Microbiome

Article	Citations
Microbiome definition re-visited: old concepts and new challenges	853
Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank	478
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences	474
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses	434
Review: microbial transformations of human bile acids	285
Gut microbiota from green tea polyphenol-dosed mice improves intestinal epithelial homeostasis and ameliorates experimental colitis	261
Earth microbial co-occurrence network reveals interconnection pattern across microbiomes	239
Specialized metabolic functions of keystone taxa sustain soil microbiome stability	212
Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity	205
Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir	191
Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens	182
Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression	176
VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition	173
METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks	167
Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance	166
Plant developmental stage drives the differentiation in ecological role of the maize microbiome	164
Fecal microbiota transplantation protects rotenone-induced Parkinson’s disease mice via suppressing inflammation mediated by the lipopolysaccharide-TLR4 signaling pathway through the microbiota-gut-br	161
Inference-based accuracy of metagenome prediction tools varies across sample types and functional categories	161
Disease-induced changes in plant microbiome assembly and functional adaptation	157
Disentangling the mechanisms shaping the surface ocean microbiota	153
Using soil bacterial communities to predict physico-chemical variables and soil quality	139
Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2	139
Lung function and microbiota diversity in cystic fibrosis	136
Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients	131
β-glucan attenuates cognitive impairment via the gut-brain axis in diet-induced obese mice	125

Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste	120
Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes	120
Rhizosphere community selection reveals bacteria associated with reduced root disease	112
Intestinal microbiota shapes gut physiology and regulates enteric neurons and glia	111
Gut microbiome composition differences among breeds impact feed efficiency in swine	110
Gut microbiota-derived indole 3-propionic acid protects against radiation toxicity via retaining acyl-CoA-binding protein	110
Direct impact of commonly used dietary emulsifiers on human gut microbiota	110
An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants	108
From gut microbiota to host appetite: gut microbiota-derived metabolites as key regulators	107
MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics	106
Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain	105
Gut microbiota-derived inosine from dietary barley leaf supplementation attenuates colitis through PPARγ signaling activation	102
Thousands of previously unknown phages discovered in whole-community human gut metagenomes	101
Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula	100
Prevotella copri increases fat accumulation in pigs fed with formula diets	99
Challenges in exploring and manipulating the human skin microbiome	99
Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas	99
Host habitat is the major determinant of the gut microbiome of fish	98
Endometrial microbiota composition is associated with reproductive outcome in infertile patients	98
Parabacteroides produces acetate to alleviate heparanase-exacerbated acute pancreatitis through reducing neutrophil infiltration	98
TLR4 regulates RORγt+ regulatory T-cell responses and susceptibility to colon inflammation through interaction with Akkermansia muciniphila	97
Gut microbiota-derived propionate mediates the neuroprotective effect of osteocalcin in a mouse model of Parkinson’s disease	96
Effect of fecal microbiota transplantation on neurological restoration in a spinal cord injury mouse model: involvement of brain-gut axis	95
Novel insights into the genetically obese (ob/ob) and diabetic (db/db) mice: two sides of the same coin	93
The extracellular vesicle of gut microbial Paenalcaligenes hominis is a risk factor for vagus nerve-mediated cognitive impairment	93
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data	87
A fiber-deprived diet causes cognitive impairment and hippocampal microglia-mediated synaptic loss through the gut microbiota and metabolites	87
Important ecophysiological roles of non-dominant Actinobacteria in plant residue decomposition, especially in less fertile soils	86
Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice	86
Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers	84
A predatory myxobacterium controls cucumber Fusarium wilt by regulating the soil microbial community	83
Gut microbiota modulation with long-chain corn bran arabinoxylan in adults with overweight and obesity is linked to an individualized temporal increase in fecal propionate	81
A synthetic probiotic engineered for colorectal cancer therapy modulates gut microbiota	81
The microbiome and mosquito vectorial capacity: rich potential for discovery and translation	81
Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios	81
Identifying biases and their potential solutions in human microbiome studies	80
A simplified synthetic community rescues Astragalus mongholicus from root rot disease by activating plant-induced systemic resistance	78
The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases	77
Towards enhancing coral heat tolerance: a “microbiome transplantation” treatment using inoculations of homogenized coral tissues	76
Bacteroides thetaiotaomicron-derived outer membrane vesicles promote regulatory dendritic cell responses in health but not in inflammatory bowel disease	76
The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota	75
Bacteria pathogens drive host colonic epithelial cell promoter hypermethylation of tumor suppressor genes in colorectal cancer	75
Eicosapentaenoic and docosahexaenoic acids attenuate hyperglycemia through the microbiome-gut-organs axis in db/db mice	74
Protists as main indicators and determinants of plant performance	72
Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria	72
Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status	70
Mechanistic insights into the attenuation of intestinal inflammation and modulation of the gut microbiome by krill oil using in vitro and in vivo models	70
The gut microbiota regulates autism-like behavior by mediating vitamin B6 homeostasis in EphB6-deficient mice	69
Gut microbiome variation modulates the effects of dietary fiber on host metabolism	69
Lactobacillus murinus alleviate intestinal ischemia/reperfusion injury through promoting the release of interleukin-10 from M2 macrophages via Toll-like receptor 2 signaling	68

Iron status influences non-alcoholic fatty liver disease in obesity through the gut microbiome	68
Enhanced mutualistic symbiosis between soil phages and bacteria with elevated chromium-induced environmental stress	68
Lessons learned from the prenatal microbiome controversy	66
Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies	66
Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria	65
Spatial heterogeneity of bacterial colonization across different gut segments following inter-species microbiota transplantation	64
The human gut archaeome: identification of diverse haloarchaea in Korean subjects	64
Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities	64
Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions	64
Developing standards for the microbiome field	63
Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation	62
Regulation of blood–brain barrier integrity by microbiome-associated methylamines and cognition by trimethylamine N-oxide	62
Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis	62
Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems	60
Glacier ice archives nearly 15,000-year-old microbes and phages	59
Joint contributions of the gut microbiota and host genetics to feed efficiency in chickens	59
Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer	59
Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys	58
Depletion of acetate-producing bacteria from the gut microbiota facilitates cognitive impairment through the gut-brain neural mechanism in diabetic mice	58
Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing	58
Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants	58
Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing	57
Estimate of the sequenced proportion of the global prokaryotic genome	57
Diet, obesity, and the gut microbiome as determinants modulating metabolic outcomes in a non-human primate model	56
Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics	56
Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field	56
Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity	56
Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease	55
The phyllosphere microbiome shifts toward combating melanose pathogen	54
Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop	54
Multifaceted roles of flavonoids mediating plant-microbe interactions	54
Gut microbiota regulation of P-glycoprotein in the intestinal epithelium in maintenance of homeostasis	53
Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse	53
Genetic and metabolic links between the murine microbiome and memory	52
Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge	52
Active virus-host interactions at sub-freezing temperatures in Arctic peat soil	52
Ultra-accurate microbial amplicon sequencing with synthetic long reads	52
Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments	51
Holo-omics for deciphering plant-microbiome interactions	51
Gut microbiota-derived ursodeoxycholic acid from neonatal dairy calves improves intestinal homeostasis and colitis to attenuate extended-spectrum β-lactamase-producing enteroaggregative Escherichia co	51
The microbiota-gut-brain axis participates in chronic cerebral hypoperfusion by disrupting the metabolism of short-chain fatty acids	51
Perinatal environment shapes microbiota colonization and infant growth: impact on host response and intestinal function	51
Antibiotic-associated dysbiosis affects the ability of the gut microbiota to control intestinal inflammation upon fecal microbiota transplantation in experimental colitis models	51
Xylitol enhances synthesis of propionate in the colon via cross-feeding of gut microbiota	50
Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle	50
Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets	49
Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome	49
Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations	49
