The microbiota of the respiratory tract: gatekeeper to respiratory health

As a library, NLM provides access to scientific literature. Inclusion in an NLM database does not imply endorsement of, or agreement with, the contents by NLM or the National Institutes of Health.

Learn more: PMC Disclaimer | PMC Copyright Notice

Nat Rev Microbiol. 2017; 15(5): 259–270.

Author information Copyright and License information PMC Disclaimer

Go to:

Key Points

• The anatomical development and maturation of the human respiratory tract is a complex multistage process that occurs not only in prenatal life but also postnatally. This maturation process depends, in part, on exposure to microbial and environmental triggers, and results in a highly specialized organ system that contains several distinct niches, each of which is subjected to specific microbial, cellular and physiological gradients.
• The respiratory microbiome during early life is dynamic and its development is affected by a range of host and environmental factors, including mode of birth, feeding type, antibiotic treatment and crowding conditions, such as the presence of siblings and day-care attendance.
• The upper respiratory tract is colonized by specialized resident bacterial, viral and fungal assemblages, which presumably prevent potential pathogens from overgrowing and disseminating towards the lungs, thereby functioning as gatekeepers to respiratory health.
• The upper respiratory tract is the primary source of the lung microbiome. In healthy individuals, the lung microbiome seems to largely consist of transient microorganisms and its composition is determined by the balance between microbial immigration and elimination.
• Next-generation sequencing has identified intricate interbacterial association networks that comprise true mutualistic, commensal or antagonistic direct or indirect relationships. Alternatively, bacterial co-occurrence seems to be driven by host and environmental factors, as well as by interactions with viruses and fungi.
• The respiratory microbiome provides cues to the host immune system that seem to be vital for immune training, organogenesis and the maintenance of immune tolerance. Increasing evidence supports the existence of a window of opportunity early in life, during which adequate microbiota sensing is essential for immune maturation and consecutive respiratory health.
• Future studies should focus on large-scale, multidisciplinary holistic approaches and adequately account for host and environmental factors. Associations that are identified by these studies can then be corroborated in reductionist surveys; for example, by using in vitro or animal studies.

Supplementary information

The online version of this article (doi:10.1038/nrmicro.2017.14) contains supplementary material, which is available to authorized users.

Subject terms: Pathogens, Microbiome, Respiratory tract diseases, Clinical microbiology, Symbiosis, Infectious-disease epidemiology

The respiratory tract spans from the nostrils to the lung alveoli and these distinct niches host a diverse microbiota. In this Review, Man, de Steenhuijsen Piters and Bogaert discuss the role of the respiratory microbiota in the maintenance of human health.

Supplementary information

The online version of this article (doi:10.1038/nrmicro.2017.14) contains supplementary material, which is available to authorized users.

Subject terms: Pathogens, Microbiome, Respiratory tract diseases, Clinical microbiology, Symbiosis, Infectious-disease epidemiology

Go to:

Abstract

The respiratory tract is a complex organ system that is responsible for the exchange of oxygen and carbon dioxide. The human respiratory tract spans from the nostrils to the lung alveoli and is inhabited by niche-specific communities of bacteria. The microbiota of the respiratory tract probably acts as a gatekeeper that provides resistance to colonization by respiratory pathogens. The respiratory microbiota might also be involved in the maturation and maintenance of homeostasis of respiratory physiology and immunity. The ecological and environmental factors that direct the development of microbial communities in the respiratory tract and how these communities affect respiratory health are the focus of current research. Concurrently, the functions of the microbiome of the upper and lower respiratory tract in the physiology of the human host are being studied in detail. In this Review, we will discuss the epidemiological, biological and functional evidence that support the physiological role of the respiratory microbiota in the maintenance of human health.

Supplementary information

The online version of this article (doi:10.1038/nrmicro.2017.14) contains supplementary material, which is available to authorized users.

Subject terms: Pathogens, Microbiome, Respiratory tract diseases, Clinical microbiology, Symbiosis, Infectious-disease epidemiology

Go to:

Main

Microbial communities have co-evolved with humans and our ancestors for millions of years and they inhabit all surfaces of the human body, including the respiratory tract mucosa. Specific sites in the respiratory tract contain specialized bacterial communities that are thought to have a major role in the maintenance of human health. In the past decade, next-generation sequencing has led to major advances in our understanding of the possible functions of the resident microbiota. So far, research has largely focused on the gut microbiota and gut microbiota-derived metabolites, and their influence on host metabolism and immunity. However, recent studies on microbial ecosystems at other body sites, including the respiratory tract, reveal an even broader role for the microbiota in human health1.

The respiratory tract is a complex organ system that is divided into the upper respiratory tract (URT) and the lower respiratory tract (LRT). The URT includes the anterior nares, nasal passages, paranasal sinuses, the nasopharynx and oropharynx, and the portion of the larynx above the vocal cords, whereas the LRT includes the portion of the larynx below the vocal cords, the trachea, smaller airways (that is, bronchi and bronchioli) and alveoli. The primary function of the respiratory tract in human physiology is the exchange of oxygen and carbon dioxide. For this purpose, the adult human airways have a surface area of approximately 70 m2, which is 40 times larger than the surface area of the skin2. This entire surface is inhabited by niche-specific bacterial communities, with the highest bacterial densities observed in the URT (Fig. 1). Over the years, evidence for the roles that bacterial communities in the URT have in preventing respiratory pathogens from establishing an infection on the mucosal surface and spreading to the LRT has accumulated. For most respiratory bacterial pathogens, colonization of the URT is a necessary first step before causing an upper, lower or disseminated respiratory infection3. Inhibition of this first step of pathogenesis for respiratory infections by the resident microbiota, a process that is also called 'colonization resistance', might be of paramount importance to respiratory health. Furthermore, if a pathogen has colonized the mucosal surface, it might be beneficial to both the microbial community and the host that these pathogens are kept at bay, preventing their overgrowth, inflammation and subsequent local or systemic spread4. In addition to this symbiotic relationship, the respiratory microbiota probably has a role in the structural maturation of the respiratory tract5 and in shaping local immunity67.

Click on image to zoom

Figure 1

Physiological and microbial gradients along the respiratory tract.

Physiological and microbial gradients exist along the nasal cavity, nasopharynx, oropharynx, trachea and the lungs. The pH gradually increases along the respiratory tract177178179180, whereas most of the increases in relative humidity (RH) and temperature occur in the nasal cavity181182183. Furthermore, the partial pressures of oxygen (pO2) and carbon dioxide (pCO2) have opposing gradients180 that are determined by environmental air conditions and gas exchange at the surface of the lungs181184185. Inhalation results in the deposition of particles from the environment into the respiratory tract; inhaled particles that are more than 10 μm in diameter are deposited in the upper respiratory tract (URT), whereas particles less than 1 μm in diameter can reach the lungs. These particles include bacteria-containing and virus-containing particles, which are typically larger than 0.4 μm in diameter186. These physiological parameters determine the niche-specific selective growth conditions that ultimately shape the microbial communities along the respiratory tract. The unit by which bacterial density is measured varies per niche; the density in the environment is depicted as bacteria per cm3 (indoor) air187, density measures in the nasal cavity and nasopharynx are shown as an estimated number of bacteria per nasal swab74, and the densities in the oropharynx and the lungs represent the estimated number of bacteria per ml of oral wash5774 or bronchoalveolar lavage (BAL)5774153, respectively.

PowerPoint slide

Current research questions address how the healthy respiratory microbiota is established and what ecological and environmental factors govern its development. Concurrently, the broad range of functions of the respiratory microbiome is starting to become clear. In this Review, we focus on the role that the respiratory microbiota has in the development and maintenance of human respiratory health.

Go to:

Anatomical development and the microbiota

Anatomical development and physiology. The development of the structures of the human respiratory tract is a complex multistage process that begins in the fourth week of gestation with the development of the nasal placodes, the oropharyngeal membrane and the lung buds89. The anatomy of the URT at birth is substantially different from the configuration in adults owing to the higher position of the larynx, which results in a large nasopharynx relative to the oropharynx10. In addition, the lack of alveoli in the newborn lungs underlines the immaturity of the LRT at birth. Indeed, the formation of alveoli begins in a late fetal stage and their development continues throughout the first three years of life11. By adulthood, many distinct subcompartments have developed in the respiratory tract, each of which has specific microbial, cellular and physiological features, such as oxygen and carbon dioxide tension, pH, humidity and temperature (Fig. 1).

Microbiota and the morphogenesis of the respiratory tract. Similar to the anatomical development of the respiratory tract, the initial acquisition of microorganisms marks the establishment of the respiratory microbiota in early life. The establishment of the respiratory microbiota is thought to have an effect on the morphogenesis of the respiratory tract. Indeed, germ-free rodents tend to have smaller lungs12 and a decreased number of mature alveoli5. The latter finding was supported by experiments in which the nasal cavities of germ-free mouse pups were colonized with Lactobacillus spp., after which the number of mature alveoli normalized5. Intriguingly, the nasopharyngeal-associated lymphoid tissue (NALT) also develops mostly after birth, which suggests that its development requires environmental cues — for example, from the local microbiota13.

Development of healthy microbiota. In contrast to the long-standing hypothesis that we are born sterile, it was recently suggested that babies acquire microorganisms in utero1415, although this suggestion is controversial16. Irrespectively, the transfer of maternal antibodies and microbial molecules in utero markedly influences postnatal immune development1718. This, in turn, primes the newborn for the substantial exposure to microorganisms that occurs after birth. During the first hours of life, a wide range of microorganisms can be detected in the URT of healthy term neonates1920. At first, these microorganisms are nonspecific and are of presumed maternal origin. During the first week of life, niche differentiation in the URT leads to a high abundance of Staphylococcus spp., followed by the enrichment of Corynebacterium spp. and Dolosigranulum spp., and the subsequent predominance of Moraxella spp.20. Microbiota profiles that are characterized by Corynebacterium spp. and Dolosigranulum spp. early in life, and Moraxella spp. at 4–6 months of age, have been shown to correlate to a stable bacterial community composition and respiratory health2122.

