ISME Journal

Article	Citations
Polymerization of dietary fructans differentially affects interactions among intestinal microbiota of colitis mice	250
Resurrection of a diatom after 7000 years from anoxic Baltic Sea sediment	235
Genome diversification of symbiotic fungi in beetle-fungus mutualistic symbioses	187
Strain identity effects contribute more to Pseudomonas community functioning than strain interactions	176
Copper stress shapes the dynamic behavior of amoebae and their associated bacteria	160
Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes	156
Complex extracellular biology drives surface competition during colony expansion in Bacillus subtilis	150
Bacterial growth and environmental adaptation via thiamine biosynthesis and thiamine-mediated metabolic interactions	144
Growth rate is a dominant factor predicting the rhizosphere effect	135
Long-term climate establishes functional legacies by altering microbial traits	128
Plankton community changes during the last 124 000 years in the subarctic Bering Sea derived from sedimentary ancient DNA	127
Staphylococcus epidermidis bacteriocin A37 kills natural competitors with a unique mechanism of action	122
Aerobic methylation of hydrogen sulfide to dimethylsulfide in diverse microorganisms and environments	121
Probiotic model for studying rhizosphere interactions of root exudates and the functional microbiome	117
Priority effects shape the structure of infant-typeBifidobacteriumcommunities on human milk oligosaccharides	109
Endosymbiont Tremblaya phenacola influences the reproduction of cotton mealybugs by regulating the mechanistic target of rapamycin pathway	108
Linking methanotroph phenotypes to genotypes using a simple spatially resolved model ecosystem	106
Correction to: Internal carbon recycling by heterotrophic prokaryotes compensates for mismatches between phytoplankton production and heterotrophic consumption	101
Conditions for the spread of CRISPR-Cas immune systems into bacterial populations	100
Resource partitioning and amino acid assimilation in a terrestrial geothermal spring	99
Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits	99
Soil minerals affect taxon-specific bacterial growth	98
Nitrogen fixation and diazotroph diversity in groundwater systems	96
Heterotrophic nitrification by Alcaligenes faecalis links organic and inorganic nitrogen metabolism	92
Symbiotic bacteria and fungi proliferate in diapause and may enhance overwintering survival in a solitary bee	92

Metabolic resource overlap impacts competition among phyllosphere bacteria	91
Correlating phylogenetic and functional diversity of the nod-free but nodulating Bradyrhizobium phylogroup	84
Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments	81
Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron	80
Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery	79
Correction to 29 articles due to inaccurate manuscript submission dates	79
Bacteria of the order Burkholderiales are original environmental hosts of type II trimethoprim resistance genes (dfrB)	76
Substrate control of sulphur utilisation and microbial stoichiometry in soil: Results of 13C, 15N, 14C, and 35S quad labelling	74
Ecological dynamics of the gut microbiome in response to dietary fiber	74
Rapid growth rate responses of terrestrial bacteria to field warming on the Antarctic Peninsula	74
Correction to: Hypervirulent Klebsiella pneumoniae employs genomic island encoded toxins against bacterial competitors in the gut	73
Marine phytoplankton downregulate core photosynthesis and carbon storage genes upon rapid mixed layer shallowing	73
Siderophores and competition for iron govern myxobacterial predation dynamics	73
Host-specific viral predation network on coral reefs	72
Genome-resolved metaproteogenomic and nanosolid characterization of an inactive vent chimney densely colonized by enigmatic DPANN archaea	72
Declines in ice cover are accompanied by light limitation responses and community change in freshwater diatoms	71
Ecological significance of extracellular vesicles in modulating host-virus interactions during algal blooms	71
Trophic modulation of endophytes by rhizosphere protists	69
Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments	69
Correction: Genomic insights from Monoglobus pectinilyticus: a pectin-degrading specialist bacterium in the human colon	65
Algae-fungi symbioses and bacteria-fungi co-exclusion drive tree species-specific differences in canopy bark microbiomes	65
Entomopathogenic pseudomonads can share an insect host with entomopathogenic nematodes and their mutualistic bacteria	62
Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion	62
Bacterial adenine cross-feeding stems from a purine salvage bottleneck	61
Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism	59
Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders	59
Rhizobium determinants of rhizosphere persistence and root colonization	59
Evolutionary history of tyrosine-supplementing endosymbionts in pollen-feeding beetles	57
Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health	56
Divergent marine anaerobic ciliates harbor closely related Methanocorpusculum endosymbionts	55
Chlamydiae as symbionts of photosynthetic dinoflagellates	55
Interplay between particle size and microbial ecology in the gut microbiome	54
Protist predation promotes antimicrobial resistance spread through antagonistic microbiome interactions	53
Impact of timing on the invasion of synthetic bacterial communities	53
Methanogenic symbionts of anaerobic ciliates are host and habitat specific	53
Gut microbiota carbon and sulfur metabolisms support Salmonella infections	52
Ecological success of extreme halophiles subjected to recurrent osmotic disturbances is primarily driven by congeneric species replacement	51
Co-existence of AMF with different putative MAT-alleles induces genes homologous to those involved in mating in other fungi: a reply to Malar et al.	50
First come, first served: superinfection exclusion in Deformed wing virus is dependent upon sequence identity and not the order of virus acquisition	49
Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake	49
Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils	49
Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients	49
Cell surface carbohydrates of symbiotic dinoflagellates and their role in the establishment of cnidarian–dinoflagellate symbiosis	48
Spatial separation of ribosomes and DNA in Asgard archaeal cells	48
Mcr-dependent methanogenesis in Archaeoglobaceae enriched from a terrestrial hot spring	48
Maximum antigen diversification in a lyme bacterial population and evolutionary strategies to overcome pathogen diversity	48
Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil	47
Frequency of change determines effectiveness of microbial response strategies	47
Well-hidden methanogenesis in deep, organic-rich sediments of Guaymas Basin	47
Bacterial–fungal interactions promote parallel evolution of global transcriptional regulators in a widespread Staphylococcus species	47

Functional conservation of microbial communities determines composition predictability in anaerobic digestion	47
Single cell dynamics and nitrogen transformations in the chain forming diatom Chaetoceros affinis	46
Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics	46
Human milk oligosaccharides modify the strength of priority effects in the Bifidobacterium community assembly during infancy	45
CRISPR-Cas in Pseudomonas aeruginosa provides transient population-level immunity against high phage exposures	45
Endosymbionts modulate virus effects on aphid-plant interactions	45
Suppression of the insect cuticular microbiomes by a fungal defensin to facilitate parasite infection	44
Dynamic nitrogen fixation in an aerobic endophyte of Populus	44
Cyanophages from a less virulent clade dominate over their sister clade in global oceans	44
Isolation of a widespread giant virus implicated in cryptophyte bloom collapse	44
Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates	43
Mortality by ribosomal sequencing (MoRS) provides a window into taxon-specific cell lysis	43
Ecosystem size-induced environmental fluctuations affect the temporal dynamics of community assembly mechanisms	43
The overlooked role of a biotin precursor for marine bacteria - desthiobiotin as an escape route for biotin auxotrophy	43
Microbial carbon, sulfur, iron, and nitrogen cycling linked to the potential remediation of a meromictic acidic pit lake	42
Marine bacteroidetes use a conserved enzymatic cascade to digest diatom β-mannan	41
Localized coevolution between microbial predator and prey alters community-wide gene expression and ecosystem function	41
Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa	41
Thermal acclimation of methanotrophs from the genusMethylobacter	41
Correction to: Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth	40
Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae)	40
Predation increases multiple components of microbial diversity in activated sludge communities	40
Heat stress reduces the contribution of diazotrophs to coral holobiont nitrogen cycling	40
Correction to: Millimeter-scale vertical partitioning of nitrogen cycling in hypersaline mats reveals prominence of genes encoding multi-heme and prismane proteins	39
Unexpected complexity of the ammonia monooxygenase in archaea	39
Niche differentiation of sulfur-oxidizing bacteria (SUP05) in submarine hydrothermal plumes	39
Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth	39
