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What Is The Human Microbiome

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As Ed Yong says in his book I Contain Multitudes, The immune system is not innately hardwired to tell the difference between a harmless symbiont and a threatening pathogen its the microbe that makes that distinction clear.

The human microbiome even affects how we smell. Different microbe species might convert sweat into the smell of onions, or testosterone into the stink of urine, which act as strong signals for our friends and foes.

These smells are highly personal: studies have found people can be identified just from their sweaty T-shirts.

Scientists also think that our microbiome may be a significant contributor to why we get jetlag.

The change in sleep patterns puts the rhythm of our gut bacteria out of sync with our own behaviour, so different species are active at the wrong times.

Read more about the body and microbiome:

Types Of Bacteria And Other Microbes

Each microbiome has a unique makeup and the combination of microbes in the body can hugely impact someones health. Certain bacteria in the body can make the difference between getting sick or not. Though the exact relationship between certain bacteria and illnesses not yet fully understood, there remains an appreciation for their roles in some human illness.

How To Help Your Microbiome

Simple daily habits make a difference. What you eat can change the microbes that live in your body. High-fiber foods feed the helpful bacteria in your colon. They also discourage the growth of some harmful ones. Probiotic foods, such as yogurt and pickled vegetables, also deliver helpful bacteria to your gut. Getting enough sleep, easing stress, and exercising may also improve your microbiome.

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About The Human Microbiome

The Human Microbiome is the collection of all the microorganisms living in association with the human body. These communities include eukaryotes, archaea, bacteria and viruses. Bacteria in an average human body number ten times more than human cells, for a total of about 1000 more genes than are present in the human genome. Because of their small size, however, microorganisms make up only about 1 to 3 percent of our body mass . These microbes are generally not harmful to us, in fact they are essential for maintaining health. For example, they produce certain vitamins that we do not have the genes to make, break down our food to extract nutrients we need to survive, teach our immune systems how to recognize dangerous invaders and even produce helpful anti-inflammatory compounds that fight off other disease-causing microbes. An ever-growing number of studies have demonstrated that changes in the composition of our microbiomes correlate with numerous disease states, raising the possibility that manipulation of these communities could be used to treat disease.

The Role Of Probiotics

Human microbiota

If microbiota are so vital to our health, how can we ensure that we have enough or the right types? You may be familiar with probiotics or perhaps already using them. These are either foods that naturally contain microbiota, or supplement pills that contain live active bacteriaadvertised to promote digestive health. Probiotic supplement sales exceeded $35 billion in 2015, with a projected increase to $65 billion by 2024. Whether you believe the health claims or think they are yet another snake oil scam, they make up a multi-billion dollar industry that is evolving in tandem with quickly emerging research.

Because probiotics fall under the category of supplements and not food, they are not regulated by the Food and Drug Administration in the U.S. This means that unless the supplement company voluntarily discloses information on quality, such as carrying the USP seal that provides standards for quality and purity, a probiotic pill may not contain the amounts listed on the label or even guarantee that the bacteria are alive and active at the time of use.

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Microbiome Intervention: Fmt And Bacterial Therapies

With an increase focus of the microbiomes role in health comes an increase focus on treating the microbiome. One of the most intriguing and promising treatments for dysbiosis is a practice called Fecal Microbiota Transplantation . The treatment uses healthy stool to restore a sick microbiome to health.

What Is The Microbiome

Picture a bustling city on a weekday morning, the sidewalks flooded with people rushing to get to work or to appointments. Now imagine this at a microscopic level and you have an idea of what the microbiome looks like inside our bodies, consisting of trillions of microorganisms of thousands of different species. These include not only bacteria but fungi, parasites, and viruses. In a healthy person, these bugs coexist peacefully, with the largest numbers found in the small and large intestines but also throughout the body. The microbiome is even labeled a supporting organ because it plays so many key roles in promoting the smooth daily operations of the human body.

Each person has an entirely unique network of microbiota that is originally determined by ones DNA. A person is first exposed to microorganisms as an infant, during delivery in the birth canal and through the mothers breast milk. Exactly which microorganisms the infant is exposed to depends solely on the species found in the mother. Later on, environmental exposures and diet can change ones microbiome to be either beneficial to health or place one at greater risk for disease.

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Can We Change Our Microbiome

Yes, we can change our microbiome to a degree. While some microbes are common to all people, some other microbes are found only in some people, or the proportion of microbial species can vary among people. We now know that certain microbes are linked to chronic inflammation and diseases, while other microbes are linked to health and the absence of inflammation.

A persons diet has a key role in what microbes live in the gut. What one eats feeds some types of microbes and not others, and this determines what lives in the gut microbial community. A goal should be to lower chronic inflammation by feeding and nurturing beneficial microbes. With a change in diet, microbial changes can occur rapidly, within a few weeks. But to maintain the microbial changes one must continue with the new dietary pattern, so as to feed and nourish the beneficial bacteria.

