I'm Dr. Josiah Zayner, former Scientist at NASA turned bioHacker who recently attempted a full-body microbiome transplant, Ask me Anything
My short bio: I recently attempted a full-body micrbiome transplant that was covered by Arielle Duhaime Ross and The Verge. My Ph.D. is in Molecular Biophysics where I studied protein and genetic engineering and then did a fellowship at NASA Ames in their Synthetic Biology program only to leave because I think Science is messed up in many ways. I am trying to change the way Science is done by things like DIY CRISPR, my BioHacking collective and company The ODIN and experiments like this full-body microbiome transplant.
Here is Part I of series of blog post I will be making covering some of the transplant
My Daily Questionaire during.before.after the experiment
Database of Samples to match in the plots below
A Principle Coordinates Analysis (PCoA) plot of my skin samples
PCoA plot of my Nose and Phlegm samples
My Proof: Here is my proof
I find this fascinating. My personal big four covering many ailments are inflammation (and immunomodulation), methylation, mitochondrial function, and endocrine balance which may be part of the cause of some of your problems. I believe that microbiome will eventually displace one of those. My question is have you had your 23andme done or some other gene testing done (perhaps you DIY'd that too) and did you do any before and after levels of inflammation factors, homocysteine, hormones, etc.?
Is it possible to test levels of horomones and homocysteine without a blood draw, lab and MDs orders? If so I should have perhaps thought bigger about those things. Yes, i have had 23andMe done I don't keep up with it much or trust it completely. The reliability of Genome Wide Association Studies has been called in to check alot. Or maybe just by me but I kind of view them with a healthy amount of skepticism and as the "microarray" of our times. But I am opinionated and not exactly an expert in that arena.
Not that I'm aware of. As far as the 23andme stuff, I've found digging through the raw data and fooling around on Google Scholar or SNPedia can give some insight. It will cross reference SNPs with papers. There are other third party tools. I agree with you somewhat on your views of the studies but it can't be totally bad and may give some leads. I think the big thing with microbiome problems are mediated through inflammation factors. As far as your other issues, methylation seems to be a factor particularly in bipolar. The methylation gene studies seems somewhat legit. I can dig up my methylation results to give you the main SNP numbers if you'd like.
Or you can use geneticgenie.org with raw data from 23andme. It's free and one of the tools I use.
I am being partly facetious. I just mean that the amount of power and associations in those studies can be pretty variable. I imagine you are correct about inflammation.
What are ways non scientists can help fix the problems you we in science? Thanks for doing the IAMA btw.
I think that by doing experiments, teaching and learning, it shows that it doesn't require a Ph.D. to do something helpful in Science for humanity.
Are you going to publish any kind of case study or anything re: your FMT, in that case?
I am pretty against academic publishing but will be updating my blog with lots of info and data Josiah Zayner Blog
Aside from issues confined directly to the GI, did you suffer any other broader, systemic symptoms? If so, I'd be very interested to hear about specific issues that you believed to be ultimately caused by gut dysbiosis, as well as which issues the FMT ultimately seemed to resolve.
I suffer from a number of health issues check out blog post including terrible post nasal drip, bipolar disorder and I was looking to see how the transplant would effect them all so I monitored lots of different aspects during the experiment(see questionaire). I don't know if any of these were related to the gut... the FMT resolved frequency of pooping(from 3+ times a day to once a day in the morning), stomach pain, bloating and even provided weight loss(I don't think I was overweight(5'9" 170) but definitely not lean). The post nasal drip or the bipolar didn't seem to resolve much, maybe 50% for the post nasal drip but much harder to quantify.
My sister had elevated levels of hphpa in her urinary organic acid test. Associated w increased dopamine production. http://abcnews.go.com/Health/anxiety-head-gut/story?id=20229136
Interesting, have not heard of that.
I have a lot of respect for what you are doing. Very cool. Can I ask how you treat bipolar and the post nasal drip?
