The Human Respiratory System and its Microbiome at a Glimpse

The recent COVID-19 pandemic promoted efforts to better understand the organizationof the respiratory microbiome and its evolution from birth to adulthood and how it interacts withexternal pathogens and the host immune system. This review aims to deepen understanding of theessential physiological functions of the resident microbiome of the respiratory system on human healthand diseases. First, the general characteristics of the normal microbiota in the different anatomicalsites of the airways have been reported in relation to some factors such as the effect of age, diet andothers on its composition and stability. Second, we analyze in detail the functions and compositionand the correct functionality of the microbiome in the light of current knowledge. Several studiessuggest the importance of preserving the micro-ecosystem of commensal, symbiotic and pathogenicmicrobes of the respiratory system, and, more recently, its relationship with the intestinal microbiome,and how it also leads to the maintenance of human health, has become better understood

Untargeted analysis of the airway proteomes of children with respiratory infections using mass spectrometry based proteomics

The upper airway – which consists mainly of the naso- and oro-pharynx - is the first point of contact between the respiratory system and microbial organisms that are ubiquitous in the environment. It has evolved highly specialised functions to address these constant threats whilst facilitating seamless respiratory exchange with the lower respiratory tract. Dysregulation of its critical homeostatic and defence functions can lead to ingress of pathogens into the lower respiratory tract, potentially leading to serious illness. Systems-wide proteomic tools may facilitate a better understanding of mechanisms in the upper airways in health and disease. In this study, we aimed to develop a mass spectrometry based proteomics method for characterizing the upper airways proteome. Naso- and oropharyngeal swab samples used in all our experiments had been eluted in the Universal Transport Media (UTM) containing significantly high levels of bovine serum albumin. Our proteomic experiments tested the optimal approach to characterize airway proteome on swab samples eluted in UTM based on the number of proteins identified without BSA depletion (Total proteome: Protocol A) and with its depletion using a commercial kit; Allprep, Qiagen (cellular proteome: Protocol B, Ci, and Cii). Observations and lessons drawn from protocol A, fed into the design and implementation of protocol B, and from B to protocol Ci and finally Cii. Label free proteome quantification was used in Protocol A (n = 6) and B (n = 4) while commercial TMT 10plex reagents were used for protocols Ci and ii (n = 83). Protocols Ci and ii were carried out under similar conditions except for the elution gradient: 3 h and 6 h respectively. Swab samples tested in this study were from infants and children with and without upper respiratory tract infections from Kilifi County Hospital on the Kenyan Coast. Protocol A had the least number of proteins identified (215) while B produced the highest number of protein identifications (2396). When Protocol B was modified through sample multiplexing with TMT to enable higher throughput (Protocol Ci), the number of protein identified reduced to 1432. Modification of protocol Ci by increasing the peptide elution time generated Protocol Cii that substantially increased the number of proteins identified to 1875. The coefficient of variation among the TMT runs in Protocol Cii was <20%. There was substantial overlap in the identity of proteins using the four protocols. Our method was were able to identify marker proteins characteristically expressed in the upper airway. We found high expression levels of signature nasopharyngeal and oral proteins, including BPIFA1/2 and AMY1A, as well as a high abundance of proteins related to innate and adaptive immune function in the upper airway. We have developed a sensitive systems-level proteomic assay for the systematic quantification of naso-oro-pharyngeal proteins. The assay will advance mechanistic studies of respiratory pathology, by providing an untargeted and hypothesis-free approach of examining the airway proteome

The microbiome of the nose - friend or foe?

Recently, multiple studies regarding the human microbiota and its role on the development of disease have emerged. Current research suggests that the nasal cavity is a major reservoir for opportunistic pathogens, which can then spread to other sections of the respiratory tract and be involved in the development of conditions such as allergic rhinitis, chronic rhinosinusitis, asthma, pneumonia, and otitis media. However, our knowledge of how nasal microbiota changes originate nasopharyngeal and respiratory conditions is still incipient. Herein, we describe how the nasal microbiome in healthy individuals varies with age and explore the effect of nasal microbiota changes in a range of infectious and immunological conditions. We also describe the potential health benefits of human microbiota modulation through probiotic use, both in disease prevention and as adjuvant therapy. Current research suggests that patients with different chronic rhinosinusitis phenotypes possess distinct nasal microbiota profiles, which influence immune response and may be used in the future as biomarkers of disease progression. Probiotic intervention may also have a promising role in the prevention and adjunctive treatment of acute respiratory tract infections and allergic rhinitis, respectively. However, further studies are needed to define the role of probiotics in the chronic rhinosinusitis.info:eu-repo/semantics/publishedVersio

The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children.

