Periodontitis is associated with airflow obstruction in the Malmö Offspring Dental Study.

AIM: To investigate the association between periodontitis and lung function in the Malmö Offspring Dental Study. MATERIALS AND METHODS: In all 1001 individuals (49.9% female, mean age: 44.6) from Malmö Offspring Dental Study were included. Periodontitis was assessed by a full-mouth examination protocol including bleeding on probing and classified according to the American Academy of Periodontology/Center for Disease Control definitions. Forced expiratory volume in 1 s (FEV1 ) and forced vital capacity (FVC) were expressed as absolute values and %predicted according to Global Lung Function Initiative reference values. FEV1 , FVC and FEV1 /FVC were analysed in relation to periodontal status using linear regression. RESULTS: Severe periodontitis was found in 7% of the population. Adjusted regression models showed significant associations between lung function and severe periodontitis with 2.1 unit lower FEV1 /FVC ratio (95% CI: -3.91, -0.23) and odds ratio (adjusted) of 2.56 (95% CI: 1.40, 4.75, p = .003) for airflow obstruction (FEV1 /FVC less than the lower limit of normal) if having severe periodontitis. Lower values of %predicted FEV1 and %predicted FVC, but not FEV1 /FVC, were found in individuals with >25% bleeding on probing. CONCLUSIONS: Severe periodontitis was associated with lower FEV1 /FVC ratio and airflow obstruction in the present cohort. More large-scale prospective studies and intervention studies are required for a comprehensive evaluation.

Indoor Airborne Microbiome and Endotoxin: Meteorological Events and Occupant Characteristics Are Important Determinants.

Airborne bacteria and endotoxin may affect asthma and allergies. However, there is limited understanding of the environmental determinants that influence them. This study investigated the airborne microbiomes in the homes of 1038 participants from five cities in Northern Europe: Aarhus, Bergen, Reykjavik, Tartu, and Uppsala. Airborne dust particles were sampled with electrostatic dust fall collectors (EDCs) from the participants' bedrooms. The dust washed from the EDCs' clothes was used to extract DNA and endotoxin. The DNA extracts were used for quantitative polymerase chain (qPCR) measurement and 16S rRNA gene sequencing, while endotoxin was measured using the kinetic chromogenic limulus amoebocyte lysate (LAL) assay. The results showed that households in Tartu and Aarhus had a higher bacterial load and diversity than those in Bergen and Reykjavik, possibly due to elevated concentrations of outdoor bacterial taxa associated with low precipitation and high wind speeds. Bergen-Tartu had the highest difference (ANOSIM R = 0.203) in ß diversity. Multivariate regression models showed that α diversity indices and bacterial and endotoxin loads were positively associated with the occupants' age, number of occupants, cleaning frequency, presence of dogs, and age of the house. Further studies are needed to understand how meteorological factors influence the indoor bacterial community in light of climate change.

Changes in Infection Prevention Practices and Occurrence of Skin Symptoms among Healthcare Workers, Cleaners and Day-care Workers in Norway during the COVID-19 Pandemic.

The COVID-19 pandemic has resulted in increased attention on infection prevention measures. This study aims to assess whether changes in hand hygiene procedures, use of personal protective equipment and moisturizers during the first year of the COVID-19 pandemic were associated with changes in the occurrence of skin symptoms among healthcare workers, cleaners, and day-care workers. A total of 602 participants (40%) responded to an electronic questionnaire, including questions on previous and current occupational exposure and skin problems. Increased frequency of hand washing, use of hand disinfectants, use of disposable gloves and moisturizers were all associated with an increased symptom score on the hands, wrists, forearms. Participants who increased their use of masks or respirators had a higher risk of facial skin symptoms, compared with those with non-increased occupational exposure. In conclusion, a change of behaviour among healthcare workers, cleaners and day-care workers during the first year of the COVID-19 pandemic, with an increase in occupational exposures and use of moisturizers, was associated with higher occurrence of facial skin symptoms and symptoms on the hands, wrists and forearms.

Ascaris exposure and its association with lung function, asthma, and DNA methylation in Northern Europe.

