Microbiome

Papers
(The median citation count of Microbiome is 8. 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 2021-02-01 to 2025-02-01.)
ArticleCitations
Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets613
Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants513
Increased methane production associated with community shifts towards Methanocella in paddy soils with the presence of nanoplastics393
Role of nasal microbiota in regulating host anti-influenza immunity in dogs386
No microorganism was detected in amniotic fluid of healthy pregnancies from the second trimester to the delivery273
Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study272
Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses265
Holo-omics for deciphering plant-microbiome interactions236
Gut microbiome variation modulates the effects of dietary fiber on host metabolism236
Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics220
Active virus-host interactions at sub-freezing temperatures in Arctic peat soil165
Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population162
Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities147
Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station146
A microbial causal mediation analytic tool for health disparity and applications in body mass index143
In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea142
A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations141
More data needed on neonatal microbiome seeding141
Obese-associated gut microbes and derived phenolic metabolite as mediators of excessive motivation for food reward135
The fusion of multi-omics profile and multimodal EEG data contributes to the personalized diagnostic strategy for neurocognitive disorders133
Decline of a distinct coral reef holobiont community under ocean acidification131
Microbial signatures and continuum in endometrial cancer and benign patients130
Lateral root enriched Massilia associated with plant flowering in maize129
The developing airway and gut microbiota in early life is influenced by age of older siblings127
Vibrio vulnificus induces the death of a major bacterial species in the mouse gut via cyclo-Phe-Pro127
Highly accurate and sensitive absolute quantification of bacterial strains in human fecal samples127
Gut-derived metabolites influence neurodevelopmental gene expression and Wnt signaling events in a germ-free zebrafish model125
The multi-kingdom microbiome of the goat gastrointestinal tract116
Maternal effects drive intestinal development beginning in the embryonic period on the basis of maternal immune and microbial transfer in chickens114
Growth rate determines prokaryote-provirus network modulated by temperature and host genetic traits114
Methanolobus use unspecific methyltransferases to produce methane from dimethylsulphide in Baltic Sea sediments114
A glimpse of the paleome in endolithic microbial communities111
Neotropical bee microbiomes point to a fragmented social core and strong species-level effects108
Stratified microbial communities in Australia’s only anchialine cave are taxonomically novel and drive chemotrophic energy production via coupled nitrogen-sulphur cycling108
Assessing the causes and consequences of gut mycobiome variation in a wild population of the Seychelles warbler104
Post-translational regulation of autophagy is involved in intra-microbiome suppression of fungal pathogens101
DNA stable isotope probing reveals the impact of trophic interactions on bioaugmentation of soils with different pollution histories100
Predicting how varying moisture conditions impact the microbiome of dust collected from the International Space Station97
Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines97
Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics97
Mosaic environment-driven evolution of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont88
Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter88
Enrichment of novel entomopathogenic Pseudomonas species enhances willow resistance to leaf beetles86
Deep-sea Bacteroidetes from the Mariana Trench specialize in hemicellulose and pectin degradation typically associated with terrestrial systems86
Degradation pathways for organic matter of terrestrial origin are widespread and expressed in Arctic Ocean microbiomes86
Exposure to Trypanosoma parasites induces changes in the microbiome of the Chagas disease vector Rhodnius prolixus85
Xylan alleviates dietary fiber deprivation-induced dysbiosis by selectively promoting Bifidobacterium pseudocatenulatum in pigs85
Sequential host-bacteria and bacteria-bacteria interactions determine the microbiome establishment of Nematostella vectensis84
Associations between habitual diet, metabolic disease, and the gut microbiota using latent Dirichlet allocation83
Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans82
Core-predominant gut fungus Kazachstania slooffiae promotes intestinal epithelial glycolysis via lysine desuccinylation in pigs82
Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition81
Linking morphology, genome, and metabolic activity of uncultured magnetotactic Nitrospirota at the single-cell level81
Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes80
Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts80
Globally distributed marine Gemmatimonadota have unique genomic potentials79
Modified PCR protocol to increase sensitivity for determination of bacterial community composition78
Shotgun metagenomic sequencing reveals the influence of artisanal dairy environments on the microbiomes, quality, and safety of Idiazabal, a raw ewe milk PDO cheese78
Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies77
Host habitat is the major determinant of the gut microbiome of fish76
Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis76
Colonization during a key developmental window reveals microbiota-dependent shifts in growth and immunity during undernutrition72
Disentangling temporal associations in marine microbial networks72