Glycoside hydrolase from the GH76 family indicates that marine Salegentibacter sp. Hel_I_6 consumes alpha-mannan from fungi	39
Taeniasis impacts human gut microbiome composition and function	39
Stainless steel corrosion via direct iron-to-microbe electron transfer by Geobacter species	38
Antibiotic-degrading resistance changes bacterial community structure via species-specific responses	38
Light-independent anaerobic microbial oxidation of manganese driven by an electrosyntrophic coculture	38
Distinct bacterial population dynamics and disease dissemination after biofilm dispersal and disassembly	38
Diversity and distribution of viruses inhabiting the deepest ocean on Earth	38
Bacterial chemolithoautotrophy in ultramafic plumes along the Mid-Atlantic Ridge	38
Role of the flagellar hook in the structural development and antibiotic tolerance of Pseudomonas aeruginosa biofilms	38
High speciation rate of niche specialists in hot springs	38
Verrucomicrobial methanotrophs grow on diverse C3 compounds and use a homolog of particulate methane monooxygenase to oxidize acetone	38
SLC24A-mediated calcium exchange as an indispensable component of the diatom cell density-driven signaling pathway	38
Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants	37
Plastoquinone synthesis inhibition by tetrabromo biphenyldiol as a widespread algicidal mechanism of marine bacteria	37
Lytic and temperate phage naturally coexist in a dynamic population model	37
Community context matters for bacteria-phage ecology and evolution	37
Genome-wide screen of genetic determinants that govern Escherichia coli growth and persistence in lake water	37
Mutualism promotes insect fitness by fungal nutrient compensation and facilitates fungus propagation by mediating insect oviposition preference	37
Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system	36
Methylotrophic methanogens and bacteria synergistically demethylate dimethylarsenate in paddy soil and alleviate rice straighthead disease	36
Honey bee symbiont buffers larvae against nutritional stress and supplements lysine	36
Lysogenic bacteriophages encoding arsenic resistance determinants promote bacterial community adaptation to arsenic toxicity	36
Hyphosphere microorganisms facilitate hyphal spreading and root colonization of plant symbiotic fungus in ammonium-enriched soil	36
Decreased efficacy of antimicrobial agents in a polymicrobial environment	36
Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium	36
Dietary intake of enrofloxacin promotes the spread of antibiotic resistance from food to simulated human gut	36
Microbial metabolomic responses to changes in temperature and salinity along the western Antarctic Peninsula	36
Gastric acid and escape to systemic circulation represent major bottlenecks to host infection by Citrobacter rodentium	35
Protistan predation selects for antibiotic resistance in soil bacterial communities	35
Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability	35
Convergent evolution of a labile nutritional symbiosis in ants	35
Oxytetracycline and heavy metals promote the migration of resistance genes in the intestinal microbiome by plasmid transfer	35
Macroecological distributions of gene variants highlight the functional organization of soil microbial systems	35
Progress and challenges in exploring aquatic microbial communities using non-targeted metabolomics	34
Active predation, phylogenetic diversity, and global prevalence of myxobacteria in wastewater treatment plants	34
Phages in the infant gut: a framework for virome development during early life	34
Life history strategies among soil bacteria—dichotomy for few, continuum for many	34
Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species	34
Increased genetic diversity loss and genetic differentiation in a model marine diatom adapted to ocean warming compared to high CO2	33
Interspecific competition can drive plasmid loss from a focal species in a microbial community	33
Intestinal persistence of Bifidobacterium infantis is determined by interaction of host genetics and antibiotic exposure	33
Strong segregation promotes self-destructive cooperation	33
Microbial invasion of a toxic medium is facilitated by a resident community but inhibited as the community co-evolves	33
Ecological relevance of flagellar motility in soil bacterial communities	33
Anaerobic hexadecane degradation by a thermophilic Hadarchaeon from Guaymas Basin	33
Community composition and physiological plasticity control microbial carbon storage across natural and experimental soil fertility gradients	33
In vivo evolution of antimicrobial resistance in a biofilm model of Pseudomonas aeruginosa lung infection	33
