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A long-awaited taxogenomic investigation of the family Halomonadaceae

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The diversity and evolution of microbial dissimilatory phosphite oxidation

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Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses

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A universe of human gut-derived bacterial prophages: unveiling the hidden viral players in intestinal microecology

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Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species

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A New Gene Family Diagnostic for Intracellular Biomineralization of Amorphous Ca Carbonates by Cyanobacteria

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A Survey on Antimicrobial Resistance Genes of Frequently Used Probiotic Bacteria, 1901 to 2022

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Mycobacteriaceae Mineralizes Micropolyethylene in Riverine Ecosystems.

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Metagenomics combined with activity-based proteomics point to gut bacterial enzymes that reactivate mycophenolate

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Structure and function of virion RNA polymerase of a crAss-like phage

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Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution

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Fast and accurate metagenotyping of the human gut microbiome with GT-Pro

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Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut

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The evolution and spread of sulfur cycling enzymes reflect the redox state of the early Earth

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Anaerobic Degradation of Aromatic and Aliphatic Biodegradable Plastics: Potential Mechanisms and Pathways

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Eukaryotic genomes from a global metagenomic dataset illuminate trophic modes and biogeography of ocean plankton

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Gut microbiome function and composition in infants from rural Kenya and association with human milk oligosaccharides

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Metagenomic Sequencing Reveals that High-Grain Feeding Alters the Composition and Metabolism of Cecal Microbiota and Induces Cecal Mucosal Injury in Sheep

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Toward a health-associated core keystone index for the human gut microbiome

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Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes

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Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes

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Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor

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Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor

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Living to the High Extreme: Unraveling the Composition, Structure, and Functional Insights of Bacterial Communities Thriving in the Arsenic-Rich Salar de Huasco Altiplanic Ecosystem

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Metabolic strategies shared by basement residents of the lost City hydrothermal field

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Subspecies-level genome comparison of Lactobacillus delbrueckii

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Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases

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Semantic design of functional de novo genes from a genomic language model

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Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan

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Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms

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Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome

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Saccharibacteria harness light energy using type-1 rhodopsins that may rely on retinal sourced from microbial hosts

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A widespread group of large plasmids in methanotrophic Methanoperedens archaea

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Genomic and phenotypic evolution of nematode-infecting microsporidia

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Effects of Co-culture on Improved Productivity and Bioresource for Microalgal Biomass Using the Floc-Forming Bacteria Melaminivora Jejuensis

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Genomic convergence between Akkermansia muciniphila in different mammalian hosts

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Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics

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No ancient DNA damage in actinobacteria from the neanderthal bone

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Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution

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Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut

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Evolutionary development and co‐phylogeny of primate‐associated bifidobacteria

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Vibrio parahaemolyticus T6SS2 effector repertoires

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Nicotinamide Riboside-Conditioned Microbiota Deflects High-Fat Diet-Induced Weight Gain in Mice

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Comparative Genomics and Physiology of Akkermansia muciniphila Isolates from Human Intestine Reveal Specialized Mucosal Adaptation

Ouwerkerk, J. P., Tytgat, H. L. P., Elzinga, J., Koehorst, J., Van den Abbeele, P., Henrissat, B., Gueimonde, M., Cani, P. D., Van de Wiele, T., Belzer, C., et al. (2022) · Microorganisms · doi:10.3390/microorganisms10081605 · Cited by 23

PHIStruct: improving phage–host interaction prediction at low sequence similarity settings using structure-aware protein embeddings

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Nitrate-driven anaerobic oxidation of ethane and butane by bacteria

Wu, M., Li, J., Lai, C.-Y., Leu, A. O., Sun, S., Gu, R., Erler, D. V., Liu, L., Li, L., Tyson, G. W., et al. (2024) · The ISME Journal · doi:10.1093/ismejo/wrad011 · Cited by 23

Sequencing effort dictates gene discovery in marine microbial metagenomes

Duarte, C. M., Ngugi, D. K., Alam, I., Pearman, J., Kamau, A., Eguiluz, V. M., Gojobori, T., Acinas, S. G., Gasol, J. M., Bajic, V., et al. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.15182 · Cited by 22

