Oral microbiota transplant

[Frank]

Any dentists, periodontists, or dental school students out there willing to participate in a safe and exciting experiment? It involves taking  a small amount of dental plaque from a healthy donor who is relatively free of caries and shows no signs of periodontal disease, then putting that plaque into the mouth of a recipient (who does suffer from PD). This would be done with the purpose of having the donor plaque bacteria colonize the recipient's mouth.

please let me know

[Inigo Howlett]

cool idea, sadly I'm not a dentist

[Frank]

i wonder if there's a training video somewhere for dentists on how to remove plaque for cleaning? For this purpose it can't be that difficult. 

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[Dakota Hamill]

A toothpick would do? Or buy a set of those metal tools dentists use.
Or make out with someone without PD? Or culture a healthy oral
microbiota of someone and make a probiotic toothpaste and brush with
it.

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[Frank]

Yes I have thought along those lines but since I am not a dentist I am
not sure of things like which location can the plaque come from such as
above or below the gum line? how must the plaque be handled in order to
keep the "good bacteria" alive? does it matter where and how to apply
the plaque to the recipient's mouth? just moving scraped plaque through
the air will likely kill off a bunch of the sample as will conditions in
the recipient's mouth such as ph, and the microbiota present there. so,
for example, how deep cleaned must the recipient's mouth be? Everyone
seems to agree with the principle of transplanting healthy oral biofilm
to a diseased mouth. I'm not sure we have figured out the details of
how to optimally do it. The good thing it that there is probably room
for error without danger of injury. so any input is valuable.

------ Original Message ------
From: "Dakota Hamill" <dko...@gmail.com>
To: "diy...@googlegroups.com" <diy...@googlegroups.com>
Sent: 3/17/2021 10:10:49 AM
Subject: Re: [DIYbio] Re: Oral microbiota transplant

>A toothpick would do? Or buy a set of those metal tools dentists use.
>Or make out with someone without PD? Or culture a healthy oral
>microbiota of someone and make a probiotic toothpaste and brush with
>it.
>
>On Tue, Mar 16, 2021 at 11:01 PM Frank <fgarc...@gmail.com> wrote:
>>
>> i wonder if there's a training video somewhere for dentists on how to remove plaque for cleaning? For this purpose it can't be that difficult.
>>
>> ------ Original Message ------
>> From: "Inigo Howlett" <inigowalk...@gmail.com>
>> To: "DIYbio" <diy...@googlegroups.com>
>> Sent: 3/16/2021 10:28:18 PM
>> Subject: [DIYbio] Re: Oral microbiota transplant
>>
>>
>> cool idea, sadly I'm not a dentist
>> On Thursday, March 11, 2021 at 5:55:26 PM UTC-5 Frank wrote:
>>>
>>> Any dentists, periodontists, or dental school students out there willing to participate in a safe and exciting experiment? It involves taking a small amount of dental plaque from a healthy donor who is relatively free of caries and shows no signs of periodontal disease, then putting that plaque into the mouth of a recipient (who does suffer from PD). This would be done with the purpose of having the donor plaque bacteria colonize the recipient's mouth.
>>>
>>> please let me know
>>
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>> Learn more at http://www.diybio.org

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>

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[Frank]

thanks! so what if you're not a dentist , some of this is common sense or basic science so any feedback is welcome

------ Original Message ------

From: "Inigo Howlett" <inigowalk...@gmail.com>

To: "DIYbio" <diy...@googlegroups.com>

Sent: 3/16/2021 10:28:18 PM

Subject: [DIYbio] Re: Oral microbiota transplant

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[Tom De Medts]

Frank,

A quick Google search for 'oral microbiota transplant' yielded at least 2 relevant hits:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5828680/

https://bmcoralhealth.biomedcentral.com/articles/10.1186/s12903-015-0109-4

My suggestion would be to figure out what has been done already, summarize it as would at a lab meeting, in 3-5 slides,

then figure out what has NOT been done yet, and proceed from there.

