npj Biofilms and Microbiomes

Papers
(The median citation count of npj Biofilms and Microbiomes is 6. 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 2021-04-01 to 2025-04-01.)
ArticleCitations
Stress triggers gut dysbiosis via CRH-CRHR1-mitochondria pathway180
Bacterial c-di-GMP signaling gene affects mussel larval metamorphosis through outer membrane vesicles and lipopolysaccharides177
A Klebsiella-phage cocktail to broaden the host range and delay bacteriophage resistance both in vitro and in vivo143
GGDEF domain as spatial on-switch for a phosphodiesterase by interaction with landmark protein HubP141
Pharmacodynamics of interspecies interactions in polymicrobial infections119
In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus106
Time-resolved compositional and dynamics analysis of biofilm maturation and dispersal via solid-state NMR spectroscopy102
The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors89
Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms81
Carbon source competition within the wound microenvironment can significantly influence infection progression76
Biofilm antimicrobial susceptibility through an experimental evolutionary lens76
Community successional patterns and inter-kingdom interactions during granular biofilm development71
Genome-wide siRNA screening reveals several host receptors for the binding of human gut commensal Bifidobacterium bifidum66
Developmental intestinal microbiome alterations in canine fading puppy syndrome: a prospective observational study64
Saliva-derived microcosm biofilms grown on different oral surfaces in vitro63
The structure of Brazilian Amazonian gut microbiomes in the process of urbanisation63
Supporting the strategic pillars of translational research in biofilms61
Biophysical properties at patch scale shape the metabolism of biofilm landscapes61
Preventing bacterial adhesion to skin by altering their physicochemical cell surface properties specifically54
Metabolic plasticity enables lifestyle transitions of Porphyromonas gingivalis54
Microbial diversity and secondary metabolism potential in relation to dark alterations in Paleolithic Lascaux Cave53
An in vitro fermentation model to study the impact of bacteriophages targeting Shiga toxin-encoding Escherichia coli on the colonic microbiota49
Long-term intake of Lactobacillus helveticus enhances bioavailability of omega-3 fatty acids in the mouse retina48
Diverse polysaccharide production and biofilm formation abilities of clinical Klebsiella pneumoniae47
A sex-dependent salivary bacterium influences oral mucositis severity after allogeneic hematopoietic cell transplantation47
Author Correction: Lactobacillus plantarum L168 improves hyperoxia-induced pulmonary inflammation and hypoalveolarization in a rat model of bronchopulmonary dysplasia47
Leptospira interrogans biofilm transcriptome highlights adaption to starvation and general stress while maintaining virulence46
Staphylococcus aureus SaeRS impairs macrophage immune functions through bacterial clumps formation in the early stage of infection46
Bacterial aggregation triggered by low-level antibiotic-mediated lysis46
Recent advances in single-cell engineered live biotherapeutic products research for skin repair and disease treatment45
Partial convergence of the human vaginal and rectal maternal microbiota in late gestation and early post-partum45
Optimization of an in vitro Pseudomonas aeruginosa Biofilm Model to Examine Antibiotic Pharmacodynamics at the Air-Liquid Interface45
Author Correction: Effect of model methanogens on the electrochemical activity, stability, and microbial community structure of Geobacter spp. dominated biofilm anodes44
Disentangling direct vs indirect effects of microbiome manipulations in a habitat-forming marine holobiont42
Bacteria contribute exopolysaccharides to an algal-bacterial joint extracellular matrix42
Machine learning analysis of sex and menopausal differences in the gut microbiome in the HELIUS study41
Combining SNAPs with antibiotics shows enhanced synergistic efficacy against S. aureus and P. aeruginosa biofilms41
Hypermutability bypasses genetic constraints in SCV phenotypic switching in Pseudomonas aeruginosa biofilms40
Oral and anal microbiome from HIV-exposed individuals: role of host-associated factors in taxa composition and metabolic pathways40
Deep generative modeling of annotated bacterial biofilm images40
A human oral commensal-mediated protection against Sjögren’s syndrome with maintenance of T cell immune homeostasis and improved oral microbiota40
Neutralization of ionic interactions by dextran-based single-chain nanoparticles improves tobramycin diffusion into a mature biofilm40
Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats39
The highly differentiated gut of Pachnoda marginata hosts sequential microbiomes: microbial ecology and potential applications38
Hydrodynamic conditions affect the proteomic profile of marine biofilms formed by filamentous cyanobacterium37
Gut commensals-derived succinate impels colonic inflammation in ulcerative colitis37
One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density37
