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Microbial ecosystems in the mouth and gut are linked to many ills (economist.com)
304 points by aluket 11 months ago | hide | past | favorite | 233 comments

Hi everyone! We’re planning to submit our formal launch on Hacker News in a few weeks, but given this post and all of the discussion around it I thought I would share a quick background now!

Bristle (bristlehealth.com) is leveraging the oral microbiome to pioneer oral health testing and care. We use metagenomic sequencing to analyze the oral microbiome from a saliva sample - looking at fungi, bacteria, and viruses - delivering evidence-based insights around oral health.

We are offering an early access program (https://www.bristlehealth.com/pages/early-access) providing oral microbiome testing and consumer research reports, with literature-backed insights accessed through an interactive web app. We’re charging users $50 and will only bill you when we ship your kit.

If you’re interested in learning more about your oral microbiome, please sign up! We literally launched yesterday and have gotten tons of interest based on exactly what’s being discussed here. We’re letting participants into the program in batches but will be turning kits around rapidly.

If anyone wants to chat more feel free to reach out to info@bristlehealth.com. As I said, we will have a dedicated HN launch with lots more information in the coming weeks, but wanted to share given the interest and that we have this ready to go.

I signed up. $50 to be a guinea pig... Well it will get me to follow where you go, which I think is interesting. Ideally this would already be tested in a clinical trial, so you wouldn't need customers to pay to be your guinea pigs, but it's a low enough sum that I'm willing to do it for the entertainment and educational value to myself.

By the way, I was looking for an About page to see the team and couldn't find one (maybe I missed it). I found your link to LinkedIn and saw one of the founders went to the same college as me. That's cool, but I think you should have a "Team" page to give customers confidence. Unless none of you are medical researchers/biologists/doctors/etc. In that case it may actually detract... But surely you at least have some on your advisory board?

Good luck and I look forward to trying out the product. I assume part of this might be to eventually sell my microbiome's genetic data, which I'm okay with. You didn't mention on the website (at least I didn't see it) whether the kit also collects cheek cells and such to get my more generalized genetic data. If that's the case, I may just consider it a $50 loss and not participate.

Thank you for participating! Co-founder and CSO here. Thanks for the feedback regarding the website, we're in the process of updating the page to improve its layout.

We absolutely will not be selling your microbiome data without your consent, and it's something the team and I are quite adamant about. We also will NOT be selling or using any of your personal genetic data without consent. Any analysis and discovery will be on completely de-identified data, and will go toward our goal of improving health care.

Thank you for supporting us, and we hope that the insights we provide in the early access may be valuable to you!

> We absolutely will not be selling your microbiome data without your consent, and it's something the team and I are quite adamant about.

Are we relying on your word on this? I have had startups change their mind on me on these sorts of things in the past. I would want some sort of assurance that my data remains private even if you change your mind and wish to make it non-private.

What happens if the company goes bankrupt and someone else buys the IP including the data? Can they do whatever they want with the data? Without some enforceable legal restrictions here the data seems to be at risk.

We follow all HIPAA requirements and de-identify our data accordingly. That said, as a company we are committed to patient privacy and I’m interested in hearing about the experiences you’ve had in the past with companies changing their minds. If you’re open to it, email us at info@bristlehealth.com and I’ll follow up with you to discuss!

Regarding the "about" page - our website is brand new and we're building out more information to coincide with announcements over the coming weeks. One of those is around our advisory board and another is relevant to your comment on clinical trials. Our team has backgrounds in genomics on both the research and commercial side! I worked at Illumina and ONT myself - other co-founders come from companies including Genentech, Twist, etc.

Is customer data protected by HIPAA?

Yes! We are 100% HIPAA compliant

You didn't answer the question asked, you answered a different question.

The question that was asked was if the customer data you collect is "protected by HIPAA," not if you choose to be "HIPAA compliment."

In other words - does the law (HIPAA) require you to handle customer data a certain way? Are you a "covered entity" under HIPAA?

I don't know much about your business, but I'm going to presume you are NOT a covered entry and HIPAA does NOT apply. I'm going to presume that because HIPAA is not a generic medical privacy law (even though people think it is), it applies to only "covered entities," which are - "Health Care Providers[1]", "Health Plans", and "Health Care Clearinghouses." You don't appear to be any of those, nobody claims to be providing any medical services, and you even provide a disclaimer that you are not providing medical services. - aka "just for funsies."

