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In the future, AI systems sanitize humans as they walk through doorways. Home surfaces self-sanitize. Food is mostly 3D printed from cleaned particles, including Vitamin K and possibly some probiotics to aid digestion. Humans are not forbidden from leaving the protected city, but few do. There's minor barrier crossing of people, but sterilizing agents penetrate clothing and clean them as they re-enter the city.

Could this spur the creation of a new auto-immune disease where the body attacks itself for lack of anything else to fight?

I want to position the environment as the cause of the new disease. Am I missing a big plot hole in this idea?

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    $\begingroup$ Why new? Allergies are basically what you described. $\endgroup$ – Mołot Nov 15 '16 at 13:20
  • $\begingroup$ @morlot could you elaborate on allergies or provide a link? $\endgroup$ – user21263 Nov 15 '16 at 13:47
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    $\begingroup$ @Molot is right. What you describe is the current prevailing scientific opinion for why allergies occur in the first world. Its well recognized now that those children who are kept in the most immaculate environments are the ones who are most likely to develop allergies. $\endgroup$ – Cort Ammon - Reinstate Monica Nov 15 '16 at 14:30
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    $\begingroup$ @Mayerz You misspelled my nickname so i got no notification. See here: en.wikipedia.org/wiki/Hygiene_hypothesis $\endgroup$ – Mołot Nov 15 '16 at 15:00
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    $\begingroup$ to be specific allergies are possibly due to the part of our immune system that evolved to deal with parasites never encountering a parasite, so they go haywire attacking harmless things that happen to be molecularly similar to some form of parasite. basically because they never have to fight a real parasite they keep casting a broader and broader net of antibodies until they catch something. $\endgroup$ – John Nov 15 '16 at 23:46
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Problems with cleanliness

One of the biggest problems with 'perfect' cleanliness and sterilization of all surfaces would be effect on gut flora. Here is an excellent summary of how gut flora is formed. Let me excerpt a few bits:

Environmental sources of the bacteria that are first to arrive into the gut of newborns are believed to be the vagina, skin, and feces of the mother, providing an inoculum that is a mix of intestinal and nonintestinal adapted species.

Regarding sanitation:

Quite recently some changes in the composition of these first colonizers have been reported, and these have been linked to more stringent hygienic conditions of delivery.

For weaning:

After the first 2 wk of life, it seems that a quite stable, feeding-related (breast vs. formula milk) microflora is established and stably maintained.

And in conclusion:

All the above suggest that our knowledge on postnatal microbial development is far from complete and that the next research efforts should be geared to illuminate our knowledge of this field, including provision of a timeline for the presence of strictly anaerobic (unculturable) bacteria.

I add these excerpts to show that there is a lot going on microbially in the human body, and we are only scratching the surface of what we know about it. Basing this on a sealed city with extreme germ-removal capability, this suggests a few different ways to enact a plot in your story:

We made some gut flora extinct and now we can't eat things

In our zeal for cleanliness, we made some gut flora extinct by sterilizing women as they give birth, or even better, growing the baby in tubes and purposefully transferring bacterial culture to the newborn. Something went wrong and now we have caused the extinction of a major type of gut flora and now we can't metabolize something important, like the amino acid lysine, or Vitamin E, or something. Horrible starvation, scurvy or rickets ensue.

We made gut flora extinct and now everyone has diabetes

A well known autoimmune disease is type 1 diabetes. This is caused by the autoimmune destruction of beta cells in the pancreas that produce insulin. The cause is unknown, but it is believed to have a combination of genetic and environmental factors. Well extinction of some gut flora could be an environmental factor, so lets say that all new children born after this gut flora extinction event get type 1 diabetes within a few years.

We tried to culture gut flora and now its mutated and killing us

Type 2 diabetes is generally caused by being overweight and getting too much sugar or saturated or trans fats. If the gut flora mutates and is now processing food INTO trans-fats, then we are going to have an immense and unhealthy amount of it in our diet. Most people get type 2 diabetes by the time they are twenty.

We tried to culture gut flora, and now everyone has psoriasis

Going with the theme of trying to keep gut flora in culture, psoriasis (another auto-immune disease) has been known to be caused by gut colonization by Staphylococcus, Malassezia, or Candida. If we get something into our gut flora culture that we can't get out (can you imagine trying to remove all the Candida from 100 trillion bacteria in a person's gut!!), then we have no choice but to transfer it to everyone, knowing that at least psoriasis is better than starvation.

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  • $\begingroup$ +1 for unintentional humor in the bolded titles (and content of course, it's helpful) $\endgroup$ – Zxyrra Nov 15 '16 at 23:51
  • $\begingroup$ I figured the AI would supplement the gut flora daily through foods and vitamins, but I hadn't considered complete extinction of specific gut flora. That could work. Thanks for the helpful answer. $\endgroup$ – A. K. Snyder Nov 16 '16 at 17:08

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