Ecology of the respiratory tract microbiome

Genome mining identifies a diversity of natural product biosynthetic capacity in human respiratory Corynebacterium strains

Corynebacterium species, integral to the healthy human upper respiratory tract (URT) microbiota, remain underexplored in microbial genomics for their potential to promote respiratory health and exclude pathobionts. This genomic study investigated the diversity and capacity for natural product synthesis within these species, as indicated by their biosynthetic gene clusters (BGCs). We aimed to map and quantify the BGC diversity in a contemporary collection of Corynebacterium strains, representative of their prevalence in the respiratory microbiota, and to elucidate intra- and interspecies variation in BGC content. The outcomes of this research could reveal key factors in maintaining the ecological balance of the upper respiratory tract and identify novel antimicrobial agents targeting respiratory pathobionts. Employing an in silico approach, we analyzed the biosynthetic potential of respiratory strains of non-diphtheriae Corynebacterium species and their reference genomes through genome sequencing and antiSMASH6 analysis. Among 161 genomes, we identified 672 BGCs, 495 of which were unique, including polyketide synthase, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptide, and siderophore families. To understand how this biosynthetic capacity compared to other respiratory bacteria, we then downloaded genomes from eight species that are associated with the URT and conducted BGC searches. We found that despite their compact genomes, Corynebacterium species possess a multitude of predicted BGCs, exceeding the diversity of natural product BGCs identified in multiple other respiratory bacteria. This research lays the foundation for future functional genomics studies on the role of Corynebacterium species in the respiratory microbiome and the discovery of novel therapeutics derived from this bacterial genus.IMPORTANCEBacterial secondary metabolites, produced by enzymes encoded by biosynthetic gene clusters, are ecologically important for bacterial communication and competition in nutrient-scarce environments and are a historically rich source of antibiotics and other medications. Human-associated Corynebacterium species, abundant in the healthy upper respiratory tract, are understudied despite evidence of their roles in promoting human health and preventing pathobiont colonization. Through genome mining of a large collection of Corynebacterium strains isolated from the human respiratory tract and publicly available genomes of other respiratory bacteria, our study suggests that Corynebacterium species have a high biosynthetic capacity and are predicted to harbor a wide range of biosynthetic gene cluster families. These findings substantially expand current knowledge regarding the production of secondary metabolites by human-associated Corynebacterium species. Our study also lays the foundations for understanding how Corynebacterium species interact in the healthy human upper respiratory tract and the potential for discovering novel biotherapeutics.

The Respiratory Tract Microbiome and Human Health

The respiratory tract microbiome (RTM) is a multi-kingdom microbial ecosystem that inhabits various niches of the respiratory system. While previously overlooked, there is now sufficient evidence that the RTM plays a crucial role in human health related to immune system training and protection against pathogens. Accordingly, dysbiosis or disequilibrium of the RTM has been linked to several communicable and non-communicable respiratory diseases, highlighting the need to unveil its role in health and disease. Here, we define the RTM and its place in microbiome medicine. Moreover, we outline the challenges of RTM research, emphasising the need for combining methodologies, including multi-omics and computational tools. We also discuss the RTM's potential for diagnosing, preventing and treating respiratory diseases and developing novel microbiome-based therapies to improve pulmonary health.

The intricate interplay among microbiota, mucosal immunity, and viral infection in the respiratory tract

The mucosal system serves as the primary barrier against respiratory diseases and plays a crucial role in combating viral infections through mucosal immunity. The resident microbial community constitutes the main component of the mucosal system and exerts a significant inhibitory impact on the invasion of exogenous agents. However, the precise relationship between resident microbiota, mucosal immunity, and viral infections remains incomplete. This review aims to summarize the regulatory interactions between the resident microbiota of the mucosal system and innate immune components such as mucosal immunity and trained immunity. By clarifying these complex relationships, this review seeks to identify potential targets for augmenting respiratory disease prevention strategies and developing novel vaccine formulations. Furthermore, we propose the possibility of integrating the fields of microbiome-based therapeutics and vaccine development to create multifunctional vaccine formulations capable of targeting mucosal immunity induction. Such an approach holds great potential in offering novel pathways and strategies for the prevention and treatment of respiratory diseases.

