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The Microbiome
Bacterial ecosystems in our bodies

A great diversity of microorganisms populate the human body. Humans have co-evolved with bacteria that live in our skin, nose, mouth, gut and other parts of the body. Each of these biological structures has a unique mixture of microbes that has adapted to reproduce and live in its specific environment. Did you ever look at the back of your tongue? The white coating in the back of your tongue is teeming with bacteria that thrive on the food that you eat and serve as guardians against pathogenic organisms that might make you sick.

Tongue

Origin of the microbiome
A fetus inside the uterus is virtually in a sterile environment without microorganisms. The act of being born by passage through the birth canal coats the body of a newborn with vaginal fluids containing a variety of bacteria. This initial microbial inoculation stimulates the immune system of the newborn to start building antibodies to combat disease. When the infant starts feeding on milk, a new population of bacteria, including Lactobacillus acidophilus, start to colonize the intestines. There are many species of Lactobacillus. These bacteria normally live in our digestive, urinary, and genital systems without causing disease. Lactobacillus is also in some fermented foods like yogurt. Lactobacillus is used therapeutically for treating and preventing diarrhea, including infectious types such as rotaviral diarrhea in children. It is also used to prevent and treat diarrhea associated with using antibiotics. One study found that 3-month-old babies with lower levels of four specific gut bacteria – Faecalibacterium, Lachnospira, Veillonella and Rothia (FLVR) had an increased risk for asthma later in life.[10]

Benefits of having bacterial partners
Researchers have estimated that for every cell of the human body there are 10 bacterial cells. An adult human may host approximately one kilogram (two pounds) of bacteria. These bacteria are constantly feeding on dead cells and secretions from our tissues and producing waste-product chemicals that prevent the growth of disease-causing bacteria. Some bacteria that reside in the intestines produce Vitamin K, which is an essential cofactor necessary for blood clotting and preventing hemorrhages. Bacterially synthesized menaquinones (Vitamin K variants) in the ileum are chemical substances that play a significant role in contributing to vitamin K requirements in humans.[1]

Some microbes in the human intestines help to break down fiber and complex carbohydrates which would otherwise be completely indigestible. These resistant starches and fiber-like carbohydrates are converted into short chain fatty acids that can be absorbed by the intestines. The intestinal bacteria help us to extract more energy from the food that we eat. Scientists now realize that different compositions of gut microbiota are present in obese persons with chronic low-grade inflammation and impaired lipid and glucose metabolism. It is thought that dietary interventions influencing microbial composition could be an option to treat metabolic syndrome.[2]

Some common microbes
Bacteria and fungi have specific habitats. The fatty acids in oily skin provide nutrition for Propionibacteria which live in the hair follicles. These bacteria may cause pimples, but they are usually kept in check by white blood cells. Corynebacteria live in the armpits and feed on the carbohydrates and aminoacids in sweat. The mouth hosts the greatest variety of bacteria, including Atopobium parvulum that ferments saliva and residual bits of food to produce bad-breath sulfur compounds. Fungi like Candida and Rhodotorula live under the fingernails. The colon, like the mouth, hosts a wide variety of microorganisms, including Escherichia coli. Some strains of E. coli can cause severe intestinal problems, but the non-pathogenic strains of E. coli produce folic acid and other B vitamins. Brevibacteria feed on dead skin cells between the toes. Shoes that have poor ventilation can promote the growth of the fungus Tinea pedis which causes a scaly infection known as Athlete's foot.

Bacterial Infections and diseases
Among the many beneficial bacteria that inhabit our bodies, there are also many microbes that can cause illnesses. There is a delicate balance between the good and bad bacteria. When this balance is disrupted perhaps through a viral infection that kills good bacteria, or by the administration of broad-spectrum antibiotics, the bad bacteria can proliferate and cause diseases.

The microbiome includes not only bacteria, but also fungi and a group of anaerobic organisms called archaea. Single cell fungi, such as Candida albicans, are called yeasts, and they are responsible for genital infections in humans when the numbers of Lactobacilli decrease. Infections can also be caused by good bacteria in the wrong places. Infections can result when the skin is broken and the bacteria get in the wound. Infective organisms that get past the skin and into the bloodstream can cause serious illness and death.

Microbial Diversity Analysis
The evaluation of microbial diversity on the human body or on a wound can be used to determine the best treatment for chronic infections. Laboratories usually analyze the genetic sequence of the 16S ribosomal RNA to classify the variety of organisms contained in the samples. The 16S ribosomal RNA (rRNA) is useful as a biomarker because it is not subject to rapid evolution and it enables identification of single-celled microbes that do not have a nucleus (prokaryotic organisms). Once the rRNA has been analyzed, it is compared to validated microbial sequencing databases to create a microbial diversity chart. The study of genetic material recovered directly from environmental samples is called metagenomics or environmental genomics; it is emerging as a supportive technology for holistic health care.

