In many modern discussions about bacteria, or germs, we find that novel descriptions are used that are more self-involved than accurate regarding the role of bacteria and microbes.  Certainly there is an increased awareness that many microbes are commensal [or "good"] and are necessary for our well-being, while others are considered "bad" and cause disease.

However, this distorts our understanding of this relationship and helps promote some of the very ideas that foster beliefs that deny the germ theory altogether.  After all, if it's about "good" versus "bad" then we have defined a classic confrontational viewpoint that supports people making claims about what constitutes the right way to live versus the wrong way.

Bacteria are often portrayed as being some type of dangerous interloper lurking about until an opportunity presents that allows it to sneak into our bodies, employing all manner of subterfuge to gain access and fool our immune systems, while others are portrayed as being vigilant in protecting our interests.  However, I would submit that as entertaining as this scenario is, it is fundamentally wrong.  Most bacteria have little impact on the organisms they inhabit, with only a small subset being pathogenic within any given creature.

With pathogens, many erroneous assumptions occur in attempting to explain how they can succeed evolutionarily if they kill their hosts, as if this were some maladaptive process at work (1).  The difficulty is not that these things may occur, but rather that our perspective is muddled because we still think anthropocentrally, by presuming that all these biological processes are targeting us as human beings.  Bear in mind that the fate for a pathogen in killing the host, is no different than the fate awaiting the "good" bacteria on the normal death of the host.  There's nothing maladaptive about it, it just goes with the territory (2).

In truth, the human body [or any organism] simply represents an environment.  As a result, we see bacteria behaving just as any organism does when presented with an environment it is familiar with versus one that is potentially hostile to it.  Every organism strives to control its environment and competitors to maximize its probability of surviving.  In many cases, that action may be detrimental to the organism, but it is incapable of acting otherwise.

It is fundamentally no different than asking the question about why the population of Easter Island cut down all their trees.  It is simply what they did, and no amount of rationalization will ever explain what someone is thinking as they cut down the last tree (3).  So it is with microbes, that are also striving to compete with the existing residents of an environment or having to cope with an environment for which they haven't specifically evolved to coexist in.

Current knowledge indicates that the human microbiota is responsible for "training" the immune system, yet it is legitimate to ask, to what end?  Is it merely to keep out competitors?  After all, it would be difficult to rationalize that bacteria, at any level, are capable of recognizing that some microbe is dangerous to humans.  In fact, resident bacteria prime the immune system to recognize themselves to avoid being targeted.  However, indigenous bacteria often don't view others as the "enemy" either, since they will often freely exchange antibiotic resistant genes with pathogens.  One could draw parallels to the same type of encounters between any animal group that encounters an indigenous group already occupying a territory.  In many cases, it is striking that the problem often doesn't actually originate with the purported pathogen, but rather with the inflammatory response to that microbe that is the difficulty [i.e. meningitis].  Certainly this doesn't change the outcome in how the human feels, but it is important to recognize that these microbes don't set out to make us sick.

In fact, it is quite telling that a particular cell death (pryoptosis) (4) is used to trigger an immune response by alerting the immune system of an invader, yet pathogenic bacteria can also release toxins which aggravate the inflammatory response.  Both release toxins, yet one is a toxin for which our immune system directs a specific response, because it recognizes it, while the other initiates a response which may make us sicker.   However, toxins aren't intended for the host.  They are intended for dealing with the bacteria in competition with each other.  In short, pathogenicity isn't as easy to identify as most think (5).

Similarly, the portals of entry for bacteria, also represent diverse strategies that have evolved to allow them to be introduced into a new environment.  Every organism has obstacles in attempting to colonize a particular territory, so each evolves a means to adapt to the circumstances to which it needs to respond (6).  Just as animals attempting to figure out how to cross a river to get to new territory, to dealing with predators that may live in that river, to attempting to cross mountains to get to environments on the other side.  While the obstacles may be different in principle, they represent the same types of responses across virtually all species.

In addition, functions like quorum sensing are often cited, as if to suggest that bacteria are somehow sneaky (7) and don't announce their presence until they have a sufficient number present and then they seek to overwhelm the immune system.  Perhaps, but it seems much more likely that these bacteria simply wait until a sufficient number are present, so that they can get on with the business of managing their colony.  Just as a single human settler didn't arrive on the west coast and decide to build Los Angeles, we humans also engage in a kind of "quorum sensing", in that when there are enough of us, then the environment shifts to accommodate that difference.

