Farm-like indoor microbiota in non-farm homes protects children from asthma development
Authors: Pauli Tuoresm√§ki
Marjut Roponen
Balamuralikrishna Jayaprakash
Petra Ina Pfefferle
Martin T√§ubel
Rob Knight
Martin Depner
Anne Hyv√§rinen
Anne M Karvonen
Bianca Schaub
Juha Pekkanen
Dick J J Heederik
Erika von Mutius
Pirkka V Kirjavainen
Georg Loss
Markus Johannes Ege
Harald Renz
Rachel I Adams
Roger Lauener
Journal: Nature Medicine (2019)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Asthma prevalence; urbanization; traditional farms; home dust microbiota; indoor microbiome
Affiliations: Environmental Health Unit, National Institute for Health and Welfare, Kuopio, Finland. ., Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland. ., Environmental Health Unit, National Institute for Health and Welfare, Kuopio, Finland., California Department of Public Health, Richmond, CA, USA., Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland., Department of Public Health, University of Helsinki, Helsinki, Finland., Department of Pediatrics, School of Medicine, University of California, San Diego, San Diego, CA, USA., Institute for Asthma and Allergy Prevention, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany., Dr von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany., Comprehensive Pneumology Center Munich, Member of the German Center for Lung Research, Munich, Germany., Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany., Comprehensive Biomaterial Bank Marburg (CBBMR), Member of the German Center for Lung Research, Philipps-University Marburg, Marburg, Germany., Children's Hospital of Eastern Switzerland, St Gallen, Switzerland., University of Zurich, Zurich, Switzerland., School of Medicine, University of St Gallen, St Gallen, Switzerland., Christine K√ºhne-Center for Allergy Care and Education, CK-CARE, Davos, Switzerland., Center for Microbiome Innovation and Departments of Pediatrics and Computer Science & Engineering, University of California San Diego, San Diego, CA, USA., Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands.

Abstract:  Asthma prevalence has increased in epidemic proportions with urbanization, but growing up on traditional farms offers protection even today1. The asthma-protective effect of farms appears to be associated with rich home dust microbiota2,3, which could be used to model a health-promoting indoor microbiome. Here we show by modeling differences in house dust microbiota composition between farm and non-farm homes of Finnish birth cohorts4 that in children who grow up in non-farm homes, asthma risk decreases as the similarity of their home bacterial microbiota composition to that of farm homes increases. The protective microbiota had a low abundance of Streptococcaceae relative to outdoor-associated bacterial taxa. The protective effect was independent of richness and total bacterial load and was associated with reduced proinflammatory cytokine responses against bacterial cell wall components ex vivo. We were able to reproduce these findings in a study among rural German children2 and showed that children living in German non-farm homes with an indoor microbiota more similar to Finnish farm homes have decreased asthma risk. The indoor dust microbiota composition appears to be a definable, reproducible predictor of asthma risk and a potential modifiable target for asthma prevention. 

Retracted: No

PubPeer comments:
 The title is clearly off-topic, as a lower risk score from a multidimensional analysis is a statistical association but not equivalent to disease protection. Overly complicated score construction after knowing the data. Suboptimal dimension reduction and multiple testing issue. Wrong labels in Fig 3c, note that replication in Gabriela was not significant. The main result could be a simple contamination problem. FaRMI is found in non farm rural children by bacterial archaeal operational taxonomic units (OTUs) of soil origin which happens both at farm and non-farm homes, see also supplement table 6. ,