Coaggregation and biofilm growth of Granulicatella spp. with Fusobacterium nucleatum and Aggregatibacter actinomycetemcomitans

Association of Corticosteroid Inhaler Type with Saliva Microbiome in Moderate-to-Severe Pediatric Asthma

Background/Objectives: Metered-dose inhalers (MDIs) and dry powder inhalers (DPIs) are common inhaled corticosteroid (ICS) inhaler devices. The difference in formulation and administration technique of these devices may influence oral cavity microbiota composition. We aimed to compare the saliva microbiome in children with moderate-to-severe asthma using ICS via MDIs versus DPIs. Methods: Saliva samples collected from 143 children (6-17 yrs) with moderate-to-severe asthma across four European countries (The Netherlands, Germany, Spain, and Slovenia) as part of the SysPharmPediA cohort were subjected to 16S rRNA sequencing. The microbiome was compared using global diversity (α and β) between two groups of participants based on inhaler devices (MDI (n = 77) and DPI (n = 65)), and differential abundance was compared using the Analysis of Compositions of Microbiomes with the Bias Correction (ANCOM-BC) method. Results: No significant difference was observed in α-diversity between the two groups. However, β-diversity analysis revealed significant differences between groups using both Bray-Curtis and weighted UniFrac methods (adjusted p-value = 0.015 and 0.044, respectively). Significant differential abundance between groups, with higher relative abundance in the MDI group compared to the DPI group, was detected at the family level [Carnobacteriaceae (adjusted p = 0.033)] and at the genus level [Granulicatella (adjusted p = 0.021) and Aggregatibacter (adjusted p = 0.011)]. Conclusions: Types of ICS devices are associated with different saliva microbiome compositions in moderate-to-severe pediatric asthma. The causal relation between inhaler types and changes in saliva microbiota composition needs to be further evaluated, as well as whether this leads to different potential adverse effects in terms of occurrence and level of severity.

Structure and composition of early biofilms formed on dental implants are complex, diverse, subject-specific and dynamic

Biofilm-associated peri-implant infections pose a major problem in modern medicine. The understanding of biofilm development is hampered by biofilm complexity and the lack of robust clinical models. This study comprehensively characterized the dynamics of early biofilm formation in the transmucosal passage of implant abutments in 12 patients. Biofilm structures and compositions were complex, diverse, subject-specific and dynamic. A total of 371 different bacterial species were detected. 100 phylogenetically diverse unnamed species and 35 taxonomically diverse disease-associated species comprised an average 4.3% and 3.1% of the community, respectively, but reached up to 12.7% and 21.7% in some samples. Oral taxa formed numerous positive associations and clusters and were characterized by a high potential for metabolic interactions. The subspecies diversity was highly patient-specific and species-dependent, with 1427 ASVs identified in total. The unprecedented depth of early biofilm characterization in this study will support the development of individualized preventive and early diagnostic strategies.

Impact of Malocclusions on Periodontopathogenic Bacterial Load and Progression of Periodontal Disease: A Quantitative Analysis

BACKGROUND

(1) Periodontal disease (PD) is a globally prevalent chronic inflammatory condition, exacerbated by the dysbiosis of the oral microbiota. This study aims to evaluate the bacterial load of specific periodontopathogenic bacteria in patients with malocclusions (MAL) compared to those without. (2) Methods: Conducted at the "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania, this pilot study involved two groups: patients with MAL and PD, and patients with PD but without MAL. We included 20 patients: 10 with MAL (9 with crowding and 1 with an open bite) and 10 without MAL. Gingival crevicular fluid was collected for bacterial DNA extraction and quantified bacterial load using real-time PCR, focusing on 12 periodontopathogenic bacteria across different complexity classes. (3) Results: The study identified significantly higher concentrations of Treponema denticola (p = 0.023, median = 4.32, IQR = 2.76-5.53 vs. median = 1.93, IQR = 0-3.19), Tannerella forsythia (p = 0.020, mean = 6.04 ± 0.72 vs. mean = 4.4 ± 1.89) and Porphyromonas gingivalis (p = 0.002, median = 5.64, IQR = 4.94-5.98 vs. median = 2.48, IQR = 0-4.05) in patients with MAL compared to those without. This suggests that MAL contributes to an environment conducive to the proliferation of specific pathogens, potentially accelerating PD progression. Additionally, Eikenella corrodens (p = 0.040, mean = 4.55 ± 1.02 vs. mean = 3.23 ± 1.56), Campylobacter rectus (p < 0.001, mean = 4.2 ± 0.56 vs. mean = 1.8 ± 1.51), Prevotella intermedia (p = 0.043, median = 5.04, IQR = 0-5.49 vs. median = 0, IQR = 0-3.39), Capnocytophaga sputigena (p = 0.011, median = 5.91, IQR = 5.47-6.17 vs. median = 4.63, IQR = 3.83-5.64), and Capnocytophaga gingivalis (p = 0.007, median = 5.87, IQR = 5.34-6.03 vs. median = 4.4, IQR = 3.5-5.71) also showed elevated concentrations, indicating the broad impacts of MAL on oral microbial profiles. (4) Conclusions: The findings demonstrate a significant relationship between MAL and increased bacterial loads, underscoring the need for its integration in managing PD. Future research should expand demographic diversity and employ longitudinal designs to better understand the causative mechanisms at play.

The effect of dental material type and masticatory forces on periodontitis-derived subgingival microbiomes

Restorative dental materials can frequently extend below the gingival margin, serving as a potential haven for microbial colonization, and altering the local oral microbiome to ignite infection. However, the contribution of dental materials on driving changes of the composition of the subgingival microbiome is under-investigated. This study evaluated the microbiome-modulating properties of three biomaterials, namely resin dental composites (COM), antimicrobial piezoelectric composites (BTO), and hydroxyapatite (HA), using an optimized in vitro subgingival microbiome model derived from patients with periodontal disease. Dental materials were subjected to static or cyclic loading (mastication forces) during biofilm growth. Microbiome composition was assessed by 16S rRNA gene sequencing. Dysbiosis was measured in terms of subgingival microbial dysbiosis index (SMDI). Biomaterials subjected to cyclic masticatory loads were associated with enhanced biofilm viability except on the antibacterial composite. Biomaterials held static were associated with increased biofilm biomass, especially on HA surfaces. Overall, the microbiome richness (Chao index) was similar for all the biomaterials and loading conditions. However, the microbiome diversity (Shannon index) for the HA beams was significantly different than both composites. In addition, beta diversity analysis revealed significant differences between composites and HA biomaterials, and between both loading conditions (static and cyclic). Under static conditions, microbiomes formed over HA surfaces resulted in increased dysbiosis compared to composites through the enrichment of periopathogens, including Porphyromonas gingivalis, Porphyromonas endodontalis, and Fretibacterium spp., and depletion of commensals such as Granulicatella and Streptococcus spp. Interestingly, cyclic loading reversed the dysbiosis of microbiomes formed over HA (depletion of periopathogenes) but increased the dysbiosis of microbiomes formed over composites (enrichment of Porphyromonas gingivalis and Fusobacterim nucleatum). Comparison of species formed on both composites (control and antibacterial) showed some differences. Commercial composites enriched Selenomonas spp. and depleted Campylobacter concisus. Piezoelectric composites effectively controlled the microbiome viability without significantly impacting the species abundance. Findings of this work open new understandings of the effects of different biomaterials on the modulation of oral biofilms and the relationship with oral subgingival infections.

Investigating oral microbiome profiles in patients with cleft lip and palate compared with the healthy control

BACKGROUND

Patients with cleft lip and palate (CLP) have an oronasal communication differed from the closed state in healthy individuals, leading to a unique oral microbiome. This study aimed to determine if variances in the oral microbiota persist among CLP patients who have received treatments for the closure of these fistulas compared to the microbiota of healthy individuals.

METHODS

Saliva samples were collected from a cohort comprising 28 CLP patients (CLP group) and 30 healthy controls (HC group). Utilizing 16S rRNA sequencing on the Illumina NovaSeq platform, we conducted a comprehensive analysis of the diversity and composition of the oral microbiota.

