npj Biofilms and Microbiomes

Article	Citations
Iron limitation-induced endophytic Ammoniphilus assemblage promotes root apoplastic iron remobilization by attenuation of salicylic acid pathways	256
Plasticity of the gut microbiome of golden snub-nosed monkeys (Rhinopithecus roxellana) in response to seasonal variation in diet	156
Partial convergence of the human vaginal and rectal maternal microbiota in late gestation and early post-partum	149
Dual-functionality of Nocardiopsis alba B57 in biocontrol and plant growth: a metabolomic approach to agricultural sustainability	127
An in vitro fermentation model to study the impact of bacteriophages targeting Shiga toxin-encoding Escherichia coli on the colonic microbiota	125
Gene horizontal transfers and functional diversity negatively correlated with bacterial taxonomic diversity along a nitrogen gradient	107
Fusobacterium nucleatum is enriched in invasive biofilms in colorectal cancer	89
In situ monitoring of Lentilactobacillus parabuchneri biofilm formation via real-time infrared spectroscopy	89
Akkermansia muciniphila inhibited the periodontitis caused by Fusobacterium nucleatum	78
Diverse polysaccharide production and biofilm formation abilities of clinical Klebsiella pneumoniae	77
Evolution of genotypic and phenotypic diversity in multispecies biofilms	72
Bacteria contribute exopolysaccharides to an algal-bacterial joint extracellular matrix	69
One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density	68
Lactobacillus plantarum L168 improves hyperoxia-induced pulmonary inflammation and hypoalveolarization in a rat model of bronchopulmonary dysplasia	67
Neutralization of ionic interactions by dextran-based single-chain nanoparticles improves tobramycin diffusion into a mature biofilm	66
Pharmacodynamics of interspecies interactions in polymicrobial infections	64
Targeted metabolomics reveals bioactive inflammatory mediators from gut into blood circulation in children with NAFLD	64
Early microbial markers of periodontal and cardiometabolic diseases in ORIGINS	64
In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus	63
The dynamics of microbiome and virome in migratory birds of southwest China	61
Harnessing vaginal inflammation and microbiome: a machine learning model for predicting IVF success	60
Ex vivo intestinal permeability assay (X-IPA) for tracking barrier function dynamics	60
Simulation of catalase-dependent tolerance of microbial biofilm to hydrogen peroxide with a biofilm computer model	59
Microbiota-host crosstalk: the role of short-term dietary restriction in neurological and metabolic dysregulation	58
Alternate-day fasting ameliorates α-synuclein pathology and suppresses inflammation via the gut-brain axis in an MPTP-induced subacute mouse model of Parkinson’s disease	57

Beyond the matrix: rethinking antibiotic tolerance in CF biofilms using 3D models	57
Donor-recipient specificity and age-dependency in fecal microbiota therapy and probiotic resolution of gastrointestinal symptoms	56
Colonization with ubiquitous protist Blastocystis ST1 ameliorates DSS-induced colitis and promotes beneficial microbiota and immune outcomes	56
The impact of antioxidant-ciprofloxacin combinations on the evolution of antibiotic resistance in Pseudomonas aeruginosa biofilms	55
Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut	54
Diffusion-based mechanism explains spatial organization in cross-feeding biofilms	54
Secreted nucleases reclaim extracellular DNA during biofilm development	53
Protecting the piglet gut microbiota against ETEC-mediated post-weaning diarrhoea using specific binding proteins	53
The gut microbiota modulate locomotion via vagus-dependent glucagon-like peptide-1 signaling	53
Interspecies competition in oral biofilms mediated by Streptococcus gordonii extracellular deoxyribonuclease SsnA	53
Social demographics determinants for resistome and microbiome variation of a multiethnic community in Southern Malaysia	52
Clostridium difficile-derived membrane vesicles promote fetal growth restriction via inhibiting trophoblast motility through PPARγ/RXRα/ANGPTL4 axis	52
Host specificity and cophylogeny in the “animal-gut bacteria-phage” tripartite system	51
Adaptation of a methanogen to Fe0 corrosion via direct contact	49
Disentangling the feedback loops driving spatial patterning in microbial communities	48