Seasonal Dynamics of Microbial Communities in PM2.5 and PM10 from a Pig Barn

Modern, intensive, high-density farming practices cause elevated concentrations of particulate matter (PM) inside livestock barns. PM in livestock barns is predominantly biological, hence, it contains abundant microorganisms. Understanding the microbial composition of PM is crucial for assessing the hazards of air emitted from livestock barns. PM10 and PM2.5 from a pig barn were collected in winter and spring, and morphological, chemical, and microbial analyses were performed. The PM samples exhibit diverse morphological characteristics. The top three elements detected in the PM samples were O, C, and Si. Other elements, including N, Al, K, Mg, Ca, Na, Zn, P, W, Ba, Fe, S, Cl, and Ti, were also identified in these samples. For bacterial α diversity, the Sobs and Chao1 indices for PM10 were significantly higher than those for PM2.5 in winter (p < 0.05), and in spring, the ACE index for PM10 was significantly higher than that for PM2.5 (p < 0.05). For fungal α diversity, the Shannon index for PM10 was significantly higher than that for PM2.5 in winter (p < 0.01), and in spring, the Ace index for PM10 was significantly higher than that for PM2.5 (p < 0.05). The β diversity results indicate that season, rather than the particle size, had a significant effect on the microbial composition in the PM samples. A total of seven bacterial pathogen genera and 16 fungal allergen genera were identified in PM samples. In winter, the relative abundances of total bacterial pathogens and fungal allergens in PM2.5 were higher than those in PM10. In contrast, the relative abundance of fungal allergens in PM10 was higher in spring than in winter. This study provides a comprehensive characterization of PM from a pig barn across the particle sizes and seasons.

The impact of environmental factors on respiratory tract microbiome and respiratory system diseases

The respiratory tract microbiome, a complex ecosystem of microorganisms colonizing the respiratory mucous layers and epithelial surfaces along with their associated microenvironment, plays a vital role in maintaining respiratory function and promoting the maturation of the respiratory immune system. Current research suggests that environmental changes can disrupt the respiratory microbiota, potentially leading to disease. This review summarizes existing research on the impact of environmental factors on the respiratory microbiome and associated diseases, aiming to offer new insights into the prevention and treatment of respiratory disease.

Upper and lower airway microbiota across infancy and childhood

BACKGROUND

The upper and lower respiratory tracts feature distinct environments and responses affecting microbial colonization but investigating the relationship between them is technically challenging. We aimed to identify relationships between taxa colonizing the nasopharynx and trachea across childhood.

METHODS

We employed V4 16S rRNA gene sequencing to profile nasopharyngeal swabs and tracheal aspirates collected from 172 subjects between 20 weeks and 18 years of age. These samples were collected prior to elective procedures over the course of 20 weeks in 2020 from subjects enrolled in a cross-sectional study. After extraction, sequencing, and quality control, we studied the remaining 147 of 172 nasopharyngeal swabs and 95 of 172 tracheal aspirates, including 80 subject-matched pairs of samples.

RESULTS

Sequencing data revealed that the nasopharynx is colonized by few, often highly abundant taxa, while the tracheal aspirates feature greater diversity. The patterns of colonization identified in the nasopharynx correlate with subject age across childhood.

CONCLUSION

Our data suggests that there are relatively few species that colonize both the nasopharyngeal tract and the trachea. Furthermore, we observe a pattern of change in the nasopharyngeal microbiota that is correlated with age, suggesting a possible developmental progression of the nasopharyngeal microbiota across childhood.

IMPACT

The airway microbiota in childhood plays important roles in respiratory health and immune development. In this work, we report on paired nasopharyngeal swab and tracheal aspirate samples from a cross-sectional cohort of children from infancy to 18 years. We find that the upper and lower airway microbiota are unlikely to share taxa and do not correlate in terms of diversity. We show that the composition of the upper airway microbiota is strongly correlated with age, with a stereotypic developmental trajectory during childhood and adolescence. Our results inform our understanding of airway microbiota assembly and may be used to predict airway disease in young children.

