House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection. Proc Natl Acad Sci U S A. 2014;111:805-810. [PMID: 24344318 DOI: 10.1073/pnas.1310750111]

A bug's view of allergic airways disease

The increase in allergic airways disease has been linked to modern urbanization and lifestyle. Recent evidence suggests that the associated reduction in microbial exposure, reduction in dietary fibre intake and increased antibiotic use may cause early dysbiosis in infancy, which predisposes to immune dysregulation and allergic airways disease later in life. This implies that there may be a window of opportunity for primary prevention strategies aimed to protect or restore the microbiome early in life and thereby decrease the risk of developing allergic airways disease. Alternatively, strategies that correct dysbiosis may aid in the treatment of established allergic airways disease.

The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review

Recent high-throughput sequencing technology has led to an expansion of knowledge regarding the microbial communities (microbiome) across various built environments (BEs). The microbiome of the BE is dependent upon building factors and conditions that govern how outdoor microbes enter and persist in the BE. Additionally, occupants are crucial in shaping the microbiome of the BE by releasing human-associated microorganisms and resuspending microbes on floors and surfaces. Therefore, both the outdoors and occupants act as major sources of microorganisms found in the BE. However, most characterizations of the microbiome of the BE have been conducted in the Western world. Notably, outdoor locations and population groups present geographical variations in outdoor and human microbiomes, respectively. Given the influences of the outdoor and human microbiomes on BE microbiology, and the geographical variations in outdoor and human microbiomes, it is likely that the microbiomes of BEs also vary by location. The summation of microbiomes between BEs contribute to a potential BE pan-microbiome, which will both consist of microbes that are ubiquitous in indoor environments around the world, and microbes that appear to be endemic to particular geographical locations. Importantly, the BE pan-microbiome can potentially question the global application of our current views on indoor microbiology. In this review, we first provide an assessment on the roles of building and occupant properties on shaping the microbiome of the BE. This is then followed by a description of geographical variations in the microbiomes of the outdoors and humans, the two main sources of microbes in BEs. We present evidence of differences in microbiomes of BEs around the world, demonstrating the existence of a global pan-microbiome of the BE that is larger than the microbiome of any single indoor environment. Finally, we discuss the significance of understanding the BE pan-microbiome and identifying universal and location-specific relationships between building and occupant characteristics and indoor microbiology. This review highlights the much needed efforts towards determining the pan-microbiome of the BE, thereby identifying general and location-specific links between the microbial communities of the outdoors, human, and BE ecosystems, ultimately improving the health, comfort, and productivity of occupants around the world.

Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges

Microorganisms have shaped our planet and its inhabitants for over 3.5 billion years. Humankind has had a profound influence on the biosphere, manifested as global climate and land use changes, and extensive urbanization in response to a growing population. The challenges we face to supply food, energy, and clean water while maintaining and improving the health of our population and ecosystems are significant. Given the extensive influence of microorganisms across our biosphere, we propose that a coordinated, cross-disciplinary effort is required to understand, predict, and harness microbiome function. From the parallelization of gene function testing to precision manipulation of genes, communities, and model ecosystems and development of novel analytical and simulation approaches, we outline strategies to move microbiome research into an era of causality. These efforts will improve prediction of ecosystem response and enable the development of new, responsible, microbiome-based solutions to significant challenges of our time.

Lung Ischemia-Reperfusion is a Sterile Inflammatory Process Influenced by Commensal Microbiota in Mice

Lung ischemia-reperfusion (IR) complicates numerous clinical processes, such as cardiac arrest, transplantation, and major trauma. These conditions generate sterile inflammation, which can cause or worsen acute lung injury. We previously reported that lung and systemic inflammation in a mouse model of ventilated lung IR depends on Toll-like receptor 4 (TLR-4) signaling and the presence of alveolar macrophages. Here, we tested the hypothesis that the intestinal microbiome has a role in influencing the inflammatory response to lung IR. Lung IR was created in intubated mechanically ventilated mice via reversible left pulmonary artery occlusion followed by reperfusion. Inflammatory markers and histology were tracked during varying periods of reperfusion (from 1 to 24 h). Separate groups of mice were given intestinally localized antibiotics for 8 to 10 weeks and then were subjected to left lung IR and analysis of lungs and plasma for markers of inflammation. Alveolar macrophages from antibiotic-treated or control mice were tested ex vivo for inflammatory responses to bacterial TLR agonists, namely, lipopolysaccharide and Pam3Cys. We found that inflammation generated by left lung IR was rapid in onset and dissipated within 12 to 24 h. Treatment of mice with intestinally localized antibiotics was associated with a marked attenuation of circulating and lung inflammatory markers as well as reduced histologic evidence of infiltrating cells and edema in the lung after IR. Alveolar macrophages from antibiotic-treated mice produced less cytokines ex vivo when stimulated with TLR agonists as compared with those from control mice. Our data indicate that the inflammatory response induced by nonhypoxic lung IR is transient and is strongly influenced by intestinal microbiota. Furthermore, these data suggest that the intestinal microbiome could potentially be manipulated to attenuate the post-IR pulmonary inflammatory response.

The rise of food allergy: Environmental factors and emerging treatments

Food allergy has rapidly increased in prevalence, suggesting an important role for environmental factors in disease susceptibility. The immune response of food allergy is characterized by IgE production, and new findings from mouse and human studies indicate an important role of the cytokine IL-9, which is derived from both T cells and mast cells, in disease manifestations. Emerging evidence suggests that route of exposure to food, particularly peanut, is important. Exposure through the skin promotes sensitization while early exposure through the gastrointestinal tract promotes tolerance. Evidence from mouse studies indicate a role of the microbiome in development of food allergy, which is supported by correlative human studies showing a dysbiosis in food allergy. There is no approved treatment for food allergy, but emerging therapies are focused on allergen immunotherapy to provide desensitization, while pre-clinical studies are focused on using adjuvants or novel delivery approaches to improve efficacy and safety of immunotherapy.

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Emerging evidence suggests that route of exposure to food allergens in early life determines sensitization versus tolerance.