ToxR is a c-di-GMP binding protein that modulates surface-associated behaviour in Pseudomonas aeruginosa	46
Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates	46
Impact of a multi-strain L. crispatus-based vaginal synbiotic on the vaginal microbiome: a randomized placebo-controlled trial	46
Integrative metagenomic and metabolomic analyses reveal the potential of gut microbiota to exacerbate acute pancreatitis	43
Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors	43
The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival	42
Rational consideration of Akkermansia muciniphila targeting intestinal health: advantages and challenges	42
Prokaryotic evolution shapes specialized communities in long term engineered pit mud ecosystem	41
Adaptation and phenotypic diversification of Bacillus thuringiensis biofilm are accompanied by fuzzy spreader morphotypes	39
Interaction between tissue-dwelling helminth and the gut microbiota drives mucosal immunoregulation	38
Gut microbes modulate the effects of the flavonoid quercetin on atherosclerosis	38
OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients	37
Latent evolution of biofilm formation depends on life-history and genetic background	36
Tanzanian gut microbiota profiles linked to high but rapidly waning yellow fever antibody titers	36
Genotoxic stress stimulates eDNA release via explosive cell lysis and thereby promotes streamer formation of Burkholderia cenocepacia H111 cultured in a microfluidic device	36
Gut-resident Phascolarctobacterium succinatutens decreases fat accumulation via MYC-driven epigenetic regulation of arginine biosynthesis	36
Environmental factors drive bacterial degradation of gastrointestinal mucus	36
Microbiome and well-being: a meta-analysis	36
Gut and oral microbiota in gynecological cancers: interaction, mechanism, and therapeutic value	35
Targeted proteomics reveal α-MSH-like Enterobacterial ClpB protein in gut microbiota of patients with anorexia nervosa	35
Multi-omic profiling reveals distinct gut microbial and metabolic landscapes in golden snub-nosed monkeys under contrasting conservation strategies	35
The Wsp chemosensory system modulates c-di-GMP-dependent biofilm formation by integrating DSF quorum sensing through the WspR-RpfG complex in Lysobacter	34
Oral and middle ear delivery of otitis media standard of care antibiotics, but not biofilm-targeted antibodies, alter chinchilla nasopharyngeal and fecal microbiomes	33
Selective inhibition of the amyloid matrix of Escherichia coli biofilms by a bifunctional microbial metabolite	33
Microbial solutions must be deployed against climate catastrophe	33
Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation	33
Endolysin selectively kills Gardnerella ex vivo in vaginal samples from women with bacterial vaginosis	33
Short term supplementation with cranberry extract modulates gut microbiota in human and displays a bifidogenic effect	32
Thwarting resistance: MgrA inhibition with methylophiopogonanone a unveils a new battlefront against S. aureus	32
Harnessing machine learning to predict antibiotic susceptibility in Pseudomonas aeruginosa biofilms	31
Matrix is everywhere: extracellular DNA is a link between biofilm and mineralization in Bacillus cereus planktonic lifestyle	31
Gut microbiota alterations are linked to COVID-19 severity in North African and European populations	31
Variation of Antigen 43 self-association modulates bacterial compacting within aggregates and biofilms	31
Synergistic effects of commensals and phage predation in suppressing colonization by pathogenic Vibrio parahaemolyticus	30
Antimicrobial and antibiotic-potentiating effect of calcium peroxide nanoparticles on oral bacterial biofilms	30

Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection	30
A rationally designed microbial consortium modulates neurodegeneration in a Drosophila melanogaster model of Parkinson’s disease	30
Author Correction: Bifidobacterium animalis Probio-M8 improves sarcopenia physical performance by mitigating creatine restrictions imposed by microbial metabolites	30
Atypical cyclic di-AMP signaling is essential for Porphyromonas gingivalis growth and regulation of cell envelope homeostasis and virulence	30
Inflammatory microbes and genes as potential biomarkers of Parkinson’s disease	29
Impact of structurally diverse polysaccharides on colonic mucin O-glycosylation and gut microbiota	29
Nisin lantibiotic prevents NAFLD liver steatosis and mitochondrial oxidative stress following periodontal disease by abrogating oral, gut and liver dysbiosis	29
Microbial mat compositions and localization patterns explain the virulence of black band disease in corals	28
Nitrate and a nitrate-reducing Rothia aeria strain as potential prebiotic or synbiotic treatments for periodontitis	28
The role of gut microbiota-gonadal axis in ovary activation of Asian honey bee (Apis cerana) queens	28
Multi-omics profiling of dairy cattle oxidative stress identifies hindgut-derived Phascolarctobacterium succinatutens exhibiting antioxidant activity	28
Coconut rhinoceros beetle digestive symbiosis with potential plant cell wall degrading microbes	28
Engineered Mycoplasma pneumoniae targeting dual-species bacterial biofilms: a novel strategy against infections	27
The cell wall lipoprotein CD1687 acts as a DNA binding protein during deoxycholate-induced biofilm formation in Clostridioides difficile	27
Identification of ferredoxin PA1551 as an antibacterial synergistic target for biofilm inhibitors against Pseudomonas aeruginosa	27
Cpx-signalling facilitates Hms-dependent biofilm formation by Yersinia pseudotuberculosis	27
Minibioreactor arrays to model microbiome response to alcohol and tryptophan in the context of alcohol-associated liver disease	27
Fusobacterium lineage profiling facilitates the clarification of the associations between non-nucleatum Fusobacterium and colorectal cancer	27
Facemask acne attenuation through modulation of indirect microbiome interactions	27
Coastal rest during the COVID-19 pandemic enhances microbial community stability and metabolic potential in a subterranean estuary	26
UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog	26
Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota	26
Spinal cord injury-induced gut dysbiosis influences neurological recovery partly through short-chain fatty acids	26
MicroMap: a network visualisation resource for human microbiome metabolism	26
Density and temperature controlled fluid extraction in a bacterial biofilm is determined by poly-γ-glutamic acid production	26
Intracellular bacteria in cancer—prospects and debates	25
Periodontitis-associated Fusobacterium nucleatum promotes ulcerative colitis by ferroptosis-mediated gut barrier disruption	25
Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism	25
Immune dysfunction during S. aureus biofilm-associated implant infections: opportunities for novel therapeutic strategies	25
Temporal turnover of viral biodiversity and functional potential in intertidal wetlands	25
Inulin-enriched Megamonas funiformis ameliorates metabolic dysfunction-associated fatty liver disease by producing propionic acid	25
Hypertension inhibition by Dubosiella newyorkensis via reducing pentosidine synthesis	24
Antibiotic treatment can exacerbate biofilm-associated infection by promoting quorum cheater development	24
Impact of trace metal supplementation on anaerobic biological methanation under hydrogen and carbon dioxide starvation	24
Economic significance of biofilms: a multidisciplinary and cross-sectoral challenge	23
The tongue biofilm metatranscriptome identifies metabolic pathways associated with the presence or absence of halitosis	23
Mesaconic acid as a key metabolite with anti-inflammatory and anti-aging properties produced by Lactobacillus plantarum 124 from centenarian gut microbiota	23
Community successional patterns and inter-kingdom interactions during granular biofilm development	23
The highly differentiated gut of Pachnoda marginata hosts sequential microbiomes: microbial ecology and potential applications	23
Recent advances in single-cell engineered live biotherapeutic products research for skin repair and disease treatment	23
Hydrodynamic conditions affect the proteomic profile of marine biofilms formed by filamentous cyanobacterium	23
The Bifidobacterium-dominated fecal microbiome in dairy calves shapes the characteristic growth phenotype of host	23
Preventing bacterial adhesion to skin by altering their physicochemical cell surface properties specifically	23
The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors	23
