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 2021-04-01 to 2025-04-01.)

Article	Citations
Stress triggers gut dysbiosis via CRH-CRHR1-mitochondria pathway	180
Bacterial c-di-GMP signaling gene affects mussel larval metamorphosis through outer membrane vesicles and lipopolysaccharides	177
A Klebsiella-phage cocktail to broaden the host range and delay bacteriophage resistance both in vitro and in vivo	143
GGDEF domain as spatial on-switch for a phosphodiesterase by interaction with landmark protein HubP	141
Pharmacodynamics of interspecies interactions in polymicrobial infections	119
In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus	106
Time-resolved compositional and dynamics analysis of biofilm maturation and dispersal via solid-state NMR spectroscopy	102
The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors	89
Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms	81
Carbon source competition within the wound microenvironment can significantly influence infection progression	76
Biofilm antimicrobial susceptibility through an experimental evolutionary lens	76
Community successional patterns and inter-kingdom interactions during granular biofilm development	71
Genome-wide siRNA screening reveals several host receptors for the binding of human gut commensal Bifidobacterium bifidum	66
Developmental intestinal microbiome alterations in canine fading puppy syndrome: a prospective observational study	64
Saliva-derived microcosm biofilms grown on different oral surfaces in vitro	63
The structure of Brazilian Amazonian gut microbiomes in the process of urbanisation	63
Supporting the strategic pillars of translational research in biofilms	61
Biophysical properties at patch scale shape the metabolism of biofilm landscapes	61
Preventing bacterial adhesion to skin by altering their physicochemical cell surface properties specifically	54
Metabolic plasticity enables lifestyle transitions of Porphyromonas gingivalis	54
Microbial diversity and secondary metabolism potential in relation to dark alterations in Paleolithic Lascaux Cave	53
An in vitro fermentation model to study the impact of bacteriophages targeting Shiga toxin-encoding Escherichia coli on the colonic microbiota	49
Long-term intake of Lactobacillus helveticus enhances bioavailability of omega-3 fatty acids in the mouse retina	48
Author Correction: Lactobacillus plantarum L168 improves hyperoxia-induced pulmonary inflammation and hypoalveolarization in a rat model of bronchopulmonary dysplasia	47
Diverse polysaccharide production and biofilm formation abilities of clinical Klebsiella pneumoniae	47

A sex-dependent salivary bacterium influences oral mucositis severity after allogeneic hematopoietic cell transplantation	47
Bacterial aggregation triggered by low-level antibiotic-mediated lysis	46
Leptospira interrogans biofilm transcriptome highlights adaption to starvation and general stress while maintaining virulence	46
Staphylococcus aureus SaeRS impairs macrophage immune functions through bacterial clumps formation in the early stage of infection	46
Optimization of an in vitro Pseudomonas aeruginosa Biofilm Model to Examine Antibiotic Pharmacodynamics at the Air-Liquid Interface	45
Recent advances in single-cell engineered live biotherapeutic products research for skin repair and disease treatment	45
Partial convergence of the human vaginal and rectal maternal microbiota in late gestation and early post-partum	45
Author Correction: Effect of model methanogens on the electrochemical activity, stability, and microbial community structure of Geobacter spp. dominated biofilm anodes	44
Disentangling direct vs indirect effects of microbiome manipulations in a habitat-forming marine holobiont	42
Bacteria contribute exopolysaccharides to an algal-bacterial joint extracellular matrix	42
Machine learning analysis of sex and menopausal differences in the gut microbiome in the HELIUS study	41
Combining SNAPs with antibiotics shows enhanced synergistic efficacy against S. aureus and P. aeruginosa biofilms	41
Hypermutability bypasses genetic constraints in SCV phenotypic switching in Pseudomonas aeruginosa biofilms	40
Oral and anal microbiome from HIV-exposed individuals: role of host-associated factors in taxa composition and metabolic pathways	40
Deep generative modeling of annotated bacterial biofilm images	40
A human oral commensal-mediated protection against Sjögren’s syndrome with maintenance of T cell immune homeostasis and improved oral microbiota	40