Birth mode and feeding type are important drivers of the early maturation of the microbiota, with children who are born vaginally and/or are breastfed transitioning towards a presumed health-promoting microbiota profile more often and more swiftly2023. These findings were corroborated by epidemiological findings that showed breastfeeding-mediated protection against infections24, which is presumably a consequence of the transfer of maternal antibodies18 and beneficial microorganisms in breast milk, such as Bifidobacterium spp. and Lactobacillus spp.2526. Conversely, the development of the respiratory microbiota can be disturbed, for example, through the use of antibiotics, which are commonly used in young children to treat infections27. Antibiotic perturbations were characterized by a decreased abundance of presumed beneficial commensal bacteria, such as Dolosigranulum spp. and Corynebacterium spp. in the URT of healthy children222829. This, in turn, might increase the risk of respiratory tract infections following antibiotic treatment30. In addition, season, vaccination, presence of siblings, day-care attendance, exposure to smoke and prior infections can also affect the infant microbiota223132333435, which indicates that the microbiota during early life is dynamic and affected by numerous host and environmental factors (Fig. 2). Host genetics seems to have a minor effect on the URT microbiota in healthy individuals, only influencing nasal bacterial density and not the composition of the microbiota36. By contrast, the composition of the sputum microbiota seems to be influenced equally by host genetics and environmental factors37.

Figure 2

Host and environmental factors that influence the respiratory microbiota.

During early life, microbial communities in the respiratory tract are highly dynamic and are driven by multiple factors, including mode of birth, feeding type, crowding conditions and antibiotic treatment. Together, these host and environmental factors can change the composition of the microbiota towards a stable community at equilibrium that is resistant to pathogen overgrowth, or, conversely, an unstable community develops that is predisposed to infection and inflammation.

PowerPoint slide

Although the gut microbiota matures into an adult-like community during the first 3 years of life38, the time that is required to establish a stable respiratory microbiota remains to be determined. Although niche differentiation occurs as early as 1 week after birth20, the respiratory microbiota evolves throughout the first few years of life213339. After the respiratory microbiota is established, antibiotic treatment remains an important perturbing factor of the microbial equilibrium throughout life40. Active smoking also affects the microbial communities in the URT3741; however, in the LRT, smoking has no clear influence on the composition of the microbiota42. Interestingly, it has been suggested that the niche-specific differences disappear again in the elderly43.

Remarkably, not only exposure to beneficial bacteria seems to be important but also the timing of these exposures seems to play a crucial part in the maintenance of respiratory health, as especially aberrant respiratory colonization patterns in infancy seem to be a major determinant of respiratory disease later in life212244. This could be due to the effect of host–microbial interactions in immune education during early life6. It has been proposed that the dynamic nature of the developing microbiota early in life might provide a window of opportunity for the modulation of the microbiota towards a beneficial composition45; however, the extent of this period of time is currently unknown.

Go to:

The microbiota of the upper respiratory tract

Gatekeeper to respiratory health. The URT consists of distinct anatomical structures that have different epithelial cell types and is exposed to various environmental factors. These diverse micro-niches are colonized by specialized bacterial communities, viruses and fungi.

The anterior nares are closest to the external environment and are lined with a skin-like keratinized squamous epithelium, including serous and sebaceous glands, the latter of which produces sebum, which leads to the enrichment of lipophilic skin colonizers, including Staphylococcus spp., Propionibacterium spp. and Corynebacterium spp.464748. Bacteria that are frequently found in other respiratory niches, including Moraxella spp., Dolosigranulum spp. and Streptococcus spp., have also been observed in the anterior nares29434849. The nasopharynx is located deeper in the nasal cavity and is covered by a stratified squamous epithelium that is punctuated by patches of respiratory epithelial cells. The composition of the bacterial communities in the nasopharynx is more diverse than in the anterior parts50 and demonstrates considerable overlap with the anterior nares; it also contains Moraxella spp., Staphylococcus spp. and Corynebacterium spp. However, other bacteria more typically inhabit the nasopharyngeal niche, most notably Dolosigranulum spp., Haemophilus spp. and Streptococcus spp.20212233. The oropharynx, which is lined with a non-keratinized stratified squamous epithelium, has more diverse bacterial communities than the nasopharynx41, which are characterized by streptococcal species, Neisseria spp., Rothia spp. and anaerobes, including Veillonella spp., Prevotella spp. and Leptotrichia spp.39415152.

In addition to bacterial inhabitants, PCR-based studies suggest the extensive presence of viral pathogens in the URT. These studies have reported an overall detection rate of 67% for respiratory viruses in healthy asymptomatic children, including human rhinovirus (HRV), human bocavirus, polyomaviruses, human adenovirus and human coronavirus3153. However, recent advances in metagenomics have revealed that the entire respiratory virome contains many other viruses. For example, the recently discovered Anelloviridae family was identified as the most prevalent virus family in the virome of the URT5455. Moreover, the healthy URT has a mycobiota that includes Aspergillus spp., Penicillium spp., Candida spp. and Alternaria spp.5657. Although the size of the respiratory mycobiome is unknown, the gut and skin mycobiomes are approximated to comprise 0.1% and 3.9%, respectively, of the total microbiome in their corresponding niches4758.

Environmental pressures, as well as microorganism–microorganism and host–microorganism interactions, influence the composition of the bacterial ecosystem in the human host and, as a consequence, its function. For various macroscale ecosystems, such as forests and coral reefs, it is well established that greater biodiversity increases the efficiency by which ecological communities are capable of using essential resources59. Similarly, the diversity of specific microscale ecosystems in the human host, such as the gut microbiota, has been associated with health outcomes. For example, increased diversity of intestinal bacteria has been linked to the absence of inflammatory bowel disease, obesity60 and resistance against acute infections by enteropathogens61. Conversely, at other body sites, such as the vagina, low bacterial diversity is considered 'healthy' as it is associated with decreased incidences of bacterial vaginosis6263 and premature birth64, which highlights the niche-specific effect of biodiversity on human health. In the respiratory tract, evidence indicates that acute URT infections, such as acute otitis media (AOM)2965, and mucosal inflammation in chronic rhinosinusitis66 are associated with a decrease in the diversity of local bacterial communities. However, other studies report a less clear association between diversity and respiratory health, which suggests that the composition of bacterial communities, in a niche- specific ecological context, also affects respiratory health52. Moreover, certain members of the microbiota, known as 'keystone species', may have exceptionally large beneficial effects on ecosystem balance, function and health67. Potential keystone species in the URT microbiota are Dolosigranulum spp. and Corynebacterium spp., as they have been strongly associated with respiratory health and the exclusion of potential pathogens, most notably Streptococcus pneumoniae, in several epidemiological and mechanistic studies21296869.

A primary function of any microbial ecosystem is to elicit a state of symbiosis, providing 'colonization resistance' against pathogens470. The principal mechanism that underlies colonization resistance is that members of a diverse local microbiome probably use all of the nutrients that are available, thereby preventing pathogens from finding the necessary resources for colonization. Although cross-sectional surveys have demonstrated associations between decreased diversity and pathogen colonization, no direct evidence exists that demonstrates that increased microbial diversity in the respiratory tract can protect against the acquisition of pathogens. However, specific members of the microbiota have been identified that can actively exclude pathogens from the nasopharyngeal niche. For example, Staphylococcus epidermidis was shown to exclude Staphylococcus aureus and destroy pre-existing biofilms through the secretion of serine proteases71. Furthermore, colonization resistance may be enhanced by interactions with the host immune system. For example, neutrophils seemed more able to kill S. pneumoniae following priming with Haemophilus influenzae72.

The URT is generally considered to be a major reservoir for potential pathogens, including S. pneumoniae, to expand and subsequently spread towards the lungs, which could potentially lead to a symptomatic infection3. Thus, establishing and maintaining a balanced microbiota in the URT that is resilient to pathogenic expansion and invasion could prove vital for respiratory health. The mechanisms that underlie a healthy respiratory microbiota, as well as specific microbiota–host interactions that support this, are considered below.

Go to:

Healthy lungs and their microbiota

The LRT comprises the conducting airways (the trachea, bronchi and bronchioles) and the alveoli, in which gas exchange takes place. The conducting airways are lined with a similar respiratory epithelium to that found in the URT, with the epithelial cells gradually shifting towards a cuboidal shape along the respiratory tree. The alveoli in the lungs are lined with functionally distinct alveolar epithelial cells. In contrast to the URT and other human mucosal sites, the LRT has traditionally been considered as sterile; however, recent studies that used next- generation sequencing discovered a wide range of diverse microbial species in samples taken from the LRT. Potential contamination of low-density specimens remains a major concern when carrying out these types of study and caution is required when interpreting the results (Box 1).

Source of the lung microbiota. In healthy individuals, bacteria enter the lungs by direct mucosal dispersion and micro-aspiration from the URT73. Culture-independent microbiota studies have confirmed that the lung microbiota largely resembles the URT microbiota when studied in healthy individuals747576. The oropharynx seems to be the main source of the lung microbiota in adults74, whereas in children the source is more likely to be both the nasopharynx and oropharynx76. This might be due to the difference in the anatomy of the URT and the frequent increased production of nasal secretions in children, which both probably enhance the dispersal of microorganisms to the lungs. Another potential source of bacteria in the LRT is the direct inhalation of ambient air, albeit, to date, its direct influence on the lung microbiome is unknown. The contribution of the gastric microbiota to the microbial community in the LRT through gastric–oesophageal reflux has, until now, been suggested to be negligible74.

Composition of the lung microbiota. As LRT sampling is particularly challenging in young infants (Box 1), current data on the composition and development of the neonatal LRT microbiota is limited to samples from intubated prematurely born infants777879. These studies showed that the LRT microbiota of premature infants is dominated by pathogenic Staphylococcus spp.7879, Ureaplasma spp.79 or Acinetobacter spp.77, which highlights the lack of complexity in these developing bacterial communities.

In healthy children and adults, a unique microbial community in the lungs was found that contained many of the bacteria that are common to the URT. A study in young children reported that although the lung microbiota was distinct from the microbiota of the URT, it was dominated by species that are also present in the URT, including Moraxella spp., Haemophilus spp., Staphylococcus spp. and Streptococcus spp., but lacked other typical URT species, such as Corynebacterium spp. and Dolosigranulum spp.76. The adult lung microbiota seems to be dominated by genera in the phyla Firmicutes (including Streptococcus spp. and Veillonella spp.) and Bacteroidetes (including Prevotella spp.)427580. Interestingly, Tropheryma whipplei seems enriched only in the LRT, which suggests that this might be one of the few bacterial species that is not derived through dispersal from the URT427580.

Studies of the LRT virome have revealed a high prevalence of members of the Anelloviridae family, in addition to a high frequency of bacteriophages818283. Furthermore, the healthy lung mycobiome was found to be predominantly composed of members of the Eremothecium, Systenostrema and Malassezia genera, and the Davidiellaceae family, with common fungi in the URT detected only in low abundance578485.