I don't treat the bipolar well. Most now just as needed clonozepam to help me sleep and reduce anxiety when in a manic phase. Depression phases haven't been as bad in recent years. I tried, seroquel and welbutrin and paxil and maybe others and all the side-effects were pretty bad so I stopped them after a few months. I have much difficulty treating my bipolar.
Post nasal drip I have tried netty potty and every brand and type of allergy medicine you can imagine. Nothing has really worked. I imagined it could be polyps or a chronic sinus infection. But who knows. CT for polyps came back inconclusive.
NAC and fish oil have helped me to a degree. Check out /r/depressionregimens. http://www.ncbi.nlm.nih.gov/pubmed/25957927
Interesting, thanks for the paper and will check it out /r/depressionregimens
Prior to the FMT, did you ever have periods of remission or at least days where you'd poop like a normal person? Did you ever find that the frequency of bowel movements was in any way associated with the bipolar/PND or overall cognitive function or physical stamina?
Interesting question. I had a steady state of long times on the toliet and 3 poops a day. Maybe one day or two days a week I would only have two. Definitely associated with stress making it worse. I wish I would have tracked better if it was associated with depression or mania or bipolar in some way because those really throw off my sleep schedule, diet and rhythm. Don't know about cognitive function either. That would have been great to track. After the transplant neither I or those close to me really saw much in terms of mood or cognitive changes besides the obvious changes that come with being in less pain such as being a little less stressed.
Prior to the FMT, what is your history with antibiotics? Had you taken broad spectrum, oral antibiotics prior or during the gut issues, or was transplant day the first? Any thoughts on whether or not the ABX may have provided the "cure" and the FMT was simply incidental?
Interesting question and totally possible. If you look at the PCoA plots of my poop you can see that a month after the experiment they cluster next to the donor and far away from my original which means that the bacteria changed but it could just have been one or two species that was wiped out by the antibiotics that was causing the issue. Good call though more of a correlation.
The gut issues have been present for a long time and can't really be traced to antibiotics. Prior to this I had probably only taken antibiotics 5 times in my life but hard to determine long-term effects so it is possible but unknown.
Did you smoke (tobacco) prior, during, or post FMT? If so, any correlations to note? Any correlation between alcohol consumption and symptoms? Can you think of any exposure to some pathogen (bacterial/fungal/viral) which may have triggered the gut issues?
Sometimes I smoke when I drink, maybe about twice a month but not around the tie of the transplant or FMT. No correlations. I have had beer shits before and drinking too many gin & tonics could cause attacks. Maybe I caught something at NASA, one of the -80C freezers broke and there where 20 year old tissue samples in there rotting and stinky for like a week, stuff like that happened all the time. I kid.
Hello! Thank you so much for doing this AMA. I'm just getting here, so pardon me if this question has already been asked, but I saw in the comments section of the Verge article that you mentioned aiming to try to help your bipolar with this--how has that been going since?
No difference sadly. No difference in much any gut brain linkage besides a craving for sweets.
Have you noticed any other changes?
Weight loss. It is kind of scaring me I guess I haven't been working out as much so maybe some muscle is going away but I keep losing weight. I haven't weighed this much in like 7 years? And it's not like I am trying. I was having trouble losing weight before the procedure. The donor is super fit.skinny.
Is it possible that increased digestive efficiency has decreased your appetite?
I don't really know. If you look at this data here Daily Questionaire it seems that I might be consuming about 200-400 less calories a day. I wonder if that is dramatic enough to see the weight loss I am seeing?
A loss of ~10lbs over ~3 months (~12 weeks) is less than a pound a week. You documented work outs but if you feel physically better (& your libido is higher) your overall physical (& sexual) activity level might be higher. You don't have a pedometer or anything, do you? Just being more aware of your diet could have affected your eating habits, as well.
I mean I did become more aware of my diet for sure. It is just really hard to tell how much. Thanks for your comments they actually make me feel a little better.
