Biohacking the Microbiome

I recently attended a meetup for Biohackers Seattle. This was a good presentation by Masha on what biohacking was — EXCEPT for one omission — nothing on the slides dealt with microbiome biohacking.

Deja Vu: Over the last two decades, I have seen many many different techniques tried to biohack myalgic encephalomyelitis. The pattern is often a few positive reports using the biohack du jour, a diverse group try it, in the larger group — the number of negative responses keep growing against a small number of positive responses. As a statistician,  I recognized the placebo effect combined with the use of only subjective evaluation and no control group. At least 80% of the items on the biohack list are familiar from these two decades of observations.

Microbiome biohacking is complex to do right

The foundation of microbiome biohacking is a comprehensive report on your gut microbiome, ideally down to the species, ideally the strain level. This report will typically have between 100 and 900 different measurements with 250 being common.


Each one of the items have impact on other items. To illustrate this, doing something to increase or decrease bifidobacterium longum – for example, taking the probiotic align results in  other bacteria increasing or decreasing. See this table for more details. We still lack complete knowledge.

Taxonomy Effect
Bacteroidaceae Decreases
Clostridiaceae Decreases
Enterobacteriaceae Decreases
Erysipelotrichaceae Decreases
Lachnospiraceae Increases
Pasteurellaceae Increases
Prevotellaceae Increases
Ruminococcaceae Increases
Streptococcaceae Decreases
Sutterellaceae Decreases
Veillonellaceae Increases
Verrucomicrobiaceae Increases
Akkermansia Increases
Anaerostipes Increases
Bacteroides Decreases
Blautia Increases
Clostridium Decreases
Dorea Increases
Escherichia Decreases
Haemophilus Increases
Holdemania Decreases
Oscillospira Increases
Prevotella Increases
Roseburia Decreases
Ruminococcus Increases
Streptococcus Decreases
Sutterella Decreases
Veillonella Increases
Firmicutes Decreases
Akkermansia muciniphila Increases
Bacteroides fragilis Decreases
Bacteroides vulgatus Decreases
Blautia producta Increases
Blautia wexlerae Increases
Escherichia coli Decreases
Holdemania filiformis Decreases
Roseburia faecis Decreases
Sutterella wadsworthensis Decreases

It is unlikely that the issue is a single bacteria being too high or too low. It is more typical that bile or serotonin producing bacteria are too many or too few. A simple naive approach would be that “serotonin is made by this one bacteria only’ or “bile is made by this one bacteria only’ — totally wrong.

A shift of bacteria can produce dozens of symptoms — and with correct biohacking, cause all of them to disappear. A simple case study that I just posted is at A reader report — 100% elimination of symptoms.

In terms of conditions, the number of statistically significant bacteria shifts reported in the medical literature (and more being reported as study sizes become larger) are:

ConditionName Bacteria Shifts
Allergies 18
Alzheimer’s disease 18
Autism 21
Autoimmune Disease 14
Brain Trauma 20
Chronic Fatigue Syndrome 30
Crohn’s Disease 23
Depression 28
Gout 23
Hashimoto’s thyroiditis 11
High Blood Pressure 10
Histamine Issues 35
Inflammatory Bowel Disease 24
Irritable Bowel Syndrome 18
Metabolic Syndrome 14
Mood Disorders 21
Parkinson’s Disease 9
Rheumatoid arthritis 24
Sjögren syndrome 21
Small Intestinal Bacterial Overgrowth  (SIBO) 8
Stress / post-traumatic stress disorder 19
Systemic Lupus Erythematosus 32
Type 2 Diabetes 18
Ulcerative colitis 9

So, you need to take things that would ideally modify all of the shifts back to normal. The items should not be items based on speculation or theory; but on actual published and peer-review studies.

I have assemble a list of such items of Gut Modifiers to assist those that wish to hack.

Microbiome Biohacking is the low hanging fruit

Less than $100 to get a report done. Even if you do not try using the Gut Modifiers, but do some other hack — you should do a before and after ubiome…. because evidence is that every biohack will alter your microbiome. Instead of a subjective report, give an objective report.  You feel less stress from eating fermented harbor seals. – There are bacteria associated with stress levels, some of those should change.