RESULTS

The analysis of the microbiota in the saliva samples revealed a total of 23 microbial phyla, 38 classes, 111 orders, 184 families, 327 genera and 612 species. The alpha diversity with microbial abundance and evenness indicated the significant difference between the CLP and HC groups. Principal coordinate analysis (PCoA) and the ADONIS test further supported the presence of distinct microorganisms between the two groups. The CLP group displayed elevated abundances of Neisseria, Haemophilus, Porphyromonas, and Granulicatella, as indicated by LefSe analysis. Conversely, Rothia, Veillonella, and Pauljensenia exhibited significant reductions in abundance in the CLP group. The results of the PICRUSt analysis indicated significant differences in the relative abundance of 25 KEGG pathways within the CLP group. Through Spearman correlation analysis, strong associations between Rothia, Veillonella, and Pauljensenia and 25 functional pathways linked to CLP were identified.

CONCLUSION

Findings of this study offer a thorough comprehension of the microbiome profiles of CLP patients after the restoration of oronasal structure and are anticipated to present innovative concepts for the treatment of CLP.

QNetDiff: a quantitative measurement of network rewiring

Bacteria in the human body, particularly in the large intestine, are known to be associated with various diseases. To identify disease-associated bacteria (markers), a typical method is to statistically compare the relative abundance of bacteria between healthy subjects and diseased patients. However, since bacteria do not necessarily cause diseases in isolation, it is also important to focus on the interactions and relationships among bacteria when examining their association with diseases. In fact, although there are common approaches to represent and analyze bacterial interaction relationships as networks, there are limited methods to find bacteria associated with diseases through network-driven analysis. In this paper, we focus on rewiring of the bacterial network and propose a new method for quantifying the rewiring. We then apply the proposed method to a group of colorectal cancer patients. We show that it can identify and detect bacteria that cannot be detected by conventional methods such as abundance comparison. Furthermore, the proposed method is implemented as a general-purpose tool and made available to the general public.

Secretome analysis and virulence assessment in Abiotrophia defectiva

Background

Abiotrophia defectiva, although infrequently occurring, is a notable cause of culture-negative infective endocarditis with limited research on its virulence. Associated with oral infections such as dental caries, exploring its secretome may provide insights into virulence mechanisms. Our study aimed to analyze and characterize the secretome of A. defectiva strain CCUG 27639.

Methods

Secretome of A. defectiva was prepared from broth cultures and subjected to mass spectrometry and proteomics for protein identification. Inflammatory potential of the secretome was assessed by ELISA.

Results

Eighty-four proteins were identified, with diverse subcellular localizations predicted by PSORTb. Notably, 20 were cytoplasmic, 12 cytoplasmic membrane, 5 extracellular, and 9 cell wall-anchored proteins. Bioinformatics tools revealed 54 proteins secreted via the 'Sec' pathway and 8 via a non-classical pathway. Moonlighting functions were found in 23 proteins, with over 20 exhibiting potential virulence properties, including peroxiredoxin and oligopeptide ABC transporter substrate-binding protein. Gene Ontology and KEGG analyses categorized protein sequences in various pathways. STRING analysis revealed functional protein association networks. Cytokine profiling demonstrated significant proinflammatory cytokine release (IL-8, IL-1β, and CCL5) from human PBMCs.

Conclusions

Our study provides a comprehensive understanding of A. defectiva's secretome, laying the foundation for insights into its pathogenicity.

The respiratory enzyme complex Rnf is vital for metabolic adaptation and virulence in Fusobacterium nucleatum

IMPORTANCE

This paper illuminates the significant question of how the oral commensal Fusobacterium nucleatum adapts to the metabolically changing environments of several extra-oral sites such as placenta and colon to promote various diseases as an opportunistic pathogen. We demonstrate here that the highly conserved Rhodobacter nitrogen-fixation complex, commonly known as Rnf complex, is key to fusobacterial metabolic adaptation and virulence. Genetic disruption of this Rnf complex causes global defects in polymicrobial interaction, biofilm formation, cell growth and morphology, hydrogen sulfide production, and ATP synthesis. Targeted metabolomic profiling demonstrates that the loss of this respiratory enzyme significantly diminishes catabolism of numerous amino acids, which negatively impacts fusobacterial virulence as tested in a preterm birth model in mice.

Granulicatella seriolae sp. nov., a Novel Facultative Anaerobe Isolated from Yellowtail Marine Fish

A bacterial strain, designated as S8T, was isolated from the gut contents of Seriola quinqueradiata from the coastal sea area of Jeju Island, South Korea. The strain is a Gram-staining positive, non-motile, non-spore-forming, facultative anaerobic coccus. Optimal growth was observed at 30 °C, pH 8.0-9.0, and 0-0.5% w/v NaCl, under anaerobic conditions. The predominant fatty acids were C18:1 ω9c, C16:0, C18:0, and C16:1 ω9c, while quinone was not detected. The genome was 2,224,566 bp long, with a GC content of 38.2%. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain S8T had 96.2% similarity with Granulicatella adiacens ATCC 49175T, its closest known species according to nomenclature. The DNA-DNA hybridization (dDDH), average nucleotide identity, and average amino acid identity values between strain S8T and G. adiacens ATCC 49175T were 25.7%, 85.5%, and 77.2%, respectively, all of which fall below the recommended threshold for species differentiation. Based on genomic, phenotypic, and phylogenetic evidence, we propose that strain S8T should be a novel species within the genus Granulicatella, for with the name Granulicatella seriolae sp. nov. is proposed. The type strain is S8T (KCTC 43438T = JCM 35604T).

Associations between Host Genetic Variants and Subgingival Microbiota in Patients with the Metabolic Syndrome

Host genetic variants may affect oral biofilms, playing a role in the periodontitis-systemic disease axis. This is the first study to assess the associations between host genetic variants and subgingival microbiota in patients with metabolic syndrome (MetS); 103 patients with MetS underwent medical and periodontal examinations and had blood and subgingival plaque samples taken. DNA was extracted and processed, assessing a panel of selected single nucleotide polymorphisms (SNPs) first (hypothesis testing) and then expanding to a discovery phase. The subgingival plaque microbiome from these patients was profiled. Analysis of associations between host genetic and microbial factors was performed and stratified for periodontal diagnosis. Specific SNPs within RUNX2, CAMTA1 and VDR genes were associated with diversity metrics with no genome-wide associations detected for periodontitis severity or Mets components at p < 10-7. Severe periodontitis was associated with pathogenic genera and species. Some SNPs correlated with specific bacterial genera as well as with microbial taxa, notably VDR (rs12717991) with Streptococcus mutans and RUNX2 (rs3749863) with Porphyromonas gingivalis. In conclusion, variation in host genotypes may play a role in the dysregulated immune responses characterizing periodontitis and thus the oral microbiome, suggesting that systemic health-associated host traits further interact with oral health and the microbiome.

Strain specificity in fusobacterial co-aggregation with colorectal cancer-relevant species

OBJECTIVES

The purpose of the present study was to characterize co-aggregation interactions between isolates of Fusobacterium nucleatum subsp. animalis and other colorectal cancer (CRC)-relevant species.

METHODS

Co-aggregation interactions were assessed by comparing optical density values following 2-h stationary strain co-incubations to strain optical density values when incubated alone. Co-aggregation was characterized between strains from a previously isolated, CRC biopsy-derived community and F. nucleatum subsp. animalis, a species linked to CRC and known to be highly aggregative. Interactions were also investigated between the fusobacterial isolates and strains sourced from alternate human gastrointestinal samples whose closest species match aligned with species in the CRC biopsy-derived community.

RESULTS

Co-aggregation interactions were observed to be strain-specific, varying between both F. nucleatum subsp. animalis strains and different strains of the same co-aggregation partner species. F. nucleatum subsp. animalis strains were observed to co-aggregate strongly with several taxa linked to CRC: Campylobacter concisus, Gemella spp., Hungatella hathewayi, and Parvimonas micra.

CONCLUSIONS

Co-aggregation interactions suggest the ability to encourage the formation of biofilms, and colonic biofilms, in turn, have been linked to promotion and/or progression of CRC. Co-aggregation between F. nucleatum subsp. animalis and CRC-linked species such as C. concisus, Gemella spp., H. hathewayi, and P. micra may contribute to both biofilm formation along CRC lesions and to disease progression.

