Human Microbiome

How to Cure Dysbiosis

1) DIET - Can maintain beneficial microbes but likely not be able to introduce absent species: fermented foods like cheese, yogurt, kimchi, kombuchi, salami, etc. - Any introduced species are transiently associated-they are gone from the gut after a day or two **The gut microbiome is highly dynamic. The proportion of resident microbial species can alter dramatically, quickly, and reproducibly with changes in diet. Although there may be no apparent change in diversity of species, the abundances of particular groups of microbes can be rapidly influenced by diet. In a recent study, human volunteers fed a high protein diet of bacon, eggs, brisket, spareribs, cheese, pork rinds, were compared with another group fed a high fiber diet composed of fruits, vegetables, grains, and beans. Noticeable differences in the gut bacteria were observed between the two groups within one day. The protein eaters had higher proportions of bacteria that can tolerate high levels of bile acids (secreted by the body to digest meat) while the plant eaters had fewer bile-tolerant bacteria, lower abundance of Prevotella species, and higher levels of expression of bacterial genes involved in carbohydrate digestion 2) PROBIOTICS - Introduction of selected bacterial species, OTC. **"Probiotics" are live microorganisms, which, when administered in adequate amounts, may confer a health benefit on the human host. Probiotics take advantage of the beneficial effects of the normal microbiota. Lactobacillus and Bifidobacteria, for example, are thought to promote health by: • Aiding in restoring intestinal microbes after antibiotic treatment • Reducing viral diarrhea in infants • Helping to prevent traveler's diarrhea • Reducing recurrent bladder infections in catheterized patients with spinal cord injuries 3) PREBIOTICS - Chemical or compound to stimulate the growth of commensal/ mutualistic bacteria, e.g. fiber 4) Fecal Microbiota Tranplants (FMT) - Remove diseased ecosystem and replace with new healthy one **Often, in the case of CDI, a healthy gut microbiota may never be reestablished, and continual bouts of disease can occur leading to death of the patient. Treatment with antibiotics has not been effective because the Clostridium pathogen can resist anti-microbial killing in its spore state. An extremely successful method, known as "fecal microbiota transplants" (FMT), can rapidly restore a normal healthy microbial community and is currently being tested and is in use in some locations. This procedure replaces the dysbiotic microbiome of CDI patients with a functioning gastrointestinal microbiome obtained from a healthy donor. FMT has been amazingly consistent in producing an overall 93% cure rate of C. difficile patients

Dysbiosis Diseases

1. Allergies = Early colonization with key species educates immature immune system, and exposure to diverse species increases tolerance. 2. Asthma = Correlated with reduced exposure to diverse microbes 3. Rheumatoid Arthritis = Enhanced levels of Prevotella copri and diminished levels of Bacteroides in new onset untreated individuals. Segmented Filamentous Bacteria (SFB) associated with autoimmune arthritis 4. Gastric cancer = Increased Helicobacter pylori associated with gastric adenocarcinoma and affected by microbiota 5. Autism = Decrease in Bacteroides fragilis. Increase in Clostridium subtypes 6. Obesity = More Lactobacillus, fewer Bacteriodetes, increased Firmicutes, Actinobacteria in some studies and contrary results in others. 7. C. difficile infection (CDI) = Drastic alterations of gut microbiota, reduced microbial diversity, loss of ability to make 2° bile acids inhibitors of germination of C. difficile spores 8. Irritable bowel syndrome (IBS) = Associated with significantly less diverse microbiota, decreased Bacteroidetes 9. Inflammatory bowel disease (IBD), Crohn's Disease (CD), Ulcerative colitis = Reduced microbial diversity, associated with large distinguishable changes in gut microbiota.CD->increased abundance of Enterobacteria, Pasteurella, Veillonella, Fusobacteria species and decreased abundance of Bacteroides and Clostridium species correlates with disease. 10. Type 1 Diabetes = Shifts in gut microbiota, low diversity, less Bfidobacteria, reduced Firmicutes to Bacteroidetes ratio 11. Type 2 Diabetes = Significantly reduction of Firmicutes associated with increased plasma glucose, less SCFA butyrate production 12. Cardiovascular Disease = Production of proatherosclerotic metabolite, trimethylamine, is dependent on intestinal microbiota (2013); Enzymes for TMA production present in Acinetobacter sp. and Klebsiella sp.

Microbiota

All of the microbes inhabiting a defined environment, such as the human body. The collection of microbes found on humans was formerly referred to as "microflora," a term now deemed incorrect as it implies that humans are colonized by tiny plants. The human microbiota does not include plants, but is composed of bacteria, fungi, archaea, protists, and viruses.