Although there are subtle regional variations of physiological parameters in the lungs (for example, of oxygen tension, pH and temperature), which, in theory, could affect microbial selection and growth, spatial microbial diversity in the lungs of healthy individuals seems almost absent758086. This supports the hypothesis that, in health, the lung microbiota is a community of transiently present microorganisms that are derived from the URT, rather than a thriving, resident community as is commonly found in chronic respiratory diseases808788. Correspondingly, a recently proposed ecological model, the adapted island model, postulates that the composition of a healthy lung microbiota is determined by the balance of microbial immigration and elimination8088. Regardless, to date, the exact function that the lung microbiome has in establishing and maintaining respiratory health is unclear, although it probably contributes substantially to mucosal immune homeostasis (Box 2).

Box 1: Technical challenges in respiratory microbiome research

Respiratory microbiome research faces general and niche-specific challenges. The absence of uniform laboratory practices (sample storage, DNA isolation and choice of 16S rRNA variable region) and bioinformatics and data analysis pipelines limits the potential to carry out accurate comparative or meta-analyses. Although different research questions require different approaches, more energy should be invested into the development of standardized operating procedures that are comparable to, for example, the Earth Microbiome project protocol152.

A specific challenge in microbiota surveys of the respiratory tract is the low density of bacterial communities that are found there, particularly in healthy individuals; densities as low as 102–103 bacteria ml−1 have been reported in bronchoalveolar lavages (BALs) of healthy individuals74153. Such low quantities of DNA preclude whole-genome sequencing, which results in hindered taxonomic resolution and functional interpretation of microbiome data. Furthermore, sampling of the lower respiratory tract (LRT) is cumbersome and is typically based on BAL or the collection of expectorated sputum. Both sampling methods carry a high risk of cross-contamination of the LRT samples with resident bacterial communities in the upper respiratory tract (URT). Distinguishing between authentic LRT communities and URT contamination is further complicated because of the anatomical link between both niches. Once bacterial DNA has been extracted, the quantity can be so low that contamination from environmental DNA invalidates the results154155. The development of standard operating procedures, including the careful use of appropriate negative controls at different stages of the sampling and laboratory workflow, can help to identify and exclude sequences from contaminating sources20156.

Box 2: Specific host–microbiota interactions that contribute to tolerance

The respiratory microbiota has been hypothesized to control mucosal immunity in early life and contribute to immune tolerance. For example, members of the Bacteroidetes phylum, such as Prevotella spp., decrease lung inflammation, neutrophil recruitment and the production of Toll-like receptor 2 (TLR2)-mediated pro-inflammatory cytokines compared with Haemophilus influenzae in a mouse model157, which could be related to the number of acyl side chains on their respective lipopolysaccharide (LPS) molecules158159160. Furthermore, in vitro activation of epithelial TLRs and nucleotide-binding oligomerization domain (NOD)-like receptors induced the release of antimicrobial peptides, such as β-defensin 2 (Ref. 138), which could potentially influence the composition of the upper respiratory tract (URT) microbiota161. The production of these antimicrobial peptides is stimulated by T helper 17 (TH17) cells162, which, in turn, were shown to be induced by specific microbial species163.

Intriguingly, immune signalling in the URT was shown to elicit responses in distally located mucosal tissues; intranasal inoculation of Staphylococcus aureus led to the TLR2-induced recruitment of monocytes to the lungs, in which they differentiated into immunosuppressive alveolar macrophages and subsequently dampened influenza virus-induced inflammatory responses164. Intranasal administration of Lactobacillus plantarum led to TLR2 and NOD2 receptor-mediated protection against lethal pneumovirus infection in the lungs of mice165. In addition, gut microbiota-induced priming of innate immune cells at the intestinal mucosa was shown to affect respiratory health; for example, through NOD1 receptor-mediated activation of the neutrophils that are required for the clearance of Streptococcus pneumoniae in the URT72166. Furthermore, in germ-free mice, inoculation with microorganisms was shown to be essential for the recruitment of dendritic cells to the lungs167, and the priming of CD8+ T cells168. Crosstalk between dendritic cells and T cells induces the release of immunoglobulin A (IgA) at the mucosal interface, which prevents pathogens from interacting with the epithelium and selects for a heterogeneous composition of the gut microbiota, facilitating the expansion of regulatory T cells (Treg cells)135 (Fig. 3).

Figure 3

Host–microbiota interactions in the respiratory tract.

Host–microbiota interactions in the respiratory tract occur mostly at the mucosal surface. Resident microorganisms prime immune cells either locally or systemically; these include epithelial cells, neutrophils and dendritic cells, which all contribute to the clearance of pathogens. Moreover, microbial signalling is necessary for the recruitment and activation of regulatory cells, such as anti-inflammatory alveolar macrophages (AMs) and regulatory T cells (Treg cells). Locally, the host will respond to microbial colonization through the release of antimicrobial peptides (AMPs) and secretory immunoglobulin A (sIgA). Sensing of the microbiota involves microfold (M) cells that activate tolerogenic dendritic cells. In addition, alveolar dendritic cells can directly sample luminal microorganisms. Together, these pathways lead to the regulation of inflammation and the induction of tolerance, which, in turn, shape resident bacterial communities. It is also plausible that early bacterial colonization is key to long-term immune regulation, which is illustrated by the microbiota-induced decrease in hypermethylation of the CXC-motif chemokine ligand 16 (Cxcl16) gene, which prevents the accumulation of inducible natural killer T cells (iNKT cells), and by the programmed death ligand 1 (PDL1)-mediated induction of tolerogenic dendritic cells (Box 3). This tolerant milieu, in turn, contributes to the normal development and maintenance of resident bacterial communities, which are also influenced by host and environmental factors (Fig. 1). AEC, alveolar epithelial cell; LPS: lipopolysaccharide; PRR: pattern recognition receptor; URT, upper respiratory tract.

PowerPoint slide

The most convincing evidence that the lung microbiota reciprocally affects local immune responses came from a study in healthy adults. In this study, specific lung bacteria (including Prevotella spp. and Veillonella spp.) were associated with an increased number of lymphocytes in bronchoalveolar lavage (BAL) fluid, TH17 cell-mediated lung inflammation and a diminished TLR4 response by alveolar macrophages126. Correspondingly, a positive correlation between the relative abundance of members of the phylum Proteobacteria and both alveolar and systemic inflammation was described for patients with acute respiratory distress syndrome (ARDS)169.

Go to:

Interbacterial relationships

Next-generation sequencing studies have revealed valuable information on both positive and negative microbial associations. By comparing sequencing data with mechanistic work, ecological interaction networks between microbial community members, or between the microbiota and the host or environment, can be partially reconstructed.

Associations between members of the microbiota can signify direct mutualism or commensalism (positive interactions), or antagonism (negative interactions). Positive interactions have been described primarily for members of the oropharyngeal microbiota; as such, Veillonella spp. were shown to induce streptococcal biofilm growth in a species-specific manner, presumably owing to shared quorum sensing systems89. These communication systems also seem to affect positive interactions between commensal and pathogenic members of the Streptococcus clade90, and between the nasopharyngeal community members Moraxella catarrhalis and H. influenzae91. Other mutualistic or commensal interactions in the nasopharyngeal microbiota exist, as illustrated by interactions between Corynebacterium spp. and Staphylococcus spp. The relationship between these species is complex and its directionality is probably species-specific or even strain-specific; Corynebacterium accolens and S. aureus mutually induce each other's growth through an unknown molecular mechanism50, whereas there are mixed reports about the interactions between Corynebacterium pseudodiphtheriticum and S. aureus465092. Furthermore, antagonistic relationships have been identified, such as those between S. aureus and S. pneumoniae32, that may, in part, be explained by the production of pneumococcal hydrogen peroxide, which results in lethal bacteriophage induction in S. aureus9394. Human experimental colonization with the commensal Neisseria lactamica reduces existing Neisseria meningitidis colonization and even protects against new meningococcal acquisition, although the exact mechanisms that underlie this antagonistic relationship are unknown95.

It could be postulated that, especially in early life, the human host may nourish and promote specific members of the microbiota, such as S. aureus, to benefit from the wide range of antimicrobial molecules that it produces; this could aid the human host in its defence against invading pathogens96. The fact that S. aureus is present in almost all infants but only sporadically causes disease at this age could, in turn, be related to specific microbial interactions; for example, co-occurrence with Corynebacterium striatum was shown to increase the commensal behaviour of S. aureus and decrease its virulence in an in vivo infection model97. Furthermore, interactions between species in the Staphylococcus genus might help to prevent S. aureus from overgrowing as well; for example, its colonization is hindered by serine protease activity in S. epidermidis71 and by the production of lugdunin by Staphylococcus lugdunensis, which is a natural antibiotic that is also active against other potential pathogens98.

Members of the microbiota might also modulate each other's growth in an indirect manner; for example, through outer membrane vesicle (OMV)-mediated immune evasion99, or by using specific properties of the local environment, as shown for C. accolens, which converts host triacylglycerols into free fatty acids (FFAs) that, in turn, limit pneumococcal growth68. A second example of these mechanisms is the frequent co-occurrence of Corynebacterium spp. and Dolosigranulum spp. in the nasopharynx202269, in which Dolosigranulum spp. might be responsible for the acidification of the local environment, which, in turn, may facilitate the expansion of Corynebacterium spp.; however, a direct interaction between these species cannot be ruled out. Given the low density and presumably transient microbiota in the LRT, it could be speculated that the diversity of this microbiota is shaped by interbacterial relationships to a lesser extent than bacterial communities in the URT, although little is known about the level of proximity and likelihood of interbacterial effects.

Bacterial associations that are detected in epidemiological surveys may also indicate the existence of joint host or environmental drivers and not the presence of direct or indirect microbial interactions per se. For example, the co-occurrence of C. accolens and Propionibacterium spp. on the lipid-rich mucosa of the anterior nares48 could be explained by solely their joint lipophilic nature. Furthermore, epidemiological data suggest positive associations between M. catarrhalis, H. influenzae and S. pneumoniae that could be mediated by biological interactions or be based on their shared association with crowding conditions (for example, the presence of young siblings and day-care attendance) and/or their frequent asymptomatic co-presence with respiratory viruses53100.

Go to:

Effect of the virome and mycobiome

Bidirectional viral–bacterial interactions. Perhaps the best-known historical example of viral–bacterial interactions in the respiratory tract comes from the Spanish flu pandemic in 1918–1919, when millions of individuals died from secondary bacterial pneumonia after an initial infection with influenza A virus101. In addition, in the absence of disease, epidemiological studies have suggested the presence of viral–bacterial interactions (reviewed in Ref. 102). The biological mechanisms that underlie these bidirectional interactions have been extensively studied, although mostly for viruses and bacteria that are known to cause respiratory diseases102.

