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The numbers are amazing. Researchers found all these microbes because of state of the art genetic analysis such as 16S rRNA gene sequencing (because most microbes can not be "cultured"). From Science Daily:

Cataloguing 10 million human gut microbial genes: Unparalleled accomplishment

Over the past several years, research on bacteria in the digestive tract (gut microbiome) has confirmed the major role they play in our health. An international consortium has developed the most complete database of microbial genes ever created. The catalogue features nearly ten million genes and will constitute a reference for all research on gut bacteria.

Research on the gut microbiome (all of the bacteria in the digestive tract) has multiplied over the past several years, helped in great part by new sequencing technologies. The gut microbiome, which scientists have labelled a "new organ" that is composed of tens of trillions of bacteria -- ten times as many as the number of cells in the human body -- is directly linked to the immune system and brain. It is a major player in chronic illnesses such as obesity and Type 2 diabetes. However, research in the field depends on access to reference gene databases (or catalogues), which is particularly important when identifying the functions of microbial genes. Few and far between, existing catalogues were created using samples from a limited number of people and geographical origins.

Most of the genes (around six million) are shared by just 1% of the population, making them quite rare. While there is substantial data today regarding the most common genes, future research will focus on determining the importance and role of these rare genes.

Thanks to this catalogue, the most clinically significant genes can be described, most notably those related to illnesses such as Type 2 diabetes, cirrhosis of the liver, cardiovascular diseases and some cancers. It will also provide a more complete picture of imbalances in the gut microbiome (dysbiosis), particularly those caused by medication.

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Much discussion about the link between gut bacteria and liver cancer, as well as the link between inflammation and cancer. Gut microbiome imbalances can cause health harms.

Bottom line: Try to improve your gut microbiome by eating a diet rich in fruits, vegetables, seeds, nuts, legumes, and whole grains.

From the Dec.4, 2014 issue of Nature: Microbiome: The bacterial tightrope

Imbalances in gut bacteria have been implicated in the progression from liver disease to cancer. The team's research, published last year, suggests that gut bacteria — which are part of the microbiome of bacteria and other microorganisms that live in and on the body — can play a crucial part in liver-cancer progression.

There are trillions of microorganisms in the human microbiome — they outnumber their host's cells by around ten to one — and their exact role in health and disease is only now starting to be explored. Studies have found that people with non-alcoholic fatty liver disease have a different composition of bacteria in their gut from healthy individuals2, 3

 Instead, she sees an emerging picture of liver disease and cancer as a process in which various factors — including a high-fat diet, alcoholism, genetic susceptibility and the microbiome — can each contribute to the progression from minor to severe liver damage, and from severe liver damage to cancer.

Flavell's research suggests that the liver has an important role in immune surveillance and helps to maintain bacterial balance in the gut. Specialized cells in the liver and intestines monitor the microbiome by keeping tabs on bacterial by-products as they pass through. These cells can detect infections and help to fight them.

But they can also pick up on subtler changes in the bacterial populations in the gut. When certain types of bacteria become too numerous — a state called dysbiosis — the immune system becomes activated and triggers inflammation, although at a lower level than it would for an infection... Now, research is emerging that suggests that dysbiosis and the immune reaction it provokes can even contribute to cancer.

He thinks that at least part of this mechanism involves disruption in the balance of the various species of bacteria in the gut. An out-of-balance microbiome promotes a constant state of inflammation, which can contribute to cancer progression, Schwabe says. This aligns with the picture that is emerging of cancer, in general, as an inflammatory process: the same immune reactions that help the body to fight infection and disease can also promote unchecked cell growth.

Some of the earliest research on the human microbiome, published in 2006, demonstrated that the balance of gut bacteria in obese people is different from that in people of healthy weight. In particular, obese people tend to have greater numbers of the bacteria that produce DCA (deoxycholic acid) and other secondary bile acids.

This line of research points to the microbiome as one potential link between obesity and liver-cancer risk . And, much like Schwabe's work, Hara's results indicate that several factors converge to promote cancer: in this case, bacteria, diet and carcinogen exposure. Here, too, the ability to stave off the disease seems to depend on maintaining the appropriate microbial balance. Overweight mice and people have a different composition of gut microbiota from their lighter counterparts, and they have higher levels of DCA, too.

