Tominaga K. (tomiken)

Coastal Vibrio as a source of antimicrobial resistance? Coastal Vibrio harbor a high diversity of underexplored antimicrobial resistance genes (ARGs). Their selective maintenance in the absence of antibiotic selection is puzzling. While their mobilization is rare, it may just be a question of time when the ecological context turns the coastal environment into a source for ARG spillover.

Coastal Vibrio as a source of antimicrobial resistance?: Trends in Microbiology https://www.cell.com/trends/microbiology/abstract/S0966-842X(26)00009-0?rss=yes

Coastal Vibrio as a source of antimicrobial resistance? Coastal Vibrio harbor a high diversity of underexplored antimicrobial resistance genes (ARGs). Their selective maintenance in the absence of antibiotic selection is puzzling. While their mobilization is rare, it may just be a question of time when the ecological context turns the coastal environment into a source for ARG spillover.

Coastal Vibrio as a source of antimicrobial resistance?: Trends in Microbiology https://www.cell.com/trends/microbiology/abstract/S0966-842X(26)00009-0?rss=yes

Copper stress upregulates oxidative stress response, histidine production and iron acquisition genes in E. coli Copper is widely used as a fast acting antimicrobial, yet the strategies that allow bacteria to survive copper stress remain incompletely understood. Here, we characterize the transcriptional responses of Escherichia coli MG1655 to excess ionic copper using RNA sequencing and a genome wide GFP based promoter library. We applied 2 mM copper, which slows growth, and 8 mM copper, a near lethal concentration. RNA seq revealed extensive transcriptome remodeling, with 487 genes upregulated at 2 mM and 364 at 8 mM. Both concentrations strongly induced canonical copper responsive systems, oxidative stress defenses, histidine biosynthesis, and multiple iron acquisition pathways - including enterobactin biosynthesis and transport - despite external iron failing to reduce copper toxicity. At 2 mM copper, additional pathways were activated, including heat shock and protein folding functions as well as lipid A, methionine and arginine biosynthesis. Copper exposure also repressed large gene sets: 486 genes at 2 mM, enriched for biofilm formation and pH elevation, and 217 genes at 8 mM, enriched for anaerobic metabolism. In contrast to the robust RNA seq results, we investigated the Horizon Discovery E. coli genome-wide GFP based promoter library as an alternative screening tool. However, in our experiments it showed low signal to noise ratios, limiting its suitability for large scale gene expression screening. ### Competing Interest Statement The authors have declared no competing interest. Estonian Research Council, PRG1496, TemTA55, TK210, TARISTU24-TK14, STP39 Horizon Europe, 101159721

Copper stress upregulates oxidative stress response, histidine production and iron acquisition genes in E. coli | bioRxiv https://www.biorxiv.org/content/10.64898/2026.03.12.711415v1?rss=1

Bacterial Stress Responses Lower mRNA-Protein Level Correlations Diverse bacterial pathogens have evolved complex regulatory mechanisms to adapt to various environmental stresses during infection. The uncertainty in mRNA-protein levels in response to environmental stressors complicates our understanding of bacterial physiology and their adaptation to stressful environments. To examine this issue, we have integrated transcriptomics and proteomics data on three human bacterial pathogens Salmonella enterica Typhimurium\[CE4.1\]\[KA4.2\], Yersinia pseudotuberculosis, and Staphylococcus aureus under ten infection-relevant stress conditions. We observed positive correlations between mRNA and protein levels, which were decreased under different stress conditions. Essential genes exhibited higher expression levels with lower variation across the conditions and stronger mRNA-protein correlations compared to non-essential genes, highlighting their [JA5.1]critical role in bacterial adaptability and survival. Moreover, we identified a substantial number of genes with stress-induced non-correlating mRNA-protein levels, particularly under conditions triggering strong stress responses. Particularly this level was dramatically lowered for osmotic stress specific genes affected by impaired translational activity under osmotic stress. Our findings highlight the prevalence of non-correlating mRNA-protein levels and the potential role of post-translational modifications in modulating protein levels in response to environmental stressors during infection. This study provides a comprehensive framework for integrating transcriptomics and proteomics data and identifies potential gene products that might significantly impact the ability of diverse bacterial pathogens to adapt to hostile infection environments. ### Competing Interest Statement The authors have declared no competing interest. Swedish Research Council, https://ror.org/03zttf063, 2021-02466 Kempe Foundation, https://ror.org/05cszw148, JCK22-0017 Medical Faculty umeå, FS 2.1.6-281-22 Swedish Research Council Excellence Center, 2022-06543 Knut and Alice Wallenberg Foundation, https://ror.org/004hzzk67, KAW 2020.0239