It's quite possible you've completed all of those steps already, in which case, I'd be curious to read your summary on

current state of the art and what you intend to do specifically...

i am assuming you'd want to perform NGS analyses of the 

healthy donor

recipient pre-transplant

recipient post-transplant (how many time points)

as you pointed out, from what specific dental location would the donor sample be obtained from?

as you also pointed out, to what specific dental locations would the donor samples be transplanted to?

So many questions.

Initially, when I read your brief one liner intro email, I was alarmed because I thought it's been established that

dental plaque is the same type of plaque that is responsible for arterial disease etc.

Then I realized 2 mistakes in my quick reading:

1. You are planning to transplant from healthy donor to diseased (PD) individual, NOT the other way around.

2. The jury is still out on whether plaque from PD is caused or simply correlated or not even that with respect to arterial plaque.

I am neither a dentist nor a medical doctor, but as a scientist I'd be very curious to know more about how your background research 

has molded your research hypothesis and protocol(s) thus far. Good luck!

- Tom

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[Frank]

To answer some of your  questions.

1. the jury is actually no longer out on the cause of PD. we know that gingivitis can be stable which means a healthy oral microbiome remains intact or it can progress to periodontal disease.  This begins with an inflammatory response to gingivsl bacteria.  but rather than end the inflammation as usual , the immune system which normally secretes lipid pro-resolving mediators, SPMs, such as resolvins, maresins, and lipoxins,  fails to do so and the inflammation becomes chronic.  inflammation destroys tissue. the  persistent Inflammation and pocket formation changes the bacterial growth environment that favors the emergence of 'periodontal pathogens' and alters the diversity and relative proportions of species leading to a a dysbiotic microflora. the dysbiotic subgingival plaque microbiome drives further inflammation which destroys tissue and perpetuates a dysbiotic milieu. Mutually reinforcement between unresolving inflammation and dysbiotic microflora perpetuates the disease.

it has now been shown that treating someone with PD with topical resolvins end the disease and results in bone regeneration.  But topical SPMs are not available.  you can, however, increase their synthesis by taking high dose omega-3.  combining that with an external  correction of the oral microbiota  could be enough to tip the  balance enough to significantly resolve the disease.

unlike many other experiments testing treatments, this is extremely safe. i can't think of  any dangers.  

As far as NGS, l am unfortunately not a millionaire so that's not happening. it's also not necessary.  the purpose of this experiment is to see if i notice a marked improvement in my PD.  I just had xrays and a periodontal evaluation . if i do this I would return to the dentist for and reevaluation. after a few months.

https://www.ncbi.nlm.nih.gov/sites/myncbi/1BWHziisucnQs/collections/60529863/public/

https://www.ncbi.nlm.nih.gov/sites/myncbi/1BWHziisucnQs/collections/60529852/public/

Best,

Frank

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[Tom De Medts]

Hi Frank,

Seems like you've given this topic quite some background research. Bravo! :)

Just curious if you've accounted for differential virome contributions to observed differences in dental health

For example, see this article - https://naturemicrobiologycommunity.nature.com/posts/61634-the-oral-virome-a-new-driver-in-periodontal-disease-and-periodontal-arthritis

This also makes me wonder if you will, and how you will screen donors for viral infection so as to prevent oral inoculation with an un-verified donor (sample)- self-reported, or tested?

Cheers!

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[Frank]

very good points and questions which i would  certainly be on the agenda in a wider experiment that had some resources. I am attempting simply to carry out a procedure that within narrow parameters of safety which most experts agree should  be relatively safe and also efficacious but which, as far I know hasn't yet been put into practice.  What makes this compelling for me is the combination of 5 factors:  

1. Immediate need to slow or halt periodontal disease 
2. High potential for significant improvement in periodontal disease progression
3. High safety profile - if basic rules are followed it is pretty safe
4. Only one or two treatments needed
5. Very low cost

I'm assuming periodontal professionals would be interested to see how that works out. They should be able to provide the details needed to design an adequate protocol. Those details would include 

• Donor selection criteria (oral characteristics and features, etc.)
• Plaque harvest sites
• Plaque harvest technique
• criteria for vehicle for the plaque such as gel
• Recipient preparation 
• Implant/placement method
• Post-transplant steps

If you can recommend a good way to find dental profession folks that would provide this type of feedback I'd appreciate it.