BACKGROUND: Ascaris infections, with a worldwide prevalence above 10%, can cause respiratory pathology. However, long-term effects on lung function in humans are largely unknown. OBJECTIVE: We investigated the associations of Ascaris exposure with lung function, asthma, and DNA methylation. METHODS: Serum Ascaris IgG antibodies were measured in 671 adults aged 18 to 47 years (46% women) from Aarhus, Bergen, and Tartu RHINESSA study centers. Seropositivity was defined as IgG above the 90th percentile. Linear and logistic regressions were used to analyze Ascaris seropositivity as associated with lung function and asthma, adjusted for age, height, and smoking and clustered by center. DNA methylation in blood was profiled by a commercial methylation assay. RESULTS: Ascaris seropositivity was associated with lower FEV1 (-247 mL; 95% CI, -460, -34) and higher odds for asthma (adjusted odds ratio, 5.84; 95% CI, 1.67, 20.37) among men but not women, also after further adjusting for house dust mite sensitivity, consistent across study centers. At a genome-wide level, Ascaris exposure was associated with 23 differentially methylated sites in men and 3 in women. We identified hypermethylation of the MYBPC1 gene, which can regulate airway muscle contraction. We also identified genes linked to asthma pathogenesis such as CRHR1 and GRK1, as well as a differentially methylated region in the PRSS22 gene linked to nematode infection. CONCLUSION: Ascaris exposure was associated with substantially lower lung function and increased asthma risk among men. Seropositive participants had sex-specific differences in DNA methylation compared to the unexposed, thus suggesting that exposure may lead to sex-specific epigenetic changes associated with lung pathology.

Exposures during the prepuberty period and future offspring's health: evidence from human cohort studies†.

Emerging evidence suggests that exposures in prepuberty, particularly in fathers-to-be, may impact the phenotype of future offspring. Analyses of the RHINESSA cohort find that offspring of father's exposed to tobacco smoking or overweight that started in prepuberty demonstrate poorer respiratory health in terms of more asthma and lower lung function. A role of prepuberty onset smoking for offspring fat mass is suggested in the RHINESSA and ALSPAC cohorts, and historic studies suggest that ancestral nutrition during prepuberty plays a role for grand-offspring's health and morbidity. Support for causal relationships between ancestral exposures and (grand-)offspring's health in humans has been enhanced by advancements in statistical analyses that optimize the gain while accounting for the many complexities and deficiencies in human multigeneration data. The biological mechanisms underlying such observations have been explored in experimental models. A role of sperm small RNA in the transmission of paternal exposures to offspring phenotypes has been established, and chemical exposures and overweight have been shown to influence epigenetic programming in germ cells. For example, exposure of adolescent male mice to smoking led to differences in offspring weight and alterations in small RNAs in the spermatozoa of the exposed fathers. It is plausible that male prepuberty may be a time window of particular susceptibility, given the extensive epigenetic reprogramming taking place in the spermatocyte precursors at this age. In conclusion, epidemiological studies in humans, mechanistic research, and biological plausibility, all support the notion that exposures in the prepuberty of males may influence the phenotype of future offspring.

Dampness, mould, onset and remission of adult respiratory symptoms, asthma and rhinitis.

STUDY QUESTION: Is dampness and indoor mould associated with onset and remission of respiratory symptoms, asthma and rhinitis among adults? MATERIALS AND METHODS: Associations between dampness, mould and mould odour at home and at work and respiratory health were investigated in a cohort of 11 506 adults from Iceland, Norway, Sweden, Denmark and Estonia. They answered a questionnaire at baseline and 10 years later, with questions on respiratory health, home and work environment. RESULTS: Baseline water damage, floor dampness, mould and mould odour at home were associated with onset of respiratory symptoms and asthma (OR 1.23-2.24). Dampness at home during follow-up was associated with onset of respiratory symptoms, asthma and rhinitis (OR 1.21-1.52). Dampness at work during follow-up was associated with onset of respiratory symptoms, asthma and rhinitis (OR 1.31-1.50). Combined dampness at home and at work increased the risk of onset of respiratory symptoms and rhinitis. Dampness and mould at home and at work decreased remission of respiratory symptoms and rhinitis. THE ANSWER TO THE QUESTION: Dampness and mould at home and at work can increase onset of respiratory symptoms, asthma and rhinitis, and decrease remission.

Asthma and selective migration from farming environments in a three-generation cohort study.