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The microbiota and dietary factors appear to play a key role in susceptibility to food allergy.

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Immunotherapy applied via different routes is currently the most promising form of experimental treatment for food allergy.

Does pet-keeping modify the association of delivery mode with offspring body size?

Caesarean-section (CS) delivery increases risk of childhood obesity, and is associated with a distinct early-life gut microbiome, which may contribute to obesity. Household pets may alter human gut microbiome composition. We examined if pet-keeping modified the association of CS with obesity at age 2 years in 639 Wayne County Health, Environment, Allergy and Asthma Longitudinal Study birth cohort participants. Pet-keeping was defined as having a dog or cat (indoors ≥1 h/day) at child age 2 years. We used logistic regression to test for an interaction between CS and pet-keeping with obesity (BMI ≥ 95th percentile) at age 2 years, adjusted for maternal obesity. A total of 328 (51.3 %) children were male; 367 (57.4 %) were African American; 228 (35.7 %) were born by CS; and 55 (8.6 %) were obese. After adjusting for maternal obesity, CS-born children had a non-significant (P = 0.25) but elevated 1.4 (95 % CI 0.8, 2.5) higher odds of obesity compared to those born vaginally. There was evidence of effect modification between current pet-keeping and delivery mode with obesity at age 2 years (interaction P = 0.054). Compared to children born vaginally without a pet currently in the home, children born via CS without a pet currently in the home had a statistically significant (P = 0.043) higher odds (odds ratio 2.00; 95 % CI 1.02, 3.93) of being obese at age 2 years. Pets modified the CS-BMI relationship; whether the underlying mechanism is through effects on environmental or gut microbiome requires specific investigation.

Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children

Variations in home characteristics, such as moisture and occupancy, affect indoor microbial ecology as well as human exposure to microorganisms. Our objective was to determine how indoor bacterial and fungal community structure and diversity are associated with the broader home environment and its occupants. Next-generation DNA sequencing was used to describe fungal and bacterial communities in house dust sampled from 198 homes of asthmatic children in southern New England. Housing characteristics included number of people/children, level of urbanization, single/multifamily home, reported mold, reported water leaks, air conditioning (AC) use, and presence of pets. Both fungal and bacterial community structures were non-random and demonstrated species segregation (C-score, P < 0.00001). Increased microbial richness was associated with the presence of pets, water leaks, longer AC use, suburban (vs. urban) homes, and dust composition measures (P < 0.05). The most significant differences in community composition were observed for AC use and occupancy (people, children, and pets) characteristics. Occupant density measures were associated with beneficial bacterial taxa, including Lactobacillus johnsonii as measured by qPCR. A more complete knowledge of indoor microbial communities is useful for linking housing characteristics to human health outcomes. Microbial assemblies in house dust result, in part, from the building's physical and occupant characteristics.

Chamber bioaerosol study: human emissions of size-resolved fluorescent biological aerosol particles

Humans are a prominent source of airborne biological particles in occupied indoor spaces, but few studies have quantified human bioaerosol emissions. The chamber investigation reported here employs a fluorescence-based technique to evaluate bioaerosols with high temporal and particle size resolution. In a 75-m(3) chamber, occupant emission rates of coarse (2.5-10 μm) fluorescent biological aerosol particles (FBAPs) under seated, simulated office-work conditions averaged 0.9 ± 0.3 million particles per person-h. Walking was associated with a 5-6× increase in the emission rate. During both walking and sitting, 60-70% or more of emissions originated from the floor. The increase in emissions during walking (vs. while sitting) was mainly attributable to release of particles from the floor; the associated increased vigor of upper body movements also contributed. Clothing, or its frictional interaction with human skin, was demonstrated to be a source of coarse particles, and especially of the highly fluorescent fraction. Emission rates of FBAPs previously reported for lecture classes were well bounded by the experimental results obtained in this chamber study. In both settings, the size distribution of occupant FBAP emissions had a dominant mode in the 3-5 μm diameter range.

Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities

The intestinal microbiota is involved in many physiological processes and it is increasingly recognized that differences in community composition can influence the outcome of a variety of murine models used in biomedical research. In an effort to describe and account for the variation in intestinal microbiota composition across the animal facilities of participating members of the DFG Priority Program 1656 "Intestinal Microbiota", we performed a survey of C57BL/6J mice from 21 different mouse rooms/facilities located at 13 different institutions across Germany. Fresh feces was sampled from five mice per room/facility using standardized procedures, followed by extraction and 16S rRNA gene profiling (V1-V2 region, Illumina MiSeq) at both the DNA and RNA (reverse transcribed to cDNA) level. In order to determine the variables contributing to bacterial community differences, we collected detailed questionnaires of animal husbandry practices and incorporated this information into our analyses. We identified considerable variation in a number of descriptive aspects including the proportions of major phyla, alpha- and beta diversity, all of which displayed significant associations to specific aspects of husbandry. Salient findings include a reduction in alpha diversity with the use of irradiated chow, an increase in inter-individual variability (beta diversity) with respect to barrier access and open cages and an increase in bacterial community divergence with time since importing from a vendor. We further observe a high degree of facility-level individuality, which is likely due to each facility harboring its own unique combination of multiple varying attributes of animal husbandry. While it is important to account and control for such differences between facilities, the documentation of such diversity may also serve as a valuable future resource for investigating the origins of microbial-driven host phenotypes.

Seasonal Dynamics of the Airborne Bacterial Community and Selected Viruses in a Children's Daycare Center

Children’s daycare centers appear to be hubs of respiratory infectious disease transmission, yet there is only limited information about the airborne microbial communities that are present in daycare centers. We have investigated the microbial community of the air in a daycare center, including seasonal dynamics in the bacterial community and the presence of specific viral pathogens. We collected filters from the heating, ventilation, and air conditioning (HVAC) system of a daycare center every two weeks over the course of a year. Amplifying and sequencing the 16S rRNA gene revealed that the air was dominated by Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes that are commonly associated with the human skin flora. Clear seasonal differences in the microbial community were not evident; however, the community structure differed when the daycare center was closed and unoccupied for a 13-day period. These results suggest that human occupancy, rather than the environment, is the major driver in shaping the microbial community structure in the air of the daycare center. Using PCR for targeted viruses, we detected a seasonal pattern in the presence of respiratory syncytial virus that included the period of typical occurrence of the disease related to the virus; however, we did not detect the presence of adenovirus or rotavirus at any time.

