Tuesday, July 24, 2012

Microbial Ecosystem Biology Paper by a friend

The following is a paper written by a friend of mine, Dominique Vyborny, for her biology class at college. I am encouraged for our future as she is of a younger generation, does not have a serious gut condition, and she is evaluating our human relationship with microbes as a complex and delicate interwoven system! This is a wonderful introduction to a breadth of topics surrounding our ecosystem. I am publishing this with her permission. I hope you enjoy it as much as I did! 

Our Inner Ecosystem:
How Our Microbiota Affect Our Health And How Probiotics May Have a Positive Impact
Dominique Vyborny Bio1323
Section 1: You Are Not Alone
With the popularity of antibacterial soaps, household cleaners, 
disinfectants, hand sanitizer, and the all too common view that germs cause disease, it’s difficult for us to conceive that our bodies are living in a healthy symbiosis with many trillions of bacteria, fungi, archaea and protozoans, both on our skin and inside our bodies. Many of these are beneficial to our wellbeing, though some are pathogenic if given an opportunity overpopulate inappropriate locations. Some beneficial bacterias in our GI tract produce nutrients such as biotin and vitamin K which can be absorbed by the body(1). Under normal conditions these microbiota live in harmony with each other, but occasionally an outside factor such as antibiotics, surgery, or immunosuppressive medications can kill off some of the good bacteria causing an opportunity for the pathogenic bacteria to flourish in unhealthy numbers. (2)
Probiotics are becoming a more popular way to help reclaim a healthy internal bacterial balance. Probiotics are defined as “live micro-organisms which when administered in adequate amounts confer a health benefit for the host”(2). Common probiotic cultures that have been proven to provide some health benefit include lactic acid bacteria, specifically, strains of Lactobacillus and Bifidobacterium. A type of yeast, Saccharomyces boulardii, has been shown to have health benefits, such as anti- inflammatory mechanisms.(3) There is also a specific strain of E. coli, specifically Escherichia coli Nissile 1917, that has been shown to have a highly responsive effect on some Crohn’s disease patients. (4)
Germ-free mice, born and raised in the absence of all microbes, suffer from several physical developmental issues: “The gut-associated lymphoid tissue (GALT), the first line of defense for the intestinal mucosa, is defective in germ free mice....Besides the developmental defects in tissue formation, the cellular and molecular of the intestinal immune system is also compromised in the absence of symbiotic bacteria.” (5)
Section 2: Every Culture Has a Culture
In countries and countries across the world we consistently encounter foods that have been fermented with non pathogenic bacteria into a stable state for storage and usage. Examples of these are brined olives, yogurt, kefir, Kim Chi, cheese, sauerkraut, sourdough, . All of these have been cultured using a variety of Lactobacillus bacterium, and until our relatively recent shift into homogenizing foods, they would contain active cultures up until the time of ingestion. Lactobacillus Plantarum most often occurs in fermented foods that are based on plant material.(6) This strain may have highly beneficial properties for those suffering from obesity, as we shall see in Section IV.
Unfortunately, with modern pasteurizing requirements, most of these foods that would normally be rich in probiotics have been stripped of their beneficial bacteria. Certain companies will reintroduce a limited amount after pasteurizing. One such company is White Mountain Bulgarian Yogurt. They then reintroduce the bacterial strains L. Acidophilus, L. Bulgaricus, S. Thermophilus and B. Bifidum. (7) The Gold Mine Natural Food Company sells a raw organic sauerkraut which is publicized to contain 7.8 million CFU’s of live lactobacillus and bifidobacterium species per gram.
We’re also seeing more options for pill-form probiotics at the local health food store. Many companies have a minimum potency guarantee, but it’s difficult to maintain appropriate conditions ideal for the health of the bacteria from manufacturer to consumer. Quite a few of these products ideally need to be refrigerated during transport to keep the bacteria alive, dormant and inactive. Some companies have come up with interesting ways to present their product, from a vegan coconut kefir that is appropriate for vegans, to a capsule that doesn’t need to be refrigerated because the bacteria is stabilized using other methods. One such company is Jarrow Formulas. They have a product called Jarro-Dophilus EPS® which is advertised as a “stable- dophilus”, meaning that it’s a shelf-stable formula and doesn’t need refrigeration, although refrigerationwillhelpextendit’sshelflife. Italsohasanentericcoating,whichwillhelpit resist the acidic environment of the stomach in order to populate the small intestines.(8) Let’s take a look at the challenges probiotics face after we ingest them.
Section 3: The Journey Home
For probiotic bacteria to be of maximum benefit, the specific strains must posses certain traits.They must either be able to survive the acidic stomach on their own, or be in a capsule that allows them to pass through the stomach and into the intestines. They must be able to colonize and reproduce in the intestines, then attach to the lining of the GI tract and become stabilized with the rest of the bacterial population. (1)
It has been suggested that, because our bodies evolved in the presence of a wide variety of bacteria and the gut microbiota evolved with our bodies, our bacteria that populate the alimentary tract have the ability to engage in cross-talk with the human host that involves several mechanisms. The host’s innate immune system is able to recognize the molecular structures of both non-pathogenic and pathogenic bacteria.(7) Basically, the body can distinguish between friend and foe. Another way that host and bacteria communicate may be through the use of hormones on the hosts end, and hormone-like chemicals produced by the bacteria. (9)
