Microbial exposure to dairy farmers' dwellings and COPD occurrence

Season, Vegetation Proximity and Building Age Shape the Indoor Fungal Communities’ Composition at City-Scale

Exposure to particular microbiome compositions in the built environment can affect human health and well-being. Identifying the drivers of these indoor microbial assemblages is key to controlling the microbiota of the built environment. In the present study, we used culture and metabarcoding of the fungal Internal Transcribed Spacer ribosomal RNA region to assess whether small-scale variation in the built environment influences the diversity, composition and structure of indoor air fungal communities between a heating and an unheated season. Passive dust collectors were used to collect airborne fungi from 259 dwellings representative of three major building periods and five building environments in one city—Lausanne (Vaud, Switzerland)—over a heating and an unheated period. A homogenous population (one or two people with an average age of 75 years) inhabited the households. Geographic information systems were used to assess detailed site characteristics (altitude, proximity to forest, fields and parks, proximity to the lake, and density of buildings and roads) for each building. Our analysis indicated that season was the factor that explained most of the variation in colonies forming unit (CFU) concentration and indoor mycobiome composition, followed by the period of building construction. Fungal assemblages were more diverse during the heating season than during the unheated season. Buildings with effective insulation had distinct mycobiome compositions from those built before 1975 — regardless of whether they were constructed with pre-1945 technology and materials or 1945 — 1974 ones. The urban landscape—as a whole—was a significant predictor of cultivable Penicillium load—the closer the building was to the lake, the higher the Penicillium load—but not of fungal community composition. Nevertheless, the relative abundance of eleven fungal taxa detected by metabarcoding decreased significantly with the urbanization gradient. When urban landscape descriptors were analyzed separately, the explanatory power of proximity to vegetation in shaping fungal assemblages become significant, indicating that land cover type had an influence on fungal community structure that was obscured by the effects of building age and sampling season. In conclusion, indoor mycobiomes are strongly modulated by season, and their assemblages are shaped by the effectiveness of building insulation, but are weakly influenced by the urban landscape.

Vitamin D3 alleviates cigarette smoke extract‑mediated epithelial‑mesenchymal transition and fibrogenesis by upregulating CC16 expression in bronchial epithelial cells

Vitamin D3 supplementation has been previously reported to inhibit the occurrence and development of chronic obstructive pulmonary disease (COPD). However, the underlying mechanism remains unclear. Epithelial-mesenchymal transition (EMT) and fibrogenesis have been associated with the development of COPD. The aim of the present study was to investigate the potential effects and mechanism of vitamin D3 in an in vitro model of cigarette smoke (CS)-induced EMT and fibrosis, with specific focus on the role of club cell protein 16 (CC16). CS extract (CSE) at different concentrations (5, 10 and 20%) was used to treat 16-HBE cells to induce EMT and fibrogenesis following which they were treated with vitamin D3. Subsequently, the 20% CSE group was selected for further experiments, where 16-HBE cells were divided into the following five groups: The control group; the CSE group; the low-dose vitamin D3 group (250 nM); the medium-dose vitamin D3 group (500 nM); and the high-dose vitamin D3 group (1,000 nM). Western blot analysis was used to detect the protein expression levels of the EMT-related proteins E-cadherin, N-cadherin, Slug and α-SMA, fibrogenesis-related proteins collagen Ⅳ and fibronectin 1, proteins involved in the TGF-β1/SMAD3 signaling pathway and CC16. Immunofluorescence was used to measure the protein expression levels of E-cadherin, N-cadherin and collagen Ⅳ. Specific CC16 knockdown was performed using short hairpin RNA transfection to investigate the role of CC16. The results of the present study found that vitamin D3 could increase the protein expression level of CC16 to inhibit the activation of the TGF-β1/SMAD3 signaling pathway; thereby reducing the 20% increase in CSE-induced EMT- and fibrogenesis-related protein expression levels. Following CC16 knockdown, the inhibitory effects of vitamin D3 on EMT- and fibrogenesis-related protein expression were partially reversed. To conclude, these results suggest that vitamin D3 can inhibit the protein expression levels of EMT- and fibrogenesis-related proteins induced by CSE, at least partially through the function of CC16. These findings are expected to provide novel theoretical foundations and ideas for the pathogenesis and treatment of COPD.

