Tominaga K. (tomiken)

Genomic and metatranscriptomic analyses reveal an active microbial hydrocarbon cycle in the photic zone Natural hydrocarbon seeps and hydrocarbons resulting from human activities are the primary conduits by which oil enters the sea. Marine Cyanobacteria, among the most abundant photosynthetic organisms in the world, produce alkanes, an additional hydrocarbon source to the sea. Alkane production proceeds via metabolism of fatty acid intermediates with a fatty acyl-ACP reductase (FAAR) and an aldehyde-deformylating oxygenase (ADO). These alkanes can be consumed with alkane hydroxylases, including alkane 1-monooxygenase (alkB). The production and consumption of alkanes in the photic zone is termed the short-term hydrocarbon cycle (STHC). Yet, an active STHC has not been substantiated through gene expression analyses. To determine if the STHC is active in the marine photic zone we evaluated over 9000 genomes to which metatranscriptome reads from a site in the Gulf of Mexico were recruited. In these samples, FAAR and ADO expression was dominated by Prochlorococcus and to a lesser extent Synechococcus. Bacterial alkane consumption via alkB was dominated by Pseudomonadota, SAR324, and Bacteroidota alkB gene expression. Additionally, archaeal alkane consumption utilizing this same n-alkane degradation pathway was observed in the transcript data by Thermoplasmatota, classified as Marine Group II and III, the most abundant planktonic archaeal groups. Active production of alkanes in the photic zone would be an important component of marine hydrocarbon cycle and more broadly of carbon cycling. Further, consumption of hydrocarbons, regardless of source, is a fundamentally important ecosystem cleanup service provided by microbes in the ocean.

Genomic and metatranscriptomic analyses reveal an active microbial hydrocarbon cycle in the photic zone | bioRxiv https://www.biorxiv.org/content/10.1101/2025.10.24.684404v1?rss=1

A Comparative Analysis: Molecular Mechanisms of Carbon Catabolite Repression in Bacteria In the environment, bacteria often encounter a mixture of different carbon sources (C-sources) that can potentially be used. However, their uptake and utilization are selective and controlled in a hierarchical order by a complex regulatory pathway named carbon catabolite repression (CCR). Currently, two major types of CCR mechanisms have been described: (a) In Escherichia coli, Bacillota (formerly Firmicutes) and Vibrio, CCR depends on the phosphorylation state of the components of the phosphoenolpyruvate–sugar phosphotransferase system (PTS) and their subsequent regulatory activity, and (b) in pseudomonads, transcripts under CCR control are repressed by the posttranscriptional regulators Hfq and Crc. The repressive effect is antagonized by Hfq- and Crc-titrating RNAs (e.g., CrcZ, CrcY, and CrcX) that are expressed in response to the preference for C-sources. In addition, the importance of CCR as a sensor linking carbon availability with the regulation of virulence, chemotaxis, quorum sensing, and antibiotic susceptibility is addressed in this article.

A Comparative Analysis: Molecular Mechanisms of Carbon Catabolite Repression in Bacteria | Annual Reviews https://www.annualreviews.org/content/journals/10.1146/annurev-micro-050624-031622?TRACK=RSS

Integrating theory and machine learning to reveal determinants of plasmid copy number Plasmids are extrachromosomal mobile genetic elements whose copy numbers (PCNs) critically influence microbial evolution, antibiotic resistance and pathogenicity. Despite their importance and immense diversity, the ecological, evolutionary and molecular factors determining PCN remain poorly understood. Here, we present a theoretical model to explain the empirical power-law relationship between plasmid size and copy number, one of the fundamental quantitative principles governing PCN control. However, this relationship alone has limited predictive power. To improve PCN prediction, we introduce a data-driven approach incorporating diverse features. Trained on >10,000 plasmids, our machine learning model achieves significantly enhanced accuracy, with plasmid-encoded protein domains emerging as key predictors. Applying this framework, we conduct the first comprehensive analysis of PCN distributions across hundreds of thousands of metagenomic plasmids (IMG/PR database) and tens of thousands of clinical isolates, uncovering niche specific taxonomic PCN hotspots and ecological adaptations. These results provide critical insights into plasmid ecology, ARG surveillance and shed lights on the gut plasmidome, a dark matter in human microbiome. ### Competing Interest Statement The authors have declared no competing interest.

