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Your Amazing Gut Microbiota, with Justin Sonneburg, PhD

Sharon Palmer

I had the amazing opportunity to attend the Annual Nutrition and Health Conference in Dallas.  One of the speakers was   Justin Sonnenburg, PgD, one the leading experts on the gut microbiota. He is such an eloquent and passionate speaker on this topic, and I always look forward to hearing this thoughts.  This is what he had to say at his presentation.

“There is no aspect of human biology that doesn’t get touched some  way by the microbiota. We are more microbial than human,  we have 10-fold the number of   microorganisms than body cells. The collective human microbiome genetic coding is 100 times greater than the human genome. Most of the microbiota are located in the gut, where they have an incredible impact on the body; the immune system is one of the greatest, but it’s not just limited to the mucosal immunity, but the immunity of the whole body. The gut microbiota impacts the host metabolism, and a number of other processes, such as the brain. If we have microbes controlling so many aspects of biology to prevent disease. The gut microbiota are   somewhat   plastic and are easily manipulated, unlike the human genome.”

“Diet is one of the most powerful best understood impacts on the gut microbiota. You can also use drugs to impact microbiota, and fecal transplants. We are undergoing efforts to map the human microbiome  and we have made tremendous strides to understanding it. Most of research today focuses on gut bacteria, it is the focus of much of the data. Still, there are incredible aspects that are poorly understood. 90% of organisms live in the gut, yet only 4 phyla are dominant.  When you narrow it down to look at phyla, there are a thousand varieties in each of our microbiota. Your neighbor has different microbiota than you do.  We have broad species in common, yet the microbiota varies widely in specific varieties. Yet, the functions of these bacteria overlap—they may have similar functions, but they are not totally identical.”

“One day we will be able to take snips and customize a peron’s treatment based on microbiota. We need to understand it mechanistically, though. The gut microbiota is an unsupervised drug factory; even autism may be influenced by the microbiota. There is work on the engineering of the gut microbiota, we can use them for therapeutic delivery and diagnostics.”

“The most abundant bacteria in the gut takes carbohydrates, and degrades them into short chain fatty acids (SCFA), which are more important in the regulatory role of the immune system. There is intense competition, many groups of bacteria are vying for complex carbohydrates, feeding off their fermentation endproducts. It is a complex ecosystem and food web, the major gateway comes in from carbohydrates that you ingest, you’re in control of this.”

“Many of us aren’t eating much dietary fiber, there is a lack of dietary fiber in westerners. America is a constipated nation, if   you   pass small stools, you have to have large hospitals,’ Dennis Burkitt once said.   One of the major dietary trends across the next decade is the need to increase fiber. The hypothesis is that increased fiber leads to increased microbiota diversity, output, and numbers; and vice versa—lower fiber intake leads to lower diversity, output and numbers.”

“When you look at the timeline of our last common ancestor, as we evolved, through hunting, fire control, farming 10-12000 years ago, and more recently processed foods, each one of these events had incredible impacts on the gut microbiota. We are creating a disbiotic microbiome. The human genome has to interact with the gut microbiota. Two different   entities evolved, and it is likely happening now in the Western world, our gut microbiota is some what foreign to our current genome.”

“Researchers studying traditional cultures, such as Malawai, show that the ancient  microbitoa looked very different, compared to one in the EU or US. In rural communities, the gut microbiota looks approximately like what it looked like 10,000 years ago. The Western microbiota is way less diverse, with ¼ to 1/3 less species in our microbiota. The study of hunter gatherer microbiota, which is how we lived for most of our human evolution, told us the same thing—the ancient microbiota was likely much more diverse. It is likely that in the past 150 – 400 years, we have been going through bottlenecks in our microbiota diversity, compared with the one we evolved with for most of our evolution. If we consumed a high fiber diet now, is it possible to bring back the microbiota community, without a fecal transpalant?  Can we recover diversity?”

“We can look to humanized gut mice, to see if they undergo dietary diversity loss. In humanized gut mice, three groups were studied: high fiber, low fiber, and fiber-defficient. If bring back fiber, did diversity come back?  Results: Diversity crashed in the low and no fiber groups. Can they recover? Yes, it came back. It shows resilience, and that the gut microbiota can recover. But some don’t come back; some species are irreversibly lost.”

“Some bacteria bloom in the absence of fiber.   They use mucus as a back up source of nutrition, they switch over to mucus, a carb-rich substance, they can ferment our mucus. The bacteria eat us when times get tough. There is tremendous plasticity in gut microbiota. In the luminal particle, it is rich in bacteria. If you have prolonged difficiency of fiber, can the microbiota decimate the mucus? Research shows that with a no fiber diet, the mucus layer changes, the microbes relocate, there is low level inflammation, as the bacteria move close to host tissue.”

“Low diversity in microbiota is associated with poor health. You can break it up into two different populations, high diversity, and low diversity of microbiota. Low diversity microbiota have more markers of poor health. However, increase in soluble fiber, increases diversity of microbiota, and it’s possible to restore diversity, with improved clinical measures.”

“Here’s what we know about microbiota diversity and human health: 1) high fiber diet leads to high diversity and high SCFA composition. 2) low fiber diet leads to low diversity and low SCFA composition. SCFA studies show that they increase abundance of T regulating cells, attenuate inflammation, and decrease macrophage. Could it be that chronic low fiber diet, predisposes us to Western diseases because of pro-inflammatory effects? SCFA decreases system immune system inflammatory responses. SCFA is   linked with better   weight and   glucose control. The multiple hit hypothesis for Western microbiota deterioration includes diet, sanitization, antibiotics, c-sections, lack of breast milk.”

“Dietary fiber is defined in many ways; I prefer the term microbiota accessible carbohydrates… When the Japanese are compared to Americans, it was found they had a gene in the microbiota that let them degrade seaweed that we don’t have. If we eat seaweed, we won’t have that gene. How to eat properly to feed microbiota? The best advice I give is to eat a lot of foods that are labeled with fiber, such as legumes, vegetables, fruits that are low GI, chia seeds—consume a wide variety diverse dietary fiber.  There is interest in   whether you gut microbiota can degrade some of these foods, such as chia and psyllium husk.”

“I really prefer fermented foods; you can decide what works for you. The natural is often best (over probiotics). With probiotics, they may be proven to work in a clinical study for something you’re trying to treat. But you can increase fermented food consumption, humans once ate huge amounts of rotting food.”

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