Microbiome #2: Improve Your Health

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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 explains the microbiome, covers the companies which provide microbiome testing and reputable companies which provide prebiotic and probiotic supplements.) This article covers the microbiome therapeutic companies and why a healthy microbiome protects you against major diseases.

Microbiome Health Therapeutic Companies

In April, 2022, microbiome therapeutic company Kaleido Bioscience declared bankruptcy amidst $360 million in outstanding debt. Among multiple mistakes, they believed their therapy was a food and not a drug. They initiated expensive trials under this premise that were not cleared by the FDA. The FDA rejected them with this warning letter. Microbiome therapeutics need to play by the same rules as regular drugs.

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:

  • Adaptive Phage Therapeutics (APT)
    • 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.
    • APT in collaboration with the Mayo Institute, identifies dangerous antibiotic resistant bacterial infection strains and provides specific bacteriophages to treat them.
    • Clinical targets include prosthetic joint, urinary tract, ophthalmic and cystic fibrosis-related lung infections as well as diabetic foot osteomyelitis.
  • Finch Therapeutics
    • Initiating a Phase 3 trial for treating Recurrent C.difficile infections, a dangerous gut infection which defies current antibiotics. 80%+ cure rate in Phase 2.
    • Trial is on clinical hold as of March, 2022 because of SARS-COVID-2 screening protocol issues.
    • The history of Finch and other C.diff therapeutic companies is quite fascinating as they attempt to turn poop into profits.
  • Ginkgo Bioworks and Synlogic
    • Developing “living medicines” based on gut bacteria to target brain and liver disorders.
    • Conducting Phase 3 clinical trial for engineered probiotic strain to lower blood Phe levels for Phenylketonuria patients. 
    • Pursuing clinical trial for engineered probiotic strain to consume methionine for  homocystinuria patients.
  • Seres Therapeutics
    • Completed C.difficile Phase 3 trial. 88% success rate vs 60% placebo rate.
    • Pursuing other antimicrobial bacteria resistant infections.
    • Pursuing ulcerative colitis.
  • Vedanta Biosciences
    • Targeting C.difficile, inflammatory bowel disease, solid tumors and gram-negative infections.
    • Targeting food allergies in combination with immunotherapy.

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. 

From this research, it is clear that improving microbiome health alleviates symptoms of serious NDs. It is also clear that treatments for NDs must also include treatments for the microbiome. Hopefully, it is abundantly clear that to keep your health, keeping a healthy microbiome is essential!

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.

In summary, keeping your gut healthy 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 is based on only 98 human adult samples. Hopefully more comprehensive databases will be available publicly from them in the future. In the meantime, commercial microbiome baseline testing companies have deeper databases and can provide you with more meaningful comparative results. 

Some companies such as Evolve Biosystems are working to make sure newborns have the right mix of gut bacteria to thrive. Having the right infant gut bacteria leads to improved later life health outcomes. Separately, several companies seek to turn the benefits of mother’s breast milk into commercial products.

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.

Microbiome Health and Antibiotics

Antibiotics, which we use to fight infections ranging from pneumonia to urinary tract infections, are 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 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.

Microbiome Health for Athletic Performance

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

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. 

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

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

Microbiome Health vs Allergies and Asthma

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.

Tests in allergic mice confirmed that providing those missing microbes did reset their immune system in favor of tolerance. In 2017 and 2018, ConsortiaTX – now ParetoBio, raised funding to pursue human trials. Vedanta BioSciences and ClostraBio also compete in this space.

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. Just drink in moderation, otherwise you’ll do more harm than good.

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