The microbiome costs of 2020 lockdown in infants

While the goal was to publish something else today, I find this topic to be more pertinent to our future as a society. Earlier today I found this paper published a couple of days ago, as a pre-print.

This substack will also be less sciency for clarity's sake.

The cost of locking down the world starts to show itself, and its long-term consequences will be disastrous. I highly recommend anyone to read the entire paper too.

Gut microbiome predicts atopic diseases in an infant cohort with reduced bacterial exposure due to social distancing

Human mucosal surfaces and body cavities harbor diverse communities of commensal microbes that play essential roles in regulation of host metabolic responses, epithelial barrier function, immune education, and immune regulation

Given that the gut microbiota provides essential, and evolution routed benefits to human development, alterations in microbial transmission through lifestyle factors linked to industrialization and western dietary habits provide a possible mechanism for the rise in chronic, non-communicable diseases in affluent societies.

There is an “immunological window of opportunity” early in life when the immune system is particularly responsive to environmental exposures (including infections, nutrition, and microbiome) that help establish the thresholds, patterns of reactivity, and functional trajectories that can have long term consequences including altered risk of immune mediated diseases. The immune response to commensal microbes is not simply a form of host defense but represents an intimate and sophisticated bidirectional dialogue that ensures a stable microenvironment is maintained with important symbiotic physiological effects on the host. These microbe-host interactions promote appropriate immune responses that effectively defend against infection, with limited collateral damage to host tissue, and without any subsequent aberrant inflammatory or allergic reactions

I think most people with any amount of interest in medicine or biology knew that the lockdowns would have a great “biological” cost on everyone, from shifting disease trends, to disrupting screening for many chronic diseases, cancers, etc to having a deep impact on socio-behavioral dynamics.

One big discussion and a common argument between different people, from experts to the average Joe is the higher incidence of chronic and autoimmune diseases in the first world, compared to the third, such observations gave birth to the old lack of Vitamin D hypothesis. Not the vitamin D you are thinking.

D in this case stands for dirty. The dirty hypothesis has been heavily discussed for years and years, the more our capacity to understand the molecular intricacies of our bodies increases, the more weight the hypothesis has. Dirty is rather powerful in many ways, everyone's favorite horse paste (Ivermectin) was discovered “in dirty” in Japan. As one can clearly read in the introduction of the paper, primary exposure at a very young age, in a simplistic sense, dictates your immune health for life.

The microbiome plays a substantial role in our immune response towards, well, almost anything really, from stress, going to depression, and of course any type of infection, we are truly an amalgamation of all our microbes, bacteria, and viruses. The shift in microbial composition also plays a significant role in both long-term Covid effects and Long Covid itself, but also in many other types of degenerative and inflammatory diseases. One such example. (FYI in relation to the substack below you can find a way to positively regulate the microbe below in this substack).

Covid infection causes long-lasting microbiome instability

The entire paper is important but the section that jumps the eye easily, and it is easier to explain to a layperson is the following, also present in the title.

Microbiome mediates the effects of environmental factors on atopic dermatitis and food allergen sensitization

The gut microbiota composition at both 6 months and 12 months was strongly predictive of atopic dermatitis diagnosis at 12 months. The atopic dermatitis-associated microbes, apart from Akkermansia (Akkermansiacaeae) and Amedibacterium (Erysipelotrichaceae), were mostly Clostridia, with all but Sarcina (Clostridiaceae) at 6 months having a positive association with atopic dermatitis. In particular Enterocloster (Lachnospiraceae), was associated at both timepoints with increased risk of atopic dermatitis.

Interestingly, our analysis revealed that rural living had a protective direct effect on atopic dermatitis, but also a predisposing microbiota-mediated effect through increased relative abundances of Intestinibacter and Eisenbergiella.

In terms of diet, atopic dermatitis was positively associated with the frequent infant consumption of starchy vegetables, fish, peanuts and pistachios, and negatively with the consumption of grain, pine nuts, and kimchi.

Higher Bifidobacterium levels at 12 months might be related to a reduction in 345 antibiotic use and a high breastfeeding rate in this cohort. Antibiotic use in infancy and 346 later childhood causes a dramatic, long-term reduction in bifidobacteria

The problem with atopic dermatitis (AD) showing up at such a young age could be described as manyfold, AD is mainly mediated by a Th2 state, an allergic state, with allergy-linked cytokines and proteins being abundant, but there are quite a few other ones present in the lesions, and one of them is IL-17, the main product of a Th17 immune response.

If you want to understand and read what I wrote about Th17, here is a link with the search query for anything mentioning Th17 in my substack. Th17 immune responses are important, but long-term activation drives many pathologies and it is directly correlated with the development of autoimmune diseases at many stages of life. The microbiome also plays an important role (intertwined really) with mitochondrial function, the production of many neurochemicals and neurotransmitters (therefore directly influencing your tryptophan metabolism aka kynurenine pathway).


Up until a (war) wound to my gut, my microbiome was pretty much incredible, the same goes for almost every other family member in the same age group, and the difference between us and other family members who are now developing immune-mediated issues is exposure to dirty. We did live in a rural region up until young adulthood too.

I am afraid the real costs of the lockdowns, and everything we discussed in this piece so far will be societal changing. A lot of children now have cognitive deficits, speech impediments, and behavioral issues, and later diseases may come and present themselves. My advice would be exposure to… well, life, and limiting antibiotics usage unless strictly needed, at some level, I am still paying the price of the absurd amount of antibiotics I had to use to survive back at the time I was wounded, and antibiotic usage at a very young age will affect a person for life (as stated in the paper itself).

I do think we can remediate, change things for the better, and recuperate ourselves, but I also think bringing such things to your attention is necessary. An informational double-edged sword… seems to be a trend here lately.

I will attempt to write something else entirely this weekend and publish it, but will now wish you all a good weekend, go live life and not pay attention to the information hamster wheel that we find ourselves in 2023.


My gratitude if you chose to support this work in any way you see fit and people who share it.

PS: Before someone annoys me, I am fully aware of the conflict of interest in the paper, I can sift through the data and information. In the end, this meme defines the last 3 years and all responses to the pandemic.