One of the main modes of action by which respiratory viruses are thought to predispose individuals to bacterial disease is through the disruption of the airway–epithelial barrier, which facilitates the adhesion of bacterial pathogens103104105. Furthermore, it was demonstrated that influenza virus infection enhances colonization (especially by pneumococci) by liberating host-derived nutrients106 and by decreasing mucociliary clearance107. In addition, respiratory viruses can modulate innate and adaptive immune responses in the host, thereby promoting bacterial colonization and infection; for example, by impairing monocyte activity108, the extended desensitization of alveolar macrophages for Toll-like receptor (TLR)-ligands109, suppressing phagocytic capacity of alveolar macrophages110, and by inhibiting the production of antimicrobial peptides that is induced by T helper 17 cells111.

Vice versa, respiratory bacteria can also promote viral infection through numerous pathways112113114115116. For example, the upregulation of adhesion receptors, such as intercellular adhesion molecule 1 (ICAM1), was shown to increase the binding of HRV and respiratory syncytial virus (RSV) to epithelial cells and amplify pro-inflammatory responses114115116. These findings were substantiated by a recent clinical study that showed that nasopharyngeal colonization by S. pneumoniae and H. influenzae in infants is associated with an amplified systemic RSV-induced host immune response, plausibly resulting in more severe RSV infection117.

Conversely, the presence of specific bacterial species in the respiratory microbiota may impede viral infections. These interactions can be either direct118119 or indirect through the host immune system. For example, infection by influenza virus was shown to be less efficient following immune priming by lipopolysaccharide (LPS)-mediated TLR4 activation of innate immune cells120121. In fact, some studies suggest that LPS signalling is necessary for appropriate immune crosstalk and immune 'readiness' for future encounters with viruses122123.

In general, the infection of bacteria by bacteriophages seems to be omnipresent. This phenomenon has even resulted in the evolution of a diverse range of antiviral defence mechanisms in commensal bacteria124. Consequently, selective infection of specific bacterial strains may regulate the composition of the bacterial community and may facilitate the adaptation of the bacterial community to novel environments by preserving its diversity125. A recent study also reported a broad overlap between species-specific bacteriophages and the bacterial community diversity in the lungs, which suggests that substantial interactions between the microbiota and bacteriophages exist in the healthy respiratory tract as well126.

Fungal–bacterial interactions. Mechanistic insight into the interactions between fungi, bacteria and the host during health is scarce. However, it has been demonstrated in vitro and in vivo that the formation of biofilms by S. aureus, Streptococcus spp. and P. aeruginosa damages respiratory epithelia, which enables fungal biofilms to develop127128129. Furthermore, P. aeruginosa stimulates the growth of Aspergillus fumigatus through sensing volatile metabolites at a distance130. Conversely, Candida albicans was shown to increase the prevalence of P. aeruginosa in mice by impeding the production of reactive oxygen species (ROS) by alveolar macrophages131. To date, the exact role and breadth of the mechanisms by which fungi contribute to a healthy equilibrium in the respiratory tract have unfortunately remained unstudied.

Although studies suggest the importance of both the respiratory virome and mycobiome in respiratory health, there is a considerable knowledge gap in their exact contributions to health compared with the role of the bacterial microbiome. However, current evidence provides an important basis for further in-depth analyses of the interactions that exist between bacteria, viruses and fungi, as well as the effect of host and environmental factors on these interactions.

Go to:

Host–bacterial interactions

As there are a vast number of commensals and potential pathogens that inhabit the mucosa of the respiratory tract, a delicate equilibrium has to be maintained between immune sensing and tolerance of non-pathogenic commensals, and the containment of resident pathogens and new invaders. This fine balance is of specific importance to the LRT, as gaseous exchange is absolutely essential for human life and the lungs are exceptionally susceptible to damage from inflammatory responses. Below, we will provide an overview of the immune components that have a role in immune homeostasis in the URT and lungs. A detailed discussion of host–bacterial interactions and their role in immune homeostasis, organogenesis and immune education is provided in Boxes 23, respectively. In addition to bacteria, viruses may also promote host immune homeostasis (discussed in Box 4).

The respiratory tract is exposed to large quantities of airborne particles from the environment. The first line of defence is the mucus layer of the nasopharynx and conducting airways. The mucus traps these particles, including microbial pathogens, which are then cleared through ciliary action towards the oral cavity. In addition, the glycoproteins in the mucus accommodate resident microorganisms and prevent infection132, as evidenced by the decrease in antibacterial cytokines and the presence of phagocytosis-impaired macrophages in the lungs of mucin-deficient mice133.

The mucus layer contains immunoglobulin A (IgA) produced by activated B cells134 and can preclude pathogens from inhabiting the mucosal surface and interacting with epithelial surface receptors. IgA is also hypothesized to be involved in the regulation and selection of commensal microorganisms and establishing mutualistic host–microbial interactions135136. Similarly, alveolar surfactant has an important role in lung innate immunity, as a deficiency in surfactant protein A has been associated with decreased bacterial phagocytosis and killing by alveolar macrophages137.

The next line of defence is the epithelial cell layer, which is essential for the spatial segregation of the microbiota and the underlying lamina propria. The respiratory tract epithelium produces various antimicrobial substances that contribute to barrier function, including human β-defensin 2 (Ref. 138). Pharyngeal and lung epithelial cells, as well as macrophages and dendritic cells, have various receptors to sense the microbiota, including innate pattern recognition receptors (PRRs), such as TLRs and nucleotide-binding oligomerization domain-like receptors (NOD-like receptors)138, which are central to balancing the activation of downstream inflammatory signalling and the maintenance of immune tolerance. The epithelium in the URT is supported by mucosa-associated lymphoid tissue (MALT), which is populated with microfold cells that transport microorganisms from the epithelium to the lamina propria, where they can activate dendritic cells139. In the lungs, dendritic cells are located within and directly below the alveolar epithelium, where they continuously sample the alveolar space140. They subsequently present processed antigens to different subsets of T cells in the lung-draining lymph node, which initiates adaptive immune responses.

Anti-inflammatory alveolar macrophages are vital in lung immune homeostasis and for regulating the crosstalk between epithelial cells, dendritic cells and T cells (reviewed in Refs 141142). These cells dampen TLR-induced inflammatory signals in epithelial cells143, suppress inflammation by inhibiting dendritic cell- mediated activation of T cells144145 and induce regulatory cells146 (Fig. 3).

In conclusion, host–microbiota interactions influence different aspects of immune system development and contribute to immune maturation, immune tolerance and resistance to bacterial infection.

Box 3: An early window of opportunity

There is increasing evidence that early environmental and microbiota-derived cues are of paramount importance for the development of lymphoid tissue in neonates and ultimately shape the host immune system in the long term. For example, nasopharyngeal-associated lymphoid tissue (NALT) organogenesis is only initiated in the first week of life and is stimulated by cholera toxin, which suggests that NALT organogenesis may require microbiota-derived signals13. Similarly, the exposure of neonatal mice to lipopolysaccharide (LPS) led to the formation of bronchus-associated lymphoid tissue (BALT), which was not observed when mice were only exposed later in life170. Furthermore, it was demonstrated that neonatal, but not adult, bacterial colonization attracts activated regulatory T cells (Treg cells) to the skin and is necessary for the induction of immune tolerance to skin commensals171. Similarly, the lung microbiota promotes the transient expression of programmed death ligand 1 (PDL1) in dendritic cells during the first two weeks of life, which is necessary for the Treg cell-mediated attenuation of allergic airway responses7. Furthermore, hypermethylation of the CXC-motif chemokine ligand 16 (Cxcl16) gene in the lungs of germ-free mice increases the expression of CXCL16 and the accumulation of invariant natural killer T cells (NKT cells), which are known for their role in inflammation and asthma6. Transplantation of the microbiotas from normal mice at neonatal, but not adult age, prevented the accumulation of NKT cells, which abrogated disease in these mice (Fig. 3).

Altogether, these data suggest that the presence of a respiratory microbiota within a specific developmental period is crucial for shaping the adaptive immune response to commensals in adult life and coordinating the delicate balance between host, microbiota and the environment towards a long-term equilibrium. Although this early period of development can be regarded as a susceptible window for aberrant microbial colonization that could lead to the induction of immune disorders, importantly, this same phase of development may also provide a window of opportunity to intervene.

Box 4: Viral–host interactions

Persistent viral infections naturally occur in humans and may regulate innate and adaptive immunity. In serum, there is an estimated daily turnover of more than 109 anellovirus particles, which is thought to induce continuous immune surveillance and influence inhabitation by other microorganisms172. Similarly, chronic infection with herpesviruses, which have co-evolved with mammals for millions of years173 and can be detected in more than 90% of humans172, protects against bacterial infections by increasing the basal expression of interferon-γ (IFNγ) and facilitating the activation of macrophages174. Likewise, acute infection with common respiratory viruses activates innate immune pathways that remain active after the virus has been cleared. For example, infection with Sendai virus in mice is associated with the interleukin-13 (IL-13)-dependent activation of natural killer T cells (NKT cells) and lung macrophages and subsequent airway hyper-reactivity175. Similarly, early infection with respiratory syncytial virus (RSV) leads to impaired regulatory T cell (Treg cell) function in mice, which increases the risk of allergic airway disease169. These findings are further supported by data from a human infant cohort study, in which persisting immune dysregulation was still detected one month after acute RSV infection176.

Go to:

Conclusions and perspectives

The development of massive parallel sequencing147 has provided us with extensive insights into the microbial ecology of human body habitats, including the respiratory tract. Studies have shown that different ecological niches in the respiratory tract are occupied by diverse microbial communities that could act as gatekeepers to respiratory health. Further studies will be required to understand the pressures that shape these communities, their precise functions and contributions to human health. Efforts should focus on reductionist approaches to understand the underlying mechanisms involved in environment–microorganism, microorganism– microorganism and microorganism–host interactions in their authentic ecological context. The use of in vitro models that enable the manipulation of specific bacterial, host or environmental factors could substantially advance our understanding of the respiratory microbiota. In addition, in vivo optical imaging techniques will help to visualize host–microbiota or intra-microbiota interactions in their spatial context in health and disease148. Data derived from these approaches could be used in mathematical models to reconstruct bacterial interactions and study host and environmental forces that govern microbial behaviour149.

