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.)

10 thoughts on “Looking into my mouth microbiome

  1. Pingback: 1p – One man bravely opens his mouth for us all to see his oral microbiome | Profit Goals

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  3. judith

    Really happy to find all this. I have been trying to understand the notion of ‘healthy biome(mouth included)for a while now so this is magic stuff. I have just spent the best few hundred quid of my life having my amalgam fillings removed(safely by the only dentist in glasgow with the knowledge and equipment) and am now on a quest to reintroduce the wildlife that should be in my mouth.Love you pioneers-will follow with bated breath(tee hee)

  4. Dr. Thornell at our dental practice- SmileWide Dental Care in Herriman, Utah has been recommending a new slightly unusual mouth rinse called “Closys” due to it being extremely effective at reducing and eliminating bacteria of all types in the mouth. Check it out! It’s practically tasteless.

    1. Alexandra Carmichael

      Fascinating, Tina! Would you like to run a study at your practice to see how Closys actually impacts the mouth microbiome?

  5. vicki

    How does the fact that different places in the mouth have different bacteria affect the interpretation of the results? the inside of the cheeks, the teeth, the gums, the top of the tongue, and the sides of the tongue all harbor different bacteria. For the uBiome test, they instruct to only swab the inside of the cheeks, and to avoid teeth etc. Assuming one can follow the instructions adequetely (not always easy), did the research you refer to specifically address cheek cell bacteria? I could easily so some of those risk referring more to gums or teeth rather than cheek, and this would lead to incorrect interpration of data – so for example, you may think youre in the clear by not having a certain kind of strep – but it could still be in your gums or teeth, just not your cheek.

  6. Gary Doolen

    I was using Closys (toothpaste & mouth rinse) for about 2 years. Recently, my dentist, Dr. Brookover in Los Alamos, NM,
    has had me switch to DioxyRinse mouth rinse and DioxyBrite toothpaste. DioxyRinse is advertised as
    containing DioxyCare ‘The Active Chlorine Dioxide System. Both DioxyRinse and DioxyBrite require mixing of
    equal parts in order to activate the chlorine dioxide.
    The DioxiBrite label says it ‘Kills germs That Cause Bad Breath!’ and that it is:
    Exceptional Cleaner and Whitener
    Neutralizes Orders
    Removes Biofilm
    Helps strengthen Enamel

    I would be quite interested in a study to see how these actually impact the mouth microbiome.
    Is anyone willing to do this? Destroying all bacteria might be quite counterproductive.

    For questions, DioxiBrite’s label lists the email address: info@dentalhealthinstitute.com.
    It also lists the website: http://www.dentalhealthinstitute.com
    Dental Health Institute (DHI), Walpole, MA 02081

  7. Gottfried Brieger

    Your comment regarding Capnocytophaga makes me think that if you can establish a link between a compromised immune system and the oral biome, this could be a useful analytical method.

  8. Was your data the regular rRNA sequencing done by uBiome? It seems to me that the taxonomic information presented here is way more precise than the rRNA data from uBiome is able to assign. I like the presentation on the uBiome website for my data because it usually stops at the genus level classification. But you have here things that are incredibly precise assignments like Peptostreptococcus sp. oral clone FL008. I don’t think it is possible for such assignments to be made accurately with the rRNA data. Or did you have metagenomic sequencing done? If not, I would really recommend using higher level classifications only.

  9. Laura Henze Russell

    The mouth (oral cavity) is key, because it is where our teeth reside, and also where our food and drink enters, and begins the digestive process. I have begun a call to integrate dental into medical care and dental records into medical records. Ubiome may provide another way into this challenge and opportunity.

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