The neonate respiratory microbiome

Over the past two decades, it has become clear that against earlier assumptions, the respiratory tract is regularly populated by a variety of microbiota even down to the lowest parts of the lungs. New methods and technologies revealed distinct microbiome compositions and developmental trajectories in the differing parts of the respiratory tract of neonates and infants. In this review, we describe the current understanding of respiratory microbiota development in human neonates and highlight multiple factors that have been identified to impact human respiratory microbiome development including gestational age, mode of delivery, diet, antibiotic treatment, and early infections. Moreover, we discuss to date revealed respiratory microbiome-disease associations in infants and children that may indicate a potentially imprinting cross talk between microbial communities and the host immune system in the respiratory tract. It becomes obvious how insufficient our knowledge still is regarding the exact mechanisms underlying such cross talk in humans. Lastly, we highlight strong findings that emphasize the important role of the gut-lung axis in educating and driving pulmonary immunity. Further research is needed to better understand the host - respiratory microbiome interaction in order to enable the translation into microbiome-based strategies to protect and improve human respiratory health from early childhood.

Evaluating the Risks of Heated Tobacco Products: Toxicological Effects on Two Selected Respiratory Bacteria and Human Lung Cells

Heated tobacco products (THPs) are increasingly promoted as potential harm reduction tools, offering an alternative to traditional cigarettes. Despite these claims, understanding of their toxicological impact on respiratory health and associated microbial communities is limited. Comprehensive investigations are needed to elucidate the biological mechanisms and potential health implications associated with their use.

METHODS

This study evaluated the toxicological effects of aerosols produced by THPs (IQOS 3 Duo with Heets "Sienna Selection") in comparison to conventional cigarette smoke (1R6F). Antibacterial activity was evaluated using Streptococcus pneumoniae and Klebsiella pneumoniae as representative species of the respiratory microbiota through agar diffusion assays and MIC/MBC determinations. Cytotoxicity was assessed in human lung fibroblast cells (MRC5) through the neutral red uptake (NRU) assay, whereas mutagenicity was investigated using the Ames test.

RESULTS

THP aerosols demonstrated the ability to inhibit the growth of both S. pneumoniae and K. pneumoniae, exerting bacteriostatic effects at lower concentrations and bactericidal effects at higher concentrations. While these antibacterial effects might initially seem beneficial against pathogens such as K. pneumoniae, they raise concerns about the potential disruption of the respiratory microbial balance, particularly in relation to S. pneumoniae. Despite these microbiological effects, THP aerosols demonstrated minimal cytotoxicity on human lung fibroblasts and lacked detectable mutagenic activity, contrasting with the significant cytotoxicity and mutagenicity caused by cigarette smoke.

CONCLUSIONS

THPs present a reduced short-term toxicological profile compared with conventional cigarettes; however, their effects on respiratory microorganisms deserve attention. The observed inhibition of commensal bacteria highlights the need to explore potential changes in the microbial ecosystem that could affect respiratory health. These findings highlight the need for additional studies to evaluate the long-term effect of THP use on respiratory microbiota and the stability of the overall microbial ecosystem.

The forecasting power of the mucin-microbiome interplay in livestock respiratory diseases

Complex respiratory diseases are a significant challenge for the livestock industry worldwide. These diseases considerably impact animal health and welfare and cause severe economic losses. One of the first lines of pathogen defense combines the respiratory tract mucus, a highly viscous material primarily composed of mucins, and a thriving multi-kingdom microbial ecosystem. The microbiome-mucin interplay protects from unwanted substances and organisms, but its dysfunction may enable pathogenic infections and the onset of respiratory disease. Emerging evidence also shows that noncoding regulatory RNAs might modulate the structure and function of the microbiome-mucin relationship. This opinion paper unearths the current understanding of the triangular relationship between mucins, the microbiome, and noncoding RNAs in the context of respiratory infections in animals of veterinary interest. There is a need to look at these molecular underpinnings that dictate distinct health and disease outcomes to implement effective prevention, surveillance, and timely intervention strategies tailored to the different epidemiological contexts.

Association between gut microbiota and acute upper respiratory tract infection: a Mendelian randomization study

Targeting specific gut microbiota (GM) species to prevent and treat acute upper respiratory tract infection (AURTI) has attracted researchers' attention, but the relationship between the two is unclear. Based on the summary data from genome-wide association studies (GWAS) on GM and five types of AURTIs (acute nasopharyngitis (common cold), acute pharyngitis, acute sinusitis, acute upper respiratory infections, and acute upper respiratory infections of multiple and unspecified sites), we performed two-sample bidirectional Mendelian randomization (MR) to assess the causal relationship. Through inverse variance weighting (IVW) method, we found that 33 potential microbial taxa can influence the occurrence of AURTI. Sensitivity analysis showed no potential horizontal pleiotropy and heterogeneity bias. We further employed multivariable Mendelian randomization to investigate the impact of potential interference factors on the significant associations previously identified, considering aspects such as comorbidities associated with AURTI, seasonal variations, pathogen specificity, and history of antibiotic allergies. Ultimately, 11 microbial taxa remained significantly associated. This study provides robust evidence for a causal relationship between GM and five types of AURTIs, thereby offering a foundation for the development of microbiota-targeted therapies and related probiotic interventions aimed at AURTI.