Influence and effect of the human microbiome in allergy and asthma

PURPOSE OF REVIEW

Studies have illustrated that the healthy human microbiome (i.e. the communities of microbes, their genomic content and interaction with the host) plays a role in the maintenance of immune homeostasis. Perturbation of these communities is an emerging characteristic of an increasing number of inflammatory diseases. The goal of this article is to review the current literature on both respiratory and gut microbiomes and their established relationship with allergy and asthma.

RECENT FINDINGS

Multiple studies have demonstrated airway microbiota dysbiosis, characterized by Proteobacteria expansion in the lower airways, to be a consistent trait of established adult asthma. Members of this phylum are associated with disease features such as bronchial hyperreactivity or corticosteroid resistance. Emerging evidence implicates the neonatal gut microbiome as playing a significant role in the development of childhood atopy, a common precursor to asthma. Murine studies have demonstrated that specific bacterial species (e.g. Lactobacillus johnsonii, Bacteroides fragilis) and microbial metabolites (e.g. the short-chain fatty acid propionate), when supplemented to animals, confer protection against allergen-induced airway disorders.

SUMMARY

The emerging view of atopy and asthma is one consistently related to inappropriate microbial community composition and function in both the airway and gastrointestinal tract. This opens up the possibility that strategies to rationally manipulate microbiota at these sites may represent a novel approach to disease prevention or management.

Composition of the gut microbiota modulates the severity of malaria

Plasmodium infections result in clinical presentations that range from asymptomatic to severe malaria, resulting in ∼1 million deaths annually. Despite this toll on humanity, the factors that determine disease severity remain poorly understood. Here, we show that the gut microbiota of mice influences the pathogenesis of malaria. Genetically similar mice from different commercial vendors, which exhibited differences in their gut bacterial community, had significant differences in parasite burden and mortality after infection with multiple Plasmodium species. Germfree mice that received cecal content transplants from "resistant" or "susceptible" mice had low and high parasite burdens, respectively, demonstrating the gut microbiota shaped the severity of malaria. Among differences in the gut flora were increased abundances of Lactobacillus and Bifidobacterium in resistant mice. Susceptible mice treated with antibiotics followed by yogurt made from these bacterial genera displayed a decreased parasite burden. Consistent with differences in parasite burden, resistant mice exhibited an elevated humoral immune response compared with susceptible mice. Collectively, these results identify the composition of the gut microbiota as a previously unidentified risk factor for severe malaria and modulation of the gut microbiota (e.g., probiotics) as a potential treatment to decrease parasite burden.

Allergies and Asthma: Do Atopic Disorders Result from Inadequate Immune Homeostasis arising from Infant Gut Dysbiosis?

Our global hypothesis is that atopic conditions and asthma develop because an individual's immune system is not able to appropriately resolve inflammation resulting from allergen exposures. We propose that the failure to appropriately down-regulate inflammation and produce a toleragenic state results primarily from less robust immune homeostatic processes rather than from a tendency to over-respond to allergenic stimuli. An individual with lower immune homeostatic capacity is unable to rapidly and completely terminate, on average over time, immune responses to innocuous allergens, increasing risk of allergic disease. A lack of robust homeostasis also increases the risk of other inflammatory conditions, such as prolonged respiratory viral infections and obesity, leading to the common co-occurrence of these conditions. Further, we posit that the development of vigorous immune homeostatic mechanisms is an evolutionary adaptation strongly influenced by both 1) exposure to a diverse maternal microbiota through the prenatal period, labor and delivery, and, 2) an orderly assemblage process of the infant's gut microbiota ecosystem shaped by breastfeeding and early exposure to a wide variety of ingested foods and environmental microbes. This early succession of microbial communities together with early allergen exposures orchestrate the development of an immune system with a robust ability to optimally control inflammatory responses and a lowered risk for atopic disorders.

Indoor microbial communities: Influence on asthma severity in atopic and nonatopic children

BACKGROUND

Allergic and nonallergic asthma severity in children can be affected by microbial exposures.

OBJECTIVE

We sought to examine associations between exposures to household microbes and childhood asthma severity stratified by atopic status.

METHODS

Participants (n = 196) were selected from a cohort of asthmatic children in Connecticut and Massachusetts. Children were grouped according to asthma severity (mild with no or minimal symptoms and medication or moderate to severe persistent) and atopic status (determined by serum IgE levels). Microbial community structure and concentrations in house dust were determined by using next-generation DNA sequencing and quantitative PCR. Logistic regression was used to explore associations between asthma severity and exposure metrics, including richness, taxa identification and quantification, community composition, and concentration of total fungi and bacteria.

RESULTS

Among all children, increased asthma severity was significantly associated with an increased concentration of summed allergenic fungal species, high total fungal concentrations, and high bacterial richness by using logistic regression in addition to microbial community composition by using the distance comparison t test. Asthma severity in atopic children was associated with fungal community composition (P = .001). By using logistic regression, asthma severity in nonatopic children was associated with total fungal concentration (odds ratio, 2.40; 95% CI, 1.06-5.44). The fungal genus Volutella was associated with increased asthma severity in atopic children (P = .0001, q = 0.04). The yeast genera Kondoa might be protective; Cryptococcus species might also affect asthma severity.

CONCLUSION

Asthma severity among this cohort of children was associated with microbial exposure, and associations differed based on atopic status.

