What Microbiome Studies Would You Like To See Happen?

We’re about to announce something exciting about some microbiome studies we’re running, but in the meantime I’d love to ask you something.

What microbiome studies would you like to see happen?

I asked this question in our latest newsletter, as well as around the office, and some inspiring and fun replies came in:

– Before and after hand washing, to see how effective it really is
– What’s in that goo that comes out of your eyes in the morning?
– Before and after colonoscopy, to see if the same microbiome returns
Chronic sinusitis, to detect any difference from normal nose/ear passages
– What happens to your gut bacteria during the transition to gluten-free
– Patients with recurrent C. diff infection
Rosacea patients, both skin and gut microbiomes
– The Hashimoto thyroiditis microbiome
Rheumatoid arthritis
– Testing the Eat Right For Your Blood Type diet and the probiotics the author recommends for each blood type
– Gut bacteria and sleep deprivation
– The bacteria on money

The 5-second rule: true or false?

Now it’s your turn. Tell us in the comments: what studies do you want to see happen?


89 thoughts on “What Microbiome Studies Would You Like To See Happen?

  1. GM

    I’d like to see a comparative study of the microbiome of infants and toddlers with and without food allergies, classified by age, sex and type of the food allergy.

    My 2-year old daughter has a milk protein allergy and we fear it is going to manifest into asthma in the next few months-years, since her immune system is recognizing some foods/other environmental allergens as threats. We have a strong reason to believe that changes in her gut microbiota would lead to significant alleviation of her symptoms, but we don’t know what the microbiome should be, and how we can get it there. There is some evidence of Lactobacillus rhamnosus GG playing some role in alleviating the symptoms, but it is a very incomplete picture.

    Its not just us – 6 million children in the US are affected by food allergies! I believe my concern would be representative of the concerns of millions of parents who try very hard to make sure their children get the best of nourishment despite having food allergies. A company like ubiome can take up the cause and help out these young children and their families, and help the little kids reach their full growth and cognitive potential! I’m quite sure a lot of parents would be very interested in participating or learning from such a study.

  2. Deepa

    I want to know what the gut flora is in children with food allergies. Though with some genetic predisposition to atopies, my son would have gotten environmental allergies if he were born in India and not here. Now he has a severe food allergy which is rare in India, especially to milk. The incidence of food allergies in children born to Indians in the US should be very high from my personal experience. I know/heard of a lot of Indian kids with food allergies here and I don’t know too many Indians here. I like to see a comparative study. I am pretty sure it has to do with some bacteria, probably mutated from glyphosate. We were eating mostly organic for years before our son was born, didn’t use cosmetics and were very careful not to use toxic personal products, etc. I also did not use antibiotics for years until I acquired an infection at the hospital after being induced, Then my delivery became complicated and I got IV antibiotics, didn’t get to touch him for almost a day, he only got IV glucose for a day. I am pretty sure got some bad bacteria from the hospital. I wish I could change that. Our apartment management also sprays the lawn routinely, which might have mutated my own bacteria.

    1. Deepa

      I also want to add that almost all the kids in our current apartment community have some immune disorder like asthma (most common), cancer or autism. So, I doubt herbicides very much. It will be good to see if apartment dwellers have a different microbiome. I did have some contact with soil and nature, though most apartment dwellers may not.

  3. Cassie S.

    How about the relationship/dynamics between healthy microbiomes and healthily functioning endocrine systems…and while we’re at it…some basic, broad, uncontroversial markers to define a generally healthy micro-biome …thinking characteristics of the populations (i.e. diversity) rather than the populations themselves.

  4. I would like to see the results of a study on probiotic supplements vs adding fermented foods to a persons diet. Which is more effective at increasing the diversity of the gut flora? Which method works faster? Would a better option be to use both a probiotic supplement together with fermented foods?

  5. Gerry Cunningham

    Prostate Cancer ( aggressive ).
    Radical Robotic Prostectomy.
    Rising PSA results after three years.
    Bowel sample before Radiotherapy.
    Bowel sample after radiotherapy

    Study would aim to look at bowel conditioning before the radiotherapy to reduce inflammatory etc effects resulting from the radiotherapy and also re-conditioning the bowel following radiotherapy effects.

    Possible that prostate or bowel tests could predict or indicate that prostate cancer is present or likely in the future.

    From bowel results could look to eliminate foods that might be linked to prostate cancer.

  6. Jen

    I would love to see studies before and after antibiotic use especially those on multiple courses both both spectrum antibiotics, topical antibiotics (I recall an ad for one that listed c diff as a possible side effect) and those that stay mostly in the bowel like Xifaxan (rifaximin). You could look at how much Xifaxan really does effect the rest of the body’s microbiome as well as how much it shifts the intestinal bacteria.

    Look at changes before and after herbal antibiotics (berberine, allicin, neem, etc) intended to treat IBS and maybe intended to treat cold/flu/sinus.