However, not everyone is convinced that individual bacterial species are to blame. Some researchers point out that dysbiosis, and therefore cancer risk, involves multiple strains of bacteria. And the bacterial mix can vary from person to person, meaning it is unlikely that scientists can pin all responsibility on a single species.

Others are looking for ways to promote the growth of healthy bacterial strains rather than target the bad ones....There is also some early clinical evidence that specially formulated probiotics — cocktails of good bacteria — can bump the microbiome back into balance. Hylemon and his colleagues gave people with cirrhosis a probiotic containing Lactobacillus bacteria and found that their blood markers of inflammation decreased along with their cognitive dysfunction (a common symptom of cirrhosis)6. Although the study was not designed to evaluate cancer risk, it does show that delivering bacteria to the gut can have positive therapeutic effects on the liver.

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More discussion of the benefits of vitamin D. From Science Daily:

Vitamin D deficiency, depression linked in international study

Vitamin D deficiency is not just harmful to physical health -- it also might impact mental health, according to a team of researchers that has found a link between seasonal affective disorder, or SAD, and a lack of sunlight. "Rather than being one of many factors, vitamin D could have a regulative role in the development of SAD," said Alan Stewart of the University of Georgia College of Education.

Stewart and Michael Kimlin from QUT's School of Public Health and Social Work conducted a review of more than 100 leading articles and found a relationship between vitamin D and seasonal depression."Seasonal affective disorder is believed to affect up to 10 percent of the population, depending upon geographical location, and is a type of depression related to changes in season," said Stewart, an associate professor in the department of counseling and human development services.

"We believe there are several reasons for this, including that vitamin D levels fluctuate in the body seasonally, in direct relation to seasonally available sunlight," he said. "For example, studies show there is a lag of about eight weeks between the peak in intensity of ultraviolet radiation and the onset of SAD, and this correlates with the time it takes for UV radiation to be processed by the body into vitamin D.

Vitamin D is also involved in the synthesis of serotonin and dopamine within the brain, both chemicals linked to depression, according to the researchers. "Evidence exists that low levels of dopamine and serotonin are linked to depression, therefore it is logical that there may be a relationship between low levels of vitamin D and depressive symptoms," said Kimlin, a Cancer Council Queensland Professor of Cancer Prevention Reseach. "Studies have also found depressed patients commonly had lower levels of vitamin D."

Vitamin D levels varied according to the pigmentation of the skin. People with dark skin often record lower levels of vitamin D, according to the researchers.

Kimlin, who heads QUT's National Health and Medical Research Council Centre for Research Excellence in Sun and Health, said adequate levels of vitamin D were essential in maintaining bone health, with deficiency causing osteomalacia in adults and rickets in children. Vitamin D levels of more than 50 nanomoles per liter are recommended by the U.S. Institute of Medicine...."A few minutes of sunlight exposure each day should be enough for most people to maintain an adequate vitamin D status."

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Makes sense. From Science Daily:

High school football players show brain changes after one season, even in absence of concussions

Some high school football players exhibit measurable brain changes after a single season of play even in the absence of concussion, according to a new study.

Dr. Whitlow and colleagues set out to determine if head impacts acquired over a season of high school football produce white matter changes in the brain in the absence of clinically diagnosed concussion.The researchers studied 24 high school football players between the ages of 16 and 18. For all games and practices, players were monitored with Head Impact Telemetry System (HITs) helmet-mounted accelerometers, which are used in youth and collegiate football to assess the frequency and severity of helmet impacts.

Risk-weighted cumulative exposure was computed from the HITs data, representing the risk of concussion over the course of the season. This data, along with total impacts, were used to categorize the players into one of two groups: heavy hitters or light hitters. There were nine heavy hitters and 15 light hitters. None of the players experienced concussion during the season.

All players underwent pre- and post-season evaluation with diffusion tensor imaging (DTI) of the brain. DTI is an advanced MRI technique, which identifies microstructural changes in the brain's white matter.

The brain's white matter is composed of millions of nerve fibers called axons that act like communication cables connecting various regions of the brain. Diffusion tensor imaging produces a measurement, called fractional anisotropy (FA), of the movement of water molecules along axons. In healthy white matter, the direction of water movement is fairly uniform and measures high in fractional anisotropy. When water movement is more random, fractional anisotropy values decrease, suggesting microstructural abnormalities.