Distinct lower respiratory tract microbiota profiles linked to airway mucus hypersecretion in children with Mycoplasma pneumoniae pneumonia

Background

Airway mucus hypersecretion (AMH) can occur in children with acute respiratory diseases, but its underlying mechanisms and relationship with the lower respiratory tract microbiota (LRTM) are not yet fully understood. This study investigates the characteristics of LRTM in children with Mycoplasma pneumoniae pneumonia (MPP) and its impact on AMH.

Methods

We collected bronchoalveolar lavage fluid and related clinical indicators from 202 children with MPP. 16S rRNA gene amplicon sequencing was used for detection and identification. Microbial diversity and characteristic genera were compared, and their abundance was analyzed for correlations with clinical factors.

Results

As the disease course (days from onset to bronchoscopy, grouped into T1, T2, T3) extended, α-diversity of the LRTM gradually increased, particularly in the T3 hypersecretion group. Moreover, significant differences were observed in the incidence of AMH, co-infection rates, peripheral white blood cell (WBC) count, and C-reactive protein levels. In AMH, Mycoplasmoides and Veillonella abundance and peripheral neutrophils were risk factors for increased secretions. In addition, in the T3 co-infection group, Streptococcus and Prevotella increased, replacing Stenotrophomonas as the dominant genus, possibly due to β-lactam antibiotic use. Prevotella abundance was strongly correlated with WBC.

Conclusion

The composition and structure of LRTM in children with MPP played a crucial role in AMH and disease progression.

Adaptability of the gut microbiota of the German cockroach Blattella germanica to a periodic antibiotic treatment

High-throughput sequencing studies have shown that diet or antimicrobial treatments impact animal gut microbiota equilibrium. However, properties related to the gut microbial ecosystem stability, such as resilience, resistance, or functional redundancy, must be better understood. To shed light on these ecological processes, we combined advanced statistical methods with 16 S rRNA gene sequencing, functional prediction, and fitness analyses in the gut microbiota of the cockroach Blattella germanica subject to three periodic pulses of the antibiotic (AB) kanamycin (n=512). We first confirmed that AB did not significantly affect cockroaches' biological fitness, and gut microbiota changes were not caused by insect physiology alterations. The sex variable was examined for the first time in this species, and no statistical differences in the gut microbiota diversity or composition were found. The comparison of the gut microbiota dynamics in control and treated populations revealed that (1) AB treatment decreases diversity and completely disrupts the co-occurrence networks between bacteria, significantly altering the gut community structure. (2) Although AB also affected the genetic composition, functional redundancy would explain a smaller effect on the functional potential than on the taxonomic composition. (3) As predicted by Taylor's law, AB generally affected the most abundant taxa to a lesser extent than the less abundant taxa. (4) Taxa follow different trends in response to ABs, highlighting "resistant taxa," which could be critical for community restoration. (5) The gut microbiota recovered faster after the three AB pulses, suggesting that gut microbiota adapts to repeated treatments.

Lactobacillus salivarius ameliorates Mycoplasma gallisepticum-induced inflammation via the JAK/STAT signaling pathway involving respiratory microbiota and metabolites

