Our human body consists of about 100 trillion cells but we carry about 1000 trillion bacteria in our intestines, that represents 10 times the amount of our own cells. (1) These bacteria are variously called our micro-flora, microbiome, gut flora, etc, along with viruses and other organisms that co-exist and co-evolved with us. Advances in rapid gene identification have enabled an explosion of knowledge related to our micro-flora, health and disease. We each carry an estimated 500 to 1000 different species of bacteria in our intestines and the balance/mix of these bacterial species can have profoundly positive or negative affects on our health. Patterns of micro-flora have been identified for a variety of human disorders including obesity, diabetes type I, several kinds of cancer and  inflammatory bowel disease to name a few. The issue of association vs. causation remains to be resolved but the beneficial and therapeutic effects of pro-biotics and fecal transplant (in rodent and human studies) in a variety of situations along with the observed deleterious effects of interrupting our micro-flora speak in favor of a causative or contributory role. (2) (3)

Accumulating evidences indicate that some diseases are triggered by abnormalities of the gut microbiota. Among these, immune-related diseases can be the promising targets for probiotcs. Several studies have proved the efficacy of probiotics for preventing such diseases including cancers, infections, allergies, inflammatory bowel diseases and autoimmune diseases. Lactobacillus casei strain Shirota (LcS) is one of the most popular probiotics, benefits of which in health maintenance and disease control have been supported by several science-based evidences.(2)

Early microbial colonization of the gut reduces the incidence of infectious, inflammatory and autoimmune diseases. Recent population studies reveal that childhood hygiene is a significant risk factor for development of inflammatory bowel disease, thereby reinforcing the hygiene hypothesis and the potential importance of microbial colonization during early life. (3)

Early-life environment significantly affects both microbial composition of the adult gut and mucosal innate immune function. We observed that a microbiota dominated by lactobacilli may function to maintain mucosal immune homeostasis and limit pathogen colonization. (3)

The human GI tract starts with the mouth and ends with the rectum. In between lay the esophagus, stomach, and intestines which consist of the duodenum, jejunum, ileum, and colon.

The surface area of the intestines equals that of a tennis court providing a huge area for absorption, digestion and interaction between our immune system and the micro-flora. This large surface area is the result of the intestinal micro-villi which produce an undulating surface resembling a series of peaks and valleys. The constant interplay between our immune system (4) and our micro-flora from birth to death along with the signaling and communication that occurs between our micro-flora and our nervous system (5,6,7) present two physiologic mechanisms for potential symbiosis (mutually beneficial interaction) vs dysbiosis (disease causing relationship).

Before birth the mouth, skin and intestine of the fetus is sterile. The first major introduction of bacteria to the infant occurs with birth  when the infant swallows bacteria in the mother’s birth canal and the infant’s skin becomes colonized by the mother’s bacteria. Infants born by cesarean section lack this initial exposure and they suffer increased risk of allergic and auto-immune disease (8). The rate of cesarean section in the US is now about 30 % and along with that increase there has been an observed increase in allergy, auto-immune and other diseases.

The second major addition to human gut and skin flora occurs with breast feeding and again breast-fed infants show decreased rates of allergy and auto-immune disease as well as decreased infections compared to bottle fed infants.

The interaction between the micro-flora and the immune system presents many complex relationships and interactions. Immune tolerance allows the immune system to recognize “self” and “friendly bacteria”  limiting the development of auto-immune disease and enhancing anti-inflammatory processes. At the other extreme recognition of “non-self”  allows for the recognition and disposal of “foreign” invaders such as infections or mutated cancer cells.

“The Old Friends Hypothesis”
Common organisms interact with dendritic cells in the GI tract, leading to increased maturation of dendritic cells. When there is interaction with these organisms again, the dendritic cells increase Treg maturation; not Th1 or Th2. This increases the baseline amount of anti-inflammatory cytokines, producing a Bystander Suppression. Another consequence of the increased number of mature dendritic cells is as they interact with self antigens, they increase the number Treg specific to these antigens. This is referred to as Specific Suppression. Together these two arms lead to tolerance of both self antigens as well as those of helpful gut organisms. (8)

Translation:  Treg or Regulatory T cells regulate the immune system and help prevent auto-immune disease and allergic reactions. Th1 and Th2,  T helper cells , on the other hand, increase inflammation and help our bodies defend against infection. The balance between Tregs and Th1, Th2 cells governs inflammatory responses.