Individuals raised on a farm appear to have less asthma than individual raised elsewhere. However, selective migration might contribute to this as may also the suggested protection from farm environment. This study investigated if parents with asthma are less likely to raise their children on a farm. This study involved three generations: 6045 participants in ECRHS/RHINE cohorts (born 1945-1973, denoted G1), their 10,121 parents (denoted G0) and their 8260 offspring participating in RHINESSA (born 1963-1998, denoted G2). G2-offspring provided information on parents not participating in ECRHS/RHINE. Asthma status and place of upbringing for all three generations were reported in questionnaires by G1 in 2010-2012 and by G2 in 2013-2016. Binary regressions with farm upbringing as outcome were performed to explore associations between parental asthma and offspring farm upbringing in G0-G1 and G1-G2. Having at least one parent with asthma was not associated with offspring farm upbringing, either in G1-G2 (RR 1.11, 95% CI 0.81-1.52) or in G0-G1 (RR 0.99, 0.85-1.15). G1 parents with asthma born in a city tended to move and raise their G2 offspring on a farm (RR 2.00, 1.12-3.55), while G1 parents with asthma born on a farm were less likely to raise their G2 offspring on a farm (RR 0.34, 0.11-1.06). This pattern was not observed in analyses of G0-G1. This study suggests that the protective effect from farm upbringing on subsequent asthma development could not be explained by selective migration. Intriguingly, asthmatic parents appeared to change environment when having children.

Cleaning at Home and at Work in Relation to Lung Function Decline and Airway Obstruction.

RATIONALE: Cleaning tasks may imply exposure to chemical agents with potential harmful effects to the respiratory system, and increased risk of asthma and respiratory symptoms among professional cleaners and in persons cleaning at home has been reported. Long-term consequences of cleaning agents on respiratory health are, however, not well described. OBJECTIVES: This study aimed to investigate long-term effects of occupational cleaning and cleaning at home on lung function decline and airway obstruction. METHODS: The European Community Respiratory Health Survey (ECRHS) investigated a multicenter population-based cohort at three time points over 20 years. A total of 6,235 participants with at least one lung function measurement from 22 study centers, who in ECRHS II responded to questionnaire modules concerning cleaning activities between ECRHS I and ECRHS II, were included. The data were analyzed with mixed linear models adjusting for potential confounders. MEASUREMENTS AND MAIN RESULTS: As compared with women not engaged in cleaning (ΔFEV1 = -18.5 ml/yr), FEV1 declined more rapidly in women responsible for cleaning at home (-22.1; P = 0.01) and occupational cleaners (-22.4; P = 0.03). The same was found for decline in FVC (ΔFVC = -8.8 ml/yr; -13.1, P = 0.02; and -15.9, P = 0.002; respectively). Both cleaning sprays and other cleaning agents were associated with accelerated FEV1 decline (-22.0, P = 0.04; and -22.9, P = 0.004; respectively). Cleaning was not significantly associated with lung function decline in men or with FEV1/FVC decline or airway obstruction. CONCLUSIONS: Women cleaning at home or working as occupational cleaners had accelerated decline in lung function, suggesting that exposures related to cleaning activities may constitute a risk to long-term respiratory health.

Agreement in reporting of asthma by parents or offspring - the RHINESSA generation study.

BACKGROUND: Self-report questionnaires are commonly used in epidemiology, but may be susceptible to misclassification, especially if answers are given on behalf of others, e.g. children or parents. The aim was to determine agreement and analyse predictors of disagreement in parents' reports of offspring asthma, and in offspring reports of parents' asthma. METHODS: In the Respiratory Health in Northern Europe, Spain and Australia (RHINESSA) generation study, 6752 offspring (age range 18-51 years) and their parents (age range 39-66 years) reported their own and each other's asthma status. Agreement between asthma reports from offspring and parents was determined by calculating sensitivity, specificity, positive and negative predictive value and Cohen's kappa. The participants' own answers regarding themselves were defined as the gold standard. To investigate predictors for disagreement logistic regression analyses were performed to obtain odds ratios (OR) with 95% confidence intervals (CI) for sex, smoking status, education, comorbidity and severity of asthma. RESULTS: Agreement was good for parental report of offspring early onset asthma (< 10 years, Cohen's kappa 0.72) and moderate for offspring later onset asthma (Cohen's kappa 0.46). Specificity was 0.99 for both, and sensitivity was 0.68 and 0.36, respectively. For offspring report of maternal and paternal asthma the agreement was good (Cohen's kappa 0.69 and 0.68), specificity was 0.96 and 0.97, and sensitivity was 0.72 and 0.68, respectively. The positive predictive value (PPV) was lowest for offspring report of maternal asthma (0.75), and highest for parents' report of early onset asthma in the offspring (0.83). The negative predictive value (NPV) was high for all four groups (0.94-0.97). In multivariate analyses current smokers (OR = 1.46 [95% CI 1.05, 2.02]) and fathers (OR = 1.31 [95% CI 1.08, 1.59]) were more likely to report offspring asthma incorrectly. Offspring wheeze was associated with reporting parental asthma incorrectly (OR = 1.60 [95% CI 1.21, 2.11]), both under- and over reporting. CONCLUSIONS: Asthma reports across generations show moderate to good agreement, making information from other generations a useful tool in the absence of direct reports.