Mycoplasma gallisepticum (MG) can cause chronic respiratory disease (CRD) in chickens, which has a significant negative economic impact on the global poultry sector. Respiratory flora is the guardian of respiratory health, and its disorder is closely related to respiratory immunity and respiratory diseases. As a common probiotic in the chicken respiratory tract, Lactobacillus salivarius (L. salivarius) has potential antioxidant, growth performance enhancing, and anti-immunosuppressive properties. However, the specific mechanism through which L. salivarius protects against MG infection has not yet been thoroughly examined. This study intends to investigate whether L. salivarius could reduce MG-induced tracheal inflammation by modulating the respiratory microbiota and metabolites. The results indicated that L. salivarius reduced MG colonization significantly and alleviated the anomalous morphological changes by using the MG-infection model. L. salivarius also reduced the level of Th1 cell cytokines, increased the level of Th2 cell cytokines, and ameliorated immune imbalance during MG infection. In addition, L. salivarius improved the mucosal barrier, heightened immune function, and suppressed the Janus kinase/Signal transducer, and activator of transcription (JAK/STAT) signaling pathway. Notably, MG infection changed the composition of the respiratory microbiota and metabolites, and L. salivarius therapy partially reversed the aberrant respiratory microbiota and metabolite composition. Our results highlighted that these findings demonstrated that L. salivarius played a role in MG-mediated inflammatory damage and demonstrated that L. salivarius, by altering the respiratory microbiota and metabolites, could successfully prevent MG-induced inflammatory injury in chicken trachea.

The intratumoral microbiota: a new horizon in cancer immunology

Over the past decade, advancements in high-throughput sequencing technologies have led to a qualitative leap in our understanding of the role of the microbiota in human diseases, particularly in oncology. Despite the low biomass of the intratumoral microbiota, it remains a crucial component of the tumor immune microenvironment, displaying significant heterogeneity across different tumor tissues and individual patients. Although immunotherapy has emerged a major strategy for treating tumors, patient responses to these treatments vary widely. Increasing evidence suggests that interactions between the intratumoral microbiota and the immune system can modulate host tumor immune responses, thereby influencing the effectiveness of immunotherapy. Therefore, it is critical to gain a deep understanding of how the intratumoral microbiota shapes and regulates the tumor immune microenvironment. Here, we summarize the latest advancements on the role of the intratumoral microbiota in cancer immunity, exploring the potential mechanisms through which immune functions are influenced by intratumoral microbiota within and outside the gut barrier. We also discuss the impact of the intratumoral microbiota on the response to cancer immunotherapy and its clinical applications, highlighting future research directions and challenges in this field. We anticipate that the valuable insights into the interactions between cancer immunity and the intratumoral microbiota provided in this review will foster the development of microbiota-based tumor therapies.

Selection versus transmission: Quantitative and organismic biology in antibiotic resistance

We aimed to determine the importance of selection (mostly dependent on the anthropogenic use of antimicrobials) and transmission (mostly dependent on hygiene and sanitation) as drivers of the spread of antibiotic-resistant bacterial populations. The first obstacle to estimating the relative weight of both independent variables is the lack of detailed quantitative data concerning the number of bacterial cells, potentially either pathogenic or harmless, and bacterial species exposed to antimicrobial action in the microbiotas of specific environments. The second obstacle is the difficulty of considering the relative importance of the transmission and selection exerting their combined effects on antibiotic resistance across eco-biological levels. As a consequence, advances are urgently required in quantitative biology and organismic biology of antimicrobial resistance. The absolute number of humans exposed to antibiotics and the absolute number of potentially pathogenic and commensal bacteria in their microbiomes should influence both the selection and transmission of resistant bacterial populations. The "whole Earth" microbiome, with astonishingly high numbers of bacterial cells and species, which are also exposed to anthropogenic antimicrobials in various biogeographical spaces, shapes the antibiotic resistance landscape. These biogeographical spaces influence various intensities of selection and transmission of potentially pathogenic bacteria. While waiting for more precise data, biostatistics analysis and mathematical or computational modeling can provide proxies to compare the influence of selection and transmission in resistant bacteria. In European countries with lower sanitation levels, antibiotic consumption plays a major role in increasing antibiotic resistance; however, this is not the case in countries with high sanitation levels. Although both independent variables are linked, their relative influence on the level of antibiotic resistance varies according to the particular location. Therefore, interventions directed to decrease antibiotic resistance should be designed "a la carte" for specific locations with particular ecological conditions, including sanitation facilities.

