Microbiome #2: Improve Your Health

Here’s how to improve your microbiome health, article #2. If you missed our first microbiome writeup with more poop jokes, here it is. Our first article explained how the microbiome works and then covered companies who provide quality microbiome testing and those who sell reputable prebiotic and probiotic supplements. This article covers the microbiome therapeutic companies and why a healthy microbiome protects you against major diseases.

Microbiome Necessity

A few quick tidbits to encourage reading further, or perhaps not (!):

• You have more bacteria in your body than your 30-40 trillion human cells.
• Your microbiome is more critical to keeping you alive than your diet.
• Without a microbiome, exposure to harmful bacteria would probably kill you.
• Digestion and bowel movements are dependent on your microbiome. Severe constipation is not a pleasant cause of death. 

Microbiome Health Therapeutic Companies

If you should develop a dangerous antibiotic resistant gut, bloodstream, lung or urinary tract infection, here are several very cool companies to know about. Each of them continue to develop microbiome therapeutics as drugs. They include:

• BioMX (formerly Adaptive Phage Therapeutics)
  • The US Department of Defense research group cataloged the bacteria and bacteriophages from sewers in cities around the world. Later, they licensed it to APT.
  • Bacteriophages feed on individual strains of bacteria in a 1-1 relationship.
  • BioMX in collaboration with the Mayo Institute, identifies dangerous antibiotic resistant bacterial infection strains and provides specific bacteriophages to treat them.
  • Clinical targets include cystic fibrosis-related lung infections as well as diabetic foot osteomyelitis.
• Seres Therapeutics [NASDAQ: MCRB]
  • Created approved FDA product, VOWST, for to prevent recurrence of C.difficile following successful Phase 3 trial. 88% success rate vs 60% placebo rate.
  • Sold VOWST for cash and sales milestone payments to Nestle Health Sciences in August, 2024.
  • Now pursuing biotherapeutics for blood stream infections.
• Vedanta Biosciences
  • Targeting Recurrent C.difficile in Phase 3 trial. First patient dosed in May, 2024.
  • Targeting inflammatory bowel disease and gram-negative infections.

Microbiome Gut-Brain Axis and Neurodegenerative Diseases

Does your microbiome protect your brain from disease? Can bacteria from your gut travel up your central nervous system (CNS) and through the blood-brain barrier (BBB)? Are there other ways that an unhealthy gut can lead to an unhealthy brain?

Dysbiosis is a significant imbalance in gut bacteria diversity. It can lead to a “leaky gut” where bacteria can enter the bloodstream and cause inflammation. Does chronic inflammation then trigger brain and body disorders? Do harmful compounds travel from the gut to the brain? Or vice-versa? Or in both directions?

All of this is being studied as scientists seek to unlock the secrets of the microbiome gut-brain axis. A compilation of this research can be found in this long, but insightful article on the Implications of Gut Microbiota on Neurodegenerative Diseases (NDs). Alzheimers, Huntingtons, Multiple Sclerosis and Parkinsons are covered. As one example, gut microbiota is critical for maintaining healthy immune cells (microglia) in the CNS to protect against unwanted invaders. 

This research confirms that improving microbiome health alleviates symptoms of serious NDs. It is also clear that treatments for NDs must also include treatments for the microbiome.

Your gut microbiota is highly sensitive to diet, sleep deprivation, circadian rhythm disturbances, chronic noise, and sedentary behavior. Not surprisingly, these are also considered risk factors for some NDs. Leading a gut healthy lifestyle significantly reduces your chances of getting many serious diseases.

Healthy Baseline Microbiome Template

So what is the desired template for a healthy baseline microbiome? In 2019, researchers at George Washington University created GutFeelingKB, a healthy human microbiome reference list and abundance profile. Although it is doubtful that one microbiome diversity fits all, it is helpful to compare your microbiome to a baseline to see where you diverge, so you can consider areas to improve your microbiome health.

Unfortunately, GutFeelingKB was based on only 98 human adult samples. Fortunately since then, leading commercial microbiome baseline testing companies such as Biohm and Viome have developed deeper databases and can provide you with more meaningful comparative results. 

For example, companies such as Infinant Health are working to make sure newborns have the right mix of gut bacteria to survive and thrive. Having the right infant gut bacteria leads to improved later life health outcomes. Other companies seek to bring the benefits of mother’s breast milk into commercial products. A 2020 study confirmed that human milk has a unique microbiome and includes stomach-protecting probiotics like Bifidobacterium breve and Lactobacillus plantarum. 

If you are curious about what you might discover if you attempt to hack your own adult microbiome to improve your health, check out this blog of a microbiome hacker from 2014-2019.

Key Bacteria That Prevent Dysbiosis:

To prevent dysbiosis, several beneficial gut bacteria are known to help maintain a healthy microbial balance. These bacteria promote gut integrity, modulate the immune system, and prevent bacterial overgrowth.