Prevalence of, and work-related risk factors for, hand eczema in a Norwegian general population (The HUNT Study).

BACKGROUND: Chemical exposures at work and at home may cause hand eczema. However, this has been scarcely described for Norway. OBJECTIVES: To investigate the prevalence of, and occupational risk factors for, hand eczema in Norway. METHODS: Among 50 805 respondents (aged ≥20 years) to the third Nord-Trøndelag Health Study (HUNT3), 5757 persons reported ever having hand eczema, and 4206 answered a hand eczema questionnaire. RESULTS: The lifetime prevalences of hand eczema were 8.4% in men and 13.8% in women (p < 0.001), with onset at age ≤10 years in 24% (men) and 20% (women), and onset at age ≥30 years in 37% (men) and 25% (women) (p < 0.001). Work-related hand eczema affected 4.8% of the population, and was most frequently associated with health/social work (29%) and occupational cleaning (20%) in women, and with farming (26%) and industrial occupations (27%) in men. Cleaning detergents (75%) and other chemicals (36%) were the most common exacerbating factors. CONCLUSIONS: The prevalence of hand eczema was 11.3%, and that of work-related hand eczema was 4.8%. Hand eczema was more common in women than in men, but with a later onset in men. Cleaning detergents were the most common aggravating factors. A large proportion of the Nord-Trøndelag population is employed in farming, providing the possibility to identify farming as an important risk factor for hand eczema.

Menopause as a predictor of new-onset asthma: A longitudinal Northern European population study.

BACKGROUND: There is limited and conflicting evidence on the effect of menopause on asthma. OBJECTIVES: We sought to study whether the incidence of asthma and respiratory symptoms differ by menopausal status in a longitudinal population-based study with an average follow-up of 12 years. METHODS: The Respiratory Health in Northern Europe study provided questionnaire data pertaining to respiratory and reproductive health at baseline (1999-2001) and follow-up (2010-2012). The study cohort included women aged 45 to 65 years at follow-up, without asthma at baseline, and not using exogenous hormones (n = 2322). Menopausal status was defined as nonmenopausal, transitional, early postmenopausal, and late postmenopausal. Associations with asthma (defined by the use of asthma medication, having asthma attacks, or both) and respiratory symptoms scores were analyzed by using logistic (asthma) and negative binomial (respiratory symptoms) regressions, adjusting for age, body mass index, physical activity, smoking, education, and study center. RESULTS: The odds of new-onset asthma were increased in women who were transitional (odds ratio, 2.40; 95% CI, 1.09-5.30), early postmenopausal (odds ratio, 2.11; 95% CI, 1.06-4.20), and late postmenopausal (odds ratio, 3.44; 95% CI, 1.31-9.05) at follow-up compared with nonmenopausal women. The risk of respiratory symptoms increased in early postmenopausal (coefficient, 0.40; 95% CI, 0.06-0.75) and late postmenopausal (coefficient, 0.69; 95% CI, 0.15-1.23) women. These findings were consistent irrespective of smoking status and across study centers. CONCLUSIONS: New-onset asthma and respiratory symptoms increased in women becoming postmenopausal in a longitudinal population-based study. Clinicians should be aware that respiratory health might deteriorate in women during reproductive aging.

Probiotic milk consumption in pregnancy and infancy and subsequent childhood allergic diseases.

