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18. The Owner's Manual: The Good, the Bad, and the Context is Everything

Good Bacteria vs Bad Bacteria?

To put it very plainly, in our everyday life, there is no such thing as good bacteria or bad bacteria. This may fly in the face of everything you’ve ever heard or read about bacteria, but it’s true. No matter what we think of Streptococcus after several bouts of strep throat or Staphylococcus after a very serious post-operative infection, those bacteria are only pathogenic under certain circumstances and usually when something has affected our ability to control their growth. We have a deep fear of bacteria that is based on centuries of battling and dying from bacterial infections, plagues, and epidemics, but that fear represents a very narrow view of the bacterial world.

Bacteria are everywhere. The ocean can be considered bacterial soup with perhaps 20 billion bacterial cells per cubic meter in open ocean water. That’s a large number, to be sure, but not particularly high population density for something as small as a bacterium, which is typically 1/100th the length of a human cell. Nonetheless, there’s a lot of ocean out there.

Bacteria are also incredible abundant in natural soils and have been estimated at 10 billion per gram of soil with perhaps 1000 different kinds. The much higher numbers in soil compared to water is partly because there is a substrate (soil particles) for the bacteria to cling to and food is abundant. Nonetheless, we can assume that bacteria are present wherever there are molecules for them to consume.

The biggest problem for microbiologists is determining just what a bacterium species is, which seems like an odd problem. Bacteria are just about the simplest organisms you can imagine. One cell, no visible structures in the cell, and their food sources are organic materials they find in the environment. If there are organic molecules somewhere in the environment, there are bacteria trying to eat them.

Each type of bacteria has a particular food preference, some type of chemical that they are especially good at breaking down for energy, and when they find that food, they proliferate. Because there are very few visible identifying characteristics and an individual bacterium is so small, it is very hard to determine what species a bacterium might be. So, it’s necessary to grow a colony of bacteria of a particular type and then test them in one of two ways: offer them a variety of food sources to see which ones they eat or obtain their genetic sequence. Both techniques then require a computer-assisted search that matches the food preferences or genetic profile to a specific species.

To complicate the identification of a bacterial species, bacteria mutate frequently and eventually that complicates proper identification. In fact, the computer-assisted identification typically brings back a report something like: “there is a XX% chance of this being Species Z”. That is, the identification of a species is rarely 100% certain. So, it’s very common just to lump bacteria into family groups, such as “coliform bacteria”, which means they resemble E. coli. (i.e., they are rod-shaped, Gram-negative, non-spore forming bacteria that contain the enzyme B-galactosidase).

In the case of the microbiome, very few bacteria are actually named, but are just listed as being members of, for example, the Proteobacteria, Firmicutes, or Bacterioidetes. As far as we’re concerned, we really just want to know what they eat and what they do. Mostly, bacteria chemically break down other molecules to get energy and nutrients. That is, they digest molecules.

They also are particularly good at defending themselves, which is probably more accurately stated as they ar good at defending the food they are trying to digest. They do this chemically also. Production of those defense and digestive chemicals is how bacteria survive in a world of billions of other bacteria and fungi species, most of which are potential competitors.

The defense chemicals that bacteria produce can take many forms but, in the world of microbes, chemical warfare is the primary mode of interaction and those chemicals often affect cell membranes of other species. This is relevant to the human relationship with bacteria because whether the bacteria are beneficial or pathogenic, the chemicals are the way the bacteria interact with our cells.

Most humans have 1000-1500 species of bacteria in their large intestine and all of them are secreting chemicals into the colon environment. This is what bacteria do. The bacteria are attempting to obtain energy and nutrients from the undigested plant materials that made it through the small intestine and are destined for excretion.

Given a sufficiently diverse bacterial community and a diversity of food materials, no one bacterial species can dominate the environment, which is also changing daily with the arrival of new and different food stuffs. So, the many species wax and wane in abundance as favored food supplies appear and then disappear. The abundance of each bacterial type can only increase in the immediate vicinity of its food supply and as that food supply moves through the colon to the anus, the majority of the associated bacteria are carried along with it. And so, any particular group of bacteria is being moved toward the exit relatively quickly (about 18-24 hours) and the interaction with the host is short-lived and pretty neutral.

So, what is a bad bacterium? Simply put, a bad bacterium is one that is allowed (for some reason) to proliferate unchecked. This happens when the controls that normally slow or stop proliferation are absent or damaged. It may be at the site of an injury where only a few types of bacteria establish and the defenses of the body are not strong enough to suppress that growth. It may be in the colon after antibiotics have ravaged the bacterial diversity and only antibiotic resistant bacteria remain. Resistant bacteria tend to be those that have a long history with the antibiotics that are used to control their growth.

In other words, if the environmental context changes, the resistance and resilience of the environment (such as the one in your colon) is compromised, and any bacteria that can take advantage of that situation can rapidly become super-abundant. Again, this is what bacteria do naturally. As I said before, C. diff, E. coli, Streptococcus, and Staphylococcus aureas are commonly occurring bacteria in the large intestine and can be identified in virtually everyone’s fecal samples. When they occur in a healthy context, they are not problematic. When the context changes, they can be deadly. And so, good, bad, or neutral completely depends on the context.

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