The respiratory enzyme complex Rnf is vital for metabolic adaptation and virulence in Fusobacterium nucleatum

A prominent oral commensal and opportunistic pathogen, Fusobacterium nucleatum can traverse to extra-oral sites such as placenta and colon, promoting adverse pregnancy outcomes and colorectal cancer, respectively. How this anaerobe sustains many metabolically changing environments enabling its virulence potential remains unclear. Informed by our genome-wide transposon mutagenesis, we report here that the highly conserved Rnf complex, encoded by the rnfCDGEAB gene cluster, is key to fusobacterial metabolic adaptation and virulence. Genetic disruption of the Rnf complex via non-polar, in-frame deletion of rnfC (Δ rnfC ) abrogates polymicrobial interaction (or coaggregation) associated with adhesin RadD and biofilm formation. The defect in coaggregation is not due to reduced cell surface of RadD, but rather an increased level of extracellular lysine, which binds RadD and inhibits coaggregation. Indeed, removal of extracellular lysine via washing Δ rnfC cells restores coaggregation, while addition of lysine inhibits this process. These phenotypes mirror that of a mutant (Δ kamAΔ ) that fails to metabolize extracellular lysine. Strikingly, the Δ rnfC mutant is defective in ATP production, cell growth, cell morphology, and expression of the enzyme MegL that produces hydrogen sulfide from cysteine. Targeted metabolic profiling demonstrated that catabolism of many amino acids, including histidine and lysine, is altered in Δ rnfC cells, thereby reducing production of ATP and metabolites including H2S and butyrate. Most importantly, we show that the Δ rnfC mutant is severely attenuated in a mouse model of preterm birth. The indispensable function of Rnf complex in fusobacterial pathogenesis via modulation of bacterial metabolism makes it an attractive target for developing therapeutic intervention.

In Vitro Selection of Lactobacillus and Bifidobacterium Probiotic Strains for the Management of Oral Pathobiont Infections Associated to Systemic Diseases

The human oral pathobionts Aggregatibacter actinomycetemcomitans, Streptococcus mitis and Streptococcus mutans, in dysbiosis-promoting conditions, lead to oral infections, which also represent a threat to human systemic health. This scenario may be worsened by antibiotic misuse, which favours multi-drug resistance, making the research on pathogen containment strategies more than crucial. Therefore, we aimed to in vitro select the most promising probiotic strains against oral pathogen growth, viability, biofilm formation, and co-aggregation capacity, employing both the viable probiotics and their cell-free supernatants (CFSs). Interestingly, we also assessed probiotic efficacy against the three-pathogen co-culture, mimicking an environment similar to that in vivo. Overall, the results showed that Lactobacillus CFSs performed better than the Bifidobacterium, highlighting Limosilactobacillus reuteri LRE11, Lacticaseibacillus rhamnosus LR04, Lacticaseibacillus casei LC04, and Limosilactobacillus fermentum LF26 as the most effective strains, opening the chance to deeper investigation of their action and CFS composition. Altogether, the methodologies presented in this study can be used for probiotic efficacy screenings, in order to better focus the research on a viable probiotic, or on its postbiotics, suitable in case of infections.

Antibiotic Resistance of Selected Bacteria after Treatment of the Supragingival Biofilm with Subinhibitory Chlorhexidine Concentrations

Due to increasing rates of antibiotic resistance and very few novel developments of antibiotics, it is crucial to understand the mechanisms of resistance development. The aim of the present study was to investigate the adaptation of oral bacteria to the frequently used oral antiseptic chlorhexidine digluconate (CHX) and potential cross-adaptation to antibiotics after repeated exposure of supragingival plaque samples to subinhibitory concentrations of CHX. Plaque samples from six healthy donors were passaged for 10 days in subinhibitory concentrations of CHX, while passaging of plaque samples without CHX served as control. The surviving bacteria were cultured on agar plates and identified with Matrix-assisted Laser Desorption/Ionization-Time of Flight-Mass spectrometry (MALDI-TOF). Subsequently, the minimum inhibitory concentrations (MIC) of these isolates toward CHX were determined using a broth-microdilution method, and phenotypic antibiotic resistance was evaluated using the epsilometertest. Furthermore, biofilm-forming capacities were determined. Repeated exposure of supragingival plaque samples to subinhibitory concentrations of CHX led to the selection of oral bacteria with 2-fold up to 4-fold increased MICs toward CHX. Furthermore, these isolates showed up to 12-fold increased MICs towards some antibiotics such as erythromycin and clindamycin. Conversely, biofilm-forming capacity was decreased. In summary, this study shows that oral bacteria are able to adapt to CHX, while also decreasing their susceptibility to antibiotics.

The Regulatory Effect of Coaggregation Between Fusobacterium nucleatum and Streptococcus gordonii on the Synergistic Virulence to Human Gingival Epithelial Cells

In subgingival plaque biofilms, Fusobacterium nucleatum is closely related to the occurrence and development of periodontitis. Streptococcus gordonii, as an accessory pathogen, can coaggregate with periodontal pathogens, facilitating the subgingival colonization of periodontal pathogens. Studies have shown that F. nucleatum can coaggregate with S. gordonii and colonize the subgingival plaque. However, most studies have focused on monocultures or coinfection of species and the potential impact of coaggregation between the two species on periodontal interactions to human gingival epithelial cells (hGECs) remains poorly understood. The present study explored the effect of coaggregation between F. nucleatum and S. gordonii on subgingival synergistic virulence to hGECs. The results showed that coaggregation inhibited the adhesion and invasion of F. nucleatum to hGECs compared with that in the F. nucleatum monoculture and coinfection group. Coaggregation and coinfection with F. nucleatum both enhanced S. gordonii adhesion to hGECs, but neither of the two groups affected S. gordonii invasion to hGECs compared with S. gordonii monoculture. The gene expression levels of TLR2 and TLR4 in hGECs in the coaggregation group were higher than those in the monoculture groups but lower than those in the coinfection group. Compared with coinfection, the coaggregation inhibited apoptosis of hGECs and promoted the secretion of the proinflammatory cytokines TNF-α and IL-6 by hGECs, showed a synergistic inflammatory effect, while coaggregation inhibited the secretion of the anti-inflammatory cytokine TGF-β1. Coaggregation enhanced the phosphorylation of p65, p38, and JNK proteins and therefore activated the NF-κB and MAPK signaling pathways. Pretreatment with a pathway antagonist/inhibitor decreased the phosphorylation levels of proteins and the secretion of TNF-α and IL-6. In conclusion, coaggregation inhibited the adhesion and invasion of F. nucleatum to hGECs. However, it enhanced the adhesion of S. gordonii to hGECs. Compared with coinfection, coaggregation inhibited the apoptosis of hGECs. The coaggregation coordinately promoted the secretion of TNF-α and IL-6 by hGECs through the TLR/NF-κB and TLR/MAPK signaling pathways while inhibiting the secretion of TGF-β1, thus aggravating the inflammatory response of hGECs.

The Effect of Benzyl Isothiocyanate on the Expression of Genes Encoding NADH Oxidase and Fibronectin-Binding Protein in Oral Streptococcal Biofilms

Recent studies have shown that antimicrobial treatment results in up- or down regulation of several virulence-associated genes in bacterial biofilms. The genes encoding NADH oxidase (nox) and fibronectin-binding protein (fbp) are known to play important roles in biofilm growth of some oral bacterial species. The objective was to study the effect of benzyl isothiocyanate (BITC), an antimicrobial agent from Miswak plant, on the expression of nox and fbp genes in some oral streptococci. The biofilms were treated with BITC and mRNA expression of nox and fbp genes was measured by comparative ΔΔCt method. The highest amount of biofilm mass was produced by A. defectiva, followed by S. gordonii, S. mutans, G. elegans and G. adiacens. Upon treatment with BITC, S. gordonii biofilms showed highest folds change in mRNA expression for both fbp and nox genes followed by S. mutans, A. defectiva, and G. adiacens. G. elegans mRNA levels for nox were extremely low. In conclusion, BITC treatment of the biofilms caused an upregulation of biofilm-associated genes fbp and nox genes in most of the tested species suggesting the significance of these genes in biofilm lifestyle of these oral bacteria and needs further investigation to understand if it contributes to antimicrobial resistance.