Integrating theory and machine learning to reveal determinants of plasmid copy number | bioRxiv https://www.biorxiv.org/content/10.1101/2025.10.23.684078v1?rss=1

Optimizing methods for virome analysis based on studies of a synthetic viral community Studies of whole viral populations--the "virome"--are yielding exciting new insights into biological systems, but methods are still being optimized. Here we describe generation and use of a synthetic viral community to assess several technical challenges important in virome analysis. Our mock community was comprised of phages lambda, T4, M13, MS2, and phi6, together with adeno-associated virus (AAV), murine hepatitis virus (MHV), and vaccinia virus (VV). We spiked the mock community into different human sample types, including stool, saliva, oropharyngeal (OP) wash, and bronchoalveolar lavage (BAL), then passed the samples through different virus enrichment protocols and analyzed by Illumina sequencing. Compared to direct metagenomic sequencing, VLP enrichment protocols greatly increased viral read yields from virus-rich samples such as from stool and saliva. Three VLP enrichment work flows were compared, and each was found to have strengths and weaknesses. Four methods for DNA amplification were compared, with three showing over-amplification of small circular ssDNA viruses, most notably GenomiPhi. Studies of viral particle stability in the presence of nuclease showed that most viral genomes were stable when protected in viral particles, but phage MS2 RNA was unexpectedly labile under some of the conditions tested. Comparison of Illumina 1000-cycle sequencing versus 300-cycle sequencing showed that longer reads supported generation of longer viral genome assemblies. Bacteriophage DNA can be modified by at least 12 different chemistries, raising the question of whether these modifications might block recovery in virome analytical protocols. We tested bacteriophage T4 DNA modified with glucosyl-hydroxymethylcytosine (ghmC) and hydroxymethylcytosine (hmC), and found that both were readily detected, though the recovery of ghmC-modified DNA was reduced. These studies together with published data help provide guidance for virome researchers optimizing analytical protocols. ### Competing Interest Statement The authors have declared no competing interest. PennCHOP Microbiome Program National Institutes of Health, https://ror.org/01cwqze88, P30AI045008, U19AI174998, R01LM014503, U54AG089323

Optimizing methods for virome analysis based on studies of a synthetic viral community | bioRxiv https://www.biorxiv.org/content/10.1101/2025.10.23.683462v1?rss=1

Escherichia coli with a 57-codon genetic code The near-universal genetic code uses 64 codons to encode the 20 canonical amino acids and protein synthesis. Here, we designed and generated Escherichia coli with a 4-megabase synthetic genome in which we replaced known occurrences of six sense codons ...

Escherichia coli with a 57-codon genetic code | Science https://www.science.org/doi/full/10.1126/science.ady4368?af=R

ParaRef: a decontaminated reference database for parasite detection in ancient and modern metagenomic datasets - Genome Biology Shotgun metagenomics holds great potential for identifying parasite DNA in biological samples, but its effectiveness is limited by widespread contamination in publicly available reference genomes, which hinders accurate detection. In this study, we systematically quantify and remove contamination from 831 published endoparasite genomes to create ParaRef, a curated reference database for species-level parasite detection. We show that decontamination significantly reduces false detection rates and improves overall detection accuracy. Our study highlights the pervasive issue of contamination in public databases and offers a resource that will enhance the reliability of parasite detection using metagenomics.

ParaRef: a decontaminated reference database for parasite detection in ancient and modern metagenomic datasets | Genome Biology | Full Text https://genomebiology.biomedcentral.com/articles/10.1186/s13059-025-03818-w

Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome Ribosomal RNA (rRNA) constitutes the core of ribosomes and is extensively chemically modified. Technical challenges have precluded systematically diss…

Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - ScienceDirect https://www.sciencedirect.com/science/article/pii/S0092867425010827?dgcid=rss_sd_all

New retron systems from environmental bacteria identify triggers of anti-phage defense and expand tools for genome editing Bacteria rely on retrons for phage defense, yet most known systems come from clinical or lab strains. This study identifies new and diverse retrons from environmental bacteria, uncovering their phage defense mechanisms and applying them as genome editing tools.