A useful rule of thumb is the "I" in HIPAA stands for insurance - if insurance is NOT involved HIPAA probably doesn't apply.

So I think your statement "Yes, we are 100% HIPAA compliment" was intentionally misleading.

[1] but only if they transmit information electronically in connection with a transaction for which HHS has adopted a standard

Hi Astura, apologies for the delay. To answer your question: no, we are not a covered entity - but we still maintain HIPAA compliant protocols with your data:

We follow all HIPAA compliant protocols in handling your data. We have additionally taken a number of security precautions beyond HIPAA compliance that mitigate the possibility of a data breach.

I appreciate you bringing this up as it is an important distinction and a good opportunity to clarify. We are not a covered entity under HIPAA as we are not (1) a health plan, (2) a health care clearinghouse, or (3) a health care provider. The laws surrounding HIPAA were enacted before genomics and consumer health became prevalent. This means that most of the companies in our space (23&me, Ancestry, Everlywell, etc.) are also not covered entities but are working with PHI (protected health information).

Covered entities are required to be HIPAA compliant to maintain the integrity of your PHI, and you can read more about those requirements here: https://www.atlantic.net/hipaa-compliant-hosting/hipaa-compl...

While Bristle is not a covered entity, we can be HIPAA compliant by enforcing the same guidelines around your PHI as are used for covered entities. This is an optional, but in our opinion critical and non-negotiable, component of our infrastructure to maintain user privacy.

> While Bristle is not a covered entity, we can be HIPAA compliant by enforcing the same guidelines around your PHI as are used for covered entities.

People respect HIPAA because sanctions for a HIPAA violation are very severe. In your case, if you have a violation, what would happen?

Absolutely positively nothing, their so-called "compliance" is strictly voluntary. That's why I'm calling them out on claiming that they are "HIPAA compliant."

If they were upfront I wouldn't give two fucks, I truly don't care. Like, I really really don't care. It's that they tried to lie is why I am called them out. They were caught with their pants down. I wouldn't be a thorn in their side if they were honest.

Did they have a choice to become a HIPAA covered entity and decided not to do it? Or that was never a choice?

The problem here is that the HIPAA legislation is outdated. Another problem is that there's almost no regulation around selling data.

My true question is: what's the business model here?

a) offering this testing service (which to be honest, sounds pretty interesting and useful)

b) selling the data of unsuspecting customers ("the 23andme model")

Sure, they could provide medical services and interface with health insurance companies, then they'd be a covered entity under HIPAA. They could employ medical staff to prescribe tests and provide test results to patients, then they'd be a covered entity under HIPAA.

I don't believe HIPAA is outdated, I believe that people just very much misunderstand it. The full title is "Health Insurance Portability and Accountability Act" - it's literally a bill to regulate health insurance companies, it was never meant to be more.

Congress could pass a general medical privacy bill tomorrow, yet they appear to be extremely uninterested in doing so, so they don't.

Their business model is probably just offering this testing service at the moment, but their weasely response when asked if their data was covered by HIPAA makes me think that they are keeping selling data on the back burner as an emergency option.

>we are not a covered entity under HIPAA

So why lie and say you are when directly asked? You could have just replied with this exact post when asked, instead you chose to blatantly lie. Why?

Did you just think nobody would notice and you'd just get away with it?

When people ask "Is customer data protected by HIPAA?" They don't mean "do you choose to follow HIPPA protocols [at the moment] with customer data?," They mean "Is customer data protected by HIPAA?" They want to know what you can legally do with their medical data, no what you currently choose to do with it. But you know that, you are playing stupid and are caught with your pants down.

We all know your competition also isn't a covered entity under HIPPA - so just admit you aren't either, don't be slimy and mealy-mouthed about it.

I’m sorry you feel that we were misleading you - that is not our intention. As I stated in my previous response: we are not a HIPAA covered entity but maintain HIPAA compliant protocols. We plan to include our data protection protocols on our site to make this information available and transparent for visitors and users. I appreciate you bringing this up!

Unless the question was answered in the first sentence ('Yes!' being one of the few single word sentences possible in English). In this perspective, the second sentence gives extra information instead of 'intentionally misleading'.

Then they need to provide additional information as to why they are considered a "covered entity" under HIPAA, because it is NOT obvious from their website why HIPPA would apply and the answer I was replying to appeared to be very mealy-mouthed based on the information given.