Author Correction: Rumen microbiome and fat deposition in sheep: insights from a bidirectional mendelian randomization study36
Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut36
Multi-way modelling of oral microbial dynamics and host-microbiome interactions during induced gingivitis36
Probiotics alleviate constipation and inflammation in late gestating and lactating sows36
Spatiotemporal bio-shielding of bacteria through consolidated geometrical structuring34
Mitochondrial dysfunction promotes microbial composition that negatively impacts on ulcerative colitis development and progression34
Depth heterogeneity of lignin-degrading microbiome and organic carbon processing in mangrove sediments33
Elongation factor Tu promotes the onset of periodontitis through mediating bacteria adhesion33
Enhancing tumor-specific recognition of programmable synthetic bacterial consortium for precision therapy of colorectal cancer33
Lactobacillus plantarum L168 improves hyperoxia-induced pulmonary inflammation and hypoalveolarization in a rat model of bronchopulmonary dysplasia32
Early microbial markers of periodontal and cardiometabolic diseases in ORIGINS31
In situ monitoring of Lentilactobacillus parabuchneri biofilm formation via real-time infrared spectroscopy31
Author Correction: Secreted nucleases reclaim extracellular DNA during biofilm development30
Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization30
Body weight index indicates the responses of the fecal microbiota, metabolome and proteome to beef/chicken-based diet alterations in Chinese volunteers29
The role of shear dynamics in biofilm formation29
Staphylococcus aureus utilizes environmental RNA as a building material in specific polysaccharide-dependent biofilms29
Trichoderma-amended biofertilizer stimulates soil resident Aspergillus population for joint plant growth promotion29
Bifidobacterium animalis Probio-M8 improves sarcopenia physical performance by mitigating creatine restrictions imposed by microbial metabolites29
Translational challenges and opportunities in biofilm science: a BRIEF for the future27
Biofilms can act as plasmid reserves in the absence of plasmid specific selection27
Rationally designed probiotics prevent shrimp white feces syndrome via the probiotics–gut microbiome–immunity axis26
The tongue biofilm metatranscriptome identifies metabolic pathways associated with the presence or absence of halitosis25
Identification of essential genes for Escherichia coli aryl polyene biosynthesis and function in biofilm formation25
Gene horizontal transfers and functional diversity negatively correlated with bacterial taxonomic diversity along a nitrogen gradient25
Niche differentiation drives microbial community assembly and succession in full-scale activated sludge bioreactors25
Akkermansia muciniphila inhibited the periodontitis caused by Fusobacterium nucleatum25
Metabolic inputs in the probiotic bacterium Lacticaseibacillus rhamnosus contribute to cell-wall remodeling and increased fitness24
Microbiome-derived antimicrobial peptides offer therapeutic solutions for the treatment of Pseudomonas aeruginosa infections24
Author Correction: Inter-species metabolic interactions in an in-vitro minimal human gut microbiome of core bacteria24
Bacteroides ovatus accelerates metformin-induced vitamin B12 deficiency in type 2 diabetes patients by accumulating cobalamin24
Sucrose addition directionally enhances bacterial community convergence and network stability of the shrimp culture system24
Role of intestinal testosterone-degrading bacteria and 3/17β-HSD in the pathogenesis of testosterone deficiency-induced hyperlipidemia in males24
Long-chain 4-aminoquinolines inhibit filamentation and increase efficacy of nystatin against Candida albicans infections in vivo24
Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts24
Ex vivo intestinal permeability assay (X-IPA) for tracking barrier function dynamics23
Synthetic periphyton as a model system to understand species dynamics in complex microbial freshwater communities23
The gut microbiota modulate locomotion via vagus-dependent glucagon-like peptide-1 signaling23
One-step preparation of antimicrobial silicone materials based on PDMS and salicylic acid: insights from spatially and temporally resolved techniques23
Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut22
The sanitary indoor environment—a potential source for intact human-associated anaerobes22
Non disseminative nano-strategy against in vivo Staphylococcus aureus biofilms22
Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance22
Environmental determinants and demographic influences on global urban microbiomes, antimicrobial resistance and pathogenicity22
Fluorescent nanosensors reveal dynamic pH gradients during biofilm formation22
The potential to produce tropodithietic acid by Phaeobacter inhibens affects the assembly of microbial biofilm communities in natural seawater21
Distinct types of multicellular aggregates in Pseudomonas aeruginosa liquid cultures21
Author Correction: Deep insights into the gut microbial community of extreme longevity in south Chinese centenarians by ultra-deep metagenomics and large-scale culturomics21