BACKGROUND The microbiota of the upper respiratory tract is increasingly recognized as a gatekeeper of respiratory health. Despite this, the microbiota of healthy adults remains understudied. To address this gap, we investigated the composition of the nasopharyngeal and oropharyngeal microbiota of healthy adults, focusing on the effect of Streptococcus pneumoniae carriage, smoking habits, and contact with children. RESULTS Differential abundance analysis indicated that the microbiota of the oropharynx was significantly different from that of the nasopharynx (P < 0.001) and highly discriminated by a balance between the classes Negativicutes and Bacilli (AUC of 0.979). Moreover, the oropharynx was associated with a more homogeneous microbiota across individuals, with just two vs. five clusters identified in the nasopharynx. We observed a shift in the nasopharyngeal microbiota of carriers vs. noncarriers with an increased relative abundance of Streptococcus, which summed up to 30% vs. 10% in noncarriers and was not mirrored in the oropharynx. The oropharyngeal microbiota of smokers had a lower diversity than the microbiota of nonsmokers, while no differences were observed in the nasopharyngeal microbiota. In particular, the microbiota of smokers, compared with nonsmokers, was enriched (on average 16-fold) in potential pathogenic taxa involved in periodontal diseases of the genera Bacillus and Burkholderia previously identified in metagenomic studies of cigarettes. The microbiota of adults with contact with children resembled the microbiota of children. Specifically, the nasopharyngeal microbiota of these adults had, on average, an eightfold increase in relative abundance in Streptococcus sp., Moraxella catarrhalis, and Haemophilus influenzae, pathobionts known to colonize the children's upper respiratory tract, and a fourfold decrease in Staphylococcus aureus and Staphylococcus lugdunensis. CONCLUSIONS Our study showed that, in adults, the presence of S. pneumoniae in the nasopharynx is associated with a shift in the microbiota and dominance of the Streptococcus genus. Furthermore, we observed that smoking habits are associated with an increase in bacterial genera commonly linked to periodontal diseases. Interestingly, our research also revealed that adults who have regular contact with children have a microbiota enriched in pathobionts frequently carried by children. These findings collectively contribute to a deeper understanding of how various factors influence the upper respiratory tract microbiota in adults. Video Abstract

The influence of lung microbiota on lung carcinogenesis, immunity and immunotherapy

Microbiota have emerged as key modulators of both the carcinogenic process and the immune response against cancer cells, and, thus, it seems to influence the efficacy of immunotherapy. While most studies have focused on analyzing the influence of gut microbiota, its composition substantially differs from that in the lung. Here, we describe how microbial life in the lungs is associated with host immune status in the lungs and, thus, how the identification of the microbial populations in the lower respiratory tract rather than in the gut might be key to understanding the lung carcinogenic process and to predict the efficacy of different treatments. Understanding the influence of lung microbiota on host immunity may identify new therapeutic targets and help to design new immunotherapy approaches to treat lung cancer

Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort

Background: Bacteria colonizing the nasopharynx play a key role as gatekeepers of respiratory health. Yet, dynamics of early life nasopharyngeal (NP) bacterial profiles remain understudied in low- and middle-income countries (LMICs), where children have a high prevalence of risk factors for lower respiratory tract infection. We investigated longitudinal changes in NP bacterial profiles, and associated exposures, among healthy infants from low-income households in South Africa. Methods: We used short fragment (V4 region) 16S rRNA gene amplicon sequencing to characterize NP bacterial profiles from 103 infants in a South African birth cohort, at monthly intervals from birth through the first 12 months of life and six monthly thereafter until 30 months. Results: Corynebacterium and Staphylococcus were dominant colonizers at 1 month of life; however, these were rapidly replaced by Moraxella- or Haemophilus-dominated profiles by 4 months. This succession was almost universal and largely independent of a broad range of exposures. Warm weather (summer), lower gestational age, maternal smoking, no day-care attendance, antibiotic exposure, or low height-for-age z score at 12 months were associated with higher alpha and beta diversity. Summer was also associated with higher relative abundances of Staphylococcus, Streptococcus, Neisseria, or anaerobic gram-negative bacteria, whilst spring and winter were associated with higher relative abundances of Haemophilus or Corynebacterium, respectively. Maternal smoking was associated with higher relative abundances of Porphyromonas. Antibiotic therapy (or isoniazid prophylaxis for tuberculosis) was associated with higher relative abundance of anerobic taxa (Porphyromonas, Fusobacterium, and Prevotella) and with lower relative abundances of health associated-taxa Corynebacterium and Dolosigranulum. HIV-exposure was associated with higher relative abundances of Klebsiella or Veillonella and lower relative abundances of an unclassified genus within the family Lachnospiraceae. Conclusions: In this intensively sampled cohort, there was rapid and predictable replacement of early profiles dominated by health-associated Corynebacterium and Dolosigranulum with those dominated by Moraxella and Haemophilus, independent of exposures. Season and antibiotic exposure were key determinants of NP bacterial profiles. Understudied but highly prevalent exposures prevalent in LMICs, including maternal smoking and HIV-exposure, were associated with NP bacterial profiles