If they have additional information they'd like to share, I'd very much like to hear it.

HIPAA applies to any circumstance around handling PHI. We handle your self-reported survey data, and microbiome data as PHI. We do NOT have to be a "covered entity" to apply HIPAA compliant protocols to our data handling. It's an additional security measure we take in handling your PHI.

>HIPAA applies to any circumstance around handling PHI.

HIPAA does not apply at all as you are not a covered entity under HIPAA, stop lying.

>We do NOT have to be a "covered entity" to apply HIPAA compliant protocols to our data handling

Yeah, but that's just your current choice. You (more or less) claimed you were obligated to abide by HIPAA, but that's a lie, you are not.

I know you though nobody would call you out on this, but I am, because I understand the law. Please be upfront when asked, and stop lying.

I'm looking forward to replies from dannygrannick and david_l_lin if they are a "covered entity" under HIPAA, because that was the question asked, and hasn't been answered yet.

We self-impose HIPAA complaint protocols despite not being a covered entity. The answer to the question: "Is customer data protected by HIPAA?" is essentially the same.

1. Any data that can be considered PHI (survey data, medical data, genetic data) is stored under HIPAA complaint guidelines. 2. Yes, we are HIPAA complaint.

And it's likely never going to be answered.

You can find our response above. Thank you for your patience, and for the engaging discussion!

There is no country field and no mention of country limitations. Can I signup from Australian?

Apologies for the lack of clarity! I can’t make any immediate guarantees around sending our kit to Australia. However, we do not collect payment until after we ship the kit, so please sign up on our early access page to hold a spot in line. If/when we reach critical mass we may be able to onboard customers from Australia.

Is there a need to account for circadian rhythms in sampling, do you ask your customers to swab at noon or before bed, or do you just include this info in model training/prediction?

At the moment, we don't account for circadian rhythms. As we explore some of the insights to the oral microbiome, that's definitely one of the avenues we'd love to dig into. We do ask customers to fill out a relatively detailed health survey, so that we can explore associations between the oral microbiome in health and disease.

> We do ask customers to fill out a relatively detailed health survey, so that we can explore associations between the oral microbiome in health and disease.

So, you're learning from customers these associations, and after a significant number of customers you could offer statistical associations to future customers?

David put it nicely (and more succinctly) in another reply: "In short, there is a network effect with our platform. Each sample we sequence contributes to a database of novel bacteria, viruses, and fungi that we can use to discover new microbes." I would just add that discoveries also apply to new associations that we can include in future reports.

A little bit of both actually - as our user base grows we create a network effect that will spur new statistical associations. We can apply those new findings to new and existing users by updating their report accordingly.

You can imagine that even if you took the test once and had (for the sake of simplicity) 1 insight being reported back, you could revisit your profile in 2 years when we have tested 10,000 users and may have 4 new insights that have been added to your report as a result of the new discoveries we've made!

TLDR; there are associations reported now, and new ones that will be reported as we grow our user base and data

I see the ANALYSIS you provide does not use my DNA but I'm unclear- are you collecting my DNA? Are you saving it or storing it, in any form, in either physical or digital form? What assurances do I have that any of the labs or other partners you use won't do this either?

Bristle CSO here. To elaborate on Esyir's reply, through saliva collection, we inevitably will have your DNA in the sample. However, our analysis selectively removes host DNA from the sample, enabling targeted sequencing of the oral microbiome. During the processing of the sample, we may capture some signal from the host genome. Our sequencing, however, captures such a low level of the host genome that we cannot derive any meaningful signal from host genetic data, and actually selectively remove that signal from the analysis to enrich for microbial signals.

We keep your saliva sample and its molecular derivatives in physical form completely DEIDENTIFIED such that it cannot be mapped back to YOU without an encrypted key.

TLDR, we do NOT use host genetic data, but cannot guarantee that none of that data will be stored somewhere in this analysis. We do not share any identifiable data with anyone. We do not analyze host genetic data.

Who has the encrypted key?

The statement is meaningless if you have the key.

We maintain the key and will never share it without your consent. The key is critical to reporting microbiome data back to the correct person. Additionally, maintaining these identifiers will be crucial when we plan to add additional health features to our platform such as dental consults, tracking the outcomes of therapeutic/preventative interventions, and improvement tracking.

