Looks like I have a serious case of missing microbes.

This is part two of my story of having my gut bacteria tested by a San Francisco company called uBiome.

If you missed the first part yesterday, it’s here:


Anyway as I was saying, one of uBiome’s in-house experts, Richard Sprague, took me through my report after I’d submitted my “poopçon” sample.

Fascinatingly, Richard explained that I had no Bifidobacterium at all.




Now, Bifidobacterium is a genus of bacteria which most people have, but I don’t.

Even more fascinatingly, Richard went on to say that low levels of Bifidobacterium can be associated with low mood and anxiety.



Most of the experiments in this area have been done with laboratory mice, but that shouldn’t put us off because mice and humans share many aspects of their physiology.

So low levels of Bifidobacterium may be indicative of low mood.

What about *no* levels, then?

As I said, wow.

Another intriguing piece of learning for me was that my bacterial diversity is very poor compared to most people’s.

It’s generally accepted that having plenty of different bacterial varieties is a good thing, but I’m way down in the 12th percentile, which means that something like 90% of people have more diverse microbiomes than me.

Without going into too much detail, one reason for this could be that I take a Lansoprazole capsule every day.

Have done for years.

They were prescribed by a doctor ages ago in an effort to cure an intermittent swallowing problem I’d had for years, and they certainly seemed to work in this respect.

I’d even been hospitalised twice before I started taking Lansoprazole, but haven’t needed any emergency admissions since then.

Lansoprazole, however, is a proton-pump inhibitor, a type of medication which significantly reduces gastric acid production.

You might imagine that an acidic environment wouldn’t be one in which microorganisms would flourish, but bacteria are funny old things.

Sometimes they actually need low pH (acidic) conditions.

So I feel a self-experiment coming on.

I’ve ordered myself a bottle of Bifidobacterium supplements, currently sitting in the fridge awaiting use, and I need to make a decision about the Lansoprazole (which isn’t a prescription medication in the USA, unlike in the UK. You can buy it in the supermarket.)

My plan is to take the supplements for a month, then get my gut bacteria checked again, while also tracking my mood.

I’ll report back, but I already find this gut-brain connection deeply interesting.

Definitely remember, as I said yesterday, that I’m neither a doctor nor a psychiatrist, so please make up your own mind about what I’ve described to you.

But wouldn’t it be truly remarkable if, in the future, depression could be treated with a daily pot of probiotic yoghurt?

13 thoughts on “Looks like I have a serious case of missing microbes.

  1. Can’t wait to hear the results, Jon! But if your other swallowing problem comes back, will you stop or carry on? Don’t let yourself have another problem and end up in the emergency room.
    Instead of this new supplement – why not try the yoghurt????
    K 🙂

  2. Really intriguing results which in turn cause lots more questions.

    Making me think too as I have a few arthritic problems and digestive issues too which often go together as do mood issues.

    More research needed I think?

  3. Jon this is very interesting.
    I am 58 and experienced many episodes of depression, fatigue, brain fog etc.
    Also hayfever, Excema. ….
    In between I was quite effective.
    Over a year ago my body started to detox through my skin. Suffered fevers, shivers, rashes. Bedridden for months.
    Doctors no help.
    Embarked on internal cleansing.
    Still in the process.
    Lots of lurking pathogens lurking.
    Since last September no depression, no brain fog, no hayfever, no allergies.
    So yes you are on the right track.
    Our internal biome affects directly our mood.
    It can be a long haul to clear up the internals at this stage in life.
    Better late than never.

  4. Also be aware that lowering your stomach acid can prevent you from absorbing essential nutrients which may affect your mood. For example, iron needs an acid environment to be absorbed and B12 has been show to be affected by PPI intake. B12 deficiency can cause not only low mood but severe depression and even psychosis.