Depending on the type of bacterial probiotic that’s ingested, the cultures may colonize different parts of the GI tract, and play different roles in maintaining the health of the human host. Certain types of bacteria can withstand the highly acidic environment of the stomach, some of them pathogenic such as Helicobacter Pylori, These bacteria use interesting methods to stay alive, such as producing large amounts of urease, which causes urea to break down into ammonia, thus buffering the stomach acid in their direct vicinity. (10) Bacteria will also colonize the small intestine, but are found in the largest numbers in the large intestine.
Section IV: Our Mirco Minions
The role that our mircoflora play may be more extensive than simply helping to crowd out pathogens. According to S. Possimiers et al:
“It is estimated that the collection of all microbial genomes in the gut comprises between 2 million and 4 million genes, which is 70-140 times more than that of it’s host. This “microbiome” encompasses all genes that are responsible for for numerous processes such as substrate breakdown, protein synthesis, biomass production, production of signaling molecules, anti-microbial compounds, and encodes biochemical pathways that humans have not evolved. Thus the intestinal microbiota can be regarded as a separate organ within the human host, which is capable of even more conversations than the human liver”.(9)
There are several diseases of the GI tract that have become more prevalent since pasteurization, irradiation, and sterilization of our foods has become the norm. Obesity has been sharply on the rise since 1980. During the 1980s and 1990s hospitalizations for peptic ulcers was on the decline but rates still remained high (11), Diagnoses’ of Crohn’s Disease(CD), a type of Irritable Bowel Disease(IBD), have been on the rise as well. There have been several studies involving these diseases and their responsiveness to probiotic treatment, or the role that gut microflora may play in causation and prevention as well as in active treatment.
In America, cases of obesity are at an all time high, with clinical obesity effecting 1 in 3 Americans. Recent studies have shown that there may be a strong link between obesity and gut microflora in animals and humans. The internal microbial balance of people suffering from obesity shows a much different bacterial profile than their more slender counterparts. (12) A study conducted by student Caroline Karlsson at Lund University in Sweden shows that in rats, an L. plantarum probiotic administered from birth until adulthood may help in controlling obesity and also seems to reduce low-level inflammation. According to Ms. Karlsson: "Rats who were given this specific lactic acid bacterium from their time in the uterus up to adult age put on significantly less weight than other rats. Both groups ate the same amount of high-energy food". There was a control group which wasn’t given any bacterial supplement, and then a third group which was given an amount of E. coli bacteria in their drinking water. The third group experienced distinct changes in their gut flora and an increased weight gain. (13) It’s been suggested that the unhealthy microbiota have the ability to increase the Caloric intake of their host, and may signal for the excess energy to be stored nearby, causing a larger amount of central body fat. (12)
The pathogenic bacteria Helicobacter pylori has been implicated in several conditions effecting human health, most commonly peptic ulcers, and as a risk factor for gastric adenocarcinoma(stomach cancer) and lymphoma. The most common to treatment for this bacteria utilizes antibiotics but due to moderate patient compliance, high cost of treatment and a resulting resistance of the bacteria, this solution is often not 100% effective. H. pylori is one of the world’s most prevalent pathogens, infecting up to 50% of the world’s population. Low socio-economic level and bad hygenic conditions are implicated as the main risk factors. Studies have been showing that the natural actions of Lactobacillus bacteria may help keep H. pylori populations in check. The suggested naturally occurring mechanism is the production of specific short chain fatty acids(SCFAs) and bacteriocins. The SCFAs lower the pH level of the gastric environment and help keep numbers in check. Bacteriocins are compounds that are small heat-resistant peptidic structures with antimicrobial activities. (10)
Crohn’s Disease(CD) is a type of Inflammatory Bowel Disease(IBD). Recently it’s been supposed that some cases of Crohn’s will respond well to a treatment of probiotics and prebiotics, if the common steroidal treatment shows no response. In a study done by S. Fujimori et al, ten active CD outpatients without history of operation for CD were enrolled in the study. Their ages ranged from 19-42. Their main symptoms were diarrhea and abdominal pain. They were put on a daily intake of both probiotics (75 billion colony forming units [CFU] daily) and prebiotics (psyllium 9.9 g daily). The probiotics were mainly comprised of Bifidobacterium and Lactobacillus. Over a 21 month period, 7 patients showed a complete response to the treatment, one patient showed a partial response, and three patients showed no response. It can thus be concluded that this treatment is safe and effective in treating active Crohn’s Disease.
Section V: In Conclusion
The microbiota and flora of the human alimentary tract are complex and interesting to study. They serve many purposes, and it can be safe to say that the human species may not have made it so far with out the help of our inner ecosystem. Preventing pathogenic disease is an important goal for our society, but learning to recognize that not all bugs are created equal, and that not all are enemies, may be the next important shift for our medical future. I hope you enjoyed learning about your own inner world, and I hope you have an opportunity to try some actively cultured foods sometime, they’re quite delicious!

