Topics and Trends in Most Cited Bacterial Genetics and Biotechnology Papers

Ranked by citations 18 months after publication

Class of 2026 (Papers Published in 2024)

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.

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Updated September 13, 2026

At a glance

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

20 papers ranked by 18-month citation count

#1 of 2,919
7818m 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

Base editinggut microbiomephage-derived particleEscherichia coliGut colonizationβ-lactamase genenon-replicative DNA vectorKlebsiella pneumoniaecurli productionpathogenic E. colimicrobiome-targeted therapiesstable bacterial editingCRISPR-derived toolsBacterial genome engineering
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#2 of 2,919
6318m 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-defence systemsanti-CRISPR proteinsAnti-restriction systemsanti-SOS proteinsCRISPR-Cas systemsRestriction-modification systemsSOS-response genesconjugationHorizontal gene transferAntibiotic resistance disseminationSingle-stranded DNA promotersMobile genetic elementsplasmid disseminationgene mobilizationPhage counter-defenceBacterial conjugationbacterial immunity evasionPlasmid establishmentgene localization on plasmids
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#3 of 2,919
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

Bacterial anti-phage defense systemsanti-phage activityDefense system interactionsnegative association analysisZorya IIDruantia IIIietAS defense systemtmn defense systemGabijaSeptu IPrrCsensory switch ATPase domainEscherichia coli strainsnegative epistasisbacterial genome analysisBacterial innate immunity
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#4 of 2,919
5518m citations

Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies

George Bouras et al.Microbial Genomics202410.1099/mgen.0.001244

George BourasThe University of Adelaide, Australia

Hybracterlong-read-first assemblyHybrid genome assemblylong-read-only assemblybacterial genome completenessplasmid recoverysmall plasmid misassemblyantimicrobial resistance genesUnicyclerassembly automation and scalabilitylong-read sequencing accuracymanually curated ground truth reference genomesgenomic variation beyond SNVsbacterial evolution genomicsassembly benchmarking
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#5 of 2,919
5518m citations

Strategies to overcome the challenges of low or no expression of heterologous proteins in Escherichia coli

Ruizhao Jiang et al.Biotechnology Advances202410.1016/j.biotechadv.2024.108417

Huimin YuTsinghua University, China

Escherichia coliheterologous protein expressioncodon optimizationinclusion body formationprotein solubilitychaperone co-expressionProtein purification tagPromoter engineeringSignal peptide (Sec)mRNA secondary structureplasmid copy numberhost strain engineeringrare codon usageprotein foldingexpression vector designtemperature-induced expressiontoxicity of recombinant proteinsSecretion systemsTranslation efficiency
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#6 of 2,919
5418m citations

Establishing a synthetic orthogonal replication system enables accelerated evolution in <i>E. coli</i>

Rongzhen Tian et al.Science202410.1126/science.adk1281

Rongzhen Tian, Jason W. ChinMedical Research Council Laboratory of Molecular Biology, United Kingdom

Orthogonal replicationContinuous evolutionmutagenesis rate elevationtigecycline resistance evolutionGFP fluorescence evolutionEscherichia colimutant O-DNAPshost polymerase orthogonalityreplicon cargo capacitymutation rate engineeringDirected evolutionsynthetic biologyselective replication
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#7 of 2,919
4418m citations

Quinolone-mediated metabolic cross-feeding develops aluminium tolerance in soil microbial consortia

Zhiyuan Ma, Meitong Jiang et al.Nature Communications202410.1038/s41467-024-54616-0

Yuting LiangInstitute of Soil Science, Chinese Academy of Sciences, China

Aluminium toleranceAcid stressMetabolic cross-feedingRhodococcus erythropolisPseudomonas aeruginosasoil bacterial consortiumquorum sensing2-heptyl-1H-quinolin-4-one (HHQ)HHQ degradationquinolone signaling moleculetryptophan biosynthesisPeptidoglycan synthesiscell wall stabilitypopulation density regulationmetabolic activity enhancementsynthetic microbial consortiasustainable agriculture in acidic soilsbeneficial bacteria for crop protection
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#9 of 2,919
3718m citations

Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication

Enea Maffei et al.Nature Communications202410.1038/s41467-023-44157-3

Alexander HarmsUniversity of Basel, Switzerland

Phage ParidePseudomonas aeruginosaDormant bacteriaAntibiotic tolerancedirect lytic replicationphage hibernationhost resuscitationmeropenemcarbapenemphage-antibiotic combinationtissue cage implant modelpersistent bacterial infectionsviral replication strategies
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#10 of 2,919
3718m citations

Darwinian Evolution of Self-Replicating DNA in a Synthetic Protocell

Zhanar Abil, Ana María Restrepo Sierra et al.Nature Communications202410.1038/s41467-024-53226-0

Christophe DanelonDelft University of Technology, Netherlands

Synthetic protocellLiposome compartmentsPURE systemPhi29 DNA polymeraseTerminal proteinSelf-replicating linear DNA templateReplication-coupled transcription-translationDarwinian evolution in vitroCell-free gene expressionDNA extraction and PCR re-encapsulationIntermittent evolution protocolSemi-continuous evolution protocolNext-generation sequencing of enriched mutationsReverse engineering of mutationsSelection advantage mutationsContext-dependent mutation effectsMinimal cell-free evolving systemSynthetic cell genetic complexityBacteriophage-derived replication machineryIn vitro DNA self-replicator
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#11 of 2,919
3618m citations

Revisiting the y-ome of <i>Escherichia coli</i>

Lisa R Moore et al.Nucleic Acids Research202410.1093/nar/gkae857

Lisa R. Moore, Peter D. KarpSRI International, United States

Escherichia coli K-12y-omefunctional gene annotationEcoCyc databaseEscherichia coli MG1655experimental evidence codesGene Ontology termsgenome curationgene characterization categoriescomputational annotation rules
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#12 of 2,919
3618m citations

Structure and mechanism of the Zorya anti-phage defence system

Haidai Hu, Philipp F Popp et al.Nature202410.1038/s41586-024-08493-8

Haidai Hu, Marc Erhardt, Simon A. Jackson, Nicholas M. I. TaylorUniversity of Copenhagen, Denmark

Zorya anti-phage defence systemBacterial anti-phage defense systemsZorA-ZorB membrane complexZorCZorDCryo-EM structureflagellar motor stator homologyMotAB-like proton channelmembrane potential-dependent defenceproton motive forceAbortive infectionnuclease domainhelicase domainMembrane depolarizationZorAB rotary motor mechanismBacterial innate immunitydefence islandPhage-bacteria arms race
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#13 of 2,919
3518m citations

Strategies to enhance stress tolerance in lactic acid bacteria across diverse stress conditions

A S Derunets et al.World Journal of Microbiology and Biotechnology202410.1007/s11274-024-03905-3

A. S. DerunetsNational Research Center Kurchatov Institute, Russia

lactic acid bacteriastress tolerance enhancementAcid stressosmotic stressoxidative stresscold stressheat stressbile salt stressstress adaptation mechanismscross-protectioncell membrane fatty acid compositionHeat shock proteins (chaperones)stress response regulatorsgenetic engineering strategiesadaptive laboratory evolutionprobiotic viabilityfreeze-drying survivalfood fermentation applicationsgastrointestinal transit survival
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#14 of 2,919
3518m citations

Phage-triggered reverse transcription assembles a toxic repetitive gene from a noncoding RNA

Max E Wilkinson et al.Science202410.1126/science.adq3977

Feng ZhangHoward Hughes Medical Institute, United States

DRT2 defense systemreverse transcriptasepseudoknotted noncoding RNAtandem repeat synthesisreconstituted promotertoxic repetitive proteinAbortive infectionBacterial anti-phage defense systemsCryo-electron microscopybiochemical reconstitutionreverse transcription in prokaryotesantiviral defense mechanismNoncoding RNA-templated DNA synthesistemplate-directed repeat elongationde novo open reading frame formationRNA-guided protein synthesisBacterial innate immunityretron-like defense system
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#15 of 2,919
3418m citations

