OOIR: Observatory of International Research

Papers

(The TQCC of npj Biofilms and Microbiomes is 16. 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 2021-08-01 to 2025-08-01.)

Article	Citations
Neutralization of ionic interactions by dextran-based single-chain nanoparticles improves tobramycin diffusion into a mature biofilm	222
Diverse polysaccharide production and biofilm formation abilities of clinical Klebsiella pneumoniae	211
Early microbial markers of periodontal and cardiometabolic diseases in ORIGINS	167
Akkermansia muciniphila inhibited the periodontitis caused by Fusobacterium nucleatum	127
An in vitro fermentation model to study the impact of bacteriophages targeting Shiga toxin-encoding Escherichia coli on the colonic microbiota	104
Gene horizontal transfers and functional diversity negatively correlated with bacterial taxonomic diversity along a nitrogen gradient	100
Bacteria contribute exopolysaccharides to an algal-bacterial joint extracellular matrix	97
Pharmacodynamics of interspecies interactions in polymicrobial infections	87
Partial convergence of the human vaginal and rectal maternal microbiota in late gestation and early post-partum	85
One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density	84
Iron limitation-induced endophytic Ammoniphilus assemblage promotes root apoplastic iron remobilization by attenuation of salicylic acid pathways	77
In situ monitoring of Lentilactobacillus parabuchneri biofilm formation via real-time infrared spectroscopy	77
Evolution of genotypic and phenotypic diversity in multispecies biofilms	74
Targeted metabolomics reveals bioactive inflammatory mediators from gut into blood circulation in children with NAFLD	71
Fusobacterium nucleatum is enriched in invasive biofilms in colorectal cancer	61
Lactobacillus plantarum L168 improves hyperoxia-induced pulmonary inflammation and hypoalveolarization in a rat model of bronchopulmonary dysplasia	57
In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus	57
Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization	57
The dynamics of microbiome and virome in migratory birds of southwest China	53
Author Correction: Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization	53
Harnessing vaginal inflammation and microbiome: a machine learning model for predicting IVF success	52
The gut microbiota modulate locomotion via vagus-dependent glucagon-like peptide-1 signaling	52
Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut	51
Diffusion-based mechanism explains spatial organization in cross-feeding biofilms	50
Ex vivo intestinal permeability assay (X-IPA) for tracking barrier function dynamics	49

