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Monday, March 02, 2009

Bacteria in Your Mouth

A paper examining the diverstiy of human salivary bacteria has recently appeared in the journal Genome Research (Nasidze et al. 2009).

The authors looked at 120 individuals from different locations all over the world. They extracted DNA from their saliva and isolated small fragments of DNA copied from a highly variable region of 16S ribosomal RNA. On average, they sequenced 120 different DNA fragments from each individual. After eliminating artifacts they were left with 14,115 fragments.

The DNA sequences were compared with a large database of bacterial sequences in order to identify the bacterial species present in the mouths of each person. In most cases it was possible to positively identify the genus although they did find 196 sequences that were not in the database. These are probably unknown species of bacteria.

ResearchBlogging.orgThere were 101 different types of bacteria (genera). Each person has between six and thirty different species of bacteria in their mouth. There are about 45 different genera in each location (e.g. Bolivia, Congo, China, California, Germany, etc.).

Some genera were seen only once while others are quite common. The most common ones are listed below.

Actinomyces: Actinomyces are rod-shaped, gram positive bacteria that can survive under both aerobic (oxygen) and anaerobic conditions. Such bacteria are called facultative anaerobes. A. naeslundii forms dental placque by adhering to the surface of your teeth.

Enterobacter: Enterobacter species belong to the γ-proteobacteria group of gram negative bacteria. They are facultative anaerobes. Enterobacter are related to Escherichia coli—no examples of E. coli were found in this study.

Fusobacterium: These are gram negative, anaerobic, bacteria that are normal inhabitants of the oral cavity. They cause periodontal disease under some (unknown?) circumstances .

Granulicatella: The Granulicatella species belong to the phylum Firmicutes. They are gram positive bacteria related to Streptococcus.

Haemophilus: These species belong to the γ-proteobacteria as well. They are rod-shaped, gram negative bacteria related to E. coli.

Leptotrichia: The Leptotrichia species are long, filamentous, gram negative, anaerobic, bacteria in the Bacteroides group.

Neisseria: Neissria is a genus in the β-proteobacteria group. They are usually small, aerobic, bacteria. N. gonorrhoeae causes gonorrhea and N. meningitidis causes meningitis but most of the species in your mouth are harmless.

Porphyromonas: These are gram negative, anaerobic, members of the Bacteriodes group. P. gingivalis is normally harmless but it can cause periodontal disease.

Prevotella: Prevotella species are gram negative, rod-shaped, anaerobic, bacteria closely related to Bacteriodes. They are among the most common bacteria in the intestines of sheep and cattle where they aid digestion.

Rothia: These gram negative bacteria belong to the phylum Actinobacteria. They are related to micrococcus.

Serratia: These are motile, rod-shaped, gram negative bacteria. S. marcescens grows in bathrooms where it is often found on tile grout. The bacteria produce a characteristic red pigment and that's why contaminated areas appear pink.

Streptococcus: Streptococcus species are small, gram negative, nonmotile, and round. They are mostly facultative anaerobes. Individual bacteria associate in long chains. It is the most common genus in mouth cultures.

Vellionella: These common species are gram negative, anaerobic cocci.

There are problems with bacterial phylogeny, especially with a classification that relies exclusively on the sequences of ribosomal RNA [Bacteria Phylogeny: Facing Up to the Problems]. Reliable trees can be constructed using concatenated sequences and these trees (see below) reveal that the main groups of bacteria diverged from each other billions of years ago.

(You can see a high resolution image here.)

Note that the Firmicutes (red) are on the same branch as Actinobacteria (olive green) but these two groups are still as distantly related as dogs and dandelions. The α-proteobacteria (orange) are also very distantly related. The diversity of bacterial species in your mouth is truly remarkable.

Stoneking's group was interested in the differences between humans and especially between groups living in different parts of the world. Stoneking was one of the original authors on the Mitochondrial Eve paper so I suspect he was looking for bacterial markers that he could use to trace human ancestry.

Unfortunately, there isn't much difference between individuals or between groups from different parts of the world. The most significant geographical variation is between the samples from the Congo and everyone else. People in the Congo have a higher percentage of Enterobacteria. The only other significant difference is that there tend to be fewer Prevotella in people from Louisiana.

The somewhat surprising conclusion is that diet, culture, and environment don't seem to play much of a role in the diversity of the human salivary microbiome.

Nasidze, I., Li, J., Quinque, D., Tang, K., and Stoneking, M. (200() Global diversity in the human salivary microbiome. Genome Res. Published in Advance February 27, 2009, [doi:10.1101/gr.084616.108] [Genome Research]

I. Nasidze, J. Li, D. Quinque, K. Tang, M. Stoneking (2009). Global diversity in the human salivary microbiome Genome Research DOI: 10.1101/gr.084616.108


  1. This is quite interesting to me. I haven't seen the paper yet, but the list of bacteria present does include the ones that I am working with, ammonia oxidizing bacteria. I think their more usual niche is on the external skin where they suppress many heterotrophic bacteria by interfering with biofilm formation and quorum sensing.


    As we know, biochemists and other biologists have yet to propose a credible theory of the origin of life. The failure to solve this problem is also a failure to refute creationist mythology fully.

    The March 2009 (84.1) Quarterly Review of Biology contains a review, by Harold Morowitz, of a new collection of papers edited by Piet Herdewijn and M. Volkan Klsakürek, Origin of Life: Chemical Approach

    Of the papers, Morowitz writes:

    "This is a book that will test the chemical knowledge of biologists, while providing a rich variety of pathways to explore in thinking about the origin of the biosphere. It may tempt others to ask the Popperian question of how we can render the scenarios vulnerable to testing or how we can develop conceptual insights to prune the plentiful array of possibilities presented in this work."

  3. Hi i was wondering if you could help me. I'm a high school student, and I am doing a science fair project on the effect of fake sugars on the bacteria in your mouth. I am completely lost on which bacteria to choose or which bacteria will work the best. I'm sorry to be bothering you, but no one else is very helpful.

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  5. Hi sir... I'm a pharmacy student and were having our research on antibacterial mouthwash.. we are going to use staphylococcus and E.coli as our test organism to have a representative gram (+) & (-) bacteria in our assay for the effectiveness of the mouthwash.. We need your comment to improve our study, your suggestions will be much appreciated. My email ad.. ( )we are hoping for your kind response. :) Thank you!

  6. There are three bacteria mis-identified as Gram Negative that are actually Gram Positive:
    Rothia, Micrococcus, and Streptococcus.