New retron systems from environmental bacteria identify triggers of anti-phage defense and expand tools for genome editing | PLOS Biology https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003042

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Acetone-mediated ammonium oxidation to dinitrogen by Zobellella taiwanensis bacteria Abstract. Bioconversion of ammonium to dinitrogen (N2) is an essential process in the nitrogen cycle, primarily driven by O2-dependent nitrification and fo

Acetone-mediated ammonium oxidation to dinitrogen by Zobellella taiwanensis bacteria | The ISME Journal | Oxford Academic https://academic.oup.com/ismej/advance-article/doi/10.1093/ismejo/wraf230/8296948?rss=1&login=false

Comparison of the Fecal Microbiota from Long-term Captive and Newly Captured Whale Sharks (<i>Rhincodon typus</i>) https://www.jstage.jst.go.jp/article/jsme2/40/3/40_ME25023/_article/-char/ja/

Non-conjugative plasmids limit their mobility to persist in nature Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it reduces diversity in populations. This ultimately leaves bacterial populations more vulnerable to being killed, for example by antibiotics.

Non-conjugative plasmids limit their mobility to persist in nature: Cell Reports https://www.cell.com/cell-reports/fulltext/S2211-1247(25)01227-6?rss=yes

Phage evolutionary relationships emerge from protein language model-based proteome representation Abstract. Viral taxonomy is a challenging task due to the propensity of viruses for recombination and the lack of universal gene markers. As a result, rece

Phage evolutionary relationships emerge from protein language model-based proteome representation | NAR Genomics and Bioinformatics | Oxford Academic https://academic.oup.com/nargab/article/7/4/lqaf134/8296763?login=true

GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy

GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes | Nucleic Acids Research | Oxford Academic https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1040/8296754?rss=1&login=true

Physiological diversity and adaptation of Rhizaria revealed by phylogenomics and comparative transcriptomics Protists are vastly diverse, forming over 20 supergroups of the eukaryotic diversity and fulfilling plentiful functions. Rhizaria is a widespread and highly abundant supergroup comprising important parasites and a huge diversity of free-living heterotrophic predators. Despite the diversity and biogeochemical importance of Rhizaria, our understanding of their physiology and metabolic capabilities remains limited, mainly due to a general lack of data and bioinformatic tools for cross-species comparisons of physiological traits. In this study, we assembled a total of 15 transcriptomes of the parasite-related bacterivorous Rhogostoma and their eukaryvorous relatives. By phylogenomic analyses and whole transcriptome comparison, we established an evolutionary framework to which we relate physiological traits. The morphologically highly similar Rhogostoma strains branch in two distinct clusters differing in orthogroups and gene expression patterns related to cell adhesion and biofilm formation. Furthermore, we reveal considerable intra-genus variation in amino acid and lipid metabolism, which might be explained by an ancient streamlining through gradual specialization to parasitism, bearing the potential for subsequent metabolic radiation. We conclude that even closely related and morphologically similar species in Rhizaria may differ distinctly in their functional repertoire. With the here established and showcased analyses, we create a basis for future characterization of the physiological traits of microeukaryotes. ### Competing Interest Statement The authors have declared no competing interest. Deutsche Forschungsgemeinschaft, 447013012, 221301018

Physiological diversity and adaptation of Rhizaria revealed by phylogenomics and comparative transcriptomics | bioRxiv https://www.biorxiv.org/content/10.1101/2025.10.20.683504v1?rss=1

Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor - Nature Ecology & Evolution Phylogenetic and biochemical analyses show a diversity of components of the DNA replication machinery in different Asgard archaea that contributed to the eukaryotic DNA replication machinery.

Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor | Nature Ecology & Evolution https://www.nature.com/articles/s41559-025-02882-6

Phages use contingency loci as a bet-hedging strategy Bacteriophages are estimated to outnumber bacteria by ~10-fold. Here, we show that phage genomes contain contingency loci (CL), hypermutable DNA regions that promote reversible frameshift mutations through DNA polymerase slippage. CL have been described in bacteria, archaea, and eukaryotes but have not previously been reported in phages. We demonstrate that CL in coliphage T2 and T4 generates genomic and phenotypic diversity in resulting progeny to evade host defense, a process known as bet-hedging. Whole genome sequencing of T2 and T4 show similar levels of CL-driven sequence variation in dozens of other putative CL. Additional sequencing of T6, T7, Secphi27, ICP1 and ICP2, alongside bioinformatics of the BASEL phage collection reveals that putative CL are widespread in phages and are encoded in every functional class of genes. Collectively, our study describes a new paradigm for understanding phage replication in which CL drive genetic diversification and population heterogeneity to rapidly evolve. ### Competing Interest Statement The authors have declared no competing interest. National Institutes of Health, GM139537, AI158433, GM088344, F31AI186463 U.S. National Science Foundation, DEB-1813069, DEB-1951307

Phages use contingency loci as a bet-hedging strategy | bioRxiv https://www.biorxiv.org/content/10.1101/2025.10.21.683753v1

Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.

Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism | Nature Microbiology https://www.nature.com/articles/s41564-025-02146-w

SmallBARNA 2026: a kingdom-wide bacterial sRNA resource Abstract. Bacterial small RNA are important context-sensitive regulators of gene expression, especially in highly pathogenic bacteria, often controlling vi

SmallBARNA 2026: a kingdom-wide bacterial sRNA resource | Nucleic Acids Research | Oxford Academic https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf999/8294348?rss=1&login=true

Cryo-EM Structures of Methanogenic Schizorhodopsins Reveal Divergent Strategies for Proton Transport and Thermal Adaptation Schizorhodopsins (SzRs) are light-driven inward proton pumps found in Asgard archaea, contrasting with most microbial rhodopsins that export protons. Some SzRs, including Methanoculleus taiwanensis SzR (MtSzR) and Methanoculleus sp. SzR (MsSzR), exhibit remarkable heat tolerance, suggesting structural adaptations to extreme environments. Here, we report cryo-electron microscopy structures of MtSzR and MsSzR at 2.4 and 2.7 Å resolutions, respectively, revealing distinct mechanisms for proton transport and thermostability. Both proteins share a cytoplasm-facing proton acceptor, yet MtSzR employs a hydrophobic gating mechanism, whereas MsSzR lacks this barrier and stabilizes its acceptor through a salt-bridge network. Thermostability also diverges: MtSzR relies on proline-rich loops and electrostatic interactions, while MsSzR achieves stability through reinforced trimerization and extensive interhelical aromatic packing. Structural and mutational analyses highlight the adaptability of SzRs and provide a framework for engineering robust photoreceptors for optogenetics and synthetic biology. ### Competing Interest Statement The authors have declared no competing interest.

Cryo-EM Structures of Methanogenic Schizorhodopsins Reveal Divergent Strategies for Proton Transport and Thermal Adaptation | bioRxiv https://www.biorxiv.org/content/10.1101/2025.10.20.683367v1

Declining ocean greenness and phytoplankton blooms in low to mid-latitudes under a warming climate Chlorophyll a is declining in low- to mid-latitude oceans, indicating reduced ocean productivity and fewer phytoplankton blooms.

Declining ocean greenness and phytoplankton blooms in low to mid-latitudes under a warming climate | Science Advances https://www.science.org/doi/full/10.1126/sciadv.adx4857?af=R

