npj Biofilms and Microbiomes

Article	Citations
An in vitro fermentation model to study the impact of bacteriophages targeting Shiga toxin-encoding Escherichia coli on the colonic microbiota	224
Dual-functionality of Nocardiopsis alba B57 in biocontrol and plant growth: a metabolomic approach to agricultural sustainability	177
Partial convergence of the human vaginal and rectal maternal microbiota in late gestation and early post-partum	146
A colon mimetic screening approach reveals Lactobacillus fermentum as a microbiome-based therapy for COPD	128
Gene horizontal transfers and functional diversity negatively correlated with bacterial taxonomic diversity along a nitrogen gradient	121
Phage-mediated expansion of the virulence gene types and enhanced ecological integration of pathogens in wild mice from human-impacted environments	115
Evolution of genotypic and phenotypic diversity in multispecies biofilms	113
Lactobacillus plantarum L168 improves hyperoxia-induced pulmonary inflammation and hypoalveolarization in a rat model of bronchopulmonary dysplasia	110
Pharmacodynamics of interspecies interactions in polymicrobial infections	105
Bacteria contribute exopolysaccharides to an algal-bacterial joint extracellular matrix	96
Machine learning and the role of the vaginal and fecal microbiome in miscarriage: a matched case-control study	92
In situ monitoring of Lentilactobacillus parabuchneri biofilm formation via real-time infrared spectroscopy	87
Plasticity of the gut microbiome of golden snub-nosed monkeys (Rhinopithecus roxellana) in response to seasonal variation in diet	87
Iron limitation-induced endophytic Ammoniphilus assemblage promotes root apoplastic iron remobilization by attenuation of salicylic acid pathways	86
Microbial messengers: decoding the gut microbiota’s role in bone health through immunomodulation and exosomal signaling	86
Fusobacterium nucleatum is enriched in invasive biofilms in colorectal cancer	86
One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density	85
Targeted metabolomics reveals bioactive inflammatory mediators from gut into blood circulation in children with NAFLD	81
Disruption of IgA-mediated aggregation at weaning favors mucus encroachment by commensal bacteria	80
Diverse polysaccharide production and biofilm formation abilities of clinical Klebsiella pneumoniae	78
Emerging non-antibiotic strategies for implant-associated biofilm infections by reprogramming the dysregulated immune microenvironment	77
Dietary copper-driven colonic dysbiosis mediates oxidative stress and butyrate deficiency to facilitate the spread of resistome in pigs	74
Akkermansia muciniphila inhibited the periodontitis caused by Fusobacterium nucleatum	73
Simulation of catalase-dependent tolerance of microbial biofilm to hydrogen peroxide with a biofilm computer model	72
Microbiota-host crosstalk: the role of short-term dietary restriction in neurological and metabolic dysregulation	72

Enzymes-enhanced antibiotic therapy reduces biofilms to undetectable levels in an implant-associated infection model	71
The impact of antioxidant-ciprofloxacin combinations on the evolution of antibiotic resistance in Pseudomonas aeruginosa biofilms	69
Diffusion-based mechanism explains spatial organization in cross-feeding biofilms	68
Harnessing vaginal inflammation and microbiome: a machine learning model for predicting IVF success	68
The microbiota-gut-brain axis: novel mechanisms and therapeutic frontiers in obesity and type 2 diabetes	68
Colonization with ubiquitous protist Blastocystis ST1 ameliorates DSS-induced colitis and promotes beneficial microbiota and immune outcomes	67
Protecting the piglet gut microbiota against ETEC-mediated post-weaning diarrhoea using specific binding proteins	65
Donor-recipient specificity and age-dependency in fecal microbiota therapy and probiotic resolution of gastrointestinal symptoms	64
The dynamics of microbiome and virome in migratory birds of southwest China	63
Multi-omics atlas of the bovine coronavirus-infected calf jejunum: reduction of Phocaeicola coprophilus and deoxycholic acid linked to Th17/Treg imbalance	62
Decoding phage communication: molecular networks, evolutionary dynamics, and therapeutic applications	62
Instance-based transfer learning enables cross-cohort early detection of colorectal cancer	62
pH regulates gut bacterial tryptophan metabolism	58