Of course, there are a few tricky circumstances around the future of the data. What happens if we go bankrupt/sell the company? I can't say for sure what will happen, but I am fully committed to the destruction of the key at any point when we realize that the identifiers do not serve a purpose.

but sharing the key would be sharing (access to) the DNA

Could we have an option of not storing biological materials after processing?

Assuming you don't store (notable) digital host data, it seems much safer, in case policy / ownership were to change, a breach happened and/or someone was compelled to produce samples/data.

Absolutely, you may request that your physical sample be destroyed after receiving your results. At present, we biobank samples in the event that the sample needs to be re-run.

Please send us an email at info@bristlehealth.com and we can ensure your physical sample is destroyed post-sequencing.

Will you be using samples to identify NEW microbiome bacteria? Or are you only identifying KNOWN bacteria?

This is a great question! In short, there is a network effect with our platform. Each sample we sequence contributes to a database of novel bacteria, viruses, and fungi that we can use to discover new microbes.

Thanks to y'all for the elaboration

I know it is not good HN policy to doubt your intentions but by emphasizing the NOT's, DEIDENTIFIED and YOU, you make me highly suspicious. Anonymization of data is difficult at best and sometimes nearly impossible so I would advise to publish the entire protocol if you want to give people assurances. The encryption key, as already stated, is pointless without an explanation how you use it and why it is employed and is otherwise just smoke and mirrors and no real security.

I completely understand your hesitation around the anonymization of data, and will have more detail around how your data will be anonymizes and used on our website shortly.

There's no way to get the oral/gun microbiome using shotgun sequencing without also picking up human data along the way. The raw sequence files will contain reads mapping to the human genome, but those are often filtered out in subsequent steps of the data processing.

From another reply -

  We also will NOT be selling or using any of your personal genetic data without consent.
"Genetic data" seems to imply that they do look up your DNA too.

Genetic data is €€€.

See Esyir's response. In short, we do NOT look up your DNA, and only look into microbial DNA. In fact, we do a host depletion step to enrich for microbial DNA prior to sequencing, then a following host depletion step prior to microbial mapping. Sequencing will inevitably pick up some signal from the host genome, but at such low levels, we cannot derive meaningful signal from the host DNA.

TLDR, we do NOT use host genetic data, but cannot guarantee that none of that data will be stored somewhere in this analysis

Is this testing service HIPAA compliant? Will you sell my data like 23andme does?

Yes and no!

Why the focus on oral? Ubiome had a great product that worked on fecal sample to determine what bacteria's are present in the intestines.

Do you see your company expanding into that area?

Our core technology is based around the oral microbiome for a number of key reasons.

1. decades of research have shown causal relationships between the oral microbiome and preventable gum disease. 2. the oral microbiome is much lower in diversity than the fecal microbiome, granting the opportunity for the development of relatively low-cost diagnostics that leverage the microbiome. 3. new and exciting studies have shown correlations between the oral microbiome and a number of systemic health indications, which we hope to continue to uncover with our platform.

If you’re interested in learning more, please drop your email at the bottom of our home page at bristlehealth.com to receive our newsletter!

Beautifully said! Also feel free to reach out to info@bristlehealth.com with any specific questions - we’ll get back to you.

Classic startup idea validation one-pager. I'm sure you'll get at least a few people signing up, but I don't think this is a good measure if people are really interested. Final price, look of the product, and the ability to market b2c matter much more.

23's success is more based on the execution of their product and marketing. They already have proven for you, there are customers in this space. Now you just need to build something great.

Thanks! We're continuing to develop and iterate the final product, and we hope that this program will provide some early user feedback. Current and new users will have their reports updated as we make changes and add new features.

US only or will you ship to other places too (in Canada myself)?

Hi everyone - looking into shipping capabilities. CA should be doable but will have to look into Europe further and will follow up tomorrow! We really appreciate the widespread interest!

I'm 90% sure we can do CAN. Sign up for early access through our website: bristlehealth.com, and we'll reach out when your kit is ready!

What about Europe?

I can’t make any immediate guarantees around sending our kit to Europe. However, we do not collect payment until after we ship the kit, so please sign up on our early access page to hold a spot in line. If/when we reach critical mass we may be able to onboard customers in Europe.

Ditto to David and we expect to have info on this in the next few days

Nothing about the mouth biome on HN, ever... and then a day before your launch, this article appears?

I feel like I'm being played.

