pepkio.com/top-papers/bacterial-genetics-and-biotechnology/2026*

## What topics and trends defined most-cited Bacterial Genetics and Biotechnology research in the Class of 2026?

The Class of 2026 for Bacterial Genetics and Biotechnology is defined by advanced structural insights and defense mechanisms. Cryo-EM structure determination and horizontal gene transfer saw the largest growth, while studies focusing broadly on Pseudomonas aeruginosa and general E. coli characterization declined.

## At a glance

| Fact | Value |
| --- | --- |
| Field | Bacterial Genetics and Biotechnology |
| Cohort label | Class of 2026 (2024 publications) |
| Papers analyzed | 2,919 |
| Papers ranked | 20 |
| Top topics in ranked papers | Bacterial anti-phage defense systems, Escherichia coli, Cryo-EM structure, Horizontal gene transfer |
| Publication window | Jan 1, 2024 – Dec 31, 2024 |
| Eligibility | Research articles; reviews excluded |
| Citation window | 18 months post-publication |
| 18m citation range | 32–78 |
| Data source | OpenAlex · Retrieved Jul 2026 |
| License | CC BY 4.0 |

## Rankings

| Rank | Title | Authors | Corresponding authors | Affiliation | Journal | 18m citations | DOI |
| ---: | --- | --- | --- | --- | --- | ---: | --- |
| 1 | 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 | 78 | 10.1038/s41586-024-07681-w |
| 2 | 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 | 63 | 10.1038/s41586-024-07994-w |
| 3 | 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 |
| 4 | Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies | George Bouras, Ghais Houtak, Ryan R Wick, Vijini Mallawaarachchi, Michael J Roach, Bhavya Papudeshi, Lousie M Judd, Anna E Sheppard, Robert A Edwards, Sarah Vreugde | George Bouras | The University of Adelaide, Australia | Microbial Genomics | 55 | 10.1099/mgen.0.001244 |
| 5 | Strategies to overcome the challenges of low or no expression of heterologous proteins in Escherichia coli | Ruizhao Jiang, Shuting Yuan, Yilong Zhou, Yuwen Wei, Fulong Li, Miaomiao Wang, Bo Chen, Huimin Yu | Huimin Yu | Tsinghua University, China | Biotechnology Advances | 55 | 10.1016/j.biotechadv.2024.108417 |
| 6 | Establishing a synthetic orthogonal replication system enables accelerated evolution in <i>E. coli</i> | Rongzhen Tian, Fabian B H Rehm, Dariusz Czernecki, Yangqi Gu, Jérôme F Zürcher, Kim C Liu, Jason W Chin | Rongzhen Tian, Jason W. Chin | Medical Research Council Laboratory of Molecular Biology, United Kingdom | Science | 54 | 10.1126/science.adk1281 |
| 7 | Quinolone-mediated metabolic cross-feeding develops aluminium tolerance in soil microbial consortia | Zhiyuan Ma, Meitong Jiang, Chaoyang Liu, Ertao Wang, Yang Bai, Mengting Maggie Yuan, Shengjing Shi, Jizhong Zhou, Jixian Ding, Yimei Xie, Hui Zhang, Yan Yang, Renfang Shen, Thomas W Crowther, Jiabao Zhang, Yuting Liang | Yuting Liang | Institute of Soil Science, Chinese Academy of Sciences, China | Nature Communications | 44 | 10.1038/s41467-024-54616-0 |
| 8 | Architecture and activation mechanism of the bacterial PARIS defence system | Amar Deep, Qishan Liang, Eray Enustun, Joe Pogliano, Kevin D Corbett | Amar Deep, Kevin D. Corbett | University of California, San Diego, United States | Nature | 43 | 10.1038/s41586-024-07772-8 |
| 9 | Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication | Enea Maffei, Anne-Kathrin Woischnig, Marco R Burkolter, Yannik Heyer, Dorentina Humolli, Nicole Thürkauf, Thomas Bock, Alexander Schmidt, Pablo Manfredi, Adrian Egli, Nina Khanna, Urs Jenal, Alexander Harms | Alexander Harms | University of Basel, Switzerland | Nature Communications | 37 | 10.1038/s41467-023-44157-3 |
| 10 | Darwinian Evolution of Self-Replicating DNA in a Synthetic Protocell | Zhanar Abil, Ana María Restrepo Sierra, Andreea R Stan, Amélie Châne, Alicia Del Prado, Miguel de Vega, Yannick Rondelez, Christophe Danelon | Christophe Danelon | Delft University of Technology, Netherlands | Nature Communications | 37 | 10.1038/s41467-024-53226-0 |
| 11 | Revisiting the y-ome of <i>Escherichia coli</i> | Lisa R Moore, Ron Caspi, Dana Boyd, Mehmet Berkmen, Amanda Mackie, Suzanne Paley, Peter D Karp | Lisa R. Moore, Peter D. Karp | SRI International, United States | Nucleic Acids Research | 36 | 10.1093/nar/gkae857 |
| 12 | Structure and mechanism of the Zorya anti-phage defence system | Haidai Hu, Philipp F Popp, Thomas C D Hughes, Aritz Roa-Eguiara, Nicole R Rutbeek, Freddie J O Martin, Ivo Alexander Hendriks, Leighton J Payne, Yumeng Yan, Dorentina Humolli, Victor Klein-Sousa, Inga Songailiene, Yong Wang, Michael Lund Nielsen, Richard M Berry, Alexander Harms, Marc Erhardt, Simon A Jackson, Nicholas M I Taylor | Haidai Hu, Marc Erhardt, Simon A. Jackson, Nicholas M. I. Taylor | University of Copenhagen, Denmark | Nature | 36 | 10.1038/s41586-024-08493-8 |
| 13 | Strategies to enhance stress tolerance in lactic acid bacteria across diverse stress conditions | A S Derunets, A I Selimzyanova, S V Rykov, A E Kuznetsov, O V Berezina | A. S. Derunets | National Research Center Kurchatov Institute, Russia | World Journal of Microbiology and Biotechnology | 35 | 10.1007/s11274-024-03905-3 |
| 14 | Phage-triggered reverse transcription assembles a toxic repetitive gene from a noncoding RNA | Max E Wilkinson, David Li, Alex Gao, Rhiannon K Macrae, Feng Zhang | Feng Zhang | Howard Hughes Medical Institute, United States | Science | 35 | 10.1126/science.adq3977 |
| 15 | PilY1 regulates the dynamic architecture of the type IV pilus machine in Pseudomonas aeruginosa | Shuaiqi Guo, Yunjie Chang, Yves V Brun, P Lynne Howell, Lori L Burrows, Jun Liu | Shuaiqi Guo, Lori L. Burrows, Jun Liu | Yale School of Medicine, United States | Nature Communications | 34 | 10.1038/s41467-024-53638-y |
| 16 | Mechanism of bacterial predation via ixotrophy | Yun-Wei Lien, Davide Amendola, Kang Soo Lee, Nina Bartlau, Jingwei Xu, Go Furusawa, Martin F Polz, Roman Stocker, Gregor L Weiss, Martin Pilhofer | Gregor L. Weiss, Martin Pilhofer | ETH Zürich, Switzerland | Science | 33 | 10.1126/science.adp0614 |
| 17 | Tracking transcription–translation coupling in real time | Nusrat Shahin Qureshi, Olivier Duss | Olivier Duss | European Molecular Biology Laboratory, Germany | Nature | 33 | 10.1038/s41586-024-08308-w |
| 18 | Autologous DNA mobilization and multiplication expedite natural products discovery from bacteria | Feng Xie, Haowen Zhao, Jiaqi Liu, Xiaoli Yang, Markus Neuber, Amay Ajaykumar Agrawal, Amninder Kaur, Jennifer Herrmann, Olga V Kalinina, Xiaoyi Wei, Rolf Müller, Chengzhang Fu | Feng Xie, Haowen Zhao, Rolf Müller, Chengzhang Fu | Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Germany | Science | 33 | 10.1126/science.abq7333 |
| 19 | Structural basis of directional switching by the bacterial flagellum | Steven Johnson, Justin C Deme, Emily J Furlong, Joseph J E Caesar, Fabienne F V Chevance, Kelly T Hughes, Susan M Lea | Steven Johnson, Susan M. Lea | NCI, United States | Nature Microbiology | 32 | 10.1038/s41564-024-01630-z |
| 20 | Structure-guided discovery of ancestral CRISPR-Cas13 ribonucleases | Peter H Yoon, Zeyuan Zhang, Kenneth J Loi, Benjamin A Adler, Arushi Lahiri, Kamakshi Vohra, Honglue Shi, Daniel Bellieny Rabelo, Marena Trinidad, Ron S Boger, Muntathar J Al-Shimary, Jennifer A Doudna | Jennifer A. Doudna | University of California, Berkeley, United States | Science | 32 | 10.1126/science.adq0553 |