Diet-microbiome interactions promote enteric nervous system resilience following spinal cord injury21
Exploring ex vivo biofilm dynamics: consequences of low ampicillin concentrations on the human oral microbiome21
Assessing the inflammatory response to in vitro polymicrobial wound biofilms in a skin epidermis model21
Colon or semicolon: gut sampling microdevices for omics insights21
Kinetics of imidazole propionate from orally delivered histidine in mice and humans21
Metabolic profiles outperform the microbiota in assessing the response of vaginal microenvironments to the changed state of HPV infection21
Decoding the RNA viromes in shrew lungs along the eastern coast of China21
Massive expansion of the pig gut virome based on global metagenomic mining21
Staphylococcus epidermidis alters macrophage polarization and phagocytic uptake by extracellular DNA release in vitro21
The Pga59 cell wall protein is an amyloid forming protein involved in adhesion and biofilm establishment in the pathogenic yeast Candida albicans20
Simulation of catalase-dependent tolerance of microbial biofilm to hydrogen peroxide with a biofilm computer model20
Author Correction: Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner20
Gut microbiota dysbiosis-mediated ceramides elevation contributes to corticosterone-induced depression by impairing mitochondrial function19
Spaceflight alters host-gut microbiota interactions19
Donor-recipient specificity and age-dependency in fecal microbiota therapy and probiotic resolution of gastrointestinal symptoms19
Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-1919
Responses of drinking water bulk and biofilm microbiota to elevated water age in bench-scale simulated distribution systems19
Hfq-binding small RNA PqsS regulates Pseudomonas aeruginosa pqs quorum sensing system and virulence19
Faecal hsa-miR-7704 inhibits the growth and adhesion of Bifidobacterium longum by suppressing ProB and aggravates hepatic encephalopathy19
The impact of antioxidant-ciprofloxacin combinations on the evolution of antibiotic resistance in Pseudomonas aeruginosa biofilms18
Root carbon inputs outweigh litter in shaping grassland soil microbiomes and ecosystem multifunctionality18
Neighborhood socioeconomic status is associated with low diversity gut microbiomes and multi-drug resistant microorganism colonization17
Transient colonizing microbes promote gut dysbiosis and functional impairment17
Diversity of bacteria within the human gut and its contribution to the functional unity of holobionts17
Protection against DSS-induced colitis in mice through FcεRIα deficiency: the role of altered Lactobacillus17
The neglected role of micronutrients in predicting soil microbial structure17
Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics17
Controlled spatial organization of bacterial growth reveals key role of cell filamentation preceding Xylella fastidiosa biofilm formation17
Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment16
Regulation of tryptophan-indole metabolic pathway in Porphyromonas gingivalis virulence and microbiota dysbiosis in periodontitis16
Clostridioides difficile bile salt hydrolase activity has substrate specificity and affects biofilm formation16
Cardiometabolic disease risk in gorillas is associated with altered gut microbial metabolism16
Active layer dynamics drives a transition to biofilm fingering16
A mannose-sensing AraC-type transcriptional activator regulates cell–cell aggregation of Vibrio cholerae16
Secreted nucleases reclaim extracellular DNA during biofilm development16
Baohuoside I targets SaeR as an antivirulence strategy to disrupt MRSA biofilm formation and pathogenicity15
Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium15
Interspecies competition in oral biofilms mediated by Streptococcus gordonii extracellular deoxyribonuclease SsnA15
Multiomics of yaks reveals significant contribution of microbiome into host metabolism15
Protecting the piglet gut microbiota against ETEC-mediated post-weaning diarrhoea using specific binding proteins15
Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees14
Bacterial vaginosis and health-associated bacteria modulate the immunometabolic landscape in 3D model of human cervix14
Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities14
Fasting-mimicking diet remodels gut microbiota and suppresses colorectal cancer progression14
Transcriptomic evidence for versatile metabolic activities of mercury cycling microorganisms in brackish microbial mats14
Competition quenching strategies reduce antibiotic tolerance in polymicrobial biofilms13
Pyoluteorin-deficient Pseudomonas protegens improves cooperation with Bacillus velezensis, biofilm formation, co-colonizing, and reshapes rhizosphere microbiome13
Combating biofilm-associated Klebsiella pneumoniae infections using a bovine microbial enzyme13
Gut microbiota-mediated secondary bile acid alleviates Staphylococcus aureus-induced mastitis through the TGR5-cAMP-PKA-NF-κB/NLRP3 pathways in mice13
Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis13
Magnetotactic bacteria and magnetofossils: ecology, evolution and environmental implications13
