ISME Journal

(The TQCC of ISME Journal is 28. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 500 papers]. The publications cover those that have been published in the past four years, i.e., from 2019-09-01 to 2023-09-01.)
Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China400
Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change350
Environmental stress destabilizes microbial networks292
Long-term nutrient inputs shift soil microbial functional profiles of phosphorus cycling in diverse agroecosystems211
Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem184
Erosion reduces soil microbial diversity, network complexity and multifunctionality183
Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae180
Chlorine disinfection promotes the exchange of antibiotic resistance genes across bacterial genera by natural transformation164
Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease155
Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment151
Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining142
Gut microbiota structure differs between honeybees in winter and summer142
Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt120
Soil microbial diversity–biomass relationships are driven by soil carbon content across global biomes119
Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean119
Niche differentiation is spatially and temporally regulated in the rhizosphere116
Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands116
Non-antibiotic pharmaceuticals enhance the transmission of exogenous antibiotic resistance genes through bacterial transformation116
Spatiotemporal dynamics of the archaeal community in coastal sediments: assembly process and co-occurrence relationship115
Phage-specific metabolic reprogramming of virocells112
Nonnutritive sweeteners can promote the dissemination of antibiotic resistance through conjugative gene transfer106
Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life101
Novel syntrophic bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics99
Ecology and evolution of antimicrobial resistance in bacterial communities97
Soil plastispheres as hotspots of antibiotic resistance genes and potential pathogens96
Stainless steel corrosion via direct iron-to-microbe electron transfer by Geobacter species90
Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification89
Syntrophus conductive pili demonstrate that common hydrogen-donating syntrophs can have a direct electron transfer option88
The planktonic protist interactome: where do we stand after a century of research?88
Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere88
Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation87
Comparative genomics reveals insights into cyanobacterial evolution and habitat adaptation84
Down to the bone: the role of overlooked endolithic microbiomes in reef coral health83
Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions83
Open challenges for microbial network construction and analysis82
Environmental heterogeneity determines the ecological processes that govern bacterial metacommunity assembly in a floodplain river system81
Chlorine disinfection facilitates natural transformation through ROS-mediated oxidative stress81
Wolbachia supplement biotin and riboflavin to enhance reproduction in planthoppers80
Comammox Nitrospira within the Yangtze River continuum: community, biogeography, and ecological drivers80
Air pollution could drive global dissemination of antibiotic resistance genes79
Characterization of a sponge microbiome using an integrative genome-centric approach78
Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments77
High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant77
Extremophilic nitrite-oxidizing Chloroflexi from Yellowstone hot springs77
The gut microbiota contributes to the development of Staphylococcus aureus-induced mastitis in mice77
Novel probiotic approach to counter Paenibacillus larvae infection in honey bees76
Achieving similar root microbiota composition in neighbouring plants through airborne signalling73
Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP)72
Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities72
Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity71
Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress69
Conserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungi68
A network approach to elucidate and prioritize microbial dark matter in microbial communities67
Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species67
The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography66
Salt-induced recruitment of specific root-associated bacterial consortium capable of enhancing plant adaptability to salt stress65
Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen65
Marked changes in diversity and relative activity of picoeukaryotes with depth in the world ocean65
Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids’ di-symbiotic systems65
Linking perturbations to temporal changes in diversity, stability, and compositions of neonatal calf gut microbiota: prediction of diarrhea65
Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy64
Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome64
Island biogeography of soil bacteria and fungi: similar patterns, but different mechanisms64
A novel bacterial thiosulfate oxidation pathway provides a new clue about the formation of zero-valent sulfur in deep sea63
