npj Biofilms and Microbiomes

Article	Citations
Analysis of microbial compositions: a review of normalization and differential abundance analysis	118
Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization	110
Three faces of biofilms: a microbial lifestyle, a nascent multicellular organism, and an incubator for diversity	92
Metagenomic analysis revealed the potential role of gut microbiome in gout	89
Interactions of plasma-activated water with biofilms: inactivation, dispersal effects and mechanisms of action	87
Economic significance of biofilms: a multidisciplinary and cross-sectoral challenge	82
Microbial predictors of healing and short-term effect of debridement on the microbiome of chronic wounds	81
Berberine attenuates choline-induced atherosclerosis by inhibiting trimethylamine and trimethylamine-N-oxide production via manipulating the gut microbiome	80
Metaproteomics characterizes human gut microbiome function in colorectal cancer	78
Seasonal dynamics of diet–gut microbiota interaction in adaptation of yaks to life at high altitude	74
Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale	64
The sources and transmission routes of microbial populations throughout a meat processing facility	63
Host development overwhelms environmental dispersal in governing the ecological succession of zebrafish gut microbiota	59
Who put the film in biofilm? The migration of a term from wastewater engineering to medicine and beyond	58
Systematic analysis of gut microbiota in pregnant women and its correlations with individual heterogeneity	54
Temporospatial shifts in the human gut microbiome and metabolome after gastric bypass surgery	53
Microbial co-occurrence network topological properties link with reactor parameters and reveal importance of low-abundance genera	52
Treatment with Anaerobutyricum soehngenii: a pilot study of safety and dose–response effects on glucose metabolism in human subjects with metabolic syndrome	50
Oral biofilms exposure to chlorhexidine results in altered microbial composition and metabolic profile	50
Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics	49
Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth	48
Parameters influencing the development of highly conductive and efficient biofilm during microbial electrosynthesis: the importance of applied potential and inorganic carbon source	45
Exposure of Salmonella biofilms to antibiotic concentrations rapidly selects resistance with collateral tradeoffs	44
Burns and biofilms: priority pathogens and in vivo models	43
Vaginal microbiota and human papillomavirus infection among young Swedish women	43

Biofilms harbour Clostridioides difficile, serving as a reservoir for recurrent infection	42
Bacterial vaginosis and health-associated bacteria modulate the immunometabolic landscape in 3D model of human cervix	41
Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis	41
Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees	40
Biofilm viability checker: An open-source tool for automated biofilm viability analysis from confocal microscopy images	39
The biofilm-associated surface protein Esp of Enterococcus faecalis forms amyloid-like fibers	39
The biofilm matrix scaffold of Pseudomonas aeruginosa contains G-quadruplex extracellular DNA structures	38
Integrated metagenomics identifies a crucial role for trimethylamine-producing Lachnoclostridium in promoting atherosclerosis	38
Identification of small molecules that interfere with c-di-GMP signaling and induce dispersal of Pseudomonas aeruginosa biofilms	37
Improved functionality of Ligilactobacillus salivarius Li01 in alleviating colonic inflammation by layer-by-layer microencapsulation	37
Interactions between gut microbiota and metabolites modulate cytokine network imbalances in women with unexplained miscarriage	36
Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization	36
Nonlinear rheological characteristics of single species bacterial biofilms	35
Gut microbiota determines the social behavior of mice and induces metabolic and inflammatory changes in their adipose tissue	34
Polymicrobial periodontal disease triggers a wide radius of effect and unique virome	34
Synergistic action of phage phiIPLA-RODI and lytic protein CHAPSH3b: a combination strategy to target Staphylococcus aureus biofilms	33
Soil microbiome manipulation triggers direct and possible indirect suppression against Ralstonia solanacearum and Fusarium oxysporum	33
Intestinal release of biofilm-like microcolonies encased in calcium-pectinate beads increases probiotic properties of Lacticaseibacillus paracasei	32
Bio-priming with a hypovirulent phytopathogenic fungus enhances the connection and strength of microbial interaction network in rapeseed	32
Human organoid biofilm model for assessing antibiofilm activity of novel agents	31
Lung microbiota associations with clinical features of COPD in the SPIROMICS cohort	31
