npj Biofilms and Microbiomes

Article	Citations
Analysis of microbial compositions: a review of normalization and differential abundance analysis	150
Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization	131
Three faces of biofilms: a microbial lifestyle, a nascent multicellular organism, and an incubator for diversity	125
Economic significance of biofilms: a multidisciplinary and cross-sectoral challenge	121
Metagenomic analysis revealed the potential role of gut microbiome in gout	117
Interactions of plasma-activated water with biofilms: inactivation, dispersal effects and mechanisms of action	106
Seasonal dynamics of diet–gut microbiota interaction in adaptation of yaks to life at high altitude	94
Berberine attenuates choline-induced atherosclerosis by inhibiting trimethylamine and trimethylamine-N-oxide production via manipulating the gut microbiome	92
Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale	81
Microbial co-occurrence network topological properties link with reactor parameters and reveal importance of low-abundance genera	81
Host development overwhelms environmental dispersal in governing the ecological succession of zebrafish gut microbiota	76
Who put the film in biofilm? The migration of a term from wastewater engineering to medicine and beyond	70
Integrated metagenomics identifies a crucial role for trimethylamine-producing Lachnoclostridium in promoting atherosclerosis	64
Burns and biofilms: priority pathogens and in vivo models	59
Biofilm viability checker: An open-source tool for automated biofilm viability analysis from confocal microscopy images	58
Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth	57
Bacterial vaginosis and health-associated bacteria modulate the immunometabolic landscape in 3D model of human cervix	55
Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis	55
Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth–gut axis	52
Biofilms harbour Clostridioides difficile, serving as a reservoir for recurrent infection	50
Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization	50
Host-microbiome interactions: Gut-Liver axis and its connection with other organs	50
Exposure of Salmonella biofilms to antibiotic concentrations rapidly selects resistance with collateral tradeoffs	49
Improved functionality of Ligilactobacillus salivarius Li01 in alleviating colonic inflammation by layer-by-layer microencapsulation	49
Identification of small molecules that interfere with c-di-GMP signaling and induce dispersal of Pseudomonas aeruginosa biofilms	48

The biofilm matrix scaffold of Pseudomonas aeruginosa contains G-quadruplex extracellular DNA structures	47
Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees	47
Interactions between gut microbiota and metabolites modulate cytokine network imbalances in women with unexplained miscarriage	46
Gut microbiota determines the social behavior of mice and induces metabolic and inflammatory changes in their adipose tissue	43
Synergistic action of phage phiIPLA-RODI and lytic protein CHAPSH3b: a combination strategy to target Staphylococcus aureus biofilms	42
Lung microbiota associations with clinical features of COPD in the SPIROMICS cohort	41
Soil microbiome manipulation triggers direct and possible indirect suppression against Ralstonia solanacearum and Fusarium oxysporum	40
Real-time monitoring of ruminal microbiota reveals their roles in dairy goats during subacute ruminal acidosis	38
Atherosclerosis amelioration by allicin in raw garlic through gut microbiota and trimethylamine-N-oxide modulation	38
The pivotal roles of gut microbiota in insect plant interactions for sustainable pest management	36
Identification of essential genes for Escherichia coli aryl polyene biosynthesis and function in biofilm formation	35
Disrupting quorum sensing alters social interactions in Chromobacterium violaceum	35
Human organoid biofilm model for assessing antibiofilm activity of novel agents	35
Experimental parameters defining ultra-low biomass bioaerosol analysis	34
A bacteriocin-based antimicrobial formulation to effectively disrupt the cell viability of methicillin-resistant Staphylococcus aureus (MRSA) biofilms	34
Diversity and infectivity of the RNA virome among different cryptic species of an agriculturally important insect vector: whitefly Bemisia tabaci	33
Gut microbiota-mediated secondary bile acid alleviates Staphylococcus aureus-induced mastitis through the TGR5-cAMP-PKA-NF-κB/NLRP3 pathways in mice	32
Human supplementation with Pediococcus acidilactici GR-1 decreases heavy metals levels through modifying the gut microbiota and metabolome	31
Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing	31