Airway microbiome signature accurately discriminates Mycobacterium tuberculosis infection status

Mycobacterium tuberculosis remains one of the deadliest infectious agents globally. Amidst efforts to control TB, long treatment duration, drug toxicity, and resistance underscore the need for novel therapeutic strategies. Despite advances in understanding the interplay between microbiome and disease in humans, the specific role of the microbiome in predicting disease susceptibility and discriminating infection status in tuberculosis still needs to be fully investigated. We investigated the impact of M.tb infection and M.tb-specific IFNγ immune responses on airway microbiome diversity by performing TB GeneXpert and QuantiFERON-GOLD assays during the follow-up phase of a longitudinal HIV-Lung Microbiome cohort of individuals recruited from two large independent cohorts in rural Uganda. M.tb rather than IFNγ immune response mainly drove a significant reduction in airway microbiome diversity. A microbiome signature comprising Streptococcus, Neisseria, Fusobacterium, Prevotella, Schaalia, Actinomyces, Cutibacterium, Brevibacillus, Microbacterium, and Beijerinckiacea accurately discriminated active TB from Latent TB and M.tb-uninfected individuals.

Time to re-set our thinking about airways disease: lessons from history, the resurgence of chronic bronchitis / PBB and modern concepts in microbiology

In contrast to significant declines in deaths due to lung cancer and cardiac disease in Westernised countries, the mortality due to 'chronic obstructive pulmonary disease' (COPD) has minimally changed in recent decades while 'the incidence of bronchiectasis' is on the rise. The current focus on producing guidelines for these two airway 'diseases' has hindered progress in both treatment and prevention. The elephant in the room is that neither COPD nor bronchiectasis is a disease but rather a consequence of progressive untreated airway inflammation. To make this case, it is important to review the evolution of our understanding of airway disease and how a pathological appearance (bronchiectasis) and an arbitrary physiological marker of impaired airways (COPD) came to be labelled as 'diseases'. Valuable insights into the natural history of airway disease can be obtained from the pre-antibiotic era. The dramatic impacts of antibiotics on the prevalence of significant airway disease, especially in childhood and early adult life, have largely been forgotten and will be revisited as will the misinterpretation of trials undertaken in those with chronic (bacterial) bronchitis. In the past decades, paediatricians have observed a progressive increase in what is termed 'persistent bacterial bronchitis' (PBB). This condition shares all the same characteristics as 'chronic bronchitis', which is prevalent in young children during the pre-antibiotic era. Additionally, the radiological appearance of bronchiectasis is once again becoming more common in children and, more recently, in adults. Adult physicians remain sceptical about the existence of PBB; however, in one study aimed at assessing the efficacy of antibiotics in adults with persistent symptoms, researchers discovered that the majority of patients exhibiting symptoms of PBB were already on long-term macrolides. In recent decades, there has been a growing recognition of the importance of the respiratory microbiome and an understanding of the ability of bacteria to persist in potentially hostile environments through strategies such as biofilms, intracellular communities, and persister bacteria. This is a challenging field that will likely require new approaches to diagnosis and treatment; however, it needs to be embraced if real progress is to be made.

Controlling the expression of heterologous genes in Bdellovibrio bacteriovorus using synthetic biology strategies

Bdellovibrio bacteriovorus HD100 is an obligate predatory bacterium that preys upon Gram-negative bacteria. It has been proposed to be applied as a "living antibiotic" in several fields such as agriculture or even medicine, since it is able to prey upon bacterial pathogens. Its interesting lifestyle makes this bacterium very attractive as a microbial chassis for co-culture systems including two partners. A limitation to this goal is the scarcity of suitable synthetic biology tools for predator domestication. To fill this gap, we have firstly adapted the hierarchical assembly cloning technique Golden Standard (GS) to make it compatible with B. bacteriovorus HD100. The chromosomal integration of the Tn7 transposon's mobile element, in conjunction with the application of the GS technique, has allowed the systematic characterization of a repertoire of constitutive and inducible promoters, facilitating the control of the expression of heterologous genes in this bacterium. PJExD/EliR proved to be an exceptional promoter/regulator system in B. bacteriovorus HD100 when precise regulation is essential, while the synthetic promoter PBG37 showed a constitutive high expression. These genetic tools represent a step forward in the conversion of B. bacteriovorus into an amenable strain for microbial biotechnology approaches.

