What are good and bad gut bacteria and what is the optimal microbiome?
These questions are recurrent when debating the importance of the colonic microbiota. They are often completed by questioning the usefulness of (very) minority bacteria.
As a whole, good and bad gut bacteria are prevalent in all of us, and their necessity changes or becomes irrelevant due to many factors. Some are even harmful, making it therefore safe to say that the optimal microbiome does not exist.
Indeed, there are minority species within all microbiota, and some are known to become, at times, pathogenic (causing or capable of causing disease).
The question is therefore relevant whether their presence represents a risk or whether, on the contrary, they can also contribute to the functionality of the symbiont (an organism living in symbiosis, a cooperative relationship).
Read on to learn all about good and bad gut bacteria and don’t allow the seemingly difficult words to scare you off!
Table of Contents
What are good and bad gut bacteria? Amphibiosis and ago-antagonism
Two concepts will help answer these questions:
The first is amphibiosis, which states that two life forms (e.g. a bacterium and a eukaryotic cell) can establish relationships that are either symbiotic (and therefore beneficial) or parasitic (and therefore potentially dangerous) depending on the context (and therefore the conditions of their shared life).
The second is ago-antagonism, which conceives of a system in which each bacterium can act for itself, or even be in conflict with the other(s), and at the same time, sometimes at the very heart of this conflictuality, act for the common interest of the structure to which it belongs (e.g. the colon or the large intestine).
The relationships between bacteria and between cells and bacteria
The concepts of amphibiosis and ago-antagonism, which are at the heart of ecology, are well suited to describe the relationships between bacteria within our colonic microbiota but also those they establish with our own cells.
As inscribed as they are in time and evolution they cannot be conceived as fixed but must be seen in all their dynamics.
Some species may, for example, be necessary or even indispensable during our childhood, adolescence, etc., but become less important or useless at other periods of our life, for example old age and vice versa.
We can also envisage that their beneficial roles in certain circumstances become rather harmful at other stages of our lives or in other situations, for example, when they increase abnormally or when our body malfunctions.
It is one of the functions of our symbiotic bacterial community in permanent interaction with us to regulate these situations while allowing or even forcing these species to proliferate or regress, to activate or inactivate themselves according to the needs or circumstances of life.
Indeed, the ecosystem they form cannot be seen as a fixed juxtaposition of individuals belonging to different species.
Each of these species has, of course, identifiable characteristics (especially when isolated) but, as symbionts, they form a community, within which the molecular supports (notably their DNA) of their characteristics evolve, interact and exchange.
Therefore, the ecosystem, which they constitute, has the capacity to adapt permanently to the liking of the circumstances by conciliating competition, cooperation, symbiosis, amphibiosis and ago-antagonism. In other words, it is alive.
Is there an ideal microbiota?
Often messages about the human colonic microbiota give the impression that the information they disseminate is universal and that they can relate to an ideal microbiota.
However, much of this data is based on analyses of fecal samples from Western donors who live in cities or have adopted these lifestyles, both of which may impact its composition.
For the most part, these data are also the result of one-off analyses that neglect the dynamic dimension.
Finally, there is no evidence that the composition of this (often) Western microbiota does not differ significantly from that of other terrestrial populations or from that of my ancestors. Why choose one over the other?
Indeed, the main source of bacteria that compose (from birth), enrich and renew our microbiota is their immediate environment, to which are added horizontal transfers in contact between close humans.
In this context, the urbanization of living and working environments has considerably increased exposure to indoor environments that are very isolated from nature and, more and more often, air-conditioned and highly sanitized, but also frequently contaminated by chemical compounds that are sometimes or often toxic.
Consequently, the bacterial populations from which the species necessary for the establishment, renewal and maintenance of the biodiversity of these microbiota are acquired, are those associated with these environments.
They often depend on very little contact with animals (except for domesticated animals, mainly dogs and cats) and with nature in general.
The environmental reservoir of accessible bacteria is depleted in its composition and, therefore, in its functionality.
To this must be added an ambient hygienism, often aggressive towards anything bacterial and less and less natural food practices.
As a race, we favor refined and cooked industrial foods that are subject to sanitary requirements imposed by their production conditions (e.g. intensive breeding) and marketing, which often require long periods of conservation to allow for transport over long distances.
This reduction of the surrounding bacterial diversity leads to an irreversable loss of species in our microbiota and, therefore, to a loss of important functionalities.
Therefore, we are obliged to note that the Western-type microbiota, which is generally used as a reference, is depleted and continues to be depleted.
Under these conditions, defining an ideal colonic microbiota is probably more or an illusion than anything else
By its very nature, the colonic microbiota can only be variable and evolving in its composition according to age, environment, diet, season, etc.
What are good and bad gut bacteria, or ideal microbiota? Conclusion
Within all microbiota live minority species. Some are known to become, at times, pathogenic.
Does the presence of these minorities represent a risk? On the other hand, can they contribute positively to the functionality of the symbiont?
Two concepts allow us to answer these questions.
According to the first called amphibiosis: two bacterial species or a bacterium and a eukaryotic cell can establish relationships that are either symbiotic (and therefore beneficial) or parasitic (and therefore potentially dangerous) depending on the conditions of their shared life.
The second is ago-antagonism, which makes it possible to conceive that each bacterium can act for itself, or even be in conflict with others, and at the same time, sometimes at the very heart of this conflict, act in the interest of the colon.
Indeed, the relationships between the bacteria within the colonic microbiota but also those they establish with its cells cannot be conceived as fixed.
On the contrary, they must be seen in all their dynamics.
Thus, some species may be necessary or even indispensable for the functions required during childhood, but become useless or even harmful at other periods of life, for example old age, and vice versa.
Their beneficial role in certain circumstances becomes rather harmful at other stages of life.
It is one of the functions of the symbiotic bacterial community in permanent interaction with its host, to regulate these situations.
So the ecosystem of which they form a part, has the capacity to adapt permanently to the liking of the circumstances by reconciling symbiosis, amphibiosis and ago-antagonism.