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Looking at the abundance (and price tags) of probiotic supplements on the shelves in natural food stores these days, you'd assume there must me a mountain of evidence supporting the benefits of these products - right?
Not exactly. It's actually a complicated and somewhat confusing landscape.
That's not to say probiotics don't have beneficial effects. Rather, it's that we rather poorly understand the mechanisms by which these benefits are created - and when we do identify the mechanism, it's generally not what we would expect.
As an example, most people (including a lot of physicians) assume that the benefits of probiotics come as a result of beneficial bacterial species in the supplement colonizing the GI tract and altering the long-term species composition of our gut. The reality is, research has shown again and again this is almost never the case. 
In a handful of studies, subjects treated with probiotics showed transient colonization (3-5 days) by the probiotic species. The vast majority of studies, however, report no meaningful change in species composition after a course of probiotics. There are a small number that reported long-term changes in species composition in the guts of their subjects - but these make up a small fraction of studies.
So if probiotics aren't actually changing the species of bacteria that live in our guts, what exactly are they doing?
There are a few ways research has shown probiotic supplements to affect our gut:
1. Effects On Epithelium Function
The epithelium is the thin layer of cells that lines our guts. This layer - a single cell thick in most places - plays a critical role in both nutrient absorption and immunity.
When working properly, the epithelium allows digested nutrients to pass through where they are absorbed into the bloodstream. Undigested food, bacteria and other large particles, however, do not pass through and are retained in the gastrointestinal (GI) tract.
This function makes the epithelium is the first layer of our immune system.
Gluten is well known to disrupt the epithelium, creating a "leaky gut" through which bacteria and undigested food particles can pass and create an inflammatory immune response.
Fortunately, probiotics have been shown to have the opposite effect, actually enhancing the junction stability of the epithelium. 
Probiotics also increase the secretion of antibodies mucin and β-defensin by epithelial cells - both of which work to neutralize pathogenic bacteria in the gut and prevent them from passing into the bloodstream. 
2. Effects On Mucosal Immunity
Coating the epithelium is a layer of mucous that also plays a critical role in the immune system of our GI system.
This mucous layer functions both as a physical barrier and a biochemical barrier, preventing pathogenic bacteria from reaching the epithelium and bloodstream.
The biochemical end of mucus immune function comes from the antibody immunoglobulin-A (IgA). Probiotics have been shown to increase secretion of IgA into the mucus layer. 
3. Interaction With Existing Gut Bacteria
Probiotics have also been shown to exert an effect on the bacteria that have already colonized the GI tract. This happens via one of two mechanisms.
First, and most intriguingly, probiotics have been shown to alter the genetic expression of some of the existing species in the GI tract. This means that while probiotics rarely change the species composition of the GI tract, they do fundamentally change the bacteria already established.
We don't yet know the full implications of this finding, but it likely plays a part in more general beneficial effects of probiotics - such as improved digestion - that previously lacked a strong explanation.
Probiotics have also been shown to restrict the growth of both pathogenic and commensal (mostly beneficial) bacteria by secreting antimicrobial compounds.
Finally, probiotics discourage the growth of pathogenic bacteria by competing with them for binding sites on the epithelium. 
Limitations In Knowledge
The first thing to note here is how incomplete our knowledge is about the action of probiotics in our GI systems.
We simply don't know much about the implications of the presence or absence of any given species in our GI system. As such, when researchers learn that probiotics change genetic expression of existing species in our gut, they're kind-of left scratching their heads as to what the precise implications of that finding actually are.
Another gap in our knowledge comes from the limitations of the methodologies used by every researcher in the field.
Thus far, researchers have only used fecal analysis to determine the effects of probiotic supplementation. This methodology gives us a pretty good picture of what's going on in the lower portions of our GI tract, but doesn't tell us a ton about what's going on in the upper regions (closer to the stomach).
It's very possible that colonization by a probiotic species could happen in an upper section of the GI tract - but not show up in a fecal analysis because that species was replaced by the species that dominate lower sections of the GI tract as the digested food moved towards the colon.
It's worth pointing out here just how young this field of research actually is. Most of the studies looked at for this article were carried out within the past 5 years. As research methodologies become more sophisticated in the coming years, our understanding of how gut flora affects our bodies and brains is poised to grow at an astounding rate.
What Are The Lessons?
Despite the significant limitations in our understanding of gut flora and probiotics, one thing is clear - both play a critical role in several aspects of health and well-being.
There is enough evidence out there demonstrating benefits of probiotic supplements that not taking them would be foolish and/or negligent.
The prevailing opinion among researchers in the field is that taking probiotic supplements 365 days a year is probably unnecessary (although none recommend against it). Cycling on and off probiotics (i.e. 4 weeks of daily supplementation followed by two weeks off) seems to be the strategy that provides the maximum benefit-to-dollar ratio.
An exception to this strategy would be if you are coming off a recent course of antibiotics, in which case supplementing with probiotics continuously for 6 months to a year will greatly accelerate the time required for your gut flora to return to a healthy state. 
Lactobacillus and bifidobacteria were the most commonly studied species, but evidence suggests that others likely play just as important of a role.
When choosing a supplement, finding one designed to deliver bacteria safely past the acidic stomach is an important factor to look for. These are generally more expensive products using technologies such as soil-bound organisms (SBO's) or inulin matrices.
It's easy to get caught up in the hype around probiotics, but it's important to remember that researchers almost universally will tell you the most important thing you can do for your gut flora health is eat foods rich in the nutrients they thrive on (referred to as prebiotics).
Soluble fiber (squash, carrots, potatoes, root vegetables), insoluble fiber (leafy greens) and resistant starches (plantains, jerusalem artichokes, sushi rice) are the three types of nutrients that pass through our own stomach acids and digestive enzymes largely undigested and are thus left for our gut bacteria to consume.
Being sure to eat a diet rich in each of these types of prebiotics is the most important step we can take to ensure healthy gut flora.