Meet the Bacteria in a Pro-Paleo, Pro-Crossfit Chiropractor

This is a guest post by Dr. Jonathan Chung DC and Dr. Grace Liu. Thanks Jonathan and Grace!

A couple of months ago, I got to interview the Gut Goddess, Dr. Grace Liu for my podcast Heal Yourself Radio. You can check out that interview here:

From Drugs to Bugs with the Gut Goddess Grace Liu

Now if you ever get a chance to talk to Grace, you’ll begin to understand that her passion and enthusiasm for poop, microbiology, and it’s relationship to gut health is highly infectious (pun intended). One of the things that came up in our conversation is the effect that antibiotics have had on the disappearance of many ancestral organisms over the years.

The fact that my medical history has never included a stint of prescribed antibiotics made the prospect of looking at my gut microbiome super interesting, so I decided to take a look. Of course, I can’t account for the fact that antibiotics may seep in through our current food and water supply, but nonetheless, I haven’t had the direct prescriptive exposure that most of us have had.

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Here is some of my relevant personal history:

Height: 5’10”
Weight: 175 lbs
Body fat: 11%

Diet: Monday through Fridays Paleo-ish. Usually no breakfast. Salad for lunch. Protein and veggies for dinner. Saturday and Sunday usually 1-2 cheat meals with Thai or Vietnamese food because I’m a sucker for rice noodles

Activity: Crossfit 3-4x/week

Stress Level: Low to medium.

Supplements: Omega-3 fish oil

3 Bowel movements/day

Antibiotics HX: Never taken.

Medical History: Past shoulder and elbow tendonosis. History of occasional gastritis.

From my view, it looks like a pretty healthy distribution compared to the other comparative values. It looks like I have a LOT more Actinobacteria than every other population average. Breaking things down at the genus level, I also found higher than average amounts of skin and mouth flora.

After reading Martin Blaser’s Missing Microbes I’m a little curious as to my H. Pylori status and seeing if that plays into my history of gastritis.

I’ll have Grace give you a deeper analysis of my poop product:

Grace’s Breakdown

I love the new uBiome dashboard that allows tracking of the major spectrums of gut flora over time. I’ll be doing this with my auto-ordered kits soon!

The breakdown is such that I suspect that you have a great gut in terms of very little known opportunistic pathogens. The production of butyrate, a major nutrient, from gut flora fermentation of fiber/food is likely very good because the abundance of known butyrate producers is high and good. Actually your gut appears to house a spectrum of butyrate-producers that I don’t commonly see — Peptinophilus — which produces butyrate apparently from protein as its major energy source. You’ve got quite the carnivore in your gut and less of the known ‘herbivores’ which I find very curious. It is about 10 to 20 times higher than I’ve seen in other Paleo diehards.

Your gut appears to be dominated by Porphyromonas which enjoys complex plant fiber like its Bacteroidetes cousins. The other major gut member on this test appears to be part of skin flora (Corynebacteria 9%), but minimal presence of any potential skin opportunistis (Cronobacteria, Staphylococcus, etc).

Campylobacter (0.2012%) might be the only potential non-commensal resident worth highlighting. Often it is associated in gastroenteritis or digestive disorders such as the microbiota signature of GERD (reflux/heartburn) and others. At higher abundances Campylobacter is correlated to low gut diversity and higher inflammatory cytokines.

Your ubiome was really interesting — not the typical ‘template’ that I see but has the major anti-inflammatory protectors and one of the lowest levels of Proteobacteria and other groups of bacteria typically associated with modern industrial guts. Your minimal or zero exposures to healthcare antibiotics may be partly responsible I suspect. After antibiotics in both human and animal studies, distinct shifts to rises in potential pathogens and reductions in beneficial gut protectors are visibly noted.

Also what I am impressed with is the nice diversity of bifidobacteria reported (in the raw taxonomy) and truly amazing abundance of one of the most important ‘gut guardians’ Bifidobacteria longum (54% of total Bifidobacteria). uBiome reports species data such as B. longum as ‘experimental’ so this data is not diagnostic. In studies of healthy human adult and infant guts, B. longum is found to be dominant out of the spectrum of bifidobacteria discovered. It has robust anti-inflammatory properties and does the job to crowd out pathogens in the gut for both babies and adults.

Bifidobacterium GENUS           0.0672%

Bifidobacterium longum           0.0363% (54% of all bifido)

Bifidobacterium catenulatum    0.0130%

Bifidobacteria tsurumiense       0.0080%

Bifidobacteria animalis             0.0049%

Bifidobacterium breve             0.0046%

Bifidobacteria adolescentis       0.0023%

Bifidobacterium bifidum           0.0000%

Overall gut diversity looked fantastic. The number of genera was fairly moderate > 90 indicating to me good diversity. The number of orders was less than mine when we contrasted the results.

Jonathan’s compared with my uBiome:

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With your exceptional current health and athletic performance, I believe it gives me hope in knowing that if we perhaps minimize antibiotics, exercise, practice good sleep, reduce stress, and essentially everything you are committed to do for optimal human health, then good gut health may be the  gift and reward.

Thank you for giving me the opportunity to check out your gut signature, Jonathan!
Twitter: Gut_Goddess


Hopkins, Mark J et al. “Degradation of cross-linked and non-cross-linked arabinoxylans by the intestinal microbiota in children.” Applied and environmental microbiology 69.11 (2003): 6354-6360.

Ezaki, Takayuki et al. “Proposal of the genera Anaerococcus gen. nov., Peptoniphilus gen. nov. and Gallicola gen. nov. for members of the genus Peptostreptococcus.” International journal of systematic and evolutionary microbiology 51.4 (2001): 1521-1528.

Turroni, Francesca et al. “Exploring the diversity of the bifidobacterial population in the human intestinal tract.” Applied and environmental microbiology 75.6 (2009): 1534-1545.