PilY1 regulates the dynamic architecture of the type IV pilus machine in Pseudomonas aeruginosa

Shuaiqi Guo et al.Nature Communications202410.1038/s41467-024-53638-y

Shuaiqi Guo, Lori L. Burrows, Jun LiuYale School of Medicine, United States

Type IV piliPseudomonas aeruginosaPilY1cryo-electron tomographysubtomogram averagingintegrative modellingPilQ secretinminor pilin complexpilus extensionpilus retraction7-fold symmetric cage-like structureschampagne-cork-shaped structureperiplasmOuter membranePilY1-minor-pilin priming complexgate-keeping mechanismbiofilm formationsurface motility
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#16 of 2,919
3318m citations

Mechanism of bacterial predation via ixotrophy

Yun-Wei Lien et al.Science202410.1126/science.adp0614

Gregor L. Weiss, Martin PilhoferETH Zürich, Switzerland

Ixotrophyfilamentous bacteriagliding motilitygrappling hookstype IX secretion systemCryo-electron microscopycryo-electron tomographytype VI secretion systemprey puncturingstable isotope labelingsingle-cell analysisinsertion sequence elementsmarine metagenomicspredator-prey dynamics
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#17 of 2,919
3318m citations

Tracking transcription–translation coupling in real time

Nusrat Shahin Qureshi et al.Nature202410.1038/s41586-024-08308-w

Olivier DussEuropean Molecular Biology Laboratory, Germany

Transcription-translation couplingribosome–RNA polymerase complexmulti-colour single-molecule fluorescence microscopytranscription elongationtranslation elongationmRNA loopingNusGTranscriptional pausingribosome collision with RNAPribosome rescue of RNAPlong-range physical couplingreconstituted transcription–translation systemreal-time tracking
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#18 of 2,919
3318m citations

Autologous DNA mobilization and multiplication expedite natural products discovery from bacteria

Feng Xie, Haowen Zhao et al.Science202410.1126/science.abq7333

Feng Xie, Haowen Zhao, Rolf Müller, Chengzhang FuHelmholtz Institute for Pharmaceutical Research Saarland (HIPS), Germany

ACTIMOTCRISPR-Cas9autologous DNA mobilizationcryptic biosynthetic gene clustersStreptomycesnatural products discoveryAntibiotic resistance disseminationlarge DNA fragment relocationreplicative plasmidsmolecular cloning limitationsbiosynthetic pathway activationchemical diversity from bacterial genomes
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#19 of 2,919
3218m citations

Structural basis of directional switching by the bacterial flagellum

Steven Johnson, Justin C Deme et al.Nature Microbiology202410.1038/s41564-024-01630-z

Steven Johnson, Susan M. LeaNCI, United States

bacterial flagellumFlagellar motor switchingstructural basisFlagellar motorrotational directionflagellar structureBacterial motilityCryo-electron microscopyFliGFliMFliNC-ring (flagellar switch complex)rotor-stator interactionclockwise rotationcounterclockwise rotationchemotaxis signalingCheY phosphorylationconformational change
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#20 of 2,919
3218m citations

Structure-guided discovery of ancestral CRISPR-Cas13 ribonucleases

Peter H Yoon et al.Science202410.1126/science.adq0553

Jennifer A. DoudnaUniversity of California, Berkeley, United States

CRISPR-Cas13Cas13anstructural-search pipelineancestral clade identificationRNA-guided ribonucleaseprogrammable RNA depletionBacterial anti-phage defense systemsCRISPR RNA processingRNA-guided nucleasessingle active site dual activitynuclease domain evolutionstructure-guided genome miningadaptive immunity in bacteriadefense-associated ribonucleasesprecision RNA editingheterologous RNA manipulation systemsEvolution of CRISPR-Casminimal Cas13 ortholog
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Dominant research themes and year-over-year shifts in Bacterial Genetics and Biotechnology

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
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
How topics shifted year over year
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 methodologyGitHubbioRxiv preprint

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 2026-10-24.

Methodology
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