Bacterial Stress Responses Lower mRNA-Protein Level Correlations | bioRxiv https://www.biorxiv.org/content/10.64898/2026.03.12.711437v1?rss=1

GradeBins: a comprehensive framework to augment metagenomic bin quality control Metagenomic binning and single-cell assembly produce draft genomes whose completeness and contamination vary with experimental and computational choices. Comparing whole bin sets remains difficult because most quality assessment tools report per-bin metrics and operate either with ground truth labels or with inference estimates. GradeBins evaluates complete bin sets under two execution modes while producing matched per-bin and bin-set summaries. For real metagenomes, inference mode integrates bin statistics, mapping depth, taxonomy, and external quality estimates from tools such as CheckM2 and EukCC to standardize per-bin and bin-set quality reporting across Bacteria, Archaea, and Eukaryotes. For synthetic or otherwise labeled datasets, ground truth mode computes base-resolved completeness, contamination, and misbinning from labeled contigs or CAMI mappings, enabling objective benchmarking of binners, parameter choices, and experimental conditions, and calibration of inference-based estimates. Across synthetic metagenomes of 10, 50, 100, 500 and 1,000 Bacteria and Archaea, and a mixed metagenome containing also Eukaryotes, GradeBins separated binner and parameter effects using Total Score and a quality-weighted bin count, together with quality tier distributions, recovery fractions, and label-aware diagnostics. Inference-mode completeness generally tracked ground truth, whereas contamination and clean-bin rates showed mode-dependent shifts that were most pronounced in the mixed community. GradeBins added low overhead in these benchmarks, with peak memory below 8 GB and runtimes typically below 30 seconds. GradeBins enables reproducible protocol comparison, regression testing, and consistent quality reporting for genome-resolved metagenomics in both benchmarking and real-data settings. The full software package is open-source and available for download at https://bbmap.org/tools/gradebins. ### Competing Interest Statement The authors have declared no competing interest. Office of Science, https://ror.org/04xm1d337, Contract No. DE-AC02-05CH11231

GradeBins: a comprehensive framework to augment metagenomic bin quality control | bioRxiv https://www.biorxiv.org/content/10.64898/2026.03.11.709163v1?rss=1

AlphaFold 3-powered discovery of phage proteins that inhibit bacterial transcription initiation Yuan et al. develop an AlphaFold 3-guided pipeline to discover phage proteins that inhibit bacterial transcription initiation. Using this approach, they identify three phage inhibitors that target distinct RNA polymerase sites and block open-complex formation through diverse structural mechanisms.

AlphaFold 3-powered discovery of phage proteins that inhibit bacterial transcription initiation: Cell Reports https://www.cell.com/cell-reports/fulltext/S2211-1247(26)00160-9?rss=yes

Discovering PETases: An Interlink Between Engineering Enzymes and Microbiomes In this review-type article, we discuss some recent trends in the identification of polyethylene terephthalate-degrading enzymes (PETases) from nature. We highlight that the discovery of novel PETase...

Discovering PETases: An Interlink Between Engineering Enzymes and Microbiomes - Jiménez - 2026 - Environmental Microbiology - Wiley Online Library https://enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.70272?af=R

Parasitic connections: a patescibacterial epibiont, its methylotrophic gammaproteobacterial host, and their phages | mBio Patescibacteriota are ultra-small bacteria with reduced genomes that rely on symbiotic interactions with other prokaryotes; however, their host specificity and associated viral parasites remain poorly characterized due to limited cultured representatives. By combining targeted cultivation with genomic and microscopy analyses, we reveal previously unrecognized host lineages and expand the known viral diversity infecting this major, but still poorly known, bacterial phylum. We describe Strigamonas methylophilicida, a new patescibacterial species of the family Absconditicoccaceae that grows as an epibiont on various methylotrophic Gammaproteobacteria. This expands the host range for this family, previously found to infect only photosynthetic partners. Using enrichment cultures and metagenomics, we retrieved complete genomes of novel phages infecting S. methylophilicida and its methylotrophic hosts, including one phage that uses a modified genetic code matching that of the patescibacterium, which shows a specific viral adaptation to infect Absconditicoccaceae hosts. Our findings reveal a previously unrecognized patescibacteria-methylotrophs-phages tripartite interaction in freshwater environments, highlight the adaptations of patescibacterial phages, and shed light on the complex ecology and evolution of host-parasite-phage dynamics in understudied bacterial lineages.