1. Lactobacillus Lactobacillus species are widely studied for their role in preventing dysbiosis. These bacteria produce lactic acid, which helps maintain an acidic environment in the gut, inhibiting the growth of pathogenic bacteria. They also play a role in modulating the immune response and maintaining the intestinal barrier​.
2. Bifidobacterium This group of bacteria is essential for gut health, particularly in infants. Bifidobacterium helps in breaking down complex carbohydrates and fibers, which produces short-chain fatty acids (SCFAs) like butyrate. SCFAs are crucial for gut health, as they provide energy for colon cells and reduce inflammation. Bifidobacterium also helps crowd out harmful bacteria and maintain the integrity of the gut lining​.
3. Akkermansia muciniphila This species is notable for its role in maintaining the mucus layer of the gut, which acts as a protective barrier. Studies show that Akkermansia helps prevent gut permeability or “leaky gut,” which is often a result of dysbiosis. A healthy population of Akkermansia muciniphila is associated with better metabolic health and reduced inflammation​.
4. Faecalibacterium prausnitzii Faecalibacterium prausnitzii is one of the most abundant bacteria in a healthy gut and is a major producer of butyrate, a short-chain fatty acid that has anti-inflammatory effects. Low levels of this bacterium are often associated with inflammatory bowel diseases and dysbiosis​.
5. Clostridia (cluster IV and XIVa) Certain strains within the Clostridia class, particularly clusters IV and XIVa, are known for promoting immune tolerance and preventing inflammation. These bacteria help regulate the immune system by inducing the production of regulatory T cells (Tregs), which suppress immune responses that can lead to autoimmune diseases and allergies​.

Maintaining a diverse and healthy population of these beneficial bacteria through a balanced diet, rich in fiber and fermented foods, can prevent dysbiosis and support comprehensive gut health. Probiotic supplements can be added when diet is not sufficient alone.

Microbiome Health Wreckers

The following are bad for your microbiome and your health:

• High dietary fat and sugar – causes leaky gut and glucose intolerance, potentially leading to diabetes and other health conditions.
• Artificial sweeteners – saccharin, sucralose. Others have minimal to no impact. 
• Emulsifiers and stabilizers, including those commonly found in ice cream and pickles.
  • Carrageenan
  • Carboxymethyl cellulose or cellulose gum
  • Polysorbate 80
• Titanium dioxide food and toothpaste additive; Animal studies only. Further research needed for humans. Best to avoid until that is completed.

Antibiotics, which we use to fight infections ranging from pneumonia to urinary tract infections, also partially wreck your microbiome. You usually recover within a few months. However, antibiotics are also losing their efficacy. Because there is not the potential for huge profits, only a few companies are seeking to find the next antibiotics. One leading candidate is teixobactin, considered a bionic predator antibiotic.

Microbiome Health for Athletic Performance

Can improving your microbiome health, also improve your athletic performance? Yes. Here’s why.

• Exercise changes microbiome
• Gut bacteria for sports performance boost and this article
• Microbiome for athletic performance
• Shake it down: Vibration impact – exercise produces more anti-inflammatory responses

For more, see Fitbiomics in our first microbiome article, a company bringing you the unique benefits found in the microbiomes of top elite athletes.

Microbiome Health for Better Mood

Gut microbiota is considered essential for healthy brain physiological processes, regulating human behavior; and affecting mental processes such as mood and cognition. 

• Gut bacteria affect your mood
• Gut bacteria linked to depression
• The Psychobiotic Revolution: Mood, Food and the New Science of the Gut-Brain Connection 

Microbiome Health vs Autoimmune Disease, Osteoarthritis, Fibromyalgia, Diabetes and Obesity

A “leaky” gut leads to chronic inflammation which then causes numerous unhealthy issues. Here’s a series of scientific articles which explain how this happens.

• Microbiome vs. Obesity
• Microbiome vs. Autoimmune disease podcast
• Microbiome vs. Diabetes and glycemic response
• Microbiome vs. Fibromyalgia
• Microbiome vs Osteoarthritis

Microbiome Health vs Allergies and Asthma

A healthy microbiome during infancy and childhood is critical in developing a balanced immune system. Studies show that babies born via C-section, those who are formula-fed, or those exposed to antibiotics early in life are more prone to developing allergies due to a less diverse gut microbiome. This lack of microbial diversity can impair the development of immune tolerance to allergens, making individuals more likely to develop allergic reactions to foods like peanuts, dairy, and eggs​.

By testing a baby’s first poop, researchers determined with 76% accuracy their risk of developing various allergies. Further research at Boston Children’s Hospital followed infants to 30 months, taking regular poop samples. They discovered a distinct group of microbes which provide protection against allergies. Certain beneficial gut bacteria, such as Clostridia and Bacteroides, have been found to support the immune system by promoting regulatory T cells that help prevent inappropriate immune responses, reducing the likelihood of allergic reactions. Tests in allergic mice confirmed that providing those missing microbes did reset their immune system in favor of tolerance.

Vedanta BioSciences, ClostraBio and many others seek to produce therapeutics to treat food allergies. These therapies will improve lives by providing more effective and accessible options beyond traditional avoidance measures and emergency treatments like epinephrine injections. 

Microbiome #2 Conclusion

Thanks for reading and taking the time to improve your microbiome health. As your reward, you may be glad to know that red wine makes more diverse gut bacteria! That said, unfortunately red wine at or after dinner disrupts a good night’s sleep. So if you like red wine, then just drink early (lunch) and in moderation (1 glass), otherwise you are probably doing more harm than good.