The results showed that both groups demonstrated global increases of FA over time, likely reflecting effects of brain development. However, the heavy-hitter group showed statistically significant areas of decreased FA post-season in specific areas of the brain, including the splenium of the corpus callosum and deep white matter tracts.

"Our study found that players experiencing greater levels of head impacts have more FA loss compared to players with lower impact exposure," Dr. Whitlow said. "Similar brain MRI changes have been previously associated with mild traumatic brain injury. However, it is unclear whether or not these effects will be associated with any negative long-term consequences."

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That's right - when thinking about having children, don't just focus on the women's age. Think about sperm quality also. From Science Daily:

Men's sperm quality declines with age, review of 90 studies confirms

Conflicting evidence about the extent to which men's semen quality declines with age -- likely lowering their fertility -- is being cleared up by new research that has collated and reviewed data from 90 previous studies from around the world.

After conducting a systematic review and meta-analysis of the studies' data, researchers from the University's Departments of Zoology and Anatomy found consistent age-related declines in semen volume and sperm performance and increases in malformed and DNA-damaged sperm. Semen quality is regarded as a proxy for how fertile a male is.

"The effects of declining semen traits with increasing male age have largely been ignored due to inconsistencies in the literature, but our work now suggests that male age affects a variety of traits. It is well recognised that reduced sperm performance can affect pregnancy success, but it is less well known that the quality of the sperm, particularly DNA quality, could affect the development and health of the offspring," Dr Johnson says.

"Our study made no attempt to estimate the rate of decline, but some well-controlled clinic-based studies have observed consistent declines with increasing age, whereas others project declines after age 35 for some traits and after age 40 for others" she says.

"Older males contribute to increased risk of obstetric complications, miscarriage, and offspring disorders such as autism, Down syndrome, epilepsy, and schizophrenia. In addition, increasing male age may be an overlooked component of couple infertility, leading to our increased use and dependency on fertility treatments, such as IVF."

The authors suggest that clinical analysis of the percentage of DNA-fragmented sperm cells and a greater focus on how well sperm swim may lead to better patient outcomes during fertility treatments of aging couples."These are likely more accurate and consistent predictors of a man's fertility status than commonly clinically measured traits such as semen volume, sperm concentration and total sperm count," Dr Johnson says.

Sperm under microscope. Credit: Fertility Associates Ltd. NZ

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Please note that the study was of people living in the Baltimore, Maryland area - so it is unknown if this would hold true for people living elsewhere. From Medical Xpress;

Virus may affect mental abilities, study reports

People with an algae virus in their throats had more difficulty completing a mental exercise than healthy people, and more research is needed to understand why, US scientists say. A study in the Proceedings of the National Academy of Sciences showed that the virus was present in about half of 92 human subjects studied, and those who had it performed worse on certain basic tasks.

The virus, known as Acanthocystis turfacea Chlorella virus 1, or ATCV-1, also appeared to limit the cognitive abilities of mice.The mice had a harder time navigating a maze and noticing new objects in their surroundings after they were infected.

It remains unclear if the virus was truly driving the drop in mental functioning. Researchers have not yet shown the cause and effect between the virus and the intelligence results."At this point we do not think that this virus should be considered as a threat to individual or public health," said lead researcher Robert Yolken, a virologist at Johns Hopkins University in Baltimore, Maryland. The virus was found by accident while scientists were analyzing microbes in the throats of healthy humans for a different study.

Experts have been studying viruses similar to ATCV-1 for 35 years, said senior author James Van Etten of the University of Nebraska, an expert on algal viruses. Van Etten joined the research four years ago when Johns Hopkins scientists found ATCV-1's DNA sequences in the brain tissue of people who had died with mental disorders such as schizophrenia.

"These viruses are ubiquitous in fresh water ponds and streams throughout the world," Van Etten said. He noted that the virus—previously thought to only infect algae—could make its way into the human body when people swallow water while swimming.There might also be another host in nature, such as mosquito larvae, he said. But the nature of the disease is still in the early stages of analysis.

It is also unknown if the virus's effects on the brain are lasting or temporary. Scientists have long understood that viruses interact with DNA, and further studies could shed more light on the role of the virus on cognition.

"As more studies like this are conducted, I believe we'll find out there's even more interaction between viruses, bacteria and fungi that are either ingested or breathed into our noses and mouths and the overall human condition," said Jordan Josephson, ear nose and throat specialist at Lenox Hill Hospital in New York, who was not involved in the study.