Fusobacterium nucleatum Subspecies Differ in Biofilm Forming Ability in vitro

Development of dysbiosis in complex multispecies bacterial biofilms forming on teeth, known as dental plaque, is one of the factors causing periodontitis. Fusobacterium nucleatum (F. nucleatum) is recognised as a key microorganism in subgingival dental plaque, and is linked to periodontitis as well as colorectal cancer and systemic diseases. Five subspecies of F. nucleatum have been identified: animalis, fusiforme, nucleatum, polymorphum, and vincentii. Differential integration of subspecies into multispecies biofilm models has been reported, however, biofilm forming ability of individual F. nucleatum subspecies is largely unknown. The aim of this study was to determine the single-subspecies biofilm forming abilities of F. nucleatum ATCC type strains. Static single subspecies F. nucleatum biofilms were grown anaerobically for 3 days on untreated or surface-modified (sandblasting, artificial saliva, fibronectin, gelatin, or poly-L-lysine coating) plastic and glass coverslips. Biofilm mass was quantified using crystal violet (CV) staining. Biofilm architecture and thickness were analysed by scanning electron microscopy and confocal laser scanning microscopy. Bioinformatic analysis was performed to identify orthologues of known adhesion proteins in F. nucleatum subspecies. Surface type and treatment significantly influenced single-subspecies biofilm formation. Biofilm formation was overall highest on poly-L-lysine coated surfaces and sandblasted glass surfaces. Biofilm thickness and stability, as well as architecture, varied amongst the subspecies. Interestingly, F. nucleatum ssp. polymorphum did not form a detectable, continuous layer of biofilm on any of the tested substrates. Consistent with limited biofilm forming ability in vitro, F. nucleatum ssp. polymorphum showed the least conservation of the adhesion proteins CmpA and Fap2 in silico. Here, we show that biofilm formation by F. nucleatum in vitro is subspecies- and substrate-specific. Additionally, F. nucleatum ssp. polymorphum does not appear to form stable single-subspecies continuous layers of biofilm in vitro. Understanding the differences in F. nucleatum single-subspecies biofilm formation may shed light on multi-species biofilm formation mechanisms and may reveal new virulence factors as novel therapeutic targets for prevention and treatment of F. nucleatum-mediated infections and diseases.

A Potential “Vitaminic Strategy” against Caries and Halitosis

Streptococcus mutans and Fusobacterium nucleatum are two key bacteria of the oral microbiota. Due to their ability to form biofilms on oral tissues, they are both involved in the onset of the most common oral diseases. F. nucleatum is also the principal producer of hydrogen sulfide (H2S), causative of the awkward bad breath of halitosis. In this study, the oral product Vea® Oris, made by vitamin E and capric/caprylic acid only, was evaluated as a potential treatment for the most common oral diseases. Different concentrations of the product were tested against both S. mutans and F. nucleatum. The effect on planktonic and biofilm growth was investigated for both strains, and for F. nucleatum, the influence on H2S production was evaluated. From our data, the product did not relevantly reduce the planktonic growth of both strains, whereas it validly counteracted biofilm assemblage. Moreover, an interesting trend of H2S reduction was highlighted. Overall, these results suggested, on the one hand, a synergistic antimicrobial–antibiofilm action of two Vea® Oris components and, together, potential modulation activity on H2S production. However, the study should be implemented to confirm these only preliminary findings, certainly extending the panel of tested bacteria and using alternative methods of detection.

Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome

BACKGROUND

Upper gastrointestinal (GI) disorders and abdominal pain afflict between 12 and 30% of the worldwide population and research suggests these conditions are linked to the gut microbiome. Although large-intestine microbiota have been linked to several GI diseases, the microbiota of the human small intestine and its relation to human disease has been understudied. The small intestine is the major site for immune surveillance in the gut, and compared with the large intestine, it has greater than 100 times the surface area and a thinner and more permeable mucus layer.

RESULTS

Using quantitative sequencing, we evaluated total and taxon-specific absolute microbial loads from 250 duodenal-aspirate samples and 21 paired duodenum-saliva samples from participants in the REIMAGINE study. Log-transformed total microbial loads spanned 5 logs and were normally distributed. Paired saliva-duodenum samples suggested potential transmission of oral microbes to the duodenum, including organisms from the HACEK group. Several taxa, including Klebsiella, Escherichia, Enterococcus, and Clostridium, seemed to displace strict anaerobes common in the duodenum, so we refer to these taxa as disruptors. Disruptor taxa were enriched in samples with high total microbial loads and in individuals with small intestinal bacterial overgrowth (SIBO). Absolute loads of disruptors were associated with more severe GI symptoms, highlighting the value of absolute taxon quantification when studying small-intestine health and function.

CONCLUSION

This study provides the largest dataset of the absolute abundance of microbiota from the human duodenum to date. The results reveal a clear relationship between the oral microbiota and the duodenal microbiota and suggest an association between the absolute abundance of disruptor taxa, SIBO, and the prevalence of severe GI symptoms. Video Abstract.

Molecular and pathogenic characterization of Vibrio parahaemolyticus isolated from seafood

Gastroenteritis infections in humans are mainly associated with consumption of Vibrio parahaemolyticus contaminated shellfish, which causes health and economic loss. Virulence factor production, antibiotic resistance profile, and biofilm-forming capacity of Vibrio parahaemolyticus isolates on food and food contact surfaces at 30 °C were investigated to evaluate the antibiotic sensitivity and pathogenic level. Strains of V. parahaemolyticus were isolated from shellfish (e.g., Crassostrea gigas, Venerupis philippinarum, Mytilus coruscus, Anadara kagoshimensis) in Korea. When examined for 17 virulence factor-encoding genes, 53.3, 73.1, 87.1, 87.9, and 90.9% of the isolates were positive for genes encoding TDH, T6SS, T3SS1, T3SS2, and Type I pilus, respectively. All isolates showed resistance to vancomycin, tetracyclines, penicillin, nalidixic acid, and doxycycline, among 26 antibiotics tested, with most isolates resistant to kanamycin (93.5%), ampicillin (96.8%), clindamycin (96.8%), tobramycin (88.7%), amikacin (83.97%), and minocycline (80.7%). Biofilm formation, cell-cell attachment, and motility were high in most isolates. These findings may assist in monitoring the epidemics of the pathogen. Continuous monitoring could help to decrease V. parahaemolyticus infections and improve seafood safety.

Efficacy of auto-aggregating aerobic denitrifiers with coaggregation traits for bioaugmentation performance in biofilm-formation and nitrogen-removal

To promote efficiency nitrogen-rich wastewater treatment from a sequencing batch biofilm reactor (SBBR), three aerobic denitrifiers (Pseudomonas mendocinaIHB602, Methylobacterium gregansDC-1 and Pseudomonas stutzeriIHB618) with dual-capacities of strong auto-aggregation and high nitrogen removal efficiency were studied. The aggregation index analysis indicated that coaggregation of the three strains co-existed was better when compared with one or two strains grown alone. Optimal coaggregation strains were used to bioaugmente a test reactor (SBBR_T), which exhibited a shorter time for biofilm-formation than uninoculated control reactor (SBBR_C). With different influent ammonia-N loads (150, 200 and 300 mg·L^-1), the average ammonia-N and nitrate-N removal efficiency were all higher than that in SBBR_C, as well as a lower nitrite-N accumulation. Microbial community structure analysis revealed coaggregation strains may successfully colonize in the bioreactor and be very tolerant of high nitrogen concentrations, and contribute to the high efficiency of inorganic nitrogen-removal and biofilm-formation.