Age-related alterations in gut homeostasis are microbiota dependent13
Veillonellaceae family members uniquely alter the cervical metabolic microenvironment in a human three-dimensional epithelial model13
Ecological change of the gut microbiota during pregnancy and progression to dyslipidemia13
A three-colour stress biosensor reveals multimodal response in single cells and spatiotemporal dynamics of biofilms13
Synergistic action of phage phiIPLA-RODI and lytic protein CHAPSH3b: a combination strategy to target Staphylococcus aureus biofilms13
Microbiome variation correlates with the insecticide susceptibility in different geographic strains of a significant agricultural pest, Nilaparvata lugens13
Csu pili dependent biofilm formation and virulence of Acinetobacter baumannii13
Novel anti-inflammatory properties of mannose oligosaccharides in the treatment of inflammatory bowel disease via LGALS3 modulation12
The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations12
Impact of SARS-CoV-2 infection on respiratory and gut microbiome stability: a metagenomic investigation in long-term-hospitalized COVID-19 patients12
Integrative analysis reveals associations between oral microbiota dysbiosis and host genetic and epigenetic aberrations in oral cavity squamous cell carcinoma12
Author Correction: Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization12
Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion12
Interaction between tissue-dwelling helminth and the gut microbiota drives mucosal immunoregulation12
Lactobacillus rhamnosus GG ameliorates hyperuricemia in a novel model12
Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization12
Burns and biofilms: priority pathogens and in vivo models12
Pulcherrimin protects Bacillus subtilis against oxidative stress during biofilm development12
Personalized prediction of glycemic responses to food in women with diet-treated gestational diabetes: the role of the gut microbiota12
Adaption mechanism and ecological role of CPR bacteria in brackish-saline groundwater12
Disentangling the feedback loops driving spatial patterning in microbial communities12
Colonization with ubiquitous protist Blastocystis ST1 ameliorates DSS-induced colitis and promotes beneficial microbiota and immune outcomes12
Gut microbiome responses to dietary intervention with hypocholesterolemic vegetable oils12
Not only for corals: exploring the uptake of beneficial microorganisms for corals by sponges11
Dietary emulsifier consumption accelerates type 1 diabetes development in NOD mice11
Biodiversity of the beneficial soil-borne fungi steered by Trichoderma-amended biofertilizers stimulates plant production11
Effect of model methanogens on the electrochemical activity, stability, and microbial community structure of Geobacter spp. dominated biofilm anodes11
Ginseng extracts improve circadian clock gene expression and reduce inflammation directly and indirectly through gut microbiota and PI3K signaling pathway11
Daily full spectrum light exposure prevents food allergy-like allergic diarrhea by modulating vitamin D3 and microbiota composition11
Adaptation of a methanogen to Fe0 corrosion via direct contact11
Integrated meta-omics approaches reveal Saccharopolyspora as the core functional genus in huangjiu fermentations11
Bacterial c-di-GMP triggers metamorphosis of mussel larvae through a STING receptor11
The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival11
Molecular characterization of the N-terminal half of TasA during amyloid-like assembly and its contribution to Bacillus subtilis biofilm formation11
Recent advances in the pathogenesis and prevention strategies of dental calculus11
Functional metagenomic analysis of quorum sensing signaling in a nitrifying community10
CO2 enhances the formation, nutrient scavenging and drug resistance properties of C. albicans biofilms10
The car tank lid bacteriome: a reservoir of bacteria with potential in bioremediation of fuel10
Dietary D-xylose promotes intestinal health by inducing phage production in Escherichia coli10
Reduced stress-associated FKBP5 DNA methylation together with gut microbiota dysbiosis is linked with the progression of obese PCOS patients10
Time-restricted feeding induces Lactobacillus- and Akkermansia-specific functional changes in the rat fecal microbiota10
Host specificity and cophylogeny in the “animal-gut bacteria-phage” tripartite system10
Gut microbiome responds compositionally and functionally to the seasonal diet variations in wild gibbons10
Author Correction: Uncharted waters: the unintended impacts of residual chlorine on water quality and biofilms10
Network mapping of root–microbe interactions in Arabidopsis thaliana10
Roles of gut microbiome-associated metabolites in pulmonary fibrosis by integrated analysis10
ToxR is a c-di-GMP binding protein that modulates surface-associated behaviour in Pseudomonas aeruginosa10
Evolution of biofilm-adapted gene expression profiles in lasR-deficient clinical Pseudomonas aeruginosa isolates9
Social demographics determinants for resistome and microbiome variation of a multiethnic community in Southern Malaysia9