Bacterial quorum sensing orchestrates longitudinal interactions to shape microbiota assembly71
Intestinal microbiome-mediated resistance against vibriosis for Cynoglossus semilaevis70
SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities70
Using strain-resolved analysis to identify contamination in metagenomics data69
Linking gastrointestinal microbiota and metabolome dynamics to clinical outcomes in paediatric haematopoietic stem cell transplantation67
Should we modulate the neonatal microbiome and what should be the goal?65
High-tannin food enhances spatial memory and scatter-hoarding in rodents via the microbiota-gut-brain axis65
Engineering a dysbiotic biofilm model for testing root caries interventions through microbial modulation64
Spatial organization of the kelp microbiome at micron scales64
Fairy: fast approximate coverage for multi-sample metagenomic binning64
Cooperation between host immunity and the gut bacteria is essential for helminth-evoked suppression of colitis62
High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains61
Aedes aegypti microbiome composition covaries with the density of Wolbachia infection61
Virome diversity shaped by genetic evolution and ecological landscape of Haemaphysalis longicornis61
Microbiomes of clownfish and their symbiotic host anemone converge before their first physical contact61
Phylogeny-guided microbiome OTU-specific association test (POST)61
Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome61
The intestinal microbiome and Cetobacterium somerae inhibit viral infection through TLR2-type I IFN signaling axis in zebrafish60
Rapid remodeling of the soil lipidome in response to a drying-rewetting event60
Melatonin alleviates heat stress-induced spermatogenesis dysfunction in male dairy goats by regulating arachidonic acid metabolism mediated by remodeling the gut microbiota60
Relative abundance data can misrepresent heritability of the microbiome58
Intestinal commensal bacteria promote Bactrocera dorsalis larval development through the vitamin B6 synthesis pathway58
The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels58
Placental TLR recognition of salivary and subgingival microbiota is associated with pregnancy complications58
Selected commensals educate the intestinal vascular and immune system for immunocompetence57
Circadian dynamics of the teleost skin immune-microbiome interface57
A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome56
Cover crop root exudates impact soil microbiome functional trajectories in agricultural soils56
Different roles of host and habitat in determining the microbial communities of plant-feeding true bugs56
High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP- and human/animal-associated bacteria55
Perturbed gut microbiome and fecal and serum metabolomes are associated with chronic kidney disease severity54
Variants of a putative baseplate wedge protein extend the host range of Pseudomonas phage K853
Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes53
Supercarriers of antibiotic resistome in a world’s large river53
Live Akkermansia muciniphila boosts dendritic cell retinoic acid synthesis to modulate IL-22 activity and mitigate colitis in mice52
Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C352
Comparative genomics analyses of Actinobacteriota identify Golgi phosphoprotein 3 (GPP34) as a widespread ancient protein family associated with sponge symbiosis52
High-fat diet-disturbed gut microbiota-colonocyte interactions contribute to dysregulating peripheral tryptophan-kynurenine metabolism52
Endogenous small intestinal microbiome determinants of transient colonisation efficiency by bacteria from fermented dairy products: a randomised controlled trial51
Gut microbiota is associated with the effect of photoperiod on seasonal breeding in male Brandt’s voles (Lasiopodomys brandtii)51
Effects of data transformation and model selection on feature importance in microbiome classification data51
Bifidobacterial carbohydrate/nucleoside metabolism enhances oxidative phosphorylation in white adipose tissue to protect against diet-induced obesity50
Biogeography, succession, and origin of the chicken intestinal mycobiome50
Signature changes in gut microbiome are associated with increased susceptibility to HIV-1 infection in MSM49
Metagenomic insights into microbial adaptation to the salinity gradient of a typical short residence-time estuary48
Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance48
Microbiota-indole 3-propionic acid-brain axis mediates abnormal synaptic pruning of hippocampal microglia and susceptibility to ASD in IUGR offspring48
Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants47
Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere47
Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem47
LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis47
Microbiota in mesenteric adipose tissue from Crohn’s disease promote colitis in mice47
Skin microbiome differentiates into distinct cutotypes with unique metabolic functions upon exposure to polycyclic aromatic hydrocarbons47
Antimicrobial peptides modulate lung injury by altering the intestinal microbiota46
Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the “Lunar Palace 365” experiment46
HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data46
Dissolved storage glycans shaped the community composition of abundant bacterioplankton clades during a North Sea spring phytoplankton bloom46
Th17 cells sense microbiome to promote depressive-like behaviors46
Microbial community regulation and performance enhancement in gas biofilters by interrupting bacterial communication45
Gut microbiome of century-old snail specimens stable across time in preservation45
Stool energy density is positively correlated to intestinal transit time and related to microbial enterotypes45
Community structure of coral microbiomes is dependent on host morphology45
