Sinus microbiome diversity depletion and Corynebacterium tuberculostearicum enrichment mediates rhinosinusitis

Post-irradiation dysbiosis in patients with nasopharyngeal carcinoma having received radiotherapy - A pilot study

OBJECTIVE

To compare the changes in the sinonasal mucosa microbiome in patients with nasopharyngeal carcinoma (NPC) before and after radiotherapy (RT), and to explore the pathogenesis of post-irradiation chronic rhinosinusitis (PI-CRS) and its association with dysbiosis.

STUDY DESIGN

Prospective cohort study.

SETTING

Unicenter, Tertiary referral hospital.

METHODS

Included patients newly diagnosed with NPC. Samples of ostiomeatal complex mucosa were collected before and after RT. Microbiome analysis was conducted using 16S rRNA sequencing, and statistical analysis was performed. Subgroup analyses based on RT modality (proton therapy or photon therapy) RESULTS: Total of 18 patients were enrolled in the study, with 62.1% receiving intensity-modulated proton therapy (IMPT). Corynebacterium was the most dominant genus identified in both the pre- and post-RT groups, with a visible increase in Staphylococcus and a decrease in Fusobacterium genus in post-RT group. Alpha-diversity did not significantly differ between groups, although the beta-diversity analysis revealed a dispersed microbiota in the post-RT group. The functional prediction indicated a higher relative abundance of taxonomies associated with biofilm formation in the post-RT group. The subgroup analysis revealed the above changes to be more significant in patients who received photon therapy (Intensity modulated radiation therapy, IMRT).

CONCLUSIONS

This is the first study to analyze the microbiome of patients with NPC after IMPT. We identified similarities between the post-RT microenvironment and that reported in patients with CRS, with a more apparent change noted in patients treated with IMRT. Further investigation is required to further elucidate the pathogenesis of PI-CRS and its relationship to post-RT dysbiosis, particularly IMPT.

Pathobiological signatures of dysbiotic lung injury in pediatric patients undergoing stem cell transplantation

Hematopoietic cell transplantation (HCT) uses cytotoxic chemotherapy and/or radiation followed by intravenous infusion of stem cells to cure malignancies, bone marrow failure and inborn errors of immunity, hemoglobin and metabolism. Lung injury is a known complication of the process, due in part to disruption in the pulmonary microenvironment by insults such as infection, alloreactive inflammation and cellular toxicity. How microorganisms, immunity and the respiratory epithelium interact to contribute to lung injury is uncertain, limiting the development of prevention and treatment strategies. Here we used 278 bronchoalveolar lavage (BAL) fluid samples to study the lung microenvironment in 229 pediatric patients who have undergone HCT treated at 32 children's hospitals between 2014 and 2022. By leveraging paired microbiome and human gene expression data, we identified high-risk BAL compositions associated with in-hospital mortality (P = 0.007). Disadvantageous profiles included bacterial overgrowth with neutrophilic inflammation, microbiome contraction with epithelial fibroproliferation and profound commensal depletion with viral and staphylococcal enrichment, lymphocytic activation and cellular injury, and were replicated in an independent cohort from the Netherlands (P = 0.022). In addition, a broad array of previously occult pathogens was identified, as well as a strong link between antibiotic exposure, commensal bacterial depletion and enrichment of viruses and fungi. Together these lung-immune system-microorganism interactions clarify the important drivers of fatal lung injury in pediatric patients who have undergone HCT. Further investigation is needed to determine how personalized interpretation of heterogeneous pulmonary microenvironments may be used to improve pediatric HCT outcomes.

Functional 2D Nanoplatforms Alleviate Eosinophilic Chronic Rhinosinusitis by Modulating Eosinophil Extracellular Trap Formation

The therapeutic outcomes of patients with eosinophilic chronic rhinosinusitis (ECRS) remain unsatisfactory, largely because the underlying mechanisms of eosinophilic inflammation are uncertain. Here, it is shown that the nasal secretions of ECRS patients have high eosinophil extracellular trap (EET) and cell-free DNA (cfDNA) levels. Moreover, the cfDNA induced EET formation by activating toll-like receptor 9 (TLR9) signaling. After demonstrating that DNase I reduced eosinophilic inflammation by modulating EET formation, linear polyglycerol-amine (LPGA)-coated TiS2 nanosheets (TLPGA) as functional 2D nanoplatforms with low cytotoxicity, mild protein adsorption, and increased degradation rate is developed. Due to the more flexible linear architecture, TLPGA exhibited higher cfDNA affinity than the TiS2 nanosheets coated with dendritic polyglycerol-amine (TDPGA). TLPGA reduced cfDNA levels in the nasal secretions of ECRS patients while suppressing cfDNA-induced TLR9 activation and EET formation in vitro. TLPGA displayed exceptional biocompatibility, preferential nasal localization, and potent inflammation modulation in mice with eosinophilic inflammation. These results highlight the pivotal feature of the linear molecular architecture and 2D sheet-like nanostructure in the development of anti-inflammation nanoplatforms, which can be exploited for ECRS treatment.

Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease

BACKGROUND

The human upper respiratory tract (URT) microbiome, like the gut microbiome, varies across individuals and between health and disease states. However, study-to-study heterogeneity in reported case-control results has made the identification of consistent and generalizable URT-disease associations difficult.

RESULTS

In order to address this issue, we assembled 26 independent 16S rRNA gene amplicon sequencing data sets from case-control URT studies, with approximately 2-3 studies per respiratory condition and ten distinct conditions covering common chronic and acute respiratory diseases. We leveraged the healthy control data across studies to investigate URT associations with age, sex, and geographic location, in order to isolate these associations from health and disease states.

CONCLUSIONS

We found several robust genus-level associations, across multiple independent studies, with either health or disease status. We identified disease associations specific to a particular respiratory condition and associations general to all conditions. Ultimately, we reveal robust associations between the URT microbiome, health, and disease, which hold across multiple studies and can help guide follow-up work on potential URT microbiome diagnostics and therapeutics.

Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes

Globally, half a billion people are employed in animal agriculture and are directly exposed to the associated microorganisms. However, the extent to which such exposures affect resident human microbiomes is unclear. Here we conducted a longitudinal profiling of the nasal and faecal microbiomes of 66 dairy farmers and 166 dairy cows over a year-long period. We compare farmer microbiomes to those of 60 age-, sex- and ZIP code-matched people with no occupational exposures to farm animals (non-farmers). We show that farming is associated with microbiomes containing livestock-associated microbes; this is most apparent in the nasal bacterial community, with farmers harbouring a richer and more diverse nasal community than non-farmers. Similarly, in the gut microbial communities, we identify more shared microbial lineages between cows and farmers from the same farms. Additionally, we find that shared microbes are associated with antibiotic resistance genes. Overall, our study demonstrates the interconnectedness of human and animal microbiomes.

Tackling Severe Neutrophilic Inflammation in Airway Disorders with Functionalized Nanosheets

Severe airway inflammatory disorders impose a significant societal burden, and the available treatments are unsatisfactory. High levels of neutrophil extracellular trap (NET) and cell-free DNA (cfDNA) were detected in the inflammatory microenvironment of these diseases, which are closely associated with persistent uncontrolled neutrophilic inflammation. Although DNase has proven to be effective in mitigating neutrophilic airway inflammation in mice by reducing cfDNA and NET levels, its clinical use is hindered by severe side effects. Here, we synthesized polyglycerol-amine (PGA) with a series of hydroxyl/amine ratios and covered them with black phosphorus (BP) nanosheets. The BP nanosheets functionalized with polyglycerol-50% amine (BP-PGA50) efficiently lowered cfDNA levels, suppressed toll-like receptor 9 (TLR9) activation and inhibited NET formation in vitro. Importantly, BP-PGA50 nanosheets demonstrated substantial accumulation in inflamed airway tissues, excellent biocompatibility, and potent inflammation modulation ability in model mice. The 2D sheet-like structure of BP-PGA50 was identified as a crucial factor for the therapeutic efficacy, and the hydroxyl/amine ratio was revealed as a significant parameter to regulate the protein resistance, cfDNA-binding efficacy, and cytotoxicity. This study shows the promise of the BP-PGA50 nanosheet for tackling uncontrolled airway inflammation, which is also significant for the treatment of other neutrophilic inflammatory diseases. In addition, our work also highlights the importance of proper surface functionalization, such as hydroxyl/amine ratio, in therapeutic nanoplatform construction for inflammation modulation.