Phylogenetic and functional characterization of Asgard primases Eukarya resemble Archaea in DNA replication. Analysis of the DNA replication machinery of Asgard archaea may provide a valuable test of the hypothesis of this phylum being the origin of Eukarya. Among the replication proteins, primase, which comprises the catalytic subunit PriS and the noncatalytic subunit PriL, synthesizes primers for extension by DNA polymerase. Here we show that Asgard primases fall into two major groups, denoted the Heimdall group and the Loki group, which are phylogenetically and structurally more closely related to eukaryotic primases and primases from non-Asgard archaea, respectively. Notably, like human PriL, PriL of the Heimdall group possesses an extra C-terminal domain, which, absent in archaeal PriL of the non-Heimdall group, presumably serves to enhance the stability of the conserved iron-sulfur cluster in PriL. We overproduced in Escherichia coli and purified the PriS and PriL subunits of the Heimdall group from the Candidatus Gerdarchaeota archaeon B18\_G1. Biochemical characterization reveals that the B18\_G1 primase is capable of primer synthesis and extension, using preferentially dNTPs as the substrates, as shown for primases from non-Asgard archaea, but, unlike the non-Asgard archaeal primases, it produces short primers, a feature typical of eukaryotic primases. These results shed significant light on the evolutionary pathway of primase, and are consistent with the hypothesis of the Asgard origin of Eukarya. ### Competing Interest Statement The authors have declared no competing interest. National Natural Science Foundation of China, 32393970, 32225003 PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), GML20240002 Shenzhen Medical Research Fund, B2301005 Shenzhen University 2035 Program for Excellent Research, 2022B002

Phylogenetic and functional characterization of Asgard primases | bioRxiv https://www.biorxiv.org/content/10.1101/2025.10.19.683342v1?rss=1

RNA viruses in water shape the viromes of shrimp and fish in aquaculture systems Aquatic environments host immense RNA viral diversity, yet the extent to which waterborne viruses influence the virome of aquatic animals remains unclear. Here, we conducted a comprehensive longitudinal metatranscriptomic analysis of water, shrimp, and fish across multiple culture stages in aquaculture systems. We identified 3,211 RNA viruses spanning 21 viral supergroups, with 97.4% representing novel species. Water exhibited the greatest viral diversity (3,093 species), followed by shrimp (1,280) and fish (398), with most viruses detected in shrimp and fish also detected in water. Diversity analyses revealed increasing richness and significant compositional shifts in 92 high-abundance viruses (>1,000 RPM) across culture stages. Viral abundance in aquatic animals was strongly correlated with that in water, and the temporal trajectories of the 16 most abundant viruses were closely synchronized between water and shrimp. Furthermore, 337 virus species were shared among shrimp and two fish species, of which 309 were present in water. These findings demonstrated that RNA viruses in water shape the composition and dynamics of aquatic animal viromes, underscoring the importance of water virome surveillance and management for disease prevention in shrimp aquaculture. ### Competing Interest Statement The authors have declared no competing interest. National Key Research and Development Program of China, 2024YFD2401202 the earmarked fund of China Agriculture Research System, CARS-48 Southern Marine Science, and Engineering Guangdong Laboratory (Zhuhai), SML2024SP003

RNA viruses in water shape the viromes of shrimp and fish in aquaculture systems | bioRxiv https://www.biorxiv.org/content/10.1101/2025.10.19.683331v1?rss=1

Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses - Nature Structural & Molecular Biology Using a new method called FoldTree, the authors compare proteins on the basis of their shape to construct more accurate family trees over long evolutionary timescales and capture distant relationships where sequence information becomes less reliable.

Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses | Nature Structural & Molecular Biology https://www.nature.com/articles/s41594-025-01649-8

Clear niche partitioning of nitrite-oxidizing bacteria from the bottom and the slope of Mariana Trench - Microbiome Background The hadal zone, characterized by extreme hydrostatic pressure and geographic isolation, hosts microbial communities uniquely adapted to these harsh conditions. While niche partitioning has been observed in other deep-sea environments, its existence within hadal trench ecosystems remains controversial. Focusing on the Mariana Trench, we investigated whether nitrite-oxidizing bacteria (NOB) exhibit depth-stratified ecological specialization between slope (6000–10,000 m) and bottom (> 10,000 m) sediments. By analysing the genomic features and ecological interactions of NOB, we aimed to resolve their functional roles in nitrogen cycling under distinct hadal microniches. Results We reconstructed 8 high-quality NOB metagenome-assembled genomes (MAGs) from 58 sediment metagenomes, revealing stark niche differentiation between depth zones. Slope-dominant NOB harboured expanded genetic arsenals for antioxidation (e.g. superoxide dismutase) and osmoprotection (compatible solute transporters), Suggesting enhanced adaptive capacity to pressure-adjacent stresses. Metatranscriptomics revealed 1.48 × (nxrA) and 1.28 × (aclA) greater expression of nitrite oxidation and carbon fixation genes in slope communities than in their bottom counterparts. Network analysis identified slope NOB as keystone taxa with elevated among-module connectivity and intramodule linkages, in contrast with bottom NOB, which exhibited localized nitrate-production gene networks. Functional profiling revealed complementary biogeochemical roles: slope NOB primarily consumed nitrite, whereas bottom populations dominated nitrate synthesis. Conclusion Our multiomics analysis revealed depth-dependent niche partitioning among hadal NOB, with transcriptional and network evidence supporting distinct pressure adaptation strategies and biogeochemical functions. The slope-bottom differentiation in stress response systems and nitrogen transformation pathways highlights how micron-scale environmental gradients drive microbial specialization in Earth’s deepest ecosystems. These findings establish NOB as critical mediators of hadal biogeochemical cycles and provide a framework for understanding microbial resilience in extreme biospheres. Video Abstract