Neutralization of ionic interactions by dextran-based single-chain nanoparticles improves tobramycin diffusion into a mature biofilm	40
Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats	39
The highly differentiated gut of Pachnoda marginata hosts sequential microbiomes: microbial ecology and potential applications	38
Hydrodynamic conditions affect the proteomic profile of marine biofilms formed by filamentous cyanobacterium	37
Gut commensals-derived succinate impels colonic inflammation in ulcerative colitis	37
One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density	37
Author Correction: Rumen microbiome and fat deposition in sheep: insights from a bidirectional mendelian randomization study	36
Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut	36
Multi-way modelling of oral microbial dynamics and host-microbiome interactions during induced gingivitis	36
Probiotics alleviate constipation and inflammation in late gestating and lactating sows	36
Spatiotemporal bio-shielding of bacteria through consolidated geometrical structuring	34
Mitochondrial dysfunction promotes microbial composition that negatively impacts on ulcerative colitis development and progression	34
Enhancing tumor-specific recognition of programmable synthetic bacterial consortium for precision therapy of colorectal cancer	33
Depth heterogeneity of lignin-degrading microbiome and organic carbon processing in mangrove sediments	33
Elongation factor Tu promotes the onset of periodontitis through mediating bacteria adhesion	33
Lactobacillus plantarum L168 improves hyperoxia-induced pulmonary inflammation and hypoalveolarization in a rat model of bronchopulmonary dysplasia	32
In situ monitoring of Lentilactobacillus parabuchneri biofilm formation via real-time infrared spectroscopy	31
Early microbial markers of periodontal and cardiometabolic diseases in ORIGINS	31
Author Correction: Secreted nucleases reclaim extracellular DNA during biofilm development	30
Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization	30
Trichoderma-amended biofertilizer stimulates soil resident Aspergillus population for joint plant growth promotion	29
Bifidobacterium animalis Probio-M8 improves sarcopenia physical performance by mitigating creatine restrictions imposed by microbial metabolites	29
Body weight index indicates the responses of the fecal microbiota, metabolome and proteome to beef/chicken-based diet alterations in Chinese volunteers	29
The role of shear dynamics in biofilm formation	29
Staphylococcus aureus utilizes environmental RNA as a building material in specific polysaccharide-dependent biofilms	29
Translational challenges and opportunities in biofilm science: a BRIEF for the future	27
Biofilms can act as plasmid reserves in the absence of plasmid specific selection	27
Rationally designed probiotics prevent shrimp white feces syndrome via the probiotics–gut microbiome–immunity axis	26
The tongue biofilm metatranscriptome identifies metabolic pathways associated with the presence or absence of halitosis	25
Identification of essential genes for Escherichia coli aryl polyene biosynthesis and function in biofilm formation	25
Gene horizontal transfers and functional diversity negatively correlated with bacterial taxonomic diversity along a nitrogen gradient	25
Niche differentiation drives microbial community assembly and succession in full-scale activated sludge bioreactors	25
Akkermansia muciniphila inhibited the periodontitis caused by Fusobacterium nucleatum	25
Metabolic inputs in the probiotic bacterium Lacticaseibacillus rhamnosus contribute to cell-wall remodeling and increased fitness	24

Microbiome-derived antimicrobial peptides offer therapeutic solutions for the treatment of Pseudomonas aeruginosa infections	24
Author Correction: Inter-species metabolic interactions in an in-vitro minimal human gut microbiome of core bacteria	24
Bacteroides ovatus accelerates metformin-induced vitamin B12 deficiency in type 2 diabetes patients by accumulating cobalamin	24
Sucrose addition directionally enhances bacterial community convergence and network stability of the shrimp culture system	24
Role of intestinal testosterone-degrading bacteria and 3/17β-HSD in the pathogenesis of testosterone deficiency-induced hyperlipidemia in males	24
Long-chain 4-aminoquinolines inhibit filamentation and increase efficacy of nystatin against Candida albicans infections in vivo	24
Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts	24
Ex vivo intestinal permeability assay (X-IPA) for tracking barrier function dynamics	23
Synthetic periphyton as a model system to understand species dynamics in complex microbial freshwater communities	23
The gut microbiota modulate locomotion via vagus-dependent glucagon-like peptide-1 signaling	23
One-step preparation of antimicrobial silicone materials based on PDMS and salicylic acid: insights from spatially and temporally resolved techniques	23
Fluorescent nanosensors reveal dynamic pH gradients during biofilm formation	22
Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance	22
Environmental determinants and demographic influences on global urban microbiomes, antimicrobial resistance and pathogenicity	22
The sanitary indoor environment—a potential source for intact human-associated anaerobes	22
Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut	22
Non disseminative nano-strategy against in vivo Staphylococcus aureus biofilms	22
Kinetics of imidazole propionate from orally delivered histidine in mice and humans	21
Metabolic profiles outperform the microbiota in assessing the response of vaginal microenvironments to the changed state of HPV infection	21
Decoding the RNA viromes in shrew lungs along the eastern coast of China	21
Massive expansion of the pig gut virome based on global metagenomic mining	21
Staphylococcus epidermidis alters macrophage polarization and phagocytic uptake by extracellular DNA release in vitro	21
The potential to produce tropodithietic acid by Phaeobacter inhibens affects the assembly of microbial biofilm communities in natural seawater	21
Distinct types of multicellular aggregates in Pseudomonas aeruginosa liquid cultures	21
Author Correction: Deep insights into the gut microbial community of extreme longevity in south Chinese centenarians by ultra-deep metagenomics and large-scale culturomics	21
Diet-microbiome interactions promote enteric nervous system resilience following spinal cord injury	21
Exploring ex vivo biofilm dynamics: consequences of low ampicillin concentrations on the human oral microbiome	21
Assessing the inflammatory response to in vitro polymicrobial wound biofilms in a skin epidermis model	21
Colon or semicolon: gut sampling microdevices for omics insights	21
Author Correction: Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner	20
The Pga59 cell wall protein is an amyloid forming protein involved in adhesion and biofilm establishment in the pathogenic yeast Candida albicans	20
Simulation of catalase-dependent tolerance of microbial biofilm to hydrogen peroxide with a biofilm computer model	20
Hfq-binding small RNA PqsS regulates Pseudomonas aeruginosa pqs quorum sensing system and virulence	19
Faecal hsa-miR-7704 inhibits the growth and adhesion of Bifidobacterium longum by suppressing ProB and aggravates hepatic encephalopathy	19
Gut microbiota dysbiosis-mediated ceramides elevation contributes to corticosterone-induced depression by impairing mitochondrial function	19
Spaceflight alters host-gut microbiota interactions	19
Donor-recipient specificity and age-dependency in fecal microbiota therapy and probiotic resolution of gastrointestinal symptoms	19
Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19	19
Responses of drinking water bulk and biofilm microbiota to elevated water age in bench-scale simulated distribution systems	19
Root carbon inputs outweigh litter in shaping grassland soil microbiomes and ecosystem multifunctionality	18
The impact of antioxidant-ciprofloxacin combinations on the evolution of antibiotic resistance in Pseudomonas aeruginosa biofilms	18
Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics	17
Controlled spatial organization of bacterial growth reveals key role of cell filamentation preceding Xylella fastidiosa biofilm formation	17
Neighborhood socioeconomic status is associated with low diversity gut microbiomes and multi-drug resistant microorganism colonization	17
Transient colonizing microbes promote gut dysbiosis and functional impairment	17
Diversity of bacteria within the human gut and its contribution to the functional unity of holobionts	17
Protection against DSS-induced colitis in mice through FcεRIα deficiency: the role of altered Lactobacillus	17
The neglected role of micronutrients in predicting soil microbial structure	17