understand ur ubiome

Christopher Kelly from Nourish Balance Thrive and I have launched a small app to view your gut microbiota data generated by uBiome, the company which offers direct to consumer kits for sequencing the microbiome of the gut, skin, nose, mouth, pregnant vagina or non-pregnant vagina, and male genitals. Using next generation barcode DNA pyrosequencing, uBiome identifies the bacteria that reside in the biome of these sites (down to genera) and quantifies their relative abundances.

We are all unique and so are our microbial signatures. Have you ordered uBiome kits? I have kits on auto-order every 1-2 months. It’s fun, #QS (quantified self) and full of insights! 10% off uBiome kits coupon.

Click HERE to see the Phylogenetic Tree App.  JSON data from AmGut and BritGut are accepted also.

ready in 6 steps

Here is an example from my uBiome data March 2015. Faecalibacterium, Roseburia, Bacteroides and Bifidobacteria are a few of the key ancestral core microbiota that are naturally found in nearly all healthy guts and is lacking in suboptimal guts. Below is my phylogenetic tree of the uBiome data which shows robust abundance of known anti-inflammatory and butyrate-producing gut flora in the Clostridiales group: Faecalibacterium, Roseburia, Blautia and Pseudobutyrvibiro. My diet at the time was moderate fiber ~30 g/day, beets, green apples, brown rice+ Paleo, glucomannan 5 g/day and soil based/bifido probiotics.

GL Clostridiales

My uBiome Phylogenetic Tree for Robust Butyrate Producers in Clostridiales (Faecalibacterium, Roseburia, Blautia, Pseudobutyrvibrio)

With weight loss and improved gut health, Faecalibacterium, Bifidobacteria, Akkermansia and Bacteroides often bounce up in gut microbiota studies. For me, Bifidobacteria was nearly non-existent in 2013. I used probiotics and Bionic Fiber to get them to start re-sprouting back to life at a level of 0.017% Bifidobacteria (with the majority over 70% being the anti-obesity and longevity strain known as Bifidobacteria longum at 0.012%). The overall Bifidobacteria longum appears to struggle. But as its populations have increased I have noticed health improvements appear to track along with it, such as ease with fat loss, better dairy tolerance and the ability to eat gluten again (occasionally) without abdominal bloating something that I haven’t been able to enjoy since the 2007.

On uBiome tests that people send to me, frequently and sadly, I observe ‘zero/undetectable’ for both or either Bifidobacteria or Bifidobacteria longum. I’m not sure why but I suspect many modern factors such as multiple courses of antibiotics, genetic factors such as FUT2 (I have this), and chronic illnesses (obesity, autoimmunity, subclinical gut infections, gastroenteritis, etc). Oligosaccharide-preferring Bifidobacteria longum has many besides benefits leanness and longevity. Other bifido are vastly different; they consume starch (Bifidobacteria animalis, Bifidobacteria adolescentis) and high relative abundance is highly correlated with celiac, gluten and food intolerances, atopy, obesity, autoimmunity, senile dementia, colorectal cancer, IBD and diverticulitis.

Both Matt Pepin, co-host of the Gut Guardians podcast, and I used Renew Life BifidoMax probiotics and others to restore Bifidobacteria longum and other vital populations. Here is Matt’s uBiome results. Restoration of some decent bifidobacteria after multiple rounds of antibiotics are evident.

What I love about tracking these changes is that I can observe shifts in the gut microbiota and see how they relate to adjustments in sleep, exercise, bionic fiber supplements and diet. I did two gut tests within a few days of each other in March 2015: uBiome and Genova. The Genova test confirmed the burgeoning recovery in Bifidobacteria and Bifidobacteria longum by both qPCR and culture. 

GL Bifido

GL bacteroidesuBiome March 2015: My Phylogenetic Tree for Bifidobacteria and Bacteroides

GL GDX qPCR BIFIDO

March 2015: Genova qPCR Stool Evaluation of Bifidobacteria and Bifidobacteria longum

GL GDX stool PCR and culture

March 2015: Genova Diagnostic Stool and Culture Test. Bifido culture results.

Recently Eli Markstrom, a Spartan warrior competitor, used uBiome stool kits to track his progress in biohacking his health and skin-gut goals such as reducing acne. As extra side benefits, Eli has seen dramatically shifted sleep, elimination of knee pain, buffering in dairy and gluten food intolerances, and eradication of digestive woes. For PaleFx Conference presentation slides of his uBiome changes, please enter information (for newsletter).

References

Wacklin, Pirjo et al. “Faecal microbiota composition in adults is associated with the FUT2 gene determining the secretor status.” PLoS One 9.4 (2014): e94863.
Lewis, Zachery T et al. “Maternal fucosyltransferase 2 status affects the gut bifidobacterial communities of breastfed infants.” Microbiome 3.1 (2015): 13.
Wacklin, Pirjo et al. “Secretor genotype (FUT2 gene) is strongly associated with the composition of Bifidobacteria in the human intestine.” PLoS One 6.5 (2011): e20113.
Remely, M et al. “Gut microbiota composition correlates with changes in body fat content due to weight loss.” Beneficial microbes (2015): 1-9.
Salazar, Nuria et al. “Inulin-type fructans modulate intestinal Bifidobacterium species populations and decrease fecal short-chain fatty acids in obese women.” Clinical nutrition 34.3 (2015): 501-507.
Dewulf, Evelyne M et al. “Insight into the prebiotic concept: lessons from an exploratory, double blind intervention study with inulin-type fructans in obese women.” Gut (2012): gutjnl-2012-303304.
Simpson, HL, and BJ Campbell. “Review article: dietary fibre–microbiota interactions.” Alimentary pharmacology & therapeutics (2015). PDF.
Grönlund, M‐M et al. “Maternal breast‐milk and intestinal bifidobacteria guide the compositional development of the Bifidobacterium microbiota in infants at risk of allergic disease.” Clinical & Experimental Allergy 37.12 (2007): 1764-1772.
Collado, Maria C et al. “Imbalances in faecal and duodenal Bifidobacterium species composition in active and non-active coeliac disease.” BMC microbiology 8.1 (2008): 232.
Gore, Claudia et al. “Bifidobacterium pseudocatenulatum is associated with atopic eczema: a nested case-control study investigating the fecal microbiota of infants.” Journal of Allergy and Clinical Immunology 121.1 (2008): 135-140.
Moro, Guido et al. “A mixture of prebiotic oligosaccharides reduces the incidence of atopic dermatitis during the first six months of age.” Archives of disease in childhood 91.10 (2006): 814-819.
Gueimonde, Miguel et al. “Qualitative and quantitative analyses of the bifidobacterial microbiota in the colonic mucosa of patients with colorectal cancer, diverticulitis and inflammatory bowel disease.” World journal of gastroenterology: WJG 13.29 (2007): 3985-3989.