Real-time monitoring of ruminal microbiota reveals their roles in dairy goats during subacute ruminal acidosis	31
Metagenomic analysis of bacterial species in tongue microbiome of current and never smokers	30
The evolutionary trajectories of P. aeruginosa in biofilm and planktonic growth modes exposed to ciprofloxacin: beyond selection of antibiotic resistance	29
Host-microbiome interactions: Gut-Liver axis and its connection with other organs	29
An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1	29
A bacteriocin-based antimicrobial formulation to effectively disrupt the cell viability of methicillin-resistant Staphylococcus aureus (MRSA) biofilms	29
Atherosclerosis amelioration by allicin in raw garlic through gut microbiota and trimethylamine-N-oxide modulation	28
Streptococcus mutans adhesion force sensing in multi-species oral biofilms	28
Disrupting quorum sensing alters social interactions in Chromobacterium violaceum	28
Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing	28
Responses of soil microbiome to steel corrosion	28
The zoonotic pathogen Leptospira interrogans mitigates environmental stress through cyclic-di-GMP-controlled biofilm production	28
Biological role of EPS from Pseudomonas syringae pv. syringae UMAF0158 extracellular matrix, focusing on a Psl-like polysaccharide	27
Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth–gut axis	27
Experimental parameters defining ultra-low biomass bioaerosol analysis	27
A multiomics approach to identify host-microbe alterations associated with infection severity in diabetic foot infections: a pilot study	26
A new BiofilmChip device for testing biofilm formation and antibiotic susceptibility	26
Identification of essential genes for Escherichia coli aryl polyene biosynthesis and function in biofilm formation	26
Network-directed efficient isolation of previously uncultivated Chloroflexi and related bacteria in hot spring microbial mats	26
Gut dysbiosis and mortality in hemodialysis patients	26
Veillonellaceae family members uniquely alter the cervical metabolic microenvironment in a human three-dimensional epithelial model	24
Gut microbiota and metabolites of α-synuclein transgenic monkey models with early stage of Parkinson’s disease	24
Impact of temperature-dependent phage expression on Pseudomonas aeruginosa biofilm formation	24
Transcriptomic evidence for versatile metabolic activities of mercury cycling microorganisms in brackish microbial mats	23
Biogeographical patterns and mechanisms of microbial community assembly that underlie successional biocrusts across northern China	23
Reduced stress-associated FKBP5 DNA methylation together with gut microbiota dysbiosis is linked with the progression of obese PCOS patients	23
Uncharted waters: the unintended impacts of residual chlorine on water quality and biofilms	22
Salivary dysbiosis in Sjögren’s syndrome and a commensal-mediated immunomodulatory effect of salivary gland epithelial cells	22
Engineered lactobacilli display anti-biofilm and growth suppressing activities against Pseudomonas aeruginosa	22

Genetic requirements and transcriptomics of Helicobacter pylori biofilm formation on abiotic and biotic surfaces	21
Diversity and infectivity of the RNA virome among different cryptic species of an agriculturally important insect vector: whitefly Bemisia tabaci	21
Biofilm-isolated Listeria monocytogenes exhibits reduced systemic dissemination at the early (12–24 h) stage of infection in a mouse model	21
Magnetotactic bacteria and magnetofossils: ecology, evolution and environmental implications	20
Detection of gut microbiota and pathogen produced N-acyl homoserine in host circulation and tissues	20
Rational consideration of Akkermansia muciniphila targeting intestinal health: advantages and challenges	20
Network mapping of root–microbe interactions in Arabidopsis thaliana	19
Inter-species Metabolic Interactions in an In-vitro Minimal Human Gut Microbiome of Core Bacteria	19
Attachment and antibiotic response of early-stage biofilms studied using resonant hyperspectral imaging	18
Fluorescent nanosensors reveal dynamic pH gradients during biofilm formation	18
Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host	18
Biofilm antimicrobial susceptibility through an experimental evolutionary lens	18
The human respiratory tract microbial community structures in healthy and cystic fibrosis infants	18
IolR, a negative regulator of the myo-inositol metabolic pathway, inhibits cell autoaggregation and biofilm formation by downregulating RpmA in Aeromonas hydrophila	18
Microbial electroactive biofilms dominated by Geoalkalibacter spp. from a highly saline–alkaline environment	18
Periodontitis associates with species-specific gene expression of the oral microbiota	17
The role of shear dynamics in biofilm formation	17