If only we were that clever

The Economist is always published on Saturday, and is regularly linked on HN.

I think more likely they timed their launch to coincide with the Economist article and then someone unrelated just happened to link the article just before their intended date.

Would love to say we thought this far ahead but this was a total coincidence through a text from a friend who is avid on HN

> Dr Sampson has tested this hypothesis in mice. He bred a strain of E. coli that cannot make Curli and injected mice with it, while injecting others with unmodified bacteria. Those that received Curli-producing bacteria expressed higher levels of synuclein and demonstrated symptoms like involuntary rigidity which, when seen in people, are associated with Parkinson’s disease. That is tantalising.

These mice were mono-colonized with E. coli, whereas both mice and humans normally have a diverse gut flora. I colonize mice with E. coli containing curli all the time and the mice do not exhibit any rigidity or symptoms of Parkinson's. So it's interesting but not quite as huge of an effect as you might think, unless your microbial flora is really disrupted. May be relevant if you have an antibiotic resistant strain of E. coli blooming in your intestine following antibiotic treatment/some other disruption of your microbiota.

A gut bacterial amyloid promotes α-synuclein aggregation and motor impairment in mice https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012599/

As someone with IBD, I really wish the hard science about bacteria would start to filter into actual treatments. I know there are possibilities there, and many patients have found avenues of success, but there is so much guesswork involved that it is very frustrating. Hopefully there will be definitive answers in the future. My gastroenterologist, who has quite a lot of training from very good schools, has absolutely nothing useful to say, in terms of the microbiome.

It's starting to filter into actual treatments. I've been doing research in the field of host-microbiome interactions for the last 8-10 years. And in the last couple of years, it's gone from a fringe to a mainstream topic.

I know a few places in Europe where they are already doing fecal microbiome transplants on a daily basis. For example, Quadram Institute & NHS Norwich. They have had some adverse events, so it's not totally safe, but I think the benefits already outweigh the risks if it's having a significant impact on your quality of life.

New research avenues include, for example, doing a phage-only transplant. And obvious things like matching donors by HLA haplotypes. Both should improve safety.

Still, I understand progress is too slow for patients. Most research institutions are pretty bad at polishing, industrializing and translating basic theories into clinical benefits. They just like to churn out small papers. I have sometimes considered to spin off as a non-profit maybe to speed things up.

Theories are beginning to be understood quite well. It's mostly about cross-reactive bacterial epitopes and self antigens [1]. Plus metabolites. A very complex network, but some epitopes are central. For example, Ro60 in Lupus or insulin in T1D and their corresponding bacterial mimics. With sufficient data, we could easily throw in a personalized cocktail of phages that could halt many autoimmune disorders and tumors with high probability. That's the vision for the next 10 years, I think.

[1] https://www.nature.com/articles/s41579-020-0367-2

As someone with IBS, totally agree with you. I wish the research would trickle down into actual treatments. I have started following a lot of research about gut etc but very little of it leads to something that can mass consumed.

I spent thousands of dollars on trying out medications, tests, visiting a number of highly trained doctors etc, nothing came up in tests and at the end almost all doctors threw their hands up and categorized my gut issues as IBS which is just a catchAll term for which there is no specific treatment other than trying out a number of things.

Fellow IBS sufferer here. I understand and share your pain.

There isn't any magic pill yet but until someone invents it I can tell you I've found great comfort following the FODMAP diet.

I've wasted ten horrible years until I discovered that Monash University diet.

Ten years of pain and expending.

Hoping it can help you as well https://www.monashfodmap.com/

For anyone who doesn't feel like viewing a slideshow website, FODMAP stands for "Fermentable Oligosaccharides Disaccharides Monosaccharides And Polyols"

Which is basically Cereals (what make beer) onions, garlic, and beans; Lactose; Fructose; and at least two of the "Sugar Alcohols".

As someone who had their gut biome wrecked by aggressive antibiotics, i was told i will probably have to take probiotics for the rest of my life, but i managed to track down two things that will 100% all the time cause pain - Garlic and Onions. I'm not entirely sure which is worse, but i'd wager garlic. For a long time i assumed it was certain types of oils, too.

Basically if you're adhering to this "Low FODMAP" diet, you're meandering between "slow carb", "atkins", and several other dietary restrictions.

That "fructose" one though, that's a doozy. There are tons of health ramifications to avoiding all of the stuff on the list, so if you suffer from intestinal stuff, it'd probably be best to experiment with each thing on the list (on the site) and see if it causes discomfort, how much, how long, etc.

