Category Archives: Allergy

Schutz vor Allergie auf dem Bauernhof: Ist das zentrale Paradigma falsch?

Keine Frage – Lebensbedingungen auf Bauernhöfen sind anders. Mehr Tiere, mehr Dreck, mehr frische Luft, alles ist anders als in einer Großstadt. Das kann auf Selektionsbedingungen zurückzuführen sein, z. B. gut  zu sehen in einer der ersten Studien vor 30 Jahren.

Clin Exp Allergy. 1999 Jan;29(1):28-34.

Auch die Eltern hatten schon weniger Allergien, und damit logischerweise auch die Kinder.

Wenn man genau hinschaut, dann haben alle Bauernhofstudien doch immer wieder dieselbe Argumentationsstruktur – weil die Bedingung X dort so, dann kann die Folge Y dort auch auf die Bedingung X zurückgeführt werden. Immer mehr Beschreibungen von X machen die Story aber nicht glaubwürdiger.

Keine der jemals beschriebenen Bedingungen X, ist aus dem Bauernhofmilieu heraus aber auch auf allgemeine Situationen mit Folge Y übertragbar gewesen, von einem einzigen weitgehend verunglückten Versuch einmal abgesehen. Keine einzige Bedingung X  ist nach 30 Jahren verallgemeinerbar, so dass nun alles doch nach einer einzigen Blase aussieht.

Natürlich hat ein hoher Endotoxin Spiegel auf den Bauernhöfen eine bestimmte Wirkung –  zumindest bei einigen Menschen und bei einigen Mäusen – aber ist das wirklich  mehr als ein modifizierender Faktor?

Da Lebensbedingungen auf dem Bauernhof angeblich protektiv sind, müsste auch mal ein einziges Kind präsentiert werden, das eigentlich eine Allergie haben muss, weil seine beiden Eltern allergisch waren.  Aber dieses Kind gab es nie, weil auch schon die Eltern keine Allergien haben.


Farming and allergy prevention could be caused by Berkson’s fallacy

Lets look at the Wikipedia definition first

Berkson’s fallacy is a result in conditional probability and statistics which is often found to be counterintuitive, and hence a veridical paradox. It is a complicating factor arising in statistical tests of proportions. Specifically, it arises when there is an ascertainment bias inherent in a study design … The most common example of Berkson’s paradox is a false observation of a negative correlation between two positive traits, i.e., that members of a population which have some positive trait tend to lack a second.

The original example is developed unsing the example of an hospital based group of patients. The only thing to know is that diabetes is a risk for cholecystitis in the general population.

Any given hospital in-patient without diabetes must have another disease (otherwise he would not be there), for example cholecystitis. And by definition this will be cholecystitis without diabetes caused by some other risk facors (female, fat, forty…) So in this group of in-patients there maybe a spurious negative association between cholecystitis and diabetes.

My example here is with families who are living on farms. Since around 1960  [Leynaert 2001] there is this interesting observation that farming families have less allergy, an effect that I found back in 1989 and that is most likely a healthy farmer effect.
This selected farm population has a lower allergy prevalence and of course their children will also have less allergy. All the negative correlations (that are interpreted as protection) with endotoxin, microbiome, etc could be caused by Berkson’s fallacy. The observation will also be even replicated as the same selection criteria are also present in the replication sample.

Many more cognitive biases could also be involved: anchoring, availability cascade, confirmation and expectation bias and of course: law of the instrument.

Revisiting Bavarian schools

The blog post has been now replaced by a full paper, online at

Presentation abstract EAACI / PAM 17.10.2019

Some mechanistic considerations are at

What is wrong with the 2011 NEJM paper?

N Engl J Med 2011;364:701-9 is another paper with 1000+ citations  that had a lasting impression on some but not all people.

First, I can’t remember of any study with such an enormous selection bias  where >94% of individuals have been lost.

Second, we should not forget that farm is not protective per se – farmers may just avoid a known allergy risk factor.  The PARSIFAL participants in this study included Steiner schools — anthroposophic medicine mostly avoids vitamin D (another ref). This is of course a major issue for any cross-sectional study that doesn’t take into account the temporality of events.

Third, in PARSIFAL dust from children’s mattresses were collected by vacuuming — it is not very likely that many helminthic eggs were transported  from stable to bedroom. In GABRIELA, only airborne dust samples  were collected which may miss helminth eggs although being highly present in stable dust.

Fourth, more  microbial exposure and more fungal taxa on farms are a trivial finding.

The inverse associations of the diversity scores with asthma were not confounded by status with respect to living on a farm because adjustment did not change the respective point estimates for asthma (Table 2), although the associations became nonsignificant.

Small sample size, borderline p-values even after a long fishing expedition? And what do these strange “probability” plots  really show – the probability of asthma or the probability to live on a farm?