Bacteriocins: potentials and prospects in health and agrifood systems

Bacteriocins are highly diverse, abundant, and heterogeneous antimicrobial peptides that are ribosomally synthesized by bacteria and archaea. Since their discovery about a century ago, there has been a growing interest in bacteriocin research and applications. This is mainly due to their high antimicrobial properties, narrow or broad spectrum of activity, specificity, low cytotoxicity, and stability. Though initially used to improve food quality and safety, bacteriocins are now globally exploited for innovative applications in human, animal, and food systems as sustainable alternatives to antibiotics. Bacteriocins have the potential to beneficially modulate microbiota, providing viable microbiome-based solutions for the treatment, management, and non-invasive bio-diagnosis of infectious and non-infectious diseases. The use of bacteriocins holds great promise in the modulation of food microbiomes, antimicrobial food packaging, bio-sanitizers and antibiofilm, pre/post-harvest biocontrol, functional food, growth promotion, and sustainable aquaculture. This can undoubtedly improve food security, safety, and quality globally. This review highlights the current trends in bacteriocin research, especially the increasing research outputs and funding, which we believe may proportionate the soaring global interest in bacteriocins. The use of cutting-edge technologies, such as bioengineering, can further enhance the exploitation of bacteriocins for innovative applications in human, animal, and food systems.

Insights into the role of the respiratory tract microbiome in defense against bacterial pneumonia

The respiratory tract microbiome (RTM) is a microbial ecosystem inhabiting different niches throughout the airway. A critical role for the RTM in dictating lung infection outcomes is underlined by recent efforts to identify community members benefiting respiratory tract health. Obligate anaerobes common in the oropharynx and lung such as Prevotella and Veillonella are associated with improved pneumonia outcomes and activate several immune defense pathways in the lower airway. Colonizers of the nasal cavity, including Corynebacterium and Dolosigranulum, directly impact the growth and virulence of lung pathogens, aligning with robust clinical correlations between their upper airway abundance and reduced respiratory tract infection risk. Here, we highlight recent work identifying respiratory tract bacteria that promote airway health and resilience against disease, with a focus on lung infections and the underlying mechanisms driving RTM-protective benefits.

The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia

Bacterial pneumonia is a considerable problem worldwide. Here, we follow the inter-kingdom respiratory tract microbiome (RTM) of a unique cohort of 38 hospitalized patients (n = 97 samples) with pneumonia caused by Legionella pneumophila. The RTM composition is characterized by diversity drops early in hospitalization and ecological species replacement. RTMs with the highest bacterial and fungal loads show low diversity and pathogen enrichment, suggesting high biomass as a biomarker for secondary and/or co-infections. The RTM structure is defined by a "commensal" cluster associated with a healthy RTM and a "pathogen" enriched one, suggesting that the cluster equilibrium drives the microbiome to recovery or dysbiosis. Legionella biomass correlates with disease severity and co-morbidities, while clinical interventions influence the RTM dynamics. Fungi, archaea, and protozoa seem to contribute to progress of pneumonia. Thus, the interplay of the RTM equilibrium, the pathogen load dynamics, and clinical interventions play a critical role in patient recovery.

Developmental progression of the nasopharyngeal microbiome during childhood and association with the lower airway microbiome

Background

The upper (URT) and lower (LRT) respiratory tract feature distinct environments and responses affecting microbial colonization but investigating the relationship between them is technically challenging. We aimed to identify relationships between taxa colonizing the URT and LRT and explore their relationship with development during childhood.

Methods

We employed V4 16S rDNA sequencing to profile nasopharyngeal swabs and tracheal aspirates collected from 183 subjects between 20 weeks and 18 years of age. These samples were collected prior to elective procedures at the Children's Hospital of Philadelphia over the course of 20 weeks in 2020, from otherwise healthy subjects enrolled in a study investigating potential reservoirs of SARS-CoV-2.

Findings

After extraction, sequencing, and quality control, we studied the remaining 124 nasopharyngeal swabs and 98 tracheal aspirates, including 85 subject-matched pairs of samples. V4 16S rDNA sequencing revealed that the nasopharynx is colonized by few, highly-abundant taxa, while the tracheal aspirates feature a diverse assembly of microbes. While no taxa co-occur in the URT and LRT of the same subject, clusters of microbiomes in the URT correlate with clusters of microbiomes in the LRT. The clusters identified in the URT correlate with subject age across childhood development.

Interpretations

The correlation between clusters of taxa across sites may suggest a mutual influence from either a third site, such as the oropharynx, or host-extrinsic, environmental features. The identification of a pattern of upper respiratory microbiota development across the first 18 years of life suggests that the patterns observed in early childhood may extend beyond the early life window.