Nasal lavage microbiome, but not nasal swab microbiome, correlates with sinonasal inflammation in children with cystic fibrosis

BACKGROUND

Cystic fibrosis (CF) is characterized by highly viscous mucus obstructing the lower and upper airways, chronic neutrophil inflammation and infection resulting not only in lung destruction but also in paranasal sinus involvement. The pathogenesis of CF-associated chronic rhinosinusitis (CRS) is still not well understood, and it remains unclear how the microbiome in the upper airways (UAW) influences paranasal sinus inflammation.

METHODS

In a cross-sectional study in pediatric patients with CF under stable disease conditions, we examined the microbiome in relation to inflammation by comparing nasal swabs (NS) and nasal lavage (NL) as two UAW sampling methods. The microbiota structure of both NS and NL was determined by 16S rRNA gene amplicon sequencing. In addition, pro-inflammatory cytokines (IL-1β, IL-6, IL-8, TNF-α) and proteases (SLPI, TIMP-1, NE/A1-AT complex) as well as neutrophil elastase activity were measured in NL.

RESULTS

Simultaneous NS and NL samples were collected from 36 patients with CF (age range: 7 - 19 years). The microbiome of NS samples was shown to be significantly lower in α-diversity and evenness compared to NL samples. NS samples were particularly found to be colonized with Staphylococcus species. NL microbiome was shown to correlate much better with the sinonasal inflammation status than NS microbiome. Especially the detection of Moraxella in NL was associated with increased inflammatory response.

CONCLUSION

Our results show that the NL microbiome reflects sinonasal inflammation better than NS and support NL as a promising tool for simultaneous assessment of the UAW microbiome and inflammation in children with CF.

Fungal and Bacterial Microbiome in Sinus Mucosa of Patients with and without Chronic Rhinosinusitis

OBJECTIVES

Dysbiosis of the sinonasal microbiome has been implicated in the pathogenesis of chronic rhinosinusitis (CRS). However, the mycobiome remains largely understudied, and microbial alterations associated with specific CRS subtypes have yet to be delineated. The objective of this study is to investigate the fungal and bacterial microbiome of sinus mucosa in CRS patients with and without nasal polyposis (CRSwNP and CRSsNP) versus healthy controls.

METHODS

Sinus mucosa was obtained from 92 patients (31 CRSsNP, 31 CRSwNP, and 30 controls) undergoing endoscopic sinus/skull base surgery. Data regarding demographics, Lund-MacKay scores, and histopathology were collected. Fungal and bacterial microbiome analysis was performed utilizing internal transcribed spacer amplicon and 16S rRNA sequencing.

RESULTS

Beta diversity of the sinonasal mycobiome differed significantly between CRS and controls (p = 0.001) and between CRSwNP and controls (p = 0.049), but not between CRSwNP and CRSsNP (p = 0.32) nor between CRSsNP and controls (p = 0.06). With respect to the bacterial microbiome, significantly lower alpha diversity was observed between CRS and controls (p < 0.001), CRSwNP versus controls (p < 0.001), and CRSsNP versus controls (p < 0.001). Beta diversity was also significantly different at the genus level between CRSwNP and CRSsNP (p = 0.019), CRSwNP and controls (p = 0.002)), and CRSsNP and controls (p < 0.001). However, alpha and beta diversity did not differ significantly between CRS patients with/without eosinophils or correlate with Lund-MacKay scores.

CONCLUSIONS

Differences in mycobiota diversity in CRS patients in comparison with controls suggest that alterations in the mycobiome may contribute to disease pathogenesis. Our findings also confirmed that diminished diversity among bacterial communities is associated with CRS and that significant differences are present in microbial composition between CRSwNP and CRSsNP.

LEVEL OF EVIDENCE

3 Laryngoscope, 134:1054-1062, 2024.

Remodeling of Paranasal Sinuses Mucosa Functions in Response to Biofilm-Induced Inflammation

Rhinosinusitis (RS) is an acute (ARS) or chronic (CRS) inflammatory disease of the nasal and paranasal sinus mucosa. CRS is a heterogeneous condition characterized by distinct inflammatory patterns (endotypes) and phenotypes associated with the presence (CRSwNP) or absence (CRSsNP) of nasal polyps. Mucosal barrier and mucociliary clearance dysfunction, inflammatory cell infiltration, mucus hypersecretion, and tissue remodeling are the hallmarks of CRS. However, the underlying factors, their priority, and the mechanisms of inflammatory responses remain unclear. Several hypotheses have been proposed that link CRS etiology and pathogenesis with host (eg, "immune barrier") and exogenous factors (eg, bacterial/fungal pathogens, dysbiotic microbiota/biofilms, or staphylococcal superantigens). The abnormal interplay between these factors is likely central to the pathophysiology of CRS by triggering compensatory immune responses. Here, we discuss the role of the sinonasal microbiota in CRS and its biofilms in the context of mucosal zinc (Zn) deficiency, serving as a possible unifying link between five host and "bacterial" hypotheses of CRS that lead to sinus mucosa remodeling. To date, no clear correlation between sinonasal microbiota and CRS has been established. However, the predominance of Corynebacteria and Staphylococci and their interspecies relationships likely play a vital role in the formation of the CRS-associated microbiota. Zn-mediated "nutritional immunity", exerted via calprotectin, alongside the dysregulation of Zn-dependent cellular processes, could be a crucial microbiota-shaping factor in CRS. Similar to cystic fibrosis (CF), the role of SPLUNC1-mediated regulation of mucus volume and pH in CRS has been considered. We complement the biofilms' "mechanistic" and "mucin" hypotheses behind CRS pathogenesis with the "structural" one - associated with bacterial "corncob" structures. Finally, microbiota restoration approaches for CRS prevention and treatment are reviewed, including pre- and probiotics, as well as Nasal Microbiota Transplantation (NMT).

The Anti-Inflammatory and Curative Exponent of Probiotics: A Comprehensive and Authentic Ingredient for the Sustained Functioning of Major Human Organs

Several billion microorganisms reside in the gastrointestinal lumen, including viruses, bacteria, fungi, and yeast. Among them, probiotics were primarily used to cure digestive disorders such as intestinal infections and diarrhea; however, with a paradigm shift towards alleviating health through food, their importance is large. Moreover, recent studies have changed the perspective that probiotics prevent numerous ailments in the major organs. Probiotics primarily produce biologically active compounds targeting discommodious pathogens. This review demonstrates the implications of using probiotics from different genres to prevent and alleviate ailments in the primary human organs. The findings reveal that probiotics immediately activate anti-inflammatory mechanisms by producing anti-inflammatory cytokines such as interleukin (IL)-4, IL-10, IL-11, and IL-13, and hindering pro-inflammatory cytokines such as IL-1, IL-6, and TNF-α by involving regulatory T cells (Tregs) and T helper cells (Th cells). Several strains of Lactobacillus plantarum, Lactobacillus rhamnosus, Lactobacillus casei, Lactobacillus reuteri, Bifidobacterium longum, and Bifidobacterium breve have been listed among the probiotics that are excellent in alleviating various simple to complex ailments. Therefore, the importance of probiotics necessitates robust research to unveil the implications of probiotics, including the potency of strains, the optimal dosages, the combination of probiotics, their habitat in the host, the host response, and other pertinent factors.

Emerging Therapies in the Medical Management of Allergic Fungal Rhinosinusitis

A non-invasive type of chronic sinusitis named allergic fungal rhinosinusitis (AFRS), which is a variant of allergic bronchopulmonary aspergillosis with nasal obstruction, was first described in 1976. The goal of this article was to provide an overview of various treatment approaches and how they can be used to control AFRS. Since this is an inflammatory disease rather than an invasive fungal infection, the treatment tries to modulate inflammation and reduce disease burden. A comprehensive treatment strategy must incorporate medicinal, surgical, biological, and immunological techniques. Owing to the chronic nature of allergic fungal rhinosinusitis and its high propensity for flare-ups and recurrence, multiple procedures are frequently required. The most likely method of establishing a long-term disease control for AFRS is a comprehensive management strategy that integrates medical, surgical, and immunological care. However, there are still disagreements regarding the exact combinations. In this review, we have mentioned different modalities in the management of AFRS, such as monoclonal antibodies, probiotic Manuka honey, and aPDT among others, some of which are promising but require further research.