N Engl J Med 2011;364:701-9 Figure 3 Does it refute any general effect of diversity?

The plots are misleading if adjustment for farm living does not change the parameter estimates for bacterial/fungal diversity. Does that really mean that farm are irrelevant?

Sixth – even many years later, the main findings of this study could not be replicated. There is not any single study that shows listeriosis (Listeria) or diphtheria (Corynebacterium)  to be protective.

Allergy protection on farms – why also studies in mice could have failed

There are  many immunological differences in humans and mice (follow my link) that a re never discussed not even in Science 2015;349/6252:1106.

Ignoring the long-standing paradox that endotoxin is also acting as a natural adjuvant to atopic inflammation, the credibility of the Science paper is further reduced.

And it is a strange experimental condition to have all animals on a standard vitamin D diet – a known co-sensitizers – and looking then for A20 which is co-regulated by vitamin D

Does a healthy worker effect explain the “allergy protection” at Bavarian farms?

Unfortunately most studies in the farming environment did not report the prevalence of parental history nor did they report the effect size of parental risk in the farming population. This is, however, a critical issue as the so called healthy worker effect HEW may be a rather trivial explanation of the results.

Specifically, it is a sampling bias: the kind of subjects that voluntarily enroll in a clinical trial and actually follow the experimental regimen are not representative of the general population. They can be expected, on average, to be healthier as they are concerned for their health [or as ill people already dropped out]

At least Braun-Fahrländer 1999 reported that allergic parents were seen much less at farms: allergic rhinitis 12.7% versus 29.4% (P=0.001). A history of allergy therefore is no more a risk factor as it is in the general population.

Leynaert 2001 showed only a slightly reduced prevalence of “allergy” (39.1% vs 41.5%, NS) while her table 4 is most interesting. The association started only after year 1960 which points towards misclassification as far as the analysis is not stratified by year of birth.

Remes 2002 showed a dose dependent effect decline between farming (36.2%) and controls (31.6%, P=0.075),

Perkin 2006 also found some significant lower prevalence in farmers 47.3% versus 57.7%, P<0.001.

A HWE is therefore likely.

In total, I found indeed six studies (Thelin 1994, Braback 2006, Chenard 2007, Thaon 2011, Elholm 2013 and Spierenburg 2015) that examined in detail a possible relationship of HWE, allergy and farming. Unfortunately the examination period in five of these studies is too short for any conclusion with Braback 2006 being the only reliable study.

Also from this study, we can safely conclude, that there is a significant HWE.


we don’t see things as they are, we see them as we are

There is an interesting meta-analysis  at JAMA Pediatrics about vitamin D supplementation during pregnancy and offspring growth, morbidity, and mortality. Nothing special, standardized methodology and even somewhat expected outcome.

In this systematic review and meta-analysis of 24 randomized clinical trials including 5405 individuals, vitamin D supplementation during pregnancy was associated with a lower risk of infants being small for gestational age and improved growth during infancy without an increased risk of fetal or neonatal mortality or congenital abnormality.

More interesting are the vitamin lobbyists writing the accompanying editorial (Bo Chawes , Klaus Bønnelykke, Hans Bisgaard) who try by nearly every sentence to devalue the findings of the meta-analysis. They are even getting to the point of

no adverse effects have been found

We don’t see things as they are, we see them as we are.

Claim to fame of the hygiene hypothesis

The recent encyclopedia article about the hygiene hypothesis seems to be well written. At least on the first instance … in reality it is more a novel than a scientific review.

For many years already, the hygiene hypothesis has been called an outdated concept; various times it was revised and transformed, and finally it gave birth to novel hypotheses.

In other words, the hypothesis has been rejected for being wrong . Even many revisions did not change that. There seem to be only one proven fact – the obsession of some authors with hygiene and nouvel Rousseauism.

Anyway, the hygiene hypothesis has promoted radical rethinking of infections, microbiota, and coevolution of mankind and microbes.

There is nothing radical in backward thinking. We still carry tons of microbes, freezer and antibiotics only did some qualitative but not so much quantitative changes,

With the advent of novel high-throughput sequencing technologies the human microbiome, which is sometimes called the ‘forgotten organ,’ has attracted much attention and is currently being implemented in a wider concept of self-foreign relationship, which may even include recognition of the nonmicrobial nonself as a vital stimulus to a well-developing immune system.

  1. So the interest is technology and not science driven.
  2. The microbiome is not an organ.
  3. The hype is already over.
  4. The Self is not defined by any bacterium.
  5. Most bacteria are excreted and not vital stimulus.