Antibiotic Therapy

Antibiotic usage can kill groups of commensal bacteria thus providing access for pathogens to take hold and multiply. Broad spectrum antibiotics have swift and dramatic effects on the composition and abundance of species found in the intestinal microbiota. It can take an extremely long time for an antibiotic-disrupted microbiome to return to its original state after the cessation of antibiotics. In some cases, the original microbiota populations are never fully restored to their prior levels after antibiotic treatment and some species can disappear and be permanently lost from the microbial population. This is readily apparent in a CDI infection. CDI is currently one the most common infections, affecting more than a million people yearly. The dramatic perturbations in microbiota proportions caused by a simple treatment of antibiotics (ex: Clindamycin) can result in severe unintended consequences, such as the onset of CDI, and so CDI is typically referred to as an "antibiotic-induced" disease because it manifests after the intestinal microbiota have been disrupted by antibiotics. The microbiomes of CDI patients are in profound dysbiosis. C. difficile is a spore-forming bacterium, any (non-growing) C. difficile spores present in the intestine will survive antibiotic treatment and later, in the absence of antibiotics, can germinate into vegetative (growing), toxin-producing cells. Subsequent treatment of CDI with antibiotics can further disrupt the colonic microbiota and can result in relentless relapses of the diarrhea, or "recurrent syndrome", marked by an indefinite cycle of infection. The levels of specific bile acids in feces from healthy individuals and those suffering with CDI indicate that a particularly pertinent microbial metabolic function is deficient in the intestines of CDI patients -the ability to convert primary bile acids into secondary bile acids. Importantly, primary bile acids can act as germinants inducing C. difficile spores to become toxin-producing vegetative cells, whereas secondary bile acids are spore germination and growth inhibitors. Primary bile acids are undetectable in feces of healthy individuals, because they are rapidly converted to secondary bile acids by beneficial intestinal bacteria. In contrast to healthy microbiota fecal samples high in secondary bile acids (germination inhibitors), the feces of CDI patients contain only primary bile acids (germinants).

Bacteria Lifestyles

Bacteria are ubiquitously found in the environment. Bacteria are found in water and soil, and in close association with all animals and plants. Their rapid growth generates enormous genetic diversity. Thus bacteria have adapted well to a wide variety of strikingly different habitats. Microbes can be found in a variety of lifestyles: Free-living - growing in soil or water or on the surfaces of plants or animals. Bacteria are often found in communities called "Biofilms," Mutualistic- describes the relationship between biological species where all parties benefit from the interaction. Our " gut microbes are likely engaged in a mutualistic relationship with the host, helping with digestion, synthesizing vitamins, and protecting against pathogens. Commensalistic- describes the scenario where one organism benefits and the other is unaffected. Parasitic- describes the interaction between organisms where one benefits at the expense of the other, and can be exemplified in the extreme case of pathogen harming a host. **Our colonizing microorganisms, the human microbiota, outnumber our own human cells. In essence, we are essentially "superorganisms" or "metaorganisms" containing trillions of human cells (of ~200 distinct types) and roughly an order of magnitude more microbial cells (comprising ~1000 - 36,000 species). Genetically, the vast majority of the genes we carry are microbial (>99% microbial and <1% human genes!). It is likely that there is an equivalent number or more microbial than human cells in the human body. The organisms comprising the human microbiota are not simply passive bystanders dwelling in and on our bodies. Together, along with human cells, the microbiota play an active role performing numerous metabolic reactions and functions. While the human genome encodes roughly 22,000 genes, pooled human microbiomes collectively sequenced so far, include greater than 9,800,000 distinct genes. The expression of these bacterial genes result in thousands of products: -proteins, sugars, enzymes, short chain fatty acids, metabolites, etc., conferring not only the ability to digest foods, but also the capability of "cross-talking" with other microbes as well as with human cells. These signaling molecules influence the development and physiology of the human host. The beneficial associations between certain key microbes and the intestinal epithelial and immune cells are the result of hundreds of thousands of years of coevolution

Microbiome

Has two definitions: Microbiome (genetic) - The collective genome of the microbes living in and on our bodies. Microbiome (ecological) - The community of microbes inhabiting our bodies.