A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria9
Riboflavin for women’s health and emerging microbiome strategies9
Adaptation and phenotypic diversification of Bacillus thuringiensis biofilm are accompanied by fuzzy spreader morphotypes9
Alternating magnetic fields and antibiotics eradicate biofilm on metal in a synergistic fashion9
Clostridium difficile-derived membrane vesicles promote fetal growth restriction via inhibiting trophoblast motility through PPARγ/RXRα/ANGPTL4 axis9
Mechanisms of fungal community assembly in wild stoneflies moderated by host characteristics and local environment9
Glycoside hydrolase processing of the Pel polysaccharide alters biofilm biomechanics and Pseudomonas aeruginosa virulence8
Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics8
Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota8
Digestive exophagy of biofilms by intestinal amoeba and its impact on stress tolerance and cytotoxicity8
Gut microbiota as a new target for anticancer therapy: from mechanism to means of regulation8
Large-scale characterisation of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population8
The BDSF quorum sensing receptor RpfR regulates Bep exopolysaccharide synthesis in Burkholderia cenocepacia via interaction with the transcriptional regulator BerB8
A meta-analysis of acetogenic and methanogenic microbiomes in microbial electrosynthesis8
Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors8
Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa8
Irrigation of the intramedullary channel improves outcome of DAIR in a sheep model8
Cell specialization in cyanobacterial biofilm development revealed by expression of a cell-surface and extracellular matrix protein8
Metaproteomic portrait of the healthy human gut microbiota8
On validly published names, correct names, and changes in the nomenclature of phyla and genera of prokaryotes: a guide for the perplexed8
In-depth insights into cervicovaginal microbial communities and hrHPV infections using high-resolution microbiome profiling8
Extracellular vesicles of the Gram-positive gut symbiont Bifidobacterium longum induce immune-modulatory, anti-inflammatory effects8
Microbiome assembly predictably shapes diversity across a range of disturbance frequencies in experimental microcosms8
Molecules-mediated bidirectional interactions between microbes and human cells8
Publisher Correction: Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis8
Yijung-tang improves thermogenesis and reduces inflammation associated with gut microbiota in hypothyroid rats8
A phosphate starvation induced small RNA promotes Bacillus biofilm formation7
Filamentous fungal biofilms: Conserved and unique aspects of extracellular matrix composition, mechanisms of drug resistance and regulatory networks in Aspergillus fumigatus7
Rational consideration of Akkermansia muciniphila targeting intestinal health: advantages and challenges7
The plant-sucking insect selects assembly of the gut microbiota from environment to enhance host reproduction7
Bacterial membrane vesicles restore gut anaerobiosis7
The hallmarks of dietary intervention-resilient gut microbiome7
Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities7
Investigating the response of the butyrate production potential to major fibers in dietary intervention studies7
Vaginal host immune-microbiome-metabolite interactions associated with spontaneous preterm birth in a predominantly white cohort7
Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates7
Mucin glycans drive oral microbial community composition and function7
Microbial co-occurrence network topological properties link with reactor parameters and reveal importance of low-abundance genera7
Bacterial capsules: Occurrence, mechanism, and function7
The regulatory framework for microbiome-based therapies: insights into European regulatory developments7
Integrative metagenomic and metabolomic analyses reveal the potential of gut microbiota to exacerbate acute pancreatitis6
Lifestyle-specific S-nitrosylation of protein cysteine thiols regulates Escherichia coli biofilm formation and resistance to oxidative stress6
Competition of two highly specialized and efficient acetoclastic electroactive bacteria for acetate in biofilm anode of microbial electrolysis cell6
Metaproteogenomic analysis of saliva samples from Parkinson’s disease patients with cognitive impairment6
High interindividual variability of indoxyl sulfate production identified by an oral tryptophan challenge test6
Alleviation of Limosilactobacillus reuteri in polycystic ovary syndrome protects against circadian dysrhythmia-induced dyslipidemia via capric acid and GALR1 signaling6
Real-time monitoring of ruminal microbiota reveals their roles in dairy goats during subacute ruminal acidosis6
Dynamics of drinking water biofilm formation associated with Legionella spp. colonization6
Periodontitis salivary microbiota exacerbates colitis-induced anxiety-like behavior via gut microbiota6
Gut microbes modulate the effects of the flavonoid quercetin on atherosclerosis6
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