Recent Understandings of Pet Allergies

Allergic reactions to pets have been recognized for at least a hundred years. Yet our understanding of the effects of all of the interactions between pet exposures and human immune responses continues to grow. Allergists, epidemiologists, and immunologists have spent years trying to better understand how exposures to pet allergens lead to allergic sensitization (the production of allergen-specific immunoglobulin class E [IgE] antibodies) and subsequent allergic disease. A major new development in this understanding is the recognition that pet exposures consist of not only allergen exposures but also changes in microbial exposures. Exposures to certain pet-associated microbes, especially in the neonatal period, appear to be able to dramatically alter how a child’s immune system develops and this in turn reduces the risk of allergic sensitization and disease. An exciting challenge in the next few years will be to see whether these changes can be developed into a realistic preventative strategy with the expectation of significantly reducing allergic disease, especially asthma.

The microbial environment and its influence on asthma prevention in early life

There is accumulating evidence to suggest that the environmental microbiome plays a significant role in asthma development. The very low prevalence of asthma in populations highly exposed to microbial environments (farm children and Amish populations) highlights its preventive potential. This microbial diversity might be necessary to instruct a well-adapted immune response and regulated inflammatory responses to other inhaled and ingested environmental elements, such as allergens, particles, and viruses. Like the internal gut microbiome, which is increasingly recognized as an important instructor of immune maturation, the external environmental microbiome might shape immune responses on the skin, airway mucosal surfaces, and potentially also the gut early in life. The diversity of the external microbial world will ensure that of the many maladapted pathways leading to asthma development, most, if not all, will be counterbalanced. Likewise, important contributors to asthma, such as allergen sensitization and allergic manifestations early in life, are being suppressed. Thus the facets of innate immunity targeted by microbes and their compounds and metabolites might be the master switch to asthma and allergy protection, which has been found in environments rich in microbial exposures.

Streptomycin treatment alters the intestinal microbiome, pulmonary T cell profile and airway hyperresponsiveness in a cystic fibrosis mouse model

Cystic fibrosis transmembrane conductance regulator deficient mouse models develop phenotypes of relevance to clinical cystic fibrosis (CF) including airway hyperresponsiveness, small intestinal bacterial overgrowth and an altered intestinal microbiome. As dysbiosis of the intestinal microbiota has been recognized as an important contributor to many systemic diseases, herein we investigated whether altering the intestinal microbiome of BALB/c Cftr(tm1UNC) mice and wild-type littermates, through treatment with the antibiotic streptomycin, affects the CF lung, intestinal and bone disease. We demonstrate that streptomycin treatment reduced the intestinal bacterial overgrowth in Cftr(tm1UNC) mice and altered the intestinal microbiome similarly in Cftr(tm1UNC) and wild-type mice, principally by affecting Lactobacillus levels. Airway hyperresponsiveness of Cftr(tm1UNC) mice was ameliorated with streptomycin, and correlated with Lactobacillus abundance in the intestine. Additionally, streptomycin treated Cftr(tm1UNC) and wild-type mice displayed an increased percentage of pulmonary and mesenteric lymph node Th17, CD8 + IL-17+ and CD8 + IFNγ+ lymphocytes, while the CF-specific increase in respiratory IL-17 producing γδ T cells was decreased in streptomycin treated Cftr(tm1UNC) mice. Bone disease and intestinal phenotypes were not affected by streptomycin treatment. The airway hyperresponsiveness and lymphocyte profile of BALB/c Cftr(tm1UNC) mice were affected by streptomycin treatment, revealing a potential intestinal microbiome influence on lung response in BALB/c Cftr(tm1UNC) mice.

Infections and Asthma

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Wheezing viral respiratory illnesses are the most common initial presentation of childhood asthma.

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Once asthma is established, viral infections, most notably rhinovirus (RV), are the most frequent trigger of severe asthma exacerbations. RV-C appears to be a particularly pathogenic virus in children with asthma.

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Evidence has recently emerged to suggest that bacterial pathogens in the lower airway may contribute to the expression of asthma. Ongoing studies are critical to our understanding of the role of the airway microbiome in asthma inception and exacerbation.

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Synergistic interactions between underlying allergy and virus infections play an important mechanistic role in asthma inception and exacerbation, and are an important therapeutic target.

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Novel therapies are needed to prevent and treat virus-induced wheezing and asthma exacerbations.

Sources of airborne microorganisms in the built environment

Each day people are exposed to millions of bioaerosols, including whole microorganisms, which can have both beneficial and detrimental effects. The next chapter in understanding the airborne microbiome of the built environment is characterizing the various sources of airborne microorganisms and the relative contribution of each. We have identified the following eight major categories of sources of airborne bacteria, viruses, and fungi in the built environment: humans; pets; plants; plumbing systems; heating, ventilation, and air-conditioning systems; mold; dust resuspension; and the outdoor environment. Certain species are associated with certain sources, but the full potential of source characterization and source apportionment has not yet been realized. Ideally, future studies will quantify detailed emission rates of microorganisms from each source and will identify the relative contribution of each source to the indoor air microbiome. This information could then be used to probe fundamental relationships between specific sources and human health, to design interventions to improve building health and human health, or even to provide evidence for forensic investigations.

The influence of the young microbiome on inflammatory diseases--Lessons from animal studies

Chronic inflammatory diseases are on the rise in the Westernized world. This rise has been correlated to a range of environmental factors, such as birth mode, rural versus urban living conditions, and use of antibiotics. Such environmental factors also influence early life gut microbiota (GM) colonization and maturation--and there is growing evidence that the negative effects of these factors on human health are mediated via GM alterations. Colonization of the gut initiates priming of the immune system from birth, driving tolerance towards non-harmful microorganisms and dietary antigens and proper reactions towards invading pathogens. This early colonization is crucial for the establishment of a healthy GM, and throughout life the balanced interaction of GM and immune system is a key element in maintaining health. An immune system out of balance increases the risk for later life inflammatory diseases. Animal models are indispensable in the studies of GM influence on disease mechanisms and progression, and focus points include studies of GM modification during pregnancy and perinatal life. Here, we present an overview of animal studies which have contributed to our understanding of GM functions in early life and how alterations affect risk and expression of certain inflammatory diseases with juvenile onset, including interventions, such as birth mode, antibiotics, and probiotics.

Distinctive Intestinal Lactobacillus Communities in 6-Month-Old Infants From Rural Malawi and Southwestern Finland

OBJECTIVE

Our aim was to compare the composition and diversity of Lactobacillus microbiota in infants living in Malawi and Southwestern Finland.