Prebiotic supplements correct oral probiotic deficiency for lasting allergy relief

The prevalence of allergic rhinitis (common allergies) has increased in the last fifty years, from less than one percent to more than twenty-six percent of the population. Today, more than one hundred million people in the US suffer seasonal or yearlong allergies. The hygiene hypothesis was proposed 30 years ago as a potential explanation for this phenomenon, and we built on it with the specific oral hygiene hypothesis. Our longitudinal pilot study suggested that oral probiotic deficiency is the cause of allergic rhinitis. This clinical trial served to verify our theory and evaluate the effectiveness of AllerPops for allergy relief. We carried out a phase II, randomized, double-blind, controlled, single-center 21-day study to investigate the efficacy of AllerPops to reduce nasal symptoms in 72 adult volunteers with seasonal/year-long nasal allergies and its impact on oral microbiome using amplicon sequencing of 16S ribosome RNA genes. The volunteers were randomly separated into two equally sized groups: a control group and an investigational group. Both groups were given at least three doses of AllerPops, taken every other day, and asked to answer questions about observed allergy symptoms. Volunteers in the investigational group cleaned their mouths before taking a dose and slowly dissolve the lozenge, while those in the control did not. Through this trial, we show that AllerPops prebiotic supplements are effective in providing sustained allergy relief (P = 0.002) and can modulate oral beneficial bacteria that produce short-chain fatty acids (SCFA), such as Fusobacteria, Butyrivibrio, and Peptostreptococcus. The clinical improvements correlated with changes in the relative abundance of probiotics significantly: Fusobacteria (R = 0.32, P = 0.009), Butyrivibrio (R = 0.25, P = 0.044), and Peptostreptococcus (R = 0.34, P = 0.005). These results point to the root cause of allergic rhinitis: the lack of oral probiotics that produce SCFA to pacify the immune systems. Future study of AllerPops' theory will help society redefine the best oral hygiene practice to protect oral probiotics so that we may prevent allergic and autoimmune diseases and dental/gum infections. The trial was retrospectively registered at clinicaltrials.com, with registration number NCT05956691, on 21/07/2023.

Efficacy and Safety of Long-Term Low-Dose Clarithromycin in Patients With Refractory Chronic Sinusitis After Endoscopic Sinus Surgery: A Prospective Clinical Trial

OBJECTIVE

To observe the efficacy and safety of postoperative long-term low-dose oral administration of clarithromycin in patients with refractory chronic rhinosinusitis (RCRS), to explore the characteristics of postoperative microbiota in the nasal cavity in patients with RCRS, and to compare the differences and changes in microbiota in the nasal cavity before and after medication.

METHODS

This was a prospective, self-controlled study. Eighteen patients with RCRS who had persistent symptoms after endoscopic sinus surgery and standard therapy with normal immunoglobulin E and eosinophil level were included. Low dose (250 mg, once daily) clarithromycin was orally administrated for 12 weeks. Symptom severity and endoscopic findings were evaluated before, after 4 weeks, and 12 weeks of treatment, and nasal cavity microbiota was analyzed simultaneously.

RESULTS

A total of 18 patients with RCRS were enrolled and 17 patients completed the study. Four weeks after oral administration of clarithromycin, significant improvement was observed in subjective symptoms including nasal congestion, rhinorrhea, postnasal drip, and general discomfort, as well as endoscopic findings including general surgical cavity condition, rhinedema, and rhinorrhea (P < .05). After continuous treatment to the 12th week, symptoms showed significant improvement compared with baseline, and endoscopic score showed significant improvement compared with both baseline and 4 weeks after treatment. Analysis of middle nasal meatus flora revealed a significant decrease of Streptococcus pneumoniae after 12 weeks of clarithromycin treatment (P < .05), while the richness, composition, and diversity were similar before and after treatment. Patients enrolled experienced no adverse drug reaction or allergic reaction, nor clinical significant liver function impairment observed.

CONCLUSION

Postoperative low-dose long-term oral administration of clarithromycin in patients with RCRS can improve the clinical symptoms and facilitate the mucosal epithelialization, with good tolerance and safety. The efficacy of clarithromycin in patients with RCRS may be related to its regulatory effect on nasal cavity microbiota.

Host-microbe interactions in chronic rhinosinusitis biofilms and models for investigation

Chronic rhinosinusitis (CRS) is a debilitating condition characterized by long-lasting inflammation of the paranasal sinuses. It affects a significant portion of the population, causing a considerable burden on individuals and healthcare systems. The pathogenesis of CRS is multifactorial, with bacterial infections playing a crucial role in CRS development and persistence. In recent years, the presence of biofilms has emerged as a key contributor to the chronicity of sinusitis, further complicating treatment and exacerbating symptoms. This review aims to explore the role of biofilms in CRS, focusing on the involvement of the bacterial species Staphylococcus aureus and Pseudomonas aeruginosa, their interactions in chronic infections, and model systems for studying biofilms in CRS. These species serve as an example of how microbial interplay can influence disease progression and exemplify the need for continued investigation and innovation in CRS research.

High throughput sequencing technology reveals alteration of lower respiratory tract microbiome in severe aspiration pneumonia and its association with inflammation

BACKGROUND

Aspiration pneumonia is a common and severe clinical condition. The microbiome present in the lower respiratory tract plays a crucial role in regulating human inflammatory response. However, the relationship between the altered lower respiratory tract microbiome and inflammation in aspiration pneumonia remains inadequately explored.

PURPOSE

To investigate the alteration of the lower respiratory tract microbiome in severe aspiration pneumonia patients and explore the potential correlation between microbiome components and inflammatory response.

METHOD

Patients in the severe aspiration pneumonia group and control group were enrolled from the intensive care unit of Jinshan Hospital, Fudan University between December 31, 2020 and August 19, 2021. Sputum specimens were collected from all participants and subsequently subjected to 16S rDNA high throughput sequencing technology. The concentration of inflammatory cytokines in serum was measured using enzyme-linked immunosorbent assay (ELISA) kits, and collected data including patients' demographic information, clinical data, and laboratory examination results were recorded for further analysis.

RESULTS

Alteration in the lower respiratory tract microbiome was observed in severe aspiration pneumonia. Compared to the control group, a significant decrease in the relative abundance of Firmicutes was found at the phylum level (P < 0.01). At the family level, the relative abundance of Corynebacteriaceae, Enterobacteriaceae and Enterococcaceae increased significantly (P < 0.001, P < 0.05, P < 0.01). There were no significant differences in community diversity of the lower respiratory tract between the two groups. Patients in the severe aspiration pneumonia group exhibited significantly higher levels of inflammation compared to those in the control group. Correlation analysis showed that the relative abundance of Corynebacteriaceae was positively correlated with the expression level of IL-1β and IL-18 (P = 0.002, P = 0.02); the relative abundance of Enterobacteriaceae was negatively correlated with IL-4 (P = 0.011); no other significant correlations have been identified between microbiome and inflammatory indicators thus far (P > 0.05).

CONCLUSIONS

Alteration of the lower respiratory tract microbiome is critically involved in inflammation and disease progression in severe cases of aspiration pneumonia. The potential inflammation regulation properties of the microbiome hold promising value for developing novel therapeutic approaches aimed at mitigating the severity of the disease.

Role of probiotics in chronic rhinosinusitis: a systematic review of randomised, controlled trials

OBJECTIVE

This review evaluated the safety profile and efficacy of probiotics in chronic rhinosinusitis and was registered with Prospero (Centre for Reviews and Dissemination number: 42020193529).

METHOD

Literature databases were searched through inception to August 2022. Randomised, controlled trials exploring adjunctive probiotics in adult chronic rhinosinusitis patients were included. From 948 records screened, 4 randomised, controlled trials were included.

RESULTS

Probiotics-associated adverse effects comprised epistaxis and abdominal pain. No reduction in Sino-Nasal Outcome Test values before 4 weeks (p = 0.58) or beyond 8 weeks (p = 0.08) of treatment or reduction of severe symptom frequency (p = 0.75) was observed. Symptom relapse in probiotic-treated patients was significantly lower across all timepoints (p = 0.045). Lower sinusitis relapse risks during treatment (risk ratio = 0.49; p = 0.019) and 8 months post-treatment (risk ratio = 0.56, p = 0.013) were observed. Probiotics demonstrated potential in improving Sino-Nasal Outcome Test symptom subscales, including sleep, psychological and rhinology subscales.

CONCLUSION

The optimal mode of probiotic administration, treatment duration and target patient subgroups requires further study to evaluate the utility of probiotics.

