The microbiome and antibiotics
Innumerable tasks are handled by the bacteria in our intestines. The goal of the bacteria is selfish, they want to feed themselves and reduce competition, but in order to do this, they end up creating a complex ecosystem which we as animals take advantage of. Some bacteria digest things for us, because breaking down a molecule into another molecule gives them energy. The nutrient they create is worthless to them, they just want to perform the conversion to get chemical energy, much the way humans do with oxygen. We effectively turn oxygen into carbon dioxide to gain chemical energy. In this way, some bacteria turn certain molecules in food into vitamins. Bifidobacterium bifidum and Bifidobacterium infantis for example create a great deal of folate, and this folate is absorbed and used by the bacteria's host.[0] More important than getting a nutrient is getting a bacterium which can produce it from multiple sources. These same two bacteria also create large amounts of thiamine, which is important for neurological health.
Interestingly, vitamin B12 is exclusively produced by microorganisms. It can be found in liver, but only because of the bacterial symbiosis which created it there. Some bacteria which produce B12 are Propionibacterium freudenreichii and Lactobacillus reuteri.
An estimated 90% of neurotransmitters are produced in the intestines.[1] In lab tests, germ-free mice -- mice with all bacteria from their intestines eliminated -- are shown to be serotonin deficient. A study suggests evidence that this serotonin deficiency can be reversed by returning certain Clostridial species of bacteria to the intestines.[2]
Another important thing to note is that, among the intestinal flora, 90% of these bacteria are anaerobes. The most significant portion of these are of the Bacteroides species.[3] Regardless of the type of anaerobic bacteria in question, it's unlikely you'll find it on the vitamin shelves. Anaerobic bacteria die in the presence of oxygen, and are difficult to keep alive outside of the human body. This means that regardless of the probiotics you take during your antibiotic regimen, you may very well still be unable to get certain bacteria which would benefit you significantly.
An exception to this seems to be spore-forming bacteria. These bacteria form spores for more efficient reproduction, since the spores are helpful in resisting many things the bacteria itself which would normally be unable to withstand, such as extreme temperature, acidic environments (like the stomach) and oxygen-rich environments.
Inadequate bacterial diversity (which often goes hand-in-hand with antibiotic use) has been implicated in a number of conditions, such as autism, autoimmune disorders such as eczema and Crohn's Disease, allergies, cancer, diabetes, and obesity. The reason for this is most likely because bacteria produce so many of the molecules which are useful to the human body, and their nature to compete with one-another also gives us greater immunity towards serious, pathogenic bacteria and fungi.
Bifidobacteria levels in particular have been shown to decrease throughout life. When a normal child is born, bifidobacteria levels dwarf all other bacteria in the microbiome.[4]
---
[0] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797147/
[1] https://www.medicalnewstoday.com/articles/292693.php
[2] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393509/