METHODS

The composition and diversity of the Lactobacillus group was analyzed in the feces of healthy 6-month-old infants living in rural Malawi (n = 44) and Southwestern Finland (n = 31), using the quantitative polymerase chain reaction method and PCR-denaturing gradient gel electrophoresis fingerprinting.

RESULTS

Malawian infants had higher counts of lactobacilli than their Finnish counterparts (7.45 log cells/g vs 6.86 log cells/g, P < 0.001, respectively) and the Lactobacillus community was richer and more diverse in the Malawian infants. Leuconostoc citreum and Weissella confusa were the predominant species in both study groups, but Malawian infants were more often colonized by these species (100% vs 74.2%, P < 0.001; 95.5% vs 41.9%, P < 0.001, respectively). Moreover, Lactobacillus ruminis, Lactobacillus gasseri, Lactobacillus acidophilus, and Lactobacillus mucosae were detected more often in the Malawian infants (59.1% vs 0.0%, P < 0.001; 38.6% vs 9.7%, P = 0.004; 29.5% vs 0.0%, P < 0.001; 22.7% vs 3.2%, P = 0.017, respectively). Lactobacillus casei group species, however, were only detected in the Finnish infants.

CONCLUSIONS

Malawian infants have a more abundant Lactobacillus microbiota with a distinct composition compared with Finnish infants. The environment, including diet and hygiene, may be among the factors influencing these differences.

Home dust microbiota is disordered in homes of low-income asthmatic children

OBJECTIVE

Exposure to microorganisms has repeatedly been found to influence development of atopic diseases, such as asthma. Innovative techniques have been developed that can comprehensively characterize microbial communities. The objective of this study was to characterize the home microbiota of asthmatic children utilizing 16S rRNA-based phylogenetic analysis by microarray.

METHODS

In this cross-sectional study, DNA was extracted from home dust and bacterial 16S rRNA genes amplified. Bacterial products were hybridized to the PhyloChip Array and scanned using a GeneArray scanner (Affymetrix, Santa Clara, CA). The Adonis test was used to determine significant differences in the whole microbiome. Welch's t-test was used to determine significant abundance differences and genus-level richness differences.

RESULTS

Nineteen homes were included in the analysis (14 asthma and five no asthma). About 1741 operational taxonomic units (OTUs) were found in at least one sample. Bacterial genus richness did not differ in the homes of asthmatics and non-asthmatics (p = 0.09). The microbial profile was significantly different between the two groups (p = 0.025). All the top 12 OTUs with significant abundance differences were increased in homes of asthmatics and belonged to one of the five phyla (p = 0.001 to p = 7.2 × 10(-6)). Nearly half of significant abundance differences belonged to the phylum Cyanobacteria or Proteobacteria.

CONCLUSIONS

These results suggest that home dust has a characteristic microbiota which is disturbed in the homes of asthmatics, resulting in a particular abundance of Cyanobacteria and Proteobacteria. Further investigations are needed which utilize high-throughput technology to further clarify how home microbial exposures influence human health and disease.

Microbiota of the indoor environment: a meta-analysis

BACKGROUND

As modern humans, we spend the majority of our time in indoor environments. Consequently, environmental exposure to microorganisms has important implications for human health, and a better understanding of the ecological drivers and processes that impact indoor microbial assemblages will be key for expanding our knowledge of the built environment. In the present investigation, we combined recent studies examining the microbiota of the built environment in order to identify unifying community patterns and the relative importance of indoor environmental factors. Ultimately, the present meta-analysis focused on studies of bacteria and archaea due to the limited number of high-throughput fungal studies from the indoor environment. We combined 16S ribosomal RNA (rRNA) gene datasets from 16 surveys of indoor environments conducted worldwide, additionally including 7 other studies representing putative environmental sources of microbial taxa (outdoor air, soil, and the human body).

RESULTS

Combined analysis of subsets of studies that shared specific experimental protocols or indoor habitats revealed community patterns indicative of consistent source environments and environmental filtering. Additionally, we were able to identify several consistent sources for indoor microorganisms, particularly outdoor air and skin, mirroring what has been shown in individual studies. Technical variation across studies had a strong effect on comparisons of microbial community assemblages, with differences in experimental protocols limiting our ability to extensively explore the importance of, for example, sampling locality, building function and use, or environmental substrate in structuring indoor microbial communities.

CONCLUSIONS

We present a snapshot of an important scientific field in its early stages, where studies have tended to focus on heavy sampling in a few geographic areas. From the practical perspective, this endeavor reinforces the importance of negative "kit" controls in microbiome studies. From the perspective of understanding mechanistic processes in the built environment, this meta-analysis confirms that broad factors, such as geography and building type, structure indoor microbes. However, this exercise suggests that individual studies with common sampling techniques may be more appropriate to explore the relative importance of subtle indoor environmental factors on the indoor microbiome.

Our interface with the built environment: immunity and the indoor microbiota

The rise of urbanization and an increasingly indoor lifestyle has affected human interactions with our microbiota in unprecedented ways. We discuss how this lifestyle may influence immune development and function, and argue that it is time that we examined ways to manipulate the indoor environment to increase our exposure to a wider phylogeny of microorganisms. An important step is to continue to engage citizen scientists in the efforts to characterize our interactions with the diverse microbial environments that we inhabit.

Humans differ in their personal microbial cloud

Dispersal of microbes between humans and the built environment can occur through direct contact with surfaces or through airborne release; the latter mechanism remains poorly understood. Humans emit upwards of 10⁶ biological particles per hour, and have long been known to transmit pathogens to other individuals and to indoor surfaces. However it has not previously been demonstrated that humans emit a detectible microbial cloud into surrounding indoor air, nor whether such clouds are sufficiently differentiated to allow the identification of individual occupants. We used high-throughput sequencing of 16S rRNA genes to characterize the airborne bacterial contribution of a single person sitting in a sanitized custom experimental climate chamber. We compared that to air sampled in an adjacent, identical, unoccupied chamber, as well as to supply and exhaust air sources. Additionally, we assessed microbial communities in settled particles surrounding each occupant, to investigate the potential long-term fate of airborne microbial emissions. Most occupants could be clearly detected by their airborne bacterial emissions, as well as their contribution to settled particles, within 1.5–4 h. Bacterial clouds from the occupants were statistically distinct, allowing the identification of some individual occupants. Our results confirm that an occupied space is microbially distinct from an unoccupied one, and demonstrate for the first time that individuals release their own personalized microbial cloud.