Pulmonary microbiome and transcriptome signatures reveal distinct pathobiologic states associated with mortality in two cohorts of pediatric stem cell transplant patients

Lung injury is a major determinant of survival after pediatric hematopoietic cell transplantation (HCT). A deeper understanding of the relationship between pulmonary microbes, immunity, and the lung epithelium is needed to improve outcomes. In this multicenter study, we collected 278 bronchoalveolar lavage (BAL) samples from 229 patients treated at 32 children's hospitals between 2014-2022. Using paired metatranscriptomes and human gene expression data, we identified 4 patient clusters with varying BAL composition. Among those requiring respiratory support prior to sampling, in-hospital mortality varied from 22-60% depending on the cluster (p=0.007). The most common patient subtype, Cluster 1, showed a moderate quantity and high diversity of commensal microbes with robust metabolic activity, low rates of infection, gene expression indicating alveolar macrophage predominance, and low mortality. The second most common cluster showed a very high burden of airway microbes, gene expression enriched for neutrophil signaling, frequent bacterial infections, and moderate mortality. Cluster 3 showed significant depletion of commensal microbes, a loss of biodiversity, gene expression indicative of fibroproliferative pathways, increased viral and fungal pathogens, and high mortality. Finally, Cluster 4 showed profound microbiome depletion with enrichment of Staphylococci and viruses, gene expression driven by lymphocyte activation and cellular injury, and the highest mortality. BAL clusters were modeled with a random forest classifier and reproduced in a geographically distinct validation cohort of 57 patients from The Netherlands, recapitulating similar cluster-based mortality differences (p=0.022). Degree of antibiotic exposure was strongly associated with depletion of BAL microbes and enrichment of fungi. Potential pathogens were parsed from all detected microbes by analyzing each BAL microbe relative to the overall microbiome composition, which yielded increased sensitivity for numerous previously occult pathogens. These findings support personalized interpretation of the pulmonary microenvironment in pediatric HCT, which may facilitate biology-targeted interventions to improve outcomes.

The Impact of Antibiotics and Steroids on the Nasal Microbiome in Patients with Chronic Rhinosinusitis: A Systematic Review According to PICO Criteria

BACKGROUND

The nasal microbiome represents the main environmental factor of the inflammatory process in chronic rhinosinusitis (CRS). Antibiotics and steroids constitute the mainstay of CRS therapies. However, their impact on microbial communities needs to be better understood. This systematic review summarizes the evidence about antibiotics' and steroids' impact on the nasal microbiota in patients with CRS.

METHODS

The search strategy was conducted in accordance with the PRISMA guidelines for systematic reviews. The authors searched all papers in the three major medical databases (PubMed, Scopus, and Cochrane Library) using the PICO tool (population, intervention, comparison, and outcomes). The search was carried out using a combination of the key terms "Microbiota" or "Microbiome" and "Chronic Rhinosinusitis".

RESULTS

Overall, 402 papers were identified, and after duplicate removal (127 papers), excluding papers off-topic (154) and for other structural reasons (110), papers were assessed for eligibility; finally, only 11 papers were included and summarized in the present systematic review. Some authors used only steroids, other researchers used only antibiotics, and others used both antibiotics and steroids. With regard to the use of steroids as exclusive medical treatment, topical mometasone and budesonide were investigated. With regard to the use of antibiotics as exclusive medical treatments, clarithromycin, doxycycline, roxithromycin, and amoxicillin clavulanate were investigated. Regarding the use of both antibiotics and steroids, two associations were investigated: systemic prednisone combined with amoxicillin clavulanate and topical budesonide combined with azithromycin.

CONCLUSIONS

The impact that therapies can have on the nasal microbiome of CRS patients is very varied. Further studies are needed to understand the role of the nasal microbiome, prevent CRS, and improve therapeutic tools for personalized medicine tailored to the individual patient.

Electrogenic Staphylococcus epidermidis colonizes nasal cavities and alleviates IL-6 progression induced by the SARS2-CoV nucleocapsid protein

AIM

Certain probiotic bacteria have been shown to possess an immunomodulatory effect and a protective effect on influenza infections. Using the Staphylococcus epidermidis K1 colonized mice model, we assessed the effect of nasal administration of glycerol or flavin mononucleotide (FMN) on the production of interleukin (IL)-6 mediated by the severe acute respiratory syndrome coronavirus 2 (SARS2-CoV) nucleocapsid protein (NPP).

METHODS AND RESULTS

FMN, one of the key electron donors for the generation of electricity facilitated by S. epidermidis ATCC 12228, was detected in the glycerol fermentation medium. Compared to the S. epidermidis ATCC 12228, the S. epidermidis K1 isolate showed significant expression of the electron transfer genes, including pyruvate dehydrogenase (pdh), riboflavin kinase (rk), 1,4-dihydroxy-2-naphthoate octaprenyltransferase (menA), and type II NADH quinone oxidoreductase (ndh2). Institute of cancer research (ICR) mice were intranasally administered with S. epidermidis K1 with or without pretreatment with riboflavin kinase inhibitors, then nasally treated with glycerol or FMN before inoculating the NPP. Furthermore, J774A.1 macrophages were exposed to NPP serum and then treated with NPP of SARS2-CoV. The IL-6 levels in the bronchoalveolar lavage fluid (BALF) of mice and macrophages were quantified using a mouse IL-6 enzyme-linked immunosorbent assay kit.

CONCLUSIONS

Here, we report that nasal administration of NPP strongly elevates IL-6 levels in both BALF and J774A.1 macrophages. It is worth noting that NPP-neutralizing antibodies can decrease IL-6 levels in macrophages. The nasal administration of glycerol or FMN to S. epidermidis K1-colonized mice results in a reduction of NPP-induced IL-6 production.

Patterns of Circulating Microbiota during the Acute Phase Following ST-Segment Elevation Myocardial Infarction Predict Long-Term Cardiovascular Events

Limited information exists regarding whether circulating microbiota could predict long-term clinical outcomes following ST-segment elevation myocardial infarction (STEMI). A total of 244 consecutive patients with STEMI were followed for 2.8 years, and 64 first major adverse cardiovascular events (MACEs) were recorded. Both microbiota abundance [Corynebacterium tuberculostearicum (HR, 1.28; 95% CI, 1.03-1.58) and Staphylococcus aureus (S. aureus) (HR, 1.16; 95% CI, 1.02-1.33) ] and microbiota clusters (Cluster 2 versus Cluster 1: HR, 1.84; 95% CI, 1.04-3.27) could independently predict MACE. Furthermore, a model based on established independent predictors alone was significantly improved by the addition of different microbiota patterns. In addition, CD14⁺⁺CD16⁺ monocytes (Mon2) had a significant mediation effect on the microbiota patterns → MACE association. The present study demonstrated that the abundance and clusters of circulating microbiota are associated with future adverse cardiovascular events independent of traditional risk factors, which were partially mediated by an increase in Mon2.

Assessment of the nasal microbiota in dogs with fungal rhinitis before and after cure and in dogs with chronic idiopathic rhinitis

BACKGROUND

Pathogenesis of canine fungal rhinitis is still not fully understood. Treatment remains challenging, after cure turbinate destruction may be associated with persistent clinical signs and recurrence of fungal rhinitis can occur. Alterations of the nasal microbiota have been demonstrated in dogs with chronic idiopathic rhinitis and nasal neoplasia, although whether they play a role in the pathogenesis or are a consequence of the disease is still unknown. The objectives of the present study were (1) to describe nasal microbiota alterations associated with fungal rhinitis in dogs, compared with chronic idiopathic rhinitis and controls, (2) to characterize the nasal microbiota modifications associated with successful treatment of fungal rhinitis. Forty dogs diagnosed with fungal rhinitis, 14 dogs with chronic idiopathic rhinitis and 29 healthy control dogs were included. Nine of the fungal rhinitis dogs were resampled after successful treatment with enilconazole infusion.

RESULTS

Only disease status contributed significantly to the variability of the microbiota. The relative abundance of the genus Moraxella was decreased in the fungal rhinitis (5.4 ± 18%) and chronic idiopathic rhinitis (4.6 ± 8.7%) groups compared to controls (51.8 ± 39.7%). Fungal rhinitis and chronic idiopathic rhinitis groups also showed an increased richness and α-diversity at species level compared with controls. Increase in unique families were associated with fungal rhinitis (Staphyloccaceae, Porphyromonadaceae, Enterobacteriaceae and Neisseriaceae) and chronic idiopathic rhinitis (Pasteurellaceae and Lactobacillaceae). In dogs with fungal rhinitis at cure, only 1 dog recovered a high relative abundance of Moraxellaceae.

CONCLUSIONS

Results confirm major alterations of the nasal microbiota in dogs affected with fungal rhinitis and chronic idiopathic rhinitis, consisting mainly in a decrease of Moraxella. Besides, a specific dysbiotic profile further differentiated fungal rhinitis from chronic idiopathic rhinitis. In dogs with fungal rhinitis, whether the NM returns to its pre-infection state or progresses toward chronic idiopathic rhinitis or fungal rhinitis recurrence warrants further investigation.