Cited References
1 JS Blake, KD Munoz, S Volpe, 2010, Nutrition, From Science to You, ISBN 10: 0-321-51319-3
2 N T Williams, Probiotics. Am J Health-Syst Pharm--Vol 67 2010, March 15. Pg 449-458
3 C. Pothoulakis, Review Article: Anti-Inflammatory Mechanisms of Action of Saccharomyces boulardii Alimentary Pharmacology and Therapeutics, 2009, 30, Pg 826-833
4 http://www.eurekalert.org/pub_releases/2011-03/asfm-pbc033111.php
5 Yun Kyung Lee, Sarkis, K. Mazmanian. Has the Microbiota Played a Critical Role in
the Evolution of the Adaptive Immune System? Science Magazine, December
24, 2010. Vol. 33, No. 6012, Pg 1768-1773
6 Edward R Farnworth, 2003, Handbook of Fermented Foods, ISBN 0-8493-1372-4 7
8 http://www.jarrow.com/product/228/Jarro_Dophilus_EPS
9 Sam Possemiers, Chalotte Grootaert, Joan Vermeiren, Gabriele Gross, Massimo
Marzorati, Willy Verstrete, and Tom Van de Wiele. The Intestinal Environment in Health and Disease-- Recent Insights on the Potential of Intestinal Bacteria to Influence Human Health. 2009 Current Pharmaceutical Design, 15, Pg2051-2065
10 M. Gotteland, O. Brunser, S. Cruchet. Systematic Review: Are probiotics useful in controlling gastric colonization by Helicobacter pylori? Alimentary Phamacology and Theraputics, 2006, 23, 1077-1086
11 Feinstein LB, Holman RC, Yorita Christensen KL, Steiner CA, Swerdlow DL. Trends in hospitalizations for peptic ulcer disease, United States, 1998–2005.
Emerg Infect Dis. 2010 Sep
12 Abstract:
DiBaise JK; Zhang H; Crowell MD; Krajmalnik-Brown R; Decker GA;
Rittmann BE, Gut Microbiota and Its Possible Relationship With Obesity, April
2008, Mayo Clinic Proceedings.;83(4) Pg 460-469,
C. Karlsson, Healthy Gut Flora Could Prevent Obesity. Lund University Magazine,
May 25th, 2011.
14 S. Fujimori, A. Tatsuguchi, K. Gudis, T. Kishida, K. Mitsui, A Ehara, T. Kobayashi, Y.

Sekita, T. Seo, C. Sakamoto. 2007. High dose probiotic and prebiotic cotherapy for remission of induction of active Crohn’s disease. 2006, Journal of Gastroenterology and Hepatology, 22, Pg 1199-1204

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