Here's an exerpt from a paper on the subject that proposes a protocol: 

"Pozhitkov and collaborators proposed to introduce health-associated oral microbiota into the oral cavity of periodontitis patients24. First, they confirmed that the microbiome of subjects with periodontitis were distinct from those of healthy or edentulous patients. Next, they tested an in vitro antimicrobial protocol to be used on the oral cavity of the recipient patient prior to OMT. It was shown that application of sodium hypochlorite (NaOCl) followed by its neutralization with sodium ascorbate buffer may be a valid option for suppressing the disease-associate microbiota to allow for a more pronounced microbial shift to a healthier microbiota. In that same study, the authors suggested an OMT procedure consisting of: (1) collecting sub- and supra-gingival plaque from a healthy donor (spouse or a partner), (2) performing deep cleaning, root planning and applying a broad-spectrum antimicrobial agent to the periodontitis patient, and finally (3) neutralizing the antimicrobial agent immediately following by a rinsing with a microbial suspension harvested from the healthy donor in the periodontitis patient24."

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5828680/

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[Tom De Medts]

Hi Frank,

Allow me to share a few thoughts, in no particular order:

1. I don't think dental professionals pr pharma might be the most motivated parties to provide an easy, cheap and long lasting fix that you are proposing :) 

I think medical insurance companies may be more motivated to pursue such work, because it means potential cost savings for them.

This is the same logic pharma will prefer to work on, for example, expensive cardiovascular drugs prescribed for a lifetime, versus 

cheap antibiotics that are prescribed for <= 1 week at time!

2. In terms of safety profile, I was reminded of how the use of antibiotics, specifically penicillin, saved so many lives in WW II and thereafter. However,

at the time, or even until much much later, we were blissfully ignorant of the potential for the evolution of multi drug resistant bacteria.

I mention this because it seems you are convinced about the safety profile of your proposed experiment, whereas, I am concerned about the possibility

of ill-health arising out of oral microbiome unknowns and unknown unknowns - I already pointed out to the possibility of virome caused pathologies.

I may be overthinking this, but I don't think I am :)

3. On one side of the coin, it is hard enough to recruit volunteers for a DIY project. Therefore, it helps if the safety profile of your experiment is very good.

But on the flip side of the coin, if something goes wrong due to your experiment, but those risks were not listed in your volunteer / recruitment consent form, 

then you might have exposure to litigation. We want to avoid these headaches, don't we? :)

4. In your protocol excerpt, what caught my attention was the suggestion of using spouse or partner as the donor in donor-recipient pairs.

Extending that a little bit, even within your nuclear or extended family, are you able to identify a healthy donor, and conduct the experiment where you ALONE are the recipient?

I realize n=1 may not be the experiment you want to perform, but this would be the smallest sized experiment, and if it is well designed and conducted,

it might even provide data to establish causality, as opposed to just correlation from an ever larger experiment.

5. We discussed how NGS of plaque might be too expensive to perform, and compare before and after samples of the recipient...vs donor sample,

However, If you detailed a project where N=1, and with close tracking of experimental intermediate time-points, not just the end-points, such data may help establish causality.

Such a proposed experiment might be worthy of submission to a funding agency to defray the costs of sequencing / consumables etc.