We don't have to consciously recognize when we have a large enough population to undertake certain activities, any more than bacteria have to maintain a "head-count" before they commence their "attack".

Even more telling is when we recognize that many of the "good" bacteria are just as damaging when they find themselves in an environment for which they are unsuited [Clostridium difficile - normal flora but can infect large intestine].  Bacteria that cause no difficulty in the gut, or in the mouth can have devastating consequences when present in other areas.  Many common bacteria can generate horrific results when a sufficiently unusual set of circumstances occur.

Another example occurs in a recent article where a different microbial interaction killed 5 individuals after a massive tornado.  We are routinely exposed to this fungus, but in the wake of this storm, it was introduced into several individuals through traumatic injuries that penetrated the skin and introduced the fungus into an environment for which it was not adapted.  As a result, we find the fungus behaving in a radical manner to preserve its survival, while the host immune system is attempting to eradicate the invader.

In effect, the entire problem is that the fungus has no idea of how to survive in the human body, so it proceeds in annihilating everything around itself in an effort to gain control over the environment, to replicate what it typically enjoys in the soil.

So, the point of this article is to consider a different perspective of how microbes interact with organisms, so that we don't view them simply as a case of the "good guys" versus the "bad guys" or worse, think that somehow we can magically determine the outcomes by creating a pristine wholesome environment for our microbial friends.  In effect, while neglect of our bodies may provide more opportunities for other bacteria to be introduced, as well as weaken the existing colonies, so can prolonged exposure to antibiotics have a devastating effect on the "balance" of microbes in our system.  Similarly, the idea that probiotics are good is probably true to a limited extend, but it would be analogous to dropping a million humans into a terrain by parachute and assuming that a city would be built.  Without more specific controls as to what bacteria are introduced and where they reside, at best it is a hit or miss proposition that anything would materially change.  After all, any bacteria that you introduce must also find a place to settle if they are to be a part of the environment, so without any "open space" available, there is no place for them to settle.

While I'm sure that some readers will find exceptions or objections to some of the discussion here, the point isn't to argue about the germ theory, but rather to promote a view that considers microbes from their perspective as organisms that are simply attempting to survive in their environment, rather than considering that they are out to either help or hurt us [the anthropocentric angle].  Given the complexity of the bacterial ecosystem that we represent, it is useful to be prudent in how radically we impinge on its residents, and to recognize that we aren't the only ones occupying this space.

(1) Consider the persistence of diseases like the plague (Yersinia pestis) which are largely transmitted through fleas. Despite killing millions of people, the plague bacteria has done little to render itself extinct, since human infection is largely accidental, being primarily an infection of rodents.  As a result, the plague [as so many other diseases] was largely a self-inflected catastrophe of human making, by creating unsanitary conditions that promoted the means for these bacteria to be introduced into environments that they might otherwise have never gained access to. Many of our most dangerous diseases are not because of biological competition or selection among microbes, but because of our close proximity to large human populations, with poor sanitation in high risk areas, and large numbers of domestic animals that may also serve as vectors.  In effect, we created the "perfect storm" of conditions [and instigated the selection process] that allowed may of these pathogens to move into new human environments.

(2) It isn't at all clear that bacteria necessarily die simply because the host does.  Since bacteria are quite capable of forming endospores in periods of stress, they could well survive for years in that form, before they are again presented with an environment in which they can grow and reproduce.  However, it is also important to note that much of the initial process of decomposition originates with the bacteria that are already resident in the body.  
"While many of the organisms isolated come from the bowel and respiratory tract, literally hundreds of species are involved in the decompositional process and decomposition would not progress without them."

(3) For those that wish to argue about Easter Island, the following two links provide a good discussion on the topic:

(4) For an interesting example of how his process is subverted by the plague bacteria.

As a result, it became apparent that many microbes previously considered non-pathogenic, or rarely pathogenic, such as Staphylococcus epidermis and Candida albicans, could cause serious disease.
(6) It is interesting to note that virtually every possible avenue for entry has the potential to be exploited by various bacterial strains.  Even phagocytes [cells that engulf and "eat" the bacteria] can be exploited by particular species that can survive inside the phagocyte and evade the immune system.  In addition, bacteria can also make their way into cells and take up residence to avoid immune system response.

(7) One can also note how frequently bacteria are referred to as being sneaky in their efforts to get into the body.  In reality they are just as sneaky as the Europeans were settling North America.  It's a quaint but misleading portrayal of what occurs.