Parasitic connections: a patescibacterial epibiont, its methylotrophic gammaproteobacterial host, and their phages | mBio https://journals.asm.org/doi/10.1128/mbio.00025-26

SypC, a symbiont outer membrane vesicle protein, impacts the development of the squid–vibrio partnership | PNAS Bacterial outer membrane vesicles (OMVs) and the cargo they carry are increasingly recognized as a means of communication between microbial symbion...

SypC, a symbiont outer membrane vesicle protein, impacts the development of the squid–vibrio partnership | PNAS https://www.pnas.org/doi/abs/10.1073/pnas.2524648123?af=R

mGem: Horses for courses in mapping bacterial small RNA interaction networks | mBio Small RNAs (sRNAs) are bacterial RNA species that are anywhere between 50 and 500 nucleotides in length. Many sRNAs employ a short sequence (as few as 6 nucleotides), known as the seed sequence, to base-pair with target transcripts (1, 2). This base-pairing is often incomplete and, in gram-negative bacteria, is frequently mediated by the RNA chaperone Hfq (3). Hfq can bind simultaneously to both an sRNA and its mRNA target, resulting in activation or repression of translation, modulation of transcript stability, or both (1). For any given sRNA, of which there may be more than a hundred encoded by the bacterium (4), there can be as few as one, or as many as several hundred target transcripts (5). Post-transcriptional control by sRNAs can therefore have far-reaching effects.

mGem: Horses for courses in mapping bacterial small RNA interaction networks | mBio https://journals.asm.org/doi/10.1128/mbio.03082-25

TerminatorNet: comprehensive identification of intrinsic transcription terminators in bacteria | Bioinformatics | Oxford Academic https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btag116/8514374?rss=1&login=true

AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2 - Nature Methods AF2BIND is a logistic regression model trained on AlphaFold2 pair features to predict small-molecule binding-site residues in proteins, without multiple sequence alignments, homology models or knowledge of the true ligand. AF2BIND was used to predict binding sites across the AF2-predicted human proteome, finding thousands of potentially new ligandable sites.

AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2 | Nature Methods https://www.nature.com/articles/s41592-026-03011-2

The recovery of 12,789 genomes revealed the diversity, function, and microbial interactions of the geothermal spring microbiome Geothermal springs, characterized by extreme physicochemical conditions, represent ecologically and evolutionarily significant habitats that foster unique microbial communities and drive adaptive evolutionary processes. Despite their importance, the complex microbial interactions and underlying mechanisms governing community assembly in these environments remain poorly understood. In this study, we conducted systematic sampling across 49 geothermal springs in Tengchong, Yunnan, over a six-year period (2016-2021), and performed metagenomic sequencing on 152 samples. We successfully reconstructed 12,789 non-redundant microbial genomes, revealing an exceptionally high level of phylogenetic and functional diversity within the spring microbiomes. Our analyses demonstrate that pH and temperature are the primary deterministic drivers shaping both microbial species composition and functional potential, thereby segregating the communities into three distinct groups: acidic, hyperthermal, and thermal. Furthermore, ecological network analysis revealed that extreme environmental conditions significantly alter network topology, resulting in less complex but more efficient microbial interaction networks. Collectively, this study provides a comprehensive resource and mechanistic insights into the microbial diversity, community structure, and species interactions in geothermal spring ecosystems. ### Competing Interest Statement The authors have declared no competing interest. National Natural Science Foundation of China, 32200002，32400002, 91951205, and 32170014

The recovery of 12,789 genomes revealed the diversity, function, and microbial interactions of the geothermal spring microbiome | bioRxiv https://www.biorxiv.org/content/10.64898/2026.03.10.710734v1?rss=1

Advancing Vibrio genetics: A platform for efficient genomic manipulation Most non-model Vibrio species lack the genetic tools needed for targeted mutagenesis, which limits the ability to functionally characterize newly identified pathways. To address this challenge, we present here efficient, robust methods for genetically manipulating Vibrio species that rely on RecA-mediated homologous recombination and two well-characterized counterselection methods, galactokinase (galK) 2-Deoxy-D-galactose (DOG-2) toxicity and the rpsLR/rpsLS streptomycin susceptibility system, both of which are active across a broad range of Vibrio species. We further characterized two genus-specific conserved promoters capable of driving high-level ectopic expression across all tested species. These promoters were incorporated into two broadly applicable, conjugatively transferable suicide backbones designed to facilitate double homologous recombination. Using these systems, we successfully disrupted polar flagellar motility in multiple Vibrio species and introduced extensive modifications to both flagellar and secretory pathways in V. diazotrophicus. Notably, although the galK system exhibited broader applicability, the rpsL system proved to be more efficient in cases where a streptomycin resistant strain could be generated. We also developed two mobilizable replicative backbones that express pH-stable fluorescent proteins for use within the genus. Collectively, these tools expand the genetic toolkit available for both gene disruption and heterologous gene expression in non-model members of the Vibrionaceae.

