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 2020-11-01 to 2024-11-01.)

Article	Citations
Analysis of microbial compositions: a review of normalization and differential abundance analysis	150
Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization	131
Three faces of biofilms: a microbial lifestyle, a nascent multicellular organism, and an incubator for diversity	125
Economic significance of biofilms: a multidisciplinary and cross-sectoral challenge	121
Metagenomic analysis revealed the potential role of gut microbiome in gout	117
Interactions of plasma-activated water with biofilms: inactivation, dispersal effects and mechanisms of action	106
Seasonal dynamics of diet–gut microbiota interaction in adaptation of yaks to life at high altitude	94
Berberine attenuates choline-induced atherosclerosis by inhibiting trimethylamine and trimethylamine-N-oxide production via manipulating the gut microbiome	92
Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale	81
Microbial co-occurrence network topological properties link with reactor parameters and reveal importance of low-abundance genera	81
Host development overwhelms environmental dispersal in governing the ecological succession of zebrafish gut microbiota	76
Who put the film in biofilm? The migration of a term from wastewater engineering to medicine and beyond	70
Integrated metagenomics identifies a crucial role for trimethylamine-producing Lachnoclostridium in promoting atherosclerosis	64
Burns and biofilms: priority pathogens and in vivo models	59
Biofilm viability checker: An open-source tool for automated biofilm viability analysis from confocal microscopy images	58
Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth	57
Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis	55
Bacterial vaginosis and health-associated bacteria modulate the immunometabolic landscape in 3D model of human cervix	55
Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth–gut axis	52
Host-microbiome interactions: Gut-Liver axis and its connection with other organs	50
Biofilms harbour Clostridioides difficile, serving as a reservoir for recurrent infection	50
Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization	50
Exposure of Salmonella biofilms to antibiotic concentrations rapidly selects resistance with collateral tradeoffs	49
Improved functionality of Ligilactobacillus salivarius Li01 in alleviating colonic inflammation by layer-by-layer microencapsulation	49
Identification of small molecules that interfere with c-di-GMP signaling and induce dispersal of Pseudomonas aeruginosa biofilms	48

The biofilm matrix scaffold of Pseudomonas aeruginosa contains G-quadruplex extracellular DNA structures	47
Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees	47
Interactions between gut microbiota and metabolites modulate cytokine network imbalances in women with unexplained miscarriage	46
Gut microbiota determines the social behavior of mice and induces metabolic and inflammatory changes in their adipose tissue	43
Synergistic action of phage phiIPLA-RODI and lytic protein CHAPSH3b: a combination strategy to target Staphylococcus aureus biofilms	42
Lung microbiota associations with clinical features of COPD in the SPIROMICS cohort	41
Soil microbiome manipulation triggers direct and possible indirect suppression against Ralstonia solanacearum and Fusarium oxysporum	40
Atherosclerosis amelioration by allicin in raw garlic through gut microbiota and trimethylamine-N-oxide modulation	38
Real-time monitoring of ruminal microbiota reveals their roles in dairy goats during subacute ruminal acidosis	38
The pivotal roles of gut microbiota in insect plant interactions for sustainable pest management	36
Human organoid biofilm model for assessing antibiofilm activity of novel agents	35
Identification of essential genes for Escherichia coli aryl polyene biosynthesis and function in biofilm formation	35
Disrupting quorum sensing alters social interactions in Chromobacterium violaceum	35
A bacteriocin-based antimicrobial formulation to effectively disrupt the cell viability of methicillin-resistant Staphylococcus aureus (MRSA) biofilms	34
Experimental parameters defining ultra-low biomass bioaerosol analysis	34
Diversity and infectivity of the RNA virome among different cryptic species of an agriculturally important insect vector: whitefly Bemisia tabaci	33
Gut microbiota-mediated secondary bile acid alleviates Staphylococcus aureus-induced mastitis through the TGR5-cAMP-PKA-NF-κB/NLRP3 pathways in mice	32
A multiomics approach to identify host-microbe alterations associated with infection severity in diabetic foot infections: a pilot study	31
Human supplementation with Pediococcus acidilactici GR-1 decreases heavy metals levels through modifying the gut microbiota and metabolome	31
Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing	31
Biogeographical patterns and mechanisms of microbial community assembly that underlie successional biocrusts across northern China	30
Gut dysbiosis and mortality in hemodialysis patients	30
Magnetotactic bacteria and magnetofossils: ecology, evolution and environmental implications	30
Responses of soil microbiome to steel corrosion	30
The role of shear dynamics in biofilm formation	30
A new BiofilmChip device for testing biofilm formation and antibiotic susceptibility	29
Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota	29
Bacteroides uniformis-induced perturbations in colonic microbiota and bile acid levels inhibit TH17 differentiation and ameliorate colitis developments	29
Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates	29
Strategy to combat biofilms: a focus on biofilm dispersal enzymes	28
Transcriptomic evidence for versatile metabolic activities of mercury cycling microorganisms in brackish microbial mats	28
Rational consideration of Akkermansia muciniphila targeting intestinal health: advantages and challenges	28
Veillonellaceae family members uniquely alter the cervical metabolic microenvironment in a human three-dimensional epithelial model	28
Gut microbiota and metabolites of α-synuclein transgenic monkey models with early stage of Parkinson’s disease	28
Reduced stress-associated FKBP5 DNA methylation together with gut microbiota dysbiosis is linked with the progression of obese PCOS patients	28
One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density	28
Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors	27
The right bug in the right place: opportunities for bacterial vaginosis treatment	27
Biofilm antimicrobial susceptibility through an experimental evolutionary lens	27
Porcine gut microbiota in mediating host metabolic adaptation to cold stress	27
Genetic requirements and transcriptomics of Helicobacter pylori biofilm formation on abiotic and biotic surfaces	26
Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis	26
Gut microbiota as an antioxidant system in centenarians associated with high antioxidant activities of gut-resident Lactobacillus	26
Inter-species Metabolic Interactions in an In-vitro Minimal Human Gut Microbiome of Core Bacteria	25
Impact of temperature-dependent phage expression on Pseudomonas aeruginosa biofilm formation	25
Gut microbiome development in early childhood is affected by day care attendance	25
Soil microbial metabolism on carbon and nitrogen transformation links the crop-residue contribution to soil organic carbon	25
Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters	24
Weaponizing volatiles to inhibit competitor biofilms from a distance	24
The role of Psl in the failure to eradicate Pseudomonas aeruginosa biofilms in children with cystic fibrosis	24