In addition to the in-depth studies of highly complex and context-dependent interspecies and host–microbiota interaction networks, holistic approaches remain important. Although studies on the composition of the respiratory tract microbiota did not show substantial differences between different developed countries, the question as to whether comparable host and environmental factors regulate the respiratory microbiota of individuals living in low/middle-income countries remains an important open question. The high burden of infectious and inflammation-related diseases in developing areas of the world might at least, in part, be related to compositional changes in the respiratory microbiota and vice versa150. Most progress can be expected from large cohort studies, in which the microbiota of healthy individuals and individuals who have an increased risk of infectious respiratory diseases is longitudinally characterized. In parallel, multi-omic (for example, transcriptomic and metabolomic) and clinical data should be integrated to study the crosstalk between host and microorganism, microbiota function, and the effect of environmental factors on the composition of the microbiota. Consequently, advances in bioinformatics will be required to appropriately combine and analyse multiple high-dimensional datasets. Methods to analyse complex combinatorial data sets are sparse, but the field is rapidly progressing by applying machine-learning algorithms and time-resolved data modelling. A multidisciplinary approach to extract patterns and associations from these studies could culminate in individualized risk assessment and preventive personalized medicine, as illustrated by a study in which dietary interventions that were made based on the gut microbiota led to the improved control of post-meal glucose levels151. Microbiota-based interventions are likely to be most beneficial in young children, as a window of opportunity within which the local microbiota primes specific features of the immune system seems to exist. Interventions during this impressionable period could redirect an aberrant developmental route, potentially influencing long-term respiratory health.

Go to:

Acknowledgements

The authors apologize to all colleagues whose work could not be cited owing to space limitations. This work was supported by the Netherlands Organization for Scientific Research through NWO-Vidi (grant 91715359 to D.B.), a Scottish Senior Clinical Fellowship award (to D.B.), the Spaarne Gasthuis Academy Hoofddorp (to W.H.M.) and Wilhelmina Children's Hospital intramural funds (to W.A.A.d.S.P.). The authors thank colleagues in Utrecht, Hoofddorp and Edinburgh for in-depth discussions in regard to topics covered in this manuscript: these discussions have substantially contributed to the content of this work.

Go to:

Glossary

Go to:

Biographies

Wing Ho Man is a medical doctor who is in the process of completing his Ph.D. in paediatric immunology and infectious diseases under the supervision of Debby Bogaert, Elisabeth Sanders and Marlies van Houten at the The Wilhelmina Children's Hospital, University Medical Centre Utrecht (UMCU), The Netherlands, and the Spaarne Gasthuis Academy, Hoofddorp, The Netherlands. He is currently investigating the human microbiome and virome of children who have lower respiratory tract infections in comparison with healthy children.

Wouter A.A. de Steenhuijsen Piters is a medical doctor and Ph.D. student at the University Medical Centre Utrecht (UMCU), The Netherlands, under the supervision of Debby Bogaert and Elisabeth Sanders. He studies the microbiome of the upper respiratory tract in association with respiratory health and disease, focusing on bioinformatic processing and data-analysis tools to answer health-related research questions. He currently works at the University of Edinburgh, UK, where he studies the development of a healthy microbiota in relation to environmental drivers and health consequences.

Debby Bogaert is a professor and physician scientist who leads a research group on the pathogenesis of respiratory infections at the Medical Research Council (MRC) Centre for Inflammation Research at the University of Edinburgh, UK. Moreover, she works as an honorary consultant in the Department of Paediatric Infectious Diseases and Immunology at the Royal Hospital for Sick Children, Edinburgh, UK. In addition, she leads a research group at the The Wilhelmina Children's Hospital, University Medical Centre Utrecht (UMCU), where she collaborates closely with clinical, environmental and public health scientists. She received her Ph.D. from Erasmus University Rotterdam, The Netherlands, where she investigated host–pathogen interactions during colonization and infection with Streptococcus pneumoniae, and worked as postdoctoral fellow at Harvard Medical School, Boston, Massachusetts, USA, where she studied pneumococcal colonization and infection in vitro and in animal models. Her current work focuses on the development of a healthy respiratory microbiome and the microbiota perturbations that are associated with respiratory disease, with the ultimate aim of developing measures to prevent or treat respiratory diseases.

PowerPoint slides

PowerPoint slide for Fig. 1(363K, ppt) PowerPoint slide for Fig. 2(358K, ppt) PowerPoint slide for Fig. 3(396K, ppt)

Go to:

Competing interests

The authors declare no competing financial interests.

Go to:

Footnotes

Wing Ho Man and Wouter A.A. de Steenhuijsen Piters: These authors contributed equally to this work.

Go to:

References

1. Lloyd-Price J, Abu-Ali G, Huttenhower C. The healthy human microbiome. Genome Med. 2016;8:51. [PMC free article] [PubMed] [Google Scholar]

2. Weibel ER. Morphometry of the Human Lung. 1963. [Google Scholar]

3. Bogaert D, De Groot R, Hermans PWM. Streptococcus pneumoniae colonisation: the key to pneumococcal disease. Lancet Infect. Dis. 2004;4:144–154. [PubMed] [Google Scholar]

4. Bäumler AJ, Sperandio V. Interactions between the microbiota and pathogenic bacteria in the gut. Nature. 2016;535:85–93. [PMC free article] [PubMed] [Google Scholar]

5. Yun Y, et al. Environmentally determined differences in the murine lung microbiota and their relation to alveolar architecture. PLoS ONE. 2014;9:e113466. [PMC free article] [PubMed] [Google Scholar]

6. Olszak T, et al. Microbial exposure during early life has persistent effects on natural killer T cell function. Science. 2012;336:489–493. [PMC free article] [PubMed] [Google Scholar]

7. Gollwitzer ES, et al. Lung microbiota promotes tolerance to allergens in neonates via PD-L1. Nat. Med. 2014;20:642–647. [PubMed] [Google Scholar]

8. Som PM, Naidich TP. Illustrated review of the embryology and development of the facial region, part 1: early face and lateral nasal cavities. Am. J. Neuroradiol. 2013;34:2233–2240. [PMC free article] [PubMed] [Google Scholar]

9. Herriges M, Morrisey EE. Lung development: orchestrating the generation and regeneration of a complex organ. Development. 2014;141:502–513. [PMC free article] [PubMed] [Google Scholar]

10. German, R. Z. & Palmer, J. B. Anatomy and development of oral cavity and pharynx. GI Motil. Onlinehttp://www.nature.com/gimo/contents/pt1/full/gimo5.html (2006).

11. Burri PH. Fetal and postnatal development of the lung. Annu. Rev. Physiol. 1984;46:617–628. [PubMed] [Google Scholar]

12. Wostmann BS. The germfree animal in nutritional studies. Annu. Rev. Nutr. 1981;1:257–279. [PubMed] [Google Scholar]

13. Fukuyama S, et al. Initiation of NALT organogenesis is independent of the IL-7R, LTβR, and NIK signaling pathways but requires the Id2 gene and CD3−CD4+CD45+ cells. Immunity. 2002;17:31–40. [PubMed] [Google Scholar]

14. Aagaard K, et al. The placenta harbors a unique microbiome. Sci. Transl Med. 2014;6:237ra65. [PMC free article] [PubMed] [Google Scholar]

15. Collado MC, Rautava S, Aakko J, Isolauri E, Salminen S. Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid. Sci. Rep. 2016;6:23129. [PMC free article] [PubMed] [Google Scholar]

16. Lauder AP, et al. Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota. Microbiome. 2016;4:29. [PMC free article] [PubMed] [Google Scholar]

17. Gomez de Agüero M, et al. The maternal microbiota drives early postnatal innate immune development. Science. 2016;351:1296–1302. [PubMed] [Google Scholar]

18. Koch MA, et al. Maternal IgG and IgA antibodies dampen mucosal T helper cell responses in early life. Cell. 2016;165:827–841. [PMC free article] [PubMed] [Google Scholar]

19. Dominguez-Bello MG, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc. Natl Acad. Sci. USA. 2010;107:11971–11975. [PMC free article] [PubMed] [Google Scholar]

20. Bosch AA, et al. Development of upper respiratory tract microbiota in infancy is affected by mode of delivery. EBioMedicine. 2016;9:336–345. [PMC free article] [PubMed] [Google Scholar]

21. Biesbroek G, et al. Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children. Am. J. Respir. Crit. Care Med. 2014;190:1283–1292. [PubMed] [Google Scholar]

22. Teo SM, et al. The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development. Cell Host Microbe. 2015;17:704–715. [PMC free article] [PubMed] [Google Scholar]

23. Biesbroek G, et al. The impact of breastfeeding on nasopharyngeal microbial communities in infants. Am. J. Respir. Crit. Care Med. 2014;190:298–308. [PubMed] [Google Scholar]

24. Duijts L, Jaddoe VWV, Hofman A, Moll HA. Prolonged and exclusive breastfeeding reduces the risk of infectious diseases in infancy. Pediatrics. 2010;126:e18–e25. [PubMed] [Google Scholar]

25. Schanche M, et al. High-resolution analyses of overlap in the microbiota between mothers and their children. Curr. Microbiol. 2015;71:283–290. [PubMed] [Google Scholar]

26. Jeurink PV, et al. Human milk: a source of more life than we imagine. Benef. Microbes. 2013;4:17–30. [PubMed] [Google Scholar]

27. Hicks LA, Taylor TH, Hunkler RJ. U.S. outpatient antibiotic prescribing, 2010. N. Engl. J. Med. 2013;368:1461–1462. [PubMed] [Google Scholar]

28. Prevaes SM, et al. Development of the nasopharyngeal microbiota in infants with cystic fibrosis. Am. J. Respir. Crit. Care Med. 2016;193:504–515. [PubMed] [Google Scholar]

29. Pettigrew MM, et al. Upper respiratory tract microbial communities, acute otitis media pathogens, and antibiotic use in healthy and sick children. Appl. Environ. Microbiol. 2012;78:6262–6270. [PMC free article] [PubMed] [Google Scholar]

30. Leibovitz E, et al. Recurrent acute otitis media occurring within one month from completion of antibiotic therapy: relationship to the original pathogen. Pediatr. Infect. Dis. J. 2003;22:209–216. [PubMed] [Google Scholar]

31. Bogaert D, et al. Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis. PLoS ONE. 2011;6:e17035. [PMC free article] [PubMed] [Google Scholar]

32. Bogaert D, et al. Colonisation by Streptococcus pneumoniae and Staphylococcus aureus in healthy children. Lancet. 2004;363:1871–1872. [PubMed] [Google Scholar]

33. Mika M, et al. Dynamics of the nasal microbiota in infancy: a prospective cohort study. J. Allergy Clin. Immunol. 2015;135:905–912.e11. [PubMed] [Google Scholar]

34. Spijkerman J, et al. Long-term effects of pneumococcal conjugate vaccine on nasopharyngeal carriage of S. pneumoniae, S. aureus, H. influenzae and M. catarrhalis. PLoS ONE. 2012;7:e39730. [PMC free article] [PubMed] [Google Scholar]

35. Greenberg D, et al. The contribution of smoking and exposure to tobacco smoke to Streptococcus pneumoniae and Haemophilus influenzae carriage in children and their mothers. Clin. Infect. Dis. 2006;42:897–903. [PubMed] [Google Scholar]