A multiomics approach to identify host-microbe alterations associated with infection severity in diabetic foot infections: a pilot study	31
Responses of soil microbiome to steel corrosion	30
The role of shear dynamics in biofilm formation	30
Biogeographical patterns and mechanisms of microbial community assembly that underlie successional biocrusts across northern China	30
Gut dysbiosis and mortality in hemodialysis patients	30
Magnetotactic bacteria and magnetofossils: ecology, evolution and environmental implications	30
Bacteroides uniformis-induced perturbations in colonic microbiota and bile acid levels inhibit TH17 differentiation and ameliorate colitis developments	29
Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates	29
A new BiofilmChip device for testing biofilm formation and antibiotic susceptibility	29
Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota	29
Rational consideration of Akkermansia muciniphila targeting intestinal health: advantages and challenges	28
Veillonellaceae family members uniquely alter the cervical metabolic microenvironment in a human three-dimensional epithelial model	28
Gut microbiota and metabolites of α-synuclein transgenic monkey models with early stage of Parkinson’s disease	28
Reduced stress-associated FKBP5 DNA methylation together with gut microbiota dysbiosis is linked with the progression of obese PCOS patients	28
One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density	28
Strategy to combat biofilms: a focus on biofilm dispersal enzymes	28
Transcriptomic evidence for versatile metabolic activities of mercury cycling microorganisms in brackish microbial mats	28
The right bug in the right place: opportunities for bacterial vaginosis treatment	27
Biofilm antimicrobial susceptibility through an experimental evolutionary lens	27
Porcine gut microbiota in mediating host metabolic adaptation to cold stress	27
Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors	27
Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis	26
Gut microbiota as an antioxidant system in centenarians associated with high antioxidant activities of gut-resident Lactobacillus	26
Genetic requirements and transcriptomics of Helicobacter pylori biofilm formation on abiotic and biotic surfaces	26
Gut microbiome development in early childhood is affected by day care attendance	25
Soil microbial metabolism on carbon and nitrogen transformation links the crop-residue contribution to soil organic carbon	25
Inter-species Metabolic Interactions in an In-vitro Minimal Human Gut Microbiome of Core Bacteria	25
Impact of temperature-dependent phage expression on Pseudomonas aeruginosa biofilm formation	25
The role of Psl in the failure to eradicate Pseudomonas aeruginosa biofilms in children with cystic fibrosis	24
Salivary dysbiosis in Sjögren’s syndrome and a commensal-mediated immunomodulatory effect of salivary gland epithelial cells	24
Network mapping of root–microbe interactions in Arabidopsis thaliana	24

Translational challenges and opportunities in biofilm science: a BRIEF for the future	24
Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters	24
Weaponizing volatiles to inhibit competitor biofilms from a distance	24
Biofilm-isolated Listeria monocytogenes exhibits reduced systemic dissemination at the early (12–24 h) stage of infection in a mouse model	23
Trichoderma-amended biofertilizer stimulates soil resident Aspergillus population for joint plant growth promotion	23
Alternating magnetic fields and antibiotics eradicate biofilm on metal in a synergistic fashion	23
Sucrose addition directionally enhances bacterial community convergence and network stability of the shrimp culture system	23
The gut microbiome-metabolome dataset collection: a curated resource for integrative meta-analysis	22
Competition of two highly specialized and efficient acetoclastic electroactive bacteria for acetate in biofilm anode of microbial electrolysis cell	22
Long-term warming in a Mediterranean-type grassland affects soil bacterial functional potential but not bacterial taxonomic composition	21
Attachment and antibiotic response of early-stage biofilms studied using resonant hyperspectral imaging	21
Evolution of biofilm-adapted gene expression profiles in lasR-deficient clinical Pseudomonas aeruginosa isolates	21
Periodontitis associates with species-specific gene expression of the oral microbiota	21
The human respiratory tract microbial community structures in healthy and cystic fibrosis infants	21
Systems view of Bacillus subtilis pellicle development	21
The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations	21
Detection of gut microbiota and pathogen produced N-acyl homoserine in host circulation and tissues	20