Gut Microbiome and COVID 19 Role of Probiotics on Gut Lung Axis

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has caused the greatest worldwide pandemic called Coronavirus-2019 (COVID-19) disease. The SARS-CoV-2 virus primarily attacks the respiratory tract, but it also disturbs the gastrointestinal system (GIT). The presence of the angiotensin-converting enzyme-2 (ACE-2) receptor in the intestinal epithelial cells, suggest the transmission of SARS-CoV-2 viruses from lungs to gut through systemic circulation. The virus detected in fecal samples of COVID-19 patients causes several gastrointestinal maladies including vomiting, diarrhea, and pain in abdomen. The gastrointestinal symptoms are associated with alterations in gut microbial composition, an increase in inflammatory cytokines and delayed virus clearance. Several studies demonstrated a decreased abundance of beneficial microbial species and increased opportunistic pathogens in the fecal samples of COVID-19 patients. The gut and lungs, share a bi-directional relationship called the “gut-lung axis” which is modulated by imbalanced gut microbiota. Since the gut microbes are suggested to play a vital role in health and disease by maintaining homeostasis of the immune system, therefore targeting the intestinal dysbiosis with beneficial microbial species, seems plausible to eventually diminish the effects of pulmonary infections and diseases. In this review, we have summarized studies demonstrating the gut-lung axis in association with gut dysbiosis in COVID-19 patients. In addition, the review also highlights the studies showing the potential role of probiotic supplementation in the amelioration of various respiratory infections and diseases. Data demonstrate that the restoration of gut microbial communities by probiotic supplementation can enhance lung capacity to combat respiratory viral infections including SARS-CoV-2