    Look for differences in people who use different anti-acids. Proton Pump Inhibitors already linked to fungal and SIBO (Small intestinal Bacterial Overgrowth) http://www.ncbi.nlm.nih.gov/pubmed/23574267

    Do people who regularly use ant-diarrheals (Virberzi, Imodium, Pepto-Bismol, Kaopectate, etc or laxatives /stool softeners have differences from those who don’t or rarely use? Which medications are the most and least disruptive?

    Look for changes after stomach flu, food poisoning, or intestinal parasite asking subjects to test asap after the illness.

    Look for changes after antifungal and antiviral (example tamiflu) treatment. Does removing some fungi or virus create differences in bacteria?

    Look at long term changes after going on FODMAP and similar diets for SIBO and ibs. Does it eventually starve the ‘good’ microbes as well as the problem ones?

    Look for changes after vaccinations since they stimulate the immune system

    Look for differences in the guts of people on psychological medications ssri, etc. since gut microbes effect our moods do psych drugs effect them

    Skin differences with people who use high efficiency washing machines and regular washing machines. Having to use heavy chemicals to cleanse the washing machine monthly so clothing does not smell putrid after washing makes me wonder what is cooking in the dang thing.

    Look at differences, if any, between people who garden organically, conventionally or maybe just have a few potted plants 😉

  7. Kim

    What type of microbiome do people with mold biotoxin illness (aka CIRS Chronic Inflammatory Response Syndrome) have

  8. maryann

    Hi, wondering about parasites–can you pick up what parasites are in the gut etc…

  9. maryann

    I also have 2 sets of granddaughters, 2 age 7 and 2 age 3. 1 of each group was born by csection. Might be fun to compare these 2 sets.

    I also wonder about testing a cancer patient before during and after chemo/radiation. I think it might be important to know what was in their biome prior to undergoing those treatments?

  10. Mary C

    Is the state of the Microbiome the common denominator between alcoholism & Alzheimer’s? What are the similarities & differences? Can prevention & intervention be as simple & earth-moving as the human biome?

  11. Something about Asbergers autism. I heard something about bacteria there. And

    2 scitzofrenia i heard thet had a differnt bacteria.

  12. Judith Oliver

    1) Bacterial populations before and after abdominal castor oil packs which support the Peyer’s patches and improve circulation/detoxification
    2) Microbiomes of heavy fast food eaters before and after a diet program and transition to healthy eating habits
    3) Microbiomes of C-section babies and natural delivery and change after probiotic implementation either in the mother or the infant, possibly matching mother’s to baby microbiomes
    4) Microbiomes of PTSD sufferers
    5) Microbiomes of people on a high protein diet for weight training before and after

  13. Jane Crowley

    Hi there, I’m in Australia and I’d love to be involved with or learn about any studies relating to the following:
    – milk kefir made from living milk kefir grains: comparisons in microbial species in different countries.
    – the family microbiome: comparisons between family members and their pets over time.
    – fermented foods: comparison of microbial species n traditionally fermented foods and the change in our microbiome from including fermented foods in our diet,
    – sauerkraut: comparison of traditional fermented sauerkraut using aerobic versus true anaerobic fermenting techniques.
    – the oral microbiome and xylitol: what exactly does birch xylitol do to our oral microbiome?
    – reducing and inducing anxiety with the use of specific microbial species, is it possible?
    – soil based probiotics: what effect does a daily dose of real living soil from a certified biodynamic farm have on the human microbiome over a month?
    – identification of the specific byproducts of well known probiotic species.
    – the ocean and its impact on the microbiome: how does a daily swim influence our microbiome?
    ……and I’ve got lots more ideas! I have been ‘experimenting’ on myself, my husband and two children for several years now (fermented foods, diet changes, probiotics, prebiotics, organic soil etc…) and I’m intrigued by the changes you can manifest in mood, behaviour and gut function by altering the human microbiome….I’d love to tackle this in a more scientific manner, or be part in formulating/taking part in studies including Australian participants.

  14. Dalayna Grace

    The state of the gut microbiome (what types of bacteria are present, what amounts, if there are more gram negative than gram positive, etc) in people who have or develop SIBO.

  15. Meredith

    I’d like to know what health conditions are linked to the new GABA consuming bacteria which has been discovered.

  16. Sonia

    I would love to know the difference between people who spend most of their time indoors and those that are outdoors.
    (work in an office, travel home on the train, dinner, TV , bed , weekends at the movies, playcenters ect)
    (work outside, train home, walk the pet, garden, dinner, tv, bed, weekends at the park, nature activities, sporting events)

  17. Anne O

    We need a study on Pediatric IBD and dietary lifestyle changes (e.g., SCD, Paleo, IBD-AID, diets). Children’s lives are devastated by this disease and so many of the harsh drugs don’t seem to work. I notice your current study is only for 18+ years of age. Please consider an IBD study for kids.

  18. Patty

    How about the effect of microwaving your food on microbe health?
    Also what is the effect of eating frozen vegetables versus fresh produce on your microbes?


  19. Patty

    If yeast thrive in warm environments, how about the effect on your microbes for those that drink hot liquids often such as coffee/tea?