36. Liu CM, et al. Staphylococcus aureus and the ecology of the nasal microbiome. Sci. Adv. 2015;1:e1400216. [PMC free article] [PubMed] [Google Scholar]

37. Lim MY, et al. Analysis of the association between host genetics, smoking, and sputum microbiota in healthy humans. Sci. Rep. 2016;6:23745. [PMC free article] [PubMed] [Google Scholar]

38. Yatsunenko T, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486:222–227. [PMC free article] [PubMed] [Google Scholar]

39. Stearns JC, et al. Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age. ISME J. 2015;9:1246–1259. [PMC free article] [PubMed] [Google Scholar]

40. Jakobsson HE, et al. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS ONE. 2010;5:e9836. [PMC free article] [PubMed] [Google Scholar]

41. Charlson ES, et al. Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS ONE. 2010;5:e15216. [PMC free article] [PubMed] [Google Scholar]

42. Morris A, et al. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am. J. Respir. Crit. Care Med. 2013;187:1067–1075. [PMC free article] [PubMed] [Google Scholar]

43. Whelan FJ, et al. The loss of topography in the microbial communities of the upper respiratory tract in the elderly. Ann. Am. Thorac. Soc. 2014;11:513–521. [PubMed] [Google Scholar]

44. Vissing NH, Chawes BLK, Bisgaard H. Increased risk of pneumonia and bronchiolitis after bacterial colonization of the airways as neonates. Am. J. Respir. Crit. Care Med. 2013;188:1246–1252. [PubMed] [Google Scholar]

45. Dominguez-Bello MG, et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat. Med. 2016;22:250–253. [PMC free article] [PubMed] [Google Scholar]

46. Frank DN, et al. The human nasal microbiota and Staphylococcus aureus carriage. PLoS ONE. 2010;5:e10598. [PMC free article] [PubMed] [Google Scholar]

47. Oh J, et al. Biogeography and individuality shape function in the human skin metagenome. Nature. 2014;514:59–64. [PMC free article] [PubMed] [Google Scholar]

48. Zhou Y, et al. Exploration of bacterial community classes in major human habitats. Genome Biol. 2014;15:R66. [PMC free article] [PubMed] [Google Scholar]

49. Wos-Oxley ML, et al. Exploring the bacterial assemblages along the human nasal passage. Environ. Microbiol. 2016;18:2259–2271. [PubMed] [Google Scholar]

50. Yan M, et al. Nasal microenvironments and interspecific interactions influence nasal microbiota complexity and S. aureus carriage. Cell Host Microbe. 2013;14:631–640. [PMC free article] [PubMed] [Google Scholar]

51. Segata N, et al. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol. 2012;13:R42. [PMC free article] [PubMed] [Google Scholar]

52. de Steenhuijsen Piters WA, et al. Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients. ISME J. 2016;10:97–108. [PMC free article] [PubMed] [Google Scholar]

53. van den Bergh MR, et al. Associations between pathogens in the upper respiratory tract of young children: interplay between viruses and bacteria. PLoS ONE. 2012;7:e47711. [PMC free article] [PubMed] [Google Scholar]

54. Wang Y, et al. Metagenomic analysis of viral genetic diversity in respiratory samples from children with severe acute respiratory infection in China. Clin. Microbiol. Infect. 2016;22:458.e1–458.e9. [PMC free article] [PubMed] [Google Scholar]

55. Wylie KM, Mihindukulasuriya KA, Sodergren E, Weinstock GM, Storch GA. Sequence analysis of the human virome in febrile and afebrile children. PLoS ONE. 2012;7:e27735. [PMC free article] [PubMed] [Google Scholar]

56. Eidi S, et al. Nasal and indoors fungal contamination in healthy subjects. Health Scope. 2016;5:e30033. [Google Scholar]

57. Charlson ES, et al. Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant. Am. J. Respir. Crit. Care Med. 2012;186:536–545. [PMC free article] [PubMed] [Google Scholar]

58. Qin J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59–65. [PMC free article] [PubMed] [Google Scholar]

59. Cardinale BJ, et al. Biodiversity loss and its impact on humanity. Nature. 2012;486:59–67. [PubMed] [Google Scholar]

60. Huttenhower C, Kostic AD, Xavier RJ. Inflammatory bowel disease as a model for translating the microbiome. Immunity. 2014;40:843–854. [PMC free article] [PubMed] [Google Scholar]

61. Kampmann C, Dicksved J, Engstrand L, Rautelin H. Composition of human faecal microbiota in resistance to Campylobacter infection. Clin. Microbiol. Infect. 2016;22:61.e1–61.e8. [PubMed] [Google Scholar]

62. Fredricks DN, Fiedler TL, Marrazzo JM. Molecular identification of bacteria associated with bacterial vaginosis. N. Engl. J. Med. 2005;353:1899–1911. [PubMed] [Google Scholar]

63. Ravel J, et al. Vaginal microbiome of reproductive-age women. Proc. Natl Acad. Sci. USA. 2011;108:4680–4687. [PMC free article] [PubMed] [Google Scholar]

64. DiGiulio DB, Stevenson DK, Shaw G, Lyell DJ, Relman DA. Reply to Keelan and Payne: microbiota-related pathways for preterm birth. Proc. Natl Acad. Sci. USA. 2015;112:E6415. [PMC free article] [PubMed] [Google Scholar]

65. Hilty M, et al. Nasopharyngeal microbiota in infants with acute otitis media. J. Infect. Dis. 2012;205:1048–1055. [PMC free article] [PubMed] [Google Scholar]

66. Abreu NA, et al. Sinus microbiome diversity depletion and Corynebacterium tuberculostearicum enrichment mediates rhinosinusitis. Sci. Transl Med. 2012;4:151ra124. [PMC free article] [PubMed] [Google Scholar]

67. Goodrich JK, et al. Human genetics shape the gut microbiome. Cell. 2014;159:789–799. [PMC free article] [PubMed] [Google Scholar]

68. Bomar L, Brugger SD, Yost BH, Davies SS, Lemon KP. Corynebacterium accolens releases antipneumococcal free fatty acids from human nostril and skin surface triacylglycerols. mBio. 2016;7:e01725-15. [PMC free article] [PubMed] [Google Scholar]

69. Laufer AS, et al. Microbial communities of the upper respiratory tract and otitis media in children. mBio. 2011;2:e00245-10. [PMC free article] [PubMed] [Google Scholar]

70. Kamada N, Chen GY, Inohara N, Núñez G. Control of pathogens and pathobionts by the gut microbiota. Nat. Immunol. 2013;14:685–690. [PMC free article] [PubMed] [Google Scholar]

71. Iwase T, et al. Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature. 2010;465:346–349. [PubMed] [Google Scholar]

72. Lysenko ES, et al. Nod1 signaling overcomes resistance of S. pneumoniae to opsonophagocytic killing. PLoS Pathog. 2007;3:e118. [PMC free article] [PubMed] [Google Scholar]

73. Huxley EJ, Viroslav J, Gray WR, Pierce AK. Pharyngeal aspiration in normal adults and patients with depressed consciousness. Am. J. Med. 1978;64:564–568. [PubMed] [Google Scholar]

74. Bassis CM, et al. Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. mBio. 2015;6:e00037-15. [PMC free article] [PubMed] [Google Scholar]

75. Segal LN, et al. Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome. 2013;1:19. [PMC free article] [PubMed] [Google Scholar]

76. Marsh RL, et al. The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx. Microbiome. 2016;4:37. [PMC free article] [PubMed] [Google Scholar]

77. Lohmann P, et al. The airway microbiome of intubated premature infants: characteristics and changes that predict the development of bronchopulmonary dysplasia. Pediatr. Res. 2014;76:294–301. [PubMed] [Google Scholar]

78. Payne MS, et al. Molecular microbiological characterization of preterm neonates at risk of bronchopulmonary dysplasia. Pediatr. Res. 2010;67:412–418. [PubMed] [Google Scholar]

79. Mourani PM, Harris JK, Sontag MK, Robertson CE, Abman SH. Molecular identification of bacteria in tracheal aspirate fluid from mechanically ventilated preterm infants. PLoS ONE. 2011;6:e25959. [PMC free article] [PubMed] [Google Scholar]

80. Dickson RP, et al. Spatial variation in the healthy human lung microbiome and the adapted island model of lung biogeography. Ann. Am. Thorac. Soc. 2015;12:821–830. [PMC free article] [PubMed] [Google Scholar]

81. Abbas, A. A. et al. The perioperative lung transplant virome: torque teno viruses are elevated in donor lungs and show divergent dynamics in primary graft dysfunction. Am. J. Transplant.10.1111/ajt.14076 (2016). [PMC free article] [PubMed]

82. Willner D, et al. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS ONE. 2009;4:e7370. [PMC free article] [PubMed] [Google Scholar]

83. Young JC, et al. Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients. Am. J. Transplant. 2015;15:200–209. [PMC free article] [PubMed] [Google Scholar]

84. van Woerden HC, et al. Differences in fungi present in induced sputum samples from asthma patients and non-atopic controls: a community based case control study. BMC Infect. Dis. 2013;13:69. [PMC free article] [PubMed] [Google Scholar]

85. Cleland EJ, et al. The fungal microbiome in chronic rhinosinusitis: richness, diversity, postoperative changes and patient outcomes. Int. Forum Allergy Rhinol. 2014;4:259–265. [PubMed] [Google Scholar]

86. Charlson ES, et al. Topographical continuity of bacterial populations in the healthy human respiratory tract. Am. J. Respir. Crit. Care Med. 2011;184:957–963. [PMC free article] [PubMed] [Google Scholar]

87. Venkataraman A, et al. Application of a neutral community model to assess structuring of the human lung microbiome. mBio. 2015;6:e02284-14. [PMC free article] [PubMed] [Google Scholar]

88. Willner D, et al. Spatial distribution of microbial communities in the cystic fibrosis lung. ISME J. 2012;6:471–474. [PMC free article] [PubMed] [Google Scholar]

89. Mashima I, Nakazawa F. The influence of oral Veillonella species on biofilms formed by Streptococcus species. Anaerobe. 2014;28:54–61. [PubMed] [Google Scholar]

90. Cook LC, LaSarre B, Federle MJ. Interspecies communication among commensal and pathogenic streptococci. mBio. 2013;4:e00382-13. [PMC free article] [PubMed] [Google Scholar]

91. Armbruster CE, et al. Indirect pathogenicity of Haemophilus influenzae and Moraxella catarrhalis in polymicrobial otitis media occurs via interspecies quorum signaling. mBio. 2010;1:e00102-10. [PMC free article] [PubMed] [Google Scholar]