Dysbiosis Causes

Ideal bacteria never introduced into or maintained in the gut (early events): 1) Aberrant initial and early colonizers 2) The "Hygiene Hypothesis" Beneficial bacteria reduced or lost entirely from the gut: 3) "Western lifestyle" -a sedentary lifestyle with an unbalanced diet, often high in fat and low in fiber. 4) Antibiotic Therapy

Functions of Symbiotic Gut Microbiota

Metabolic = Synthesis of vitamins (vitamin K), Harvest maximal energy through digestion (fermentaton of complex polysaccharides), and Control of gut epithelial cell differentiation and proliferation Immune and Structural = Immune system development and immunomodulation, enhancement of intestinal barrier integrity (tight junctions), prevention of intestinal barrier dysfunction, and induction of IgA antibodies Protective = Competition for niche (space, epithelial receptors), competition for nutrients, and production of anti-microbial factors and peptides

Transplantation of Human Microbiota into Germ-free Mice

Mice receiving the "O" microbiota from the obese twin became obese, even though they did not increase their food intake. Mice receiving the "L" microbiota remained lean. Analysis of the obese and lean microbiota revealed differences in the metabolic potential of the different bacterial communities within the microbiomes. The obese gut microbiota had increased enzymatic ability to break down amino acids and carbohydrates. The lean gut microbiota was capable of increased fermentation of short chain fatty acids and production of certain chemical compounds or metabolites affecting lipid metabolism. Animals colonized with these differently-derived microbiota showed marked changes in weight. These experiments showed that human gut microbiota can confer particular traits. Lean microbiota don't infiltrate O mice when cohoused in one bin; O mice still become fat and L mice still become lean.

Dysbiosis

Microbiota from healthy people has revealed striking differences in bacterial diversity in some cases, suggesting that a healthy or "symbiotic" gut microbiome is important for maintaining good health. A symbiotic microbiome plays an active role in human health by performing a number of beneficial metabolic tasks. A perturbation or disruption of the microbiome can result in a reduction or loss of beneficial microbial species and consequently a decrease in the metabolic activities essential for health, a state referred to as "dysbiosis". Dysbiosis is correlated with detrimental changes in health and can be observed strikingly in the gut microbiomes of people with intestinal diseases, such as inflammatory bowel disease (IBD) and C. difficile infections (CDI). Surprisingly, dysbiosis of the gut microbiome has been reported to impact physiological systems that go beyond the gastrointestinal tract, and can be associated with asthma, diabetes, rheumatoid arthritis, cardiovascular disease, neurological disorders, and more. These "extra-intestinal" diseases might result from a decrease in protective beneficial microbes and an increase in numbers of detrimental species producing harmful metabolites that can be absorbed through the intestinal wall into the circulatory system resulting in negative health consequences, far from the confines of the intestinal tract.

Aberrant Initial and Early Colonizers

Normal vs Caesarean delivery - The mode of delivery and choice of early feeding can impact initial gut colonization, that may have long term consequences. Lack of early colonization with our co-evolved optimal microbes may not provide the correct signals at critical developmental time points required for educating our immune system and has been correlated with the manifestation of early childhood allergies. Notably, gastrointestinal tracts of infants born by Cesarean delivery (Csection) are initially colonized by bacteria normally associated with the skin surface, and babies born by C-section have been reported to be prone to allergies and metabolic diseases. Breast milk vs. Synthetic Formula - Surprisingly, mother's milk is not sterile as previously thought. It contains "probiotics" or beneficial bacteria (Bfidobacterium infantis) and "prebiotics" or nutrients that select for the persistence and growth of beneficial bacteria (thus limiting the colonization of harmful or pathogenic bacteria). Bfidobacteria are able to digest the complex oligosaccharides (prebiotic) present in breast milk allowing them to flourish and dominate, thus preventing less desirable bacteria from establishing residence, and setting the stage for proper development of the immune system and promotion of gut barrier integrity. Interestingly, the composition of breast milk has been found to differ with respect to the gender of the infant, with mothers producing a much higher percentage of fat in milk for male babies. Formula-fed infants do not benefit from the innate tailoring differences in milk composition nor are they seeded with beneficial bacteria and prebiotics found in mother's milk and as a result, they have substantial differences in the microbes that colonize their intestinal tract. **As we age, our microbiome composition also changes. Unborn individuals are sterile until they pass through the mother's birth canal (or via C-section) and if they are breast-fed as babies (leads to more Actinobacteria and Proteobacteria with less Firmicutes). Normal diet with solid food leads to removal of Actinobacteria and onset of Bacteroidetes as a baby/toddler (malnutrition as a toddler leads to much larger amount of Proteobacteria). As an adult, your microbiota consists mainly of Firmicutes with some bacteroidetes (obese individuals have larger amount of Proteobacteria).