Impact of domestic mould exposure on Aspergillus biomarkers and lung function in patients with chronic obstructive pulmonary disease

Patients with chronic obstructive pulmonary disease (COPD) are frequently colonised or sensitised by Aspergillus, but clinical significance remains unclear. Furthermore, little is known on the impact of indoor mould exposure during COPD. In this study, we assessed the relationship between domestic mould exposure, Aspergillus biomarkers and COPD severity during acute exacerbation and at stable state. Aspergillus section Fumigati culture in sputum and anti-Aspergillus antibodies detection (IgG and precipitins) were followed up in COPD patients that were prospectively recruited during exacerbation (n = 62), and underwent a visit at stable state after 18 months (n = 33). Clinical characteristics were collected at inclusion. Electrostatic dust collectors (EDCs) were used to measure domestic mould contamination. Aspergillus section Fumigati was more frequently detected during exacerbation (16.9%) than at stable state (4.0%), but the frequency of patients presenting with anti-Aspergillus antibodies was similar (32.2% and 33.3%, respectively). Aspergillus section Fumigati detection was associated with a higher body-mass index (BMI) during exacerbation, whereas patients with anti-Aspergillus antibodies presented a lower BMI and forced expiratory volume in 1 s, as well as a higher frequency of inhaled corticoids and higher total mould and Penicillium exposure at final visit (P < 0.05). The frequency of patients with anti-Aspergillus antibodies was higher for total mould counts >30 CFU/cm² (P = 0.03). Aspergillosis was diagnosed in 2 patients (6.1%) who presented increased levels of antibodies. Our data suggest that anti-Aspergillus antibodies are associated with chronic lung function alteration and/or domestic mould exposure, thereby supporting the consideration of indoor mould contamination and anti-Aspergillus antibodies kinetics in COPD management.

Indoor Microbial Exposures and Chronic Lung Disease: From Microbial Toxins to the Microbiome

Effects of environmental microbial exposures on human health have long been of interest. Microbes were historically assumed to be harmful, but data have suggested that microbial exposures can modulate the immune system. We focus on the effects of indoor environmental microbial exposure on chronic lung diseases. We found contradictory data in bacterial studies using endotoxin as a surrogate for bacterial exposure. Contradictory data also exist in studies of fungal exposure. Many factors may modulate the effect of environmental microbial exposures on lung health, including coexposures. Future studies need to clarify which method of assessing environmental microbial exposures is most relevant.

Characterization of chronic obstructive pulmonary disease in dairy farmers

BACKGROUND

Although farming is often considered a risk factor for COPD, data regarding the burden and characteristics of COPD in dairy farmers are sparse and conflicting.

OBJECTIVES

To characterize COPD in dairy farmers.

METHODS

4788 subjects entered two parallel COPD screening programs, one in agricultural workers and one in general practice from 2011 to 2015. Subjects with COPD were invited to participate in the characterization phase of the study. Those who accepted were included in two subgroups: dairy farmers with COPD (DF-COPD) (n = 101) and non-farmers with COPD (NF-COPD) (n = 85). Patients with COPD were frequency-matched with subjects with normal spirometry for age, sex and tobacco smoking (pack-years and status) (DF-controls n = 98, NF-controls n = 89). All subjects from these four groups underwent lung function and exercise testing, questionnaires and blood analysis.

RESULTS

The frequency of COPD in dairy farmers was 8.0% using the GOLD criterion and 6.2% using the lower limit of normal criterion and was similar in non-farming subjects (7.3% and 5.2%, respectively) although dairy farmers had lower tobacco consumption (screening phase). DF-COPD had better pulmonary function, exercise capacity and quality of life, fewer symptoms and comorbidities than NF-COPD, and higher levels of some Th2 biomarkers (MCP-2, periostin) (characterization phase). In farmers, COPD was not related to occupational exposure factors, supporting the role of host factors.

CONCLUSION

COPD secondary to organic dust exposure (dairy farming) appears less severe and associated with fewer comorbidities than COPD secondary to tobacco smoking.

In Patients with Mild-to-Moderate COPD, Tobacco Smoking, and Not COPD, Is Associated with a Higher Risk of Cardiovascular Comorbidity

Background

Comorbidities including cardiovascular diseases are very common in chronic obstructive pulmonary disease (COPD) secondary to tobacco smoking and contribute to the overall severity of the disease. In non-smoking COPD, which accounts for about 25% of COPD cases worldwide, current knowledge on the frequency and determinants of comorbidities remains scarce. The aims of the current study were to assess the frequency of major comorbidities and to evaluate their determinants in a group of non-selected patients with mild-to-moderate COPD who were exposed to organic dust (dairy farmers), to tobacco smoking, or to both, and in controls without COPD who were exposed to organic dust (dairy farmers), or to tobacco smoking, or to both, or who were without exposure.