Molecular and Structural Parallels between Gluten Pathogenic Peptides and Bacterial-Derived Proteins by Bioinformatics Analysis

Gluten-related disorders (GRDs) are a group of diseases that involve the activation of the immune system triggered by the ingestion of gluten, with a worldwide prevalence of 5%. Among them, Celiac disease (CeD) is a T-cell-mediated autoimmune disease causing a plethora of symptoms from diarrhea and malabsorption to lymphoma. Even though GRDs have been intensively studied, the environmental triggers promoting the diverse reactions to gluten proteins in susceptible individuals remain elusive. It has been proposed that pathogens could act as disease-causing environmental triggers of CeD by molecular mimicry mechanisms. Additionally, it could also be possible that unrecognized molecular, structural, and physical parallels between gluten and pathogens have a relevant role. Herein, we report sequence, structural and physical similarities of the two most relevant gluten peptides, the 33-mer and p31-43 gliadin peptides, with bacterial pathogens using bioinformatics going beyond the molecular mimicry hypothesis. First, a stringent BLASTp search using the two gliadin peptides identified high sequence similarity regions within pathogen-derived proteins, e.g., extracellular proteins from Streptococcus pneumoniae and Granulicatella sp. Second, molecular dynamics calculations of an updated α-2-gliadin model revealed close spatial localization and solvent-exposure of the 33-mer and p31-43 peptide, which was compared with the pathogen-related proteins by homology models and localization predictors. We found putative functions of the identified pathogen-derived sequence by identifying T-cell epitopes and SH3/WW-binding domains. Finally, shape and size parallels between the pathogens and the superstructures of gliadin peptides gave rise to novel hypotheses about activation of innate immunity and dysbiosis. Based on our structural findings and the similarities with the bacterial pathogens, evidence emerges that these pathologically relevant gluten-derived peptides could behave as non-replicating pathogens opening new research questions in the interface of innate immunity, microbiome, and food research.

Synergistic interactions prevail in multispecies biofilms formed by the human gut microbiota on mucin

Bacterial species in the human gut predominantly exist in the form of mixed-species biofilms on mucosal surfaces. In this study, the biofilm-forming ability of many human gut bacterial strains (133 strains recovered from human faeces) on mucin-coated and non-coated polystyrene surfaces was determined. A significant variation (P < 0.05) in the biofilm-forming ability of many bacterial species on both surfaces was noticed. Based on some preliminary trials, four bacterial species were selected (Bifidobacterium bifidum, Bifidobacterium longum subsp. infantis, Parabacteroides distasonis and Bacteroides ovatus), which could not form any abundant biofilm individually under the in vitro conditions investigated, but produced abundant biofilms when co-cultured in different combinations of two, three and four species, giving an evidence of synergistic interactions in multispecies biofilm formation. There was a 4.74-fold increase in the biofilm mass when all strains developed a biofilm together. Strain-specific qPCR analysis showed that B. bifidum was the most dominant species (56%) in the four-species biofilm after 24 h, followed by B. longum subsp. infantis (36.2%). Study involving cell free supernatant of the cooperating strains showed that cell viability as well as physical presence of cooperating cells were prerequisites for the observed synergy in biofilms. The molecular mechanism behind these interactions and subsequent effects on the functionality of the strains involved were not determined in our study but merit further work.

Granulicatella adiacens: An uncommon diagnosis of prosthetic hip joint infection. A case report with review of the literature

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Prosthetic hip infection caused by Granulicatella adiacens.

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Diagnosis was achieved using broad range 16S PCR gene analysis at an early stage, after joint aspiration and culture failed to yield a pathogen.

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Granulicatella adiacens is a nutritionally variant streptococcus (NVS).

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Staged revision surgery together with administration of appropriate antibiotics resulted in cure.

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Diagnosis challenging, and often delays appropriate antibiotic administration.

We report a case of prosthetic hip infection in a 79 year old man caused by Granulicatella adiacens. The diagnosis was achieved using broad range 16S PCR gene analysis at an early stage, after joint aspiration and culture failed to yield a pathogen. Staged revision surgery together with administration of appropriate antibiotics resulted in cure. Granulicatella adiacens is a nutritionally variant streptococcus (NVS). It has been increasingly reported to cause significant morbidities involving various systems. Its insidious growth due to complex growth requirements, has made its diagnosis challenging, and often delays appropriate antibiotic administration.

Oral Pathogen Fusobacterium nucleatum Coaggregates With Pseudomonas aeruginosa to Modulate the Inflammatory Cytotoxicity of Pulmonary Epithelial Cells

Chronic obstructive pulmonary disease (COPD) is the third leading cause of mortality worldwide, and inflammatory damage induced by bacterial infections is an important contributor to the etiology of COPD. Fusobacterium nucleatum, a recognized periodontal pathogen, is considered as a biomarker of lung function deterioration of COPD patients coinfected with Pseudomonas aerugionsa, but the underlying mechanism is still unclear. This study established single- and dual-species infection models, bacterial simultaneous and sequential infection models, and found that F. nucleatum could coaggregate with P. aeruginosa to synergistically invade into pulmonary epithelial cells and transiently resist P. aeruginosa-induced cytotoxic damage to amplify IL-6 and TNF-α associated inflammation in pulmonary epithelial cells simultaneously infected with P. aeruginosa and F. nucleatum. Furthermore, F. nucleatum pretreatment or subsequential infection could maintain or even aggravate P. aeruginosa-induced inflammatory cytotoxicity of pulmonary epithelial cells. These results indicate that oral pathogen F. nucleatum coaggregates with P. aeruginosa to facilitate bacterial invasion and modulates the inflammatory cytotoxicity of pulmonary epithelial cells, which may contribute to lung function deterioration of COPD patients accompanied with P. aeruginosa and F. nucleatum coinfection.

Microbial population shift and metabolic characterization of silver diamine fluoride treatment failure on dental caries

The objective of this pilot study was to describe the microbial profiles present in the plaque and saliva of children who continued to develop new carious lesions following treatment with silver diamine fluoride ("nonresponders") compared to caries active, caries-free, and children immediately receiving SDF treatment for untreated caries in order to identify potential microbial differences that may relate to a re-incidence of caries. Saliva and plaque samples from infected and contralateral sites were obtained from twenty children who were either caries free, had active carious lesions, were caries active and received SDF treatment immediately before sampling, or had previously received SDF treatment and developed new caries. In total, 8,057,899 Illumina-generated sequence reads from 60 samples were obtained. Reads were processed using the Quantitative Insights Into Microbial Ecology pipeline. Group differences were assessed using Analysis of Variance Models and Tukey Honest Significant Differences. To identify significant taxa between treatment groups, Linear discriminant analysis Effect Size (LefSe) and Analysis of Differential Abundance Taking Sample Variation Into Account were used. Differential abundant analysis indicated that members of the Lachnospiraceae family were significantly enriched in non-responders and the genus Tannerella and species Granulicatella adiances were also highly abundant in this group. LefSe analysis between non-responders and SDF-treated groups revealed that genera Leptotrichia and Granulicatella were enriched in non-responders. We observed the highest abundance of phosphotransferase system and lowest abundance of lipopolysaccharide synthesis in non-responders. The microbiome in dental biofilms is responsible for initiation and progression of dental caries. SDF has been shown to be effective in arresting the progression carious lesions, in part due to its antimicrobial properties. Findings suggest that the differential abundance of select microbiota and specific pathway functioning in individuals that present with recurrent decay after SDF treatment may contribute to a potential failure of silver diamine fluoride to arrest dental caries. However, the short duration of sample collection following SDF application and the small sample size emphasize the need for further data and additional analysis.

Fusobacterium nucleatum Secretes Outer Membrane Vesicles and Promotes Intestinal Inflammation

Multiple studies have implicated microbes in the development of inflammation, but the mechanisms remain unknown. Bacteria in the genus Fusobacterium have been identified in the intestinal mucosa of patients with digestive diseases; thus, we hypothesized that Fusobacterium nucleatum promotes intestinal inflammation. The addition of >50 kDa F. nucleatum conditioned media, which contain outer membrane vesicles (OMVs), to colonic epithelial cells stimulated secretion of the proinflammatory cytokines interleukin-8 (IL-8) and tumor necrosis factor (TNF). In addition, purified F. nucleatum OMVs, but not compounds <50 kDa, stimulated IL-8 and TNF production; which was decreased by pharmacological inhibition of Toll-like receptor 4 (TLR4). These effects were linked to downstream effectors p-ERK, p-CREB, and NF-κB. F. nucleatum >50-kDa compounds also stimulated TNF secretion, p-ERK, p-CREB, and NF-κB activation in human colonoid monolayers. In mice harboring a human microbiota, pretreatment with antibiotics and a single oral gavage of F. nucleatum resulted in inflammation. Compared to mice receiving vehicle control, mice treated with F. nucleatum showed disruption of the colonic architecture, with increased immune cell infiltration and depleted mucus layers. Analysis of mucosal gene expression revealed increased levels of proinflammatory cytokines (KC, TNF, IL-6, IFN-γ, and MCP-1) at day 3 and day 5 in F. nucleatum-treated mice compared to controls. These proinflammatory effects were absent in mice who received F. nucleatum without pretreatment with antibiotics, suggesting that an intact microbiome is protective against F. nucleatum-mediated immune responses. These data provide evidence that F. nucleatum promotes proinflammatory signaling cascades in the context of a depleted intestinal microbiome.IMPORTANCE Several studies have identified an increased abundance of Fusobacterium in the intestinal tracts of patients with colon cancer, liver cirrhosis, primary sclerosing cholangitis, gastroesophageal reflux disease, HIV infection, and alcoholism. However, the direct mechanism(s) of action of Fusobacterium on pathophysiological within the gastrointestinal tract is unclear. These studies have identified that F. nucleatum subsp. polymorphum releases outer membrane vesicles which activate TLR4 and NF-κB to stimulate proinflammatory signals in vitro Using mice harboring a human microbiome, we demonstrate that F. nucleatum can promote inflammation, an effect which required antibiotic-mediated alterations in the gut microbiome. Collectively, these results suggest a mechanism by which F. nucleatum may contribute to intestinal inflammation.

