Here's an excellent article on research studies in animals -
http://www.nature.com/nri/journal/v11/n10/full/nri3061.html?WT.ec_id=NRI-201110.
It's not that long, so hopefully, you'll be able to read it. If not, here are the important points to note, as I see them, with my comments following:
1) ...the intestinal microbiota has widespread implications in the field of immunology, and researchers are being compelled to explain how the microbiota contributes to and/or affects their studies.
COMMENT: Although this paper comes from an Immune magazine, it's important to note that the intestinal micribiota (flora) affects every system, organ, gland, tissue, and cell in the body. What they are noting is that the microbiota affects everything in a study. That's something that's generally not considered, but applies to every study that's ever been done, or will be done.
2) ...much more research is needed to understand and tease out specific interactions between the gut microbiota and the immune system.
COMMENT: Much, much, much more research is needed. This tells us that with all the research that's been done, this very important piece hasn't ever been considered. As I say again and again, we know about 1% of what takes place in the body. Maybe, I was being too generous.
3) ...intestinal microbiota has a role beyond the local gut immune response. This is not surprising, as the microbiota is involved in various physiological processes, including the breakdown and absorption of nutrients, the production of vitamins and hormones and the prevention of colonization by pathogens (colonization resistance).
COMMENT: It affects everthing else. Another function to consider is that the microbiota help to transform and reduce chemicals and heavy metals. Our expsoures to chemical toxins is so high, that without an intact intestinal microbiota, we will be att greater risk to the toxins we encounter.
4) ...several extraintestinal disorders have been linked to changes in gut microbiota populations. These include allergies, asthma, diabetes, obesity, cancer and, very recently, neuropathologies.
COMMENT: These type of research results have been coming out for years. If we consider just cancer, obesity, diabetes, and neuropathologies alone, addressing intestinal microbiota imbalances may be the biggest cure target ever. That then means that anything that creates these imbalances would in all likelihood be the biggest threat to human health and life - ANTIBIOTICS - which means "against life". Pasteur, who originally promoted the germ theory, via plagiarism, later recounted that theory and stated that the intestinal terrain(microbiota) was everything, as was the conclusion of the scientist Beauchamp, who he stole it from.
5) ******it is now becoming crucial for immunologists to consider the effects of the gut microbiota on - EVERY - animal experiment, as EVEN THE SMALLEST CHANGES to the commensal population can have drastic effects on the results obtained. *********
COMMENT: Note the use of the word, "crucial" in this study. The make-up of the intestinal flora can have "drastic effects on the results", even the "SMALLEST" chnages. So again, we look at whether or not this has been considered in any study past or present - NO. So will it be? The final paragraphs of this study seem to be stating no.
6) ...studies have shown that treating animals with different antibiotics or using faecal transplants can alter their microbiota profiles and result in different responses to bacterial infections.
COMMENT: Research out of Stanford in 2009 has shown that as much as 30% of the microbiota/flora can be destroyed by one round of antibiotics. While most species will repopulate, some never come back, thus permanently altering the microbiota and thus the health and possible life expectancy of an individual. The use of fecal transplants as noted above can also alter the microbiota profiles. This may be good when replenishing the microflora in someone who has had it destroyed by antibiotics.
7) A recent paper from Richard Flavell's group showed that fostering mouse pups with genetically different mothers establishes a microbiota profile in the pups that resembles the foster mother rather than the birth mother, and this was linked to changes in disease susceptibility.
COMMENT: Different foster mothers create different microbiota profiles. It wasn't the birth mothers who had the dominant role to play. It was the long-term exposure to the foster moms that created the dominant intestinal profile.
8) It is well accepted that environmental and dietary differences can shape the commensal populations in otherwise genetically identical strains of mice. For instance, the simple but instrumental study by Dan Littman's group showed that the same strains of mice from two North American suppliers (Taconic and Jackson Laboratories) have different dominant microbial communities in the gut.
COMMENT: Epigenetics. Ever wonder why you never here anything about the influence of genetics anymore, when it was always in the news for decades? It was proven that genetics weren't as influential as previously thought. What they did discover is that the environment that we're exposed to on a daily basis has greater influence. Here we have the same two strains but from two different suppliers, exhibiting different microbial profiles. Different environments, different results.
9) ...variations in diet can also affect the growth and development of different microorganisms, thereby producing different intestinal microbiota profiles.
COMMENT: Environment, environment, environment.
-A little side note here to consider, as the world environment changes around us, expect this to have an immediate effect on our health. Global warming, air pollution, toxic chemicals, etc., will change us.
10) Beyond diet and environment, a recent study has found that, even within the same facility, moving young mice from one room to another can shift the microbial populations that dominate the gut. Furthermore, mice exposed to stress in a social disruption model were found to have significant changes in their gut microbiota profiles, and this led to increased susceptibility to bacterial infection.
COMMENT: Wow. Environment, environment, environment.
11) ***these studies introduce concerns for data obtained using animal models that have not previously considered the role of the microbiota.*******
COMMENT: That means every study that's EVER been done using animal models. That easily translates to every human study also, as the same concerns apply to every intestinal microbiota. Many people consider research results to be conclusive, but this new study shows that most research results are probably flawed.
The authors of the study go on to discuss the solutions for this and the obvious enormous challenges that such solutions present. This translates to the obvious conclusion that the solutions can't be implemented at our current level of knowledge and therefore, this problem will continue to persist, at least for several decades, maybe generations, more.
In 2001, The World Health Organization stated that Antibiotic Resistance is one of the "3" main threats to human health in the world today.
In 2004, The U.S. Center for Disease Control directed all MDs to do susceptibility testing for infections prior to prescribing antibiotics. Less than 5% follow this directive.
This wound up being a longer post than I thought it would, so my apologies for the length. It's probably difficult to state these type of issues succinctly and briefly without considering all that needs to be considered.
It wasn't my origical intent to comment on each section, but I thought that would help to explain my understanding and views on what was listed.