MicroICS: predictive phenotyping of Listeria monocytogenes biofilms from three-dimensional structural features	57
Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut	55
Secreted nucleases reclaim extracellular DNA during biofilm development	54
Ex vivo intestinal permeability assay (X-IPA) for tracking barrier function dynamics	54
Beyond the matrix: rethinking antibiotic tolerance in CF biofilms using 3D models	53
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	53
Modulation of gut microbiota and its metabolite Equol by Huaier granule suppresses hepatocellular carcinoma via the gut-liver axis	51
The gut microbiota modulate locomotion via vagus-dependent glucagon-like peptide-1 signaling	51
Interspecies competition in oral biofilms mediated by Streptococcus gordonii extracellular deoxyribonuclease SsnA	51
PGPR-mediated enhancement of soil nutrients, rhizosphere microbial ecology, and plant growth: a review	49
Clostridium difficile-derived membrane vesicles promote fetal growth restriction via inhibiting trophoblast motility through PPARγ/RXRα/ANGPTL4 axis	49
The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival	48
An antifungal effector from a plant-parasitic nematode modulates host fungal community composition and supports ecological fitness	46
Social demographics determinants for resistome and microbiome variation of a multiethnic community in Southern Malaysia	46
Interaction between tissue-dwelling helminth and the gut microbiota drives mucosal immunoregulation	45
Functional roles of degraders and non-degraders in anaerobic trophic networks converting lignocellulose into monocarboxylates	45
Disentangling the feedback loops driving spatial patterning in microbial communities	45
Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates	44
Host specificity and cophylogeny in the “animal-gut bacteria-phage” tripartite system	43
ToxR is a c-di-GMP binding protein that modulates surface-associated behaviour in Pseudomonas aeruginosa	43
Adaptation of a methanogen to Fe0 corrosion via direct contact	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
Integrative metagenomic and metabolomic analyses reveal the potential of gut microbiota to exacerbate acute pancreatitis	41
Precision Prediction of Microbial Ecosystem Impact on Host Metabolism Using Genome-Resolved Metagenomics	41
Spermidine is a common component of the eDNA-dependent biofilm matrix	41
Gut microbes modulate the effects of the flavonoid quercetin on atherosclerosis	40
Herbivory-triggered assemblage of sunflower rhizosphere microbiome enhances herbivore tolerance through plant–soil feedback	40
Impact of a multi-strain L. crispatus-based vaginal synbiotic on the vaginal microbiome: a randomized placebo-controlled trial	39
Disruption of bile acid homeostasis potentiates Paneth cell ablation by activating the intestinal Farnesoid X receptor in necrotizing enterocolitis	39
Targeted proteomics reveal α-MSH-like Enterobacterial ClpB protein in gut microbiota of patients with anorexia nervosa	39
Thwarting resistance: MgrA inhibition with methylophiopogonanone a unveils a new battlefront against S. aureus	38
The Wsp chemosensory system modulates c-di-GMP-dependent biofilm formation by integrating DSF quorum sensing through the WspR-RpfG complex in Lysobacter	38
Research advances in the identification of gut keystone bacteria and formulation of suitable dietary intervention strategies for restoring gut homeostasis	38
Bacterial inoculation drives microbiome-mediated resistance to a soil-borne pathogen in wheat	38
Oral and middle ear delivery of otitis media standard of care antibiotics, but not biofilm-targeted antibodies, alter chinchilla nasopharyngeal and fecal microbiomes	37
Unraveling the microbial landscape in prostate cancer: pathogenesis to therapy	37

Rattus norvegicus and Rattus tanezumi as hub hosts for viral diversity and potential spillover on Hainan Island, China	36
Latent evolution of biofilm formation depends on life-history and genetic background	36
Beyond estrobolome 1.0: unraveling endocrine-microbiome axis as a driver and therapeutic target in hormone-driven cancers	36
Complement and neutrophils are actively involved at the cervicovaginal interface in cases of adverse microbial composition, cervical shortening and spontaneous preterm birth	36
Trehalose ameliorates severe acute pancreatitis by modulating gut microbial metabolism	36