Advancing Vibrio genetics: A platform for efficient genomic manipulation | bioRxiv https://www.biorxiv.org/content/10.64898/2026.03.10.710856v1

Advancing Vibrio genetics: A platform for efficient genomic manipulation Most non-model Vibrio species lack the genetic tools needed for targeted mutagenesis, which limits the ability to functionally characterize newly identified pathways. To address this challenge, we present here efficient, robust methods for genetically manipulating Vibrio species that rely on RecA-mediated homologous recombination and two well-characterized counterselection methods, galactokinase (galK) 2-Deoxy-D-galactose (DOG-2) toxicity and the rpsLR/rpsLS streptomycin susceptibility system, both of which are active across a broad range of Vibrio species. We further characterized two genus-specific conserved promoters capable of driving high-level ectopic expression across all tested species. These promoters were incorporated into two broadly applicable, conjugatively transferable suicide backbones designed to facilitate double homologous recombination. Using these systems, we successfully disrupted polar flagellar motility in multiple Vibrio species and introduced extensive modifications to both flagellar and secretory pathways in V. diazotrophicus. Notably, although the galK system exhibited broader applicability, the rpsL system proved to be more efficient in cases where a streptomycin resistant strain could be generated. We also developed two mobilizable replicative backbones that express pH-stable fluorescent proteins for use within the genus. Collectively, these tools expand the genetic toolkit available for both gene disruption and heterologous gene expression in non-model members of the Vibrionaceae.

Advancing Vibrio genetics: A platform for efficient genomic manipulation | bioRxiv https://www.biorxiv.org/content/10.64898/2026.03.10.710856v1

piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE Abstract. piqtree (pronounced pie-cue-tree) is an easy to use, open-source Python package that provides Python script based control of IQ-TREE’s phylogenet

piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE | Molecular Biology and Evolution | Oxford Academic https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msag061/8512395

Unravelling the molecular diversity of marine cyanobacterial communities in the lagoon of Nouméa (New Caledonia): impact of a cyclonic event | ISME Communications | Oxford Academic https://academic.oup.com/ismecommun/advance-article/doi/10.1093/ismeco/ycag032/8509918?login=true

Bringing the genetically minimal cell to life on a computer in 4D We present a whole-cell spatial and kinetic model for the ∼100 min cell cycle of the genetically minimal bacterium JCVI-syn3A. We simulate the complet…

Bringing the genetically minimal cell to life on a computer in 4D - ScienceDirect https://www.sciencedirect.com/science/article/pii/S0092867426001741?via%3Dihub

Conditional activation of Cas13 enforces lysogeny in a native type VI-A CRISPR host - Nature Microbiology RNA-targeting CRISPR in Listeria seeligeri restricts the lytic cycle of temperate phages but tolerates prophage acquisition while also preventing induction—a system that enables acquisition of beneficial prophages while mitigating the risks of lysis.

Conditional activation of Cas13 enforces lysogeny in a native type VI-A CRISPR host | Nature Microbiology https://www.nature.com/articles/s41564-026-02288-5

Oxford Nanopore enhanced accuracy of long-read amplicons applied to microbial whole-genome sequencing | Microbiology Spectrum Recent advances in genome sequencing have greatly improved our ability to study microbes and detect infections. One such technology, Oxford Nanopore Technologies (ONT), can read long stretches of nucleic acids. ONT is also portable and can sequence in real time, making it useful in clinical settings. However, ONT accuracy is known to be lower than traditional short-read methods, limiting its widespread use. Fortunately, many strategies have emerged to overcome this limitation: better ONT chemistry, better basecaller, and hybrid approaches combining ONT with highly accurate short reads. Another promising method uses molecular barcodes or “Unique Molecular Identifiers” (UMIs) to make long reads at high accuracy, reaching accuracy levels similar to the existing short-read technologies. In our study, we optimized this UMI-based method and successfully applied it to human blood samples spiked with common infection-causing bacteria. The results showed a significant drop in ONT error rate, suggesting that this approach could make ONT a reliable tool for diagnosing infections and analyzing microbial DNA in clinical samples.