BACKGROUND: Whether probiotics, which can influence the microbiome, prevent infant eczema or allergic disease remains an open question. Most studies have focused on high-risk infants. OBJECTIVES: We sought to assess whether consumption of probiotic milk products protects against atopic eczema, rhinoconjunctivitis, and asthma in early childhood in a large population-based pregnancy cohort (the Norwegian Mother and Child Cohort study). METHODS: We examined associations between consumption of probiotic milk products in pregnancy and infancy with questionnaire-reported atopic eczema, rhinoconjunctivitis, and asthma in 40,614 children. Relative risks (RRs) were calculated by using general linear models adjusted for potential confounders. RESULTS: Consumption of probiotic milk in pregnancy was associated with a slightly reduced relative risk (RR) of atopic eczema at 6 months (adjusted RR, 0.94; 95% CI, 0.89-0.99) and of rhinoconjunctivitis between 18 and 36 months (adjusted RR, 0.87; 95% CI, 0.78-0.98) compared with no consumption during pregnancy. Maternal history of allergic disease did not notably influence the associations. When both the mother (during pregnancy) and infant (after 6 months of age) had consumed probiotic milk, the adjusted RR of rhinoconjunctivitis was 0.80 (95% CI, 0.68-0.93) relative to no consumption by either. Probiotic milk consumption was not associated with asthma at 36 months. CONCLUSIONS: In this population-based cohort consumption of probiotic milk products was related to a reduced incidence of atopic eczema and rhinoconjunctivitis, but no association was seen for incidence of asthma by 36 months of age.

Pregnancy outcomes as related to in utero exposure to air pollution and greenness: The Life-GAP Project.

Background: Lower birth weight and preterm birth may increase the risk of adverse health outcomes later in life. We examined whether maternal exposure to air pollution and greenness during pregnancy is associated with offspring birth weight and preterm birth. Methods: We analyzed data on 4286 singleton births from 2358 mothers from Respiratory Health in Northern Europe, a prospective questionnaire-based cohort study (1990-2010). Mixed-effects regression models with random intercepts for mothers and centers were used to estimate the association of exposures to particulate matter (PM2.5 and PM10), nitrogen dioxide (NO2), ozone (O3), black carbon (BC), and greenness (Normalized Difference Vegetation Index in 300m-buffers [NDVI300m]) with birth outcomes, adjusting for potential confounders. Results: Median (interquartile range [IQR]) exposures to PM2.5, PM10, NO2, O3, BC, and NDVI300m during pregnancy were 8.4(5.0) µg/m3, 14.4(8.3) µg/m3, 14.0(11.0) µg/m3, 54.7(10.2) µg/m3, 0.47(0.41) µg/m3, and 0.31(0.20), respectively. IQR increases in air pollution exposures during pregnancy were associated with decreased birth weight and the strongest association was seen for PM2.5 (-49g; 95% confidence interval [CI] = -83, -16). However, O3 showed an opposite association. IQR increase in NDVI300m was associated with an increase in birth weight of 25 g (95% CI = 7, 44). Preterm birth was not associated with the exposures. Conclusion: Increased greenness and decreased air pollution may contribute to healthier pregnancies and improve overall health in the next generation. This emphasizes the need to adopt policies that target the reduction of air pollution emissions and exposure of the population.

The impact of gingivitis reduction on lung function: a randomized trial under intensified oral hygiene.

BACKGROUND: Periodontal disease and lung function impairment were found to be associated with low-grade systemic or local inflammation, and it might be that gingival/periodontal inflammation triggers lung function due to systemic inflammation or the transfer of oral bacteria or its components to the lung. A recent observational study in non-smoking subjects showed that lung volumes and flow rates were significantly reduced by 71-185 ml for severe gingivitis regardless of the adjustment for potential confounders. The result did not show any confounding by smoking, and the association between gingivitis and lower lung function was not modified by systemic inflammation. The designed interventional trial primarily aims to test the hypothesis that gingivitis reduction by optimized daily oral hygiene, professional tooth cleaning and antibacterial chlorhexidine (CHX)-containing mouth rinse improves lung function in terms of forced vital capacity (FVC) by at least 2%. The secondary objective will test the hypothesis that gingivitis reduction improves forced expiratory volume in 1 s (FEV1) and forced expiratory flow at 25-75% of the pulmonary volume (FEF25-75) by at least 2%. Furthermore, the influence of the oral microbiome will be taken into account. METHODS: The study has to include 120 non-smoking subjects aged between 18 and 30 years with biofilm-induced gingivitis. The chosen "waiting control group design" will compare the immediate intervention group with the delayed intervention group, which serves as a control group. Dental and gingival status, lung function and oral microbiome will be recorded. The intensified preventive intervention-professional tooth cleaning, one-stage full-mouth disinfection with CHX and safeguarding an optimal daily oral hygiene by each subject-cannot be blinded, but the outcome measurement in terms of lung function tests is blind. DISCUSSION: This proposed multidisciplinary study has several strengths. Only one previous intervention study with patients with severe periodontitis (mostly smokers) has been performed. It is novel to include non-smoking subjects with mild and potentially reversible oral inflammation. Furthermore, this research is innovative, because it includes evidence-based interventions for gingivitis reduction, standardized measures of the outcome on lung function and oral microbiome and combines expertise from dentistry, lung physiology, oral microbiology and epidemiology/statistical modelling. TRIAL REGISTRATION: German Clinical Trial Register DRKS00028176. Registered on February 2022.