Killing bacteria
The germ theory of disease was demonstrated at the beginning of the 20th century. Robert Koch's research on tuberculosis demonstrated that bacteria were capable of causing disease. In 1928, Alexander Fleming discovered penicillin, a drug with powerful antibacterial properties. Both of these discoveries contributed to advances in sanitation and treatment of infectious diseases that extended significantly the average lifespan of people. The implementation of proper waste disposal practices, emphasis on cleaning surfaces for food preparation, instruction of proper hand washing with soap and the use of antibiotics reduced the incidence of infectious diseases substantially, so that by the end of the 20th century the major causes of death were degenerative conditions such as cardiovascular disease and cancer caused by exposure to radiation, tobacco smoke or other carcinogenic substances.

Antibiotic-resistant bacteria
In the last half of the 20th century doctors were making extensive use of antibiotics for anything that seemed to be an infection, but the antibiotics were completely ineffective for treating diseases caused by viruses like the common cold. It was soon discovered that certain bacterial infections that had previously responded to penicillin could not be cured any more, and new antibiotics had to be used. What had happened was that new strains of bacteria had developed resistance to the antibiotics. This happened through the simple process of evolution. The few organisms that were not killed by the antibiotic survived and proliferated to create more resistant strains. At the beginning of the 21st century medical practitioners were concerned that the indiscriminate use of antibiotics had created superbugs that could not be killed with antibiotics, such as Methicillin-resistant Staphylococcus aureus (MRSA). Diseases caused by these bacteria can result in difficult-to-treat infections that may even be fatal.

The use of broad-spectrum antibiotics has also been recognized as the trigger for intestinal infections by hypervirulent strains of Clostridium dificile, an organism that is usually kept in check by the normal bacteria in the gut. An antibiotic may help to clear an infection in the ear or in another part of the body, but as a consequence, most of the normal bacteria in the digestive system are also killed. Once the good bacteria are gone, the bad bacteria proliferate and a patient may suffer from cramps, diarrhea and other digestive maladies. Approximately 110,000 deaths per year are the result of fulminant Clostridium difficile infections.[3] A recent trend in the treatment of these infections is to try to restore the colonic microflora by introducing healthy bacterial flora through infusion of stool from a healthy donor. This procedure is known as fecal bacteriotherapy or fecal transplantation and it has been highly effective in treating recurrent C. difficile in adults.

Tissue samples of patients with Crohn's disease and inflammatory bowel disease have shown a relative depletion of the common bacterium Faecalibacterium prausnitzii. Subsequent experiments have shown that F. prausnitzii has strong anti-inflammatory response, and now this bacterium is recognized as one of the "good" microbes of the human microbiome.[6]

Gut bacteria can influence the brain
One of the most surprising results of the study of the microbiome has been that the intestinal microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Researchers have found that some individuals with these disorders, including Autism Spectrum Disorder (ASD), display a variety of gastrointestinal abnormalities and that oral treatment with the human commensal Bacteroides fragilis corrects gut permeability, alters microbial composition, and ameliorates defects in communicative, stereotypic, anxiety-like and sensorimotor behaviors.[4] Commonly used oral antibiotics alter the normal gut microbiota which play an important role in metabolizing plant polysaccharides, promoting gastrointestinal motility, maintaining water balance, producing some vitamins, and competing against pathogenic bacteria. Loss of normal gut flora can result in the overgrowth of pathogenic flora, which can in turn cause constipation and other problems. However, in one small study of children with autism, treatment with the minimally absorbed glycopeptide antibiotic vancomycin resulted in short-term improvement in ASD symptoms, supporting a direct role for the antibiotic-sensitive gut bacteria in ASD. Researchers are now focusing on the possibility that gut-brain interactions could also be a direct result of chemical substances produced by microbial metabolism.[5]

Artificial sweeteners can make you fat
For many years, the diet industry has been promoting the use of artificial sweeteners such as sucralose, aspartame and saccharin as a way reduce calories to lose weight and prevent diabetes, but it turns out that obesity may not only be the result of extra calories. Epidemiological studies have found that consumption of diet soda is associated with the development of metabolic syndrome, which is a combination of conditions that include abdominal obesity, high blood pressure and elevated fasting plasma glucose.[7]  Additional research has found that artificial sweeteners induce glucose intolerance by altering the composition and function of the bacteria in the intestines.[8]  The gut is populated by two major phyla of microorganisms called Bacteroidetes and Firmicutes which maintain a certain balance based on the diet. When the carbohydrates in the diet are reduced by artificial sweeteners, the population of Bacteroidetes is reduced and the Firmicutes increase. Firmicutes produce enzymes that are more efficient at extracting energy from food, and this promotes the storage of fat.