The Fungal and Bacterial Interface in the Respiratory Mycobiome with a Focus on Aspergillus spp

The heterogeneity of the lung microbiome and its alteration are prevalently seen among chronic lung diseases patients. However, studies to date have primarily focused on the bacterial microbiome in the lung rather than fungal composition, which might play an essential role in the mechanisms of several chronic lung diseases. It is now well established that Aspergillus spp. colonies may induce various unfavorable inflammatory responses. Furthermore, bacterial microbiomes such as Pseudomonas aeruginosa provide several mechanisms that inhibit or stimulate Aspergillus spp. life cycles. In this review, we highlighted fungal and bacterial microbiome interactions in the respiratory tract, with a focus on Aspergillus spp.

A Review on the Nasal Microbiome and Various Disease Conditions for Newer Approaches to Treatments

Introduction: Commensal bacteria have always played a significant role in the maintenance of health and disease but are being unravelled only recently. Studies suggest that the nasal microbiome has a significant role in the development of various disease conditions. Search engines were used for searching articles having a nasal microbiome and disease correlation. In olfactory dysfunction, dysbiosis of the microbiome may have a significant role to play in the pathogenesis. The nasal microbiome influences the phenotype of CRS and is also capable of modulating the immune response and plays a role in polyp formation. Microbiome dysbiosis has a pivotal role in the development of Allergic Rhinitis; but, yet known how is this role played. The nasal microbiome has a close association with the severity and phenotype of asthma. They contribute significantly to the onset, severity, and development of asthma. The nasal microbiome has a significant impact on the immunity and protection of its host. The nasal microbiome has been a stimulus in the development of Otitis Media and its manifestations. Studies suggest that the resident nasal microbiome is responsible for the initiation of neurodegenerative diseases like Parkinson's Disease.Materials and Methods: Literature search from PubMed, Medline, and Google with the Mesh terms: nasal microbiome AND diseases. Conclusion: With increasing evidence on the role of the nasal microbiome on various diseases, it would be interesting to see how this microbiome can be modulated by pro/pre/post biotics to prevent a disease or the severity of illness.

Treatment Strategy of Uncontrolled Chronic Rhinosinusitis with Nasal Polyps: A Review of Recent Evidence

Chronic rhinosinusitis (CRS) is recognized as a heterogeneous disease with a wide range of clinical features, resulting in significant morbidity and cost to the healthcare system. While the phenotypic classification is determined by the presence or absence of nasal polyps and comorbidities, the endotype classification has been established based on molecular biomarkers or specific mechanisms. Research on CRS has now developed based on information based on three major endotypes: types 1, 2, and 3. Recently, biological therapies targeting type 2 inflammation have been clinically expanded and may be applied to other inflammatory endotypes in the future. The purpose of this review is to discuss the treatment options according to the type of CRS and summarize recent studies on new therapeutic approaches for patients with uncontrolled CRS with nasal polyps.

The Nasal Bacteria Microbiome Comparison Among Fungal Ball Sinusitis, Chronic Sinusitis with Polyps

To evaluate the composition of the microbial community of the middle nasal in paranasal sinus fungus ball (FB), chronic sinusitis with nasal polyps (CRSwNP) and healthy controls, providing new insights into the pathogenesis of FB and CRSwNP. Through 16 s rRNA gene high-throughput sequencing to determine the microbial characterization from patients with FB (n = 29) and CRSwNP (n = 10), and healthy controls (n = 4). The FB group had significantly lower αdiversity and significantly different β diversity compared to the other groups. All three groups mainly consisted of four bacterial phyla (Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria). In the FB group, the highest relative abundance was found in Proteobacteria (47.04%). However, pairwise comparisons resulted in statistically significant differences only for Firmicutes (CRSwNP, p = 0.003, Control, p = 0.008). The CRSwNP group was statistically different from the control group in TM7(p = 0.010), Chloroflexi(p = 0.018) and Bacteroidete(p = 0.027). At the genus level, the FB group had the highest relative abundance of Haemophilus (11.53%), followed by Neisseria (7.39%), and Neisseria abundance (p < 0.001) was significantly different from the remaining two groups. Ruminococcacea abundance (p < 0.001) and Comamonadaceae abundance (p < 0.001) were increased in the CRSwNP group. The relative abundance of Lactobacillus (p < 0.001), Bacteroides S24_7 (p < 0.001), and Desulfovibrio (p < 0.001) was significantly decreased in the FB and CRSwNP groups compared to the control group. The imbalance of the microbial community is related to the pathogenesis of sinusitis.

Comparative Genomic and Metagenomic Investigations of the Corynebacterium tuberculostearicum Species Complex Reveals Potential Mechanisms Underlying Associations To Skin Health and Disease

Corynebacterium are a diverse genus and dominant member of the human skin microbiome. Recently, we reported that the most prevalent Corynebacterium species found on skin, including Corynebacterium tuberculostearicum and Corynebacterium kefirresidentii, comprise a narrow species complex despite the diversity of the genus. Here, we apply high-resolution phylogenomics and comparative genomics to describe the structure of the C. tuberculostearicum species complex and highlight genetic traits which are enriched or depleted in it relative to other Corynebacterium. Through metagenomic investigations, we also find that individual species within the complex can associate with specific body sites. Finally, we discover that one species from the complex, C. kefirresidentii, increases in relative abundance during atopic dermatitis flares, and show that most genomes of this species encode a colocalized set of putative virulence genes. IMPORTANCE Corynebacterium are commonly found bacteria on the human skin. In this study, we perform comparative genomics to gain insight into genetic traits which differentiate a phylogenetically related group of Corynebacterium, the Corynebacterium tuberculostearicum species complex, that includes the most prevalent species from the genus in skin microbiomes. After resolving the presence of distinct species within the complex, we applied metagenomic analysis to uncover biogeographic associations of individual species within the complex with specific body sites and discovered that one species, commonly found in the nares of individuals, increases in abundance across multiple body sites during atopic dermatitis flares.

Associations of Microbial Diversity with Age and Other Clinical Variables among Pediatric Chronic Rhinosinusitis (CRS) Patients

Chronic rhinosinusitis (CRS) is a heterogenous disease that causes persistent paranasal sinus inflammation in children. Microorganisms are thought to contribute to the etiology and progression of CRS. Culture-independent microbiome analysis offers deeper insights into sinonasal microbial diversity and microbe-disease associations than culture-based methods. To date, CRS-related microbiome studies have mostly focused on the adult population, and only one study has characterized the pediatric CRS microbiome. In this study, we analyzed the bacterial diversity of adenoid tissue, adenoid swab, maxillary sinus, and sinus wash samples from 45 pediatric CRS patients recruited from the Johns Hopkins All Children's Hospital (JHACH) in St. Petersburg, FL, USA. The alpha diversity in these samples was associated with baseline nasal steroid use, leukotriene receptor antagonist (LTRA) use, and total serum immunoglobulin (Ig) E (IgE) level. Streptococcus, Moraxella, and Haemophilus spp. were most frequently identified from sinus cultures and the sequenced 16S rRNA gene content. Comparative analyses combining our samples with the samples from the previous microbiome study revealed differentially abundant genera between patients with pediatric CRS and healthy controls, including Cutibacterium and Moraxella. Additionally, the abundances of Streptobacillus and Staphylococcus were consistently correlated with age in both adenoid- and sinus-derived samples. Our study uncovers new associations of alpha diversity with clinical parameters, as well as associations of specific genera with disease status and age, that can be further investigated.

Upper airway microbiome transplantation for patients with chronic rhinosinusitis

BACKGROUND

Chronic or recurrent rhinosinusitis without polyps (CRSsNP) is characterized by a persistent inflammation of the sinonasal mucosa. The underlying cause is unclear but increasing interest has been directed toward changes in the sinonasal microbiome as a potential driver.

METHODS

Twenty-two patients diagnosed with CRSsNP were treated with antibiotics for 13 days, followed by 5 consecutive days of nasal microbiome transplants from healthy donors. Outcome measures were 22-item Sino-Nasal Outcome Test (SNOT-22) questionnaire, total nasal symptom score (TNSS), endoscopic grading, 16S ribosomal RNA (rRNA) next generation sequencing (microbiome analysis), and nasal lavage fluid analysis of inflammatory cytokines. Patients were examined at the start of the study and after antibiotic treatment as well as 10 days and 3 months after the transplant series.

RESULTS

At the end of the study, patients reported significantly reduced SNOT-22 scores and microbiome analysis showed significantly increased abundance and diversity. No significant change was observed for TNSS or endoscopic scoring.

CONCLUSION

Nasal microbiome transplants obtained from healthy individuals and administered as nasal lavages to patients with CRSsNP are feasible. The patients reported significant and lasting reduction of symptoms and these findings were associated with a lasting increase in abundance and diversity of the local bacterial flora. The observations, which need to be confirmed by randomized controlled trials, may constitute a new treatment avenue for these difficult to treat patients where antibiotics only provide short lasting symptom control.