Further information on this study and the virus. From Medical Xpress:

Researchers identify algae-virus DNA in humans

From Newsweek:

American Researchers Discover 'Stupidity Virus'

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Natural ways that may help GERD symptoms without drugs : eating smaller portions, losing weight, not lying down for 2 hours after eating, and avoiding alcohol, cigarettes, and "trigger" foods.From Health Day News:

Could Popular Heartburn Drugs Upset Your 'Good' Gut Bugs?

Heartburn drugs such as Prilosec and Nexium may disrupt the makeup of bacteria in the digestive system, potentially boosting the risk of infections and other problems, a small new study suggests.

According to Harvard Medical School, billions of dollars are spent annually on antacid drugs in an attempt to combat heartburn, ulcers and gastroesophageal reflux disease, also known as GERD. Old standbys such as Maalox and Mylanta have been supplanted by more effective, more expensive drugs, including proton pump inhibitors. These include Prevacid (lansoprazole) and Protonix (pantoprazole) in addition to Prilosec (omeprazole) and Nexium (esomeprazole).

Long-term use of proton pump inhibitors has been linked to infection with a germ called Clostridium difficile, which causes severe diarrhea, he said. Researchers have also connected the medications to vitamin deficiencies, bone fractures and pneumonia, among other conditions.

In the new study, researchers sought to understand what happens to the trillions of germs in the digestive system when people take omeprazole, the generic name for the drug best known as Prilosec.Ten participants, aged 18 to 57, took 20 or 40 milligrams of the drug a day for 28 days. Researchers analyzed the study participants' stool samples to understand the germs in their guts.

"These microbes have evolved with us to participate in our normal development and metabolism, and perform certain functions that we would not be able to accomplish without their help," DiBaise said. Many scientists believe that people's risk of disease goes up when their normal germ makeup changes, he said.

The researchers found evidence that the medications disrupted the balance of bacteria in the digestive systems of the participants, and the changes lasted for at least a month after they discontinued the drug. It didn't seem to matter whether they took the higher or lower dose, DiBaise said.

DiBaise cautioned that the study doesn't prove that the drug causes users to become more vulnerable to C. difficile infections. However, it shows that the drug "creates a situation in the gut microbial environment that may increase an individual's susceptibility," he said.

What should users do for now? According to DiBaise, proton pump inhibitors are "the most effective medications to treat gastroesophageal reflux disease." If patients don't have the most severe symptoms, he said, other types of heartburn drugs might help. Also recommended: eating smaller portions, losing weight, not lying down for two hours after eating, and avoiding alcohol, cigarettes and "trigger" foods.

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Based on the study results, the researchers suggest that even older couples in bad marriages could benefit from marriage counseling.From Science Daily:

Bad marriage, broken heart?

Older couples in a bad marriage -- particularly female spouses -- have a higher risk for heart disease than those in a good marriage, finds the first nationally representative study of its kind.

Liu analyzed five years of data from about 1,200 married men and women who participated the National Social Life, Health and Aging Project. Respondents were aged 57-85 at the beginning of the study...Liu set out to learn how marital quality is related to risk of heart disease over time, and whether this relationship varies by gender and/or age. Among her findings:

Negative martial quality (e.g., spouse criticizes, spouse is demanding) has a bigger effect on heart health than positive marital quality (e.g., spousal support). In other words, a bad marriage is more harmful to your heart health than a good marriage is beneficial.

The effect of marital quality on cardiovascular risk becomes much stronger at older ages. Over time, the stress from a bad marriage may stimulate more, and more intense, cardiovascular responses because of the declining immune function and increasing frailty that typically develop in old age, Liu said.

Marital quality has a bigger effect on women's heart health than it does on men's, possibly because women tend to internalize negative feelings and thus are more likely to feel depressed and develop cardiovascular problems, Liu said.

Heart disease leads to a decline in marital quality for women, but not for men. This is consistent with the longstanding observation that wives are more likely to provide support and care to sick husbands, while husbands are less likely to take care of sick wives.

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Bottom line: Try to avoid artificial sweeteners!

From Scientific American: Artificial Sweeteners May Have Despicable Impacts on Gut Microbes

I find it ironic that Thanksgiving coincides with American Diabetes Month. In honor of that irony, two recently published studies have suggested a possible link between what you eat, how it impacts the behavior of the microbes living in your gut, and type II diabetes.