High fiber diets lower inflammation in the gut and body, while low fiber diets increase inflammation. A Western style diet with lots of highly processed foods, lots of meat, high-fat foods, little dietary fiber, refined grains, sugary drinks and desserts feeds microbes that are linked to chronic inflammation and disease. On the other hand, a diet rich in real whole plant foods and fiber, such as fruits, vegetables, whole grains, nuts, legumes, and seeds is linked to beneficial microbes and health.

Several large projects have been studying the human microbiome, such as the Human Microbiome Project and the American Gut Project .

The Human Microbiome Project

What is the Human Microbiome?

The Human Microbiome Project was supported by the National Institutes of Health Common Fund from 2007 through 2016, with the mission of generating resources that would enable the comprehensive characterization of the human microbiome and analysis of its role in human health and disease. This area of the website focuses on the first of a two-phase effort, frequently referred to as HMP1, which ran from 2008 through 2013. From the Common Fund website:

The Human Microbiome Project has transitioned from Common Fund support. Common Fund programs are strategic investments that achieve a set of high-impact goals within a 5-10 year timeframe. At the conclusion of each program, deliverables transition to other sources of support or use by the broader scientific community. The HMP was supported by the Common Fund from 2007 to 2016. Non-HMP investment in microbiome research at the NIH has increased over forty-fold since the inception of the HMP and spans over 20 of the NIH Institutes and Centers. Please note that since the HMP is no longer supported by the Common Fund, the program website is being maintained as an archive and will not be updated on a regular basis.

HMP1 characterized the microbial communities found at several different sites on the human body: nasal passages, oral cavity, skin, gastrointestinal tract, and urogenital tract, and examined the role of these microbes in human health and disease. The 5 stated aims of the project were

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Health Benefits Of The Microbiome

On the basis of the currently available literature, the gut microbiome is known to contribute to a number of important functions in the host, from protective, immunomodulatory, metabolic to trophic roles. These are promoted via a number of mechanisms. For example, members of the gut microbiome can produce anti-inflammatory factors, pain relieving compounds, antioxidants, and vitamins to protect and nurture the body. Additionally, they may prevent attachment and action of harmful bacteria that can produce toxins causing chronic disease. This close and specific contact with human cells, exchanging nutrients and metabolic wastes, makes symbiotic bacteria essentially a human organ.

Onset Of Type 2 Diabetes

Researchers from Stanford University and the Jackson Laboratory of Genomic Medicine worked together to perform a longitudinal analysis on the biological processes that occur in the microbiome of patients at risk for Type 2 Diabetes. T2D affects nearly 20 million Americans with at least 79 million pre-diabetic patients, and is partially characterized by marked shifts in the microbiome compared to healthy individuals. The project aimed to identify molecules and signaling pathways that play a role in the etiology of the disease.

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Where Does My Intestinal Microbiome Come From

Your intestinal microbiome is primarily determined largely by your genetics . How is that possible you might ask? Well, your immune system is inherited from your parents . It is your immune system that determines which bugs will be allowed to colonize in those early years. Of course, your intestinal microbiome is also shaped by environmental factors natural delivery versus ceasaeran section, breastmilk versus formula fed , antibiotic exposure and many other exposures shape the intestinal microbiome in those early years. Not surpisingly, the development of a robust and diverse intestinal microbiome has been associated a long list of health related outcomes in infancy, childhood and adults .; The North American Society of Pediatric Gastroenterology, Hepatology and Nutrition has previously outlined the importance of establishment of health microbiome early in life.

What Is The Gut Microbiota

The Human Microbiome

The gut microbiota used to be called the microflora of the gut.

Around this time, in 1996, Dr. Rodney Berg, of Louisiana State Universitys Microbiology and Immunology department, wrote about the gut microbiota, summing up its profound importance.

The indigenous gastrointestinal tract microflora has profound effects on the anatomical, physiological, and immunological development of the host, Dr. Berg wrote, in a paper published in Trends in Microbiology.

The paper adds:

The indigenous microflora stimulates the host immune system to respond more quickly to pathogen challenge and, through bacterial antagonism, inhibits colonization of the GI tract by overt exogenous pathogens.

This symbiotic relationship benefits humans, and the presence of this normal flora includes microorganisms that are so present in the environment that they can be found in practically all animals from the same habitat.

However, these native microbes also include harmful bacteria that can overcome the bodys defenses that separate them from vital systems and organs. Examples include

In summary, there are beneficial bacteria in the gut, and there are harmful bacteria that can cross into wider systems and can cause local infections of the GI tract. These infections include food poisoning and other GI diseases that result in diarrhea and vomiting.

The gut microbiota contains over 3 million genes, making it 150 times more genetically varied than the human body.

  • disease

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Does The Microbiome Really Affect Behaviour

Its hard to tell if the microbiome is responsible for changes in diseases and behaviour, or if diseases and behaviour are responsible for the microbiome.

Experts are piecing together how gut microbes influence the brain through the hormones and molecules they produce but no one knows how important these are.

Drug companies, keen for new ways to treat neurological disorders, are investing money into research.

