The "Hygiene Hypothesis"

[Recusant]

I recalled a conversation here in which the hygiene hypothesis came up, but a site search revealed that it was from 2012 in the midst of a long thread devoted to non-religious pet peeves. Not ideal for thread necromancy, so . . .

"'Natural Protection From Asthma And Allergies': Scientists Isolate Bacteria Behind The Immune System Farm Effect" | Science Alert

For decades, scientists have theorized that kids actually need to get a bit dirty for their immune systems to develop fully.

It's known as the 'hygiene hypothesis'. And, as childhood rates of allergies, asthma, and hay fever rose drastically in industrialized Western nations, scientists noticed the same did not go for children raised on farms.

"Girls and boys who grow up on farms and are exposed to a wider variety of microbes have the problem far less often," says epidemiologist Markus Ege, of LMU University Hospital and the Institute of Asthma and Allergy Prevention at Helmholtz Munich in Germany.

That phenomenon is known as 'the farm effect'.

Now, Ege and his colleagues have found exactly which bacterial species mediate the farm effect in rural European children. This discovery goes some way towards verifying the hygiene hypothesis once and for all.

[Continues . . .]

The paper is behind a paywall.

Abstract:

Background

The inverse association of farm exposure with asthma and atopic conditions has been attributed to the diversity of environmental bacteria and fungi, but the specific taxa and the underlying mechanisms remain elusive.

Methods

We performed sequencing of the bacterial 16S ribosomal ribonucleic acid (16S rRNA) gene in mattress dust samples from 1018 schoolchildren from two German populations of the cross-sectional GABRIELA (Multidisciplinary Study to Identify the Genetic and Environmental Causes of Asthma in the European Community [GABRIEL] Advanced Study) survey. Bacterial metabolic pathways and enzymes were assessed bioinformatically, and metabolites were measured by using mass spectrometry. Statistical methods included network, interaction, and mediation analyses.

Results

Within the highly diverse microbial exposure in a farm environment, the study identified nine gram-positive environmental bacterial genera, whose composite score explained two thirds of the inverse association of farm exposure and asthma in a mediation analysis. The effect was independent of gram-negative farm-associated bacteria. A PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) analysis revealed nine pathways, whose enzymes were encoded by the identified genera and whose metabolites were detected in cowshed dust by using mass spectrometry. The metabolites included ligands of the human aryl hydrocarbon receptor (kynurenine and xanthine) and the peroxisome proliferator-activated receptor-γ (α-linoleic and stearidonic acid). Single nucleotide polymorphisms of the corresponding human receptor genes interacted with the composite score of the bacterial genera for asthma. Fungi and bacteriophages co-occurred with the beneficial bacteria but did not carry the protective effect. All results were replicated in independent populations.

Conclusions

In this analysis, the inverse association of childhood asthma and farm exposure was largely mediated by exposure to gram-positive bacterial genera. Gene–environment interactions of a compound score of these bacteria with human receptors recognizing bacterial metabolites suggest novel approaches to asthma prevention.

[billy rubin]

where exactly on a farm do these . . . metabolites?  exist?

manure? chicken feed? raw milk?