Results from a study by researchers in Israel, published in the journal Nature in October, have suggested that consumption of artificial sweeteners—found in over 6,000 food products—can lead to changes in the gut microbiome, and have put forth an explanation for how this alteration might be associated with diseases such as type II diabetes.

Jotham Suez, a PhD candidate and lead author of the study explains, “We asked people who do not regularly consume artificial sweeteners to add them to their diet for one week, and saw that the majority of these subjects had poorer glycemic responses.” And like humans, mice that were given saccharin-spiked water also developed marked glucose intolerance compared to mice drinking sugar water, or water alone.

Their experiment revealed that mice did exhibit different microbiome profiles after consuming artificial sweeteners, just as with the human volunteers who had developed glucose intolerance. And importantly, the humans who did not show glucose intolerance after consuming artificial sweeteners also did not see changes in the community composition of their microbiome.

Consequently, this change in microbial community in mice also modified how the microbiota functioned as a group to regulate metabolism. Pathways that impact the transport of sugar in the body were found to have decreased function after saccharin treatment and, notably, there was an increased abundance of short-chain fatty acids (SCFAs), which are implicated in lipid biosynthesis.

An investigation done by an independent group of researchers in Canada found similar results in a study published in October in the journal PLoS ONE. Although conducted using rats instead of mice, and with a different artificial sweetener (aspartame instead of saccharin) this study also found an increased risk of glucose intolerance. In addition, both studies showed that propionate—a SCFA highly involved in sugar production—is increased in animals consuming artificial sweeteners (although, unfortunately, propionate concentrations in humans weren’t assessed in the Nature study).

But the take home point is this: findings from two independent studies suggest that messing with the microbiome may have despicable consequences. Artificial sweeteners were originally intended to stave off the increasing obesity and metabolic disease epidemic, but instead they may have directly contributed to it.

In other words, consuming artificial sweeteners appears to throw metabolism out of whack by upsetting the critical balance of the biota in the gut—just as how chaos would surely ensue if you were to throw Gru’s minions out of whack.

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Great reasons to eat walnuts. Yes, this study was done in mice, but it (as supported by other research) should also apply to humans.From Medical Xpress:

'Tis the season to indulge in walnuts

Researchers at UC Davis and other institutions have found that diets rich in whole walnuts or walnut oil slowed prostate cancer growth in mice. In addition, both walnuts and walnut oil reduced cholesterol and increased insulin sensitivity. The walnut diet also reduced levels of the hormone IGF-1, which had been previously implicated in both prostate and breast cancer. The study was published online in the Journal of Medicinal Food. 

Davis and colleagues have been investigating the impact of walnuts on health for some time. A previous study found that walnuts reduced prostate tumor size in mice; however, there were questions about which parts of the nuts generated these benefits. 

In the current study, researchers used a mixture of fats with virtually the same fatty acid content as walnuts as their control diet. The mice were fed whole walnuts, walnut oil or the walnut-like fat for 18 weeks. The results replicated those from the previous study. While the walnuts and walnut oil reduced cholesterol and slowed prostate cancer growth, in contrast, the walnut-like fat did not have these effects, confirming that other nut components caused the improvements - not the omega-3s.

While the study does not pinpoint which combination of compounds in walnuts slows cancer growth, it did rule out fiber, zinc, magnesium and selenium. In addition, the research demonstrated that walnuts modulate several mechanisms associated with cancer growth.

"The energy effects from decreasing IGF-1 seem to muck up the works so the cancer can't grow as fast as it normally would," Davis said. "Also, reducing cholesterol means cancer cells may not get enough of it to allow these cells to grow quickly." In addition, the research showed increases in both adiponectin and the tumor suppressor PSP94, as well as reduced levels of COX-2, all markers for reduced prostate cancer risk.

Although results in mice don't always translate to humans, Davis said his results suggest the benefits of incorporating walnuts into a healthy diet. Other research, such as the PREDIMED human study, which assessed the Mediterranean diet, also found that eating walnuts reduced cancer mortality.

Still, Davis recommends caution in diet modification. "In our study the mice were eating the equivalent of 2.6 ounces of walnuts," he said. "You need to realize that 2.6 ounces of walnuts is about 482 calories. That's not insignificant, but it's better than eating a serving of supersized fries, which has 610 calories. In addition to the cancer benefit, we think you also get cardiovascular benefits that other walnut research has demonstrated.