Blog: Microbiome & Fiber Archives » BIOME ONBOARD AWARENESS: THE SCIENCE BEHIND FOOD, OUR MICROBIOME, AND DISEASE

SUMMARY: This is not a 1950s sci-fi movie. This is what is likely happening now in your gut according to an amazing study just now publishing in Cell. If you are eating the Standard American Diet, the normal, helpful bacteria in your gut are not getting natural whole food fiber. Instead they are being fed fiber additives supplemented in processed foods, or isolated fiber supplements you are buying. Surprisingly, both the fiber additives and the supplements FAIL to feed your microbiome, and instead, they CANNIBALIZE the mucus lining for fuel, at least for mice, according to this study. Repeat: Fiber Additives Starve Gut Microbes. They Eat Mucus Lining. That compromises the intestinal barrier role in preventing pathogen infection. Bottom line: EAT WHOLE FOOD BASED FIBER to feed your microbiome, AND DON’T COUNT ON THE FIBER ADDED IN PROCESSED FOODS OR THE SUPPLEMENTS YOU TAKE FOR THAT FIBER. No wonder so many are sick.

“While this work was in mice, the take-home message from this work for humans amplifies everything that doctors and nutritionists have been telling us for decades: Eat A LOT OF FIBER FROM DIVERSE NATURAL SOURCES,” says Martens. “Your diet directly influences your microbiota, and from there it may influence the status of your gut’s mucus layer and tendency toward disease. But it’s an open question of whether we can cure our cultural lack of fiber with something more purified and easy to ingest [fiber supplements or that added to processed foods] than a lot of broccoli.” —Eric Martens, Ph.D., an associate professor of microbiology at the University of Michigan Medical School who led the research along with his former postdoctoral fellow Mahesh Desai, Ph.D., now at the Luxembourg Institute of Health.

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SUMMARY (updated Aug 2018): Dr. Rob Knight’s talk, Saturday, October 18, 2014, listed eleven factors that optimize the gut microbiome based on the American Gut Data cautioning all is preliminary. These are listed below along with an interesting article =&1=&Can We Eat Our Way To A Healthier Microbiome? It’s Complicated=&2=&” in which Dr. Knight and Jeff Leach (founders of crowd sourcing project “American Gut”) discuss the microbiome diet. A KEY finding was that the more vegs consumed (30 different each week is BEST), the more diverse the microbiome, and that is thought to be associated with health and improved immune status since MANY chronic diseases (see the below Table) have changes in microbiome diversity AND composition, [Cantinean et al 2018]. A 2018 update on the American Gut data just published, [McDonald et al 2018], and it still says to eat 30 different vegs each week! This post also provides insight into what the microbiome experts are saying about translation of microbiome research into clinical practice. And last, my synopsis of Dr. Knight’s talk is provided (see below the light bulb) along with my listing of fav microbiome researcher labs whose work is discussed in this post! Use them and PUBMED for your own disease prevention or mitigation research. Always. Stick with the evidence for answers as this blog does.

Microbiome and associated health problems

[Cantinean et al 2018], Figure 1 shows the link:

Source: [Catinean et al 2018] An overview on the interplay between nutraceuticals and gut microbiota, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5855885/

Table 1, lists links between several diseases and changes of microbiota:

Disease Changes in microbiota’s diversity and composition Consequences Reference

Inflammatory bowel disease Less bacterial diversity ↓ the number of Bacteroides and Firmicutes decreasing the concentration of butyrate Lucas López et al. (2017)

Irritable bowel syndrome—diarrhea ↑Enterobacteriaceae↓Faecalibacterium prausnitzii not known Dupont (2014)

Constipation ↑Firmicutes(Lachnospiraceae and Ruminococcaceae)↓Bacteroidetes (Prevotella) increasing the production of butyrate Zhu et al. (2014)

Obesity Changes in the ratio of Bacteroidetes/Firmicutes↓ the abundance Akkermansia muciniphila↑ the abundance Campylobacter, Shigella, Prevotella decreasing the production of butyrate Festi et al. (2014),Tremaroli & Bäckhed (2012)

Diabetes T2 ↓Bifidobacterium spp significant association of Parabacteroides with diabetic patients not known Wu et al. (2010)

↓Firmicutes↑Bacteroidetes, Proteobacteria it is possible to determine endotoxemia → oxidative stress → IL1, IL6, TNF α Marlene (2013)

Diabetes T1 ↓Lactobacillus, Bifidobacterium, Blautia coccoides–Eubacterium rectale, Prevotella decreasing the production of butyrate decreasing the synthesis of mucin increasing the intestinal permeability Murri et al. (2013)

↓Clostidium clusters IV and XIV (species that produce butyrate) decreasing the production of butyrate De Goffau et al. (2014)

Dyslipidemia ↓Lactobacillus decreasing enzymatic deconjugation of bile acids → increasing the level of cholesterol Kumar et al. (2012), Ramakrishna (2013)

Nonalcoholic steatohepatitis ↓Firmicutes↓Faecalibacterium and Anaerosporobacter (order Clostridiales)↑Parabacteroides and Allisonella (order Aeromonadales) increase in luminal gut ethanol production metabolism of dietary choline release of lipopolysaccharides increasing small intestinal bacterial overgrowth increasing endotoxemia increasing lipopolysaccharide →↑ insulin resistance and ↑ TNF alpha Compare et al. (2012), Wong et al. (2013) and Machado & Cortez-Pinto (2012)