The "Hygiene Hypothesis"

Over 25 years ago, the "hygiene hypothesis," was proposed to explain the steady yearly increase in allergies (eczema and hay fever). It inferred that a declining family size, improvement in living standards, and increased personal hygiene, could be responsible for decreased cross-infection that is necessary for normal human immune system development. This hypothesis is supported by a marked increase in asthma, type I diabetes, IBD, and other diseases in developed countries compared with undeveloped countries. A large study demonstrated that children growing up on farms, exposed to a far greater diversity of soil and animal microbes, had less allergies and asthma compared with children raised in cities with diminished microbial diversity. Lack of early exposure to diverse species is strongly correlated with an over responsive immune system and autoimmune disease.

"Western lifestyle"

The Western lifestyle has long been implicated as a contributor to developing maladies such as atherosclerosis and cardiovascular disease. Coronary heart disease accounts for the highest proportion of deaths in the United States and is also a major cause of death worldwide. Globally, the number of deaths due to cardiovascular diseases have increased over 30% in past 2 decades. Recent focus on the contribution of the intestinal microbiota with respect to coronary illness has led to the elucidation of how the production of one proatherosclerotic metabolite is dependent on the human microbiome and illustrates how a product produced by species in the microbiome could adversely affect human health. Researchers have determined recently that dietary phosphatidylcholine (lecithin) found in eggs, and L-carnitine found in red meat are metabolized to trimethyline (TMA) by constituents of the intestinal microbiota. TMA is subsequently absorbed into the host bloodstream and is modified by enzymes in the liver to trimethylamine-N-oxide (TMAO), a proatherosclerotic metabolite. The researchers claim that there is a dose-dependent relationship between high levels of TMAO found in plasma and an increased likelihood of a major adverse cardiovascular event. The production of TMA from lecithin and L-carnitine was shown to be strictly dependent on gut microbiota. The researchers observe that individuals consuming a Western diet are more likely to harbor gut microbes that result in the production of TMAO that may lead to or exacerbate cardiovascular and metabolic diseases. This preliminary study spurned a number of far reaching speculative conclusions that red meat consumption can result in heart disease. While gut bacteria can indeed metabolize meat and eggs to a metabolite that is purported to be linked to heart disease, interestingly, there are many other foods, including cauliflower, peas, carrots, and seafood that generate much higher levels of TMAO.

Locations of Bacteria in Body

There is tremendous variation from one site to the next (ex: nasopharynx, inside of elbows, GI tract, mouth, etc.) and the numbers of species at some locations can exceed hundreds of thousands. Furthermore, places in the body previously thought to be sterile, such as the small intestine, stomach, and lungs, are now known to harbor microbial communities. The microbiota of each human is unique, influenced by each individual's genetic makeup, early microbial colonizers, diet, and other modulators, such as exposure to antibiotics. As a result, the microbiome varies in composition and abundance of species between each human being. 1. The gastrointestinal tract is where most of our microbiota are found. The lower intestine, the colon, contains the highest density of microbes of all other environments on earth, reaching 1012 bacteria/gram of feces. These microbes are largely anaerobic and are composed of 5-7 prevalent bacterial groups; the two dominant bacterial groups are Bacteroidetes and Firmicutes. There is great variability in the presence and proportions of these groups between people and there are many different "healthy" microbiota patterns capable of performing the essential beneficial metabolic tasks for the host. **Initial bacteria colonization - A human infant is thought to be sterile prior to birth, but becomes colonized soon after exposure to distinct bacterial species found in the mother's birth canal. These species, as well as bacteria present within human breast milk, are the earliest colonizers of the human GI tract, enabling the infant to digest milk and providing the groundwork for the establishment of the core intestinal microbiota. Over weeks, months, and years, a complex highly evolved gastrointestinal microbiome develops. There appear to be early critical time points when specific interactions between commensal microbiota constituents and the cells of the developing immune system must occur to ensure the proper education of both innate and adaptive immune cells. Lack of these key pivotal signalling interactions between the our commensal bacteria and the immature intestinal immune cells has been proposed to lead to long-lived sequellae of allergic reactions and conditions. It takes a long time to establish a stabilized human microbiome. By 2 -3 years, a matured gut microbiome produces metabolites, digests complex carbohydrates, maintains intestinal epithelial barrier function, and continually influences host physiology, thus setting the stage for life-long good health. Notably, once this core microbiome is established, it is thought to be much less sensitive to major fluctuations, such as the loss or introduction of new species without a dramatic perturbation

Human Microbe Mutualism

What Microbes Gain: 1. Nutrients 2. Shelter 3. Dispersal What Humans Gain: 1. Protection from pathogens 2. Production of essential vitamins (e.g., vitamin K) 3. Maximum value from digestion 4. Development and regulation of the immune system 5. Metabolic regulation 6. Barrier integrity and maintenance of the gut lumenal epithelium