I feel concerned for you. It's interesting and scary to think how much microbes might affect our ability to metabolize things and weight. Please do see a doctor if you feel concerned if only to get a basic blood and vitamin panel done. So many things including stress or a difference in your GI tract causing less pooping might be causing it. Thank you for sharing your journey both the ups and downs even if I think it's all a bit crazy pants, good luck.
I will don't worry!
Do you plan on creating any bio-synthetic (super) suits? Or ever thought of the idea, just for the fun of it?
Of course I have thought about it. I mean if bacteria are an extension of us, how can we harness them to give us super powers. Totally being serious. Something I hope to explore to extend humans beyond our innate evolution.
How did you choose your donor? Did you collect data on him beforehand?
That was a tough one because alot of people I asked were afraid to participate. What I was looking for was: 1. Someone free of GI issues, mental health issues and post nasal drip issues. 2. Free of Hepatitis and HIV 3. Fit 4. Local to the Bay Area so I could get fresh samples
They say at least for C. diff that outcomes improve if a family member donates but I didn't have any local. Fortunately, I ended up finding someone who fit all the criteria above.
How similar is your diet to this person's diet? Does it matter?
The donor drank less alcohol and ate more sweets. Besides that I don't think anything was too abnormal between our diets.
Also what about things like raw milk? Did you ever try to modulate your bacteria via other methods?
No, not really. I am a strong advocate of human bacteria just because the communities are so complex. Ya' know?
I wonder if human breast milk would replace a fecal transplant, given a purpose of it is to colonize the baby's gut with healthy bacteria.
Try it and document it. Seems like a pretty safe experiment.
Why are you not working with the science community? Wouldn't you rather that your experiments gain the support of the community, rather then have the community think you are a crazy mad scientist with meaningless results?
The Science community is pretty dogmatic and has its own standards that I think inhibit progressive Science. Science is not inclusitory, it's elitist and wasteful.
I couldn't publish my results in most respectable journals just simply for the fact that my experiment doesn't have an IRB, IEC approval for testing on human subjects.
I hope people would judge the experiment on the data and protocol rather than by their biases but maybe I am just a Crazy Mad Scientist.
From the article, the results of your fecal microorganisms seem good almost to good (I don't have the background to interpret the plots you provided), which is the reason corroboration by the science community and strict guidelines are required. The only way your results would mean anything is if the "right" people think it means something. In your case the "right" people is the medical and scientific community, and you threw their rules and guidelines right out of the window. Those rules and guidelines were put in place for important reasons, such as safety, and providing accurate and repeatable results.
Btw, The pee team at Ames says hi
I think the "right" people already think it means something i.e. the general populace. I can just see that by the overwhelming response.
Basically, the plot shows based on distance the relatedness of the microbiomes of each sample taken. If you look at poop for instance and look at what each number is related to you can see a clear pattern of my gut microbiota shifting away from my old microbiome(low numbers) to the donor's microbiome(59 and 60). The samples taken in March from myself(50, 51, 52 ,53) all sit near 59 and 60. You can also start seeing a gradual change from 40 and 45 towards 59 and 60 indicating that something is happening. 42 is a little off but if you look at the diary I kept my bowel movements were strange that day for some reason the stool was liquidy, why? I don't know.
All this data together is pretty good evidence that compared to before my microbiome in my gut shifted to one similar to the donors.
I'm not saying that my experiment in any way is similar to Nobel Prize winner Barry Marshall's as talked about in The Verge article but Scientists pushing boundaries and going outside normal safety guidelines has pushed alot of things forward.
The traditional Scientific community is good for most Science but in my opinion not all Science.
Any regrets? Also, single or double coated pills? And does the poop have to be ingested immediately after defecation? What is the time window?
Taking antibiotics was pretty brutal. I don't know if I regret it but if I had to do it again I would try it without it. I did only singly coated pills which was maybe an oversight on my part but it ended up working out in the end. You can see in the PCoA plot of poop that my new poop microbiota slowly start to resemble the donors until a month later when they are pretty closely related.