The role of Psl in the failure to eradicate Pseudomonas aeruginosa biofilms in children with cystic fibrosis	17
Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors	17
Gut microbiome development in early childhood is affected by day care attendance	17
Evolution of biofilm-adapted gene expression profiles in lasR-deficient clinical Pseudomonas aeruginosa isolates	17
Human supplementation with Pediococcus acidilactici GR-1 decreases heavy metals levels through modifying the gut microbiota and metabolome	16
The hallmarks of dietary intervention-resilient gut microbiome	16
Characterization of oral virome and microbiome revealed distinctive microbiome disruptions in paediatric patients with hand, foot and mouth disease	16
Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters	16
Carbohydrates from Pseudomonas aeruginosa biofilms interact with immune C-type lectins and interfere with their receptor function	16
Alternating magnetic fields and antibiotics eradicate biofilm on metal in a synergistic fashion	16
A regulatory network involving Rpo, Gac and Rsm for nitrogen-fixing biofilm formation by Pseudomonas stutzeri	16
Competition of two highly specialized and efficient acetoclastic electroactive bacteria for acetate in biofilm anode of microbial electrolysis cell	16
Translational challenges and opportunities in biofilm science: a BRIEF for the future	16
Porcine gut microbiota in mediating host metabolic adaptation to cold stress	16
Artificial consortium demonstrates emergent properties of enhanced cellulosic-sugar degradation and biofuel synthesis	15
The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia	15
Cytochrome bd promotes Escherichia coli biofilm antibiotic tolerance by regulating accumulation of noxious chemicals	15
Sucrose addition directionally enhances bacterial community convergence and network stability of the shrimp culture system	15
Systems view of Bacillus subtilis pellicle development	15
Reduction of alternative electron acceptors drives biofilm formation in Shewanella algae	14
Weaponizing volatiles to inhibit competitor biofilms from a distance	14
The right bug in the right place: opportunities for bacterial vaginosis treatment	14
Quantifying the effects of antibiotic treatment on the extracellular polymer network of antimicrobial resistant and sensitive biofilms using multiple particle tracking	14
Microrheology of Pseudomonas aeruginosa biofilms grown in wound beds	13
The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations	13
Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut	13
Soil microbial metabolism on carbon and nitrogen transformation links the crop-residue contribution to soil organic carbon	13
Time-restricted feeding induces Lactobacillus- and Akkermansia-specific functional changes in the rat fecal microbiota	13
Biofilms can act as plasmid reserves in the absence of plasmid specific selection	13
Role of adhesion forces in mechanosensitive channel gating in Staphylococcus aureus adhering to surfaces	13
Gut microbiota as an antioxidant system in centenarians associated with high antioxidant activities of gut-resident Lactobacillus	13
Gut microbiota-mediated secondary bile acid alleviates Staphylococcus aureus-induced mastitis through the TGR5-cAMP-PKA-NF-κB/NLRP3 pathways in mice	13
Long-term warming in a Mediterranean-type grassland affects soil bacterial functional potential but not bacterial taxonomic composition	12
Nisin probiotic prevents inflammatory bone loss while promoting reparative proliferation and a healthy microbiome	12
Automated quantification of Candida albicans biofilm-related phenotypes reveals additive contributions to biofilm production	12
In situ monitoring of Lentilactobacillus parabuchneri biofilm formation via real-time infrared spectroscopy	12
Deep insights into the gut microbial community of extreme longevity in south Chinese centenarians by ultra-deep metagenomics and large-scale culturomics	12
Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates	12
Lifestyle-specific S-nitrosylation of protein cysteine thiols regulates Escherichia coli biofilm formation and resistance to oxidative stress	12
Microbiome variation correlates with the insecticide susceptibility in different geographic strains of a significant agricultural pest, Nilaparvata lugens	12
Trichoderma-amended biofertilizer stimulates soil resident Aspergillus population for joint plant growth promotion	12
Impact of spatial proximity on territoriality among human skin bacteria	12
The gut microbiome-metabolome dataset collection: a curated resource for integrative meta-analysis	12
No hints at glyphosate-induced ruminal dysbiosis in cows	12
Neutralization of ionic interactions by dextran-based single-chain nanoparticles improves tobramycin diffusion into a mature biofilm	12
Temperature-regulated heterogeneous extracellular matrix gene expression defines biofilm morphology in Clostridium perfringens	12