What sort of agencies? I am not sure, where you live / work etc., but here are some suggestions:

https://www.pacb.com/smrt-science/smrt-grant/

https://www.dnagenotek.com/US/company/programs/grants-contests/gut-microbiome-grant-program.html (program closed, and was for gut, but no harm in asking?)

https://microbe.med.umich.edu/opportunities/faculty-postdoctoral/2021-microbiome-research-pilot-grant-opportunity (not sure if open to outsiders)

https://www.nidcr.nih.gov/grants-funding/grant-programs/oral-microbiota-bacterial-disease-program - directly relevant, and may help to say hi to Tamara McNealy directly and make your inquiries

https://hmpdacc.org - not sure how much of this is focused only on the gut component...

https://www.openbiome.org - they have a stool bank in Mass, not sure if they are or will be interested in oral u-biome transplants...

6. There is an aspect to biofilm in all microbial communities, and I have not explored whether there might be potential collaborators and funders for DIY projects on this topic.

7. "If you can recommend a good way to find dental profession folks that would provide this type of feedback I'd appreciate it."

I think your best resources are the corresponding authors of papers that are most relevant to your proposed study.

However, having spent nearly 2 decades in tier 1 universities in the US, I will suggest that you strike a relationship with these people

via a progression of emails, starting with simple questions about their work, and importantly learning why and what the 

challenges are in conducting the experiments you are proposing. Rather than saying you want to explore this, it may be better

to ask why they have not pursued such experiments.... After all, if your proposed experiments are such no-brainers, then why have they not been 

performed / reported for a large cohort yet? For DIYbio projects, I think it's sometimes MORE important to understand why entities with more 

resources have NOT conducted those studies. As a DIYer with much less time, energy and $$ than academia and corporates, I would take a bigger hit

if I ignored the challenges / obstacles that bigger player(s) face(d).

8. Who could help you with the dental transplant protocol?

Unfortunately, I don't know and have no idea. Had some extremely lateral ideas, but not sure if and how any of them might work, will list them below anyways:

• Association of dental hygienists - https://www.adha.org?
  
• A maverick dentist, like Patch Adams was to general physicians? BTW, Dr. Adams is still alive and well (link), may be you can ping him to find some maverick dentists? :)
  
• How about in a veterinary context? Extrapolatable to humans? (but you want this to work for you, right? - may be a bad suggestion, sorry)
  
• health or dental insurance company ? https://www.deltadental.com

I know I may NOT be helping you with the answers you seek, and this long email from me may even sound very negative and discouraging, but that is NOT AT ALL my intention.

I'd rather have you see the pitfalls now and succeed later, than paint some rosy picture that ignores future challenges. To reiterate, I do want you to succeed :)

Cheers!

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/em53682345-f0cc-47d8-ab74-60a3c16ccf86%40cabron.

[Frank]

thank you for taking so much time to answer my comments. 

answers below

------ Original Message ------

From: "Tom De Medts" <tdm...@gmail.com>

To: "DIYbio" <diy...@googlegroups.com>

Sent: 3/22/2021 1:18:12 PM

Subject: Re: Re[4]: [DIYbio] Re: Oral microbiota transplant

Hi Frank,

Allow me to share a few thoughts, in no particular order:

1. I don't think dental professionals pr pharma might be the most motivated parties to provide an easy, cheap and long lasting fix that you are proposing :) 

I think medical insurance companies may be more motivated to pursue such work, because it means potential cost savings for them.

This is the same logic pharma will prefer to work on, for example, expensive cardiovascular drugs prescribed for a lifetime, versus 

cheap antibiotics that are prescribed for <= 1 week at time!

agreed. even more poignant is the twenty years it has taken to do something with the discovery of SPMs - proresolving mediators which have been shown to practically eliminate PD . if widely used  it would put a big dent in the lucrative implant business. 

2. In terms of safety profile, I was reminded of how the use of antibiotics, specifically penicillin, saved so many lives in WW II and thereafter. However,

at the time, or even until much much later, we were blissfully ignorant of the potential for the evolution of multi drug resistant bacteria.

I mention this because it seems you are convinced about the safety profile of your proposed experiment, whereas, I am concerned about the possibility

of ill-health arising out of oral microbiome unknowns and unknown unknowns - I already pointed out to the possibility of virome caused pathologies.