Genome-centric investigation of bile acid metabolizing microbiota of dairy cows and associated diet-induced functional implications	32
Reduced trace gas oxidizers as a response to organic carbon availability linked to oligotrophs in desert fertile islands	32
Microbial controls over soil priming effects under chronic nitrogen and phosphorus additions in subtropical forests	32
Virus–pathogen interactions improve water quality along the Middle Route of the South-to-North Water Diversion Canal	32
Pulsed, continuous or somewhere in between? Resource dynamics matter in the optimisation of microbial communities	32
Proteomes of native and non-native symbionts reveal responses underpinning host-symbiont specificity in the cnidarian–dinoflagellate symbiosis	32

Syntrophic entanglements for propionate and acetate oxidation under thermophilic and high-ammonia conditions	32
Metagenome-derived virus-microbe ratios across ecosystems	32
Production of structurally diverse sphingolipids by anaerobic marine bacteria in the euxinic Black Sea water column	32
Selection of photosynthetic traits by turbulent mixing governs formation of cyanobacterial blooms in shallow eutrophic lakes	31
Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus	31
Genetic and species rearrangements in microbial consortia impact biodegradation potential	31
Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities	31
Aminolipids in bacterial membranes and the natural environment	31
Population differentiation of Rhodobacteraceae along with coral compartments	31
Flavonoid-attracted Aeromonas sp. from the Arabidopsis root microbiome enhances plant dehydration resistance	31
Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil	31
Heme cross-feeding can augment Staphylococcus aureus and Enterococcus faecalis dual species biofilms	31
Lysis of Escherichia coli by colicin Ib contributes to bacterial cross-feeding by releasing active β-galactosidase	31
Correction to: Anaerobic hydrocarbon biodegradation by alkylotrophic methanogens in deep oil reservoirs	31
Abiotic factors shape mosquito microbiomes that enhance host development	30
Enzyme promiscuity in natural environments: alkaline phosphatase in the ocean	30
Transportome remodeling of a symbiotic microalga inside a planktonic host	30
Pollutant profile complexity governs wastewater removal of recalcitrant pharmaceuticals	30
Microbiome science of human excrement composting	30
Pathobiont and symbiont contribute to microbiota homeostasis through Malpighian tubules–gut countercurrent flow in Bactrocera dorsalis	30
Correction to: Dispersal of microbes from grassland fire smoke to soils	30
Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment	30
Drivers and consequences of microbial community coalescence	29
Palmitoleic acid as a coordinating molecule between the invasive pinewood nematode and its newly associated fungi	29
Phylogenomic resolution of marine to freshwater dinoflagellate transitions	29
Bacterial type VI secretion system helps prevent cheating in microbial communities	29
Gut microbiota contribute to variations in honey bee foraging intensity	29
Catestatin selects for colonization of antimicrobial-resistant gut bacterial communities	29
Urea-based mutualistic transfer of nitrogen in biological soil crusts	29
Coevolution of marine phytoplankton and Alteromonas bacteria in response to pCO2 and coculture	29
Transitivity and intransitivity in soil bacterial networks	29
Led astray by 16S rRNA: phylogenomics reaffirms the monophyly of Methylobacterium and lack of support for Methylorubrum as a genus	29
Spatial sensing as a strategy for public goods regulation by gut microbes	29
Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean	28
Asgard ESCRT-III and VPS4 reveal conserved chromatin binding properties of the ESCRT machinery	28
Sulfoquinovose is a widespread organosulfur substrate for Roseobacter clade bacteria in the ocean	28
Intracellular common gardens reveal niche differentiation in transposable element community during bacterial adaptive evolution	28
Wide-ranging organic nitrogen diets of freshwater picocyanobacteria	28
Resistance evolution can disrupt antibiotic exposure protection through competitive exclusion of the protective species	28
Spatial organization of a soil cyanobacterium and its cyanosphere through GABA/Glu signaling to optimize mutualistic nitrogen fixation	28
Protozoal food vacuoles enhance transformation in Vibrio cholerae through SOS-regulated DNA integration	28
Niche partitioning of the ubiquitous and ecologically relevant NS5 marine group	28
Flavobacterial exudates disrupt cell cycle progression and metabolism of the diatom Thalassiosira pseudonana	28
Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis	28
Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies	28
