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The Gut Microbiome

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Fun (and Mostly Fun) Introductory Microbiome Videos

The Virome (Viruses/Phages) The Mycobiome (Fungi/Yeasts) Parasites. Children, Babies, Pregnancy and Birth. Aging and the Microbiome. Scientific Papers. The Gut Microbiota News Watch 2016 Top 10 - Gut Microbiota for Health. Excitement over the microbiome needs to be kept in check. — The American Microbiome Institute. Harnessing the amazing work of the 40 trillion chemists in your gut microbiome. Deep in your gut, 40 trillion chemists are hard at work helping you digest your lunch, making essential vitamins and nutrients you can’t produce on your own, protecting you from disease, and more.

Harnessing the amazing work of the 40 trillion chemists in your gut microbiome

These talented creatures are bacteria, fungi, and other single-celled organisms. These organisms live together in complex communities called microbiomes. They reside all over your body — and far beyond it. Microbiomes have been found anywhere scientists choose to look for them, from the hottest deserts to lakes hidden deep beneath Antarctic ice. Me, myself, us. WHAT’S a man?

Me, myself, us

Or, indeed, a woman? Biologically, the answer might seem obvious. A human being is an individual who has grown from a fertilised egg which contained genes from both father and mother. A growing band of biologists, however, think this definition incomplete. They see people not just as individuals, but also as ecosystems. The Microbiome. Everyone’s got a personal collection of microbiota.

The Microbiome

You could think of yours as your unique internal pet—at up to 3 percent of your body mass, it’s as hefty as a teacup Yorkie or a large guinea pig—requiring care and feeding. In turn, your microbiota provide essential services: extracting energy from food, absorbing and generating vitamins and amino acids and forming barriers against infective invaders. If researchers are correct, your microbiota might also fight diabetes, obesity and cancer; stimulate your immune system; break down toxins; and boost your overall health.

Change Your Microbiome, Change Yourself. If you think you’re only human, you’d better think again.

Change Your Microbiome, Change Yourself

Single-celled bacteria living in and on our bodies outnumber human cells by at least 3 to 1 — and perhaps as much as 10 to 1. The latest estimates from the American Academy of Microbiology put our bodies at 37 trillion human cells and our microbiomes — as those bugs are collectively called — at 100 trillion.

Yes, that’s right, our skin and guts, mouths and noses, along with every other body surface, are home to 100,000,000,000,000 microscopic bugs. The typical human microbiome is said to represent about 1,000 different species, with wide variation from one person to the next in exactly which species. If it’s still hard to fathom just how big a single microbiome is, consider this: That same report says those microbes, each vanishingly small and seemingly weightless on its own, add up to something like 2.5 pounds.

If these statistics have you reaching for the hand sanitizer, slow down. A Lifestyle Prescription for Optimal Health: Microbiota – the Indispensable “Organ” – 4. A Lifestyle Prescription for Optimal Health: Microbiota – the Indispensable “Organ” – 4 We are not alone, neither in our social settings nor as individuals.

A Lifestyle Prescription for Optimal Health: Microbiota – the Indispensable “Organ” – 4

Gut reaction: the surprising power of microbes. ‘So, what’s in the thermos?”

Gut reaction: the surprising power of microbes

I asked. I was standing in a lift at Washington University in St Louis, with Professor Jeff Gordon and two of his students, one of whom was holding a metal canister. “Just some faecal pellets in tubes,” she said. “They’re microbes from healthy children, and also from some who are malnourished. There is no such thing as a ‘good’ or a ‘bad’ microbe. In the 1870s, German physician Robert Koch was trying to curtail an epidemic of anthrax that was sweeping local farm animals.

There is no such thing as a ‘good’ or a ‘bad’ microbe

Other scientists had seen a bacterium, Bacillus anthracis, in the victims’ tis­sues. Koch injected this microbe into a mouse – which died. Scientists bust myth that our bodies have more bacteria than human cells. Red blood cells dominate our total cell count by number (though not by mass).

Scientists bust myth that our bodies have more bacteria than human cells

It's often said that the bacteria and other microbes in our body outnumber our own cells by about ten to one. That's a myth that should be forgotten, say researchers in Israel and Canada. The ratio between resident microbes and human cells is more likely to be one-to-one, they calculate. A 'reference man' (one who is 70 kilograms, 20–30 years old and 1.7 metres tall) contains on average about 30 trillion human cells and 39 trillion bacteria, say Ron Milo and Ron Sender at the Weizmann Institute of Science in Rehovot, Israel, and Shai Fuchs at the Hospital for Sick Children in Toronto, Canada. Those numbers are approximate — another person might have half as many or twice as many bacteria, for example — but far from the 10:1 ratio commonly assumed.