Increasing flavonoid concentrations in root exudates enhance associations between arbuscular mycorrhizal fungi and an invasive plant63
Engineering rhizobacteria for sustainable agriculture62
Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere62
Prokaryotic taxonomy and nomenclature in the age of big sequence data62
“Candidatus Dechloromonas phosphoritropha” and “Ca. D. phosphorivorans”, novel polyphosphate accumulating organisms abundant in wastewater treatment systems59
Natural diets promote retention of the native gut microbiota in captive rodents59
Heterotrophy in the earliest gut: a single-cell view of heterotrophic carbon and nitrogen assimilation in sponge-microbe symbioses59
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity58
Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem58
Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column58
The functional repertoire contained within the native microbiota of the model nematode Caenorhabditis elegans58
Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities58
The soil microbial food web revisited: Predatory myxobacteria as keystone taxa?57
Small phytoplankton dominate western North Atlantic biomass57
Drought and plant litter chemistry alter microbial gene expression and metabolite production57
Non-antibiotic pharmaceuticals promote the transmission of multidrug resistance plasmids through intra- and intergenera conjugation56
Active sulfur cycling in the terrestrial deep subsurface56
Candida albicans promotes tooth decay by inducing oral microbial dysbiosis56
Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo55
A genomic view of the microbiome of coral reef demosponges55
Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants54
Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil53
The relationship between fecal bile acids and microbiome community structure in pediatric Crohn’s disease53
Mercury methylation by metabolically versatile and cosmopolitan marine bacteria53
Life-history strategies of soil microbial communities in an arid ecosystem53
Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype53
The subgingival microbiome associated with periodontitis in type 2 diabetes mellitus52
Interspecies bacterial competition regulates community assembly in the C. elegans intestine51
Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments51
Host genetic effects upon the early gut microbiota in a bovine model with graduated spectrum of genetic variation51
Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters51
Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika50
Unraveling negative biotic interactions determining soil microbial community assembly and functioning50
Mixotrophy in marine picocyanobacteria: use of organic compounds by Prochlorococcus and Synechococcus50
Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions50
Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo 13C and 2H metabolic network mapping50
Unusual marine cyanobacteria/haptophyte symbiosis relies on N2 fixation even in N-rich environments50
Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs49
Niche-adaptation in plant-associated Bacteroidetes favours specialisation in organic phosphorus mineralisation48
Niche partitioning of methane-oxidizing bacteria along the oxygen–methane counter gradient of stratified lakes48
Coprophagy prevention alters microbiome, metabolism, neurochemistry, and cognitive behavior in a small mammal48
Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)48
Consequences of microbial diversity in forest nitrogen cycling: diverse ammonifiers and specialized ammonia oxidizers47
Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes47
Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles47
Groundwater cable bacteria conserve energy by sulfur disproportionation47
Artificial sweeteners stimulate horizontal transfer of extracellular antibiotic resistance genes through natural transformation47
Niche-based assembly of bacterial consortia on the diatom Thalassiosira rotula is stable and reproducible47
Social networks strongly predict the gut microbiota of wild mice46
Sustained RNA virome diversity in Antarctic penguins and their ticks46
Selective carbon sources influence the end products of microbial nitrate respiration46
Potential utilization of terrestrially derived dissolved organic matter by aquatic microbial communities in saline lakes46
Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups46
Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves45
Sucrose triggers a novel signaling cascade promoting Bacillus subtilis rhizosphere colonization45
Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations45
Mycelial network-mediated rhizobial dispersal enhances legume nodulation45
Intra-colony channels in E. coli function as a nutrient uptake system45
Microbial carrying capacity and carbon biomass of plastic marine debris45
CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa45
Relationships between nitrogen cycling microbial community abundance and composition reveal the indirect effect of soil pH on oak decline45
It does not always take two to tango: “Syntrophy” via hydrogen cycling in one bacterial cell43
Anaerobic ammonium oxidation is a major N-sink in aquifer systems around the world43
Iron competition triggers antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus43
