OOIR: Observatory of International Research

Papers

(The TQCC of npj Biofilms and Microbiomes is 17. 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 2021-05-01 to 2025-05-01.)

Article	Citations
Early microbial markers of periodontal and cardiometabolic diseases in ORIGINS	188
Diverse polysaccharide production and biofilm formation abilities of clinical Klebsiella pneumoniae	185
Lactobacillus plantarum L168 improves hyperoxia-induced pulmonary inflammation and hypoalveolarization in a rat model of bronchopulmonary dysplasia	146
Pharmacodynamics of interspecies interactions in polymicrobial infections	146
Gene horizontal transfers and functional diversity negatively correlated with bacterial taxonomic diversity along a nitrogen gradient	109
Neutralization of ionic interactions by dextran-based single-chain nanoparticles improves tobramycin diffusion into a mature biofilm	94
An in vitro fermentation model to study the impact of bacteriophages targeting Shiga toxin-encoding Escherichia coli on the colonic microbiota	88
Partial convergence of the human vaginal and rectal maternal microbiota in late gestation and early post-partum	79
Bacteria contribute exopolysaccharides to an algal-bacterial joint extracellular matrix	77
In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus	76
Akkermansia muciniphila inhibited the periodontitis caused by Fusobacterium nucleatum	73
Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization	69
In situ monitoring of Lentilactobacillus parabuchneri biofilm formation via real-time infrared spectroscopy	65
One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density	65
Colonization with ubiquitous protist Blastocystis ST1 ameliorates DSS-induced colitis and promotes beneficial microbiota and immune outcomes	63
Author Correction: Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization	63
Donor-recipient specificity and age-dependency in fecal microbiota therapy and probiotic resolution of gastrointestinal symptoms	56
The dynamics of microbiome and virome in migratory birds of southwest China	56
Secreted nucleases reclaim extracellular DNA during biofilm development	55
Simulation of catalase-dependent tolerance of microbial biofilm to hydrogen peroxide with a biofilm computer model	55
Ex vivo intestinal permeability assay (X-IPA) for tracking barrier function dynamics	51
The gut microbiota modulate locomotion via vagus-dependent glucagon-like peptide-1 signaling	50
Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut	49
Protecting the piglet gut microbiota against ETEC-mediated post-weaning diarrhoea using specific binding proteins	47
Interspecies competition in oral biofilms mediated by Streptococcus gordonii extracellular deoxyribonuclease SsnA	47

The impact of antioxidant-ciprofloxacin combinations on the evolution of antibiotic resistance in Pseudomonas aeruginosa biofilms	47
Veillonellaceae family members uniquely alter the cervical metabolic microenvironment in a human three-dimensional epithelial model	47
Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors	46
Fluorescent nanosensors reveal dynamic pH gradients during biofilm formation	46
Alternating magnetic fields and antibiotics eradicate biofilm on metal in a synergistic fashion	45
ToxR is a c-di-GMP binding protein that modulates surface-associated behaviour in Pseudomonas aeruginosa	44
Integrative metagenomic and metabolomic analyses reveal the potential of gut microbiota to exacerbate acute pancreatitis	43
Host specificity and cophylogeny in the “animal-gut bacteria-phage” tripartite system	43
Social demographics determinants for resistome and microbiome variation of a multiethnic community in Southern Malaysia	43
Interaction between tissue-dwelling helminth and the gut microbiota drives mucosal immunoregulation	41
Adaptation and phenotypic diversification of Bacillus thuringiensis biofilm are accompanied by fuzzy spreader morphotypes	40
Gut microbes modulate the effects of the flavonoid quercetin on atherosclerosis	40
Adaptation of a methanogen to Fe0 corrosion via direct contact	40
Disentangling the feedback loops driving spatial patterning in microbial communities	40
Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates	40
Clostridium difficile-derived membrane vesicles promote fetal growth restriction via inhibiting trophoblast motility through PPARγ/RXRα/ANGPTL4 axis	39
The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival	39
Daily full spectrum light exposure prevents food allergy-like allergic diarrhea by modulating vitamin D3 and microbiota composition	39
Rational consideration of Akkermansia muciniphila targeting intestinal health: advantages and challenges	38
Competition of two highly specialized and efficient acetoclastic electroactive bacteria for acetate in biofilm anode of microbial electrolysis cell	38
Gut and oral microbiota in gynecological cancers: interaction, mechanism, and therapeutic value	35
Microbial solutions must be deployed against climate catastrophe	35
Thwarting resistance: MgrA inhibition with methylophiopogonanone a unveils a new battlefront against S. aureus	35
Matrix is everywhere: extracellular DNA is a link between biofilm and mineralization in Bacillus cereus planktonic lifestyle	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
Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation	34
Oral and middle ear delivery of otitis media standard of care antibiotics, but not biofilm-targeted antibodies, alter chinchilla nasopharyngeal and fecal microbiomes	34
OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients	33
Latent evolution of biofilm formation depends on life-history and genetic background	33
Selective inhibition of the amyloid matrix of Escherichia coli biofilms by a bifunctional microbial metabolite	32
The Wsp chemosensory system modulates c-di-GMP-dependent biofilm formation by integrating DSF quorum sensing through the WspR-RpfG complex in Lysobacter	31
Short term supplementation with cranberry extract modulates gut microbiota in human and displays a bifidogenic effect	31
Metagenomic analysis revealed the potential role of gut microbiome in gout	31
Author Correction: Bifidobacterium animalis Probio-M8 improves sarcopenia physical performance by mitigating creatine restrictions imposed by microbial metabolites	30
Antimicrobial and antibiotic-potentiating effect of calcium peroxide nanoparticles on oral bacterial biofilms	30
Variation of Antigen 43 self-association modulates bacterial compacting within aggregates and biofilms	30
Nisin lantibiotic prevents NAFLD liver steatosis and mitochondrial oxidative stress following periodontal disease by abrogating oral, gut and liver dysbiosis	29
Coconut rhinoceros beetle digestive symbiosis with potential plant cell wall degrading microbes	28
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
Atypical cyclic di-AMP signaling is essential for Porphyromonas gingivalis growth and regulation of cell envelope homeostasis and virulence	27
Temporal turnover of viral biodiversity and functional potential in intertidal wetlands	26
Cpx-signalling facilitates Hms-dependent biofilm formation by Yersinia pseudotuberculosis	26
Impact of trace metal supplementation on anaerobic biological methanation under hydrogen and carbon dioxide starvation	26
Impact of structurally diverse polysaccharides on colonic mucin O-glycosylation and gut microbiota	26
Minibioreactor arrays to model microbiome response to alcohol and tryptophan in the context of alcohol-associated liver disease	26
The cell wall lipoprotein CD1687 acts as a DNA binding protein during deoxycholate-induced biofilm formation in Clostridioides difficile	26
Nitrate and a nitrate-reducing Rothia aeria strain as potential prebiotic or synbiotic treatments for periodontitis	26
Microbial mat compositions and localization patterns explain the virulence of black band disease in corals	26
Antibiotic treatment can exacerbate biofilm-associated infection by promoting quorum cheater development	25

Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism	25
Facemask acne attenuation through modulation of indirect microbiome interactions	25
Hypertension inhibition by Dubosiella newyorkensis via reducing pentosidine synthesis	25
The Bifidobacterium-dominated fecal microbiome in dairy calves shapes the characteristic growth phenotype of host	25
Intracellular bacteria in cancer—prospects and debates	24
Spinal cord injury-induced gut dysbiosis influences neurological recovery partly through short-chain fatty acids	24
Inulin-enriched Megamonas funiformis ameliorates metabolic dysfunction-associated fatty liver disease by producing propionic acid	24
Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota	24
Density and temperature controlled fluid extraction in a bacterial biofilm is determined by poly-γ-glutamic acid production	24
Hydrodynamic conditions affect the proteomic profile of marine biofilms formed by filamentous cyanobacterium	23
Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut	23
Recent advances in single-cell engineered live biotherapeutic products research for skin repair and disease treatment	23
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	22
The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors	22
The highly differentiated gut of Pachnoda marginata hosts sequential microbiomes: microbial ecology and potential applications	22
Staphylococcus aureus utilizes environmental RNA as a building material in specific polysaccharide-dependent biofilms	22
Developmental intestinal microbiome alterations in canine fading puppy syndrome: a prospective observational study	22
Body weight index indicates the responses of the fecal microbiota, metabolome and proteome to beef/chicken-based diet alterations in Chinese volunteers	22
Deep generative modeling of annotated bacterial biofilm images	22
Preventing bacterial adhesion to skin by altering their physicochemical cell surface properties specifically	22
Time-resolved compositional and dynamics analysis of biofilm maturation and dispersal via solid-state NMR spectroscopy	22
Spaceflight alters host-gut microbiota interactions	21
Mitochondrial dysfunction promotes microbial composition that negatively impacts on ulcerative colitis development and progression	21
Gut microbiome responses to dietary intervention with hypocholesterolemic vegetable oils	21
Staphylococcus epidermidis alters macrophage polarization and phagocytic uptake by extracellular DNA release in vitro	21
Community successional patterns and inter-kingdom interactions during granular biofilm development	21
Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance	21
Long-chain 4-aminoquinolines inhibit filamentation and increase efficacy of nystatin against Candida albicans infections in vivo	21
Gut microbiota-mediated secondary bile acid alleviates Staphylococcus aureus-induced mastitis through the TGR5-cAMP-PKA-NF-κB/NLRP3 pathways in mice	20
Non disseminative nano-strategy against in vivo Staphylococcus aureus biofilms	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	19
Environmental determinants and demographic influences on global urban microbiomes, antimicrobial resistance and pathogenicity	19
Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion	19
Bacterial c-di-GMP triggers metamorphosis of mussel larvae through a STING receptor	19
Ecological change of the gut microbiota during pregnancy and progression to dyslipidemia	19
Publisher Correction: Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis	18
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
In-depth insights into cervicovaginal microbial communities and hrHPV infections using high-resolution microbiome profiling	17
On validly published names, correct names, and changes in the nomenclature of phyla and genera of prokaryotes: a guide for the perplexed	17
Topical prebiotic nitrate: optimizing the ‘hang-time’, source and dose for specific oral or systemic effects	17
Bacterial capsules: Occurrence, mechanism, and function	17
Extracellular vesicles of the Gram-positive gut symbiont Bifidobacterium longum induce immune-modulatory, anti-inflammatory effects	17
Akkermansia muciniphila in the small intestine improves liver fibrosis in a murine liver cirrhosis model	17
Periodontitis salivary microbiota exacerbates colitis-induced anxiety-like behavior via gut microbiota	17
Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization	17