92. Wos-Oxley ML, et al. A poke into the diversity and associations within human anterior nare microbial communities. ISME J. 2010;4:839–851. [PubMed] [Google Scholar]

93. Regev-Yochay G, Trzcinski K, Thompson CM, Malley R, Lipsitch M. Interference between Streptococcus pneumoniae and Staphylococcus aureus: in vitro hydrogen peroxide-mediated killing by Streptococcus pneumoniae. J. Bacteriol. 2006;188:4996–5001. [PMC free article] [PubMed] [Google Scholar]

94. Selva L, et al. Killing niche competitors by remote-control bacteriophage induction. Proc. Natl Acad. Sci. USA. 2009;106:1234–1238. [PMC free article] [PubMed] [Google Scholar]

95. Deasy AM, et al. Nasal inoculation of the commensal Neisseria lactamica inhibits carriage of Neisseria meningitidis by young adults: a controlled human infection study. Clin. Infect. Dis. 2015;60:1512–1520. [PubMed] [Google Scholar]

96. Janek D, Zipperer A, Kulik A, Krismer B, Peschel A. High frequency and diversity of antimicrobial activities produced by nasal Staphylococcus strains against bacterial competitors. PLoS Pathog. 2016;12:e1005812. [PMC free article] [PubMed] [Google Scholar]

97. Ramsey MM, Freire MO, Gabrilska RA, Rumbaugh KP, Lemon KP. Staphylococcus aureus shifts toward commensalism in response to Corynebacterium species. Front. Microbiol. 2016;7:1230. [PMC free article] [PubMed] [Google Scholar]

98. Zipperer A, et al. Human commensals producing a novel antibiotic impair pathogen colonization. Nature. 2016;535:511–516. [PubMed] [Google Scholar]

99. Tong TT, Mörgelin M, Forsgren A, Riesbeck K. Haemophilus influenzae survival during complement-mediated attacks is promoted by Moraxella catarrhalis outer membrane vesicles. J. Infect. Dis. 2007;195:1661–1670. [PubMed] [Google Scholar]

100. de Steenhuijsen Piters WA, Sanders EA, Bogaert D. The role of the local microbial ecosystem in respiratory health and disease. Philos. Trans. R. Soc. B Biol. Sci. 2015;370:20140294. [PMC free article] [PubMed] [Google Scholar]

101. Taubenberger JK, Reid AH, Fanning TG. The 1918 influenza virus: a killer comes into view. Virology. 2000;274:241–245. [PubMed] [Google Scholar]

102. Bosch AA, Biesbroek G, Trzcinski K, Sanders EAM, Bogaert D. Viral and bacterial interactions in the upper respiratory tract. PLoS Pathog. 2013;9:e1003057. [PMC free article] [PubMed] [Google Scholar]

103. Sajjan U, Wang Q, Zhao Y, Gruenert DC, Hershenson MB. Rhinovirus disrupts the barrier function of polarized airway epithelial cells. Am. J. Respir. Crit. Care Med. 2008;178:1271–1281. [PMC free article] [PubMed] [Google Scholar]

104. Avadhanula V, et al. Respiratory viruses augment the adhesion of bacterial pathogens to respiratory epithelium in a viral species- and cell type-dependent manner. J. Virol. 2006;80:1629–1636. [PMC free article] [PubMed] [Google Scholar]

105. Ramphal R, Small PM, Shands JW, Fischlschweiger W, Small PA. Adherence of Pseudomonas aeruginosa to tracheal cells injured by influenza infection or by endotracheal intubation. Infect. Immun. 1980;27:614–619. [PMC free article] [PubMed] [Google Scholar]

106. Siegel SJ, Roche AM, Weiser JN. Influenza promotes pneumococcal growth during coinfection by providing host sialylated substrates as a nutrient source. Cell Host Microbe. 2014;16:55–67. [PMC free article] [PubMed] [Google Scholar]

107. Pittet LA, Hall-Stoodley L, Rutkowski MR, Harmsen AG. Influenza virus infection decreases tracheal mucociliary velocity and clearance of Streptococcus pneumoniae. Am. J. Respir. Cell Mol. Biol. 2010;42:450–460. [PMC free article] [PubMed] [Google Scholar]

108. Raza MW, Blackwell CC, Elton RA, Weir DM. Bactericidal activity of a monocytic cell line (THP-1) against common respiratory tract bacterial pathogens is depressed after infection with respiratory syncytial virus. J. Med. Microbiol. 2000;49:227–233. [PubMed] [Google Scholar]

109. Didierlaurent A, et al. Sustained desensitization to bacterial Toll-like receptor ligands after resolution of respiratory influenza infection. J. Exp. Med. 2008;205:323–329. [PMC free article] [PubMed] [Google Scholar]

110. Sun K, Metzger DW. Inhibition of pulmonary antibacterial defense by interferon-γ during recovery from influenza infection. Nat. Med. 2008;14:558–564. [PubMed] [Google Scholar]

111. Robinson KM, et al. Influenza A virus exacerbates staphylococcus aureus pneumonia in mice by attenuating antimicrobial peptide production. J. Infect. Dis. 2014;209:865–875. [PMC free article] [PubMed] [Google Scholar]

112. Ni K, et al. Pharyngeal microflora disruption by antibiotics promotes airway hyperresponsiveness after respiratory syncytial virus infection. PLoS ONE. 2012;7:e41104. [PMC free article] [PubMed] [Google Scholar]

113. Wyde PR, Six HR, Ambrose MW, Throop BJ. Muramyl peptides and polyinosinic-polycytodylic acid given to mice prior to influenza virus challenge reduces pulmonary disease and mortality. J. Biol. Response Mod. 1990;9:98–102. [PubMed] [Google Scholar]

114. Sajjan US. H. influenzae potentiates airway epithelial cell responses to rhinovirus by increasing ICAM-1 and TLR3 expression. FASEB J. 2006;20:2121–2123. [PubMed] [Google Scholar]

115. Gulraiz F, Bellinghausen C, Bruggeman CA, Stassen FR. Haemophilus influenzae increases the susceptibility and inflammatory response of airway epithelial cells to viral infections. FASEB J. 2015;29:849–858. [PubMed] [Google Scholar]

116. Bellinghausen C, et al. Exposure to common respiratory bacteria alters the airway epithelial response to subsequent viral infection. Respir. Res. 2016;17:68. [PMC free article] [PubMed] [Google Scholar]

117. de Steenhuijsen Piters, W. A. A. et al. Nasopharyngeal microbiota, host transcriptome and disease severity in children with respiratory syncytial virus infection. Am. J. Respir. Crit. Care Med. 1104–1115 (2016). This clinical study shows that the composition of the microbiota of the nasopharynx during early RSV infection is strongly associated with the differential expression of genes that are linked to innate immune pathways that, in turn, are associated with increased RSV disease severity.

118. Scheiblauer H, Reinacher M, Tashiro M, Rott R. Interactions between bacteria and influenza A virus in the development of influenza pneumonia. J. Infect. Dis. 1992;166:783–791. [PubMed] [Google Scholar]

119. Tashiro M, Ciborowski P, Klenk H-D, Pulverer G, Rott R. Role of Staphylococcus protease in the development of influenza pneumonia. Nature. 1987;325:536–537. [PubMed] [Google Scholar]

120. Short KR, et al. Bacterial lipopolysaccharide inhibits influenza virus infection of human macrophages and the consequent induction of CD8+ T cell immunity. J. Innate Immun. 2014;6:129–139. [PMC free article] [PubMed] [Google Scholar]

121. Ichinohe T, et al. Microbiota regulates immune defense against respiratory tract influenza A virus infection. Proc. Natl Acad. Sci. USA. 2011;108:5354–5359. [PMC free article] [PubMed] [Google Scholar]

122. Amit I, et al. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science. 2009;326:257–263. [PMC free article] [PubMed] [Google Scholar]

123. Abt MC, et al. Commensal bacteria calibrate the activation threshold of innate antiviral immunity. Immunity. 2012;37:158–170. [PMC free article] [PubMed] [Google Scholar]

124. Pride DT, Salzman J, Relman DA. Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses. Environ. Microbiol. 2012;14:2564–2576. [PMC free article] [PubMed] [Google Scholar]

125. Williams HTP. Phage-induced diversification improves host evolvability. BMC Evol. Biol. 2013;13:17. [PMC free article] [PubMed] [Google Scholar]

126. Segal LN, et al. Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Nat. Microbiol. 2016;1:16031. [PMC free article] [PubMed] [Google Scholar]

127. Boase S, et al. Bacterial-induced epithelial damage promotes fungal biofilm formation in a sheep model of sinusitis. Int. Forum Allergy Rhinol. 2013;3:341–348. [PubMed] [Google Scholar]

128. Diaz PI, et al. Synergistic interaction between Candida albicans and commensal oral streptococci in a novel in vitro mucosal model. Infect. Immun. 2012;80:620–632. [PMC free article] [PubMed] [Google Scholar]

129. Xu H, et al. Streptococcal co-infection augments Candida pathogenicity by amplifying the mucosal inflammatory response. Cell. Microbiol. 2014;16:214–231. [PMC free article] [PubMed] [Google Scholar]

130. Briard B, Heddergott C, Latgé J-P. Volatile compounds emitted by Pseudomonas aeruginosa stimulate growth of the fungal pathogen Aspergillus fumigatus. mBio. 2016;7:e00219. [PMC free article] [PubMed] [Google Scholar]

131. Roux D, et al. Candida albicans impairs macrophage function and facilitates Pseudomonas aeruginosa pneumonia in rat. Crit. Care Med. 2009;37:1062–1067. [PubMed] [Google Scholar]

132. Linden SK, Sutton P, Karlsson NG, Korolik V, McGuckin MA. Mucins in the mucosal barrier to infection. Mucosal Immunol. 2008;1:183–197. [PMC free article] [PubMed] [Google Scholar]

133. Roy MG, et al. Muc5b is required for airway defence. Nature. 2014;505:412–416. [PMC free article] [PubMed] [Google Scholar]

134. Kiyono H, Fukuyama S. NALT- versus Peyer's-patch-mediated mucosal immunity. Nat. Rev. Immunol. 2004;4:699–710. [PMC free article] [PubMed] [Google Scholar]

135. Kawamoto S, et al. Foxp3+ T cells regulate immunoglobulin A selection and facilitate diversification of bacterial species responsible for immune homeostasis. Immunity. 2014;41:152–165. [PubMed] [Google Scholar]

136. Sutherland DB, Suzuki K, Fagarasan S. Fostering of advanced mutualism with gut microbiota by immunoglobulin A. Immunol. Rev. 2016;270:20–31. [PubMed] [Google Scholar]