Deep embeddings to comprehend and visualize microbiome protein space

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Phylogenetic classification of ten novel species belonging to the genus Bifidobacterium comprising B. phasiani sp. nov., B. pongonis sp. nov., B. saguinibicoloris sp. nov., B. colobi sp. nov., B. simiiventris sp. nov., B. santillanense sp. nov., B. miconis sp. nov., B. amazonense sp. nov., B. pluvialisilvae sp. nov., and B. miconisargentati sp. nov

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Evidence of microbial reductive dehalogenation in deep-sea cold seeps and its implications for biogeochemical cycles

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Comparative metagenomics highlight a widespread pathway involved in catabolism of phosphonates in marine and terrestrial Serpentinizing ecosystems

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Comparative Genomics and Pan-Genome Driven Prediction of a Reduced Genome of Akkermansia muciniphila

Bukhari, S. A. R., Irfan, M., Ahmad, I., & Chen, L. (2022) · Microorganisms · doi:10.3390/microorganisms10071350 · Cited by 18

Comparative Transcriptomics Sheds Light on Remodeling of Gene Expression during Diazotrophy in the Thermophilic Methanogen Methanothermococcus thermolithotrophicus

Maslać, N., Sidhu, C., Teeling, H., & Wagner, T. (2022) · mBio · doi:10.1128/mbio.02443-22 · Cited by 18

Mriyaviruses: small relatives of giant viruses

Yutin, N., Mutz, P., Krupovic, M., & Koonin, E. V. (2024) · mBio · doi:10.1128/mbio.01035-24 · Cited by 18

A new microsporidian parasite, Ordospora pajunii sp. nov (Ordosporidae), of Daphnia longispina highlights the value of genomic data for delineating species boundaries

de Albuquerque, N. R. M., Haag, K. L., Fields, P. D., Cabalzar, A., Ben‐Ami, F., Pombert, J., & Ebert, D. (2022) · Journal of Eukaryotic Microbiology · doi:10.1111/jeu.12902 · Cited by 18

Comparative pangenomic analysis of predominant human vaginal lactobacilli strains towards population-specific adaptation: understanding the role in sustaining a balanced and healthy vaginal microenvironment

Bhattacharya, A., Das, S., Bhattacharjee, M. J., Mukherjee, A. K., & Khan, M. R. (2023) · BMC Genomics · doi:10.1186/s12864-023-09665-y · Cited by 16

Gut microbiota drives structural variation of exogenous probiotics to enhance colonization

Jiang, S., Huang, S., Zhang, Z., Ma, W., Han, Z., Song, Y., Huo, D., Cui, W., & Zhang, J. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2503371 · Cited by 15

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Schoelmerich, M. C., Ly, L., West-Roberts, J., Shi, L.-D., Shen, C., Malvankar, N. S., Taib, N., Gribaldo, S., Woodcroft, B. J., Schadt, C. W., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49548-8 · Cited by 14

Genome Sequence of Citrobacter Sp. Strain A1, a Dye-Degrading Bacterium

Chan, G. F., Gan, H. M., & Rashid, N. A. A. (2012) · Journal of Bacteriology · doi:10.1128/jb.01285-12 · Cited by 13

Resistome analysis of Escherichia coli isolates from layers in Hungary

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Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics

Arikawa, K., & Hosokawa, M. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.09.010 · Cited by 13

Genomic Characteristion of Opportunistic Pathogen Kluyvera Reveals a Novel CTX-M Subgroup

Yu, K., Huang, Z., Lan, R., Morris, J. G., Xiao, Y., Fu, S., Gao, H., Bai, X., Li, K., & Wang, D. (2023) · Microorganisms · doi:10.3390/microorganisms11122836 · Cited by 12

Enhanced terrestrial Fe(II) mobilization identified through a novel mechanism of microbially driven cave formation in Fe(III)-rich rocks