Clear niche partitioning of nitrite-oxidizing bacteria from the bottom and the slope of Mariana Trench | Microbiome | Full Text https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02192-w

Multi-environment deep mutational scanning reveals the distribution of temperature-sensitive variants in a bacterial kinase Ghose et al. perform multi-temperature deep mutational scanning to provide a comprehensive accounting of variants with altered temperature-dependent behavior in a model kinase, challenging previous assumptions surrounding temperature sensitivity and adaptation. Heat-sensitive variants were distributed across the protein structure and affected expression, whereas heat-resistant variants showed increased enzymatic activity, not stability.

Multi-environment deep mutational scanning reveals the distribution of temperature-sensitive variants in a bacterial kinase: Cell Reports https://www.cell.com/cell-reports/fulltext/S2211-1247(25)01217-3?rss=yes

Defensive fungal symbiosis on insect hindlegs Dinidorid stinkbugs were reported to possess a conspicuous tympanal organ on female hindlegs. In this study, we show that this organ is specialized to retain microbial symbionts rather than to perceive sound. The organ’s surface is not membranous but ...

Defensive fungal symbiosis on insect hindlegs | Science https://www.science.org/doi/10.1126/science.adp6699

Microbial hydrocarbon degradation potential of the Baltic Sea ecosystem - Microbiome Background The Baltic Sea receives petroleum hydrocarbons from various point sources. The degradation of these contaminants in the environment is typically facilitated by a variety of microorganisms that possess a range of genes and metabolic functions related to the degradation of various hydrocarbon substrates. However, our understanding of natural attenuation and the microbial capacity to degrade these contaminants within the Baltic Sea ecosystem remains limited. In this study, we compiled metagenomes from the benthic and pelagic ecosystems across the Baltic Sea to identify microorganisms and characterize their genes and metabolic functions involved in the degradation of hydrocarbon compounds. Results Known hydrocarbon-degrading phyla, i.e., Pseudomonadota, Myxococcota A, Actinomycetota, and Desulfobacterota, were identified within the Baltic Sea metagenome-assembled genomes (MAGs). Notably, 80% of the MAGs exhibited multiple hydrocarbon degradation gene annotations (> 10 reads per kilobase million). Aerobic degradation was the predominant pathway for hydrocarbon degradation across environmental samples. Hydrocarbon degradation gene abundances varied among samples and Baltic Sea subbasins, with long-chain alkanes and dibenzothiophene compounds being the preferred substrates. Species richness and diversity of both benthic and pelagic microorganisms positively correlated with hydrocarbon degradation gene diversity, with the pelagic ecosystem exhibiting significantly higher richness and diversity compared to the benthic ecosystem. Additionally, the composition of the hydrocarbon degradation genes across the Baltic Sea subbasins was influenced by oil spill history, with areas that experienced higher spill volumes showing lower microbial diversity, suggesting potential enrichment of specific hydrocarbon degraders. Among the environmental factors assessed, depth played a significant role in shaping the composition of genes involved in hydrocarbon degradation within the Baltic Sea. Conclusions Using metagenomics, we profiled the native microorganisms associated with hydrocarbon degradation in the Baltic Sea. This knowledge will aid in understanding the natural capacities of microbial communities, potentially linked to the natural attenuation of hydrocarbon pollutants in the area. Insights into microbial degradation potential can enhance predictions of petroleum pollutant persistence and accumulation, support mitigation strategies for marine pollution, and reveal the ecological resilience of native microbial communities in marine ecosystems. Video Abstract Graphical Abstract