Chicken cecal microbiota reduces abdominal fat deposition by regulating fat metabolism	19
Deep insights into the gut microbial community of extreme longevity in south Chinese centenarians by ultra-deep metagenomics and large-scale culturomics	19
Fluorescent nanosensors reveal dynamic pH gradients during biofilm formation	19
Artificial consortium demonstrates emergent properties of enhanced cellulosic-sugar degradation and biofuel synthesis	19
Carbohydrates from Pseudomonas aeruginosa biofilms interact with immune C-type lectins and interfere with their receptor function	19
Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism	19
The hallmarks of dietary intervention-resilient gut microbiome	19
A regulatory network involving Rpo, Gac and Rsm for nitrogen-fixing biofilm formation by Pseudomonas stutzeri	18
The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia	18
Quantifying the effects of antibiotic treatment on the extracellular polymer network of antimicrobial resistant and sensitive biofilms using multiple particle tracking	18
In situ monitoring of Lentilactobacillus parabuchneri biofilm formation via real-time infrared spectroscopy	17
Gut microbiome dysregulation drives bone damage in broiler tibial dyschondroplasia by disrupting glucose homeostasis	17
Microbiome variation correlates with the insecticide susceptibility in different geographic strains of a significant agricultural pest, Nilaparvata lugens	17
Characterization of oral virome and microbiome revealed distinctive microbiome disruptions in paediatric patients with hand, foot and mouth disease	17
Inflammatory microbes and genes as potential biomarkers of Parkinson’s disease	17
Extracellular vesicles of the Gram-positive gut symbiont Bifidobacterium longum induce immune-modulatory, anti-inflammatory effects	17
The neglected role of micronutrients in predicting soil microbial structure	17
Biofilms can act as plasmid reserves in the absence of plasmid specific selection	17
Cytochrome bd promotes Escherichia coli biofilm antibiotic tolerance by regulating accumulation of noxious chemicals	17
Gut microbiome responses to dietary intervention with hypocholesterolemic vegetable oils	17
Nisin probiotic prevents inflammatory bone loss while promoting reparative proliferation and a healthy microbiome	16
Glycoside hydrolase processing of the Pel polysaccharide alters biofilm biomechanics and Pseudomonas aeruginosa virulence	16
Neutralization of ionic interactions by dextran-based single-chain nanoparticles improves tobramycin diffusion into a mature biofilm	16
Gut microbiome determines therapeutic effects of OCA on NAFLD by modulating bile acid metabolism	16
Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics	16
Time-restricted feeding induces Lactobacillus- and Akkermansia-specific functional changes in the rat fecal microbiota	16
The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors	16
Gut microbiome signatures of extreme environment adaption in Tibetan pig	15
No hints at glyphosate-induced ruminal dysbiosis in cows	15
Antimicrobial potential of known and novel probiotics on in vitro periodontitis biofilms	15
Reduction of alternative electron acceptors drives biofilm formation in Shewanella algae	15
In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus	15
Identification and characterization of novel endolysins targeting Gardnerella vaginalis biofilms to treat bacterial vaginosis	15
Mucin glycans drive oral microbial community composition and function	15
Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut	15
Protease activities of vaginal Porphyromonas species disrupt coagulation and extracellular matrix in the cervicovaginal niche	14
Colonization with ubiquitous protist Blastocystis ST1 ameliorates DSS-induced colitis and promotes beneficial microbiota and immune outcomes	14
Microbiome-derived antimicrobial peptides offer therapeutic solutions for the treatment of Pseudomonas aeruginosa infections	14
Large-scale characterisation of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population	14
Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium	14
Microrheology of Pseudomonas aeruginosa biofilms grown in wound beds	14
Microbiome assembly predictably shapes diversity across a range of disturbance frequencies in experimental microcosms	14
Csu pili dependent biofilm formation and virulence of Acinetobacter baumannii	14
Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment	13
Proteome-wide prediction of bacterial carbohydrate-binding proteins as a tool for understanding commensal and pathogen colonisation of the vaginal microbiome	13
Nitrate and a nitrate-reducing Rothia aeria strain as potential prebiotic or synbiotic treatments for periodontitis	13