I used fresh poop. There can be an argument that glycerol frozen poop would work just as well but I was trying to do more than just cure C. diff. I kept the poop cool(~4C) in a fridge to try and prevent too much microbial growth and used it for ~a week after collection. The problem is that other stuff is going to want to grow on the poop sooo the window is probably not to large.
Do you farts smell different?
Hahaha. Legit question. I am actually anosmic(can't smell) so I wouldn't know but have not had any friends or roommates comment to the likes.
whoa! didn't know you were anosmic! a coworker might be anosmic due to drinking (alcohol). wonder if that's the case for you, too?
As far as I know I have been anosmic since before drinking age. I don't really remember smells so I don't know if I ever really could. I have also broken my nose a number of times. The worst is never being able to smell yourself. I grew up never knowing if I was stinky or not, hah.
I have suffered from allergies most of my life and asthma and anxiety in recent years. I have been trying to improve my stomach bacteria to hopefully help some or all of these problems, and to support my overall health.
I live in Japan and have been doing this by increasing my regular intake of yogurt, Natto (and other Japanese fermented foods, and also increasing my intake of fiber.
It does seem to be helping with allergies and maybe asthma, but it is so hard to tell.
Specifically, I no longer am allergic or asthmatic to cats, but it is impossible to prove that it can be partially or completely attributed to gut bacteria as their are other possible explanations.
What is your opinion about this kind of approach and also the connection between the flora in our digestive tract and these kinds of illnesses?
I think that documentation is key. Understand that when you are experimenting on yourself you can collect a wealth of information that can be useful to others even if the experiments don't work. If you change your diet try and start a questionaire or diary like this(My Diary)
People are attributing gut bacteria to alot of diseases but I think you should take it with a dose of skepticism. Fermented foods can be good because some can be considered a probiotic or prebiotic.
There are so many types of bacteria and bacterial communities. The bacterial communities in human guts are very unique. Though there has been research that shows probiotics can help with things, I think that human bacteria is the best form of treatment.
Do you like pancakes?
They're ok. I have always been more of a salty person both in terms of food and personality.
Bacon pancakes then.
Making bacon pancakes. I take some bacon and I put it in a pancake.
Did anyone else read "microphone implant" at first?
That would have helped my rap career and life long goals of being a member of the Wu-Tang Clan.
Why did you choose pills and not an enema? Seems like it would increase your chances of getting sick to do it this way. Glad you didn't, though!
I could be mislead but there have been a bunch of studies in the past few years at least for C. diff that show oral fecal transplants are just as effective as colonoscopies and enemas, &c. Seemed easier, less messy, required less sample. But I don't imagine different results with that method? Glad I didn't get sick either!
Do/did you have any interesting medical diagnostics pertaining to your issues, beyond "ouch, my butt hurts"? Anomalous results which don't seem directly correlated to gut health?
I have had lots of blood work done over the years nothing abnormal. I have heart arrythmias and high blood pressure sometimes.
What are your biggest long term worries with the FMT?
Relapse, haha. Always the biggest worry I guess. And everyone making fun of me for eating poop.
I think it's all an odd way to go about an experiment but I support total body autonomy. You and others should be able to try things like this. Although I might reserve the right to think trying it yourself is not something I'd do. Good luck with no relapses. If you do revert back to IBS symptoms will you try again?
I don't know if I would do it again. It was arduous. Definitely wouldn't do the antibiotics. I agree that it was very odd, in fact very surreal.
Hello, first, thank you for this experience and for your precious feedback. I'm wondering if FMT could solve or at least be good to treat diabetes? Do you have an opinion on this? Thx.
Diabetes as far as I know is a disease that effects the islet cell of the pancreas so I don't think it would help at all.
