Microbiome

Papers
(The median citation count of Microbiome is 11. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-05-01 to 2024-05-01.)
ArticleCitations
Microbiome definition re-visited: old concepts and new challenges876
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences489
Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank484
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses451
Review: microbial transformations of human bile acids294
Gut microbiota from green tea polyphenol-dosed mice improves intestinal epithelial homeostasis and ameliorates experimental colitis275
Earth microbial co-occurrence network reveals interconnection pattern across microbiomes241
Specialized metabolic functions of keystone taxa sustain soil microbiome stability216
Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir197
Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens191
VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition184
Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression180
METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks179
Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance172
Fecal microbiota transplantation protects rotenone-induced Parkinson’s disease mice via suppressing inflammation mediated by the lipopolysaccharide-TLR4 signaling pathway through the microbiota-gut-br171
Plant developmental stage drives the differentiation in ecological role of the maize microbiome168
Disease-induced changes in plant microbiome assembly and functional adaptation164
Using soil bacterial communities to predict physico-chemical variables and soil quality142
Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2140
Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients135
β-glucan attenuates cognitive impairment via the gut-brain axis in diet-induced obese mice130
Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste123
Rhizosphere community selection reveals bacteria associated with reduced root disease122
Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes121
Gut microbiome composition differences among breeds impact feed efficiency in swine115
Direct impact of commonly used dietary emulsifiers on human gut microbiota114
Intestinal microbiota shapes gut physiology and regulates enteric neurons and glia113
An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants112
Gut microbiota-derived indole 3-propionic acid protects against radiation toxicity via retaining acyl-CoA-binding protein112
Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain111
From gut microbiota to host appetite: gut microbiota-derived metabolites as key regulators108
Gut microbiota-derived inosine from dietary barley leaf supplementation attenuates colitis through PPARγ signaling activation104
Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula103
Challenges in exploring and manipulating the human skin microbiome103
Thousands of previously unknown phages discovered in whole-community human gut metagenomes102
Endometrial microbiota composition is associated with reproductive outcome in infertile patients101
TLR4 regulates RORγt+ regulatory T-cell responses and susceptibility to colon inflammation through interaction with Akkermansia muciniphila101
Host habitat is the major determinant of the gut microbiome of fish101
Parabacteroides produces acetate to alleviate heparanase-exacerbated acute pancreatitis through reducing neutrophil infiltration100
Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas100
Prevotella copri increases fat accumulation in pigs fed with formula diets99
Effect of fecal microbiota transplantation on neurological restoration in a spinal cord injury mouse model: involvement of brain-gut axis99
Gut microbiota-derived propionate mediates the neuroprotective effect of osteocalcin in a mouse model of Parkinson’s disease99
Novel insights into the genetically obese (ob/ob) and diabetic (db/db) mice: two sides of the same coin97
The extracellular vesicle of gut microbial Paenalcaligenes hominis is a risk factor for vagus nerve-mediated cognitive impairment96
A fiber-deprived diet causes cognitive impairment and hippocampal microglia-mediated synaptic loss through the gut microbiota and metabolites93
Important ecophysiological roles of non-dominant Actinobacteria in plant residue decomposition, especially in less fertile soils90
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data88
A simplified synthetic community rescues Astragalus mongholicus from root rot disease by activating plant-induced systemic resistance86
Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers85
A synthetic probiotic engineered for colorectal cancer therapy modulates gut microbiota84
Identifying biases and their potential solutions in human microbiome studies83
Gut microbiota modulation with long-chain corn bran arabinoxylan in adults with overweight and obesity is linked to an individualized temporal increase in fecal propionate83
The microbiome and mosquito vectorial capacity: rich potential for discovery and translation82
Bacteroides thetaiotaomicron-derived outer membrane vesicles promote regulatory dendritic cell responses in health but not in inflammatory bowel disease78
Towards enhancing coral heat tolerance: a “microbiome transplantation” treatment using inoculations of homogenized coral tissues78
The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases78
Bacteria pathogens drive host colonic epithelial cell promoter hypermethylation of tumor suppressor genes in colorectal cancer76
Eicosapentaenoic and docosahexaenoic acids attenuate hyperglycemia through the microbiome-gut-organs axis in db/db mice75
The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota75
Gut microbiome variation modulates the effects of dietary fiber on host metabolism75
Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria74
Protists as main indicators and determinants of plant performance72
The gut microbiota regulates autism-like behavior by mediating vitamin B6 homeostasis in EphB6-deficient mice71
Mechanistic insights into the attenuation of intestinal inflammation and modulation of the gut microbiome by krill oil using in vitro and in vivo models71
Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status71
Lactobacillus murinus alleviate intestinal ischemia/reperfusion injury through promoting the release of interleukin-10 from M2 macrophages via Toll-like receptor 2 signaling71
Enhanced mutualistic symbiosis between soil phages and bacteria with elevated chromium-induced environmental stress69
Iron status influences non-alcoholic fatty liver disease in obesity through the gut microbiome68
Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria67
Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities66
Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies66
Lessons learned from the prenatal microbiome controversy66
The human gut archaeome: identification of diverse haloarchaea in Korean subjects65
Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation65
Developing standards for the microbiome field64
Spatial heterogeneity of bacterial colonization across different gut segments following inter-species microbiota transplantation64
Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis63