  20. Judy

    I would like to know if pacifier use in babies affects diversity of their GI bacteria as well as any correlation with dental and intestinal health issues later in life

  21. Colin Hood

    I would love to see a study performed on how various physical activities can affect our microbiomes. Specifically higher level athletes, or anyone who performs consistent, multiple hours a day of training (strength & conditioning, dancers, yoga/Martial arts practitioners, outdoor enthusiasts). Interested to see the affects of how a very physical daily lifestyle can effect the many system of systems that can perhaps help shift our paradigms towards more accountable, actionable adaily movement within our society.

  22. Rebecca Savastio

    I’m really shocked that there is no active study on the microbiome and obesity. I think this should be next on your list.

  23. Joe

    It’s been 1 1/2 years since my successful home FMT to reverse my IBS-D. I’d like to see the FDA relax it’s IND requirements somewhat, that make a clinical trial so burdensome for studying the benefits of an FMT for many different diseases. I have been so happy with my successful FMT to reverse my disease. I didn’t get my diary back, that is the only exception. Everything is back, no more ‘flares’ of IBS. I only wish that more people could experience the return to health that I have found. It’s frustrating to have my health back, and yet to see other people struggle with diseases connected with damage to the microbiome, when I know firsthand there is a solution.

    I continue to examine my life for products that may be harmful to my good bacteria, and take steps to eliminate them. We make so many mistakes. We have ignored the elephant in the room, and have approved a long list of products without testing to see whether they harm our good, helpful bacteria. Sadly, there are so many mistakes we make.

    Since finding the best donor is critical to the success of FMTs, and reversing disease, I believe we need 10-fold larger effort to find and recruit the best donors, so our FMT trials will be successful. Dr Colleen Kelly has my observations on which steps we can take to improve success rates. The ideal donor is a crucial step to an FMT.

    Since the average American has already lost 40% of this ecosystem it does make it a challenge to find the best donor. We should also consider this for the treatment aspect. We need this diversity, the greater the diversity, the better our health. Remember too, that many of us carry some bad actors, and that our good bacteria keep these bad ones inline. But, don’t stop there. These bad actors have a role in training our immune system. The concept of implanting just good bacteria does not establish a healthy ecosystem. We don’t want a ‘pine forest plantation’, we want a ‘natural rain forest’. So, I know there are efforts to just implant only good bacteria, but this is not really the right approach.

    Moving forward. I believe our oral microbiome plays an enormous role in the establishment of the connecting microbiomes throughout the intestinal tract. We are, however, disrupting this oral microbiome. We, unwittingly, drink chlorinated water on a daily basis. While it is very important in our water supply for preventing water borne diseases, it is a mistake for us to ingest a product that indiscriminately kills bacteria, inside of us. We have from 600 to 800 species of bacteria in our oral microbiome. What is interesting is that some of these bacteria are anaerobic, the ones that populate 90% of our gut microbiome. I believe there is an important, very natural role being played by the oral microbiome in populating the connecting microbiomes, however we’ve been unwittingly disrupting it.

    What else do we do to the oral microbiome ? Well, let’s think about mouthwash. It kills bacteria. We approved this product for human consumption without having any idea how important the human microbiome is to our health, and that when we kill species of good bacteria and disrupt balances of good vs bad bacteria, we in turn affect our health.
    I suggest that we strongly need to re-evaluate the wisdom of daily using a product that kills bacteria. I believe it disrupts the oral microbiome flora, which in turn has a cascading affect on subsequent microbiomes.

    Let’s think about toothpaste as well. If we read the label, it says,”if more is consumed than is normally used for brushing, call a poison control center immediately”. This should give us pause. We don’t have studies that determine if toothpaste is harmful to our good oral bacteria. Does it disrupt this ecosystem ? I’m not against flossing and brushing, not at all. But, we need to re-think this. First, and foremost, we need to get the added sugars our of diets, they feed the bad bacteria of our oral, and our gut microbiomes. So, when we eliminate this first mistake in our diet (sugar), then perhaps we can better assess the necessity of toothpaste . Our processed foods have added sugars, the trouble is they feed our bad bacteria. Our food producers add them because they compete for our food dollar, yet when we understand the microbiome, it’s
    really an epic mistake.

    Granted, we’ve made good progress in 2016. We’ve banned the foolish practice of adding antibacterials to hand soaps. We’ve also banned low level antibiotics used in animal feed to increase weight gain. This will take affect Jan 1st, 2017. We now need to encourage our medial professionals all across the USA to reduce the number of antibiotics given, when possible. It’s all to clear that antibiotics have a devastating affect on the microbiome. Sure, we need them to save lives. But, we need to reduce use, when possible.

    One last thing, I predict and hope that home fermentation of vegetables and fruits will become commonplace. Sorry for the long post.

  24. Sharm

    It would be interesting to see a study done on Hashimoto’s thyroiditis and why when stool testing is done they seem to be missing the same gut flora.

  25. I would like to see a Ubiome test for kids. My son is liveing with Autism and has had many gut issues over his 13 years and I think with kids on the Spectrum this would be a Huge resource to actually know whether you are addressing the core issues with a non-verbal kid who can’t share whhat he is feeling inside his body in a meaningful way.

    Hoping this is a test that is developed soon!

    Bill Munro

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