Bridging the membrane lipid divide: bacteria of the FCB group superphylum have the potential to synthesize archaeal ether lipids43
Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea43
Inside out: microbiota dynamics during host-plant adaptation of whiteflies43
Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria42
Protists as catalyzers of microbial litter breakdown and carbon cycling at different temperature regimes42
Role of glucosyltransferase R in biofilm interactions between Streptococcus oralis and Candida albicans42
Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi42
Fungal communities decline with urbanization—more in air than in soil42
The effect of phage genetic diversity on bacterial resistance evolution42
Dark septate endophyte improves salt tolerance of native and invasive lineages of Phragmites australis42
High cell densities favor lysogeny: induction of an H20 prophage is repressed by quorum sensing and enhances biofilm formation in Vibrio anguillarum42
Seasonality of interactions between a plant virus and its host during persistent infection in a natural environment42
A large-scale assessment of lakes reveals a pervasive signal of land use on bacterial communities41
Fecal filtrate transplantation protects against necrotizing enterocolitis41
A role for gut microbiota in host niche differentiation41
Variable influences of soil and seed-associated bacterial communities on the assembly of seedling microbiomes41
Metagenomic and chemical characterization of soil cobalamin production41
Divergent symbiont communities determine the physiology and nutrition of a reef coral across a light-availability gradient40
Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira40
The thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV oxidizes subatmospheric H2 with a high-affinity, membrane-associated [NiFe] hydrogenase40
The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization40
Root-associated microorganisms reprogram plant life history along the growth–stress resistance tradeoff40
A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum40
Host specificity of microbiome assembly and its fitness effects in phytoplankton39
Bayesian modeling reveals host genetics associated with rumen microbiota jointly influence methane emission in dairy cows39
Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms39
Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling39
Benchmarking microbial growth rate predictions from metagenomes39
Plant communities mediate the interactive effects of invasion and drought on soil microbial communities39
Ecological succession in the vaginal microbiota during pregnancy and birth38
Solutions in microbiome engineering: prioritizing barriers to organism establishment38
Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients38
Intracellular symbionts drive sex ratio in the whitefly by facilitating fertilization and provisioning of B vitamins38
Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt38
Global ecotypes in the ubiquitous marine clade SAR8638
A phylogenetically novel cyanobacterium most closely related to Gloeobacter38
Burkholderia insecticola triggers midgut closure in the bean bug Riptortus pedestris to prevent secondary bacterial infections of midgut crypts37
Diversity and distribution of viruses inhabiting the deepest ocean on Earth37
Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation37
Intracellular amorphous Ca-carbonate and magnetite biomineralization by a magnetotactic bacterium affiliated to the Alphaproteobacteria37
Polysaccharide niche partitioning of distinct Polaribacter clades during North Sea spring algal blooms37
Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog37
Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber37
Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes36
The oxidation of hydrocarbons by diverse heterotrophic and mixotrophic bacteria that inhabit deep-sea hydrothermal ecosystems36
Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities36
Plant-microbe interactions in the phyllosphere: facing challenges of the anthropocene36
The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity36
Genomic, transcriptomic, and proteomic insights into the symbiosis of deep-sea tubeworm holobionts36
Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment35
Maize germplasm chronosequence shows crop breeding history impacts recruitment of the rhizosphere microbiome35
Inter-species interactions alter antibiotic efficacy in bacterial communities35
Temperature-dependent changes to host–parasite interactions alter the thermal performance of a bacterial host35
Transcriptome plasticity underlying plant root colonization and insect invasion by Pseudomonas protegens35
Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes35
A cosmopolitan fungal pathogen of dicots adopts an endophytic lifestyle on cereal crops and protects them from major fungal diseases35
Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection35
Microbial metabolism and necromass mediated fertilization effect on soil organic carbon after long-term community incubation in different climates35
The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition35
Evolutionary compromises in fungal fitness: hydrophobins can hinder the adverse dispersal of conidiospores and challenge their survival35
Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow34