Given the many molecule classes regulating immune functions across individuals such as short RNAs, the hygiene hypothesis may eventually come back as a surprising explanation of the phenomena evoked by crowding, day care, sibship size, orofecally transmitted diseases, and respiratory infections.

Why that?
A comeback of the hygiene hypothesis by short RNA?
The listed phenomena are not intrinsically related, but are occuring only at the same time scale.

Even the old birth order effect might be rediscovered as epigenetic programming someday. Admittedly, these notions are entirely hypothetical, but without hypotheses, proven or not, science hardly advances.

So if David Strachan’s birth order effect would be really caused by  epigenetic programming – why would that be related to hygiene at all?

Science is is not so much about proven or unproven but about reasonable and non reasonable hypotheses.



ArXiv is operational since 1991, bioRxiv since 2013 and since 2019 there is now also medrxiv. More details  at

The main arguments in favour of sharing work in its preliminary form are, firstly, that science works faster if work is made available sooner after it is completed and, secondly, that articles are improved by feedback from a wider group of readers, alongside formal peer review by a few experts. Simple estimates suggest that halving the delay to sharing a research result can double the speed at which research progresses. Ambitious research funders are now embracing preprints and other measures that aim to accelerate the pace of research.

Although there was a mixed reception in the beginning, see Science back in 2017

MedArXiv will have a hard time attracting preprints if mainstream medical journal editors decide they won’t publish final versions of the papers. Currently, The BMJ and The Lancet are among the few medical journals that have explicitly said that posting a preprint doesn’t preclude publication; Nature and Science, which both occasionally publish medical studies, have the same policy. But at the JAMA Network, which publishes a dozen journals, the issue is hotly debated.

@MedArXiv opened on June 6. So far they have only 304 followers on Twitter (and no allergy paper in the archive).

As the current “Allergy” editor and the publisher (John Wiley and Sons A/S)  agreed to preprints last week, I have submited now my first preprint paper.

Vitamin D polygenic risk score is not associated with any disease

It is one of the minor papers in a minor journal but nevertheless has some big impact: A phenome-wide Mendelian-randomization study of genetically determined vitamin D on multiple health outcomes using the UK Biobank – Int J Epidemiol. 2019 Sep 13

Existing studies suggest that a low vitamin D level is associated with more than 130 outcomes. … We then implemented a Mendelian Randomization-Phenome Wide Association Study (MR-PheWAS) analysis on data from 339 256 individuals of White British origin from UK Biobank. We first ran a PheWAS analysis to test the associations between a 25(OH)D polygenic risk score and 920 disease outcomes…The PheWAS analysis did not identify any health outcome associated with the 25(OH)D polygenic risk score.

The message is clear – we know it for years.

Vitamin D Warnhinweis

Das Deutsche Ärzteblatt hat einen Warnhinweis “Fachgesellschaften warnen vor unkritischem Umgang mit Nahrungs­ergänzungsmitteln” allem Internet Hype zum Trotz

“Die Werbeaussage, wonach jeder Mensch eine Extraportion Vitamine oder Mineralstoffe zur Aufrechterhaltung der Leistungsfähigkeit und Gesundheit braucht, ist schlicht und einfach falsch“, sagte Jürgen Schölmerich, Facharzt für Gastroenterologie und ehemaliger ärztlicher Direktor und Vorstandsvorsitzender des Universitätsklinikums Frankfurt am Main. Nur für wenige Personengruppen, etwa Schwangere oder Veganer, seien bestimmte Nahrungsergänzungsmittel-Präparate tatsächlich empfohlen.

Why do we have so much atopic dermatitis?

I think it is quite reasonable that childhood skin care practices is involved in the increase in atopic dermatis (AD) according to a recent review.

Kelleher and colleagues found skin barrier dysfunction precedes AD development. Thus, soaps and detergents may aggravate preexisting tendencies to skin barrier dysfunction and promote skin inflammation and initiate AD in susceptible individuals. Whether skin care practices have changed over time to explain the increase in AD incidence remains unknown, but high bathing frequency and the use of fragranced lotions are commonplace in US children, two practices potentially harmful to the skin barrier. Protecting the skin barrier early in life with emollients appears to reduce the risk of AD development.

More mutations, more asthma?

While some researchers still believe that genetics cannot be responsible for the asthma epidemic as the prevalence increased with only two generations I have no doubt that (within the gene by environment framework) any environmental change is a necessary but not sufficient cause.
I would count also epigenetic changes as “genetic” while there seems now even direct evidence of an increased mutational load in humans

While the overall deleterious homozygosity has consistently decreased, risk alleles have steadily increased in frequency over that period of time. Those that increased most are associated with diseases such as asthma, Crohn disease, diabetes and obesity, which are highly prevalent in present-day populations.

