Meet your second digestive system
You are carrying a large population of microorganisms, most of them in your colon. The usual shorthand is "good bacteria and bad bacteria". That framing is comfortable, popular, and not much use.
Why good-versus-bad breaks down
The same organism can be harmless in one context and a problem in another. Some depend on the presence of others to behave usefully. Many have no clear moral position at all — they are simply metabolising what is available.
A more useful frame is occupational. Think of a workshop rather than a battlefield. Different workers arrive with different tools, take on different materials, and produce different outputs.
Three ways they differ
They use different substrates. A microbe that can break into resistant starch may be unable to touch a branched plant gum, and vice versa. The enzymes are specific, in the same way yours are — this is the same principle you met in Chapter 3, applied to organisms with a far wider toolkit than ours.
They do different jobs. Some are primary degraders: they attack intact plant structures and open them up. Others cannot do that at all, and live on the fragments the first group releases.
They produce different things. The metabolic output differs by organism. Some yield mainly one short-chain fatty acid, some another, some produce gases as a by-product.
The handover that makes it a community
This is where it stops being a list of species and becomes a system.
Certain organisms release acetate as they break fibre down. Others take that acetate and convert it into butyrate. Cultured strains of butyrate producers have been shown to draw a substantial majority of their butyrate carbon from acetate made by someone else (Duncan et al., 2004).
So the butyrate in your colon is often not the work of one organism. It is the output of a relay. Which means having the butyrate-makers present is not sufficient — they need the organisms that feed them, and those need something to break down.
That is the mechanistic case for eating a range of plant fibres rather than a lot of one, and it is worth noticing that it follows from how the community works rather than from anything a supplement company asserts.
Go deeper: keystone organisms
Some substrates depend on particular specialists. Resistant starch, for example, is degraded most effectively when a specific primary degrader is present; without it, the starch is used far less efficiently even if other organisms are abundant (Ze et al., 2012).
The practical implication is uncomfortable for anyone selling a simple story: the same fibre can behave differently in two people, because the community receiving it is different. Fermentation studies of the same fibre across individuals do show substantial variation.
Not an army of good and bad. A workshop of specialists, where one worker's output is the next one's raw material.
What to hold on to
Diversity of microbes is a consequence of diversity of substrate. Feed a narrow range of materials and you support a narrower community; feed a wider range and more specialists have something to work on.
We have used the word fermentation several times now without defining it. That is next.