Anecdotally the onions are way worse for me than garlic, although the latter doesn't do me any favor.

To anyone wanting to learn about FODMAPs, Monash University blog (1) helps to understand this very complex topic.

(1) https://www.monashfodmap.com/blog/

Low fodmap was of enormous help to me too. For years I thought I had gluten issues, as most bread caused me trouble.

Turns out every wheat product with the exception of sourdough wheat bread is high fodmap! I tried low fodmap and nearly instantly got a lot better. And I can now eat some fodmaps by reintroducing in lower amounts.

Highly recommend anyone with ibs try this. It is complicated but you can get free or cheap apps that let you search ingredients fast to figure out what to remove.

And the great part is the intolerance is quantity based. So, celery in a recipe? No problem. Just don’t eat a massive amount of it. Very much unlike any kind of hard avoidance plan.

This won’t solve all issues but give it an honest shot. Mine has moved from seriously debilitating to minor inconvenience.

Exactly, that have been my personal experience too.

Identifying the triggers, and keeping an eye on quantity are the keys for me. It isn't an easy process but it makes a world of difference as you say.

Was diagnosed with IBS just after university, then (similarly) spent 10 years suffering and experimenting when I ended up switching to an ultra-low carb diet for unrelated reasons. Within weeks, I started to feel better and for the next 12 years felt great - so much so, that my family (wanting me to enjoy something sweet) started buying me "Keto-friendly" bars with < 2g of net carbs, but also with erythritol. That was a mistake, as within weeks of enjoying the bars, I was back to dealing with IBS. I'm six weeks into trying to undo the 'damage', and starting to feel a bit better, but I'd definitely advise people who have IBS to always be cautious with trigger foods - certainly the ones that personally cause them issues, but also others on the list.

That's a good advice. I wish you the best with your recovery.

Thanks, yes I have been following fodmap for years now and reduced my gluten intake as well and that has helped a bit. Although its only recommended for 3 to 6 months.

I have also slowly been introducing foods I have been avoiding back and so far I have been able to tolerate them well

Yes, the key is to try to have the less restrictive diet without the food that triggers your symptoms.

About gluten, in my case I found out that it wasn't the problem but fructans.

(I didn't downvote). For comparison, imagine you signed up with the username "Oracle" and posted "Fellow data storage sufferer here. I understand and share your pain. There isn't any magic pill yet but until someone invents it I can tell you I've found great comfort using the Oracle database" and a link to a "purchase Oracle" page.

You might be a well-meaning person, but you're hard to distinguish from a bot pushing a fad diet with online courses, a for-pay app, a shop, "find a dietician" services, certifications, etc. Preying on offering hope to the sick and desperate is common and people are cynical and wary of it, and even genuine well-meaning people are prone to sharing dubious alternative medicine suggestions which they honestly believe help but aren't proven to do anything more than the placebo effect. If you were a long-standing HN commentor, you'd probably get more benefit of the doubt; signing up as "fodmap" to link to an apparently for-profit fodmap service with an emotional message makes it easy to assume bad faith astroturfing at a glance - focused username, commercial link, fringe/alternative/woo treatment, claims of health cure for incurable condition, SEO style message ("As a fellow sufferer, believe me, I know, I've been there, trust me, just one easy credit card payment").

[I wrote this for your deleted comment;]

I agree with your overall message but in this case I would like to point out one thing - a lot of fad diets were first adopted by people and then researched to see if they are helpful where as Fodmap has been specifically researched for the gut and only after it has been shown to be helpful, its now being recommended by doctors.

Obviously you should talk to your doctor before adopting the diet. It may not provide all of the nutrients that your body needs and its normally only recommended for 3 to ~6 months. Its may also not work well for some variants of IBS / IBD / other gut issues and may even be a detriment - so talk to your doctor.

Personally its been helpful for me. A lot of people also may not need to do fodmap and instead just do a elimination diet. For example you may not know it but may be suffering from lactose intolerance or gluten intolerance and so on. Probably easier to try that first as well.

I don't have an "overall message"; they asked why they were being downvoted for sharing a genuine opinion, and I explained how much the comment looks like an advert. I am already convinced that gut microbiome affects people and diet affects people.

I did remove my question because I understood that it didn't add up anything interesting to the discussion.

