During the 1990’s, antibacterial soaps went from a being a small-scale medical industry product to a billion dollar consumer industry. Soap manufacturers poured in millions into advertizing, and quickly nearly every household in the western world had antibacterial soaps at their sinks.
The pitch for antibacterial soaps was fairly simple - bacteria cause disease, so killing the bacteria on our hands at every opportunity would surely reduce the occurrence of disease.
Furthermore, the antibacterial ingredients seemed to have no toxicity issues for humans - so where was the risk?
Well, we’ve learned quite a bit in the intervening 20 years-or-so. Our understanding of the bacteria that inhabit our skin and digestive tract has changed pretty dramatically, and we now know that most of these bacteria are not only harmless, but quite beneficial and necessary for our health.
Nuking the bacteria on our skin with antibacterials several times a day no longer seems like such a great idea.
Triclosan: The Secret Toxin
By far the most common antibacterial ingredient over the past 20 years has been triclosan. A survey done in 2007 showed that 76% of commercial soaps contained triclosan. 
Triclosan works by disrupting a critical enzyme (called ENR) that bacteria use in the synthesis of fatty acids. When ENR is disrupted by triclosan, the bacteria can no longer form or repair cell walls, resulting in the death of the cell.
Because humans do not have the ENR enzyme, triclosan initially seemed to not have any toxicity issues for us.
As we’ll discuss below, we now know that triclosan does in fact have meaningful effects in the body.
Because triclosan is particularly adept at leaching into our bloodstream via our skin, any toxicity are a major concern. A 2007 study done on over 2,500 participants showed that 75% had biologically-significant levels of triclosan in their urine. 
Because our skin is a permeable membrane, it’s good practice to assume that any chemicals in your soaps and skin care products will also end up in your bloodstream (which is why I recommend using only food-grade skin care products whenever possible). Some chemicals are more likely to leach into our bodies, and triclosan appears to be among these.
Issue #1: Hormone Disruption
In recent years, it’s been noted that triclosan shares a few key chemical similarities with triiodothyronine (T3), one of the primary hormones produced and regulated by our thyroid gland. (both molecules have two phenyl rings bearing a total of three halogen substitutions)
As you might expect, this chemical similarity between triclosan and T3 creates problems for the thyroid gland and the associated cell receptors throughout the body.
Several studies have demonstrated that exposure to triclosan produces a dose-dependent decrease in serum levels of both T3 and T4 thyroid hormones. 
These thyroid hormones are a primary regulator of metabolic activity throughout the body - so reducing levels of T3 and T4 in the body could lead to weight gain, decreased energy levels and the other symptoms commonly associated with hypothyroidism.
Troublingly, triclosan has also been shown to have estrogenic activities in the body.  Other synthetic foreign estrogens (such as BPA) have been linked to feminization and decreased sperm counts in men  - and weight gain and inflammation in women. 
Issue #2: Allergic Sensitization
Several studies in recent years have correlated triclosan exposure with increased allergic sensitivity in human studies.
Researchers found that children who showed levels of triclosan in their urine were significantly more likely to develop increased sensitization to both aeroallergens and food allergens. 
Interestingly, all studies found that males were more likely to experience an increase in allergic sensitization as a result of triclosan exposure. 
Issue #3: Disrupts Gut Microbiome
This is likely the biggest problem that triclosan exposure creates. In recent years we’ve learned so much about the role our gut microbes play in everything from immunity to digestion to weight management - the potential health impacts of disrupting our microbiome is huge.
There;s no question that exposure to triclosan disrupts the microbes in our digestive system. A 2006 study found significant alterations in fecal bacteria of mice exposed to levels of triclosan similar to what is commonly found in human urine samples. 
Researchers looking at the correlation of triclosan and allergic sensitization didn’t propose a mechanism for how such a phenomena could occur in the body. My own opinion is that this is very likely a byproduct of gut flora disruption.
Our gut bacteria play a huge role in the formation of our immune system. From the time we’re born, our gut bacteria “train” our immune cells to recognize what is a threat and what is not a threat (and thus, what to attack and what not to attack).
Allergies are effectively an unneeded reaction of our immune system to organic particles that are not actually a threat to the body (like pollens or proteins in food). When gut flora is disrupted by triclosan, the interaction of the gut flora with the immune system is also disrupted, possibly leading to a poorly tuned immune system and thus, allergic sensitization.
This is just one example of countless examples of how disruption of gut flora (by triclosan or other antibiotics/antimicrobials) could negatively impact our health.
Not Just Triclosan
Triclosan is the most widely used and thus, most widely studied antimicrobial compound used in consumer products. It would be foolish, however, to assume that other antimicrobial ingredients in soaps or skin care products are any safer.
While other antimicrobials may not share the hormone-disrupting properties of triclosan, we know for certain that they will disrupt the microbiome of our skin and gut if given the opportunity (it’s what these chemicals are designed to do, after all).
As we’ve discussed, triclosan is quite good at leaching into our bloodstream through our skin even from normal use of antibacterial soap products. This is due largely to triclosan being a relatively small, water-soluble molecule - characteristics shared by most other antimicrobial compounds used in consumer products. We should assume that these chemicals will be just as likely to absorb through the skin as triclosan.
Indeed, several studies investigating triclosan toxicity have also looked at triclocarbon, another common antimicrobial, and found it too leaches readily into the bloodstream from consumer soap products.
The reality is, these antimicrobial products are not only dangerous, but unnecessary. Studies have shown that traditional soaps are just as effective in removing bacteria from the hands.