GUT MICROBIOTA AND NUTRITION NEWSLETTER #28
April 2021
Dear Friends,
A very special welcome this month to our new subscribers who learned about Natasha's work through Instagram Live! We're so glad you have joined us on this journey to understand more about the science of gut microbiota and diet.
This month, we bring you some research on how several factors can affect the microbiome, the mucosal barrier, and inflammation: long-term dietary patterns, intermittent fasting during Ramadan, and a fungus called Debaryomyces hansenii. For the sport dietitians, you’ll find a new study on FODMAP consumption in endurance athletes and its association with gastrointestinal symptoms. We also share a landmark study on a microbiota-led intervention for malnutrition. And Kristina’s practice tip this month is called “Bacteria 101”.
We’re also excited to announce that, along with our co-author Dr. Ed Ishiguro, we’ve signed on with Academic Press for a 2nd Edition of our Gut Microbiota textbook! This means we’re setting out to update the manuscript with the important new studies and frameworks on diet and gut microbiota that have emerged since we submitted our previous manuscript in 2017. The updated edition will appear in early 2023. Stay tuned here for our progress!
Natasha and Kristina
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Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome
A new study published in Gut discusses novel insights into the relationship between diet, gut bacteria, and intestinal inflammation. The study examined 173 different diet factors and correlated these with the gut microbiomes of over 1425 participants. Processed foods and animal-derived foods were consistently associated with higher abundances of possibly detrimental bacteria: Firmicutes and Ruminococcus species of the Blautia genus, as well as endotoxin synthesis pathways. Beneficial short-chain fatty acid-producing bacteria and pathways of nutrient metabolism were associated with consumption of plant foods and fish. Specific foods were associated with microbes known to protect the intestinal mucosal lining and have anti-inflammatory effects.
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Remodeling of the gut microbiome during Ramadan-associated intermittent fasting
An interesting study from the Netherlands reveals that Ramadan-associated intermittent fasting resulted in potentially beneficial changes in the microbiome. This prospective study looked at healthy, young males fasting during the month of Ramadan. Intermittent fasting was observed over a period of 16 hours from dawn to sunset. The researchers confirmed that the intermittent fasting resulted in significant changes in microbial composition, with the abundance of the order Clostridiales significantly increased after fasting, along with increased abundance of the Lachnospiraceae and Ruminococcaceae families. Intermittent fasting provoked upregulation of short-chain fatty acid-producing Lachnospiraceae, which is a possible explanation for the positive health effects associated with intermittent fasting. After cessation of Ramadan fasting, the microbial composition shifted back to baseline.
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Debaryomyces is enriched in Crohn's disease intestinal tissue and impairs healing in mice
The link between specific microbes and inflammation has been of longstanding interest in IBD. Debaryomyces hansenii is a salt-tolerant fungus used in the food industry for surface ripening of cheese and meat products. Researchers have discovered this fungus in high abundance in the inflamed mucosal tissues of individuals living with Crohn’s disease, while only 1 of 10 healthy people harbored the fungus in their guts. When this fungus was transferred to mice it led to impaired mucosal wound healing. Treating the mice with antifungal medication eliminated the fungus and allowed the wounds to heal, suggesting that targeting this microbe could have therapeutic value for CD.
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High Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols (FODMAP) Consumption Among Endurance Athletes and Relationship to Gastrointestinal Symptoms
The FODMAP diet has shown promise in treating the lower gastrointestinal symptoms frequently experienced by endurance athletes. This was an exploratory study looking at the dietary strategies of 430 endurance athletes surrounding exercise, specifically in relation to the FODMAP content of foods or sports nutrition products and the development of gastrointestinal symptoms. A high proportion of athletes (60%) reported a high FODMAP food for a pre-race meal. More frequent nutrition product use -- particularly solid, gel/gummy, and homemade products -- was often related to increased frequency of GI symptoms. Few athletes (15.1%) consumed a habitual diet that would be considered low in FODMAPs. The authors conclude that FODMAP intake by endurance athletes is high, both surrounding exercise and as a matter of habit, and may be contributing to GI symptoms experienced during exercise.