Reduce risk of cancer
Nancy Turner, professor in the nutrition and food science department of Texas A&M University, was able to show that dried plums promote retention of beneficial bacteria throughout the colon, and by doing so they may reduce the risk of colon cancer, which is one of the leading causes of death in the U.S.[9] The microbiota affect the health of the host organism through physical interactions and, indirectly, through their metabolism. Previous research has shown that disruptions to the microbiota may initiate intestinal inflammation that can promote development of colon cancer. Adding dried plums to the diet increased Bacteroidetes and reduced Firmicutes in the distal colon without affecting the proportions found in the proximal colon. An experiment with rats showed that dried plums significantly reduced the number of aberrant crypts in the colon, which are the earliest observable precancerous lesions. This suggests that regularly eating dried plums may be a viable dietary strategy to help reduce the risk of colon cancer. Other studies have shown that some types of intestinal bacteria may boost the body's ability to fight malignancy by slowing the growth of tumors or by enhancing the effectiveness of cancer immunotherapy drugs.[11] Learn more about cancer prevention.

How to maintain a healthy microbiome
Foods with soluble fiber, such as oatmeal and plums, are good substrates for the growth of beneficial bacteria in the colon. Fermented products with active cultures such as yogurt and kefir have some of the probiotic bacteria necessary to maintain a healthy digestive system, so eat them regularly. When bathing or showering, use plain soaps and avoid soaps with antibacterial agents that could promote the development of resistant bacteria. Keep your teeth clean to avoid cavities and gum diseases, but don't obsess about killing millions of germs like advertised in mouth wash commercials because many more millions of bacteria will repopulate your mouth in less than 30 minutes. Learn to live with your microbiome.

Learn about Hygiene
References
  1. Conly JM, Stein K., The production of menaquinones (vitamin K2) by intestinal bacteria and their role in maintaining coagulation homeostasis, Prog Food Nutr Sci. 1992 Oct-Dec;16(4):307-43. PMID: 1492156
  2. Remely M, et al., Effects of short chain fatty acid producing bacteria on epigenetic regulation of FFAR3 in type 2 diabetes and obesity, Gene, 2014 Mar 1;537(1):85-92. doi: 10.1016/j.gene.2013.11.081. Epub 2013 Dec 8. PMID: 24325907
  3. Fecal bacteriotherapy
  4. Hsiao EY, et al., Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders, Cell, 2013 Dec 19;155(7):1451-63. doi: 10.1016/j.cell.2013.11.024. Epub 2013 Dec 5.
  5. Krajmalnik-Brown, Rosa et al. Gut bacteria in children with autism spectrum disorders: challenges and promise of studying how a complex community influences a complex disease. Microbial Ecology in Health and Disease, [S.l.], v. 26, mar. 2015. ISSN 1651-2235. DOI:http://dx.doi.org/10.3402/mehd.v26.26914.
  6. Moises Velasquez-Manoff, Gut Microbiome - The Peacekeepers, Science, March 2015, p.54.
  7. P. L. Lutsey, L. M. Steffen and J. Stevens, "Dietary Intake and the Development of the Metabolic Syndrome. The Atherosclerosis Risk in Communities Study", Circulation, Jan. 22, 2008, PMID 18212291
  8. Jotham Suez, Tal Korem, David Zeevi, Gili Zilberman-Schapira, Christoph A. Thaiss, Ori Maza, David Israeli, Niv Zmora, Shlomit Gilad, Adina Weinberger, Yael Kuperman, Alon Harmelin, Ilana Kolodkin-Gal, Hagit Shapiro, Zamir Halpern, Eran Segal, Eran Elinav. Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature, 2014; DOI: 10.1038/nature13793
  9. Paul Schattenberg, Texas A&M AgriLife, Research shows dried plums can reduce risk of colon cancer
  10. Marie-Claire Arrieta, et al., Early infancy microbial and metabolic alterations affect risk of childhood asthma, Science Translational Medicine, 30 SEP 2015 : 307RA152
  11. Maria-Luisa Alegre and Thomas F. Gajewski, Germ Warefare, Scientific American, April 2016, p.50.


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