🦠 Category

microbiology

552 papers

Microbiology explores the invisible world of tiny life forms that shape our health, environment, and even the air we breathe. From bacteria and viruses to fungi and parasites, this field investigates how these microscopic organisms interact with us and each other, driving everything from disease outbreaks to beneficial fermentation processes. Understanding them is crucial for developing new medicines, improving food safety, and combating global health challenges.

At Gist.Science, we make the latest discoveries in this dynamic field accessible to everyone. We process every new preprint uploaded to bioRxiv in this category, transforming dense academic findings into both clear, plain-language explanations and detailed technical summaries. This ensures that whether you are a student, a researcher, or simply curious, you can grasp the significance of cutting-edge science without getting lost in jargon.

Below are the most recent papers in microbiology, curated and summarized directly from the bioRxiv server to keep you at the forefront of discovery.

🦠 microbiology

Evaluation of Oxford Nanopore Sequencing for Antimicrobial Resistance Surveillance in Salmonella: Comparison with Phenotypic Antimicrobial Susceptibility in a Large-Scale Study

This large-scale study evaluating Oxford Nanopore sequencing on 1,490 *Salmonella* isolates from Taiwan demonstrates that while genotypic resistance generally correlates with phenotypic results, specific discrepancies driven by breakpoint definitions, gene expression, and unknown determinants highlight the need for careful interpretation to leverage whole-genome sequencing as a superior alternative to conventional antimicrobial susceptibility testing for surveillance and treatment guidance.

Hong, Y.-P., Liao, Y.-S., Wan, Y.-W., Kuo, S.-C., Teng, R.-H., Liang, S.-Y., Chang, J.-H., Wei, H.-L., Chiou, C.-S.2026-05-19
🦠 microbiology

A complete-genome view of phylum Nanobdellota and recurrent Form III RuBisCO transfer between archaea and Patescibacteriota

This study expands the genomic representation of the archaeal phylum Nanobdellota by 52-fold through 208 new complete genomes from Baltic Sea and groundwater metagenomes, establishes a new SeqCode nomenclature for a dominant order, and provides evidence for recurrent archaea-to-Patescibacteriota transfers of Form III RuBisCO.

Nielsen, T. N., Lui, L. M.2026-05-18
🦠 microbiology

Repurposing antiviral drugs as a new avenue for Klebsiella pneumoniae decolonization

This study demonstrates that repurposing antiviral drugs offers a promising new avenue for decolonizing the gastrointestinal tract of antibiotic-resistant *Klebsiella pneumoniae*, as six identified compounds showed strain-specific and context-dependent antibacterial activity relevant to the human gut environment.

Anderson, N., Todd, K., Casiano, M., Maheswaran, N., Blankenberger, A., Singh, A., Relich, R. F., Tilston-Lunel, N. L. (…)2026-05-17
🦠 microbiology

Apparent generalism in Pseudomonas aeruginosa is underpinned by Convergent, Cryptic Specialization

This study reveals that the apparent ecological generalism of *Pseudomonas aeruginosa* is actually driven by convergent, cryptic specialization, where distinct genomic adaptations to specific environments emerge repeatedly across the phylogeny rather than being confined to deep lineages.

Mehlferber, E. C., Irby, I., Yarter, M., Lowery, N., Lowhorn, R., Appaji, Y., Eum, J., Song, H., Stone, B., Brown, S. P.2026-05-16
🦠 microbiology

Combined lactate- and phosphate-dependent cytoplasmic acidification drives Mycobacterium tuberculosis growth arrest at acidic pH

This study reveals that *Mycobacterium tuberculosis* growth arrest at acidic pH on lactate is driven by phosphate-dependent cytoplasmic acidification and proton motive force dissipation, which can be suppressed by mutations in phosphate transporters that upregulate the SenX3/RegX3 regulon to restore growth.

Kibiloski, A. P., Dechow, S. J., Abdalla, B. J., Murdoch, H. M., Tischler, A. D., Abramovitch, R. B.2026-05-16
🦠 microbiology

Disentangling Production and Persistence of Extracellular Virions in Grassland Soils with SIP-Viromics

By applying a genome-resolved stable isotope probing viromics approach to rewetted grassland soils, this study reveals that while only a small fraction of extracellular virions are actively produced during the first week, the majority persist as a stable "viral seed bank" targeting rapidly resuscitating bacterial hosts, thereby serving as a crucial genetic reservoir for microbial turnover and biogeochemical cycling following environmental disturbance.

Trubl, G., Roux, S., Kellom, M., Vyshenska, D., Tomatsu, A., Singh, K., Kimbrel, J., Eloe-Fadrosh, E. A., Malmstrom, R. (…)2026-05-15
🦠 microbiology

A Bioinformatic Pipeline for Consensus Taxonomic Classification of Long-Read Amplicons

The paper introduces the Amplicon Consensus Taxonomy (ACT) pipeline and its associated ACT-DB reference database, a robust workflow that integrates multiple classification tools to achieve superior taxonomic resolution for Oxford Nanopore long-read amplicons by effectively identifying novel and low-abundance taxa while minimizing overclassification.

Paulsen, A. A., LaSarre, B., Delp, D., Beattie, G. A., Halverson, L. J.2026-05-15
🦠 microbiology

Ticks and tickborne diseases in the upper Midwestern United States: role for citizen science in assessing exposure risk

This study utilized a citizen science program in the upper Midwestern United States to map tick ranges and found that while *Amblyomma americanum* has not yet established in the region, adult *Ixodes scapularis* ticks exhibit high prevalence of multiple pathogens, including *Borrelia burgdorferi*, providing critical data for assessing local tickborne disease risks.

Linz, A. M., Marcis, C., Payant, C., Donnerbauer, L., Donnerbauer, A., Gruenling, E., Boese, K., Heuer, G., Boehm, A., U (…)2026-05-15