137. LeVine AM, et al. Distinct effects of surfactant protein A or D deficiency during bacterial infection on the lung. J. Immunol. 2000;165:3934–3940. [PubMed] [Google Scholar]

138. Uehara A, Fujimoto Y, Fukase K, Takada H. Various human epithelial cells express functional Toll-like receptors, NOD1 and NOD2 to produce anti-microbial peptides, but not proinflammatory cytokines. Mol. Immunol. 2007;44:3100–3111. [PubMed] [Google Scholar]

139. Kim D-Y, et al. The airway antigen sampling system: respiratory M cells as an alternative gateway for inhaled antigens. J. Immunol. 2011;186:4253–4262. [PubMed] [Google Scholar]

140. Jahnsen FL, et al. Accelerated antigen sampling and transport by airway mucosal dendritic cells following inhalation of a bacterial stimulus. J. Immunol. 2006;177:5861–5867. [PubMed] [Google Scholar]

141. Kopf M, Schneider C, Nobs SP. The development and function of lung-resident macrophages and dendritic cells. Nat. Immunol. 2014;16:36–44. [PubMed] [Google Scholar]

142. Hussell T, Bell TJ. Alveolar macrophages: plasticity in a tissue-specific context. Nat. Rev. Immunol. 2014;14:81–93. [PubMed] [Google Scholar]

143. Westphalen K, et al. Sessile alveolar macrophages communicate with alveolar epithelium to modulate immunity. Nature. 2014;506:503–506. [PMC free article] [PubMed] [Google Scholar]

144. Holt PG, et al. Downregulation of the antigen presenting cell function(s) of pulmonary dendritic cells in vivo by resident alveolar macrophages. J. Exp. Med. 1993;177:397–407. [PMC free article] [PubMed] [Google Scholar]

145. Holt PG, Schon-Hegrad MA, Oliver J. MHC class II antigen-bearing dendritic cells in pulmonary tissues of the rat. Regulation of antigen presentation activity by endogenous macrophage populations. J. Exp. Med. 1988;167:262–274. [PMC free article] [PubMed] [Google Scholar]

146. Soroosh P, et al. Lung-resident tissue macrophages generate Foxp3+ regulatory T cells and promote airway tolerance. J. Exp. Med. 2013;210:775–788. [PMC free article] [PubMed] [Google Scholar]

147. Margulies M, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005;437:376–380. [PMC free article] [PubMed] [Google Scholar]

148. Mills B, Bradley M, Dhaliwal K. Optical imaging of bacterial infections. Clin. Transl Imaging. 2016;4:163–174. [PMC free article] [PubMed] [Google Scholar]

149. McLoughlin K, Schluter J, Rakoff-Nahoum S, Smith AL, Foster KR. Host selection of microbiota via differential adhesion. Cell Host Microbe. 2016;19:550–559. [PubMed] [Google Scholar]

150. Liu L, et al. Global, regional, and national causes of child mortality: an updated systematic analysis for 2010 with time trends since 2000. Lancet. 2012;379:2151–2161. [PubMed] [Google Scholar]

151. Zeevi D, et al. Personalized nutrition by prediction of glycemic responses. Cell. 2015;163:1079–1095. [PubMed] [Google Scholar]

152. Caporaso JG, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6:1621–1624. [PMC free article] [PubMed] [Google Scholar]

153. Goleva E, et al. The effects of airway microbiome on corticosteroid responsiveness in asthma. Am. J. Respir. Crit. Care Med. 2013;188:1193–1201. [PMC free article] [PubMed] [Google Scholar]

154. Salter SJ, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12:87. [PMC free article] [PubMed] [Google Scholar]

155. Biesbroek G, et al. Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection. PLoS ONE. 2012;7:e32942. [PMC free article] [PubMed] [Google Scholar]

156. Dickson RP, et al. Enrichment of the lung microbiome with gut bacteria in sepsis and the acute respiratory distress syndrome. Nat. Microbiol. 2016;1:16113. [PMC free article] [PubMed] [Google Scholar]

157. Larsen JM, et al. Chronic obstructive pulmonary disease and asthma-associated Proteobacteria, but not commensal Prevotella spp., promote Toll-like receptor 2-independent lung inflammation and pathology. Immunology. 2015;144:333–342. [PMC free article] [PubMed] [Google Scholar]

158. Bäckhed F, Normark S, Schweda EKH, Oscarson S, Richter-Dahlfors A. Structural requirements for TLR4-mediated LPS signalling: a biological role for LPS modifications. Microbes Infect. 2003;5:1057–1063. [PubMed] [Google Scholar]

159. Coats SR, Reife RA, Bainbridge BW, Pham TT-T, Darveau RP. Porphyromonas gingivalis lipopolysaccharide antagonizes Escherichia coli lipopolysaccharide at Toll-like receptor 4 in human endothelial cells. Infect. Immun. 2003;71:6799–6807. [PMC free article] [PubMed] [Google Scholar]

160. Munford RS. Sensing Gram-negative bacterial lipopolysaccharides: a human disease determinant? Infect. Immun. 2008;76:454–465. [PMC free article] [PubMed] [Google Scholar]

161. Salzman NH, et al. Enteric defensins are essential regulators of intestinal microbial ecology. Nat. Immunol. 2010;11:76–83. [PMC free article] [PubMed] [Google Scholar]

162. Kao C-Y, et al. IL-17 markedly up-regulates β-defensin-2 expression in human airway epithelium via JAK and NF-κB signaling pathways. J. Immunol. 2004;173:3482–3491. [PubMed] [Google Scholar]

163. Atarashi K, et al. Th17 cell induction by adhesion of microbes to intestinal epithelial cells. Cell. 2015;163:367–380. [PMC free article] [PubMed] [Google Scholar]

164. Wang J, et al. Bacterial colonization dampens influenza-mediated acute lung injury via induction of M2 alveolar macrophages. Nat. Commun. 2013;4:2106. [PMC free article] [PubMed] [Google Scholar]

165. Rice TA, et al. Signaling via pattern recognition receptors NOD2 and TLR2 contributes to immunomodulatory control of lethal pneumovirus infection. Antiviral Res. 2016;132:131–140. [PMC free article] [PubMed] [Google Scholar]

166. Clarke TB, et al. Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity. Nat. Med. 2010;16:228–231. [PMC free article] [PubMed] [Google Scholar]

167. Herbst T, et al. Dysregulation of allergic airway inflammation in the absence of microbial colonization. Am. J. Respir. Crit. Care Med. 2011;184:198–205. [PubMed] [Google Scholar]

168. Naik S, et al. Commensal–dendritic-cell interaction specifies a unique protective skin immune signature. Nature. 2015;520:104–108. [PMC free article] [PubMed] [Google Scholar]

169. Krishnamoorthy N, et al. Early infection with respiratory syncytial virus impairs regulatory T cell function and increases susceptibility to allergic asthma. Nat. Med. 2012;18:1525–1530. [PMC free article] [PubMed] [Google Scholar]

170. Rangel-Moreno J, et al. The development of inducible bronchus-associated lymphoid tissue depends on IL-17. Nat. Immunol. 2011;12:639–646. [PMC free article] [PubMed] [Google Scholar]

171. Scharschmidt TC, et al. A wave of regulatory T cells into neonatal skin mediates tolerance to commensal microbes. Immunity. 2015;43:1011–1021. [PMC free article] [PubMed] [Google Scholar]

172. Virgin HW, Wherry EJ, Ahmed R. Redefining chronic viral infection. Cell. 2009;138:30–50. [PubMed] [Google Scholar]

173. McGeoch DJ, Rixon FJ, Davison AJ. Topics in herpesvirus genomics and evolution. Virus Res. 2006;117:90–104. [PubMed] [Google Scholar]

174. Barton ES, et al. Herpesvirus latency confers symbiotic protection from bacterial infection. Nature. 2007;447:326–329. [PubMed] [Google Scholar]

175. Kim EY, et al. Persistent activation of an innate immune response translates respiratory viral infection into chronic lung disease. Nat. Med. 2008;14:633–640. [PMC free article] [PubMed] [Google Scholar]

176. Mejias A, et al. Whole blood gene expression profiles to assess pathogenesis and disease severity in infants with respiratory syncytial virus infection. PLoS Med. 2013;10:e1001549. [PMC free article] [PubMed] [Google Scholar]

177. England RJ, Homer JJ, Knight LC, Ell SR. Nasal pH measurement: a reliable and repeatable parameter. Clin. Otolaryngol. Allied Sci. 1999;24:67–68. [PubMed] [Google Scholar]

178. Brunworth JD, Garg R, Mahboubi H, Johnson B, Djalilian HR. Detecting nasopharyngeal reflux: a novel pH probe technique. Ann. Otol. Rhinol. Laryngol. 2012;121:427–430. [PubMed] [Google Scholar]

179. Ayazi S, et al. A new technique for measurement of pharyngeal pH: normal values and discriminating pH threshold. J. Gastrointest. Surg. 2009;13:1422–1429. [PubMed] [Google Scholar]

180. West JB. Regional differences in the lung. Chest. 1978;74:426. [PubMed] [Google Scholar]

181. Keck, T. & Lindemann, J. Numerical simulation and nasal air-conditioning. GMS Curr. Top. Otorhinolaryngol. Head Neck Surg.10.3205/cto000072 (2010). [PMC free article] [PubMed]

182. Ingenito EP, et al. Indirect assessment of mucosal surface temperatures in the airways: theory and tests. J. Appl. Physiol. 1987;63:2075–2083. [PubMed] [Google Scholar]

183. McFadden ER, et al. Thermal mapping of the airways in humans. J. Appl. Physiol. 1985;58:564–570. [PubMed] [Google Scholar]

184. Morgan NJ, MacGregor FB, Birchall MA, Lund VJ, Sittampalam Y. Racial differences in nasal fossa dimensions determined by acoustic rhinometry. Rhinology. 1995;33:224–228. [PubMed] [Google Scholar]

185. Walsh JH, et al. Evaluation of pharyngeal shape and size using anatomical optical coherence tomography in individuals with and without obstructive sleep apnoea. J. Sleep Res. 2008;17:230–238. [PubMed] [Google Scholar]

186. Hatch TF. Distribution and deposition of inhaled particles in respiratory tract. Bacteriol. Rev. 1961;25:237–240. [PMC free article] [PubMed] [Google Scholar]

187. Prussin AJ, Marr LC. Sources of airborne microorganisms in the built environment. Microbiome. 2015;3:78. [PMC free article] [PubMed] [Google Scholar]

Articles from Nature Reviews. Microbiology are provided here courtesy of Nature Publishing Group