Patients and Methods

A total of 4665 subjects (2323 dairy farmers and 2342 non-farmers) including 355 patients with COPD and 4310 controls with normal spirometry were recruited through a large COPD screening program. Self-reported physician-diagnosed diseases with plausible links to COPD were recorded in this cross-sectional study.

Results

Whatever the exposure, cardiovascular comorbidities were not more frequent in patients with COPD than their counterparts without airflow limitation. A higher risk of major cardiovascular comorbidities was associated with tobacco smoking and a lower risk was associated with exposure to organic dusts.

Conclusion

Tobacco smoking (but not COPD) is associated with higher frequency of cardiovascular comorbidities. By contrast, being a dairy farmer exposed to organic dusts is associated with a lower frequency of the same comorbidities. This reinforces the crucial need for controlling established cardiovascular risk factors even in patients with mild-to-moderate COPD.

Fingerprinting ambient air to understand bioaerosol profiles in three different environments in the south east of England

Molecular and chemical fingerprints from 10 contrasting outdoor air environments, including three agricultural farms, three urban parks and four industrial sites were investigated to advance our understanding of bioaerosol distribution and emissions. Both phospholipid fatty acids (PLFA) and microbial volatile organic compounds (MVOC) profiles showed a different distribution in summer compared to winter. Further to this, a strong positive correlation was found between the total concentration of MVOCs and PLFAs (r = 0.670, p = 0.004 in winter and r = 0.767, p = 0.001 in summer) demonstrating that either chemical or molecular fingerprints of outdoor environments can provide good insights into the sources and distribution of bioaerosols. Environment specific variables and most representative MVOCs were identified and linked to microbial species emissions via a MVOC database and PLFAs taxonomical classification. While similar MVOCs and PLFAs were identified across all the environments suggesting common microbial communities, specific MVOCs were identified for each contrasting environment. Specifically, 3,4-dimethylpent-1-yn-3-ol, ethoxyethane and propanal were identified as key MVOCs for the industrial areas (and were correlated to fungi, Staphylococcus aureus (Gram positive bacteria) and Gram negative bacteria, R = 0.863, R = 0.618 and R = 0.676, respectively) while phthalic acid, propene and isobutane were key for urban environments (correlated to Gram negative bacteria, fungi and bacteria, R = 0.874, R = 0.962 and R = 0.969 respectively); and ethanol, 2-methyl-2-propanol, 2-methyl-1-pentene, butane, isoprene and methyl acetate were key for farms (correlated to fungi, Gram positive bacteria and bacteria, R = 0.690 and 0.783, R = 0.706 and R = 0.790, 0.761 and 0.768). The combination of MVOCs and PLFAs markers can assist in rapid microbial fingerprinting of distinct environmental influences on ambient air quality.

Indoor Microbiome: Quantification of Exposure and Association with Geographical Location, Meteorological Factors, and Land Use in France

The indoor microbial community is a mixture of microorganisms resulting from outdoor ecosystems that seed the built environment. However, the biogeography of the indoor microbial community is still inadequately studied. Dust from more than 3000 dwellings across France was analyzed by qPCR using 17 targets: 10 molds, 3 bacteria groups, and 4 mites. Thus, the first spatial description of the main indoor microbial allergens on the French territory, in relation with biogeographical factors influencing the distribution of microorganisms, was realized in this study. Ten microorganisms out of 17 exhibited increasing abundance profiles across the country: Five microorganisms (Dermatophagoïdes pteronyssinus, Dermatophagoïdes spp., Streptomyces spp., Cladosporium sphaerospermum, Epicoccum nigrum) from northeast to southwest, two (Cryptococcus spp., Alternaria alternata) from northwest to southeast, Mycobacteria from east to west, Aspergillus fumigatus from south to north, and Penicillium chrysogenum from south to northeast. These geographical patterns were partly linked to climate and land cover. Multivariate analysis showed that composition of communities seemed to depend on landscapes, with species related to closed and rather cold and humid landscapes (forests, located in the northeast) and others to more open, hot, and dry landscapes (herbaceous and coastal regions, located in the west). This study highlights the importance of geographical location and outdoor factors that shape communities. In order to study the effect of microorganisms on human health (allergic diseases in particular), it is important to identify biogeographic factors that structure microbial communities on large spatial scales and to quantify the exposure with quantitative tools, such as the multi-qPCR approach.

