OOIR: Observatory of International Research

Papers

(The TQCC of npj Biofilms and Microbiomes is 18. 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 2021-10-01 to 2025-10-01.)

Article	Citations
In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus	232
Neutralization of ionic interactions by dextran-based single-chain nanoparticles improves tobramycin diffusion into a mature biofilm	223
Evolution of genotypic and phenotypic diversity in multispecies biofilms	137
Iron limitation-induced endophytic Ammoniphilus assemblage promotes root apoplastic iron remobilization by attenuation of salicylic acid pathways	115
Targeted metabolomics reveals bioactive inflammatory mediators from gut into blood circulation in children with NAFLD	115
Plasticity of the gut microbiome of golden snub-nosed monkeys (Rhinopithecus roxellana) in response to seasonal variation in diet	112
Lactobacillus plantarum L168 improves hyperoxia-induced pulmonary inflammation and hypoalveolarization in a rat model of bronchopulmonary dysplasia	94
Dual-functionality of Nocardiopsis alba B57 in biocontrol and plant growth: a metabolomic approach to agricultural sustainability	94
An in vitro fermentation model to study the impact of bacteriophages targeting Shiga toxin-encoding Escherichia coli on the colonic microbiota	84
Gene horizontal transfers and functional diversity negatively correlated with bacterial taxonomic diversity along a nitrogen gradient	77
Diverse polysaccharide production and biofilm formation abilities of clinical Klebsiella pneumoniae	76
Partial convergence of the human vaginal and rectal maternal microbiota in late gestation and early post-partum	70
Early microbial markers of periodontal and cardiometabolic diseases in ORIGINS	66
In situ monitoring of Lentilactobacillus parabuchneri biofilm formation via real-time infrared spectroscopy	66
Pharmacodynamics of interspecies interactions in polymicrobial infections	63
Bacteria contribute exopolysaccharides to an algal-bacterial joint extracellular matrix	61
Akkermansia muciniphila inhibited the periodontitis caused by Fusobacterium nucleatum	61
Fusobacterium nucleatum is enriched in invasive biofilms in colorectal cancer	58
One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density	58
Colonization with ubiquitous protist Blastocystis ST1 ameliorates DSS-induced colitis and promotes beneficial microbiota and immune outcomes	57
The gut microbiota modulate locomotion via vagus-dependent glucagon-like peptide-1 signaling	55
The dynamics of microbiome and virome in migratory birds of southwest China	54
Donor-recipient specificity and age-dependency in fecal microbiota therapy and probiotic resolution of gastrointestinal symptoms	53
Ex vivo intestinal permeability assay (X-IPA) for tracking barrier function dynamics	53
Simulation of catalase-dependent tolerance of microbial biofilm to hydrogen peroxide with a biofilm computer model	52