Future Areas Of Research

The microbiome is a living dynamic environment where the relative abundance of species may fluctuate daily, weekly, and monthly depending on diet, medication, exercise, and a host of other environmental exposures. However, scientists are still in the early stages of understanding the microbiomes broad role in health and the extent of problems that can occur from an interruption in the normal interactions between the microbiome and its host.

Some current research topics:

  • How the microbiome and their metabolites influence human health and disease.
  • What factors influence the framework and balance of ones microbiome.
  • The development of probiotics as a functional food and addressing regulatory issues.

Specific areas of interest:

  • Factors that affect the microbiome of pregnant women, infants, and the pediatric population.
  • Manipulating microbes to resist disease and respond better to treatments.
  • Differences in the microbiome between healthy individuals and those with chronic disease such as diabetes, gastrointestinal diseases, obesity, cancers, and cardiovascular disease.
  • Developing diagnostic biomarkers from the microbiome to identify diseases before they develop.
  • Alteration of the microbiome through transplantation of microbes between individuals .

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What Is Niehs Doing

NIEHS studies the microbiome to gain a better understanding of its complex relationships with the environment, and how these interactions may contribute to human health and disease. This knowledge could help us revolutionize the way new chemicals are tested for toxicity, and design prevention and treatment strategies for diseases that have environmental causes.

NIEHS-supported research related to the microbiome includes the environmental factors described below.

Chronic stress NIEHS researchers found chronic stress disturbs the gut microbiome in mice, triggering an immune response and promoting the development of colitis, a chronic digestive disease characterized by inflammation of the inner lining of the colon.4

Artificial sweeteners A NIEHSfunded study found sucralose, a widelyused artificial sweetener, changes the gut microbiome in mice and may increase the risk of developing chronic inflammation.5 In a separate study, they found that acesulfamepotassium, another artificial sweetener, induced weight gain in male, but not female, mice.6

Diet NIEHS researchers showed a highfat diet shaped the gut microbiome of mice in a way that predisposed them to gain weight and develop obesity.7

Caesarean delivery NIEHSfunded research indicates the way a newborn enters the world, by C-section or natural birth, and what is eaten, formula or breast milk, during the first six weeks of life may affect the type of microbes in the gut microbiome.8

The Human Microbiome: 20 Reasons Why Microbes Are Important

The human microbiome and what we do to it

March 24, 2017 by Eirik

The trillions of microorganisms that live in and on you affect pretty much everything that goes on inside your body. They affect your eyesight, how well your liver functions, your cognitive abilities, and the workings of your digestive system, among other things. If youre a regular reader of, this is something you undoubtedly know. However, if youre new to this site and/or have never paid much attention to the role microbes play in human health, then youre probably unaware of the fact that the trillions of critters that call your body home greatly influence your health and well-being.

Over the years Ive written dozens of articles on the human microbiome, many of which include in-depth discussions about how bacteria affect human health. I realise that not everybody is interested in reading these long and comprehensive articles; they just want some quick and simple information and advice that help them understand why microbes are important and what they can do to take better care of their microbiome. For that reason, I sometimes create infographics that explain things I believe everyone should know about human-associated microorganisms.

If you like the infographic, then please share it with your friends and family!

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Our Evolving Understanding Of The Healthy Microbiome

Early studies sought to identify the normal set of microbes that colonize healthy people, primarily in the gut, by culture and characterization of physiological properties. Such studies best highlight organisms that grow well in the lab environment, such as Escherichia coli. This bias led to the perception that E. coli is an abundant and prevalent member of the human gut microbiome . The introduction of strictly anaerobic techniques in the 1970s allowed the recovery of more than 300 bacterial species from the gut alone ; furthermore, the counting of viable cells within standardized serial dilutions in selective media permitted quantification of these species. A summary of four large studies from this era looking at stool samples from 141 Americans on different diets found that bacteria of the genus Bacteroides and anaerobic cocci were both prevalent and abundant, whereas the genus Clostridium was ubiquitous in lower abundance, though no single species was observed in all subjects. Other prevalent but lower-abundance bacteria included members of the genera Bifidobacterium, Eubacterium, Lactobacillus, and Streptococcus, as well as facultative anaerobes such as Escherichia.

What Is A Healthy Microbiome

A healthy microbiome is one that is balanced in equilibrium or homeostasis, and is a sign of health. Researchers have studied the gut and its microbiome more than any other site of the body, thus much of the current knowledge of the human microbiome is really about the gut microbiome. The gut is incredibly important for healthy functioning of the body. Chronic inflammation and some diseases are now being linked to the microbes in the gut.

Researchers still do not know exactly what microbes constitute a healthy gut microbiome, but some patterns are emerging.;

Diversity of microbes, and the mix of microbes is important. The more diverse the gut microbiome , the healthier it is, and the more it can adapt to disturbances. Also, the actual mix of types of microbes involved in a healthy gut microbiome is important. This is also true for other microbiomes throughout the body. Healthy communities don’t have just one important species of bacteria or other microbes, but a mix of microbes, and some mixes work better than others for preventing infections and for health.

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