Drivers and implications of distance decay differ for ectomycorrhizal and foliar endophytic fungi across an anciently fragmented landscape	27
Evolution of rhizobial symbiosis islands through insertion sequence-mediated deletion and duplication	27
Iron and sulfate reduction structure microbial communities in (sub-)Antarctic sediments	27
Correction: Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity	27
Population dynamics of microbial cross-feeding are determined by co-localization probabilities and cooperation-independent cheater growth	27
Wet-dry cycles protect surface-colonizing bacteria from major antibiotic classes	27
Functional genome-centric view of the CO-driven anaerobic microbiome	27
Virophage infection mode determines ecological and evolutionary changes in a host-virus-virophage system	27
Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds	27
Correction: Non-antibiotic pharmaceuticals enhance the transmission of exogenous antibiotic resistance genes through bacterial transformation	26
Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane	26
Conversion of marginal land into switchgrass conditionally accrues soil carbon but reduces methane consumption	26
Correction: Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus	26
Spatial regulation of cell motility and its fitness effect in a surface-attached bacterial community	26
Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef	26
Correction to: Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks	26
Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom	26
Catabolic protein degradation in marine sediments confined to distinct archaea	25
Correction: Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria	25
Whole genome sequences reveal the Xanthomonas perforans population is shaped by the tomato production system	25
Harnessing solar power: photoautotrophy supplements the diet of a low-light dwelling sponge	25
Scarless excision of an insertion sequence restores capsule production and virulence in Acinetobacter baumannii	25
Correction: Lysogenic bacteriophages encoding arsenic resistance determinants promote bacterial community adaptation to arsenic toxicity	25
Active lithoautotrophic and methane-oxidizing microbial community in an anoxic, sub-zero, and hypersaline High Arctic spring	25
Water-driven microbial nitrogen transformations in biological soil crusts causing atmospheric nitrous acid and nitric oxide emissions	25
Motility mediates satellite formation in confined biofilms	24
Distinct microbial hydrogen and reductant disposal pathways explain interbreed variations in ruminant methane yield	24
Pleomorphic viruses establish stable relationship with marine hyperthermophilic archaea	24
Bacteria use a catabolic patchwork pathway of apparently recent origin for degradation of the synthetic buffer compound TRIS	24
Microorganisms oxidize glucose through distinct pathways in permeable and cohesive sediments	24
Rhizoviticin is an alphaproteobacterial tailocin that mediates biocontrol of grapevine crown gall disease	24
Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities	24
Climate acts as an environmental filter to plant pathogens	24
Adaptation strategies of giant viruses to low-temperature marine ecosystems	23
Lineage-specific energy and carbon metabolism of sponge symbionts and contributions to the host carbon pool	23
Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates	23
Scallop-bacteria symbiosis from the deep sea reveals strong genomic coupling in the absence of cellular integration	23
Divergent molecular strategies drive evolutionary adaptation to competitive fitness in biofilm formation	23
Metagenomic time series reveals a Western English Channel viral community dominated by members with strong seasonal signals	23
Taxonomic and functional stability overrules seasonality in polar benthic microbiomes	23
Diurnal transcriptional variation is reduced in a nitrogen-fixing diatom endosymbiont	23
Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay	23
Hidden genomic diversity drives niche partitioning in a cosmopolitan eukaryotic picophytoplankton	23
Globally distributed bacteriophage genomes reveal mechanisms of tripartite phage–bacteria–coral interactions	23
Large attachment organelle mediates interaction between Nanobdellota archaeon YN1 and its host	23
Active prophages in coral-associated Halomonas capable of lateral transduction	23
Idiosyncratic genome evolution of the thermophilic cyanobacterium Synechococcus at the limits of phototrophy	23
Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing	22
Humic acid-dependent respiratory growth of Methanosarcina acetivorans involves pyrroloquinoline quinone	22
Hot spring distribution and survival mechanisms of thermophilic comammox Nitrospira	22