Secreted nucleases reclaim extracellular DNA during biofilm development	49
Interspecies competition in oral biofilms mediated by Streptococcus gordonii extracellular deoxyribonuclease SsnA	49
Simulation of catalase-dependent tolerance of microbial biofilm to hydrogen peroxide with a biofilm computer model	48
Colonization with ubiquitous protist Blastocystis ST1 ameliorates DSS-induced colitis and promotes beneficial microbiota and immune outcomes	48
Donor-recipient specificity and age-dependency in fecal microbiota therapy and probiotic resolution of gastrointestinal symptoms	47
Protecting the piglet gut microbiota against ETEC-mediated post-weaning diarrhoea using specific binding proteins	46
The impact of antioxidant-ciprofloxacin combinations on the evolution of antibiotic resistance in Pseudomonas aeruginosa biofilms	46
Social demographics determinants for resistome and microbiome variation of a multiethnic community in Southern Malaysia	45
Clostridium difficile-derived membrane vesicles promote fetal growth restriction via inhibiting trophoblast motility through PPARγ/RXRα/ANGPTL4 axis	45
Alternating magnetic fields and antibiotics eradicate biofilm on metal in a synergistic fashion	43
ToxR is a c-di-GMP binding protein that modulates surface-associated behaviour in Pseudomonas aeruginosa	41
Gut microbes modulate the effects of the flavonoid quercetin on atherosclerosis	41
Host specificity and cophylogeny in the “animal-gut bacteria-phage” tripartite system	41
Interaction between tissue-dwelling helminth and the gut microbiota drives mucosal immunoregulation	41
Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors	41
Adaptation and phenotypic diversification of Bacillus thuringiensis biofilm are accompanied by fuzzy spreader morphotypes	40
The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival	39
Disentangling the feedback loops driving spatial patterning in microbial communities	39
Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates	38
Adaptation of a methanogen to Fe0 corrosion via direct contact	38
Rational consideration of Akkermansia muciniphila targeting intestinal health: advantages and challenges	38
Integrative metagenomic and metabolomic analyses reveal the potential of gut microbiota to exacerbate acute pancreatitis	38
Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation	37
Microbial solutions must be deployed against climate catastrophe	37
OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients	37
Oral and middle ear delivery of otitis media standard of care antibiotics, but not biofilm-targeted antibodies, alter chinchilla nasopharyngeal and fecal microbiomes	36
Latent evolution of biofilm formation depends on life-history and genetic background	35
Genotoxic stress stimulates eDNA release via explosive cell lysis and thereby promotes streamer formation of Burkholderia cenocepacia H111 cultured in a microfluidic device	34
Tanzanian gut microbiota profiles linked to high but rapidly waning yellow fever antibody titers	34
Matrix is everywhere: extracellular DNA is a link between biofilm and mineralization in Bacillus cereus planktonic lifestyle	34
The Wsp chemosensory system modulates c-di-GMP-dependent biofilm formation by integrating DSF quorum sensing through the WspR-RpfG complex in Lysobacter	32
Selective inhibition of the amyloid matrix of Escherichia coli biofilms by a bifunctional microbial metabolite	31
Environmental factors drive bacterial degradation of gastrointestinal mucus	31
Thwarting resistance: MgrA inhibition with methylophiopogonanone a unveils a new battlefront against S. aureus	30
Metagenomic analysis revealed the potential role of gut microbiome in gout	30
Gut and oral microbiota in gynecological cancers: interaction, mechanism, and therapeutic value	30
Short term supplementation with cranberry extract modulates gut microbiota in human and displays a bifidogenic effect	30
Antimicrobial and antibiotic-potentiating effect of calcium peroxide nanoparticles on oral bacterial biofilms	29
Coconut rhinoceros beetle digestive symbiosis with potential plant cell wall degrading microbes	29
Impact of structurally diverse polysaccharides on colonic mucin O-glycosylation and gut microbiota	29
Microbial mat compositions and localization patterns explain the virulence of black band disease in corals	28
Atypical cyclic di-AMP signaling is essential for Porphyromonas gingivalis growth and regulation of cell envelope homeostasis and virulence	28
Nitrate and a nitrate-reducing Rothia aeria strain as potential prebiotic or synbiotic treatments for periodontitis	28
Variation of Antigen 43 self-association modulates bacterial compacting within aggregates and biofilms	28
Author Correction: Bifidobacterium animalis Probio-M8 improves sarcopenia physical performance by mitigating creatine restrictions imposed by microbial metabolites	28
The role of gut microbiota-gonadal axis in ovary activation of Asian honey bee (Apis cerana) queens	27
Multi-omics profiling of dairy cattle oxidative stress identifies hindgut-derived Phascolarctobacterium succinatutens exhibiting antioxidant activity	27
Inflammatory microbes and genes as potential biomarkers of Parkinson’s disease	27
Gut microbiota alterations are linked to COVID-19 severity in North African and European populations	27
The cell wall lipoprotein CD1687 acts as a DNA binding protein during deoxycholate-induced biofilm formation in Clostridioides difficile	27

