uBiome's attempt to define references ranges for the microbiome

uBiome just released a new study:
16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome

I’ve never done any microbiome testing, but I bet their ranges will be of interest to anyone doing so, especially those watching for trends over time.


I’m starting to go through the studies that identified the clinically relevant taxa. From am initial look some of the studies are a bit s mall (n=30). Too early to say much until i complete the meta analysis. Either way, this is a good first start in understanding how (if) the mircrobiome can be leveraged to help these conditions which a lot of folks really struggle with.

Also, i believe genova dx has done a similar study but not sure if its published.

To put this into perspective, I tested the same stool in 2 different places and got greatly varying results of Faecalibacterium, one of the taxa mentioned in this study, differed by quite a bit.

Gut (3/10/2017) - 0.49%
Gut (3/10/2017) - 15.85%

Looking at all my tests, it seems that abundance is quite modulated on high I sample (toilet paper vs sampling from a hat – usually from the hat I mix it a bit more).

Gut (3/10/2017) - 0.49%
Gut (3/10/2017) - 15.85%
Gut (3/02/2017) - 9.61%
Gut (1/28/2017) - 1.27%
Gut (11/12/2016) - 0.28%
Gut (7/28/2016) - 10.54%
Gut (7/20/2016) - 11.14%
Gut (7/17/2016) - 4.32%
Gut (7/13/2016) - 13.73%
Gut (5/27/2016) - 0.26%
Gut (3/24/2016) - < 0.01%
Gut (3/02/2016) - 7.59%
Gut (2/17/2016) - 7.52%
Gut (1/11/2016) - 11.77%
Gut (11/29/2015) - 0.20%
Gut (9/10/2015) - 0.15%
Anything (9/10/2015) - 0.02%
Gut (6/23/2015) - 9.30%

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Has anyone else been tested by ubiome? I would be curios to probe their results.

I’ve done two round with ubiome. The first round had some complications, but I did get data from the second. I’ve also submitted a sample to Thryve and am looking forward to their results. See below for my last ubiome summary in relation to the reference ranges: https://blog.adafruit.com/2017/05/04/healthy-gut-reference-ranges/

what do things look like at the family level? Are you willing to post your raw data (json file)? I’d be happy to take a look at it and show you how you compare to me.

Sure, I am happy to share and discuss.

Raw JSON file @ family level from uBioMe April 1st 2017 sample.


I’m on a LCHF diet, fanatical fermenter and I run at least one ultra mountain marathon every month 62-100+ miles in length.

Thanks. I MTB in central PA fairly regularly.

Here are the results from a genus and phyla perspective. The sample you gave me was taken April 2017 so you are the last sample in this bunch and I am the 17 samples before it.

Have you thought about submitting this sample for the ubiome smartgut program? Its currently in pilot stage and I believe free.

@Mikey_Sklar Here’s the same plot but colored differently. I also cleaned up the sample names on the plot. Shows the differences i little better i think.

@Mikey_Sklar Here’s the same data but another colormap. Not sure which one I like. You?

You might want to also consider reaching out to @sprague

Hey Isaac, just curious, what you used to make these visualizations. Was it something you programmed or some software? They look fantastic.

Thanks Jacob. I made them using Python, pandas, and matplotlib. Code is here: https://github.com/isaacgerg/ubiome_longitudinal_analysis

If I had more time, I’d like to make a webservice where you can upload these ubiome json files it automatically makes the plots for you. Someone is free to make that though using my code :slight_smile: