Microbiome

Papers
(The TQCC of Microbiome is 27. 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 2020-11-01 to 2024-11-01.)
ArticleCitations
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses566
Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank501
Review: microbial transformations of human bile acids359
Gut microbiota from green tea polyphenol-dosed mice improves intestinal epithelial homeostasis and ameliorates experimental colitis339
Specialized metabolic functions of keystone taxa sustain soil microbiome stability281
METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks242
Fecal microbiota transplantation protects rotenone-induced Parkinson’s disease mice via suppressing inflammation mediated by the lipopolysaccharide-TLR4 signaling pathway through the microbiota-gut-br241
Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir237
Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens223
VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition218
Disease-induced changes in plant microbiome assembly and functional adaptation216
Plant developmental stage drives the differentiation in ecological role of the maize microbiome208
Intestinal microbiota shapes gut physiology and regulates enteric neurons and glia156
An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants143
Rhizosphere community selection reveals bacteria associated with reduced root disease143
Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain142
Direct impact of commonly used dietary emulsifiers on human gut microbiota141
From gut microbiota to host appetite: gut microbiota-derived metabolites as key regulators139
TLR4 regulates RORγt+ regulatory T-cell responses and susceptibility to colon inflammation through interaction with Akkermansia muciniphila132
Novel insights into the genetically obese (ob/ob) and diabetic (db/db) mice: two sides of the same coin127
Gut microbiota-derived inosine from dietary barley leaf supplementation attenuates colitis through PPARγ signaling activation125
Challenges in exploring and manipulating the human skin microbiome125
Thousands of previously unknown phages discovered in whole-community human gut metagenomes124
Endometrial microbiota composition is associated with reproductive outcome in infertile patients123
Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas121
Host habitat is the major determinant of the gut microbiome of fish121
Gut microbiota-derived propionate mediates the neuroprotective effect of osteocalcin in a mouse model of Parkinson’s disease119
Effect of fecal microbiota transplantation on neurological restoration in a spinal cord injury mouse model: involvement of brain-gut axis116
Parabacteroides produces acetate to alleviate heparanase-exacerbated acute pancreatitis through reducing neutrophil infiltration114
Prevotella copri increases fat accumulation in pigs fed with formula diets114
A fiber-deprived diet causes cognitive impairment and hippocampal microglia-mediated synaptic loss through the gut microbiota and metabolites114
Important ecophysiological roles of non-dominant Actinobacteria in plant residue decomposition, especially in less fertile soils113
Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers113
A simplified synthetic community rescues Astragalus mongholicus from root rot disease by activating plant-induced systemic resistance108
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data103
A synthetic probiotic engineered for colorectal cancer therapy modulates gut microbiota100
Identifying biases and their potential solutions in human microbiome studies97
Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation94
Eicosapentaenoic and docosahexaenoic acids attenuate hyperglycemia through the microbiome-gut-organs axis in db/db mice92
Lactobacillus murinus alleviate intestinal ischemia/reperfusion injury through promoting the release of interleukin-10 from M2 macrophages via Toll-like receptor 2 signaling91
The microbiome and mosquito vectorial capacity: rich potential for discovery and translation90
Multifaceted roles of flavonoids mediating plant-microbe interactions90
The microbiota-gut-brain axis participates in chronic cerebral hypoperfusion by disrupting the metabolism of short-chain fatty acids89
Towards enhancing coral heat tolerance: a “microbiome transplantation” treatment using inoculations of homogenized coral tissues86
Regulation of blood–brain barrier integrity by microbiome-associated methylamines and cognition by trimethylamine N-oxide85
The phyllosphere microbiome shifts toward combating melanose pathogen83
Gut microbiome variation modulates the effects of dietary fiber on host metabolism82
Enhanced mutualistic symbiosis between soil phages and bacteria with elevated chromium-induced environmental stress80
The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota80
Depletion of acetate-producing bacteria from the gut microbiota facilitates cognitive impairment through the gut-brain neural mechanism in diabetic mice79
Protists as main indicators and determinants of plant performance79
Gut microbiota-derived ursodeoxycholic acid from neonatal dairy calves improves intestinal homeostasis and colitis to attenuate extended-spectrum β-lactamase-producing enteroaggregative Escherichia co77
Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities76
Iron status influences non-alcoholic fatty liver disease in obesity through the gut microbiome75
Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts75
Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge74
Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems73
Lessons learned from the prenatal microbiome controversy73
Joint contributions of the gut microbiota and host genetics to feed efficiency in chickens73
Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies73
Ultra-accurate microbial amplicon sequencing with synthetic long reads72
Antibiotic-associated dysbiosis affects the ability of the gut microbiota to control intestinal inflammation upon fecal microbiota transplantation in experimental colitis models70
Spatial heterogeneity of bacterial colonization across different gut segments following inter-species microbiota transplantation70
Commensal microbe-derived acetate suppresses NAFLD/NASH development via hepatic FFAR2 signalling in mice70
Gut dysbiosis promotes prostate cancer progression and docetaxel resistance via activating NF-κB-IL6-STAT3 axis70
Gut microbiota-derived metabolites mediate the neuroprotective effect of melatonin in cognitive impairment induced by sleep deprivation69
Integrated meta-omics reveals new ruminal microbial features associated with feed efficiency in dairy cattle68
Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies67
Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing66
Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing66
Glacier ice archives nearly 15,000-year-old microbes and phages66
Plant domestication shapes rhizosphere microbiome assembly and metabolic functions65
Gut microbiota regulation of P-glycoprotein in the intestinal epithelium in maintenance of homeostasis64
Dynamics of dark fermentation microbial communities in the light of lactate and butyrate production64
Perinatal environment shapes microbiota colonization and infant growth: impact on host response and intestinal function61
Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop61
Active virus-host interactions at sub-freezing temperatures in Arctic peat soil61
Diet, obesity, and the gut microbiome as determinants modulating metabolic outcomes in a non-human primate model61
A comprehensive evaluation of microbial differential abundance analysis methods: current status and potential solutions61
Holo-omics for deciphering plant-microbiome interactions61
Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field61
Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity61
HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes60
Host-microbiota interaction-mediated resistance to inflammatory bowel disease in pigs59
Lactobacillus reuteri tryptophan metabolism promotes host susceptibility to CNS autoimmunity59
Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations59
Effects of caloric restriction on the gut microbiome are linked with immune senescence58
Ageing and rejuvenation models reveal changes in key microbial communities associated with healthy ageing58
Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake57
Metabolite-based dietary supplementation in human type 1 diabetes is associated with microbiota and immune modulation57
Xylitol enhances synthesis of propionate in the colon via cross-feeding of gut microbiota56
Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer56
Orally administered Odoribacter laneus improves glucose control and inflammatory profile in obese mice by depleting circulating succinate54
Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome54
High-dose saccharin supplementation does not induce gut microbiota changes or glucose intolerance in healthy humans and mice53
Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats53
Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens53
Characterization of the human skin resistome and identification of two microbiota cutotypes53
A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere53
HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data52
Gammaproteobacteria, a core taxon in the guts of soil fauna, are potential responders to environmental concentrations of soil pollutants52
The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes51
Urban wastewater bacterial communities assemble into seasonal steady states51
PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes51
Glutamic acid reshapes the plant microbiota to protect plants against pathogens50
Inhalable antibiotic resistomes emitted from hospitals: metagenomic insights into bacterial hosts, clinical relevance, and environmental risks50
The functional evolution of termite gut microbiota49
Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream49
New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal49
The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut49
Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses49
A philosophical perspective on the prenatal in utero microbiome debate48
Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics48
Cognitive behavioral therapy for irritable bowel syndrome induces bidirectional alterations in the brain-gut-microbiome axis associated with gastrointestinal symptom improvement48
Specific metabolites drive the deterministic assembly of diseased rhizosphere microbiome through weakening microbial degradation of autotoxin48
Understanding the host-microbe interactions using metabolic modeling48
Polyamine metabolism links gut microbiota and testicular dysfunction47
Associations between habitual diet, metabolic disease, and the gut microbiota using latent Dirichlet allocation47
Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years47
Vaginal microbiome-host interactions modeled in a human vagina-on-a-chip47
Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites47
Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes46
The diet rapidly and differentially affects the gut microbiota and host lipid mediators in a healthy population46
Signature changes in gut microbiome are associated with increased susceptibility to HIV-1 infection in MSM46
Decoding the RNA viromes in rodent lungs provides new insight into the origin and evolutionary patterns of rodent-borne pathogens in Mainland Southeast Asia46
A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)45
Long-term effect of epigenetic modification in plant–microbe interactions: modification of DNA methylation induced by plant growth-promoting bacteria mediates promotion process45
Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques45
Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity45
Chicken jejunal microbiota improves growth performance by mitigating intestinal inflammation45
Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection45
Modulating gut microbiota in a mouse model of Graves’ orbitopathy and its impact on induced disease45
Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions44
Development of fungal-mediated soil suppressiveness against Fusarium wilt disease via plant residue manipulation44
Reduced chemodiversity suppresses rhizosphere microbiome functioning in the mono-cropped agroecosystems44
Elucidating the role of the gut microbiota in the physiological effects of dietary fiber44
Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements43
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 students43
Gut microbiome mediates the protective effects of exercise after myocardial infarction43
The plant microbiota signature of the Anthropocene as a challenge for microbiome research42
Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome42
Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation42
Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms42
Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy42
Gut dysbiosis induces the development of mastitis through a reduction in host anti-inflammatory enzyme activity by endotoxemia42
SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment41
Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes41
Acquisition of oral microbiota is driven by environment, not host genetics41
Early life microbial exposures shape the Crassostrea gigas immune system for lifelong and intergenerational disease protection41
Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes41
Antimicrobial resistance in Antarctica: is it still a pristine environment?40
Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach40
Remodeling of the maternal gut microbiome during pregnancy is shaped by parity40
Soil conditions and the plant microbiome boost the accumulation of monoterpenes in the fruit of Citrus reticulata ‘Chachi’40
The bacterial communities of Alaskan mosses and their contributions to N2-fixation40
Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity39
Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling39
Microbial community characterization of shrimp survivors to AHPND challenge test treated with an effective shrimp probiotic (Vibrio diabolicus)39
Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh39
Vitamin B12 produced by Cetobacterium somerae improves host resistance against pathogen infection through strengthening the interactions within gut microbiota39
Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity38
Gut microbiota-derived ursodeoxycholic acid alleviates low birth weight-induced colonic inflammation by enhancing M2 macrophage polarization38
A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations38
Gut microbiota response to antibiotics is personalized and depends on baseline microbiota38
Gardnerella vaginalis alters cervicovaginal epithelial cell function through microbe-specific immune responses38
Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes38
Honey bee genetics shape the strain-level structure of gut microbiota in social transmission38
Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria38
Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes38
Genomic evidence for sulfur intermediates as new biogeochemical hubs in a model aquatic microbial ecosystem38
Post-translational regulation of autophagy is involved in intra-microbiome suppression of fungal pathogens38
Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals38
Beneficial effect of the short-chain fatty acid propionate on vascular calcification through intestinal microbiota remodelling38
Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA37
Polinton-like viruses are abundant in aquatic ecosystems37
Gut microbiota–derived metabolite 3-idoleacetic acid together with LPS induces IL-35+ B cell generation37
Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments37
Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits37
SCAPP: an algorithm for improved plasmid assembly in metagenomes37
Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage37
Potential and expression of carbohydrate utilization by marine fungi in the global ocean37
Dietary calcium phosphate strongly impacts gut microbiome changes elicited by inulin and galacto-oligosaccharides consumption37
Xylan alleviates dietary fiber deprivation-induced dysbiosis by selectively promoting Bifidobacterium pseudocatenulatum in pigs36
Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression36
Elevated atmospheric CO2 alters the microbial community composition and metabolic potential to mineralize organic phosphorus in the rhizosphere of wheat36
HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi36
Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis36
Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis36
Batch effects account for the main findings of an in utero human intestinal bacterial colonization study35
Unmasking viral sequences by metagenomic next-generation sequencing in adult human blood samples during steroid-refractory/dependent graft-versus-host disease35
Reduced B12 uptake and increased gastrointestinal formate are associated with archaeome-mediated breath methane emission in humans35
Synergistic action of the gut microbiota in environmental RNA interference in a leaf beetle35
Characterization of diazotrophic root endophytes in Chinese silvergrass (Miscanthus sinensis)35
Investigation of fiber utilization in the rumen of dairy cows based on metagenome-assembled genomes and single-cell RNA sequencing35
Opportunistic bacteria with reduced genomes are effective competitors for organic nitrogen compounds in coastal dinoflagellate blooms34
Subcellular view of host–microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan–microbe symbiosis34
A mixed community of skin microbiome representatives influences cutaneous processes more than individual members34
Association of gut microbiota with metabolism in juvenile Atlantic salmon34
Characterization of TMAO productivity from carnitine challenge facilitates personalized nutrition and microbiome signatures discovery34
Depth-dependent variability of biological nitrogen fixation and diazotrophic communities in mangrove sediments34
Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale34
Considerations for mosquito microbiome research from the Mosquito Microbiome Consortium33
Spatial organization of the kelp microbiome at micron scales33
Integrating metagenomic binning with flux balance analysis to unravel syntrophies in anaerobic CO2 methanation33
Characterization of the public transit air microbiome and resistome reveals geographical specificity33
Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics33
The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA33
Accurate identification and quantification of commensal microbiota bound by host immunoglobulins33
Bog ecosystems as a playground for plant–microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria32
Perturbed gut microbiome and fecal and serum metabolomes are associated with chronic kidney disease severity32
Supercarriers of antibiotic resistome in a world’s large river32
Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity32
Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome32
Whole lung tissue is the preferred sampling method for amplicon-based characterization of murine lung microbiota31
Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-231
In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem31
LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis31
Increasing the power of interpretation for soil metaproteomics data31
Strain-level analysis reveals the vertical microbial transmission during the life cycle of bumblebee31
Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research31
Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities31
Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes31
The global distribution and environmental drivers of the soil antibiotic resistome30
Microbiota in mesenteric adipose tissue from Crohn’s disease promote colitis in mice30
Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance30
Gut microbiota of the young ameliorates physical fitness of the aged in mice30
High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method30
Cooperation between host immunity and the gut bacteria is essential for helminth-evoked suppression of colitis30
The oral microbiome, pancreatic cancer and human diversity in the age of precision medicine30
Dissolved storage glycans shaped the community composition of abundant bacterioplankton clades during a North Sea spring phytoplankton bloom30
Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes30
Diet and gut microbiome interactions of relevance for symptoms in irritable bowel syndrome29
Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species29
Gut metabolites predict Clostridioides difficile recurrence29
Human gut-derived B. longum subsp. longum strains protect against aging in a d-galactose-induced aging mouse model29
Metabolic framework of spontaneous and synthetic sourdough metacommunities to reveal microbial players responsible for resilience and performance29
Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals29
Mucin O-glycan-microbiota axis orchestrates gut homeostasis in a diarrheal pig model29
Virus diversity and interactions with hosts in deep-sea hydrothermal vents29
The gut microbiome and antibiotic resistome of chronic diarrhea rhesus macaques (Macaca mulatta) and its similarity to the human gut microbiome29
Gut microbiome signatures linked to HIV-1 reservoir size and viremia control28
Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR28
Sulfate-dependant microbially induced corrosion of mild steel in the deep sea: a 10-year microbiome study28
Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs28
Ecological interactions and the underlying mechanism of anammox and denitrification across the anammox enrichment with eutrophic lake sediments27
Blockage of bacterial FimH prevents mucosal inflammation associated with Crohn’s disease27
Stool energy density is positively correlated to intestinal transit time and related to microbial enterotypes27
Distinct B cell subsets in Peyer’s patches convey probiotic effects by Limosilactobacillus reuteri27
High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP- and human/animal-associated bacteria27
Zearalenone disturbs the reproductive-immune axis in pigs: the role of gut microbial metabolites27
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