Composition and diversity analysis of the lung microbiome in patients with suspected ventilator-associated pneumonia

Background

Ventilator-associated pneumonia (VAP) is associated with high morbidity and health care costs, yet diagnosis remains a challenge. Analysis of airway microbiota by amplicon sequencing provides a possible solution, as pneumonia is characterised by a disruption of the microbiome. However, studies evaluating the diagnostic capabilities of microbiome analysis are limited, with a lack of alignment on possible biomarkers. Using bronchoalveolar lavage fluid (BALF) from ventilated adult patients suspected of VAP, we aimed to explore how key characteristics of the microbiome differ between patients with positive and negative BALF cultures and whether any differences could have a clinically relevant role.

Methods

BALF from patients suspected of VAP was analysed using 16s rRNA sequencing in order to: (1) differentiate between patients with and without a positive culture; (2) determine if there was any association between microbiome diversity and local inflammatory response; and (3) correctly identify pathogens detected by conventional culture.

Results

Thirty-seven of 90 ICU patients with suspected VAP had positive cultures. Patients with a positive culture had significant microbiome dysbiosis with reduced alpha diversity. However, gross compositional variance was not strongly associated with culture positivity (AUROCC range 0.66–0.71). Patients with a positive culture had a significantly higher relative abundance of pathogenic bacteria compared to those without [0.45 (IQR 0.10–0.84), 0.02 (IQR 0.004–0.09), respectively], and an increased interleukin (IL)-1β was associated with reduced species evenness (r_s = − 0.33, p < 0.01) and increased pathogenic bacteria presence (r_s = 0.28, p = 0.013). Untargeted 16s rRNA pathogen detection was limited by false positives, while the use of pathogen-specific relative abundance thresholds showed better diagnostic accuracy (AUROCC range 0.89–0.998).

Conclusion

Patients with positive BALF culture had increased dysbiosis and genus dominance. An increased caspase-1-dependent IL-1b expression was associated with a reduced species evenness and increased pathogenic bacterial presence, providing a possible causal link between microbiome dysbiosis and lung injury development in VAP. However, measures of diversity were an unreliable predictor of culture positivity and 16s sequencing used agnostically could not usefully identify pathogens; this could be overcome if pathogen-specific relative abundance thresholds are used.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13054-022-04068-z.

Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies

The human microbiome is composed of a collection of dynamic microbial communities that inhabit various anatomical locations in the body. Accordingly, the coevolution of the microbiome with the host has resulted in these communities playing a profound role in promoting human health. Consequently, perturbations in the human microbiome can cause or exacerbate several diseases. In this Review, we present our current understanding of the relationship between human health and disease development, focusing on the microbiomes found across the digestive, respiratory, urinary, and reproductive systems as well as the skin. We further discuss various strategies by which the composition and function of the human microbiome can be modulated to exert a therapeutic effect on the host. Finally, we examine technologies such as multiomics approaches and cellular reprogramming of microbes that can enable significant advancements in microbiome research and engineering.

Nasal microbiome in chronic rhinosinusitis

Chronic rhinosinusitis (CRS) is defined as an inflammatory disorder of the paranasal sinuses and of the nasal mucosa that lasts 12 weeks or longer. In CRS microbes contribute to the disease pathogenesis. Clinical microbiology is focused on finding single pathogens that causes the disease and the main goal is the use of antibiotics to kill bacteria. Efforts to achieve a better understanding of CRS include the study of the sinus microbiome, and to evaluate the ability of probiotics to augment homeostasis and modulate the immune response of the host mucosa. This review provides an update on the role of the microbiome in CRS. The study was conducted using two databases: PubMed and Science Direct. We searched for articles in English that matched the review topic. We first used the abstracts of articles to assess whether they met the inclusion criteria. We also reviewed the references of the selected articles and read those with titles that might be of interest. Several studies have shown that endogenous microbiome dysbiosis can impact mucosa health and disease severity. Some bacterial species presenting protective or pathogenic effect. Antimicrobial agents can create a similar disruption and impact the nasal microbiome balance. On the other hand, probiotics offers a promising avenue for developing systemic and topical therapies geared towards strategic manipulation of the biological host load, thereby augmenting immune homeostasis. A better comprehension of sinus-nasal microbiome in healthy and in CRS patients and the link with different CRS phenotype can help in developing new prognostics, diagnostics, and therapeutics strategies. Going forward, the use of probiotics can restore the native sinus ecology with significant therapeutic and preventive implications.

Chronic and Recurrent Sinusitis in Children, as Manifestation of Immune Dysfunction and Atopic Background

Rhinosinusitis in children, as in adults, can be classified by duration (acute, recurrent, and chronic) and by cause (viral, bacterial, and inflammatory) and needs to be treated accordingly after careful investigation which include through clinical history, laboratory tests, and, if necessary, nasal endoscopy and imaging studies.

Factors Limiting the Translatability of Rodent Model-Based Intranasal Vaccine Research to Humans

The intranasal route of vaccination presents an attractive alternative to parenteral routes and offers numerous advantages, such as the induction of both mucosal and systemic immunity, needle-free delivery, and increased patient compliance. Despite demonstrating promising results in preclinical studies, however, few intranasal vaccine candidates progress beyond early clinical trials. This discrepancy likely stems in part from the limited predictive value of rodent models, which are used frequently in intranasal vaccine research. In this review, we explored the factors that limit the translatability of rodent-based intranasal vaccine research to humans, focusing on the differences in anatomy, immunology, and disease pathology between rodents and humans. We also discussed approaches that minimize these differences and examined alternative animal models that would produce more clinically relevant research.

Alloiococcus otitidis-Cause of Nonspecific Acute Sinusitis: First Case Report and Review of Literature

Although most sinus infections are viral, potential bacterial pathogens such as Streptococcus pneumoniae, Haemophilus influenza and Moraxella catarrhalis can migrate during a viral respiratory infection from the nasopharynx into the sinus cavity causing sinusitis. Alloiococcus otitidis is a commensal of the external auditory canal and is considered one of the potential middle ear pathogens. Unlike most otopathogens, A. otitidis is rarely found in the nasopharynx of healthy individuals. This difficult-to-culture organism has not previously been described as a causative agent of sinusitis. Here we describe one case of acute sinusitis due to A. otitidis and review previous knowledge of this controversial organism based on recent literature.

Chronic Rhinosinusitis, S. aureus Biofilm and Secreted Products, Inflammatory Responses, and Disease Severity

Chronic rhinosinusitis (CRS) is a persistent inflammation of the nasal cavity and paranasal sinuses associated with tissue remodelling, dysfunction of the sinuses’ natural defence mechanisms, and induction of different inflammatory clusters. The etiopathogenesis of CRS remains elusive, and both environmental factors, such as bacterial biofilms and the host’s general condition, are thought to play a role. Bacterial biofilms have significant clinical relevance due to their potential to cause resistance to antimicrobial therapy and host defenses. Despite substantial medical advances, some CRS patients suffer from recalcitrant disease that is unresponsive to medical and surgical treatments. Those patients often have nasal polyps with tissue eosinophilia, S. aureus-dominant mucosal biofilm, comorbid asthma, and a severely compromised quality of life. This review aims to summarise the contemporary knowledge of inflammatory cells/pathways in CRS, the role of bacterial biofilm, and their impact on the severity of the disease. Here, an emphasis is placed on S. aureus biofilm and its secreted products. A better understanding of these factors might offer important diagnostic and therapeutic perceptions for recalcitrant disease.

5-α reductase inhibition by Epilobioum fleischeri extract modulates facial microbiota structure

Background

Facial skin is a particularly complex environment made of different skin types such as sebaceous (forehead) and dry (cheeks). The skin microbiota composition on different facial sites has not yet been addressed.

Methods

We conducted a 4‐week‐long, single‐centre, randomized and placebo‐controlled clinical study involving 23 Caucasian females. We assessed both bacterial composition on five different facial areas and the microbiome modulatory effects resulting from the topical application of a plant extract (Epilobium fleischeri). Skin microbiome samples were collected before and after 4 weeks of product application. Microbiota profiling was performed via 16S rRNA gene sequencing, and relative abundance data were used to calculate differentials via a multinomial regression model.

Results

Via ‘reference frames’, we observed shifts in microbial composition after 4 weeks of twice‐daily product application and identify certain microbiota species, which were positively associated with the application of the product containing the Epilobium fleischeri extract. Staphylococcus hominis, Staphylococcus epidermidis, and Micrococcus yunnanensis appeared to be significantly enriched in the final microbiota composition of the active treatment group.

Conclusion

Facial skin was found to be colonized by an heterogenous microbiota, and the Epilobium fleischeri extract had a modulatory effect on commensal bacteria on the different facial sites.