Oxford Nanopore enhanced accuracy of long-read amplicons applied to microbial whole-genome sequencing | Microbiology Spectrum https://journals.asm.org/doi/full/10.1128/spectrum.02856-25?af=R

Molecular clock dating using complex mixture models: applied to ancient symbionts | Molecular Biology and Evolution | Oxford Academic https://academic.oup.com/mbe/article/43/3/msag039/8489165?login=true

Genomic perplexity and the evolution of context-dependent function | Molecular Biology and Evolution | Oxford Academic https://academic.oup.com/mbe/article/43/3/msag041/8497498

tRNA gene arrays: emerging roles in bacterial persistence and adaptive evolution Bacterial tRNA genes often form arrays that are thought to enhance translational efficiency. Recent work shows that tRNA gene arrays also regulate persistence in Burkholderia, correlating with phylogenetic relationships. These findings implicate tRNA gene arrays in niche-specific adaptive evolution, extending bacterial persistence beyond survival under lethal stresses.

tRNA gene arrays: emerging roles in bacterial persistence and adaptive evolution: Trends in Microbiology https://www.cell.com/trends/microbiology/fulltext/S0966-842X(26)00034-X?rss=yes#f0005

A proteostasis clock underlies the timing of bacterial dormancy and antibiotic tolerance | bioRxiv https://www.biorxiv.org/content/10.64898/2026.03.09.710435v1?rss=1

Semirandom DNA adducts regulate a filamentous defence-associated reverse transcriptase | bioRxiv https://www.biorxiv.org/content/10.64898/2026.03.07.710306v1?rss=1

High throughput in situ imaging reveals widely occurring diel vertical migration among phytoplankton | ISME Communications | Oxford Academic https://academic.oup.com/ismecommun/advance-article/doi/10.1093/ismeco/ycag049/8512076?rss=1&login=false

Illuminating the newly produced viruses within the virosphere with BONCAT and single virus genomic sequencing technologies | ISME Communications | Oxford Academic https://academic.oup.com/ismecommun/advance-article/doi/10.1093/ismeco/ycag048/8507969?rss=1&login=false

Sub-daily virus sampling at the Bermuda Atlantic Time Series reveals diel and depth-structured population dynamics without community-level shifts Viruses are often studied in disease settings, but in the ocean they outnumber cells and shape ecosystems, yet their dynamics remain poorly understood. In this study, high-resolution sampling of blue-ocean waters revealed little community-level change but extensive depth- and diel-driven population dynamics beneath the surface.

Sub-daily virus sampling at the Bermuda Atlantic Time Series reveals diel and depth-structured population dynamics without community-level shifts | PLOS Biology https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003474

Sub-daily virus sampling at the Bermuda Atlantic Time Series reveals diel and depth-structured population dynamics without community-level shifts Viruses are often studied in disease settings, but in the ocean they outnumber cells and shape ecosystems, yet their dynamics remain poorly understood. In this study, high-resolution sampling of blue-ocean waters revealed little community-level change but extensive depth- and diel-driven population dynamics beneath the surface.

Sub-daily virus sampling at the Bermuda Atlantic Time Series reveals diel and depth-structured population dynamics without community-level shifts | PLOS Biology https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003474

Viruses in marine sediments: a review of their effect on biogeochemistry and microbial interactions | Applied and Environmental Microbiology In the ocean, viruses are known to mediate the carbon cycle, keeping dissolved organic carbon (DOC) in the microbial loop and preventing its movement into secondary consumers (1). However, few direct measurements of this carbon flux exist, and recent considerations of the ocean system consider that viruses can not only loop carbon in the dissolved pool but also participate in a carbon shuttle through the creation of aggregates that pellet or can be part of a viral vent that releases carbon into the atmosphere (2). While the pelagic ocean has been well reviewed for viral contributions to microbial diversity and biogeochemical cycling, less attention has been paid in recent years to the sedimentary portion of the ocean, where carbon is potentially stored over geological time, but viral influence can still be felt. Here, we review the literature on viruses in sedimentary ecosystems and their potential role in biogeochemistry and microbial diversity.

Viruses in marine sediments: a review of their effect on biogeochemistry and microbial interactions | Applied and Environmental Microbiology https://journals.asm.org/doi/10.1128/aem.00275-25?utm_source=twitter&utm_medium=social&utm_content=ASM&utm_id=falcon&utm_campaign=MicrobiologyMonday