Forest tree growth is linked to mycorrhizal fungal composition and function across Europe34
Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom34
Ammonia oxidation at pH 2.5 by a new gammaproteobacterial ammonia-oxidizing bacterium34
Electrogenic sulfide oxidation mediated by cable bacteria stimulates sulfate reduction in freshwater sediments34
Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway34
A mycovirus modulates the endophytic and pathogenic traits of a plant associated fungus34
Temporal and spatial dynamics in the apple flower microbiome in the presence of the phytopathogen Erwinia amylovora34
Compensatory mutations modulate the competitiveness and dynamics of plasmid-mediated colistin resistance in Escherichia coli clones34
In vitro interaction network of a synthetic gut bacterial community34
Synthetic bacterial community derived from a desert rhizosphere confers salt stress resilience to tomato in the presence of a soil microbiome33
Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations33
Quorum sensing controls persistence, resuscitation, and virulence of Legionella subpopulations in biofilms33
Multi-omic meta-analysis identifies functional signatures of airway microbiome in chronic obstructive pulmonary disease33
Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment33
Metabolic potentials of archaeal lineages resolved from metagenomes of deep Costa Rica sediments33
A widely distributed hydrogenase oxidises atmospheric H2 during bacterial growth33
Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage33
A symbiotic nutrient exchange within the cyanosphere microbiome of the biocrust cyanobacterium, Microcoleus vaginatus33
Decline in symbiont-dependent host detoxification metabolism contributes to increased insecticide susceptibility of insects under high temperature33
Desulfurivibrio spp. mediate sulfur-oxidation coupled to Sb(V) reduction, a novel biogeochemical process32
Light exposure mediates circadian rhythms of rhizosphere microbial communities32
Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales32
Trophic cooperation promotes bacterial survival of Staphylococcus aureus and Pseudomonas aeruginosa32
Global distribution of a chlorophyll f cyanobacterial marker32
T6SS secretes an LPS-binding effector to recruit OMVs for exploitative competition and horizontal gene transfer32
Lytic bacteriophage have diverse indirect effects in a synthetic cross-feeding community32
Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient32
Biotin provisioning by horizontally transferred genes from bacteria confers animal fitness benefits32
Fungal foraging behaviour and hyphal space exploration in micro-structured Soil Chips32
Production of ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces species31
Organic nitrogen utilisation by an arbuscular mycorrhizal fungus is mediated by specific soil bacteria and a protist31
Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline31
Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health31
The microbiome of alpine snow algae shows a specific inter-kingdom connectivity and algae-bacteria interactions with supportive capacities31
Host genetics exerts lifelong effects upon hindgut microbiota and its association with bovine growth and immunity31
The CRISPR-Cas systems were selectively inactivated during evolution of Bacillus cereus group for adaptation to diverse environments31
Temporal tracking of quantum-dot apatite across in vitro mycorrhizal networks shows how host demand can influence fungal nutrient transfer strategies31
Anaerobic metabolism of Foraminifera thriving below the seafloor30
Cable bacteria extend the impacts of elevated dissolved oxygen into anoxic sediments30
Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation30
Insights into the dynamics between viruses and their hosts in a hot spring microbial mat30
Microbial storage and its implications for soil ecology30
Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents30
Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes30
A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances30
Small changes in rhizosphere microbiome composition predict disease outcomes earlier than pathogen density variations30
Diversity and biogeography of SAR11 bacteria from the Arctic Ocean29
Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean29
Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome29
Biodiversity of protists and nematodes in the wild nonhuman primate gut29
Direct quantification of ecological drift at the population level in synthetic bacterial communities29
Anthropogenic dissolved organic carbon and marine microbiomes29
New insights into the distributions of nitrogen fixation and diazotrophs revealed by high-resolution sensing and sampling methods29
Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire29
Recovery of fen peatland microbiomes and predicted functional profiles after rewetting28
Diverse coral reef invertebrates exhibit patterns of phylosymbiosis28
Human gut-microbiome-derived propionate coordinates proteasomal degradation via HECTD2 upregulation to target EHMT2 in colorectal cancer28
Land-use change has host-specific influences on avian gut microbiomes28
Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment28
Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO2, but strongly affected by drought28
Symbiont replacements reset the co-evolutionary relationship between insects and their heritable bacteria28