Plant sex affects plant-microbiome assemblies of dioecious Populus cathayana trees under different soil nitrogen conditions45
Rhizosphere community selection reveals bacteria associated with reduced root disease45
Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments45
Gut microbiota-derived inosine from dietary barley leaf supplementation attenuates colitis through PPARγ signaling activation43
Commensal microbe-derived acetate suppresses NAFLD/NASH development via hepatic FFAR2 signalling in mice43
Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance43
Soil conditions and the plant microbiome boost the accumulation of monoterpenes in the fruit of Citrus reticulata ‘Chachi’43
Colonocyte-derived lactate promotes E. coli fitness in the context of inflammation-associated gut microbiota dysbiosis43
Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data43
H2 generated by fermentation in the human gut microbiome influences metabolism and competitive fitness of gut butyrate producers43
Protists as main indicators and determinants of plant performance42
Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation42
Oligofructose improves small intestinal lipid-sensing mechanisms via alterations to the small intestinal microbiota42
Metal(loid) speciation and transformation by aerobic methanotrophs42
Gut dysbiosis promotes prostate cancer progression and docetaxel resistance via activating NF-κB-IL6-STAT3 axis42
Location-specific signatures of Crohn’s disease at a multi-omics scale42
Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes42
Antioxidant potential of Pediococcus pentosaceus strains from the sow milk bacterial collection in weaned piglets42
Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome42
Population mixing mediates the intestinal flora composition and facilitates invasiveness in a globally invasive fruit fly41
Global distribution, diversity, and ecological niche of Picozoa, a widespread and enigmatic marine protist lineage41
Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome41
Microbiome and tryptophan metabolomics analysis in adolescent depression: roles of the gut microbiota in the regulation of tryptophan-derived neurotransmitters and behaviors in human and mice41
Identification of the mutual gliding locus as a factor for gut colonization in non-native bee hosts using the ARTP mutagenesis41
Integrated multi-omics analysis reveals the positive leverage of citrus flavonoids on hindgut microbiota and host homeostasis by modulating sphingolipid metabolism in mid-lactation dairy cows consumin41
Blocked conversion of Lactobacillus johnsonii derived acetate to butyrate mediates copper-induced epithelial barrier damage in a pig model40
Gut microbiota contributes to bisphenol A-induced maternal intestinal and placental apoptosis, oxidative stress, and fetal growth restriction in pregnant ewe model by regulating gut-placental axis40
PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation40
Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet40
Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles39
A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mi39
Depletion of acetate-producing bacteria from the gut microbiota facilitates cognitive impairment through the gut-brain neural mechanism in diabetic mice38
Deciphering the gut microbiome of grass carp through multi-omics approach38
Correction to: Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans38
Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides38
Correction: Sodium levels and grazing pressure shape natural communities of the intracellular pathogen Legionella38
Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans38
Correction: Gut microbiota-derived propionate mediates the neuroprotective effect of osteocalcin in a mouse model of Parkinson’s disease38
Microbial active functional modules derived from network analysis and metabolic interactions decipher the complex microbiome assembly in mangrove sediments38
From dysbiosis to defense: harnessing the gut microbiome in HIV/SIV therapy38
Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human38
SCAPP: an algorithm for improved plasmid assembly in metagenomes38
Sodium levels and grazing pressure shape natural communities of the intracellular pathogen Legionella38
Salivary proteomics and metaproteomics identifies distinct molecular and taxonomic signatures of type-2 diabetes37
Effects of melatonin on rumen microorganisms and methane production in dairy cow: results from in vitro and in vivo studies37
The microbiota of cork and yellow stain as a model for a new route for the synthesis of chlorophenols and chloroanisoles from the microbial degradation of suberin and/or lignin37
A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere37
Darier’s disease exhibits a unique cutaneous microbial dysbiosis associated with inflammation and body malodour37
Analysis of early childhood intestinal microbial dynamics in a continuous-flow bioreactor37
Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution36
Bacteroides salyersiae is a potent chondroitin sulfate-degrading species in the human gut microbiota36
Host selection is not a universal driver of phyllosphere community assembly among ecologically similar native New Zealand plant species36
Bacillus species are core microbiota of resistant maize cultivars that induce host metabolic defense against corn stalk rot36
Exploring the landscape of symbiotic diversity and distribution in unicellular ciliated protists35
The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet35
Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition35
Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium35
Natural plant disease suppressiveness in soils extends to insect pest control35
Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake34
The plasma viral communities associate with clinical profiles in a large-scale haematological patients cohort34
Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes34
Spatiotemporal variation of the indoor mycobiome in daycare centers34
