While there doesn't seem to be a direct relationship between poor methylation and poor digestion, the two often occur together, which can be caused by the effects of poor methylation on the functioning of the liver and gallbladder, resulting in the gallbladder not being able to perform it's important role in proper digestion and detoxification. He says that the gallbladder is the most methylation-sensitive organ in the body. The liver needs the enzymes involved in methylation to make bile, which is made from cholesterol. If you can't make adequate bile, you can't excrete fats out of your body. There are some things that hinder the release of bile, which include "High stress lifestyles, low stomach acid, estrogen dominance, toxin and pesticide exposure can all stop the bile from being released. All these things hurt our methylation cycle, which in turn hurts the gallbladder."
Bile is critical for proper digestion of fats. It is an emulsifier and a detergent so it breaks fat up into smaller pieces which can then be absorbed. If there isn't enough bile, deficiencies of fat-soluble vitamins can occur. Bile also works like soap in that it "rinses out" particles of food and bacteria from the walls of the small intestines, the same way that detergent rinses these things off of your dishes. If this process doesn't work properly than bacteria can grow too high up in the intestines and cause SIBO. If insufficient bile is excreted it can also lead to leaky gut. Without adequate gallbladder function, there are more cracks and spaces between the cells lining the gut. The gallbladder concentrates the toxins and junk that the liver is trying to get rid of, so if it gets emptied less and less frequently and fully problems can occur. The liver is trying to get rid of things like pesticides, flame retardants, heavy metals, food additives, and medications. A major part of detoxification is simply producing bile when we eat. Bile is also important for clearing excess estrogen so hormonal balance can also be affected.
Poor methylation means poor detoxification. If methylation, sulfation, and glutathione aren't working well (oxalate can reduce sulfation even more) the body switches to an alternative pathway called UGT (glucoronidation), in which things are detoxified by being "stuck" to glucose. Unfortunately this results in thick and sticky bile which can hinder it's function and even keep it from leaving the gallbladder. The bile should have a relatively thin consistency, like that of dish detergent, rather than the more molasses-like thickness that it can take on when a lot of sugar is used for detox. There is research showing that giving taurine and sulfur to mice with thick bile corrected the problem. Estrogen must also be detoxed via the bile, so increased estrogen levels (such as pregnancy) or the taking of birth control pills and/or hormone replacement therapy can exacerbate this problem. This also explains why gallbladder disease seems to occur more often during pregnancy.
Choline (as phosphatidyl choline) removes excess cholesterol but if the gallbladder isn't working right it may not be able to do this, so in some cases high cholesterol is simply the result of the gallbladder being unable to remove it. Phosphatidyl choline also protects the gut lining from irritation caused by bile in the GI tract. Without enough phosphatidyl choline fat cannot be removed from the liver which then leads to liver disease.
This is what he has to say about correcting the problem "So the way we prevent this is through optimizing methylation by increasing taurine, phosphatidylcholine, folate, B12, and TMG. Taurine is produced by the methyl cycle, and when taurine is given to rats with gallbladder sludge, their bile gets slippery again and rescues their liver from damage.5 The methylation genes PEMT and BHMT are found in the liver and they make choline phospholipids which are necessary to keep the bile flowing. Choline protects the liver and gallbladder against damage from the detergent action of bile and it promotes movement of cholesterol into the bile so it can be removed from the body. When we run out of choline, cholesterol and fat literally get stuck in our liver and muscles, leading to fatty liver disease and muscle damage." (On an interesting and possibly related note, I recently read a theory that suggests that insulin-resistance and diabetes may be caused by bits of fat being inside the cells and "mucking up" the insulin receptors. At the bottom of this post is a more detailed list of the supplements that Dr Rostenberg recommends.