Mining indigenous honeybee gut microbiota for Lactobacillus with probiotic potential

The present study was done to explore the diversity of lactic acid bacteria (LAB) associated with the gastrointestinal tract (GIT) of honeybee species endemic to northeastern Pakistan. Healthy worker bees belonging to Apis mellifera, A. dorsata, A. cerana and A. florea were collected from hives and the surroundings of a major apiary in the region. The 16S rRNA amplicon sequencing revealed a microbial community in A. florea that was distinct from the others in having an abundance of Lactobacillus and Bifidobacteria. However, this was not reflected in the culturable bacteria obtained from these species. The isolates were characterized for safety parameters, and 20 LAB strains deemed safe were evaluated for resistance to human GIT stresses like acid and bile, adhesion and adhesiveness, and anti-pathogenicity. The five most robust strains, Enterococcus saigonensis NPL780a, Lactobacillus rapi NPL782a, Lactobacillus kunkeei NPL783a, and NPL784, and Lactobacillus paracasei NPL783b, were identified through normalized Pearson (n) principal components analysis (PCA). These strains were checked for inhibition of human pathogens, antibiotic resistance, osmotic tolerance, metabolic and enzymatic functions, and carbohydrate utilization, along with antioxidative and cholesterol-removing potential. The findings suggest at least three strains (NPL 783a, 784 and 782a) as candidates for further in vitro and in vivo investigations of their potential health benefits and application as novel probiotic adjuncts.

Identification of bacterial biofilms on desalination reverse osmosis membranes from the mediterranean sea

Nanofiltration and reverse osmosis are two of the most effective surface water treatment processes. They provide water of high quality and eliminate a large amount of microorganisms, organic matter and micropollutants. However, the main limitation of membrane nanofiltration is fouling, which imposes an additional cost. This study focused on the search for microorganisms capable of reducing the performance of nanofilters and also to study autoaggregation and biofilms formation by bacterial strains isolated from the nanomembranes used in the seawater desalination plant of Souk Tlata (Algeria). It provides new microbiological data on the desalination of seawater in the southern Mediterranean basin. The results revealed 14 bacterial species isolated from six fouled reverse osmosis membranes; their quantities were significant with the dominance of Raoultella sp., Klebsiella sp., Staphylococcus sp., Stenotrophomonas sp., Micrococcus sp., and Escherichia coli. In addition, electron imaging of nanomembrane surfaces revealed complex structures of microorganisms forming biofilms.

Polymicrobial Biofilm Interaction Between Histophilus somni and Pasteurella multocida

Histophilus somni and Pasteurella multocida are two of multiple agents responsible for bovine respiratory disease (BRD) in cattle. Following respiratory infection of calves with H. somni, P. multocida may also be isolated from the lower respiratory tract. Because H. somni may form a biofilm during BRD, we sought to determine if P. multocida can co-exist with H. somni in a polymicrobial biofilm in vitro and in vivo. Interactions between the two species in the biofilm were characterized and quantified by fluorescence in situ hybridization (FISH). The biofilm matrix of each species was examined using fluorescently tagged lectins (FTL) specific for the exopolysaccharide (EPS) using confocal laser scanning microscopy. Bacterial interactions were determined by auto-aggregation and biofilm morphology. Pasteurella multocida and H. somni were evenly distributed in the in vitro biofilm, and both species contributed to the polymicrobial biofilm matrix. The average biomass and biofilm thickness, and the total carbohydrate and protein content of the biofilm, were greatest when both species were present. Polymicrobial bacterial suspensions auto-aggregated faster than single species suspensions, suggesting physical interactions between the two species. Almost 300 P. multocida genes were significantly differentially regulated when the bacteria were in a polymicrobial biofilm compared to a mono-species biofilm, as determined by RNA-sequencing. As expected, host genes associated with inflammation and immune response were significantly upregulated at the infection site following H. somni challenge. Encapsulated P. multocida isolates not capable of forming a substantial biofilm enhanced an in vitro polymicrobial biofilm with H. somni, indicating they contributed to the polymicrobial biofilm matrix. Indirect evidence indicated that encapsulated P. multocida also contributed to a polymicrobial biofilm in vivo. Only the EPS of H. somni could be detected by FTL staining of bovine tissues following challenge with H. somni. However, both species were isolated and an immune response to the biofilm matrix of both species was greater than the response to planktonic cells, suggesting encapsulated P. multocida may take advantage of the H. somni biofilm to persist in the host during chronic BRD. These results may have important implications for the management and prevention of BRD.

Gardnerella vaginalis Enhances Atopobium vaginae Viability in an in vitro Model

Bacterial vaginosis (BV) is the most common vaginal infection among women of reproductive age. A hallmark of BV is the presence of a highly structured polymicrobial biofilm on the vaginal epithelium, presumably initiated by facultative anaerobes of the genus Gardnerella, which then becomes a scaffold for other species to adhere to. One of the species often found incorporated in Gardnerella mediated biofilms is Atopobium vaginae. Interestingly, A. vaginae is very rarely found without the presence of Gardnerella. However, not much is known regarding the interactions between A. vaginae and Gardnerella species. This study assessed biological interactions between Gardnerella vaginalis and A. vaginae. In our in vitro model, by using specific Gardnerella and A. vaginae Peptide Nucleic Acid (PNA)-Fluorescence In Situ Hybridization (FISH) probes, we confirmed that A. vaginae was able to incorporate a pre-formed G. vaginalis biofilm, accounting for up to 20% of the total number of biofilm cells. However, our findings showed that almost 92% of A. vaginae cells lost viability after 48 h of mono-species planktonic growth, but were able to maintain viability when co-cultured with Gardnerella or after pre-conditioning with cell-free supernatant of Gardnerella cultures. While the in vitro conditions are very different from the in vivo microenvironment, this study contributes to a better understanding of why A. vaginae vaginal colonization rarely occurs in the absence of Gardnerella. Overall, this highlights the importance of microbial interactions between BV-associated bacteria and demands more studies focused on the polymicrobial bacterial communities found in BV.

Contribution of different adherent properties of Granulicatella adiacens and Abiotrophia defectiva to their associations with oral colonization and the risk of infective endocarditis

Granulicatella adiacens (G. adiacens) and Abiotrophia defectiva (A. defectiva) colonize the oral cavity and form part of the normal flora in the intestinal and genitourinary tracts. As reported previously, the frequency of isolation of G. adiacens from the oral cavity was much higher than that of A. defectiva. However, it has been reported that compared with G. adiacens, A. defectiva was isolated at considerably higher frequencies from the blood of patients with infective endocarditis (IE). Hence, in this study, the in vitro interaction of G. adiacens and A. defectiva strains with host surfaces and biofilm formation was examined to assess whether their different adhesive properties contribute to their associations with oral colonization and IE, respectively. G. adiacens exhibited an increased binding ability to saliva-coated hydroxyapatite beads than A. defectiva following the addition of CaCl₂. Furthermore, biofilm formation was observed only for G. adiacens with the use of a polystyrene tube and scanning electron microscopy analysis. Conversely, A. defectiva displayed significantly greater adherence to human umbilical vein endothelial cells and immobilized fibronectin than G. adiacens. These findings suggest that differences in binding properties to host components imply specific binding mechanisms in G. adiacens and A. defectiva, which might mediate selective colonization in the oral cavity or are associated with the pathogenicity of endocarditis.

