Can we eat to selectively grow specific bacteria?

Recently, I was reading that different types of bacteria thrive on different types of prebiotic. Thus, in theory, one could selectively feed (and therefore increase) a specific beneficial bacterial population. This led me into a line of questioning around how do bacteria eat? Specifically, how do we know that a given prebiotic is consumed by a particular bacteria, as opposed to being consumed by all bacteria, or whichever ones get first access? Are there classes of bacteria similar to animals (e.g., omnivore, carnivore, etc.)?

First, a little basic background: bacterial cells are bound by a cell envelope that consists of an inner cytoplasmic membrane and an outer cell wall. The bacterial cell wall is rigid and, like the cell wall in plant cells, gives bacteria their shape. Bacteria rely on diffusion, a process where molecules move from an area of higher concentration to an area of lower concentration, to move molecules into the cell and through the cytoplasmic membrane. Bacteria also excrete enzymes to dissolve molecules outside the cell to allow them to pass through the membrane via diffusion. Sometimes simple diffusion needs assistance from proteins to allow molecules to pass into the cell, a process called facilitated diffusion. Another method — active transport — requires energy to transport molecules to overcome the concentration gradient and allow particles to pass through the membrane.

In a 2019 study in Cell, scientists raised gnotobiotic mice (mice without any gut bacteria) in sterile conditions and gave them a set of 20 bacterial species found in the human gut. At the start of the experiment, the mice all had the same set of microbes from human donors. The study found that by feeding the mice different prebiotic fibers, that different proportions of bacterial species are selectively increased. For example, mice that ate a lot of pea fiber or citrus pectin had a much higher proportion of a bacteria called Bacteroides thetaiotaomicron at the end of the experiment. On the other hand, mice that were fed high proportions of beta-glucan and barley bran experienced a pronounced increase in Bacteroides ovatus.

Furthermore, the effects of the diet were markedly able to increase the relative proportions of bacteria. For example, the relative abundance of these bacterial community members was increased from 10%-20% to nearly 50%. Furthermore, these results were reproducible across two separate experiments. Interestingly, there were no pronounced threshold or saturation effects of these fibers at the concentrations tested. Thus, based on the evidence we have, it seems the more of a type of fiber that is eaten, the more a particular population will flourish. However, I would expect that there would be some kind of saturation effect. But, for the time being, more prebiotic fiber is better when it comes to growing a particular population of bacteria.

However, the growth of one population mad inadvertently impact the ability of another population to grow. Even with a relatively simplified number of bacterial species, competition between bacterial species is not always crystal clear. B. thetaiotaomicron, which thrives on pea fiber, did not increase upon omission of another species (B. cellulosilyticus) and in the presence of pea fiber. In contrast, B. vulgatus expanded in the absence of B. cellulosilyticus when pea fiber is present. Oddly, O. splanchnicus expanded in the absence of B. cellulosilyticus, but only in the absence of pea fiber as well. Clearly, there are some complex interactions between species. And this is a relatively simplified system of 20 species, whereas our gut microbiome contains between 100-1000 different species, based on different estimates.

As I recently discovered, not all fiber is the same. Each fiber molecule often contains a variety of long-chain polysaccharides that we can’t break down without the help of gut bacteria. To find out exactly which polysaccharide molecules increased the numbers of specific microbes, additional experiments looked at various bacterial species. For the Bacteroides thetaiotaomicron, for example, the increase in abundance is driven by a molecule in pea fiber called arabinan. The investigators were able to determine that various species of the Bacteroides genus have overlapping capacities to degrade the arabinan present in pea fiber. Does that mean that all species of a genus are able to eat the same types of food? Furthermore, do various species of the same genus perform the same functions? These are open questions for another blog post.