Author Correction: Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization	51
Secreted nucleases reclaim extracellular DNA during biofilm development	51
Protecting the piglet gut microbiota against ETEC-mediated post-weaning diarrhoea using specific binding proteins	49
Diffusion-based mechanism explains spatial organization in cross-feeding biofilms	49
Harnessing vaginal inflammation and microbiome: a machine learning model for predicting IVF success	48
Interspecies competition in oral biofilms mediated by Streptococcus gordonii extracellular deoxyribonuclease SsnA	47
Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut	47
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	46
Clostridium difficile-derived membrane vesicles promote fetal growth restriction via inhibiting trophoblast motility through PPARγ/RXRα/ANGPTL4 axis	46
Gut microbes modulate the effects of the flavonoid quercetin on atherosclerosis	45
Disentangling the feedback loops driving spatial patterning in microbial communities	45
Adaptation and phenotypic diversification of Bacillus thuringiensis biofilm are accompanied by fuzzy spreader morphotypes	44
Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors	44
The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival	44
ToxR is a c-di-GMP binding protein that modulates surface-associated behaviour in Pseudomonas aeruginosa	44
Adaptation of a methanogen to Fe0 corrosion via direct contact	43
Impact of a multi-strain L. crispatus-based vaginal synbiotic on the vaginal microbiome: a randomized placebo-controlled trial	43
Prokaryotic evolution shapes specialized communities in long term engineered pit mud ecosystem	42
Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates	41
Rational consideration of Akkermansia muciniphila targeting intestinal health: advantages and challenges	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	40
Integrative metagenomic and metabolomic analyses reveal the potential of gut microbiota to exacerbate acute pancreatitis	39
Environmental factors drive bacterial degradation of gastrointestinal mucus	37
Endolysin selectively kills Gardnerella ex vivo in vaginal samples from women with bacterial vaginosis	36
Gut-resident Phascolarctobacterium succinatutens decreases fat accumulation via MYC-driven epigenetic regulation of arginine biosynthesis	35
Matrix is everywhere: extracellular DNA is a link between biofilm and mineralization in Bacillus cereus planktonic lifestyle	34
Latent evolution of biofilm formation depends on life-history and genetic background	34
OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients	34
Genotoxic stress stimulates eDNA release via explosive cell lysis and thereby promotes streamer formation of Burkholderia cenocepacia H111 cultured in a microfluidic device	34
Microbial solutions must be deployed against climate catastrophe	33
Tanzanian gut microbiota profiles linked to high but rapidly waning yellow fever antibody titers	33
Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation	32
Thwarting resistance: MgrA inhibition with methylophiopogonanone a unveils a new battlefront against S. aureus	32
Oral and middle ear delivery of otitis media standard of care antibiotics, but not biofilm-targeted antibodies, alter chinchilla nasopharyngeal and fecal microbiomes	31
The Wsp chemosensory system modulates c-di-GMP-dependent biofilm formation by integrating DSF quorum sensing through the WspR-RpfG complex in Lysobacter	30
Short term supplementation with cranberry extract modulates gut microbiota in human and displays a bifidogenic effect	30
Selective inhibition of the amyloid matrix of Escherichia coli biofilms by a bifunctional microbial metabolite	30
Gut and oral microbiota in gynecological cancers: interaction, mechanism, and therapeutic value	30
Multi-omics profiling of dairy cattle oxidative stress identifies hindgut-derived Phascolarctobacterium succinatutens exhibiting antioxidant activity	29
A rationally designed microbial consortium modulates neurodegeneration in a Drosophila melanogaster model of Parkinson’s disease	29
Inflammatory microbes and genes as potential biomarkers of Parkinson’s disease	29
Antimicrobial and antibiotic-potentiating effect of calcium peroxide nanoparticles on oral bacterial biofilms	29
Variation of Antigen 43 self-association modulates bacterial compacting within aggregates and biofilms	28
Impact of structurally diverse polysaccharides on colonic mucin O-glycosylation and gut microbiota	28
Author Correction: Bifidobacterium animalis Probio-M8 improves sarcopenia physical performance by mitigating creatine restrictions imposed by microbial metabolites	28
Microbial mat compositions and localization patterns explain the virulence of black band disease in corals	27
Atypical cyclic di-AMP signaling is essential for Porphyromonas gingivalis growth and regulation of cell envelope homeostasis and virulence	26
Synergistic effects of commensals and phage predation in suppressing colonization by pathogenic Vibrio parahaemolyticus	26