I may be overthinking this, but I don't think I am :)

it's about risk vs benefit. as a sufferer of chronic periodontal disease who has an inflammatory phenotype and several other chronic-inflammation related conditions, the potential benefits of this procedure far outweigh the risks.

3. On one side of the coin, it is hard enough to recruit volunteers for a DIY project. Therefore, it helps if the safety profile of your experiment is very good.

But on the flip side of the coin, if something goes wrong due to your experiment, but those risks were not listed in your volunteer / recruitment consent form, 

then you might have exposure to litigation. We want to avoid these headaches, don't we? :)

due to the nature of this procedure, the recipient bares almost all the risk. I will be the recipient, no one else, and I accept the risks.

4. In your protocol excerpt, what caught my attention was the suggestion of using spouse or partner as the donor in donor-recipient pairs.

Extending that a little bit, even within your nuclear or extended family, are you able to identify a healthy donor, and conduct the experiment where you ALONE are the recipient?

I realize n=1 may not be the experiment you want to perform, but this would be the smallest sized experiment, and if it is well designed and conducted,

it might even provide data to establish causality, as opposed to just correlation from an ever larger experiment.

interestingly, my parents and all but one sibling are free of both PD and dental caries. My mother who is in her 80's has every natural tooth still in her mouth, no caries, and has always had a fairly casual oral hygiene regimen. the question of why I am different is a good one but the subject of a different discussion. 

5. We discussed how NGS of plaque might be too expensive to perform, and compare before and after samples of the recipient...vs donor sample,

However, If you detailed a project where N=1, and with close tracking of experimental intermediate time-points, not just the end-points, such data may help establish causality.

Such a proposed experiment might be worthy of submission to a funding agency to defray the costs of sequencing / consumables etc.

What sort of agencies? I am not sure, where you live / work etc., but here are some suggestions:

https://www.pacb.com/smrt-science/smrt-grant/

https://www.dnagenotek.com/US/company/programs/grants-contests/gut-microbiome-grant-program.html (program closed, and was for gut, but no harm in asking?)

https://microbe.med.umich.edu/opportunities/faculty-postdoctoral/2021-microbiome-research-pilot-grant-opportunity (not sure if open to outsiders)

https://www.nidcr.nih.gov/grants-funding/grant-programs/oral-microbiota-bacterial-disease-program - directly relevant, and may help to say hi to Tamara McNealy directly and make your inquiries

https://hmpdacc.org - not sure how much of this is focused only on the gut component...

https://www.openbiome.org - they have a stool bank in Mass, not sure if they are or will be interested in oral u-biome transplants...

6. There is an aspect to biofilm in all microbial communities, and I have not explored whether there might be potential collaborators and funders for DIY projects on this topic.

7. "If you can recommend a good way to find dental profession folks that would provide this type of feedback I'd appreciate it."

I think your best resources are the corresponding authors of papers that are most relevant to your proposed study.

However, having spent nearly 2 decades in tier 1 universities in the US, I will suggest that you strike a relationship with these people

via a progression of emails, starting with simple questions about their work, and importantly learning why and what the 

challenges are in conducting the experiments you are proposing. Rather than saying you want to explore this, it may be better

to ask why they have not pursued such experiments.... After all, if your proposed experiments are such no-brainers, then why have they not been 

performed / reported for a large cohort yet? For DIYbio projects, I think it's sometimes MORE important to understand why entities with more 

resources have NOT conducted those studies. As a DIYer with much less time, energy and $$ than academia and corporates, I would take a bigger hit

if I ignored the challenges / obstacles that bigger player(s) face(d).

All this makes sense if I were simply interested in conducting an experiment that has nothing to do with me personally. This is a case where I actually have a need to address my own PD sooner rather than later. There is a real time issue, not enough time for what you suggest. However, if a quick and dirty approach were to succeed then I think I would have more leverage to pursue a more proper experimental process to repeat the procedure according to best practices.  Thus, if I don't find the input I'm seeking soon I may go ahead and rely on common sense and my own medical knowledge and hope for the best.  

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