Acute coronary syndromes not know trimethylamine is formed by gut microbiota from nutrients which contain l-carnitine, choline, phosphatidylcholine followed by the formation of trimethylamine N-oxide (TMAO) by hepatic enzymes increasing the plasmatic level of TMAO–increasing the risk of myocardial infarction and stroke Trøseid (2017)

Autistic spectrum disorders ↑Clostridium histolyticum (Clostridium clusters I and II)↑Bacteroidetes, Desulfovibrio↓Firmicutes increasing the production of neurotoxins Parracho et al. (2005), De Angelis et al. (2013)

Allergy ↑Lactobacillus, Enterococcus increasing of allergic sensitization Kirjavainen et al. (2002)

low diversity of microbiota ↑Bacteroidales↓Clostridiales not know Hua et al. (2016)

Dr. Rob Knight’s eleven point punch list of things that seem to be beneficial to the microbiome are:

Source: Dr. Rob Knight_11 Factors Affect Microbiome from American Gut Data, biomeonboardawareness.com/

Eat lots of plants: 5 to 30 different varieties each week preferably. This finding is so profound that “American Gut” will soon change participant food journal requirements to “only ask for frequency on consumption of holistic food within the past month, instead of the three week food journal. This change is warranted since the long term diet, especially meat and fiber consumption, has been shown to have the largest effect on the microbiome.”

Aging increases microbiome diversity: Microbiomes are more diverse at age 50 to 60 then populations in their twenties (see above slides).

Having an IBD diagnosis means your microbiome is altered. NOTE: Many chronic and autoimmune diseases are also following suit.

The time of year alters the microbiome with a more diverse microbiome being with sun and outdoor exposure.

Antibiotics wipe the microbiome with some folks recovering relatively soon whereas others do not recover the pre-antibiotic microbiome even one year later.

Males vs females: The sex for a given microbiome can now be accurately predicted.

Sleep 8 hours for a more diverse microbiome. Less than 6 hours yields a less diverse microbiome.

BMI but it only subtly affects the microbiome.

Plants: eating 6 to 10 each week is good, but eating 30 plus different varieties is best. (See further discussion below.)

Alcohol: one drink is helpful, more than one reduces diversity.

Frequent exercisers have a more diverse microbiome and it is best if exercise is outdoors rather than indoors.

What’s up with plants and the microbiome?

Here is a great read where Dr. Knight and Jeff Leach talk about plants (and their fiber): Can We Eat Our Way To A Healthier Microbiome? It’s Complicated. In sum, “eating too little fiber could starve the bacteria we want around. “When we starve our bacteria they eat us,” Leach says. “They eat the mucus lining – the mucin in our large intestine.” Knight adds that when we do keep our bacteria well fed, they, in turn, give off nutrients that nourish the cells that line our guts. Fiber, Knight says, “is thought to be good for your gut health over all.” You can read the post, Fiber Additives Starve Gut Microbes. They Eat Mucus Lining for more on all that! Bottom line: Harness this information to positively nudge your microbiome towards health. Note too that everyone is uniquely different so the right diet depends a lot on the individual’s lifestyle AND that individual’s microbes. More tips from the article are:

There are a lot of different ways to get fiber. Leach recommends getting it from vegetables. Eat a variety of veggies, and eat the whole thing, he recommends. “If you’re going to eat asparagus, eat the whole plant, not just the tips,” he says.

Fiber was also central to Leach’s suggestion to Stein to eat more garlic and leek. Those vegetables contain high levels of a type of fiber called inulin, which feeds actinobacteria in our guts. In fact, inulin is considered a prebiotic, since it feeds the good bacteria, or probiotics, that live inside us.

Garlic actually has antimicrobial properties, which paradoxically, could also be good thing for our microbiomes. One study shows that garlic hurts some of the bad bacteria in our guts while leaving the good guys intact. [Filocamo et al 2012]

Eat fermented foods which contain probiotics along with foods that feed those probiotics. Fermented foods like kimchi, sauerkraut and yogurt might be surer sources of probiotics. Researchers are unclear about whether these have any lasting effect on the composition of our microbiome, but in some cases they do seem to help. “Epidemiologically there seems to be some evidence that eating fermented food is beneficial rather than harmful,” Knight says. But researchers are still trying to figure out why.

⇒ A key benefit of fiber beyond regularity, is that when the microbiome ferments it, short chain fatty acids (SCFAs) are produced.

This study, from Nutrition & Diabetes, summarizes SCFA nicely: “Colonic fermentation is a complex process that occurs through the interactions of many microbial species and involves the anaerobic breakdown of dietary fibre, protein and peptides.^{1, 2, 3} The principal end products of colonic fermentation are the short chain fatty acids (SCFAs) acetate, propionate and butyrate, the gases hydrogen, carbon dioxide and methane^{4, 5, 6} and energy, which is used by the microbiota for growth and maintenance of cellular functions.⁷ Small amounts of branched chain fatty acids (iso-butyrate, valerate and iso-valerate) are also formed from protein and amino acid degradation. The amount and type of dietary fibre are among the major determinants of gut microbial composition and SCFA production patterns.⁸ In humans, the SCFA produced account for 5–10% of total dietary energy.⁹) [Fernandes et al 2014]

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