Source: Ref. 1 A particular overestimate in Luckey’s work relates to the proportion of bacteria in our guts, Milo and colleagues say. Counting Cells. A person likely carries the same number of human and microbial cells, according to a new estimate.

Counting Cells

Human blood prepared on a slideFLICKR, SMALLER.PATHOLOGICAL.CAMicrobiologist Thomas Luckey, who in 1972 estimated that the number of microbial cells in and on the human body outnumbers those carrying the human genome by 10 to 1, was wrong: people are not more microbe than human, scientists now suggest. According to new research from scientists in Israel and Canada, a 5”7’, 20-year-old man weighing 70 kilograms (154 pounds) likely harbors some 30 trillion human cells (the vast majority of which are red blood cells) and 39 trillion bacteria. “The numbers are similar enough that each defecation event may flip the ratio to favour human cells over bacteria,” the researchers wrote in a paper posted to the preprint server bioRxiv last week (January 6). But the exact number may not matter, said Peer Bork, a bioinformatician at the European Molecular Biology Laboratory in Heidelberg, Germany. Microbiome: Your Body Houses 10x More Bacteria Than Cells.

What happens in the gut doesn’t stay in the gut – it sometimes affects the brain.

Microbiome: Your Body Houses 10x More Bacteria Than Cells

Animal studies have started to show that the microbiome, from its staging ground in the bowel, can influence the development of its host’s brain. Rochellys Diaz Heijtz found that germ-free mice, without any microbiome, were more active, less anxious and less risk-averse than usual. Their brains differed in the activity of over a hundred genes that provide cells with energy, influence chemical communications in the brain and strengthen the connection between nerve cells. Heijtz could even shift her germ-free mice towards “normal” behaviour and genetic activity by giving them a microbiome transplant, but this only worked early in their lives. But later, Javier Bravo at University College Cork managed to change the behaviour of normal adult mice by feeding them with a probiotic bacterium called Lactobacillus rhamnosus, often found in yoghurts and dairy products. Fast Facts about the Microbiome. The Environment Within: Exploring the Role of the Gut Microbiome.

The Human Microbiome - Interactive Website. There Is No ‘Healthy’ Microbiome. But Mr. Leach did not have C. difficile. He experimented on himself because he views the Western microbiome as “a hot microbial mess,” he wrote on his blog. Poor diets, antibiotics and overly sanitized environments have gentrified the Western gut, he wrote, “potentially dragging us closer to ill health.” The Hadza, with their traditional hunter-gatherer lifestyle, carry diverse microbial communities that are presumably closer to a healthier and disappearing ideal. The More Diverse Your Gut Flora.

This is a post from the Gut Critters blog that ended November 18, 2016. Ray Medina gave permission for his material to be copied as long as it was attributed to him and not used for commercial purposes. – kiraonysko

What Are Beneficial Gut Bacteria. The Many Vital Functions of Beneficial Gut Flora. Gut microbiota: The good, the bad and the ugly - next frontier in understanding human health. 7 Things You Had No Idea Gut Bacteria Could Do. The gut microbiome: how does it affect our health? The bacteria in our gut are estimated to weight up to 2 kg. Most of us are aware that the bacteria in our gut play an important role in digestion.

When the stomach and small intestine are unable to digest certain foods we eat, gut microbes jump in to offer a helping hand, ensuring we get the nutrients we need. In addition, gut bacteria are known to aid the production of certain vitamins - such as vitamins B and K - and play a major role in immune function. But increasingly, researchers are working to find out more about how gut bacteria - particularly the bacteria that is unique to us individually - influence our health and risk of disease. Perhaps most studied is how gut microbiota affects an individual's risk of obesity and other metabolic conditions.

Gut microbes switch host genes on and off under influence of diet. The researchers found diet-induced changes in gut microbiota have different effects on host gene expression. The study - by a team at the University of Wisconsin-Madison (UW-Madison) - is published in the journal Molecular Cell. Genes - strips of DNA contained in chromosomes - are the blueprint for making organisms and sustaining life. However, while their DNA makeup is relatively fixed, genes respond to changes in environment. Interactions with the environment do not change the genes, but they alter their expression by switching them on and off through chemical tags on the DNA. Microbiome Fingerprints. Four microbial features distinguish the the microbiome of the starred person from the microbiomes of four other people.PNAS, E.A.