Low Vitamin D Status Is Associated with Epithelial-Mesenchymal Transition in Patients with Chronic Obstructive Pulmonary Disease

Vitamin D deficiency is correlated with the increased morbidity of chronic obstructive pulmonary disease (COPD). However, the mechanisms underlying these effects have largely remained elusive. This study analyzed the correlations among COPD, vitamin D concentration, and epithelial-mesenchymal transition (EMT). Ninety-five patients with newly diagnosed COPD and 190 age- and sex-matched healthy subjects were recruited for this research. Serum 25(OH)D levels were detected, and pulmonary EMT biomarkers and TGF-β/Smad signaling were evaluated. Serum 25(OH)D level was remarkably decreased in COPD patients compared with that in control subjects. Furthermore, serum 25(OH)D concentration gradually decreased in COPD patients ranging from grade 1-2 to 4. However, reduced expression of the epithelial biomarker E-cadherin and increased expression of the mesenchymal biomarkers vimentin and α-SMA were found in COPD patients. Mechanistic analysis showed that pulmonary nuclear vitamin D receptor (VDR) was decreased in patients with COPD. In contrast, TGF-β/Smad signaling was obviously activated in COPD patients. Furthermore, the level of serum TGF-β in COPD patients increased in parallel with COPD severity. Serum 25(OH)D concentration was inversely associated with TGF-β levels in COPD patients. In vitro experiments showed that active vitamin D3 inhibits TGF-β-induced Smad2/3 phosphorylation in MRC-5 cells. Furthermore, vitamin D concentration was inversely correlated with TGF-β/Smad signaling and EMT in COPD patients, suggesting EMT as a vital mediator of COPD development in patients with low vitamin D concentrations.

Major Differences in the Diversity of Mycobiomes Associated with Wheat Processing and Domestic Environments: Significant Findings from High-Throughput Sequencing of Fungal Barcode ITS1

Occupational exposure to grain dust is associated with both acute and chronic effects on the airways. However, the aetiology of these effects is not completely understood, mainly due to the complexity and variety of potentially causative agents to which workers are exposed during cereals process. In this study, we characterized the mycobiome during different steps of wheat processing—harvesting, grain unloading and straw handling—and compared it to mycobiomes of domestic environments—rural and urban. To do so, settled dust was collected at a six month interval for six weeks in the close proximity of 142 participants, 74 occupationally exposed to wheat dust—freshly harvested or stored—and 68 not occupationally exposed to it. Fungal community composition was determined in those samples by high-throughput sequencing of the primary fungal barcode marker internal transcribed spacer 1 (ITS1). The comparison of different mycobiomes revealed that fungal richness, as well as their composition, was much higher in the domestic environment than at the workplace. Furthermore, we found that the fungal community composition strongly differed between workplaces where workers handled freshly harvested wheat and those where they handled stored wheat. Indicator species for each exposed population were identified. Our results emphasize the complexity of exposure of grain workers and farmers and open new perspectives in the identification of the etiological factors responsible for the respiratory pathologies induced by wheat dust exposure.

Is atopy a risk indicator of chronic obstructive pulmonary disease in dairy farmers?

Abstract

Allergic mechanisms related to environmental and occupational exposure have been suggested to contribute to the development of chronic obstructive pulmonary disease (COPD).

Objectives

To investigate the relationships between atopy markers, persistent airflow limitation (PAL) and occupational exposure in dairy farmers.

Methods

Clinical and biological (total IgE and 21 allergen specific IgE) markers of atopy were assessed in 101 dairy farmers with PAL (DF-PAL), 85 non-farmers with PAL (NF-PAL) (both groups were prospectively included from a screening program performed between 2011 and 2015), and matched controls, i.e. 98 farmers without PAL (DF-controls) and 89 non-farming subjects without PAL (NF-controls). Occupational exposure in farmers was estimated using a validated questionnaire.

Results

Prevalence of allergy history was significantly higher in DF-PAL and in NF-PAL than in controls. Polysensitization, and sensitization to seasonal and food allergens were more frequent in DF-PAL than in DF-controls, respectively: 13.8% vs 1% (adjusted odds ratio (aOR): 17.5 (2.2–134), 11.9% vs 3.1% (aOR: 4.4 (1.2–7.2) and 16.8% vs 4.1% (aOR: 5.2 (1.7–7.2)). The prevalence of atopy markers was similar between NF-PAL patients and NF-controls.

Conclusions

PAL in farmers is associated with a high rate of markers of atopy, supporting atopy as a risk indicator.

Clinical trial registered with ClinicalTrials.gov (NCT02540408).

Electronic supplementary material

The online version of this article (10.1186/s12931-019-1082-2) contains supplementary material, which is available to authorized users.