Environmental protection from allergic diseases: From humans to mice and back

Allergic diseases have a strong environmental component, illustrated by the rapid rise of their prevalence in the Western world. Environmental exposures have been consistently shown to either promote or protect against allergic disease. Here we focus on protective exposures and the pathways they regulate. Traditional farming, natural environments with high biodiversity, and pets in the home (particularly dogs) have the most potent and consistent allergy-protective effects and are actively investigated to identify the environmental and host-based factors that confer allergy protection. Recent work emphasizes the critical protective role of microbial diversity and its interactions with the gut/lung and skin/lung axes-a cross-talk through which microbial exposure in the gut or skin powerfully influences immune responses in the lung.

The respiratory microbiome and innate immunity in asthma

PURPOSE OF REVIEW

The purpose of this study is to summarize recent studies of the lower respiratory microbiome in asthma, the role of innate immunity in asthma and strategies to understand complex microbiome-immune interactions in asthma.

RECENT FINDINGS

Recent evidence indicates that the composition of lower respiratory microbiota in asthmatic individuals, across a spectrum of disease severity, is altered compared with healthy individuals. Attributes of this altered airway microbiome have been linked to clinical and inflammatory features of asthma. The importance of innate immune cells and mucosal defense systems in asthma is increasingly appreciated and may be dysregulated in the disease.

SUMMARY

Interactions between the respiratory microbiome and innate mucosal immunity in asthma are complex and a challenge to dissect. Multiple avenues of investigation, leveraging a variety of methodologies, will need to be pursued to understand functional relationships to clinical and inflammatory phenotypes seen in asthma.

Novel microbiome-based therapeutics for chronic rhinosinusitis

The human microbiome, i.e. the collection of microbes that live on, in and interact with the human body, is extraordinarily diverse; microbiota have been detected in every tissue of the human body interrogated to date. Resident microbiota interact extensively with immune cells and epithelia at mucosal surfaces including the airways, and chronic inflammatory and allergic respiratory disorders are associated with dysbiosis of the airway microbiome. Chronic rhinosinusitis (CRS) is a heterogeneous disease with a large socioeconomic impact, and recent studies have shown that sinus inflammation is associated with decreased sinus bacterial diversity and the concomitant enrichment of specific sinus pathogens. Here, we discuss the potential role for probiotic supplementation for CRS in light of this increasing understanding of the airway microbiome and microbial interactions with the host. We focus on the ecological significance of microbiome-based probiotic supplementation and potential interactions with the gastrointestinal tract and consider microbial administration methods for treatment of CRS.

The pediatric microbiome and the lung

PURPOSE OF REVIEW

Many pediatric lung diseases are characterized by infection. These infections are generally diagnosed, studied, and treated using standard culture methods to identify 'traditional pathogens'. Based on these techniques, healthy lungs have generally been thought to be sterile. However, recent advances in culture-independent microbiological techniques challenged this paradigm by identifying diverse microbes in respiratory specimens (respiratory microbiomes) from both healthy people and those with diverse lung diseases. In addition, growing evidence suggests a link between gastrointestinal microbiomes and inflammatory diseases of various mucosal surfaces, including airways.

RECENT FINDINGS

This article reviews the rapidly developing field of respiratory microbiome research, emphasizing recent progress made employing increasingly sophisticated technologies. Although many of the relevant studies have focused on adults with cystic fibrosis, recent research has included children and adults with other respiratory diseases, as well as healthy individuals. These studies suggest that even healthy children have airway microbiomes, and that both respiratory and gastrointestinal microbiomes often differ between healthy people and those with different types and severities of airway disease. The causal relationships between microbiomes, disease type and progression, and treatments such as antibiotics must now be defined.

SUMMARY

The advent of culture-independent microbiological techniques has transformed how we think about the relationship between microbes and airway disease. More research is required to translate these findings to improved therapies and preventive strategies.

Microbiota in allergy and asthma and the emerging relationship with the gut microbiome

Asthma and atopy, classically associated with hyper-activation of the T helper 2 (Th2) arm of adaptive immunity, are among the most common chronic illnesses worldwide. Emerging evidence relates atopy and asthma to the composition and function of the human microbiome, the collection of microbes that reside in and on and interact with the human body. The ability to interrogate microbial ecology of the human host is due in large part to recent technological developments that permit identification of microbes and their products using culture-independent molecular detection techniques. In this review we explore the roles of respiratory, gut, and environmental microbiomes in asthma and allergic disease development, manifestation, and attenuation. Though still a relatively nascent field of research, evidence to date suggests that the airway and/or gut microbiome may represent fertile targets for prevention or management of allergic asthma and other diseases in which adaptive immune dysfunction is a prominent feature.

Helsinki alert of biodiversity and health

Urban living in built environments, combined with the use of processed water and food, may not provide the microbial stimulation necessary for a balanced development of immune function. Many chronic inflammatory disorders, including allergic, autoimmune, metabolic, and even some behavioural disorders, are linked to alteration in the human commensal microbiota. Sedentary lifestyle is associated with reduced exposure to a broad spectrum of environmental micro-organisms and surplus energy balance, both risk factors of chronic inflammatory disorders. According to the Biodiversity Hypothesis, an environment with diverse macrobiota and microbiota modifies and enriches the human microbiota, which in turn is crucial in the development and maintenance of appropriate immune function. These issues were discussed in the symposium 'Chronic Inflammation, Lifestyle and Environment', held in Helsinki, 20-22 August 2014, under the sponsorship of the Yrjö Jahnsson Foundation. This paper briefly outlines the recent findings in the context of the environment, lifestyle, and health; discusses the forces that undermine immune tolerance in urban environments; and highlights the possibilities to restore broken immune tolerance among urban dwellers, summarizing the main messages in four statements and calling for actions to combat major public health threats.