Nisin lantibiotic prevents NAFLD liver steatosis and mitochondrial oxidative stress following periodontal disease by abrogating oral, gut and liver dysbiosis	27
Facemask acne attenuation through modulation of indirect microbiome interactions	26
Impact of trace metal supplementation on anaerobic biological methanation under hydrogen and carbon dioxide starvation	26
Cpx-signalling facilitates Hms-dependent biofilm formation by Yersinia pseudotuberculosis	26
Hypertension inhibition by Dubosiella newyorkensis via reducing pentosidine synthesis	25
Minibioreactor arrays to model microbiome response to alcohol and tryptophan in the context of alcohol-associated liver disease	25
Intracellular bacteria in cancer—prospects and debates	25
Spinal cord injury-induced gut dysbiosis influences neurological recovery partly through short-chain fatty acids	24
Density and temperature controlled fluid extraction in a bacterial biofilm is determined by poly-γ-glutamic acid production	24
Temporal turnover of viral biodiversity and functional potential in intertidal wetlands	24
Antibiotic treatment can exacerbate biofilm-associated infection by promoting quorum cheater development	24
Inulin-enriched Megamonas funiformis ameliorates metabolic dysfunction-associated fatty liver disease by producing propionic acid	24
The Bifidobacterium-dominated fecal microbiome in dairy calves shapes the characteristic growth phenotype of host	24
Immune dysfunction during S. aureus biofilm-associated implant infections: opportunities for novel therapeutic strategies	24
Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota	24
Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism	23
Economic significance of biofilms: a multidisciplinary and cross-sectoral challenge	23
Deep generative modeling of annotated bacterial biofilm images	22
The highly differentiated gut of Pachnoda marginata hosts sequential microbiomes: microbial ecology and potential applications	22
Time-resolved compositional and dynamics analysis of biofilm maturation and dispersal via solid-state NMR spectroscopy	22
Recent advances in single-cell engineered live biotherapeutic products research for skin repair and disease treatment	22
Preventing bacterial adhesion to skin by altering their physicochemical cell surface properties specifically	22
Hydrodynamic conditions affect the proteomic profile of marine biofilms formed by filamentous cyanobacterium	21
Community successional patterns and inter-kingdom interactions during granular biofilm development	21
The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors	21
Mitochondrial dysfunction promotes microbial composition that negatively impacts on ulcerative colitis development and progression	21
Long-chain 4-aminoquinolines inhibit filamentation and increase efficacy of nystatin against Candida albicans infections in vivo	20
Staphylococcus aureus utilizes environmental RNA as a building material in specific polysaccharide-dependent biofilms	20
Body weight index indicates the responses of the fecal microbiota, metabolome and proteome to beef/chicken-based diet alterations in Chinese volunteers	20
Non disseminative nano-strategy against in vivo Staphylococcus aureus biofilms	20
The tongue biofilm metatranscriptome identifies metabolic pathways associated with the presence or absence of halitosis	20
Ecological change of the gut microbiota during pregnancy and progression to dyslipidemia	19
Staphylococcus epidermidis alters macrophage polarization and phagocytic uptake by extracellular DNA release in vitro	19
Synthetic periphyton as a model system to understand species dynamics in complex microbial freshwater communities	19
Gut microbiome responses to dietary intervention with hypocholesterolemic vegetable oils	19
Metagenomic analysis reveals the novel role of vaginal Lactobacillus iners in Chinese healthy pregnant women	19
Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance	19
Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms	19
Spaceflight alters host-gut microbiota interactions	19
Gut microbiota-mediated secondary bile acid alleviates Staphylococcus aureus-induced mastitis through the TGR5-cAMP-PKA-NF-κB/NLRP3 pathways in mice	19
Environmental determinants and demographic influences on global urban microbiomes, antimicrobial resistance and pathogenicity	19
Irrigation of the intramedullary channel improves outcome of DAIR in a sheep model	18
The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations	18
Polybacterial intracellular macromolecules shape single-cell inflammatory profiles in upper airway epithelia	18
The car tank lid bacteriome: a reservoir of bacteria with potential in bioremediation of fuel	18
Alginate exopolymer significantly modulates the viscoelastic properties and resilience of bacterial biofilms	18
Periodontitis salivary microbiota exacerbates colitis-induced anxiety-like behavior via gut microbiota	18
On validly published names, correct names, and changes in the nomenclature of phyla and genera of prokaryotes: a guide for the perplexed	18
Bacterial c-di-GMP triggers metamorphosis of mussel larvae through a STING receptor	18
Publisher Correction: Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis	18
Author Correction: Bacterial biofilm-derived H-NS protein acts as a defense against Neutrophil Extracellular Traps (NETs)	18
In-depth insights into cervicovaginal microbial communities and hrHPV infections using high-resolution microbiome profiling	18
Extracellular vesicles of the Gram-positive gut symbiont Bifidobacterium longum induce immune-modulatory, anti-inflammatory effects	17
Topical prebiotic nitrate: optimizing the ‘hang-time’, source and dose for specific oral or systemic effects	17
(p)ppGpp imposes graded transcriptional changes to impair motility and promote antibiotic tolerance in biofilms	17
Bacterial capsules: Occurrence, mechanism, and function	17
Carbohydrates from Pseudomonas aeruginosa biofilms interact with immune C-type lectins and interfere with their receptor function	17
Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion	17
Infant gut microbiota and SCFAs mediate the association between early-life human milk microbiota and neurodevelopment	17
Akkermansia muciniphila in the small intestine improves liver fibrosis in a murine liver cirrhosis model	17
Vaginal pharmacomicrobiomics modulates risk of persistent and recurrent bacterial vaginosis	16
Gut microbiota and SCFAs improve the treatment efficacy of chemotherapy and immunotherapy in NSCLC	16
Bifidobacterium longum NSP001-derived extracellular vesicles ameliorate ulcerative colitis by modulating T cell responses in gut microbiota-(in)dependent manners	16
Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases	16
PreLect: Prevalence leveraged consistent feature selection decodes microbial signatures across cohorts	16
Geocaulosphere soil bacterial community drives potato common scab outcomes beyond pathogen abundance	16
Microbiome modulation of implant-related infection by a novel miniaturized pulsed electromagnetic field device	16
Host-microbiome relationship in depression: can human induced pluripotent stem cells play a role in unravelling mechanisms?	16
Gender differences in global antimicrobial resistance	16
Microbial melatonin metabolism in the human intestine as a therapeutic target for dysbiosis and rhythm disorders	16