## Topic trends

### What Topics Define the Class of 2026?

In the 2024 cohort for Bacterial Genetics and Biotechnology, the landscape is heavily influenced by deep structural and mechanistic analyses. The most prominent topics include bacterial anti-phage defense systems and Escherichia coli (both at 12% normalized frequency). The widespread application of advanced imaging is evident, with cryo-EM structure and cryo-electron microscopy each appearing in 10% of the highly cited papers. Horizontal gene transfer also features prominently at 10%. Additionally, the field demonstrates a strong focus on applied genetic engineering and cellular mechanics, as shown by the prevalence of base editing, bacterial innate immunity, bacterial conjugation, and studies on the outer membrane. This distribution indicates a mature field where foundational organisms like E. coli serve as models for high-resolution structural biology and the characterization of complex genetic mobility and defense networks.

*Leading research themes*

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

The transition from 2023 to 2024 reveals a distinct shift toward high-resolution structural analysis and specific molecular machinery. The largest absolute increases were seen in cryo-EM structure (rising by 0.08 in normalized frequency) and horizontal gene transfer (+0.06). We also observed a sudden emergence of research into the flagellar motor apparatus, with terms like C-ring (flagellar switch complex), flagellar motor, FliG, and FliM surging from near zero to significant presence. Conversely, broader organism-level studies experienced relative declines. Pseudomonas aeruginosa saw the steepest drop (-0.06), and general mentions of Escherichia coli decreased by 0.04, even as specific strains like E. coli MG1655 rose. Topics such as antimicrobial resistance and mobile genetic elements remained flat. This evolution suggests that the field is moving away from broad phenotypic characterization toward precise, structure-function elucidation of bacterial nanomachines and complex gene transfer events.

*How topics shifted year over year*

## Cite this ranking

```
Pepkio Research Index (PRI). Topics and Trends in Most Cited Bacterial Genetics and Biotechnology Papers, Class of 2026. https://pri.pepkio.com/top-papers/bacterial-genetics-and-biotechnology/2026. Accessed 2026-10-28.

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
```