Air pollution and endocrine disruptors induce human microbiome imbalances: A systematic review of recent evidence and possible biological mechanisms

A rich body of literature indicates that environmental factors interact with the human microbiome and influence its composition and functions contributing to the pathogenesis of diseases in distal sites of the body. This systematic review examines the scientific evidence on the effect of environmental toxicants, air pollutants and endocrine disruptors (EDCs), on compositional and diversity of human microbiota. Articles from PubMed, Embase, WoS and Google Scholar where included if they focused on human populations or the SHIME® model, and assessed the effects of air pollutants and EDCs on human microbiome. Non-human studies, not written in English and not displaying original research were excluded. The Newcastle-Ottawa Scale was used to assess the quality of individual studies. Results were extracted and presented in tables. 31 studies were selected, including 24 related to air pollutants, 5 related to EDCs, and 2 related to EDC using the SHIME® model. 19 studies focussed on the respiratory system (19), gut (8), skin (2), vaginal (1) and mammary (1) microbiomes. No sufficient number of studies are available to observe a consistent trend for most of the microbiota, except for streptococcus and veillionellales for which 9 out of 10, and 3 out of 4 studies suggest an increase of abundance with exposure to air pollution. A limitation of the evidence reviewed is the scarcity of existing studies assessing microbiomes from individual systems. Growing evidence suggests that exposure to environmental contaminants could change the diversity and abundance of resident microbiota, e.g. in the upper and lower respiratory, gastrointestinal, and female reproductive system. Microbial dysbiosis might lead to colonization of pathogens and outgrowth of pathobionts facilitating infectious diseases. It also might prime metabolic dysfunctions disrupting the production of beneficial metabolites. Further studies should elucidate the role of environmental pollutants in the development of dysbiosis and dysregulation of microbiota-related immunological processes.

Review: The Nose as a Route for Therapy. Part 2 Immunotherapy

The nose provides a route of access to the body for inhalants and fluids. Unsurprisingly it has a strong immune defense system, with involvement of innate (e.g., epithelial barrier, muco- ciliary clearance, nasal secretions with interferons, lysozyme, nitric oxide) and acquired (e.g., secreted immunoglobulins, lymphocytes) arms. The lattice network of dendritic cells surrounding the nostrils allows rapid uptake and sampling of molecules able to negotiate the epithelial barrier. Despite this many respiratory infections, including SARS-CoV2, are initiated through nasal mucosal contact, and the nasal mucosa is a significant "reservoir" for microbes including Streptococcus pneumoniae, Neisseria meningitidis and SARS -CoV-2. This review includes consideration of the augmentation of immune defense by the nasal application of interferons, then the reduction of unnecessary inflammation and infection by alteration of the nasal microbiome. The nasal mucosa and associated lymphoid tissue (nasopharynx-associated lymphoid tissue, NALT) provides an important site for vaccine delivery, with cold-adapted live influenza strains (LAIV), which replicate intranasally, resulting in an immune response without significant clinical symptoms, being the most successful thus far. Finally, the clever intranasal application of antibodies bispecific for allergens and Intercellular Adhesion Molecule 1 (ICAM-1) as a topical treatment for allergic and RV-induced rhinitis is explained.

Role and Function of Regulatory T Cell in Chronic Rhinosinusitis with Nasal Polyposis

Chronic rhinosinusitis with nasal polyps (CRSwNP) is a subtype of chronic rhinosinusitis characterized by high edema in the stroma, albumin deposition, and formation of pseudocysts. The pathogenesis of CRSwNP is not yet fully understood. Regulatory T (Treg) cells are a subset of CD4+ T cells that play a suppressive immunoregulatory role in the process of CRSwNP. Recent studies have found that there was a significant reduction in Treg cells in polyp tissues, which leads to the onset of CRSwNP. An imbalance between Th17 and Treg cells can also aggravate inflammation toward the Th2 type. This review focuses on our understanding of the function and role of Treg cells and their regulatory factors and clinical significance in CRSwNP. We also summarize the current drug treatments for CRSwNP with Tregs as the potential therapeutic target, which will provide new ideas for the treatment of CRSwNP in the future.

Unravelling the role of the microbiome in chronic rhinosinusitis

Chronic rhinosinusitis (CRS) is a complex, heterogenous condition with likely infectious and inflammatory causative factors. Renewed interest in the role that microbes play in this condition has stemmed from advancements in microbe identification and parallel research that has implicated the role of the microbiome in other chronic inflammatory conditions. This clinical commentary provides a review of the current literature relevant to chronic rhinosinusitis. Particular focus is paid to factors specific to the investigation of the sinonasal microbiome, evidence for the role of dysbiosis in the disease state and influences that may impact the microbiome. Possible mechanisms of disease and therapeutic implications through microbial manipulation are also reviewed, as are deficiencies and limitations of the current body of research.

Pulmonary microbiome and gene expression signatures differentiate lung function in pediatric hematopoietic cell transplant candidates

Impaired baseline lung function is associated with mortality after pediatric allogeneic hematopoietic cell transplantation (HCT), yet limited knowledge of the molecular pathways that characterize pretransplant lung function has hindered the development of lung-targeted interventions. In this study, we quantified the association between bronchoalveolar lavage (BAL) metatranscriptomes and paired pulmonary function tests performed a median of 1 to 2 weeks before allogeneic HCT in 104 children in The Netherlands. Abnormal pulmonary function was recorded in more than half the cohort, consisted most commonly of restriction and impaired diffusion, and was associated with both all-cause and lung injury-related mortality after HCT. Depletion of commensal supraglottic taxa, such as Haemophilus, and enrichment of nasal and skin taxa, such as Staphylococcus, in the BAL microbiome were associated with worse measures of lung capacity and gas diffusion. In addition, BAL gene expression signatures of alveolar epithelial activation, epithelial-mesenchymal transition, and down-regulated immunity were associated with impaired lung capacity and diffusion, suggesting a postinjury profibrotic response. Detection of microbial depletion and abnormal epithelial gene expression in BAL enhanced the prognostic utility of pre-HCT pulmonary function tests for the outcome of post-HCT mortality. These findings suggest a potentially actionable connection between microbiome depletion, alveolar injury, and pulmonary fibrosis in the pathogenesis of pre-HCT lung dysfunction.

Endotypes of chronic rhinosinusitis: Relationships to disease phenotypes, pathogenesis, clinical findings, and treatment approaches

Chronic rhinosinusitis (CRS) is a common clinical syndrome that produces significant morbidity and costs to our health system. The study of CRS has progressed from an era focused on phenotype to include endotype-based information. Phenotypic classification has identified clinical heterogeneity in CRS based on endoscopically observed features such as presence of nasal polyps, presence of comorbid or systemic diseases, and timing of disease onset. More recently, laboratory-based findings have established CRS endotype based upon specific mechanisms or molecular biomarkers. Understanding the basis of widespread heterogeneity in the manifestations of CRS is advanced by findings that the three main endotypes, Type 1, 2, and 3, orchestrate the expression of three distinct large sets of genes. The development and use of improved methods of endotyping disease in the clinic are ushering in an expansion of the use of biological therapies targeting Type 2 inflammation now and perhaps other inflammatory endotypes in the near future. The purpose of this review is to discuss the phenotypic and endotypic heterogeneity of CRS from the perspective of advancing the understanding of the pathogenesis and improvement of treatment approaches and outcomes.

Nasopharyngeal microbiome reveals the prevalence of opportunistic pathogens in SARS-CoV-2 infected individuals and their association with host types

The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is causing a severe global health emergency owing to its highly infectious nature. Although the symptoms of SARS-CoV-2 are well known but its impact on nasopharyngeal microbiome is poorly studied. The present cross-sectional study was intended to understand the perturbation in the nasopharyngeal microbiome composition within the infected (n = 63) and non-infected (n = 26) individuals using 16S rRNA gene based targeted amplicon sequencing and their association with host types and the prevalence of opportunistic pathogens at the stage of infection. The results confirmed that number of OTUs were significantly (p < 0.05) decreased in the SARS-CoV-2 infected individuals in comparison to non-infected individuals. Pairwise Wilcoxon test showed a significant (p < 0.05) increase in the abundance of Proteobacteria in infected individuals compared to non-infected ones and vice-versa for Fusobacteria and Bacteroidetes. Similarity percentage (SIMPER) analysis showed the increment in the abundance of opportunistic pathogens (Haemophilus, Stenotrophomonas, Acinetobacter, Moraxella, Corynebacterium 1, Gemella, Ralstonia, and Pseudomonas) involved in secondary infection. Furthermore, this study highlighted the microbial community structure of individuals within and across the families. In this study, we also performed the assesment of microbiome associated with host types (age and genders) and COVID-19 conditions (symptomatic and asymptomatic). The data suggested that the host types/conditions during the COVID-19 infection are potential factors in enrichment of specific bacterial communities in upper respiratory tract.