Regulation of blood–brain barrier integrity by microbiome-associated methylamines and cognition by trimethylamine N-oxide63
Joint contributions of the gut microbiota and host genetics to feed efficiency in chickens61
Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing60
Depletion of acetate-producing bacteria from the gut microbiota facilitates cognitive impairment through the gut-brain neural mechanism in diabetic mice60
Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems60
Glacier ice archives nearly 15,000-year-old microbes and phages60
Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys59
Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer59
Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants59
Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing58
The phyllosphere microbiome shifts toward combating melanose pathogen58
Multifaceted roles of flavonoids mediating plant-microbe interactions57
The microbiota-gut-brain axis participates in chronic cerebral hypoperfusion by disrupting the metabolism of short-chain fatty acids57
Diet, obesity, and the gut microbiome as determinants modulating metabolic outcomes in a non-human primate model57
Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity57
Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field57
Estimate of the sequenced proportion of the global prokaryotic genome57
Gut microbiota-derived ursodeoxycholic acid from neonatal dairy calves improves intestinal homeostasis and colitis to attenuate extended-spectrum β-lactamase-producing enteroaggregative Escherichia co56
Antibiotic-associated dysbiosis affects the ability of the gut microbiota to control intestinal inflammation upon fecal microbiota transplantation in experimental colitis models55
Ultra-accurate microbial amplicon sequencing with synthetic long reads55
Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease55
Gut microbiota regulation of P-glycoprotein in the intestinal epithelium in maintenance of homeostasis55
Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge54
Commensal microbe-derived acetate suppresses NAFLD/NASH development via hepatic FFAR2 signalling in mice54
Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse54
Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments54
Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop53
Holo-omics for deciphering plant-microbiome interactions53
Active virus-host interactions at sub-freezing temperatures in Arctic peat soil52
Perinatal environment shapes microbiota colonization and infant growth: impact on host response and intestinal function52
Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies51
Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets50
Gut dysbiosis promotes prostate cancer progression and docetaxel resistance via activating NF-κB-IL6-STAT3 axis50
Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle50
Dynamics of dark fermentation microbial communities in the light of lactate and butyrate production50
Xylitol enhances synthesis of propionate in the colon via cross-feeding of gut microbiota50
Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome50
Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations50
HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes49
Ageing and rejuvenation models reveal changes in key microbial communities associated with healthy ageing49
Reservoirs of antimicrobial resistance genes in retail raw milk48
Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts48
Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens48
Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms47
Gammaproteobacteria, a core taxon in the guts of soil fauna, are potential responders to environmental concentrations of soil pollutants47
Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses47
Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream47
Expanding magnetic organelle biogenesis in the domain Bacteria46
The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut46
Host-microbiota interaction-mediated resistance to inflammatory bowel disease in pigs46
A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere46
Integrated meta-omics reveals new ruminal microbial features associated with feed efficiency in dairy cattle46
Metabolite-based dietary supplementation in human type 1 diabetes is associated with microbiota and immune modulation46
Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria45
Recent infection by Wolbachia alters microbial communities in wild Laodelphax striatellus populations45
New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal45
Associations between habitual diet, metabolic disease, and the gut microbiota using latent Dirichlet allocation45
Skin microbiota analysis-inspired development of novel anti-infectives45
Characterization of the human skin resistome and identification of two microbiota cutotypes44
Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats44
A comprehensive evaluation of microbial differential abundance analysis methods: current status and potential solutions44
High-dose saccharin supplementation does not induce gut microbiota changes or glucose intolerance in healthy humans and mice43
Polyamine metabolism links gut microbiota and testicular dysfunction43
A philosophical perspective on the prenatal in utero microbiome debate42
Modulating gut microbiota in a mouse model of Graves’ orbitopathy and its impact on induced disease42
Trophic interactions as determinants of the arbuscular mycorrhizal fungal community with cascading plant-promoting consequences42
Depth-related variability in viral communities in highly stratified sulfidic mine tailings42
Topography of the respiratory tract bacterial microbiota in cattle42
Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites42
Orally administered Odoribacter laneus improves glucose control and inflammatory profile in obese mice by depleting circulating succinate41
Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection41
Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer41
Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity41
Inhalable antibiotic resistomes emitted from hospitals: metagenomic insights into bacterial hosts, clinical relevance, and environmental risks41
Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial41
Decoding the RNA viromes in rodent lungs provides new insight into the origin and evolutionary patterns of rodent-borne pathogens in Mainland Southeast Asia41
Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques41
Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms40
Understanding the host-microbe interactions using metabolic modeling40
Effects of caloric restriction on the gut microbiome are linked with immune senescence40
Glutamic acid reshapes the plant microbiota to protect plants against pathogens40
Adaptive matching between phyllosphere bacteria and their tree hosts in a neotropical forest40
Maternal gut microbes shape the early-life assembly of gut microbiota in passerine chicks via nests40
The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge39
Gut microbiota-derived metabolites mediate the neuroprotective effect of melatonin in cognitive impairment induced by sleep deprivation39
Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake39
Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation38
Development of fungal-mediated soil suppressiveness against Fusarium wilt disease via plant residue manipulation38
HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data38
Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter38
A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes38
Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics38
Gut microbiome mediates the protective effects of exercise after myocardial infarction38
Urban wastewater bacterial communities assemble into seasonal steady states38
Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions37
Microbial dark matter filling the niche in hypersaline microbial mats37
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 students37
Plant domestication shapes rhizosphere microbiome assembly and metabolic functions37
The bacterial communities of Alaskan mosses and their contributions to N2-fixation37
Vaginal microbiome-host interactions modeled in a human vagina-on-a-chip37
Remodeling of the maternal gut microbiome during pregnancy is shaped by parity37
The functional evolution of termite gut microbiota37
Cognitive behavioral therapy for irritable bowel syndrome induces bidirectional alterations in the brain-gut-microbiome axis associated with gastrointestinal symptom improvement37
Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota36
Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements36
Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes36
SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment36
Long-term effect of epigenetic modification in plant–microbe interactions: modification of DNA methylation induced by plant growth-promoting bacteria mediates promotion process36
A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations36
The plant microbiota signature of the Anthropocene as a challenge for microbiome research36
Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments36
Post-translational regulation of autophagy is involved in intra-microbiome suppression of fungal pathogens36
Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach35
Microbial community characterization of shrimp survivors to AHPND challenge test treated with an effective shrimp probiotic (Vibrio diabolicus)35
Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals35
The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes35
Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes35
PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes35
Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years35
Honey bee genetics shape the strain-level structure of gut microbiota in social transmission35
Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity34
Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome34
Characterization of TMAO productivity from carnitine challenge facilitates personalized nutrition and microbiome signatures discovery34
Genomic evidence for sulfur intermediates as new biogeochemical hubs in a model aquatic microbial ecosystem34
Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA34
Dietary calcium phosphate strongly impacts gut microbiome changes elicited by inulin and galacto-oligosaccharides consumption34
Investigating host-microbiome interactions by droplet based microfluidics33
Chicken jejunal microbiota improves growth performance by mitigating intestinal inflammation33
SCAPP: an algorithm for improved plasmid assembly in metagenomes33
Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh33
Acquisition of oral microbiota is driven by environment, not host genetics33
Subcellular view of host–microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan–microbe symbiosis33
Batch effects account for the main findings of an in utero human intestinal bacterial colonization study33
Lactobacillus reuteri tryptophan metabolism promotes host susceptibility to CNS autoimmunity33
Signature changes in gut microbiome are associated with increased susceptibility to HIV-1 infection in MSM33
Gut microbiota response to antibiotics is personalized and depends on baseline microbiota32
Elucidating the role of the gut microbiota in the physiological effects of dietary fiber32
Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses32
Gut microbiota–derived metabolite 3-idoleacetic acid together with LPS induces IL-35+ B cell generation32
Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes32
Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community32
Correction to: Microbiome definition re-visited: old concepts and new challenges31
Synergistic action of the gut microbiota in environmental RNA interference in a leaf beetle31
Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling31
Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria31
Accurate identification and quantification of commensal microbiota bound by host immunoglobulins31
The diet rapidly and differentially affects the gut microbiota and host lipid mediators in a healthy population31
Bog ecosystems as a playground for plant–microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria31
Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale31
A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)30
Disruption of ruminal homeostasis by malnutrition involved in systemic ruminal microbiota-host interactions in a pregnant sheep model30
Unmasking viral sequences by metagenomic next-generation sequencing in adult human blood samples during steroid-refractory/dependent graft-versus-host disease30
Xylan alleviates dietary fiber deprivation-induced dysbiosis by selectively promoting Bifidobacterium pseudocatenulatum in pigs30
Reduced chemodiversity suppresses rhizosphere microbiome functioning in the mono-cropped agroecosystems30
Molecular repertoire of Deinococcus radiodurans after 1 year of exposure outside the International Space Station within the Tanpopo mission30
Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites30
Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy30
Specific metabolites drive the deterministic assembly of diseased rhizosphere microbiome through weakening microbial degradation of autotoxin30
Potential and expression of carbohydrate utilization by marine fungi in the global ocean30
High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method30
A mixed community of skin microbiome representatives influences cutaneous processes more than individual members29
Climate mediates continental scale patterns of stream microbial functional diversity29
Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage29
Polinton-like viruses are abundant in aquatic ecosystems29
Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome29
Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities29
Gardnerella vaginalis alters cervicovaginal epithelial cell function through microbe-specific immune responses29
Early-life gut dysbiosis linked to juvenile mortality in ostriches28
Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes28
Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes28
Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals28
Association of gut microbiota with metabolism in juvenile Atlantic salmon28
0.10223412513733