Looking into my mouth microbiome

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 RuBiome 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:

OctMouth[grepl("Streptococcus",OctMouth$tax_name),]$tax_name

## [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 gobbleygook 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.