Effect of Antibiotic Exposure on Upper Respiratory Tract Bacterial Flora

Background

The human microbiota modulates the immune system and forms the surface flora. Antibiotic administration causes dysbiosis in the intestinal flora. It is not clear if antibiotic administration in the community effects the upper airway flora in the mid-term or long-term. This study aims to define long-term influence of antibiotics on upper airway flora.

Material/Methods

In this prospective study, aerobic microbiological analysis of nasal and nasopharyngeal surfaces was performed. Antibiotic administration history of the last 6 months was retrieved using the social insurance database. Culture results of antibiotic-treated and antibiotic-naïve subjects were compared by Pearson’s chi-square test or Fisher’s exact test.

Results

A total of 210 subjects were included in the study. Normal flora were documented in 86 nasal swabs and 99 nasopharyngeal swabs. Most of the remaining cases demonstrated gram-positive bacterial overgrowth. There were 113 subjects who did not receive any antibiotic, and 93% of the remaining 97 patients received broad-spectrum antibiotics. Statistical analysis showed that nasal and nasopharyngeal flora did not change upon antibiotic administration, but antibiotic administration during the last month caused increased methicillin resistance development of coagulase-negative Staphylococcus and Staphylococcus aureus microorganisms.

Conclusions

Antibiotic exposure did not lead to perturbations in general composition of upper airway flora within 6 months, although the incidence of methicillin resistance in coagulase-positive and -negative Staphylococci demonstrated significant increases when patients received antibiotic during the last month. This should be considered in case of broad-spectrum antibiotic administration, since methicillin resistance increases the morbidity and mortality of nosocomial Staphylococcus infections.

Sinonasal mycosis following transfrontal craniotomy in three dogs

CASE DESCRIPTION

Three dogs were presented for investigation of chronic nasal discharge and epistaxis 141, 250, and 357 days after undergoing transfrontal craniotomy to treat an intracranial meningioma (2 dogs) or a meningoencephalocele (1 dog).

CLINICAL FINDINGS

CT findings were consistent with destructive rhinitis and frontal sinusitis in all 3 dogs, with results of histologic examination and fungal culture of samples obtained during frontal sinusotomy confirming mycotic infection. Frontal sinusotomy revealed fungal plaques covering a combination of bone and residual surgical tissue adhesive at the site of the previous craniotomy in all 3 dogs. Aspergillus spp were identified in all 3 dogs, and Chrysosporium sp was also identified in 1 dog.

TREATMENT AND OUTCOME

Surgical curettage was followed by antifungal treatment (topical clotrimazole in 2 dogs and oral itraconazole for 3 months in 1 dog). Nasal discharge improved in the short-term but recurred in all dogs 99, 118, and 110 days after frontal sinusotomy. One dog received no further treatment, 1 dog received an additional 8.5 months of oral itraconazole treatment, and 1 dog underwent 2 additional surgical debridement procedures. At last follow-up, 2 dogs were alive 311 and 481 days after frontal sinusotomy; the third dog was euthanized because of status epilepticus 223 days after frontal sinusotomy.

CLINICAL RELEVANCE

Sinonasal mycosis should be considered as a potential complication in dogs developing persistent mucopurulent nasal discharge, intermittent epistaxis, and intermittent sneezing following transfrontal craniotomy. The pathophysiology may be multifactorial, and potential risk factors, including use of surgical tissue adhesive in the frontal sinus, require further investigation.

Defining the microbiome of the head and neck: A contemporary review

OBJECTIVE

The purpose of this paper is to define the microbiome of the head and neck by characterizing and distinguishing the commensal bacteria from pathogenic species.

STUDY DESIGN

Literature review.

METHODS

Pubmed and Google scholar databases were queried for relevant articles. Keywords such as "middle ear microbiome", "outer ear microbiome", "sinonasal microbiome", "tonsil microbiome", and "laryngeal microbiome" were utilized separately to identify articles pertaining to each topic of study. All applicable abstracts were chosen for initial review and relevant abstracts were then selected for review of the full texts. Articles that did not study the human microbiome, those not written primarily in English, those that were not readily available for full review, and case reports were excluded from the study.

RESULTS

Limited studies that investigate the microbial environments of isolated anatomic subsites in the head and neck exist, however the comprehensive microbiome of the head and neck has yet to be completely defined. Based on this review, various studies of the ears, larynx, tonsils and sinus microbiomes exist and yield valuable information, however they are limited in scope and anatomic subsite. In this literature review, these studies are compiled in order to create a comprehensive text inclusive of the known microbial elements of the major anatomic subsites of the head and neck, namely the tonsils, larynx, sinus, outer ear and middle ear.

CONCLUSIONS

The significance of the human microbiome in identifying and preventing disease has been established in various physiologic systems, however there is limited research on the microbiome of the head and neck. Understanding the microbiome of the head and neck can help differentiate disease-prone patients from normal patients and guide treatment regimens and antibiotic usage, to aid in resistance control and limit adverse effects of antibiotic overuse. Understanding the elements that lead to dysbiosis can help treat and even prevent common conditions as tonsillitis and rhinosinusitis. In this review, we provide a comprehensive review to serve as an initial background for future studies to define the head and neck microbiome distinguished by all relevant subsites.

The Role of Probiotics in Chronic Rhinosinusitis Treatment: An Update of the Current Literature

Chronic rhinosinusitis (CRS) is a significant health problem. It affects 5–12% of the general population. The causes that underlie the onset of CRS are not yet well known. However, many factors may contribute to its onset, such as environmental factors and the host’s general condition. Medical treatment mainly uses local corticosteroids, nasal irrigation, and antibiotics. In recent years, a new therapeutic approach that employs the use of probiotics emerged. Probiotics have been extensively studied as a therapy for dysbiosis and inflammatory pathologies of various parts of the body. We aimed to examine the studies in vivo and in vitro and clinicals reports in the existing literature to update probiotics’ role in rhinosinusitis chronic medical treatment.

Novel strategies for inhibition of bacterial biofilm in chronic rhinosinusitis

An important role has been recently reported for bacterial biofilm in the pathophysiology of chronic diseases, such as chronic rhinosinusitis (CRS). CRS, affecting sinonasal mucosa, is a persistent inflammatory condition with a high prevalence around the world. Although the exact pathological mechanism of this disease has not been elicited yet, biofilm formation is known to lead to a more significant symptom burden and major objective clinical indicators. The high prevalence of multidrug-resistant bacteria has severely restricted the application of antibiotics in recent years. Furthermore, systemic antibiotic therapy, on top of its insufficient concentration to eradicate bacteria in the sinonasal biofilm, often causes toxicity, antibiotic resistance, and an effect on the natural microbiota, in patients. Thus, coming up with alternative therapeutic options instead of systemic antibiotic therapy is emphasized in the treatment of bacterial biofilm in CRS patients. The use of topical antibiotic therapy and antibiotic eluting sinus stents that induce higher antibiotic concentration, and decrease side effects could be helpful. Besides, recent research recognized that various natural products, nitric oxide, and bacteriophage therapy, in addition to the hindered biofilm formation, could degrade the established bacterial biofilm. However, despite these improvements, new antibacterial agents and CRS biofilm interactions are complicated and need extensive research. Finally, most studies were performed in vitro, and more preclinical animal models and human studies are required to confirm the collected data. The present review is specifically discussing potential therapeutic strategies for the treatment of bacterial biofilm in CRS patients.

Variations in facial conformation are associated with differences in nasal microbiota in healthy dogs

Background

Extrinsic and intrinsic factors have been shown to influence nasal microbiota (NM) in humans. Very few studies investigated the association between nasal microbiota and factors such as facial/body conformation, age, and environment in dogs. The objectives are to investigate variations in NM in healthy dogs with different facial and body conformations. A total of 46 dogs of different age, living environment and from 3 different breed groups were recruited: 22 meso−/dolichocephalic medium to large breed dogs, 12 brachycephalic dogs and 12 terrier breeds. The nasal bacterial microbiota was assessed through sequencing of 16S rRNA gene (V1-V3 regions) amplicons.

Results

We showed major differences in the NM composition together with increased richness and α-diversity in brachycephalic dogs, compared to meso−/dolichocephalic medium to large dogs and dogs from terrier breeds.

Conclusion

Healthy brachycephalic breeds and their unique facial conformation is associated with a distinct NM profile. Description of the NM in healthy dogs serves as a foundation for future researches assessing the changes associated with disease and the modulation of NM communities as a potential treatment.