  5. Have know this many years, was pointed out by daughter’s psychologist in Austin. Since we all do probiotics anyway to keep a happy population we reap the rewards as you are about to. Another thing for happy person and gut is to give up the wheat. It’s not that big a deal if you don’t eat bread anyway (who needs yeast into the bargain and all the fat and sugar (butter & marmalade). 3 months off the wheat has been amazing both for husband depression/anxiety and my thyroid and cortisol overload. Why not go whole hog and ditch the over the top with gluten modern wheat, you maybe a heck of a lot happier and healthier before you can say Jack Robinson (sort of!) Good on you & well done for getting this info out there.

  6. I think you are onto something very powerful here. The health of the gut amazingly affects just about every other part of a healthy (or unheathy) individual.

    Just beware of some advertised pro-biotic yoghurts that (a) have sweeteners added with additional chemicals to stop the bacteria feeding on the sugar…not good… (b) are often pasteurised after the fermentation process which kills all good bacteria !

    I have heard that an excelent form of pro-biotic comes from home cultured Kefir, popular in Europe – “Kefir is a unique cultured dairy product that is one of the most probiotic rich foods on the planet and has incredible medicinal benefits for healing issues like leaky gut.” Can search up to find more about it.
    From reading about it I would say that liquid forms of probiotic (unsweetened / unchemicaled / unpasturised) are ikely to be the most effective above dry pills to be assimilated by the gut.

    Because our foods generally (especially in the USA) are under attack by “the Agenda” to generally weaken us and bring us into submission to the governing superpowers, it is generally best to eductae ourselves thoroughly on nutritional indformation that our bodies need to function at their optimum.

    Avoid processed and sugary foods and other refined carbohydrates – they add to the bad bacteria in the gut and kill the good – no wonder the increasing levels of depression and anxiety in the US. All the medications that they continually try to put us on such as antidepressant treatments also probably harm gut flora…there is a higher level Agenda, it is not just chance.

    Avoid also tap water or use a very good filter – so many chemicals and drugs in the water supply that harm our biological balance and wellbeing.

    Find a very good multivitamin and testosterone booster for men as all the chemicals in the world around us including our daily cleaning and hygeine products produce oestrogen mimickers and other hormone imbalances in our bodies.

    Diet / Brief but intense daily Exercise / Reading and Meditation on good things – like the Bible are all key to healthy body / hormone balance and self actualisation rather than self subversion that the media continually hollers in our ears….!

    Your doing great things Jon, thanks !

  7. Very interesting.

    I made a similar but different discovery.
    I was given Terbinafine tablets (250mg once per day) for “brittle nail condition”, which is a fungal infection – possibly needing twelve months to cure fully. I noticed, after a month or two, that I lost significant amounts of weight, because quite simply my appetite dwindled. I mentioned this to someone else who had taken these tablets and they said that they had lost their TASTE too. Not with me however.

    I am very happy that my appetite dwindled and am now much fitter but have nevertheless stopped taking the tablets. I believe that some bug bacteria (or fungus) might have been causing my appetite to be slightly high in the first place.

    I do not suffer from depression or low moods so this is not relevant to that scenario – but I thought I would add this information anyway because of the quite unexpected and beneficial results.

  8. I hope you get good results from the supplements. I do recommend you check about leaky gut syndrome. Also it may help taking fermented foods. Best wishes

  9. The digestive system is the 2nd brain. I suspect that you will need more than supermarket bought product to change the flora though.
    It sounds gross but fecal transplants have been shown on Tv over here in Europe. ….something lovely for you to think about……

  10. Hi Jon,

    Very interesting.

    You want to read a book by Guilia Enders called “Gut”, very informative about our microbiomes.

    I’m a pharmacist and whilst knowing nothing about your medical history and your reason for taking the PPI, from experience it’s really common for people to be taking these drugs for years and years with no idea of why! Not 100% sure what condition it is you mention, but it might be worth consulting your GP (or gastroenterologist) whether it’s safe for you to stop. PPIs can also cause vitamin deficiencies (notably B12) so might also be worth getting tested to make sure you’re not deficient. Anyway, hope that’s useful and you don’t mind me sticking my oar in on your medicines!

    Best Wishes,

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