Phyllosphere microbiome responses to spray-induced gene silencing targeting Phytophthora infestans in potato	36
Intermittent fasting exacerbates microplastic-induced gut inflammation via Rikenella-mediated regulation of purine metabolism and Th17/Treg balance	35
Multi-omic profiling reveals distinct gut microbial and metabolic landscapes in golden snub-nosed monkeys under contrasting conservation strategies	35
Tanzanian gut microbiota profiles linked to high but rapidly waning yellow fever antibody titers	35
Individual variability shapes ex vivo responses to resistant starch in inflammatory bowel disease derived microbiomes	34
OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients	34
Selective inhibition of the amyloid matrix of Escherichia coli biofilms by a bifunctional microbial metabolite	34
Endolysin selectively kills Gardnerella ex vivo in vaginal samples from women with bacterial vaginosis	34
Matrix is everywhere: extracellular DNA is a link between biofilm and mineralization in Bacillus cereus planktonic lifestyle	33
Environmental factors drive bacterial degradation of gastrointestinal mucus	33
Gut and oral microbiota in gynecological cancers: interaction, mechanism, and therapeutic value	33
Short term supplementation with cranberry extract modulates gut microbiota in human and displays a bifidogenic effect	33
Genotoxic stress stimulates eDNA release via explosive cell lysis and thereby promotes streamer formation of Burkholderia cenocepacia H111 cultured in a microfluidic device	33
Coconut rhinoceros beetle digestive symbiosis with potential plant cell wall degrading microbes	32
Gut-resident Phascolarctobacterium succinatutens decreases fat accumulation via MYC-driven epigenetic regulation of arginine biosynthesis	32
Microbial solutions must be deployed against climate catastrophe	32
Author Correction: Bifidobacterium animalis Probio-M8 improves sarcopenia physical performance by mitigating creatine restrictions imposed by microbial metabolites	32
Microbiome and well-being: a meta-analysis	32
The gut microbiota mediates depression-like behaviors in mice with chronic Echinococcus multilocularis infection	31
Multi-omics profiling of dairy cattle oxidative stress identifies hindgut-derived Phascolarctobacterium succinatutens exhibiting antioxidant activity	31
Microbial mat compositions and localization patterns explain the virulence of black band disease in corals	31
Antimicrobial and antibiotic-potentiating effect of calcium peroxide nanoparticles on oral bacterial biofilms	31
Dietary fiber deficiency exacerbates intestinal inflammation via miR-6240-enriched gut extracellular vesicles	31
Synergistic effects of commensals and phage predation in suppressing colonization by pathogenic Vibrio parahaemolyticus	31
A rationally designed microbial consortium modulates neurodegeneration in a Drosophila melanogaster model of Parkinson’s disease	30
Nitrate and a nitrate-reducing Rothia aeria strain as potential prebiotic or synbiotic treatments for periodontitis	30
Inflammatory microbes and genes as potential biomarkers of Parkinson’s disease	30
Gut microbiota alterations are linked to COVID-19 severity in North African and European populations	30
Copper as a central element critical to interkingdom interactions within a polymicrobial wound environment	30
Impact of structurally diverse polysaccharides on colonic mucin O-glycosylation and gut microbiota	30
Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection	29
Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota	29
Nisin lantibiotic prevents NAFLD liver steatosis and mitochondrial oxidative stress following periodontal disease by abrogating oral, gut and liver dysbiosis	29
The cell wall lipoprotein CD1687 acts as a DNA binding protein during deoxycholate-induced biofilm formation in Clostridioides difficile	29
Coastal rest during the COVID-19 pandemic enhances microbial community stability and metabolic potential in a subterranean estuary	29
Harnessing machine learning to predict antibiotic susceptibility in Pseudomonas aeruginosa biofilms	29
The role of gut microbiota-gonadal axis in ovary activation of Asian honey bee (Apis cerana) queens	29
Identification of ferredoxin PA1551 as an antibacterial synergistic target for biofilm inhibitors against Pseudomonas aeruginosa	28
Engineered Mycoplasma pneumoniae targeting dual-species bacterial biofilms: a novel strategy against infections	28
