There is a new angle in Probiotic health. People in "Developed Counties" actually have less diversity of gut flora than people exhibit in less developed Countries. This lack of diversity is completely understandable from a sanitation point of view. But, it is with greater diversity that the gut immune system functions at its peak. Diversity means a greater number of different types of bacterium in the intestinal tract all interacting in harmony for the health of the body.
While many nutritionists cite the sanitation aspect as a positive to protect health against problematic germs, some researchers are now not so sure. There is another factor too, cooked food. ref There appears to be cross-talk for immunity between the different types of organisms that historically have inhabited the human intestinal tract. This goes beyond the scope of any probiotic formula currently available in the marketplace. 
Over the last 10 years, IBD, inflammatory bowel disease, or IBS, research has progressed to the point that now the entire "microflora" is viewed as faulty. The new theory is that IBD is no longer an autoimmune disease but rather an immunodeficient condition. Of course many researchers are looking at genetic mutations as the cause. A basic shift in type of bacteria and other organisms occurs based mostly upon diet and environmental exposure. ref Changes develop from a normal balance of organisms to less firmicutes and greater bacteriodes, as occurs in developed countries from increased eating of farmed animal meat and sugar. This study looked at Herbals and functional foods on intestinal bacteria types. The normal bacterium make up changes as well, lactobacillus in small intestines and bifidobacteria in colon. This further results in disruption of microbial diversitification toward more of the phylum Proteobacteria, a situation often found in IBD. This phylum includes Escherichia coli, or E-coli. A little E-coli is necessary, but with too much or unnatural conditions, disease can develop. These changes go from mostly anaerobic, without oxygen, to more aerobic which changes the conditions and pH balance in the intestinal tract leading to a dysbiosis of the entire microflora, resulting in IBD.
NEW TWIST: This reference reveals a new concept. While the bacterial types and amounts were similar between IBD subjects and healthy controls, there was a layer difference in that more degraded mucus was found in the cells attached to the gut lining. This would cloud looking at just the number of bacteria and types but give light to other functions such as layering of bacterium, attachment, and placement, as well as other "house" cleaning and elimination body activities.
Another group has gone even deeper and presents this new aspect. Back to the beginning diversity thing. These changes have come about over time with the introduction and proliferation of antibiotics plus the many sterile environments generated in developed countries. This has produced a pretty big shift in the types of and make up of the human gut microflora. Certain players normally present in the microflora became absent or missing. These include many intestinal parasites, including protozonans and helminths. While these are capable of causing disease, when held in check, they play a positive role talking with the usual host bacteria genera in the human microbiotia. Thus, a sterile environment creates a dysbiosis and the proper immune functions and messages are impaired, leading to a compromised immune system and greater susceptibility to IBD. ref
FACT: When cattle moved form the green pasture grass into grain feed lots, one vital change occurred with the marbleization and tenderization of meat. Inside the cows multi-chambered stomach, grains feed a completely different type of bacteria than does grass. These different bacteria that now predominate do not build the same types of fat as the grass loving bacteria would. Omega 6 fats dramatically increase while omega 3 decrease, plus the CLA content of milk and cheese also decreased. Literally, meat goes from a healthy protein and fat food into the junk food category, capable of generating disease conditions. These actions unset an historically balanced ratio of Omega 6 to Omega 3 fats. This ratio went from under 4 to 1 up to 15 to 1. Over 4-1, it becomes harder for the body to limit chronic inflammation. CLA is a type of fat that controls how the body deals with and stores fat.
This situation will take some time to study and research how to safely change back to a healthy gut flora. It may take some generations and dramatic lifestyle as well as food production changes. Although today with the mobility of airplane travelers from different Countries, this is rapidly changing in large Metropolitan cities. Look at this report on bacteria found in NYC subways. ref This should jump-start your primordial pump to want to safeguard your good intestinal tract flora preventative factors to effectively deal with this bacterial diversification attack. Look at this report of bacteria trading genes between normal bacteria and pathogenic under gut inflammation conditions. This next article is a good summary of intestinal actions leading to microflora disruption here. Did you notice that the improper use of the wrong type or dosage of probiotics is one possible cause, as well as antibiotics? And this last report goes a little further into causes of intestinal dysbiosis here.
PRECAUTIONARY Sidebar: A new situation is emerging from the ever increasing dosages of probiotics in the marketplace. Scientists know that bacteria can mutate from breaks in their DNA. And that these mutated new bacteria can influence other bacteria in many ways, some adverse. With higher dosage probiotics, the likelihood of DNA breaks is increased. ref It may be prudent to stay with lower dosages, 10-25 billion, until this new issue can be examined. Plus, make sure to only take clinically documented strains with a strain code listed after the bacteria name. ref ie. Lactobacillus Acidophilus LA-14. ref
In the meantime, the use of clinically studied bacteria for IBD is the best protocol for that condition available right now. Make sure you only use documented strains that include a bacteria code and were found to have beneficial effects on IBD. Prebioitics such as FOS, GOS, and inulin have shown value on their own, even without added bacteria since they feed and control the existing good bacteria.
While diet is a major player, unless food production methods change, this really limits healthy choices. Farmed fish, vegetable oil fried foods, and grain lot beef are all junk foods. They change the diet from good fats to detrimental ones and unbalanced ratios. Plus, farmed fish rarely eat krill to make carotinoids, the element that give fish its salmon color.
Major Change in Infant Health
A change in bacteria for infants in Developed Countries represents perhaps the single most dramatic bacteria wipeout in history. All infants in less developed Countries still are born with this bacteria, Bifidobacterium Longum Subspecies Infantis. In the United States, over the last century, this bacteria is being wiped out to the point that today 90% of infants born NO LONGER EXHIBIT this most vital bacteria. This bacteria is the only one that will digest 100% of human milk carbohydrates. Blame antibiotics and cesarean births, improper diet, plus super sanitation. article