Dynamics of dark fermentation microbial communities in the light of lactate and butyrate production	48
Commensal microbe-derived acetate suppresses NAFLD/NASH development via hepatic FFAR2 signalling in mice	48
Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses	47
Ageing and rejuvenation models reveal changes in key microbial communities associated with healthy ageing	47
HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes	47
Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream	47
Reservoirs of antimicrobial resistance genes in retail raw milk	46
Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens	46
Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms	46
Gut dysbiosis promotes prostate cancer progression and docetaxel resistance via activating NF-κB-IL6-STAT3 axis	46
Gammaproteobacteria, a core taxon in the guts of soil fauna, are potential responders to environmental concentrations of soil pollutants	46
Expanding magnetic organelle biogenesis in the domain Bacteria	45
Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria	45
Associations between habitual diet, metabolic disease, and the gut microbiota using latent Dirichlet allocation	45
Gut bacterial ClpB-like gene function is associated with decreased body weight and a characteristic microbiota profile	44
Metabolite-based dietary supplementation in human type 1 diabetes is associated with microbiota and immune modulation	44
Host-microbiota interaction-mediated resistance to inflammatory bowel disease in pigs	44
Recent infection by Wolbachia alters microbial communities in wild Laodelphax striatellus populations	44
Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies	44
Characterization of the human skin resistome and identification of two microbiota cutotypes	43
Trophic interactions as determinants of the arbuscular mycorrhizal fungal community with cascading plant-promoting consequences	42
High-dose saccharin supplementation does not induce gut microbiota changes or glucose intolerance in healthy humans and mice	42
A philosophical perspective on the prenatal in utero microbiome debate	42
A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere	42
New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal	42
Skin microbiota analysis-inspired development of novel anti-infectives	41
Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer	41
Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques	41
A comprehensive evaluation of microbial differential abundance analysis methods: current status and potential solutions	41
The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut	41
Decoding the RNA viromes in rodent lungs provides new insight into the origin and evolutionary patterns of rodent-borne pathogens in Mainland Southeast Asia	40
Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts	40

Maternal gut microbes shape the early-life assembly of gut microbiota in passerine chicks via nests	40
Modulating gut microbiota in a mouse model of Graves’ orbitopathy and its impact on induced disease	40
Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial	40
Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity	40
Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms	40
Glutamic acid reshapes the plant microbiota to protect plants against pathogens	40
Topography of the respiratory tract bacterial microbiota in cattle	40
Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats	40
Polyamine metabolism links gut microbiota and testicular dysfunction	40
Understanding the host-microbe interactions using metabolic modeling	40
Depth-related variability in viral communities in highly stratified sulfidic mine tailings	39
Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites	39
Adaptive matching between phyllosphere bacteria and their tree hosts in a neotropical forest	39
Orally administered Odoribacter laneus improves glucose control and inflammatory profile in obese mice by depleting circulating succinate	39
Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection	39
Integrated meta-omics reveals new ruminal microbial features associated with feed efficiency in dairy cattle	38
Inhalable antibiotic resistomes emitted from hospitals: metagenomic insights into bacterial hosts, clinical relevance, and environmental risks	38
HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data	38
Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter	38
Isolation and characterization of diverse microbial representatives from the human skin microbiome	38
Development of fungal-mediated soil suppressiveness against Fusarium wilt disease via plant residue manipulation	38
The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge	38
A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes	38
Effects of caloric restriction on the gut microbiome are linked with immune senescence	37
Microbial dark matter filling the niche in hypersaline microbial mats	37
SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment	36
Urban wastewater bacterial communities assemble into seasonal steady states	36
Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation	36
Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements	36
Remodeling of the maternal gut microbiome during pregnancy is shaped by parity	36
Long-term effect of epigenetic modification in plant–microbe interactions: modification of DNA methylation induced by plant growth-promoting bacteria mediates promotion process	36
Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics	35
Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions	35
Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years	35
A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations	35
Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota	35
Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach	35
Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments	35
Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals	35
Gut microbiome mediates the protective effects of exercise after myocardial infarction	35
Post-translational regulation of autophagy is involved in intra-microbiome suppression of fungal pathogens	35
The plant microbiota signature of the Anthropocene as a challenge for microbiome research	34
The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes	34
The functional evolution of termite gut microbiota	34
Gut microbiota-derived metabolites mediate the neuroprotective effect of melatonin in cognitive impairment induced by sleep deprivation	34
The bacterial communities of Alaskan mosses and their contributions to N2-fixation	34
Plant domestication shapes rhizosphere microbiome assembly and metabolic functions	34
Microbial community characterization of shrimp survivors to AHPND challenge test treated with an effective shrimp probiotic (Vibrio diabolicus)	34
Indoor bacterial, fungal and viral species and functional genes in urban and rural schools in Shanxi Province, China–association with asthma, rhinitis and rhinoconjunctivitis in high school students	34
Cognitive behavioral therapy for irritable bowel syndrome induces bidirectional alterations in the brain-gut-microbiome axis associated with gastrointestinal symptom improvement	34
Vaginal microbiome-host interactions modeled in a human vagina-on-a-chip	34
Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes	34
Characterization of TMAO productivity from carnitine challenge facilitates personalized nutrition and microbiome signatures discovery	34
Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake	33
Investigating host-microbiome interactions by droplet based microfluidics	33
Genomic evidence for sulfur intermediates as new biogeochemical hubs in a model aquatic microbial ecosystem	33
Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh	33
Acquisition of oral microbiota is driven by environment, not host genetics	33
Signature changes in gut microbiome are associated with increased susceptibility to HIV-1 infection in MSM	33
Batch effects account for the main findings of an in utero human intestinal bacterial colonization study	33
Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes	33
Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity	32
Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses	32
Elucidating the role of the gut microbiota in the physiological effects of dietary fiber	32
Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA	32
Honey bee genetics shape the strain-level structure of gut microbiota in social transmission	32
SCAPP: an algorithm for improved plasmid assembly in metagenomes	32
PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes	32
Dietary calcium phosphate strongly impacts gut microbiome changes elicited by inulin and galacto-oligosaccharides consumption	32
Subcellular view of host–microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan–microbe symbiosis	32
Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community	32
The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation	31
Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome	31
Gut microbiota response to antibiotics is personalized and depends on baseline microbiota	31
Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale	31
Chicken jejunal microbiota improves growth performance by mitigating intestinal inflammation	31
Disruption of ruminal homeostasis by malnutrition involved in systemic ruminal microbiota-host interactions in a pregnant sheep model	30
Gut microbiota–derived metabolite 3-idoleacetic acid together with LPS induces IL-35+ B cell generation	30
Correction to: Microbiome definition re-visited: old concepts and new challenges	30
Lactobacillus reuteri tryptophan metabolism promotes host susceptibility to CNS autoimmunity	30
Accurate identification and quantification of commensal microbiota bound by host immunoglobulins	30
Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling	30
Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites	30
High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method	30
Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy	29
Polinton-like viruses are abundant in aquatic ecosystems	29
Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes	29
Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities	29
Synergistic action of the gut microbiota in environmental RNA interference in a leaf beetle	29
Xylan alleviates dietary fiber deprivation-induced dysbiosis by selectively promoting Bifidobacterium pseudocatenulatum in pigs	29
The diet rapidly and differentially affects the gut microbiota and host lipid mediators in a healthy population	29
Molecular repertoire of Deinococcus radiodurans after 1 year of exposure outside the International Space Station within the Tanpopo mission	29
Unmasking viral sequences by metagenomic next-generation sequencing in adult human blood samples during steroid-refractory/dependent graft-versus-host disease	29
Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome	29