The endotoxin phantom – discrepancies in the NEJM 2002 farm paper

N Engl J Med 2002; 347:869-877 made a strong point that the farm effect is mediated by endotoxin but showed just a 1,7 fold higher endotoxin exposure at farms.

N Engl J Med 2002; 347:869-877 table 1 shows environmental exposure between farm and non-farming households

LPS therefore can not even explain the farm protection as endotoxin effects are so much similar between farming and non-farming (table 2. Why is only the result of the total sample given here and not the farm result?).

N Engl J Med 2011; 364:701-709 table 2 endotoxin effect is not stronger at farms – more some unspecific immunosuppressive effect?

What is the reason for the lower IL10 capacity in Figure 2D to respond to LPS exposure – exhaustion, adaptation? And even more important: What is the reason for the lower allergy rate at farms?

If we now go back to table 1 there is a 5,0 fold Der p1 excess in farm – much higher than the 1,7 fold increase of endotoxin.

As nearly all allergens have helminth homologues –  the question is what did the authors really measure? Da Costa Santiago 2015 has a nice table that could give an answer.

J Immunol. 2015 Jan 1;194(1):93-100 shows Der p1 homologs

Der p1 is a cysteine protease of 25kDa that has homologues for example in Loa loa. Loa loa is unlikely at Bavarian farms – and more common in tropical Africa. Cysteine proteases are nevertheless a big tool for helminths –  in Schistosoma japonicum a cathepsin B2 cysteine protease is considered the main penetration tool.

Usually cysteine proteases are not allergenic, but the excessive (and rather isolated) rise combined with a reduced Der  p1 sensitization in the children,  is definitely an unusual finding. The Dermatophagoides pteronyssinus habitat is cosmopolitan, house dust,  influenced by altitude and climate, but there is no known reasons for this excess in farms. Is the Der p1 value just a false positive and has it helminthic and not mite origin?

I am therefore blasting Der p1  sequence (P08176) against all known cow endoparasite genomes. Fasciola has a strong hit with CL6, a papain family cysteine protease with e+48.

Wormbase blastp results – e+ values are somewhat lower than my local blast result at the same locus

With an identity values between 40% and 70% there could well be a confusion of mite Der p1 and  helminth (Fasciola?) CL6, which should be tested for cross-reactivity.

The story even gets more interesting when reading more about parasites

Helminth parasites have complicated life cycles … at the same time as skewing the immune system toward a Th2-driven response, they have a general suppressive effect on the host immune system that prevents their elimination and reduces immune-mediated tissue damage. It has been suggested that cytokines of the anti-inflammatory network, particularly IL-10 and transforming growth factor- (TGF-), that are produced in response to continual stimulation of the immune system by parasite antigens, are pivotal to regulating the damage they cause and that, coincidentally, these have a bystander protective affect against allergic reactions.

This is exactly what N Engl J Med 2002; 347:869-877 showed: increasingly exhausted IL10 capacity. May the x-axis label should not be LPS but  CL6?

N Engl J Med 2002; 347:869-877 Figure 2. Smoothed Plots of the Log-Transformed Capacity of Peripheral-Blood Leukocytes (PBL) to Produce Interleukin-10 (Panel D) after Stimulation with Lipopolysaccharide (LPS) or Staphylococcal Enterotoxin B (SEB) in Relation to the Log-Transformed Endotoxin-Load Values.



The Amish paradox in NEJM 2016 explained

A recent study in the NEJM found remarkable differences in the asthma prevalence between Amish and Hutterite populations. The lifestyle of both communities is similar but their farming practice is distinct as the Amish follow a more traditional style of outdoor grazing whereas the Hutterities use industrialized farming practices. Gene expression data in the Amish children have been interpreted as „intense exposure to microbes“ because protection of experimental asthma by Amish derived house dust was nearly abrogated in mice deficient for MyD88.

Any helminth exposure has been excluded due to low IgE and eosinophil counts in the children while I still think that this could be an explanation in particular as the attempt to show an effect of bacterial exposure was unsuccessful since the discovery of the farming effect.

One difference between conventional stable (Hutterites) and outdoor grazing (Amish) is the higher helminthic infection rate on pasture, mainly with Fasciola, Ostertagia, Eimeria, Cooperia, Dictyocaulus and Trichostrongylos species.

Infected cattle rarely demonstrate clinical disease, while it is known that Fasciola (as for example Schistosome) has numerous immunosuppressive functions in the host. IgE is not always raised as Fasciola can degrade human immunoglobulin or even induce eosinophil apoptosis.

Re-analysis of Gene Expression Network using (String Consortium 2019). The gene expression network in Amish children {Stein et al., 2016, #73074} in the upper area has similarities with the network observed in sheep after Fasciola infection {Fu et al., 2017, #6751} module #1 and #3, in the lower plot.