High-resolution metagenomic reconstruction of the freshwater spring bloom34
Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host33
Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques33
Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale33
F. prausnitzii potentially modulates the association between citrus intake and depression33
Metabolic modeling of the International Space Station microbiome reveals key microbial interactions33
Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants33
Metagenome-validated combined amplicon sequencing and text mining-based annotations for simultaneous profiling of bacteria and fungi: vaginal microbiota and mycobiota in healthy women32
Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners32
Review: microbial transformations of human bile acids32
Microbiota-derived indoles alleviate intestinal inflammation and modulate microbiome by microbial cross-feeding31
MGS2AMR: a gene-centric mining of metagenomic sequencing data for pathogens and their antimicrobial resistance profile31
Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation31
A Lactobacillus consortium provides insights into the sleep-exercise-microbiome nexus in proof of concept studies of elite athletes and in the general population31
Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean31
VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution31
Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism31
Clean room microbiome complexity impacts planetary protection bioburden30
Disruption of fish gut microbiota composition and holobiont’s metabolome during a simulated Microcystis aeruginosa (Cyanobacteria) bloom30
Characterisation of the koala (Phascolarctos cinereus) pouch microbiota in a captive population reveals a dysbiotic compositional profile associated with neonatal mortality30
Novel biological aqua crust enhances in situ metal(loid) bioremediation driven by phototrophic/diazotrophic biofilm30
Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes30
Gut microbiota regulation of P-glycoprotein in the intestinal epithelium in maintenance of homeostasis30
N/S element transformation modulating lithospheric microbial communities by single-species manipulation30
Using the collaborative cross to identify the role of host genetics in defining the murine gut microbiome30
Anthropogenic activities mediate stratification and stability of microbial communities in freshwater sediments29
animalcules: interactive microbiome analytics and visualization in R29
Gut microbiota-derived ursodeoxycholic acid alleviates low birth weight-induced colonic inflammation by enhancing M2 macrophage polarization29
Combined effect of microbially derived cecal SCFA and host genetics on feed efficiency in broiler chickens29
Unique microbial landscape in the human oropharynx during different types of acute respiratory tract infections29
Enhanced IgA coating of bacteria in women with Lactobacillus crispatus-dominated vaginal microbiota29
Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome29
Core species and interactions prominent in fish-associated microbiome dynamics29
A synbiotic mixture of selected oligosaccharides and bifidobacteria assists murine gut microbiota restoration following antibiotic challenge29
Gut dysbiosis induces the development of mastitis through a reduction in host anti-inflammatory enzyme activity by endotoxemia29
Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments29
Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes29
Lactiplantibacillus plantarum enables blood urate control in mice through degradation of nucleosides in gastrointestinal tract29
Determination of antibiotic resistance patterns and genotypes of Escherichia coli isolated from wild birds28
Investigation of fiber utilization in the rumen of dairy cows based on metagenome-assembled genomes and single-cell RNA sequencing28
Evolutionary diversification and succession of soil huge phages in glacier foreland28
Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report28
Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation27
Nutrient dynamics in coral symbiosis depend on both the relative and absolute abundance of Symbiodiniaceae species27
Metabolite-based dietary supplementation in human type 1 diabetes is associated with microbiota and immune modulation27
The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules27
Experimental community coalescence sheds light on microbial interactions in soil and restores impaired functions27
Supergroup F Wolbachia with extremely reduced genome: transition to obligate insect symbionts27
Characterizing the gut phageome and phage-borne antimicrobial resistance genes in pigs27
Considerations for mosquito microbiome research from the Mosquito Microbiome Consortium26
Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR26
Presence and role of viruses in anaerobic digestion of food waste under environmental variability26
Reproducible and opposing gut microbiome signatures distinguish autoimmune diseases and cancers: a systematic review and meta-analysis26
Microbial colonisation rewires the composition and content of poplar root exudates, root and shoot metabolomes26
Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states26
Growth of sulfate-reducing Desulfobacterota and Bacillota at periodic oxygen stress of 50% air-O2 saturation25
Modulating gut microbiota in a mouse model of Graves’ orbitopathy and its impact on induced disease25
Mosquito sex and mycobiota contribute to fructose metabolism in the Asian tiger mosquito Aedes albopictus25
Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters25
Cross-kingdom inhibition of bacterial virulence and communication by probiotic yeast metabolites25
Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages25
An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics25
Sulfur-cycling chemolithoautotrophic microbial community dominates a cold, anoxic, hypersaline Arctic spring25
0.12028002738953