FRANZOSA ET AL. People harbor distinctive sets of microbes, the genetic signatures of which can be used to identify individuals participating in the Human Microbiome Project, according to work published today (May 11) in PNAS. “Each of us personally has a specific set of bugs that are an extension of us, just the same way that our own genome is a part of what defines us,” said coauthor Curtis Huttenhower, a biostatistician at the Harvard School of Public Health. The study suggests that microbiome sequencing may someday have utility in criminal investigations, for example, but it also raises questions about how microbiome sequence data should best be handled to protect the privacy of study participants. Sure enough, the team was able to correctly identify a person’s stool microbiome more than 80 percent of the time. New Catalog of Human Gut Microbes. An updated analysis of the gut microbiome extends the list of known bacterial genes to 9.8 million.

WIKIMEDIA, MATTOSAURUSAn expanded catalog of nearly 9.8 million genes from the human gut microbiome spans a cohort of bacteria three times larger than that used to create previous gene lists. The results, published this week (July 6) in Nature Biotechnology, integrate data from newly sequenced samples and previous studies to provide near-complete gene sets for most gut microbes. Microbial Menagerie. It’s in the Genes. Immune cells surrounding hair follicles in mouse skin. These hair follicles are home to a diverse array of commensal bacteria.FLICKR, NIAIDScouring the genomes and body-wide microbial communities of 93 people, researchers have discovered a link between the composition of the microbiome and genetic variation in innate immunity, phagocyte function, and other immune pathways.

Divided by language, united by gut bacteria – people have three common gut types - Not Exactly Rocket Science. Europe is a divided land. How does the gut microbiome recover after diarrhea? — The American Microbiome Institute. Diarrhea is an important global health challenge that kills nearly two million people each year. Even when it is not lethal it can have important detrimental impacts, especially on children. Biofilm Bacteria Control Distant Cells Using Long-Range Electrical Signals. Your gut's trick for controlling the bacteria that live in it. By Sam Wong. Our immune system selectively chooses which gut bacteria to keep, and which to eliminate — The American Microbiome Institute. Immune cells are educated in the gut to not attack beneficial bacteria — The American Microbiome Institute.

The gastrointestinal tract is made up of trillions of bacteria that are largely ignored by the body’s immune system. Why is it that the body’s immune system knows to ignore these beneficial bacteria that are so important for our ability to live a healthy life? Short-chain fatty acids and their effect on dendritic cells — The American Microbiome Institute. Short-chain fatty acids (SCFA) are metabolites produced from microbiota fermentation. Sex, body mass index, and dietary fiber correlated with microbiome composition — The American Microbiome Institute. On last week’s podcast, we talked with Erica and Justin Sonnenburg about how the food we eat, and specifically dietary fiber, is important for “feeding” our microbiomes. Gut Bacteria Vary with Diet. Prevotella in the gut appears to improve glucose tolerance — The American Microbiome Institute.

Interview with Gary Wu: Reducing the incidence of metabolic and immune diseases through a better understanding of diet and microbiota - Gut Microbiota for Health. How Diet Influences Host-Microbiome Communication in Mice. The microbiome may affect vaccination efficacy — The American Microbiome Institute. The microbiome of an isolated Amazon population. Human gut microbiome evolution: From hunter-gatherers to a western lifestyle. First snapshot of Inuit gut microbiome shows similarities to Western microbiome. Rare Microbes and Antibiotic Resistance. A Wash On the Wild Side: How I Learned To Stop Worrying and Love My Microbiome.

Going Feral: my one-year journey to acquire the healthiest gut microbiome in the world (you heard me!) How Good Gut Bacteria Could Transform Your Health (Page 2) - EatingWell. Bacteria and Humans Have Been Swapping DNA for Millennia. Vegetables’ Microbial Tenants. Burn injuries lead to changes in the gut microbiome — The American Microbiome Institute. ICU patients lose helpful gut bacteria within days of hospital admission - Scienmag. Traditional societies’ and modern societies’ microbiomes differ — The American Microbiome Institute. Cohabiting family members share microbiota with one another and with their dogs. Diverse Microbes in Hunter-Gatherers’ Guts. New insights into gut microbial community variation from the two largest cohorts to date - Gut Microbiota for Health. Gut Microbes for Life. What's in Your Poo? - Scientific American Blog Network. This Personal Poop Banking Service Lets You Save Your Poop.

On the Origins and Control of Community Types in the Human Microbiome. Gut's Microbial Community Shown to Influence Host Gene Expression. The hologenome: How our relationship with microbes drives our evolution. Vitamin D and the Microbiome. Bad Bacteria Thrive on Unhealthy Tissue and Cells. Spinal Injuries Impact Gut Microbiome. Intestinal Alkaline Phosphatase And Gut Health. There's Nothing Infantile About Bifidobacterium Infantis.

Was I too hard on Bifidobacteria? Saccharomyces boulardii. Chapter 12: Human Microbiome Analysis.