Microbial hydrocarbon degradation potential of the Baltic Sea ecosystem | Microbiome | Full Text https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02211-w

IDBac: an open-access web platform and compendium for the identification of bacteria by MALDI-TOF mass spectrometry. The identification of bacteria is central to the microbiological sciences. While gene sequencing methods have been the standard to identify bacteria, use of MALDI-TOF mass spectrometry (MS) in clinical microbiology provides high-throughput identification to the subspecies level. However, biotyping has yet to be adopted outside of clinical settings due to the lack of a centralized public database of MS protein signatures that would facilitate strain identification via spectral comparison. Herein we present the IDBac web platform, a crowd-sourced central knowledgebase of protein MS signatures of >1400 strains spanning 6 bacterial phyla. Accompanying the knowledgebase is analysis infrastructure to identify unknown isolates, probe relationships within culture collections, and visualize specialized metabolite differences within groups of closely related bacteria. We highlight this utility by demonstrating the dereplication of bacterial isolates using the seed knowledgebase, identifying trends in culture collections using metadata integration, and reporting the discovery of a new metabolite from a Paraburkholderia isolate. ### Competing Interest Statement MW is a co-founder of Ometa Labs LLC. Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community Trust National Institute of General Medical Sciences of the NIH, R01GM125943, R21GM148870, R01GM129344, R25GM051765, R01AI155694, R35GM147235 National Science Foundation graduate research fellowship program National Institutes of Health, 5U24DK133658-02, R35GM150870 Office of the Director and the National Center for Complementary and Integrative Health, T32AT007533 U.S. Department of Energy Joint Genome Institute

IDBac: an open-access web platform and compendium for the identification of bacteria by MALDI-TOF mass spectrometry. | bioRxiv https://www.biorxiv.org/content/10.1101/2025.10.15.682631v1

GhostFold: Accurate protein structure prediction using structure-constrained synthetic coevolutionary signals The accuracy of protein structure prediction models such as AlphaFold2 is tightly coupled to the depth and quality of multiple sequence alignments (MSAs), posing a persistent challenge for proteins with few or no identifiable homologs. We present GhostFold, a method for conjuring structure-constrained synthetic MSAs from a single amino acid sequence, bypassing the need for traditional homology searches. Leveraging the ProstT5 protein language model and the 3Di structural alphabet, GhostFold projects a query sequence into a tokenized structural representation and iteratively back-translates to generate an ensemble of diverse, fold-consistent sequences. These synthetic alignments (pseudoMSAs) encode emergent coevolutionary constraints that are sufficient for high-accuracy structure prediction of difficult targets such as orphan proteins and hypervariable antibody loops. GhostFold consistently matches or exceeds the performance of MSA-based and language model-based structure predictors while being computationally lightweight and independent of large sequence databases. Notably, we observe a decoupling of confidence metrics (e.g., pLDDT) from prediction accuracy when using pseudoMSAs, suggesting that AlphaFold2's internal confidence calibration is strongly influenced by the statistical properties of natural sequence alignments. These results establish that structure-guided synthetic MSAs can functionally substitute for evolutionary data, offering a scalable and generalizable solution to one of the central limitations in computational structural biology. GhostFold represents a shift from passive data mining to intelligent sequence synthesis, redefining how structural priors are encoded in deep learning-based protein folding. ### Competing Interest Statement BB is an equity shareholder in Infinimmune and a member of their Scientific Advisory Board. National Institute of Allergy and Infectious Diseases, P01-AI177683, U19-AI135995, R01-AI171438, P30-AI036214, UM1-AI144462 James B. Pendleton Charitable Trust, https://ror.org/04tw4j633

GhostFold: Accurate protein structure prediction using structure-constrained synthetic coevolutionary signals | bioRxiv https://www.biorxiv.org/content/10.1101/2025.10.13.682177v1?rss=1