Characterization of Proximal Small Intestinal Microbiota in Patients With Suspected Small Intestinal Bacterial Overgrowth: A Cross-Sectional Study

OBJECTIVES

The composition of the small intestinal microbiota has not yet been characterized thoroughly using culture-independent techniques. We compared small intestinal microbial communities in patients with and without small intestinal bacterial overgrowth (SIBO) using culture-dependent and culture-independent bacterial identification approaches.

METHODS

Small bowel aspirate and mucosal samples were collected from patients with suspected SIBO. The aspirates were cultured to diagnose SIBO, defined as ≥10 colony-forming units/mL coliform or ≥10 colony-forming units/mL upper aerodigestive tract bacteria. Bacteria in the aspirates and mucosa were identified using 16S rRNA gene sequencing. We compared small intestinal microbiome composition between groups with and without a culture-based SIBO diagnosis.

RESULTS

Analysis of the aspirate and mucosal microbial communities from 36 patients revealed decreased α-diversity but no differences in β-diversity in patients with SIBO compared with those without SIBO. There were no significant differences in the relative abundance of individual taxa from the aspirates or mucosa after adjustment for false discovery rate between patients with and without SIBO. Subgroup analysis revealed significant differences in mucosal β-diversity between the coliform and upper aerodigestive tract subgroups. Relative abundances of a mucosal Clostridium spp. (P = 0.05) and an aspirate Granulicatella spp. (P = 0.02) were higher in coliform SIBO vs non-SIBO subgroups. The microbial composition and relative abundance of multiple taxa significantly differed in the mucosal and aspirate specimens.

DISCUSSION

Culture-based results of small bowel aspirates do not correspond to aspirate microbiota composition but may be associated with species richness of the mucosal microbiota.

Antimicrobial capacity of Leucocyte-and Platelet Rich Fibrin against periodontal pathogens

Various studies have described the biological properties of the Leucocyte- and Platelet Rich Fibrin (L-PRF) such as the antimicrobial effect against wound bacteria, but less is known about the effect against periodontal pathogens. The aim of this study was to evaluate the antibacterial properties of the L-PRF membrane and L-PRF exudate against the main periopathogens cultured on agar plates and in planktonic solution. This study demonstrated the antibacterial effect of the L-PRF membrane against P. intermedia, F. nucleatum, and A. actinomycetemcomitans, but especially against P. gingivalis. The L-PRF exudate also showed a strong inhibition against P. gingivalis on agar plates. No inhibition could be observed for the other bacterial strains. Moreover, L-PRF exudate decreased the number of viable P.gingivalis in a planktonic solution in a dose-dependent way. However, A. actinomycetemcomitans showed an increased growth in planktonic solution when in contact with the L-PRF exudate.

Proteomic Analysis and Virulence Assessment of Granulicatella adiacens Secretome

Despite reports on the occurrence of Granulicatella adiacens in infective endocarditis, few mechanistic studies on its virulence characteristics or pathogenicity are available. Proteins secreted by this species may act as determinants of host-microbe interaction and play a role in virulence. Our aim in this study was to investigate and functionally characterize the secretome of G. adiacens. Proteins in the secretome preparation were digested by trypsin and applied to nanoLC-ESI-MS/MS. By using a combined mass spectrometry and bioinformatics approach, we identified 101 proteins. Bioinformatics tools predicting subcellular localization revealed that 18 of the secreted proteins possessed signal sequence. More than 20% of the secretome proteins were putative virulence proteins including serine protease, superoxide dismutase, aminopeptidase, molecular chaperone DnaK, and thioredoxin. Ribosomal proteins, molecular chaperones, and glycolytic enzymes, together known as "moonlighting proteins," comprised fifth of the secretome proteins. By Gene Ontology analysis, more than 60 proteins of the secretome were grouped in biological processes or molecular functions. KEGG pathway analysis disclosed that the secretome consisted of enzymes involved in biosynthesis of antibiotics. Cytokine profiling revealed that secreted proteins stimulated key cytokines, such as IL-1β, MCP-1, TNF-α, and RANTES from human PBMCs. In summary, the results from the current investigation of the G. adiacens secretome provide a basis for understanding possible pathogenic mechanisms of G. adiacens.

Chronic Inflammation as a Link between Periodontitis and Carcinogenesis

Periodontitis is characterized by a chronic inflammation produced in response to a disease-associated multispecies bacterial community in the subgingival region. Although the inflammatory processes occur locally in the oral cavity, several studies have determined that inflammatory mediators produced during periodontitis, as well as subgingival species and bacterial components, can disseminate from the oral cavity, contributing therefore, to various extraoral diseases like cancer. Interestingly, carcinogenesis associated with periodontal species has been observed in both the oral cavity and in extra oral sites. In this review, several studies were summarized showing a strong association between orodigestive cancers and poor oral health, presence of periodontitis-associated bacteria, tooth loss, and clinical signs of periodontitis. Proinflammatory pathways were also summarized. Such pathways are activated either by mono- or polymicrobial infections, resulting in an increase in the expression of proinflammatory molecules such as IL-6, IL-8, IL-1β, and TNF-α. In addition, it has been shown that several periodontitis-associated species induce the expression of genes related to cell proliferation, cell cycle, apoptosis, transport, and immune and inflammatory responses. Intriguingly, many of these pathways are linked to carcinogenesis. Among them, the activation of Toll-like receptors (TLRs) and antiapoptotic pathways (such as the PI3K/Akt, JAK/STAT, and MAPK pathways), the reduction of proapoptotic protein expression, the increase in cell migration and invasion, and the enhancement in metastasis are addressed. Considering that periodontitis is a polymicrobial disease, it is likely that mixed species promote carcinogenesis both in the oral cavity and in extra oral tissues and probably—as observed in periodontitis—synergistic and/or antagonistic interactions occur between microbes in the community. To date, a good amount of studies has allowed us to understand how monospecies infections activate pathways involved in tumorigenesis; however, more studies are needed to determine the combined effect of oral species in carcinogenesis.

Isolation and characterization of Sphingomonadaceae from fouled membranes

Membrane filtration systems are widely applied for the production of clean drinking water. However, the accumulation of particles on synthetic membranes leads to fouling. Biological fouling (i.e., biofouling) of reverse osmosis and nanofiltration membranes is difficult to control by existing cleaning procedures. Improved strategies are therefore needed. The bacterial diversity on fouled membranes has been studied, especially to identify bacteria with specialized functions and to develop targeted approaches against these microbes. Previous studies have shown that Sphingomonadaceae are initial membrane colonizers that remain dominant while the biofilm develops. Here, we characterized 21 Sphingomonadaceae isolates, obtained from six different fouled membranes, to determine which physiological traits could contribute to colonization of membrane surfaces. Their growth conditions ranged from temperatures between 8 and 42 oC, salinity between 0.0 and 5.0% w/v NaCl, pH from 4 and 10, and all isolates were able to metabolize a wide range of substrates. The results presented here show that Sphingomonadaceae membrane isolates share many features that are uncommon for other members of the Sphingomonadaceae family: all membrane isolates are motile and their tolerance for different temperatures, salt concentrations, and pH is high. Although relative abundance is an indicator of fitness for a whole group, for the Sphingomonadaceae it does not reveal the specific physiological traits that are required for membrane colonization. This study, therefore, adds to more fundamental insights in membrane biofouling.

'NetShift': a methodology for understanding 'driver microbes' from healthy and disease microbiome datasets

The combined effect of mutual association within the co-inhabiting microbes in human body is known to play a major role in determining health status of individuals. The differential taxonomic abundance between healthy and disease are often used to identify microbial markers. However, in order to make a microbial community based inference, it is important not only to consider microbial abundances, but also to quantify the changes observed among inter microbial associations. In the present study, we introduce a method called 'NetShift' to quantify rewiring and community changes in microbial association networks between healthy and disease. Additionally, we devise a score to identify important microbial taxa which serve as 'drivers' from the healthy to disease. We demonstrate the validity of our score on a number of scenarios and apply our methodology on two real world metagenomic datasets. The 'NetShift' methodology is also implemented as a web-based application available at https://web.rniapps.net/netshift.

