Facultative mutualists: It's good to have a lot of friends.
The wide variety of foods we eat means that we ingest a wide variety of chemical substances. As mentioned before, plants possess hundreds of thousands of secondary metabolites, most of which are related to defense against herbivores, and many of which probably present digestive challenges for us.
All of these chemicals are toxins of one sort or another and their toxicity to us will depend on the concentration in the plant tissues. It would be absurd to think that the human gut is capable of handling them all. For one, with our paltry 20,000 genes, we just don’t have the capacity to deal with such a variety.
Perhaps more importantly, food moves through our small intestine in about 90 minutes, and all of our digestion and absorption must be accomplished in that amount of time. Obviously, we can handle simple digestive tasks in the form of proteins, fats, and simple carbohydrates, and the absorption of important vitamins and minerals. Chemically complex substances that are difficult to break down cannot be managed in 90 minutes and, in fact, might require more energy than they actually provide.
Thus, adaptations for handling such foods never happened in our evolutionary history because it was unnecessary for survival. And we are either unaffected by plant toxins or we stopped eating certain plants because of the toxic effects. So, when it comes to slow-to-digest substances, we digest what we can and the rest passes on to the colon and through our system. We certainly don’t need bacteria to handle the food material that we can’t digest; in an evolutionary sense, we don’t really care if it gets digested or not. In fact, things that we can’t digest easily are usually not even referred to as “food”.
Nonetheless, although we possess a repository of undigested material in our large intestine that we as humans are unable to use, that certainly does not mean that material is unusable. As with every ecosystem, we expect that unused resources are soon discovered by organisms that can make use of them.
However, everything about our colon suggests that we have slowed down the movement of undigested food for some reason, but not because we need more time to digest it. In comparison to the small intestine, the large intestine is less muscular and has much slower contractions, which leads to a retention time of up to 24 hours even though the colon is a much shorter organ.
This sudden hitting of the brakes when food material enters the colon does not suggest in any way that we are finished with this food because it’s unusable, but rather that we are going to hold on to it for a while longer, much longer than would seem necessary. And the only reason seems to be that the indigestible stuff helps us create an environment suitable for the microbiome, which also strongly suggests that the microbiome offers us something we need.
The tremendous diversity of bacteria in the colon does not imply that all bacteria are necessary or even beneficial. This is a niche filled with food and the many hundreds of species merely reflect the diversity of food material, not a diversity of beneficial mutualisms. It’s very likely that a great percentage of the species are benign and opportunistically filling a niche.
All of the bacteria produce enzymes that break down durable, complex, structural components of the food we send to them. These enzymes form a chemical soup that breaks chemical bonds in the food molecules. This process releases energy and breaks off smaller molecules that can be easier for other bacteria to break down further. What may be the most important aspect of the process of digesting cellulose from plants is that each bacterial species has one or more genes for producing enzymes that humans cannot produce.
Thus, living in our gut is a community of tens of trillions of tiny cells that collectively possess millions of genes and, in a sense, we have access to those genes or at least to the gene products. Between the basic life-history properties of BUGS and their tremendous range of biochemical capacity, we have access to a system that provides very rapid responses using an arsenal of chemical weapons that we, as BIGS, could never have evolved independently. By consuming our omnivore diet, we maintain this vast array of functions and abilities even if we don’t need them every day or even every month.
In this sense, bacterial diversity provides for human digestive flexibility. For example, people who eat a wide variety of food types, including spices, have a much more diverse digestive microbiome than someone raised on a diet of processed white bread, fried chicken, and mashed potatoes, and who never gets adventurous with food.
The high diversity microbiome is better able to handle food challenges without gastric upset and flatulence. It can handle the new food quickly and with a minimum of fuss. The low diversity microbiome handles the foods it knows well, but it might not be able to accommodate new food types, and it may take longer to adjust if it is able to adjust at all. A good example of that inflexibility is frequently seen in people eating very spicy food for the first time or, actually, anywhere from 3-24 hours after they eat that food.
The human ability to provide a safe harbor for ten thousand species of bacteria (and counting) means that even if most of them are just hitchhikers, their presence can act as a safety net in a dynamic world, a chemical insurance policy against unforeseen events. Just as some bacteria may be obligate mutualists and we must have them for normal development, it is possible that a microbiome of facultative mutualists is just as necessary, just as obligate in a sense, for humans to persist in an ever-changing world.
That is, each particular species of bacteria may not be absolutely necessary, but the possession of the diverse and healthy microbiome is absolutely necessary, regardless of the exact makeup of that community. In that sense, anything that interferes with the normal functioning of a such a microbiome would be a danger to human health.