Premature infants have an increased risk of a developing a very severe illness called necrotizing enterocolitis. Human studies have demonstrated significant risk reduction for this problem with the administration of pro-biotics to infants in neonatal intensive care units. (9)

Similarly, administration of pro-biotics during the first few years of life (to mother and child)  have been associated with decreased risk of eczema in children. While some studies suggest reduction of allergies and asthma in children, the regular use of probiotics remains undecided relative to preventing food allergies or asthma (10, 11).

Due to the recent exponential increase in food allergies and atopic disorders, effective allergy prevention has become a public health priority in many developed regions. Important preventive strategies include the promotion of breastfeeding and vaginal deliveries, judicious use of perinatal antibiotics, as well as the avoidance of maternal tobacco smoking. Breastfeeding for at least 6 months and introduction of complementary solids from 4-6 months are generally recommended. Complex oligosaccharides in breast milk support the establishment of bifidobacteria in the neonatal gut which stimulate regulatory T lymphocyte responses and enhance tolerance development…Perinatal supplementation with probiotics and/or prebiotics may reduce the risk of atopic dermatitis, but no reliable effect on the prevention of food allergy or respiratory allergies has so far been found. A randomized trial on maternal fish oil supplementation during pregnancy found that atopic dermatitis and egg sensitization in the first year of life were significantly reduced, but no preventive effect for food allergies was demonstrated. (10)

Thus birth by cesarean section increases risk and  breast feeding decreases risk of immune related problems (allergies, auto-immune disease and infection ). Use of probiotics for mother and child decrease the risk of eczema but the use of probiotics in preventing asthma or food allergy remains unsettled. There are a host of possible probiotics available that include various combinations of “healthy bacteria”. Future posts will discuss some of these.

Our micro-flora are constantly exposed to potential changing agents. Known influences include antibiotics (as medications or in the foods that we eat), stress, sleep, and diet. Because of the ubiquitous use of antibiotics in agriculture and animal husbandry, and the sometimes excessive use of antibiotics in medicine our microbiome is frequently changed by external factors. Many experts on the microbiome  consider these influences harmful and attribute the rising rates of several diseases as consequences of disruption in our gut flora.

Clostridium Difficile Colitis , a serious infection or overgrowth of the bacterium Clostridium difficile in the intestine occurs most commonly as a result of antibiotic administration to treat infections. This serious problem responds to anti-biotic treatment (ironically both the cause and cure) 90% of the time with the first round of treatment but there is a high incidence of recurrence due to the fact that C-difficile spores are resistant to antibiotics and can cause recurrent infection. In refractory or recurrent C-difficile cases a fecal transplant (FMT or fecal microbiota transplant) from a healthy human results in a 90 to 95% cure rate with the first treatment.

Antibiotic usage disrupts the normal gut flora and leads to an increased predisposition to CDI. The risk of recurrent CDI after initial treatment of the first infection is approximately 20–25% [Kelly and Lamont, 2008; Khanna et al. 2012g] and is further increased up to 60% with the use of additional systemic antibiotics and subsequent CDI recurrences [Hu et al. 2009]. The pathophysiology of recurrent CDI involves ongoing disruption of the normal fecal flora and an inadequate host immune response. Standard CDI treatment with antibiotics such as metronidazole and vancomycin further disrupts colonic microbial communities that normally keep expansion of C. difficile populations in check. Since C. difficile spores are resistant to antibiotic therapy for CDI, they can germinate to vegetative forms after treatment has been discontinued and lead to recurrent CDI. (12)

The authors of this study review the data for fecal microbiota transplant and summarize by stating:

Therefore, existing literature suggests that fecal transplant is safe and effective with over 500 cases of recurrent CDI with no serious adverse events reported to date. FMT appears to be an appropriate treatment option for multiple CDI recurrences and may be considered for refractory moderate to severe C. difficile diarrhea, failing standard therapy. The FDA had recently announced that an Investigational New Drug Application would be required for use of FMT for CDI, but this was later changed to the use of an informed consent process to ensure communication of potential risks.