Salivary dysbiosis in Sjögren’s syndrome and a commensal-mediated immunomodulatory effect of salivary gland epithelial cells	24
Network mapping of root–microbe interactions in Arabidopsis thaliana	24
Translational challenges and opportunities in biofilm science: a BRIEF for the future	24
Alternating magnetic fields and antibiotics eradicate biofilm on metal in a synergistic fashion	23
Sucrose addition directionally enhances bacterial community convergence and network stability of the shrimp culture system	23
Biofilm-isolated Listeria monocytogenes exhibits reduced systemic dissemination at the early (12–24 h) stage of infection in a mouse model	23
Trichoderma-amended biofertilizer stimulates soil resident Aspergillus population for joint plant growth promotion	23
Competition of two highly specialized and efficient acetoclastic electroactive bacteria for acetate in biofilm anode of microbial electrolysis cell	22
The gut microbiome-metabolome dataset collection: a curated resource for integrative meta-analysis	22
The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations	21
Long-term warming in a Mediterranean-type grassland affects soil bacterial functional potential but not bacterial taxonomic composition	21
Attachment and antibiotic response of early-stage biofilms studied using resonant hyperspectral imaging	21
Evolution of biofilm-adapted gene expression profiles in lasR-deficient clinical Pseudomonas aeruginosa isolates	21
Periodontitis associates with species-specific gene expression of the oral microbiota	21
The human respiratory tract microbial community structures in healthy and cystic fibrosis infants	21
Systems view of Bacillus subtilis pellicle development	21
Detection of gut microbiota and pathogen produced N-acyl homoserine in host circulation and tissues	20
Chicken cecal microbiota reduces abdominal fat deposition by regulating fat metabolism	19
Deep insights into the gut microbial community of extreme longevity in south Chinese centenarians by ultra-deep metagenomics and large-scale culturomics	19
Fluorescent nanosensors reveal dynamic pH gradients during biofilm formation	19
Artificial consortium demonstrates emergent properties of enhanced cellulosic-sugar degradation and biofuel synthesis	19
Carbohydrates from Pseudomonas aeruginosa biofilms interact with immune C-type lectins and interfere with their receptor function	19
Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism	19
The hallmarks of dietary intervention-resilient gut microbiome	19
A regulatory network involving Rpo, Gac and Rsm for nitrogen-fixing biofilm formation by Pseudomonas stutzeri	18
The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia	18
Quantifying the effects of antibiotic treatment on the extracellular polymer network of antimicrobial resistant and sensitive biofilms using multiple particle tracking	18
Cytochrome bd promotes Escherichia coli biofilm antibiotic tolerance by regulating accumulation of noxious chemicals	17
Gut microbiome responses to dietary intervention with hypocholesterolemic vegetable oils	17
In situ monitoring of Lentilactobacillus parabuchneri biofilm formation via real-time infrared spectroscopy	17
Gut microbiome dysregulation drives bone damage in broiler tibial dyschondroplasia by disrupting glucose homeostasis	17
Microbiome variation correlates with the insecticide susceptibility in different geographic strains of a significant agricultural pest, Nilaparvata lugens	17
Characterization of oral virome and microbiome revealed distinctive microbiome disruptions in paediatric patients with hand, foot and mouth disease	17
Inflammatory microbes and genes as potential biomarkers of Parkinson’s disease	17
Extracellular vesicles of the Gram-positive gut symbiont Bifidobacterium longum induce immune-modulatory, anti-inflammatory effects	17
The neglected role of micronutrients in predicting soil microbial structure	17
Biofilms can act as plasmid reserves in the absence of plasmid specific selection	17