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A Microbiota-Directed Food Intervention for Undernourished Children
This paper is the culmination of years of incredible work from the lab of Jeff Gordon, which led to an elegant and inexpensive new treatment for children with malnutrition. In previous work, Gordon and colleagues had found that children with malnutrition showed immature development of their gut microbiota compared with normally-developing children. Given the known impact of diet on gut microbiota, they investigated which combinations of local foods might be able to correct the gut microbiota deficit in the malnourished kids. They developed a therapeutic diet using these foods, and in this latest paper, they tested the intervention in a group of malnourished children -- finding that, indeed, the children who received the new intervention showed better growth than those who received the standard intervention. This research is an excellent example of how focusing on the gut microbiota can lead to simple but powerful dietary interventions for health.
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Kristina's Practice Tip: Bacteria 101
When I was starting out as a science writer more than a decade ago, I knew about as much about bacteria as the average person – which is to say, a few facts I remembered from high school biology; information from news stories about contamination of processed meats; and messages from cleaning product ads that implied I would feel amazing if I used their product to eliminate 99.9% of bacteria from the surfaces of my home.
As I started writing more and more about bacteria, talking with microbiologists and medical professionals for various assignments, I realized that my previous views on bacteria were extremely limited -- and frankly, inaccurate. I was so used to thinking of bacteria as categorically harmful that I hadn't paid attention to their many beneficial functions. Human life is not even possible without the bacteria living in our bodies and in our environment. (See this video for a 'thought experiment' on what the world would be like with no microbes.)
In the current era, because of rapidly advancing science and greater awareness, we are gradually coming to realize that not only do bacteria surround us wherever we go, but they also play a critical role in maintaining our health. After years of writing almost exclusively about bacteria and other microorganisms, I'm obsessed with the beneficial microbes -- not just for the sheer joy of learning about them, but because in the years ahead, we're going to be bombarded with messages about new products (both foods and drugs) that will target our resident gut microbes so the 'good' can out-compete the 'bad'. I'm convinced we need to equip ourselves to evaluate the messages we'll encounter as these areas of food and biotechnology continue to advance.
So, we begin with the basics. What are bacteria, and what do you need to know when you talk about them?
- On the 'tree of life' that shows the relationships between all life forms, bacteria make up one of the three branches. The other branches are archaea (an ancient single-celled life form, similar to bacteria), and eukaryotes, which are essentially ALL forms of complex life. According to current theories, billions of years ago only bacteria and archaea existed, and at some point a single archaeon combined with a single bacterium, leading to the very first complex life form. All of the living things we know -- from mushrooms to marmosets -- followed from that event.
- Every bacterium is a single cell enclosed within a cell wall -- a tiny sac of life. What it looks like and what it does depends on its genetic makeup. Bacteria can live independently, unlike viruses, which need to hijack other cells in order to survive and reproduce.
- Out of all the microbial species on Earth, fewer than 1% of them make humans ill. Only around 1400 human pathogens (many of them bacterial) have been described by scientists, but these pathogens have become famous while the neutral or beneficial microbes have been relatively ignored.
- In the early days of microbiology, scientists studied bacteria by culturing them in Petri dishes. They found out a lot in that manner, but what really changed the game was when they learned to sequence the genes of bacteria a couple of decades ago. For the first time it was possible to find out the identities of all the bacteria in a certain place -- even the ones that didn't grow in the lab -- by taking a 'snapshot' of their combined genes and figuring out which bacteria all of the genes belonged to. This is the foundation of microbiome science.
- Bacteria are classified according to a naming system: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species, and Strain. Bacteria of the same strain are clones of each other (give or take a few genes – bacteria have been known to share!). It's common to refer to bacteria by genus and species, for example: Bifidobacterium lactis. But when we talk about bacteria, and probiotic bacteria in particular, we should really be talking about bacterial strains: so, Bifidobacterium lactis BB-12. (Note that there are no italics for the strain designation.) As I argued in this article, since scientific studies focus on which probiotic strain(s) confer a particular health benefit, we need to get used to talking about bacterial strains and what they do. Talking in generalities about bacterial species will only get us so far -- they will not allow us to properly interpret a probiotic label or link the probiotics to any health benefits.
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