Coconut rhinoceros beetle digestive symbiosis with potential plant cell wall degrading microbes	26
Gut microbiota alterations are linked to COVID-19 severity in North African and European populations	26
Density and temperature controlled fluid extraction in a bacterial biofilm is determined by poly-γ-glutamic acid production	25
Nitrate and a nitrate-reducing Rothia aeria strain as potential prebiotic or synbiotic treatments for periodontitis	25
Facemask acne attenuation through modulation of indirect microbiome interactions	25
The role of gut microbiota-gonadal axis in ovary activation of Asian honey bee (Apis cerana) queens	25
Nisin lantibiotic prevents NAFLD liver steatosis and mitochondrial oxidative stress following periodontal disease by abrogating oral, gut and liver dysbiosis	25
Temporal turnover of viral biodiversity and functional potential in intertidal wetlands	25
The cell wall lipoprotein CD1687 acts as a DNA binding protein during deoxycholate-induced biofilm formation in Clostridioides difficile	25
Cpx-signalling facilitates Hms-dependent biofilm formation by Yersinia pseudotuberculosis	24
The Bifidobacterium-dominated fecal microbiome in dairy calves shapes the characteristic growth phenotype of host	24
Antibiotic treatment can exacerbate biofilm-associated infection by promoting quorum cheater development	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	24
Minibioreactor arrays to model microbiome response to alcohol and tryptophan in the context of alcohol-associated liver disease	24
Hypertension inhibition by Dubosiella newyorkensis via reducing pentosidine synthesis	23
Immune dysfunction during S. aureus biofilm-associated implant infections: opportunities for novel therapeutic strategies	23
Inulin-enriched Megamonas funiformis ameliorates metabolic dysfunction-associated fatty liver disease by producing propionic acid	23
Spinal cord injury-induced gut dysbiosis influences neurological recovery partly through short-chain fatty acids	23
Economic significance of biofilms: a multidisciplinary and cross-sectoral challenge	23
Impact of trace metal supplementation on anaerobic biological methanation under hydrogen and carbon dioxide starvation	23
Preventing bacterial adhesion to skin by altering their physicochemical cell surface properties specifically	22
Intracellular bacteria in cancer—prospects and debates	22
Community successional patterns and inter-kingdom interactions during granular biofilm development	22
Hydrodynamic conditions affect the proteomic profile of marine biofilms formed by filamentous cyanobacterium	22
Staphylococcus aureus utilizes environmental RNA as a building material in specific polysaccharide-dependent biofilms	22
Periodontitis-associated Fusobacterium nucleatum promotes ulcerative colitis by ferroptosis-mediated gut barrier disruption	22
The highly differentiated gut of Pachnoda marginata hosts sequential microbiomes: microbial ecology and potential applications	22
The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors	22
Body weight index indicates the responses of the fecal microbiota, metabolome and proteome to beef/chicken-based diet alterations in Chinese volunteers	21
Mitochondrial dysfunction promotes microbial composition that negatively impacts on ulcerative colitis development and progression	21
Mesaconic acid as a key metabolite with anti-inflammatory and anti-aging properties produced by Lactobacillus plantarum 124 from centenarian gut microbiota	21
Deep generative modeling of annotated bacterial biofilm images	21
The tongue biofilm metatranscriptome identifies metabolic pathways associated with the presence or absence of halitosis	21
Recent advances in single-cell engineered live biotherapeutic products research for skin repair and disease treatment	21
Time-resolved compositional and dynamics analysis of biofilm maturation and dispersal via solid-state NMR spectroscopy	21
Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance	20
Synthetic periphyton as a model system to understand species dynamics in complex microbial freshwater communities	20
Spaceflight alters host-gut microbiota interactions	20
Ecological change of the gut microbiota during pregnancy and progression to dyslipidemia	20
Staphylococcus epidermidis alters macrophage polarization and phagocytic uptake by extracellular DNA release in vitro	20
Metagenomic analysis reveals the novel role of vaginal Lactobacillus iners in Chinese healthy pregnant women	20
Environmental determinants and demographic influences on global urban microbiomes, antimicrobial resistance and pathogenicity	20
Long-chain 4-aminoquinolines inhibit filamentation and increase efficacy of nystatin against Candida albicans infections in vivo	20
Non disseminative nano-strategy against in vivo Staphylococcus aureus biofilms	20
Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms	20
Gut microbiome responses to dietary intervention with hypocholesterolemic vegetable oils	20
Bacterial c-di-GMP triggers metamorphosis of mussel larvae through a STING receptor	19
In-depth insights into cervicovaginal microbial communities and hrHPV infections using high-resolution microbiome profiling	19
Parabacteroides as a promising target for disease intervention: current stage and pending issues	19
Alginate exopolymer significantly modulates the viscoelastic properties and resilience of bacterial biofilms	19
The car tank lid bacteriome: a reservoir of bacteria with potential in bioremediation of fuel	19
Temporal dynamics, microdiversity, and ecological functions of viral communities during cyanobacterial blooms in Lake Taihu	19
(p)ppGpp imposes graded transcriptional changes to impair motility and promote antibiotic tolerance in biofilms	19
Gut microbiota-mediated secondary bile acid alleviates Staphylococcus aureus-induced mastitis through the TGR5-cAMP-PKA-NF-κB/NLRP3 pathways in mice	19
Irrigation of the intramedullary channel improves outcome of DAIR in a sheep model	19
Infant gut microbiota and SCFAs mediate the association between early-life human milk microbiota and neurodevelopment	19
Publisher Correction: Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis	19
Author Correction: Bacterial biofilm-derived H-NS protein acts as a defense against Neutrophil Extracellular Traps (NETs)	18
Periodontitis salivary microbiota exacerbates colitis-induced anxiety-like behavior via gut microbiota	18
The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations	18
Vaginal pharmacomicrobiomics modulates risk of persistent and recurrent bacterial vaginosis	18
Bacterial capsules: Occurrence, mechanism, and function	18
Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion	18
Host-microbiome relationship in depression: can human induced pluripotent stem cells play a role in unravelling mechanisms?	18
PreLect: Prevalence leveraged consistent feature selection decodes microbial signatures across cohorts	18
Polybacterial intracellular macromolecules shape single-cell inflammatory profiles in upper airway epithelia	18
On validly published names, correct names, and changes in the nomenclature of phyla and genera of prokaryotes: a guide for the perplexed	18
Microfluidic investigation of the impacts of flow fluctuations on the development of Pseudomonas putida biofilms	18
Extracellular vesicles of the Gram-positive gut symbiont Bifidobacterium longum induce immune-modulatory, anti-inflammatory effects	18