Bacteroides uniformis-induced perturbations in colonic microbiota and bile acid levels inhibit TH17 differentiation and ameliorate colitis developments	11
Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics	11
The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors	11
Gut microbiome dysregulation drives bone damage in broiler tibial dyschondroplasia by disrupting glucose homeostasis	11
Influence of phosphate dosing on biofilms development on lead in chlorinated drinking water bioreactors	11
Gut microbiome responses to dietary intervention with hypocholesterolemic vegetable oils	11
In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus	11
Treatment with a neutrophil elastase inhibitor and ofloxacin reduces P. aeruginosa burden in a mouse model of chronic suppurative otitis media	11
Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota	11
One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density	11
Association of a dysbiotic oral microbiota with the development of focal lymphocytic sialadenitis in IκB-ζ-deficient mice	10
Staphylococcus aureus utilizes environmental RNA as a building material in specific polysaccharide-dependent biofilms	10
Identification and characterization of novel endolysins targeting Gardnerella vaginalis biofilms to treat bacterial vaginosis	10
Glycoside hydrolase processing of the Pel polysaccharide alters biofilm biomechanics and Pseudomonas aeruginosa virulence	10
Proteome-wide prediction of bacterial carbohydrate-binding proteins as a tool for understanding commensal and pathogen colonisation of the vaginal microbiome	10
Microbiome-derived antimicrobial peptides offer therapeutic solutions for the treatment of Pseudomonas aeruginosa infections	10
Donor-dependent fecal microbiota transplantation efficacy against necrotizing enterocolitis in preterm pigs	9

Longitudinal characterization of multispecies microbial populations recovered from spaceflight potable water	9
CO2 enhances the formation, nutrient scavenging and drug resistance properties of C. albicans biofilms	9
The neglected role of micronutrients in predicting soil microbial structure	9
Metabolic plasticity enables lifestyle transitions of Porphyromonas gingivalis	9
Inflammatory microbes and genes as potential biomarkers of Parkinson’s disease	9
Protease activities of vaginal Porphyromonas species disrupt coagulation and extracellular matrix in the cervicovaginal niche	9
Inactivation and sensitization of Pseudomonas aeruginosa by microplasma jet array for treating otitis media	9
The phosphorylated regulator of chemotaxis is crucial throughout biofilm biogenesis in Shewanella oneidensis	9
Environmental stress perception activates structural remodeling of extant Streptococcus mutans biofilms	9
Antimicrobial potential of known and novel probiotics on in vitro periodontitis biofilms	9
Extracellular amoebal-vesicles: potential transmission vehicles for respiratory viruses	9
Biofilms preserve the transmissibility of a multi-drug resistance plasmid	9
Microbiome assembly predictably shapes diversity across a range of disturbance frequencies in experimental microcosms	9
Assessing the inflammatory response to in vitro polymicrobial wound biofilms in a skin epidermis model	9
The effect of toxic pyridine-alkaloid secondary metabolites on the sunbird gut microbiome	9
The microbiota-gut-kidney axis mediates host osmoregulation in a small desert mammal	9
Assessing saliva microbiome collection and processing methods	8
Clinically adaptable polymer enables simultaneous spatial analysis of colonic tissues and biofilms	8
Ecological change of the gut microbiota during pregnancy and progression to dyslipidemia	8
Saliva-derived microcosm biofilms grown on different oral surfaces in vitro	8
Developmental intestinal microbiome alterations in canine fading puppy syndrome: a prospective observational study	8
Optotracing for selective fluorescence-based detection, visualization and quantification of live S. aureus in real-time	8
Four species of bacteria deterministically assemble to form a stable biofilm in a millifluidic channel	8
Functional metagenomic analysis of quorum sensing signaling in a nitrifying community	8
Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment	8
GGDEF domain as spatial on-switch for a phosphodiesterase by interaction with landmark protein HubP	8
Tumour microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients	8
Distinct colon mucosa microbiomes associated with tubular adenomas and serrated polyps	8
Large-scale characterisation of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population	8
Colonization with ubiquitous protist Blastocystis ST1 ameliorates DSS-induced colitis and promotes beneficial microbiota and immune outcomes	8
The structure of Brazilian Amazonian gut microbiomes in the process of urbanisation	8