Optimization of bacterial DNA and endotoxin extraction from settled airborne dust.

Collecting and obtaining sufficient amount of airborne particles for multiple microbial component assessments can be challenging. A passive dust sampling device, the electrostatic dust fall collector (EDC) has been established for assessing airborne exposures including endotoxin and glucans. Recently, with advances in next-generation sequencing techniques, EDCs were used to collect microbial cells for DNA sequencing analysis to promote the study of airborne bacterial and fungal communities. However, low DNA yields have been problematic when employing passive sampling with EDC. To address this challenge, we attempted to increase the efficiency of extraction. We compared DNA extraction efficiency of bacterial components from EDCs captured on filters through filtration using five extraction techniques. By measuring the abundance, diversity and structure of bacterial communities using qPCR and amplicon sequencing targeting 16S rRNA genes, we found that two techniques outperformed the rest. Furthermore, we developed protocols to simultaneously extract both DNA and endotoxin from a single EDC cloth. Our technique promotes a high quality to price ratio and may be employed in large epidemiological studies addressing airborne bacterial exposure where a large number of samples is needed.

Food hypersensitivity: an examination of factors influencing symptoms and temporal changes in the prevalence of sensitization in an adult sample.

BACKGROUND/OBJECTIVES: Food hypersensitivity (FHS) is common, but little is known about the factors associated with severe reactions, age of onset and whether sensitization persists. This study examines the factors associated with self-reported severe food reactions, onset age and the changes in prevalence of sensitization to foods over time in an adult sample. SUBJECTS/METHODS: We used data from adults taking part in the European Community Respiratory Health Survey (ECRHS) III (2010-2014) who provided information on food hypersensitivity, including symptoms, suspected culprit food and onset age (n = 4865). A subsample from six countries had serum food-specific IgE tested for 25 core foods and also in 10 years earlier (ECRHS II). We applied logistic regression and McNemar's test for analyses. RESULTS: The prevalence of self-reported FHS was 13.5% at ECRHS III. Of those providing information on symptoms (n = 611), 26.4% reported severe reactions. About 80% of 1033 reported food-specific reactions (reported by 596 participants) began after age 15. History of asthma (odds ratio OR 2.12 95% confidence interval CI 1.13-3.44) and a younger age of onset of FHS (OR 1.02, 95% CI 1.01-1.03, per year) were associated with higher risks of a lifetime experience of severe food reactions. In the subsample with IgE tested in both surveys (n = 1612), the overall prevalence of sensitization to foods did not change over 10 years. CONCLUSION: Our findings support previous observations of more severe food reactions in people with asthma and that most FHS reported by this sample started after age 15. We found no evidence of changes in the prevalence of sensitization to food in adults followed for 10 years.

Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action.

The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish "gold standard" protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory 'omics' features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices.

Pet keeping and tobacco exposure influence CD14 methylation in childhood.

BACKGROUND: Several CD14 gene-environment interactions in relation to the development of allergic diseases have been reported, but the underlying biological mechanisms are unclear. We recently showed that CD14 methylation increased during childhood, parallelling a decreased impact of CD14 polymorphisms on soluble CD14 levels. Here, we aim to explore whether environmental stimuli during childhood affects CD14 methylation, thereby providing a biological mechanism through which environment may modulate genetic effect. METHODS: CD14 methylation levels were quantified in 157 children from the prospective Environment and Childhood Asthma birth cohort at ages 2 and 10. Associations between CD14 methylation levels and house dust levels of endotoxin, ß(1,3)-glucans (at 2 yr only), allergens (dog, cat, and house dust mite), pet keeping and tobacco smoke exposure (TSE; questionnaire data) at 2 and 10 yr were explored. RESULTS: Children in homes without pets had larger increases in CD14 methylation through childhood (2-10 yr) compared with children with pets (2.1% increase (p = 0.003) vs. 0.4% decrease (n.s.), global p = 0.04). At 10 yr of age, lower CD14 methylation values were found in children with pets compared with children without pets at both 2 and 10 yr (5.4% vs. 7.5% [p = 0.02]). A similar trend was detected for TSE; children not exposed show larger increases in CD14 methylation, most pronounced in school-age girls exposed vs. not exposed to tobacco (5.5% vs. 7.5% methylation, p = 0.037). CONCLUSION: Pet keeping and TSE appears to limit increase in CD14 methylation from 2 to 10 yr of age. This may partly explain the diverging CD14 allele associations with allergic diseases detected in different environments.