I am probably too late to this but the entire thing is so interesting. I am curious about your CRISPR machines what have you used them for? Is this the beginning of the zombie apocalypse ?
We are mostly working on democratizing the CRISPR tool so anyone can use it but we have projects in the works at The ODIN for editing beer brewing yeast.
There are lots of people doing DIY FMT on a regular basis, a community that will be very interested in the Verge article. What did you think about Arielle's comments that your intentions came across as misguided? Or her comment that you didn't follow a standard FMT protocol?
I know Arielle and she is super cool and there is always the person someone is trying to portray and the person they actually are. I doubt that she was being malicious. Standard FMT protocols are for treating C. diff, which I was not trying to do. We talked a bunch about this stuff. I think her being skeptical is good. A good Scientist.Science reporter.experimenter is always skeptical in my opinion. Of course I didn't do everything 100% perfect, of course I could have done more research and probed people in the DIY FMT community. This is Science though, not perfect.
What is this community called?
No specific name but you can find communities on facebook like Bacteriotherapy and forums and blogs on the internet.
What advice can you give science fiction writers? In terms of accuracy and imagination..
The best Science fiction to me is the stuff that is either so far in the future it is hard to criticize(i.e. Star Trek, Star Wars) or that is built off of realistic technology or ideas. The best ideas I have occur after large influxes of new information. i.e. if you want to write about Space, read about it, learn about it, see what others predict. Spend time thinking, doing nothing else but thinking. Go for a 30 minute walk, sit and stare at the wall. For me, creativity takes effort and time and the assimilation of new information.
Try and think about mundane things in a new way, what will a garden look like in 100 years? Will people be growing plants that have been biological engineered to make medicine or extract elemental gold?
Try and think of 6 impossible things before breakfast. A lightsaber is something mundane, a sword, that was futurized, a laser sword. Impossible, a laser would continue out, you wouldn't be able to control the length. Someone though performed the mental gymnastics of saying that they invented some technology that causes the plasma beam to loop on itself or maybe just "The Force". Sometimes, impossible only seems impossible because there is no reason to try and make it possible.
What was it like working at Ames? Was the research less basic and more applied?
Most research at NASA is applied but in a very lose sense as the goal of NASA is space travel and exploration. I tell people that working at NASA is like everyone imagines the government to be, alot of people don't even work. My first mentor showed up one day a month, my last day there no one in my building was around to say goodbye to.
They waste alot of money, we ordered a few pieces of equipment around $100,000 that were never used for the entire time I was there(2 years) because government money is usually "use it or lose it.". Others at the same price or higher are used once or twice every 6 months. I can do the same research at our lab at The ODIN and I built the lab for under $5,000.
You need to fill out forms for everything.
When they started GeneLab the only person actually working in the lab at the time would goto lunch with us. One day he said he would catch up as they were taking a group picture and we saw 15 or more people gathering for the picture. We asked them who they were and he told us they were "Project Managers", NASA has soooo many project managers that really don't do much work.
Last time I checked, about 55% of the NASA workforce is over the age of 55 and no one really retires. Would you if you didn't even need to come into work each day to collect a paycheck? There is nothing wrong with people over the age 55 but because NASA doesn't have the constant influx of Science talks or even access to cutting edge Science journals people are still doing experiments that they learned 20 years ago.
If you think NASA is some high tech research place you are wrong, the water in our lab was brown in color so after we cleaned anything we needed to rinse it again in purified water. There are not even projectors in most of the conference rooms. A bunch of people I know still used CRT monitors.
The quality of research is some times horrendous. I volunteered to be a reviewer for a NASA conference(ICES). I received a technical paper(from people at Johnson) that was almost a word for word copy of the paper they submitted from the previous year, they also plagarized a figure from another paper and when I demanded it be rejected, people said I was overreacting....
This is not to say there are not good hardworking people at NASA but it is a decaying institution that has an amazing social media branch to keep people thinking that everything is amazing and awesome.
Private space is the future.
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