Tonsils as an in vivo model : Virus infections, microbiome, and immune responses

Tonsillectomy and adenotomy are two of the most common operations in the otorhinolaryngology field. Recurrent infections and hypertrophy are the main indications for these surgical procedures. Palatine tonsils and nasopharyngeal tonsil (adenoid) continuously interact with our environment. Tonsils consist of mucosa associated lymphoid tissue and serve as a site for bacteria, viruses, and other antigens to be presented to the immune cells. Physiologically complex tonsil tissue is crucial in inducing and maintaining immune responses. However, the underlying mechanisms of the pathological conditions are not fully understood. This thesis primarily aimed to investigate tonsillar virus infections, microbiome, and their association with immune responses. The diagnostics and immunomodulatory effects of human bocavirus 1 (HBoV1) were particularly emphasised. Elective adeno-/tonsillectomy patients of all ages were recruited from Satakunta Central Hospital 2008–2009 and Turku University Hospital 2013–2015. Adeno-/tonsillectomy was performed according to routine clinical procedures; tonsil tissues, nasopharyngeal aspirate (NPA), and serum samples were collected. Virus diagnostics was done by polymerase chain reaction (PCR); the expression of cytokine and transcription factors was analysed by reverse-transcription PCR. RNA sequencing was used for microbial profiling. Our results support earlier data that respiratory virus infections in palatine tonsil tissue, adenoid tissue, and NPA are common (with a total detection rate of 94%) in non-acutely ill adeno-/tonsillectomy patients. Additionally, in one or more of the sample sites, human herpesviruses 6 and 7 and the Epstein-Barr virus were commonly found (67%, 51%, and 35%, respectively). High HBoV1 DNA loads in NPA had no correlation with serology or messenger RNA results. Furthermore, HBoV1 infection was associated with suppressed expression of tonsillar cytokines, suggesting the immunosuppressive capacity of the virus. Our study revealed that atopy associated with lower intratonsillar bacterial diversity, suggesting differences in microbial balance between atopic and non-atopic subjects. Palatine tonsil and adenoid tissues serve as an in vivo model to investigate viruses, bacteria, and their interactions with local immune responses.Risakudos in vivo -mallina – virusinfektiot, mikrobiomi ja immuunivasteet Nielurisa- ja kitarisaleikkaus ovat yleisiä toimenpiteitä korva-, nenä- ja kurkkutautien alalla. Leikkausindikaatio on useimmiten risatulehdukset ja risojen liikakasvu. Nielu- ja kitarisat ovat jatkuvasti vuorovaikutuksessa ympäristön kanssa. Risakudos koostuu limakalvon ja lymfaattisen kudoksen yhdistelmästä ja toimii antigeenin ja immuunijärjestelmän solujen kohtaamispaikkana. Fysiologisesti monimuotoinen risakudos toimii merkittävässä roolissa immuunivasteiden aktivoinnissa ja muokkaamisessa. Tämän väitöskirjan tarkoituksena oli tutkia risakudoksen virusinfektioita, mikrobiomia ja niiden yhteyttä immuunivasteisiin. Erityisesti tutkittiin bokaviruksen (HBoV1) diagnostiikkaa ja HBoV1 infektion yhteyttä immuunivasteisiin.Aineistoon kerättiin kaiken ikäisiä kita- ja nielurisaleikkauspotilaita Satakunnan keskussairaalasta vuosina 2008–2009 ja Turun Yliopistollisesta keskussairaalasta vuosina 2013–2015. Leikkauspotilaista otettiin verinäytteet, nenän imulimanäytteet (NPA) ja risakudosnäytteet. Virukset analysoitiin polymeraasiketjureaktio (PCR) menetelmällä. Sytokiinigeenien ilmentymistä tutkittiin käänteistranskriptaasipolymeraariketjureaktiolla (RT-PCR) ja RNA-sekvensointia käytettiin risakudoksen mikrobiomin kartoittamiseen. Kroonista risasairautta sairastavien leikkauspotilaiden risakudoksissa ja nenän imulimassa esiintyy runsaasti hengitystieviruksia (esiintyvyys 94 %), kuten aikaisemmin on osoitettu. Herpesvirus 6 (HHV6), herpesvirus 7 (HHV7) Epstein-Barr virus olivat yleisiä (67 %, 51 %, 35 %) yhdessä tai useammassa näytelaadussa. HBoV1 korkea virusmäärä ei korreloinut vasta-ainetasoihin tai lähetti RNA tuloksiin. HBoV1 oli yhteydessä risakudoksen sytokiinigeenien vähäisempään ilmaantuvuuteen viitaten HBoV1:n kapasiteettiin muokata immuunivastetta. Lisäksi tutkimuksessa kävi ilmi, että atooppisilla potilailla nielurisakudoksen bakteerien monimuotoisuus on alhaisempi. Nielu- ja kitarisa soveltuvat käytettäväksi in vivo mallina tutkittaessa risakudoksen viruksia, bakteereja ja niiden vaikutusta immuunivasteisiin

Potential contribution of beneficial microbes to face the COVID-19 pandemic

The year 2020 will be remembered by a never before seen, at least by our generation, global pandemic of COVID-19. While a desperate search for effective vaccines or drug therapies is on the run, nutritional strategies to promote immunity against SARS-CoV-2, are being discussed. Certain fermented foods and probiotics may deliver viable microbes with the potential to promote gut immunity. Prebiotics, on their side, may enhance gut immunity by selectively stimulating certain resident microbes in the gut. Different levels of evidence support the use of fermented foods, probiotics and prebiotics to promote gut and lungs immunity. Without being a promise of efficacy against COVID-19, incorporating them into the diet may help to low down gut inflammation and to enhance mucosal immunity, to possibly better face the infection by contributing to diminishing the severity or the duration of infection episodes.Fil: Antunes, Adriane E.C.. Universidade Estadual de Campinas; BrasilFil: Vinderola, Celso Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Lactología Industrial. Universidad Nacional del Litoral. Facultad de Ingeniería Química. Instituto de Lactología Industrial; ArgentinaFil: Xavier-Santos, Douglas. Universidade Estadual de Campinas; BrasilFil: Sivieri, Katia. Universidade Estadual Paulista Julio de Mesquita Filho; Brasi

Manipulation of the Upper Respiratory Microbiota to Reduce Incidence and Severity of Upper Respiratory Viral Infections: A Literature Review.

There is a high incidence of upper respiratory viral infections in the human population, with infection severity being unique to each individual. Upper respiratory viruses have been associated previously with secondary bacterial infection, however, several cross-sectional studies analyzed in the literature indicate that an inverse relationship can also occur. Pathobiont abundance and/or bacterial dysbiosis can impair epithelial integrity and predispose an individual to viral infection. In this review we describe common commensal microorganisms that have the capacity to reduce the abundance of pathobionts and maintain bacterial symbiosis in the upper respiratory tract and discuss the potential and limitations of localized probiotic formulations of commensal bacteria to reduce the incidence and severity of viral infections