Exposure to Antibacterial Chemicals Is Associated With Altered Composition of Oral Microbiome.

Antimicrobial chemicals are used as preservatives in cosmetics, pharmaceuticals, and food to prevent the growth of bacteria and fungi in the products. Unintentional exposure in humans to such chemicals is well documented, but whether they also interfere with human oral microbiome composition is largely unexplored. In this study, we explored whether the oral bacterial composition is affected by exposure to antibacterial and environmental chemicals. Gingival fluid, urine, and interview data were collected from 477 adults (18-47 years) from the RHINESSA study in Bergen, Norway. Urine biomarkers of triclosan, triclocarban, parabens, benzophenone-3, bisphenols, and 2,4- and 2,5-dichlorophenols (DCPs) were quantified (by mass spectrometry). Microbiome analysis was based on 16S amplicon sequencing. Diversity and differential abundance analyses were performed to identify how microbial communities may change when comparing groups of different chemical exposure. We identified that high urine levels (>75th percentile) of propyl parabens were associated with a lower abundance of bacteria genera TM7 [G-3], Helicobacter, Megasphaera, Mitsuokella, Tannerella, Propionibacteriaceae [G-2], and Dermabacter, as compared with low propylparaben levels (<25th percentile). High exposure to ethylparaben was associated with a higher abundance of Paracoccus. High urine levels of bisphenol A were associated with a lower abundance of Streptococcus and exposure to another environmental chemical, 2,4-DCP, was associated with a lower abundance of Treponema, Fretibacterium, and Bacteroidales [G-2]. High exposure to antibacterial and environmental chemicals was associated with an altered composition of gingiva bacteria; mostly commensal bacteria in the oral cavity. Our results highlight a need for a better understanding of how antimicrobial chemical exposure influences the human microbiome.

Cow Farmers' Homes Host More Diverse Airborne Bacterial Communities Than Pig Farmers' Homes and Suburban Homes.

Living on a farm has been linked to a lower risk of immunoregulatory disorders, such as asthma, allergy, and inflammatory bowel disease. It is hypothesized that a decrease in the diversity and composition of indoor microbial communities is a sensible explanation for the upsurge in immunoregulatory diseases, with airborne bacteria contributing to this protective effect. However, the composition of this potentially beneficial microbial community in various farm and suburban indoor environments is still to be characterized. We collected settled airborne dust from stables and the associated farmers' homes and from suburban homes using electrostatic dust collectors (EDCs) over a period of 14 days. Then, quantitative PCR (qPCR) was used to assess bacterial abundance. The V3-V4 region of the bacterial 16S rRNA gene was amplified and sequenced using Ilumina MiSeq in order to assess microbial diversity. The Divisive Amplicon Denoising Algorithm (DADA2) algorithm was used for the inference of amplicon sequence variants from amplicon data. Airborne bacteria were significantly more abundant in farmers' indoor environments than in suburban homes (p < 0.001). Cow farmers' homes had significantly higher bacterial diversity than pig farmers' and suburban homes (p < 0.001). Bacterial taxa, such as Firmicutes, Prevotellaceae, Lachnospiraceae, and Lactobacillus were significantly more abundant in farmers' homes than suburban homes, and the same was true for beneficial intestinal bacterial species, such as Lactobacillus amylovorus, Eubacterium hallii, and Faecalibacterium prausnitzii. Furthermore, we found a higher similarity between bacterial communities in individual farmers' homes and their associated cow stables than for pig stables. Our findings contribute with important knowledge on bacterial composition, abundance, and diversity in different environments, which is highly valuable in the discussion on how microbial exposure may contribute to the development of immune-mediated diseases in both children and adults.