Washing your hands might be a good way to keep you from getting sick but in some cases, “dirt” can do you good.
Researchers found that people living in less cleanly regions of the world develop far less autoimmune diseases. For example, people living in Thailand are 10 times less likely to get Inflammatory Bowel Disease then people living in Finland, one of the richest countries in the world with high sanitary standards. Thai people are also about 100 times less likely to develop the autoimmune disease type 1 diabetes, and if this is not already enough, in Thailand, the risk to develop allergies is 10 times lower as well. [1, 2]
However, in Thailand, you also are much more likely to catch infectious diseases of any kind.
What sounds a little bit like a trade-off between autoimmune diseases and infectious disease could be exactly that – a trade-off. Research over the last years has shown a connection between extreme hygiene and autoimmune diseases, which culminated in the proposal of the “hygiene hypothesis”.
A rather extreme comparison is done by a French scientist who showed that while the incidence of many infectious diseases went down, the frequency of autoimmune diseases went through the roof. 
Wait… isn't it a good thing that we have eradicated most infectious diseases in the western world?
Yes, it is! While the comparison of infectious diseases and autoimmune diseases is absolutely valid, it is rather extreme. You don’t have to catch severe infection to not develop an autoimmune disease.
However, spending your life in an almost sterile bubble brings the disadvantage that your immune system lacks “education”.
In his Ted Talk, Moises Velazquez-Manoff proposes that “evolution turns the unavoidable into the necessary” and explains that a body that has evolved being surrounded by microorganisms needs the microorganisms to stay healthy.
Our bodies have being in a close symbiotic relationship with microbes and suddenly we started to sterilize our food and sanitize our homes and on top of it, we swallow antibiotics every other year, which literally acts like an atomic bomb on our gut bacteria.
There is a lot of research out there supporting the theory that microbes educate our immune system. For instance, if you are living on a farm you are three times less likely to develop hay fever and the same applies to having a pet as a kid. Both, living on a farm and having a pet will expose you to much more microbes than living in an pet-free apartment in the city. [4, 5]
It goes much further than simple allergies. As an example, researchers found that “breastfeeding is associated with a lower risk for multiple sclerosis”. 
Another big study found that countries that have lower hygiene standards had a lower risk for Alzheimer’s disease. 
There are also clinical trials that show how a parasitic worm improves the symptoms of the devastating autoimmune diseases Multiple Sclerosis and Inflammatory Bowel Disease. They do it by suppressing the immune system, which is exactly what the drugs do that are prescribed against these diseases. [8, 9]
Does this mean that we should go back to the good old times where we got killed by microbes and not by our own immune system?
No, what I am getting at is that we haven't just reduced infectious microorganism but we have also reduced non-infectious, beneficial microbes. Our Microbiome.
Babies born by C-section, not being breastfed and the use of multiple courses of antibiotics early in life can leave the diversity of our microbiome diminished and we slowly start to get a fairly good understanding on how the microbiome educates our immune system already early in life.
Even if you are already suffering from autoimmune diseases, it might not be too late to do something against it. Promising research shows that resetting our microbiome can do miracles to our health. [10, 11, 12]
Take Home Message: Our immune system relies on the communication with microbes to stay healthy!
Ng et al., Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies, The Lancet, 2017
Jean-Francois Bach, The effect of infections on susceptibility to autoimmune diseases and allergic diseases, NEJM, 2002
O’Connor et al. Early-life home environment and risk of asthma among inner-city children. Journal of Allergy and Clinical Immunology DOI: 10.1016/j.jaci.2017.06.040 (2017)
Riedler et al., Austrian children living on a farm have less hay fever, asthma and allergic sensitization, Clinical and Experimental Allergy, 2000
Silja et al., Breastfeeding is associated with lower risk for multiple sclerosis, Multiple Sclerosis Journal, 2012
Fox et al., Hygiene and the world distribution of Alzheimer’s disease: Epidemiological evidence for a relationship between microbial environment and age-adjusted disease burden, Evolution, Medicine and Public Health, 2013
Fleming et al., Probiotic helminth administration in relapsing–remitting multiple sclerosis: a phase 1 study, Mult Scler, 2011
Broadhurst et al., IL-22+ CD4+ T Cells Are Associated with Therapeutic Trichuris trichiura Infection in an Ulcerative Colitis Patient, Science Translational Medicine, 2010
Dr. Tim Spector - The Diet Myth
Dr. David Perlmutter - Brain Maker
Raphael Kellman - Microbiome Diet