Foliar metal micronutrients reshape rhizosphere soil multifunctionality by filtering microbial life-history strategies	28
Facemask acne attenuation through modulation of indirect microbiome interactions	28
Gut microbiota–GABA axis dysregulation underlies polystyrene microplastic (PS-MP) neurotoxicity in rainbow trout: a role for oxidative stress and blood–brain barrier disruption	28
Fusobacterium lineage profiling facilitates the clarification of the associations between non-nucleatum Fusobacterium and colorectal cancer	28
MicroMap: a network visualisation resource for human microbiome metabolism	28
Minibioreactor arrays to model microbiome response to alcohol and tryptophan in the context of alcohol-associated liver disease	28
Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism	27
Temporal turnover of viral biodiversity and functional potential in intertidal wetlands	27
Hypertension inhibition by Dubosiella newyorkensis via reducing pentosidine synthesis	27
Density and temperature controlled fluid extraction in a bacterial biofilm is determined by poly-γ-glutamic acid production	27
The gut-heart axis in heart failure: a systematic review and meta-analysis of gut microbiota and metabolites	27
UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog	27
Spinal cord injury-induced gut dysbiosis influences neurological recovery partly through short-chain fatty acids	27
Role of starvation survival response mechanisms on ribosome integrity, antibiotic tolerances, and virulence of Pseudomonas aeruginosa biofilms	27
Antibiotic treatment can exacerbate biofilm-associated infection by promoting quorum cheater development	27
The Bifidobacterium-dominated fecal microbiome in dairy calves shapes the characteristic growth phenotype of host	27
Inulin-enriched Megamonas funiformis ameliorates metabolic dysfunction-associated fatty liver disease by producing propionic acid	26
Periodontitis-associated Fusobacterium nucleatum promotes ulcerative colitis by ferroptosis-mediated gut barrier disruption	26
High-resolution visualization of biofilm matrix development in space and time using fluorescent stains for cellulose	26
The effects of oral probiotic intervention on brain structure and function in human adults: a systematic review	26
Intracellular bacteria in cancer—prospects and debates	26
Drug repurposing for glucosyltransferase inhibition for targeted oral biofilm disruption	26
Phage endolysin enables targeted manipulation of the small intestinal microbiota and uncovers niche overlap between oral and butyrate-producing taxa	26
Impact of trace metal supplementation on anaerobic biological methanation under hydrogen and carbon dioxide starvation	26
Immune dysfunction during S. aureus biofilm-associated implant infections: opportunities for novel therapeutic strategies	26
Hydrodynamic conditions affect the proteomic profile of marine biofilms formed by filamentous cyanobacterium	26
Time-resolved compositional and dynamics analysis of biofilm maturation and dispersal via solid-state NMR spectroscopy	26
The tongue biofilm metatranscriptome identifies metabolic pathways associated with the presence or absence of halitosis	25
Deep generative modeling of annotated bacterial biofilm images	25
Recent advances in single-cell engineered live biotherapeutic products research for skin repair and disease treatment	25
Mitochondrial dysfunction promotes microbial composition that negatively impacts on ulcerative colitis development and progression	25
The highly differentiated gut of Pachnoda marginata hosts sequential microbiomes: microbial ecology and potential applications	25
Joint contributions of host genetics and heritable gut microbiota to semen quality variation in Duroc boars	24
Mesaconic acid as a key metabolite with anti-inflammatory and anti-aging properties produced by Lactobacillus plantarum 124 from centenarian gut microbiota	24
Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms	24
Novel antimicrobial peptides and peptide-microbiome crosstalk in Appalachian salamander skin	24

Non disseminative nano-strategy against in vivo Staphylococcus aureus biofilms	24
Community successional patterns and inter-kingdom interactions during granular biofilm development	24
Preventing bacterial adhesion to skin by altering their physicochemical cell surface properties specifically	24