Hospital-associated microbiota and implications for nosocomial infections

The rise of high-throughput sequencing technologies and culture-independent microbial surveys has the potential to revolutionize our understanding of how microbes colonize, move about, and evolve in hospital environments. Genome analysis of individual organisms, characterization of population dynamics, and microbial community ecology are facilitating the identification of novel pathogens, the tracking of disease outbreaks, and the study of the evolution of antibiotic resistance. Here we review the recent applications of these methods to microbial ecology studies in hospitals and discuss their potential to influence hospital management policy and practice and to reduce nosocomial infections and the spread of antibiotic resistance.

Helicobacter pylori update: gastric cancer, reliable therapy, and possible benefits

Helicobacter pylori infection contributes to the development of diverse gastric and extragastric diseases. The infection is necessary but not sufficient for the development of gastric adenocarcinoma. Its eradication would eliminate a major worldwide cause of cancer death, therefore there is much interest in identifying how, if, and when this can be accomplished. There are several mechanisms by which H pylori contributes to the development of gastric cancer. Gastric adenocarcinoma is one of many cancers associated with inflammation, which is induced by H pylori infection, yet the bacteria also cause genetic and epigenetic changes that lead to genetic instability in gastric epithelial cells. H pylori eradication reduces both. However, many factors must be considered in determining whether treating this bacterial infection will prevent cancer or only reduce its risk-these must be considered in designing reliable and effective eradication therapies. Furthermore, H pylori infection has been proposed to provide some benefits, such as reducing the risks of obesity or childhood asthma. When tested, these hypotheses have not been confirmed and are therefore most likely false.

The microbiome in asthma

The application of recently developed sensitive, specific, culture-independent tools for identification of microbes is transforming concepts of microbial ecology, including concepts of the relationships between the vast complex populations of microbes associated with ourselves and with states of health and disease. Although most work initially focused on the community of microbes (microbiome) in the gastrointestinal tract and its relationship to gastrointestinal disease, interest has expanded to include study of the relationships of the airway microbiome to asthma and its phenotypes and to the relationships between the gastrointestinal microbiome, development of immune function, and predisposition to allergic sensitization and asthma. Here we provide our perspective on the findings of studies of differences in the airway microbiome between asthmatic patients and healthy subjects and of studies of relationships between environmental microbiota, gut microbiota, immune function, and asthma development. In addition, we provide our perspective on how these findings suggest the broad outline of a rationale for approaches involving directed manipulation of the gut and airway microbiome for the treatment and prevention of allergic asthma.

Asthma myths, controversies, and dogma

Although the symptom complex we call asthma has been well described since antiquity, our understanding of the causes and therapy of asthma has evolved. Even with this evolution in our understanding, there are persistent myths (widely held but false beliefs) and dogma (entrenched beliefs) regarding the causes, classification, and therapy of asthma. It is sobering that some of the knowledge we hold dear today, will become the mythology of tomorrow.

Green areas around homes reduce atopic sensitization in children

Background

Western lifestyle is associated with high prevalence of allergy, asthma and other chronic inflammatory disorders. To explain this association, we tested the ‘biodiversity hypothesis’, which posits that reduced contact of children with environmental biodiversity, including environmental microbiota in natural habitats, has adverse consequences on the assembly of human commensal microbiota and its contribution to immune tolerance.

Methods

We analysed four study cohorts from Finland and Estonia (n = 1044) comprising children and adolescents aged 0.5–20 years. The prevalence of atopic sensitization was assessed by measuring serum IgE specific to inhalant allergens. We calculated the proportion of five land-use types – forest, agricultural land, built areas, wetlands and water bodies – in the landscape around the homes using the CORINE2006 classification.

Results

The cover of forest and agricultural land within 2–5 km from the home was inversely and significantly associated with atopic sensitization. This relationship was observed for children 6 years of age and older. Land-use pattern explained 20% of the variation in the relative abundance of Proteobacteria on the skin of healthy individuals, supporting the hypothesis of a strong environmental effect on the commensal microbiota.

Conclusions

The amount of green environment (forest and agricultural land) around homes was inversely associated with the risk of atopic sensitization in children. The results indicate that early-life exposure to green environments is especially important. The environmental effect may be mediated via the effect of environmental microbiota on the commensal microbiota influencing immunotolerance.

Innate immunity in the lung regulates the development of asthma

The lung, while functioning as a gas exchange organ, encounters a large array of environmental factors, including particulate matter, toxins, reactive oxygen species, chemicals, allergens, and infectious microbes. To rapidly respond to and counteract these elements, a number of innate immune mechanisms have evolved that can lead to lung inflammation and asthma, which is the focus of this review. These innate mechanisms include a role for two incompletely understood cell types, invariant natural killer T (iNKT) cells and innate lymphoid cells (ILCs), which together produce a wide range of cytokines, including interleukin-4 (IL-4), IL-5, IL-13, interferon-γ, IL-17, and IL-22, independently of adaptive immunity and conventional antigens. The specific roles of iNKT cells and ILCs in immunity are still being defined, but both cell types appear to play important roles in the lungs, particularly in asthma. As we gain a better understanding of these innate cell types, we will acquire great insight into the mechanisms by which allergic and non-allergic asthma phenotypes develop.