Aggregatibacter actinomycetemcomitans H-NS promotes biofilm formation and alters protein dynamics of other species within a polymicrobial oral biofilm

Aggregatibacter actinomycetemcomitans is a Gram-negative organism, strongly associated with aggressive forms of periodontitis. An important virulence property of A. actinomycetemcomitans is its ability to form tenacious biofilms that can attach to abiotic as well as biotic surfaces. The histone-like (H-NS) family of nucleoid-structuring proteins act as transcriptional silencers in many Gram-negative bacteria. To evaluate the role of H-NS in A. actinomycetemcomitans, hns mutant derivatives of serotype a strain D7S were generated. Characteristics of the hns mutant phenotype included shorter and fewer pili, and substantially lower monospecies biofilm formation relative to the wild type. Furthermore, the D7S hns mutant exhibited significantly reduced growth within a seven-species oral biofilm model. However, no apparent difference was observed regarding the numbers and proportions of the remaining six species regardless of being co-cultivated with D7S hns or its parental strain. Proteomics analysis of the strains grown in monocultures confirmed the role of H-NS as a repressor of gene expression in A. actinomycetemcomitans. Interestingly, proteomics analysis of the multispecies biofilms indicated that the A. actinomycetemcomitans wild type and hns mutant imposed different regulatory effects on the pattern of protein expression in the other species, i.e., mainly Streptococcus spp., Fusobacterium nucleatum, and Veillonella dispar. Gene ontology analysis revealed that a large portion of the differentially regulated proteins was related to translational activity. Taken together, our data suggest that, apart from being a negative regulator of protein expression in A. actinomycetemcomitans, H-NS promotes biofilm formation and may be an important factor for survival of this species within a multispecies biofilm.

A member of a specific group of gene-regulating proteins promotes biofilm formation by a bacterium associated with aggressive forms of gum disease. Forming biofilms helps the bacterium to cause persistent infections. Researchers at Karolinska Institutet and Umeå University (Sweden), and University of Zürich (Switzerland), led by Jan Oscarsson at Umeå University, investigated the role of the “histone-like” protein H-NS in Aggregatibacter actinomycetemcomitans infections. These proteins are known to suppress the activity of specific genes in many bacteria, a property confirmed in this research. By studying mutant bacterial strains deficient in H-NS protein, the researchers demonstrated that this protein promotes the formation of biofilms by the bacteria. The results suggest that H-NS plays a significant role in allowing Aggregatibacter actinomycetemcomitans to thrive in biofilms containing mixed populations of bacteria. This effect appears to involve activating production of hair-like appendages called pili on the bacterial surface.

Cytokine induction of peripheral blood mononuclear cells by biofilms and biofilm supernatants of Granulicatella and Abiotrophia spp

Granulicatella and Abiotrophia species are the normal oral flora bacteria that can occasionally cause infective endocarditis. Although substantial data exists in the literature demonstrating occurrence of these species in infective endocarditis, only a few mechanistic studies on their pathogenicity are found. The aim of this study was to investigate the ability of Granulicatella and Abiotrophia species to elicit immune response from human peripheral blood mononuclear cells (PBMC). Biofilms and biofilm supernatants of Granulicatella elegans CCUG 38949, Granulicatella adiacens CCUG 27809 and Abiotrophia defectiva CCUG 27639 were used to stimulate PBMCs for 24 h. Cytokines produced were first screened using a human cytokine membrane array kit. Further, pro-inflammatory cytokines TNF-α, IL-β, and IL-17 were quantified by ELISA. The cytokine profiler array showed the induction of 15 different cytokines/chemokines including IL-1β, IL-6, IL-8, TNF-α, MCP-1, MIP-1α/MIP-1β and RANTES. ELISA quantification revealed that G. adiacens biofilm induced significantly higher (P < 0.05) levels of IL-1β, i.e., 1931 (183) pg/ml than G. elegans or A. defectiva. However, in the case of biofilm supernatants A. defectiva was the strongest, inducing 2104 (574) pg/ml. Biofilm supernatants, but not biofilms from all three species induced TNF-α only weakly. IL-17 was undetectable from any of the stimulated samples. In conclusion, Granulicatella and Abiotrophia are potent inducers of inflammatory mediators from human PBMCs. However, biofilms and biofilm supernatants from these species seem to selectively elicit stimulation of certain cytokines.

Agriculturally important microbial biofilms: Present status and future prospects

Microbial biofilms are a fascinating subject, due to their significant roles in the environment, industry, and health. Advances in biochemical and molecular techniques have helped in enhancing our understanding of biofilm structure and development. In the past, research on biofilms primarily focussed on health and industrial sectors; however, lately, biofilms in agriculture are gaining attention due to their immense potential in crop production, protection, and improvement. Biofilms play an important role in colonization of surfaces - soil, roots, or shoots of plants and enable proliferation in the desired niche, besides enhancing soil fertility. Although reports are available on microbial biofilms in general; scanty information is published on biofilm formation by agriculturally important microorganisms (bacteria, fungi, bacterial-fungal) and their interactions in the ecosystem. Better understanding of agriculturally important bacterial-fungal communities and their interactions can have several implications on climate change, soil quality, plant nutrition, plant protection, bioremediation, etc. Understanding the factors and genes involved in biofilm formation will help to develop more effective strategies for sustainable and environment-friendly agriculture. The present review brings together fundamental aspects of biofilms, in relation to their formation, regulatory mechanisms, genes involved, and their application in different fields, with special emphasis on agriculturally important microbial biofilms.

Trace Mineral Micronutrients and Chronic Periodontitis-a Review

Trace mineral micronutrients are imperative for optimum host response. Populations worldwide are prone to their insufficiency owing to lifestyle changes or poor nutritional intake. Balanced levels of trace minerals like iron (Fe), zinc (Zn), selenium (Se) and copper (Cu) are essential to prevent progression of chronic conditions like periodontitis. Their excess as well as deficiency is detrimental to periodontal health. This is specifically true in relation to Fe. Furthermore, some trace elements, e.g. Se, Zn and Cu are integral components of antioxidant enzymes and prevent reactive oxygen species induced destruction of tissues. Their deficiency can worsen periodontitis associated with systemic conditions like diabetes mellitus. With this background, the present review first focusses on the role of four trace minerals, namely, Fe, Zn, Se and Cu in periodontal health followed by an appraisal of the data from case control studies related to their association with chronic periodontitis.

Mature Biofilm Degradation by Potential Probiotics: Aggregatibacter actinomycetemcomitans versus Lactobacillus spp

The biofilm degradation of Aggregatibacter actinomycetemcomitans is essential as a complete periodontal disease therapy, and here we show the effects of potential probiotic bacteria such as Lactobacillus spp. for the biofilm of several serotypes of A. actinomycetemcomitans strains. Eight of the 13 species showed the competent biofilm degradation of ≥ 90% reduction in biofilm values in A. actinomycetemcomitans Y4 (serotype b) as well as four of the seven species for the biofilm of A. actinomycetemcomitans OMZ 534 (serotype e). In contrast, the probiotic bacteria did not have a big impact for the degradation of A. actinomycetemcomitans SUNY 75 (serotype a) biofilm. The dispersed A. actinomycetemcomitans Y4 cells through the biofilm detachment were still viable and plausible factors for the biofilm degradation were not due to the lactic acid and low pH conditions. The three enzymes, protease, lipase, and amylase may be responsible for the biofilm degradation; in particular, lipase was the most effective enzyme for the biofilm degradation of A. actinomycetemcomitans Y4 along with the protease activity which should be also important for the other serotypes. Remarkable lipase enzyme activities were detected from some of the potential probiotics and a supporting result using a lipase inhibitor presented corroborating evidence that lipase activity is one of the contributing factors for biofilm degradation outside of the protease which is also another possible factor for the biofilm of the other serotype of A. actinomycetemcomitans strains. On the other hand, the biofilm of A. actinomycetemcomitans SUNY 75 (serotype a) was not powerfully degraded by the lipase enzyme because the lipase inhibitor was slightly functional for only two of potential probiotics.