Announcing the uBiome Smoking Study on the Oral Microbiome


uBiome Seeks Citizen Scientists to Explore Smoking’s Effect on Mouth Bacteriasmokingstudy

uBiome, the leading microbial genomics company, seeks smokers, ex-smokers, and non-smokers to take part in a free ground-breaking study investigating the effects of tobacco smoking on the mouth’s microbial make-up.


San Francisco, California – July 15th, 2015 – Although tobacco use in the United States is in slow decline, almost one in five adults is a smoker. While a great deal has been learned over the past fifty years about smoking’s serious health implications, it has only recently become feasible to investigate its impact on the oral microbiome. Biotech startup uBiome is giving smokers, ex-smokers, and non-smokers the chance to contribute to important research while also receiving their individual data showing the bacterial composition of their own mouth. Study participants will get a free at-home, mail-in mouth testing kit. They will also learn how their microbiome compares to those of other smokers, non-smokers, and ex-smokers.

How to take part in the study:

The microbiome consists of the bacteria living in and on the human body, making up between three and six pounds of an individual’s overall weight. Bacteria can be both helpful and harmful. They play a crucial role in digesting food and synthesizing vitamins. However, they also contribute to serious issues such as autoimmune disorders, diabetes, heart conditions, bowel conditions, and skin conditions. The bacteria which make up the human microbiome are distributed across many different parts of the body – in the gut, ears, nose, genitals or mouth, for instance. The mouth alone can be home to around 1,000 different bacterial species.

Oral bacteria can cause tooth decay and gum disease, with figures showing that nearly 42 percent of periodontitis (gum disease) in the United States is attributable to tobacco smoking. There may be other links between smoking and the microbiome. For example a recent study by University Hospital Zurich suggested that the gut microbiomes of ex-smokers differ from those of smokers in a way which might partly account for the weight-gain often seen when people stop smoking. Potential weight-gain is a frequently cited reason for smokers refusing to give up, so understanding more about the interrelationship between bacteria, smoking, and weight change would be invaluable.

Jessica Richman, co-founder and CEO of uBiome, says the tobacco smoking study has significant potential. “Despite the known health risks, about 42 million Americans smoke. One way or another we’re all affected by smoking. Everyone either knows a smoker or is one themselves. We need to know more than we do, so this crucial study will shine a light on some of the unknowns. What difference does it make to the oral microbiome, for instance, if someone took up smoking as a teenager rather than coming to it later in life?”

Almost eighteen of every 100 U.S. adults aged 18 years or older currently smoke cigarettes. Although smoking rates in the U.S. have halved since 1964, the rate of decline has slowed. Smoking dropped from nearly 21 of every 100 adults  in 2005 to nearly 18 of every 100 adults in 2013. Cigarette smoking is the leading cause of preventable disease and death in the United States, accounting for more than 480,000 deaths every year, or 1 in 5 of all deaths.

Dr. Zachary Apte, CTO and co-founder of uBiome, says the oral microbiome samples from smokers, ex-smokers and non-smokers will be scrutinized in the company’s state of the art laboratory. “Just ten years ago it would have cost millions of dollars to analyze just one single person’s microbiome. Our sequencing service, based on research from the NIH Human Microbiome Project, can now do it for $89. For the first time, this makes large-scale research like uBiome’s new smoking study possible.”

uBiome’s mission is to use big data to understand the human microbiome by giving consumers the power to learn about their bodies, perform experiments, and see how current research studies apply to them. uBiome was launched in 2012 by UCSF scientists and Stanford and Cambridge technologists after a crowd-funding campaign raised over $350,000 from citizen scientists, roughly triple the initial goal. uBiome is now funded by Andreesen Horowitz, Y Combinator, and other leading angel investors.

Those interested in participating in the uBiome tobacco smoking study and getting a free mouth microbiome kit can find details here:


Alexandra Carmichael

Looking into my mouth microbiome

I’m so excited to give you another of Richard Sprague’s insightful and pioneering posts about his personal microbiome investigation. Thank you for sharing your findings with us, Richard!

The gut biome is interesting enough, but bacteria colonize just about every part of the body, so recently I’ve been studying my uBiome mouth test results. The simple GitHub uBiome utilities I use for analyzing my gut will work for that too, so here’s a short example of how I did it:

First I loaded my uBiome data into two variables, one for each sample: June 2014 (junMouth) and the other from October 2014 (OctMouth), after a visit to my dentist.

Let’s see which species are new in the later (October) sample:

octToJunChange <- span=""> uBiome_sample_unique(OctMouth,junMouth)
##   count                        missing.tax_name
## 1  3640                  bacterium NLAE-zl-P562
## 2  2725                 Streptococcus sanguinis
## 3  2075               Capnocytophaga gingivalis
## 4  1969 Peptostreptococcus sp. oral clone FG014
## 5  1618                 Granulicatella adiacens

One of those species, Streptococcus sanguinis looks interesting. Wikipedia says this:

S. sanguinis is a normal inhabitant of the healthy human mouth where it is particularly found in dental plaque, where it modifies the environment to make it less hospitable for other strains of Streptococcus that cause cavities, such as Streptococcus mutans.

No cavities? Nice! More good news: this quick check confirms that I don’t have any S. mutans:

## [1] Streptococcus                      Streptococcus pseudopneumoniae    
## [3] Streptococcus sanguinis            Streptococcus constellatus        
## [5] Streptococcus anginosus group      Streptococcus sp. oral clone GM006
## [7] Streptococcus thermophilus         Streptococcus oralis              
## [9] Streptococcus gordonii            
## 250 Levels: [Eubacterium] sulci ... Veillonellaceae

Then I look at the species that disappeared (went extinct) between the two samples:

junToOctChange <- span=""> uBiome_sample_unique(junMouth,OctMouth)
##   count                        missing.tax_name
## 1  6034                Capnocytophaga granulosa
## 2  4153 Peptostreptococcus sp. oral clone FL008
## 3  3375         Prevotella sp. oral clone ID019
## 4  2691                   Streptococcus rubneri
## 5  1571                       Prevotella buccae

Anything in the genus Capnocytophaga is an opportunistic pathogen, so I say good riddance. Usually they’re fine, but if your immune system dips they can turn bad.

Streptococcus rubneri was discovered a couple years ago, so little is known about it.

Prevotella buccae is more interesting. It seems to be implicated in periodonal disease (yuk!) but that genus is involved too in breaking down proteins and carbohydrates.

Hard to say what’s really going on. Meanwhile, here are the biggest changes (increase) since the first sample:

junToOctCompare <- span=""> uBiome_compare_samples(junMouth,OctMouth)
##                                  tax_name count_change
## 64         Streptococcus pseudopneumoniae        62007
## 68         Veillonella sp. oral taxon 780         8065
## 41                       Neisseria oralis         4693
## 2  Abiotrophia sp. oral clone P4PA_155 P1         2308
## 28                 Granulicatella elegans         1987

Whoah! That first one, Streptococcus pseudopneumoniae, looks nasty! Wikipedia says it may cause pneumonia, though a recent medical journal says more hopefully that it “treads the fine line between commensal and pathogen”

…which is a scientific gobbledygook way of saying nobody has a clue. All the more reason to keep testing, submitting, and getting more data. I just sent two more kits to uBiome, and will let you know more as soon as I get back the results.

(This post was originally published here.)