Lung microbiota-mediated biotransformation of mogroside preserves pulmonary barrier integrity and attenuates PM2.5-induced inflammation via NF-κB–Th17 modulations	24
L-citrulline protects testicular Sertoli cell function by mitigating DNA damage via the gut-testis axis of sheep fed a high-concentrate diet	24
Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance	24
Long-chain 4-aminoquinolines inhibit filamentation and increase efficacy of nystatin against Candida albicans infections in vivo	24
Metagenomic analysis reveals the novel role of vaginal Lactobacillus iners in Chinese healthy pregnant women	23
Spaceflight alters host-gut microbiota interactions	23
Staphylococcus epidermidis alters macrophage polarization and phagocytic uptake by extracellular DNA release in vitro	23
Environmental determinants and demographic influences on global urban microbiomes, antimicrobial resistance and pathogenicity	23
Stenotrophomonas maltophilia alleviates Alzheimer’s disease model phenotype by inhibiting Aβ aggregation via autophagy	22
The gut commensal Bacteroides thetaiotaomicron harbors prevalent class A and D β-lactamases with cross-taxa dissemination potential	22
Prucalopride, a serotonin type 4 receptor agonist, induces fast anxiolytic/antidepressant effects and concomitant changes in the gut microbiota	22
Association of gut microbiome with mobility impairment in the Hispanic Community Health Study/Study of Latinos	22
Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion	22
Ecological change of the gut microbiota during pregnancy and progression to dyslipidemia	22
Garvicin Q-producing Lactococcus garvieae LG3092: its role in mitigating dysbiosis and H. pylori-associated gastritis	22
Modeling diet-gut microbiome interactions and prebiotic responses in Thai adults	22
Publisher Correction: Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis	22
Gut microbiota-mediated secondary bile acid alleviates Staphylococcus aureus-induced mastitis through the TGR5-cAMP-PKA-NF-κB/NLRP3 pathways in mice	22
Irrigation of the intramedullary channel improves outcome of DAIR in a sheep model	22
Author Correction: Bacterial biofilm-derived H-NS protein acts as a defense against Neutrophil Extracellular Traps (NETs)	22
Multi-omics framework integrating genetics microbiome and immunity for understanding motor neuron degeneration pathogenesis	22
Pseudomonas plecoglossicida disrupts intestinal homeostasis through manipulation of palmitoleic acid microbial metabolism	22
Polybacterial intracellular macromolecules shape single-cell inflammatory profiles in upper airway epithelia	21
Microbiome and metabolic disruption in acute vs. severe and enduring anorexia nervosa	21
Temporal dynamics, microdiversity, and ecological functions of viral communities during cyanobacterial blooms in Lake Taihu	21
In-depth insights into cervicovaginal microbial communities and hrHPV infections using high-resolution microbiome profiling	21
Alginate exopolymer significantly modulates the viscoelastic properties and resilience of bacterial biofilms	21
On validly published names, correct names, and changes in the nomenclature of phyla and genera of prokaryotes: a guide for the perplexed	21
Periodontitis salivary microbiota exacerbates colitis-induced anxiety-like behavior via gut microbiota	21
The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations	20
Emergent roles of infant gut microbes during the utilization of human milk oligosaccharides	20
Author Correction: Inulin-enriched Megamonas funiformis ameliorates metabolic dysfunction-associated fatty liver disease by producing propionic acid	20
(p)ppGpp imposes graded transcriptional changes to impair motility and promote antibiotic tolerance in biofilms	20
Bacterial capsules: Occurrence, mechanism, and function	20
Extracellular vesicles of the Gram-positive gut symbiont Bifidobacterium longum induce immune-modulatory, anti-inflammatory effects	20
Geocaulosphere soil bacterial community drives potato common scab outcomes beyond pathogen abundance	20
Parabacteroides as a promising target for disease intervention: current stage and pending issues	20
Infant gut microbiota and SCFAs mediate the association between early-life human milk microbiota and neurodevelopment	20
Topical prebiotic nitrate: optimizing the ‘hang-time’, source and dose for specific oral or systemic effects	20
Bacterial c-di-GMP triggers metamorphosis of mussel larvae through a STING receptor	20