Mitochondrial dysfunction promotes microbial composition that negatively impacts on ulcerative colitis development and progression	23
Body weight index indicates the responses of the fecal microbiota, metabolome and proteome to beef/chicken-based diet alterations in Chinese volunteers	22
Time-resolved compositional and dynamics analysis of biofilm maturation and dispersal via solid-state NMR spectroscopy	22
L-citrulline protects testicular Sertoli cell function by mitigating DNA damage via the gut-testis axis of sheep fed a high-concentrate diet	21
Novel antimicrobial peptides and peptide-microbiome crosstalk in Appalachian salamander skin	21
Staphylococcus aureus utilizes environmental RNA as a building material in specific polysaccharide-dependent biofilms	21
Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance	21
Non disseminative nano-strategy against in vivo Staphylococcus aureus biofilms	21
Deep generative modeling of annotated bacterial biofilm images	21
Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms	21
Metagenomic analysis reveals the novel role of vaginal Lactobacillus iners in Chinese healthy pregnant women	21
Ecological change of the gut microbiota during pregnancy and progression to dyslipidemia	20
Gut microbiota-mediated secondary bile acid alleviates Staphylococcus aureus-induced mastitis through the TGR5-cAMP-PKA-NF-κB/NLRP3 pathways in mice	20
Staphylococcus epidermidis alters macrophage polarization and phagocytic uptake by extracellular DNA release in vitro	20
Long-chain 4-aminoquinolines inhibit filamentation and increase efficacy of nystatin against Candida albicans infections in vivo	20
Gut microbiome responses to dietary intervention with hypocholesterolemic vegetable oils	20
Author Correction: Bacterial biofilm-derived H-NS protein acts as a defense against Neutrophil Extracellular Traps (NETs)	20
Spaceflight alters host-gut microbiota interactions	20
Synthetic periphyton as a model system to understand species dynamics in complex microbial freshwater communities	20
The car tank lid bacteriome: a reservoir of bacteria with potential in bioremediation of fuel	20
Environmental determinants and demographic influences on global urban microbiomes, antimicrobial resistance and pathogenicity	20
Publisher Correction: Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis	19
Irrigation of the intramedullary channel improves outcome of DAIR in a sheep model	19
Parabacteroides as a promising target for disease intervention: current stage and pending issues	19
On validly published names, correct names, and changes in the nomenclature of phyla and genera of prokaryotes: a guide for the perplexed	19
Infant gut microbiota and SCFAs mediate the association between early-life human milk microbiota and neurodevelopment	19
Bacterial c-di-GMP triggers metamorphosis of mussel larvae through a STING receptor	19
Temporal dynamics, microdiversity, and ecological functions of viral communities during cyanobacterial blooms in Lake Taihu	19
Garvicin Q-producing Lactococcus garvieae LG3092: its role in mitigating dysbiosis and H. pylori-associated gastritis	19
The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations	19
Alginate exopolymer significantly modulates the viscoelastic properties and resilience of bacterial biofilms	19
Microbiome and metabolic disruption in acute vs. severe and enduring anorexia nervosa	19
Polybacterial intracellular macromolecules shape single-cell inflammatory profiles in upper airway epithelia	19
Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion	18
Bacterial capsules: Occurrence, mechanism, and function	18
Extracellular vesicles of the Gram-positive gut symbiont Bifidobacterium longum induce immune-modulatory, anti-inflammatory effects	18

Emergent roles of infant gut microbes during the utilization of human milk oligosaccharides	18
(p)ppGpp imposes graded transcriptional changes to impair motility and promote antibiotic tolerance in biofilms	18
In-depth insights into cervicovaginal microbial communities and hrHPV infections using high-resolution microbiome profiling	18
Periodontitis salivary microbiota exacerbates colitis-induced anxiety-like behavior via gut microbiota	18
Multi-omics framework integrating genetics microbiome and immunity for understanding motor neuron degeneration pathogenesis	18