Parker, C. W., Senko, J. M., Auler, A. S., Sasowsky, I. D., Schulz, F., Woyke, T., & Barton, H. A. (2022) · Scientific Reports · doi:10.1038/s41598-022-21365-3 · Cited by 12

Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes

Meyer, B. H., Adam, P. S., Wagstaff, B. A., Kolyfetis, G. E., Probst, A. J., Albers, S. V., & Dorfmueller, H. C. (2022) · eLife · doi:10.7554/elife.67448 · Cited by 12

Genome-guided Investigation of Antibiotic Substances produced by Allosalinactinospora lopnorensis CA15-2T from Lop Nor region, China

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Short-Term Warming Induces Cyanobacterial Blooms and Antibiotic Resistance in Freshwater Lake, as Revealed by Metagenomics Analysis

Manna, B., Jay, E., Zhang, W., Zhou, X., Lyu, B., Thomas, G. M., & Singhal, N. (2024) · Water · doi:10.3390/w16182655 · Cited by 11

Semantic search using protein large language models detects class II microcins in bacterial genomes

Kulikova, A. V., Parker, J. K., Davies, B. W., & Wilke, C. O. (2024) · mSystems · doi:10.1128/msystems.01044-24 · Cited by 10

Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems

Johnson, S. R., Weigele, P. R., Fomenkov, A., Ge, A., Vincze, A., Eaglesham, J. B., Roberts, R. J., & Sun, Z. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkae1175 · Cited by 10

Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes

Kananen, K., Veseli, I., Quiles Pérez, C. J., Miller, S. E., Eren, A. M., & Bradley, P. H. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbaf039 · Cited by 10

Investigating antimicrobial resistance genes in probiotic products for companion animals

Kerek, A., Szabó, E., Szabó, Á., Papp, M., Bányai, K., Kardos, G., Kaszab, E., Bali, K., & Jerzsele, Á. (2024) · Frontiers in Veterinary Science · doi:10.3389/fvets.2024.1464351 · Cited by 9

Whole genome analysis and in vivo safety assessment of probiotic candidate Lactobacillus acidophilus L177

Liu, Y., Zheng, H., Wang, J., Xin, J., Wu, R., Zhang, J., Zhong, Z., Liu, H., Huang, Y., Fu, H., et al. (2025) · BMC Microbiology · doi:10.1186/s12866-025-04099-w · Cited by 9

A multi-modal deep language model for contaminant removal from metagenome-assembled genomes

Zou, B., Wang, J., Ding, Y., Zhang, Z., Huang, Y., Fang, X., Cheung, K. C., See, S., & Zhang, L. (2024) · Nature Machine Intelligence · doi:10.1038/s42256-024-00908-5 · Cited by 9

Protein language models uncover carbohydrate-active enzyme function in metagenomics

Thurimella, K., Mohamed, A. M. T., Li, C., Vatanen, T., Graham, D. B., Owens, R. M., La Rosa, S. L., Plichta, D. R., Bacallado, S., & Xavier, R. J. (2025) · BMC Bioinformatics · doi:10.1186/s12859-025-06286-y · Cited by 9

A cascade of sulfur transferases delivers sulfur to the sulfur‐oxidizing heterodisulfide reductase‐like complex

Tanabe, T. S., Bach, E., D'Ermo, G., Mohr, M. G., Hager, N., Pfeiffer, N., Guiral, M., & Dahl, C. (2024) · Protein Science · doi:10.1002/pro.5014 · Cited by 9

Comprehensive Metagenomic Analysis of Veterinary Probiotics in Broiler Chickens

Kerek, Á., Román, I. L., Szabó, Á., Papp, M., Bányai, K., Kardos, G., Kaszab, E., Bali, K., Makrai, L., & Jerzsele, Á. (2024) · Animals · doi:10.3390/ani14131927 · Cited by 8

Whole Genome Sequencing and Extracellular Metabolite Profiling of Lactiplantibacillus plantarum FRT4: Insights into Probiotic Functionality

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Several independent adaptations of archaea to hypersaline environments

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Staged microbial consortium valorizes cattle manure wastewater and promotes maize growth

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