Biofilms preserve the transmissibility of a multi-drug resistance plasmid	13
Staphylococcus aureus utilizes environmental RNA as a building material in specific polysaccharide-dependent biofilms	13
Tumour microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients	13
Assessing saliva microbiome collection and processing methods	13
Lifestyle-specific S-nitrosylation of protein cysteine thiols regulates Escherichia coli biofilm formation and resistance to oxidative stress	13
Intracellular bacteria in cancer—prospects and debates	13
Atypical cyclic di-AMP signaling is essential for Porphyromonas gingivalis growth and regulation of cell envelope homeostasis and virulence	13
Distinct colon mucosa microbiomes associated with tubular adenomas and serrated polyps	13
Modulating biofilm can potentiate activity of novel plastic-degrading enzymes	12
Role of mucus-bacteria interactions in Enterotoxigenic Escherichia coli (ETEC) H10407 virulence and interplay with human microbiome	12
The phosphorylated regulator of chemotaxis is crucial throughout biofilm biogenesis in Shewanella oneidensis	12
Phenotypic correlates of the working dog microbiome	12
Filamentous fungal biofilms: Conserved and unique aspects of extracellular matrix composition, mechanisms of drug resistance and regulatory networks in Aspergillus fumigatus	12
Metabolic plasticity enables lifestyle transitions of Porphyromonas gingivalis	12
How probiotics, prebiotics, synbiotics, and postbiotics prevent dental caries: an oral microbiota perspective	12
Longitudinal characterization of multispecies microbial populations recovered from spaceflight potable water	12
Mechanisms of fungal community assembly in wild stoneflies moderated by host characteristics and local environment	12

Activity-based protein profiling identifies alternating activation of enzymes involved in the bifidobacterium shunt pathway or mucin degradation in the gut microbiome response to soluble dietary fiber	11
CO2 enhances the formation, nutrient scavenging and drug resistance properties of C. albicans biofilms	11
Assessing the inflammatory response to in vitro polymicrobial wound biofilms in a skin epidermis model	11
Neighborhood socioeconomic status is associated with low diversity gut microbiomes and multi-drug resistant microorganism colonization	11
Inactivation and sensitization of Pseudomonas aeruginosa by microplasma jet array for treating otitis media	11
A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria	11
Pulcherrimin protects Bacillus subtilis against oxidative stress during biofilm development	11
Early microbial markers of periodontal and cardiometabolic diseases in ORIGINS	11
Limosilactobacillus mucosae-derived extracellular vesicles modulates macrophage phenotype and orchestrates gut homeostasis in a diarrheal piglet model	11
Treatment with a neutrophil elastase inhibitor and ofloxacin reduces P. aeruginosa burden in a mouse model of chronic suppurative otitis media	11
A meta-analysis of acetogenic and methanogenic microbiomes in microbial electrosynthesis	11
The effect of toxic pyridine-alkaloid secondary metabolites on the sunbird gut microbiome	11
Akkermansia muciniphila inhibited the periodontitis caused by Fusobacterium nucleatum	10
Functional metagenomic analysis of quorum sensing signaling in a nitrifying community	10
Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation	10
Niche differentiation drives microbial community assembly and succession in full-scale activated sludge bioreactors	10
Donor-dependent fecal microbiota transplantation efficacy against necrotizing enterocolitis in preterm pigs	10
GGDEF domain as spatial on-switch for a phosphodiesterase by interaction with landmark protein HubP	10
In-depth insights into cervicovaginal microbial communities and hrHPV infections using high-resolution microbiome profiling	10
The microbiota-gut-kidney axis mediates host osmoregulation in a small desert mammal	10
Clostridioides difficile bile salt hydrolase activity has substrate specificity and affects biofilm formation	10
Metagenomic and metatranscriptomic insights into sulfate-reducing bacteria in a revegetated acidic mine wasteland	10
Biophysical properties at patch scale shape the metabolism of biofilm landscapes	10
Daily full spectrum light exposure prevents food allergy-like allergic diarrhea by modulating vitamin D3 and microbiota composition	10
Socioeconomic disparities and household crowding in association with the fecal microbiome of school-age children	10
Active layer dynamics drives a transition to biofilm fingering	10
Impaired amino acid uptake leads to global metabolic imbalance of Candida albicans biofilms	10
Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota	9
Biofilm cultivation facilitates coexistence and adaptive evolution in an industrial bacterial community	9
Three-dimensional low shear culture of Mycobacterium bovis BCG induces biofilm formation and antimicrobial drug tolerance	9
Distinct types of multicellular aggregates in Pseudomonas aeruginosa liquid cultures	9
The structure of Brazilian Amazonian gut microbiomes in the process of urbanisation	9
Spinal cord injury-induced gut dysbiosis influences neurological recovery partly through short-chain fatty acids	9
Extracellular amoebal-vesicles: potential transmission vehicles for respiratory viruses	9
Bacterial lipopolysaccharide modulates immune response in the colorectal tumor microenvironment	9
Saliva-derived microcosm biofilms grown on different oral surfaces in vitro	9
Inulin-enriched Megamonas funiformis ameliorates metabolic dysfunction-associated fatty liver disease by producing propionic acid	9
Four species of bacteria deterministically assemble to form a stable biofilm in a millifluidic channel	9
Ecological change of the gut microbiota during pregnancy and progression to dyslipidemia	9
The tongue biofilm metatranscriptome identifies metabolic pathways associated with the presence or absence of halitosis	9
Investigating the oral microbiome in retrospective and prospective cases of prostate, colon, and breast cancer	8
Bactericidal synergism between phage endolysin Ply2660 and cathelicidin LL-37 against vancomycin-resistant Enterococcus faecalis biofilms	8
Developmental intestinal microbiome alterations in canine fading puppy syndrome: a prospective observational study	8
Antibiotic treatment can exacerbate biofilm-associated infection by promoting quorum cheater development	8
Vaginal microbiome topic modeling of laboring Ugandan women with and without fever	8
Biodiversity of the beneficial soil-borne fungi steered by Trichoderma-amended biofertilizers stimulates plant production	8
Body weight index indicates the responses of the fecal microbiota, metabolome and proteome to beef/chicken-based diet alterations in Chinese volunteers	8
Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments	8
Variation of Antigen 43 self-association modulates bacterial compacting within aggregates and biofilms	8
Synthetic periphyton as a model system to understand species dynamics in complex microbial freshwater communities	8
Mitochondrial dysfunction promotes microbial composition that negatively impacts on ulcerative colitis development and progression	8
Probiotics alleviate constipation and inflammation in late gestating and lactating sows	7
Dietary fat promotes antibiotic-induced Clostridioides difficile mortality in mice	7
Vaccination with an HIV T-cell immunogen induces alterations in the mouse gut microbiota	7
Nasal symbiont Staphylococcus epidermidis restricts the cellular entry of influenza virus into the nasal epithelium	7
ToxR is a c-di-GMP binding protein that modulates surface-associated behaviour in Pseudomonas aeruginosa	7
The sanitary indoor environment—a potential source for intact human-associated anaerobes	7
Interspecies competition in oral biofilms mediated by Streptococcus gordonii extracellular deoxyribonuclease SsnA	7
Impaired flux of bile acids from the liver to the gut reveals microbiome-immune interactions associated with liver damage	7
Bacterial biofilm functionalization through Bap amyloid engineering	7
BCM3D 2.0: accurate segmentation of single bacterial cells in dense biofilms using computationally generated intermediate image representations	7
Bacterial capsules: Occurrence, mechanism, and function	7
The car tank lid bacteriome: a reservoir of bacteria with potential in bioremediation of fuel	7
Author Correction: Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization	7
Enhancing tumor-specific recognition of programmable synthetic bacterial consortium for precision therapy of colorectal cancer	7
Dissecting the impact of dietary fiber type on atherosclerosis in mice colonized with different gut microbial communities	7
Impact of the repurposed drug thonzonium bromide on host oral-gut microbiomes	7
The Wsp chemosensory system modulates c-di-GMP-dependent biofilm formation by integrating DSF quorum sensing through the WspR-RpfG complex in Lysobacter	7
Gut microbiome responds compositionally and functionally to the seasonal diet variations in wild gibbons	7
Controlled spatial organization of bacterial growth reveals key role of cell filamentation preceding Xylella fastidiosa biofilm formation	7
The Pga59 cell wall protein is an amyloid forming protein involved in adhesion and biofilm establishment in the pathogenic yeast Candida albicans	7