In the area of obesity rodent studies have demonstrated that fecal transplants from thin to obese subjects results in significant weight loss. Measurable differences in the microbiome of obese vs thin humans have been identified.

The prevalence of obesity and related disorders such as metabolic syndrome has vastly increased throughout the world. Recent insights have generated an entirely new perspective suggesting that our microbiota might be involved in the development of these disorders. Studies have demonstrated that obesity and metabolic syndrome may be associated with profound microbiotal changes, and the induction of a metabolic syndrome phenotype through fecal transplants corroborates the important role of the microbiota in this disease. (13)

The issue of gut flora and obesity deserves a dedicated post. Multiple research articles and review articles have been published on the topic of fecal transplantation in relation to obesity, diabetes, metabolic syndrome, autoimmune disease and cancer. (14,15,16)

Diabetes, obesity, allergy, auto-immune disease, infections, psychiatric disorders and cancer represent examples of the potential interplay between the human microbiome, human health and disease. Multiple sources of information suggest a cause and effect relationship. The results of fecal transplantation in human and rodent studies, manipulation of the gut flora with pro-biotics and pre-biotics, data on the effects of vaginal vs cesarean delivery, and the benefits of breast feeding all proclaim the importance of our micro-flora.

Most traditional cultures have one or more forms of fermented foods. Examples include yogurt, kefir, sauerkraut, kim chee, beet kvass, kombucha. Almost any food can be fermented to produce health promoting probiotics and there is a growing movement for home-fermentation and/or consumption of purchased fermented foods. In addition to the pro-biotic nature of fermented foods and beverages, fermentation offers other potential health benefits. These include reduction of the anti-nutrients found  in various neolithic  foods (such as mineral binding phytic acid found in grains and legumes, digestive enzyme inhibitors found in soy and other legumes). Other potential health benefits include the production of Vitamin K2 found in many fermented foods.

This discussion barely scratches the surface of gut flora, health and disease. Future posts will address how our gut bacteria produce essential nutrients and affect mental health as well as physical health. Other important topics include how our activity, food, sleep and stress affect the our gut ecology. The system is dynamic with effects going in both directions.

Following the references below you will find links to NPR discussions of related topics. You can choose to read the articles and/or listen to the NPR interviews and reports.

Peace, happiness and longevity.

BOB

(1) Microbes in Gastrointestinal Health and Disease

(2) Probiotics as efficient immunopotentiators: Translational role in cancer prevention

(3) Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces.

(4) Has the microbiota played a critical role in the evolution of the adaptive immune system?

(5) It’s a Gut Feeling – how the gut microbiota affect… [J Physiol. 2014] – PubMed – NCBI

(6) Metabolic tinkering by the gut microbiome: Impl… [Gut Microbes. 2014] – PubMed – NCBI

(7) The gut-brain axis rewired: adding a functional vaga… [FASEB J. 2014] – PubMed – NCBI

(8) Cesarean versus vaginal delivery: long-term infant outcomes and the hygiene hypothesis.

(9) Probiotics for prevention of necrotizing enterocolitis in preterm infants.

(10) Preventing atopy and allergic disease.

(11) Gut microbiota and allergic disease: new findings.

(12) Clostridium Difficile Colitis ,

(13) Gut microbiome, obesity, and metabolic dysfunc… [J Clin Invest. 2011] – PubMed – NCBI

(14) Fecal microbiota transplantation: indications, methods, evidence, and future directions.

(15) Fecal microbiota transplantation: past, present and future.

(16) Therapeutic potential of fecal microbiota transplantation.

Here are the NPR and other links.

Interview: Martin Blaser, Author Of ‘Missing Microbes’ : NPR

FDA Backs Off On Regulation Of Fecal Transplants : Shots – Health News : NPR

Human Microbiome Project – Home | NIH Common Fund

Staying Healthy May Mean Learning To Love Our Microbiomes : Shots – Health News : NPR

Gut Bacteria Might Guide The Workings Of Our Minds : Shots – Health News : NPR

Worried That Your Baby’s Sick? There May Be An Upside : Shots – Health News : NPR