Another project suggestion: oral weathermaps

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Andrew Hessel

Feb 15, 2009, 2:02:56 PM2/15/09
Last week, I was at the dentist.  These trips haven't changed much since I was a child:  X-rays, oral inspection, cleaning with metal pick and floss, fluoride rinse, admonition about brushing, flossing, etc, and a freebie toothbrush.

My dental clinic seems like a well-run car dealership.  I'm getting regularly scheduled maintenance but little more.  The focus is prevention, managing expectations and, ultimately, mediocre care.

Teeth are complex, living structures.  And they aren't alone.  The mouth is colonized by bacteria shortly after birth.  They grow easily there, feeding on the plentiful sugars and other foods to found there.  To a bacteria, each tooth is an entire planet, with a population of billions.

Bacteria form complex ecosystems on their teeth-planets.  There are hundreds of species known considered "normal flora" in the mouth; these were identified by culturing, which means there may be 10X or 100X more, plus viruses and fungi.  It is these microorganisms that ultimately determine whether one has cavities, health gums, bad breath, etc.

Saliva helps control microbial growth.  Brushing and flossing helps knock back the population numbers to a more manageable level.  Still, the bacteria have formidable defenses, including the ability to organize into biofilms that are very resistant to chemical or mechanical attack.  They also swap genes all the time.

Most dentists recognize Streptococcus mutans, which converts sugar to acids that can attack enamel, as a prominent microbial cause of cavities.  But what about gingivitis, periodontal disease, or even foul breath?  Chances are good there are complex ecosystems that haven't been teased apart yet with modern gene-based identification technologies.

I propose a DIYbio oral weathermap, something along these lines:

1.  Brushing of teeth with a moistened brush (no toothpaste) then spitting into a commercial spit kit.

2.  The 16S ribosomal RNA genes amplified and sequenced.  The species and relative proportions thereof could be determined, produce a "weathermap" of bacteria.  (We might be able to find a sponsor for this work, given it has downstream commercial applications.)

3.  Correlate results to known oral histories.  We could get copies of our dental charts if necessary.  Mouths with health gums and no cavities would represent the gold standard "balance" of bacteria, while bacterial patterns that correlate with high cavities or more serious diseases would flag the mouth for more vigilant attention, or possible treatment.

4.  Time-course studies could be done.  How do the numbers change over a typical day in a normal mouth?  In a cavity prone mouth?

5.  Explore treatment considerations, eg alternatives for balancing the oral flora back to a healthy mix in ways that ideally do not require lengthy approval processes.  We might think about what could be done with bacterocins, natural compounds, or peptides known to selectively knock back various species, block attachment (see the related 2008 MIT iGEM project here), or interfere with biofilm formation.

Anyone trained in dentistry out in DIY world? :)


Bryan Bishop

Feb 15, 2009, 2:15:27 PM2/15/09
On Sun, Feb 15, 2009 at 1:02 PM, Andrew Hessel wrote:
> I propose a DIYbio oral weathermap, something along these lines:

Yesterday there was this huge, massive oral weather storm when
millions of individuals embraced each other for valentine's day.
Kissing is an important and vital component of any diybio oral
weathermap initiative :-).

- Bryan
1 512 203 0507

Julie Norville

Feb 15, 2009, 2:58:34 PM2/15/09
This sounds like a good idea.


Feb 15, 2009, 6:56:17 PM2/15/09
Interesting idea Julie and Andrew,
I saw a video that might work into your idea. This guy, built a printer, I think you could user a regular inkjet printer, to spray or print small squares of DNA solution on glass. He took samples of every known virus and printed it on glass. He then took samples from someone's nose, mouth etc., multiplied the DNA, attach a florescent strand to the DNA and dip the glass in it. What ever glowed, since like DNA sticks to each other, showed what virus or viruses were found. It can be done for bacteria too. You could use the glass to quickly take samples of the commercial spit kit. 

Anyone trained in dentistry out in DIY world? :)


Andrew Hessel

Feb 15, 2009, 10:40:55 PM2/15/09
Yes, microarrays would work, but we'd have to know what we are looking for, since the probes would have to be designed.  Nimblegen arrays are fantastic, btw.
Andrew Hessel
Biostrategy consultant


Feb 15, 2009, 10:56:03 PM2/15/09
You could make the chip with what you find. You wouldn't have to predetermine what you are looking for. Of course I'm not sure how one would separate all the microbes to begin with.
You could do a sample of non-cavity and cavity mouths. Use what you find to put on a chip. Then find common microbes that exist between the two. You wouldn't even have to know what they were to begin with. Just find the matching microbes by matching the DNA. Once you have you the data then determine what the microbes are.
Just a thought.

Bryan Bishop

Feb 15, 2009, 10:59:16 PM2/15/09
On Sun, Feb 15, 2009 at 9:56 PM, Frankco wrote:
> You could make the chip with what you find. You wouldn't have to
> predetermine what you are looking for. Of course I'm not sure how one would
> separate all the microbes to begin with.

That would be by shuffling around samples within the diybio community,
as well as trained microbe watchers who read from books and technical
manuals on microbe microscopic identification techniques.


Nov 30, 2014, 8:34:50 PM11/30/14
Hey, I know this thread is old, but I'm very interested in this project idea, especially when combined with other CAMBRA or preventative dentistry methods. Did anything come of this project? If so please let me know!

Brian Degger

Dec 9, 2014, 7:34:30 AM12/9/14
We can start with the literature/database already in existence ;)

The goal of creating the Human Oral Microbiome Database (HOMD) is to
provide the scientific community with comprehensive information o­n
the approximately 700 prokaryote species that are present in the human
oral cavity. Approximately 49% are officially named, 17% unnamed (but
cultivated) and 34% are known o­nly as uncultivated phylotypes. The
HOMD presents a provisional naming scheme for the currently unnamed
species so that strain, clone, and probe data from any laboratory can
be directly linked to a stably named reference scheme. The HOMD links
sequence data with phenotypic, phylogenetic, clinical, and
bibliographic information. Genome sequences for oral bacteria
determined as part of this project, the Human Microbiome Project, and
other sequencing projects are being added to the HOMD as they become
available. Genomes for 315 oral taxa (46% of taxa o­n HOMD) are
currently available o­n HOMD. The HOMD site offers easy to use tools
for viewing all publically available oral bacterial genomes. Welcome!

Primary Investigators: Tsute Chen, Floyd E. Dewhirst, Jacques Izard,
Bruce J. Paster, Anne Tanner, and William G. Wade

Current Research Contributors: Alice Kirega, Sonia Vartoukian, and Larry Yang
Past Research Contributors: Oxana Baranova, Jessica Blanton, Derrick
Fouts, Akila Ganesan, Erin Klein, Abby Lakshmanan, Cori Leonetti,
Emmanuel Mongodin, Alexandra Rybalka, Derek Spencer, Hayley Thompson,
Griffin Weigle, and Wen-Han Yu

This project is supported by: Grant R37-DE016937 "A Foundation for the
Oral Microbiome and Metagenome" from The National Institute of Dental
and Craniofacial Research
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Brian Degger
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