Environmentally determined differences in the murine lung microbiota and their relation to alveolar architecture

Commensal bacteria control the micro-ecology of metazoan epithelial surfaces with pivotal effect on tissue homeostasis and host defense. In contrast to the upper respiratory tract, the lower respiratory tract of healthy individuals has largely been considered free of microorganisms. To understand airway micro-ecology we studied microbiota of sterilely excised lungs from mice of different origin including outbred wild mice caught in the natural environment or kept under non-specific-pathogen-free (SPF) conditions as well as inbred mice maintained in non-SPF, SPF or germ-free (GF) facilities. High-throughput pyrosequencing of reverse transcribed 16S rRNA revealed metabolically active murine lung microbiota in all but GF mice. The overall composition across samples was similar at the phylum and family level. However, species richness was significantly different between lung microbiota from SPF and non-SPF mice. Non-cultivatable Betaproteobacteria such as Ralstonia spp. made up the major constituents and were also confirmed by 16S rRNA gene cloning analysis. Additionally, Pasteurellaceae, Enterobacteria and Firmicutes were isolated from lungs of non-SPF mice. Bacterial communities were detectable by fluorescent in situ hybridization (FISH) at alveolar epithelia in the absence of inflammation. Notably, higher bacterial abundance in non-SPF mice correlated with more and smaller size alveolae, which was corroborated by transplanting Lactobacillus spp. lung isolates into GF mice. Our data indicate a common microbial composition of murine lungs, which is diversified through different environmental conditions and affects lung architecture. Identification of the microbiota of murine lungs will pave the path to study their influence on pulmonary immunity to infection and allergens using mouse models.

The microbiota, chemical symbiosis, and human disease

Our understanding of mammalian-microbial mutualism has expanded by combing microbial sequencing with evolving molecular and cellular methods, as well as unique model systems. Here, the recent literature linking the microbiota to diseases of three of the key mammalian mucosal epithelial compartments-nasal, lung, and gastrointestinal tract-is reviewed with a focus on new knowledge about the taxa, species, proteins, and chemistry that promote health and impact progression toward disease. The information presented is further organized by specific diseases now associated with the microbiota: Staphylococcus aureus infection and rhinosinusitis in the nasal-sinus mucosa, as well as cystic fibrosis, chronic obstructive pulmonary disorder, and asthma in the pulmonary tissues. For the vast and microbially dynamic gastrointestinal compartment, several disorders are considered, including obesity, atherosclerosis, Crohn's disease, ulcerative colitis, drug toxicity, and even autism. Our appreciation of the chemical symbiosis ongoing between human systems and the microbiota continues to grow and suggests new opportunities for modulating this symbiosis using designed interventions.

Microbiome diversity and asthma and allergy risk

The prevalence of asthma and allergy has been constantly increasing in Westernized countries in the last decades. Asthma and allergies are complex diseases with a local tissue inflammation that are determined by genetic and environmental factors. Because the commensal microflora is crucial to maintain inflammatory homeostasis and to induce immune regulation, the microbiome may play an important role for the development of allergic conditions. New techniques such as next-generation sequencing methods give the opportunity to explore the microbial community structure of the human body comprehensively. In this review, we will discuss the available literature concerning the human microbiota and asthma and allergy development and occurrence. The focus is on studies of the local microbiome of the place of inflammation, the gastrointestinal microbiome, and the influence of intrinsic factors relating to the host and extrinsic factors relating to the external environment on the microbiome.

Allergic sensitization and the environment: latest update

The prevalence of asthma and other allergic diseases is still increasing both in developed and developing countries. Allergic sensitization against common inhalant allergens is common and, although not sufficient, a necessary step in the development of allergic diseases. Despite a small number of proteins from certain plants and animals being common allergens in humans, we still do not fully understand who will develop sensitization and to which allergens. Environmental exposure to these allergens is essential for the development of sensitization, but what has emerged clearly in the literature in the recent years is that the adjuvants to which an individual is exposed at the same time as the allergen are probably an equally important determinant of the immune response to the allergen. These adjuvants act on all steps in the development of sensitization from modifying epithelial barriers, to facilitating antigen presentation, to driving T-cell responses, to altering mast cell and basophil hyperreactivity. The adjuvants come from biogenic sources, including microbes and the plants and animals that produce the allergens, and from man-made sources (anthropogenic), including unintended by-products of combustion and chemicals now ubiquitous in modern life. As we better understand how individuals are exposed to these adjuvants and how the exposure influences the likelihood of an allergic response, we may be able to design individual and community-level interventions that will reverse the increase in allergic disease prevalence, but we are not there yet.

Longitudinal analysis of microbial interaction between humans and the indoor environment

The bacteria that colonize humans and our built environments have the potential to influence our health. Microbial communities associated with seven families and their homes over 6 weeks were assessed, including three families that moved their home. Microbial communities differed substantially among homes, and the home microbiome was largely sourced from humans. The microbiota in each home were identifiable by family. Network analysis identified humans as the primary bacterial vector, and a Bayesian method significantly matched individuals to their dwellings. Draft genomes of potential human pathogens observed on a kitchen counter could be matched to the hands of occupants. After a house move, the microbial community in the new house rapidly converged on the microbial community of the occupants' former house, suggesting rapid colonization by the family's microbiota.

Urban microbiomes and urban ecology: how do microbes in the built environment affect human sustainability in cities?

Humans increasingly occupy cities. Globally, about 50% of the total human population lives in urban environments, and in spite of some trends for deurbanization, the transition from rural to urban life is expected to accelerate in the future, especially in developing nations and regions. The Republic of Korea, for example, has witnessed a dramatic rise in its urban population, which now accounts for nearly 90% of all residents; the increase from about 29% in 1955 has been attributed to multiple factors, but has clearly been driven by extraordinary growth in the gross domestic product accompanying industrialization. While industrialization and urbanization have unarguably led to major improvements in quality of life indices in Korea and elsewhere, numerous serious problems have also been acknowledged, including concerns about resource availability, water quality, amplification of global warming and new threats to health. Questions about sustainability have therefore led Koreans and others to consider deurbanization as a management policy. Whether this offers any realistic prospects for a sustainable future remains to be seen. In the interim, it has become increasingly clear that built environments are no less complex than natural environments, and that they depend on a variety of internal and external connections involving microbes and the processes for which microbes are responsible. I provide here a definition of the urban microbiome, and through examples indicate its centrality to human function and wellbeing in urban systems. I also identify important knowledge gaps and unanswered questions about urban microbiomes that must be addressed to develop a robust, predictive and general understanding of urban biology and ecology that can be used to inform policy-making for sustainable systems.