Thank you for answering anyway. Your comment helps me to see why my post could be seen as not well intentioned.

I have IBS symptoms basically fully in times of stress, days on end, otherwise things are fairly normal. I wonder if either my understanding of IBS is false, or it's not biome related for me.

I suffer from IBS as well and out of all the things that flares up my IBS, stress is a prominent one. Reading research papers, its been seen that gut biome changes based on stress - look up gut-brain connection, theres been a few books written about it as well.

Its a fairly new thing - from about 15 years back. Nowadays one of the treatments that a gastroenterologist could recommend if they have exhausted everything else is low dose anti-depressant.

Key is to identify what is causing stress and treat that

I agree. For me, relaxing breathing techniques help me when having an stress episode.

Check out hyperbiotics. They had a submission here a while back, and have both probiotic and prebiotic products. They were started by microbiome researchers.

Also I’ve heard promising things about fecal transplants for biome restoration.

I had Ibd for 10 years, did a microbiota transplant and, literally, the day after it was gone. I am not sure why this treatment is not being pushed for Ibd,bbut it was nothing short of miracolous.

Completely anecdotal, personal experience. It wasn't Accutane but when I was a pimply teen, in an effort to remedy the acne, I was prescribed doxycycline and another topical antibacterial ointment; in any case, I never had heartburn or experienced depression prior to that but a few months after starting those meds, both started. It's likely unrelated but whenever I read how crucial biomes are - I can't help but wonder. For the record, I preferred the acne.

Anecdotally I wonder about this sometimes too. I took Accutane mostly because I had a parent that really drove me to take it (I think projecting some of their own issues with acne onto my completely normal amount of teenage acne) and I definitely feel like it changed my mood during and after taking it. I didn't drink at all on it either. It's a drug that you shouldn't be able to have a teenager take unless it's approved by a panel of dermatologists or something. I had no idea of the severity of the side effects from it when I took it.

I took this when I was a teenager too, acne was horrible even with a proper skincare routine. Getting access to Accutane was easy, only took 1 session with a Dermatologist who asked me basic questions on what my routine was. In hindsight I wonder if this should have been harder to access.

Of course it worked and I feel like I gotboff relatively lucky with the side-effects. One benefit was dry(er) skin/hair, which sounds bad but oily skin/hair was relatively worse to live with. I also never knew how bad some side-effects could have been which is why I said I was lucky.

However what I'll never know is - whether I'd be different if I never took it. Some side-effects are so out of the ordinary that even if I have it, I'll never effectively be able to say "yes, that was because I took Accutane when I was younger". Even being lucky, I still wished I just let the hormonal acne play out.

Edit: I just had a quick glance on the list of side-effects and for example, I've had back pain since I was a teen, and I thought it was just my form that was the cause even though I'd watch tens of hours of videos on proper form, people I know would use way worse form and never suffer an injury. Minor anxiety and even being susceptible to being sick. Some of these apply but they are also very common in those taking Isotretinoin (besides the anxiety; 1/1000-10000) but sadly I can't ever know whether the cause was due to the medication.

Oh wow, this happened to me too.

Not depression, but severe GERD that started after a course of doxycycline prescribed for acne.

It's not as bad now as it used to be, but I don't remember having these issues at all beforehand.

Interesting. I took oxytetracycline for acne for several years as a teenager in the late 1980s. I wonder if anyone has done a study on the long-term effects of that.

oh my, I was prescribed a course of doxycycline once, and those were gloomiest and angriest couple weeks of my life. I felt like I'm a sociopath, just didn't care about people emotionally. And that bitter taste all the time, like my saliva just become bitter.

I had the pleasure to work with a top geneticist whose domain of specialty was the microbiome, and he continually insisted there are tons of discoveries to be made in the arena (which he and those researchers we sequenced for did often, from dentistry to studies of the monitor lizard to chrons disease, just all over in subjects you might not expect).

Less on topic, I learned how to read scientific papers and filter bullshit ones (even in respectable journals) from good ones under his tutelage, and am forever grateful to the vast array of science and tech I was exposed to while supporting the tech side of a "every major sequencer" sequencing lab.

Who did you work for? I am interested in getting more involved in this exact field and would appreciate any helpful direction :) I am digesting anything I can find on the topic, but I feel it is greatly underappreciated still, as I agree there is MUCH to be discovered.

I updated my profile with an email, please feel free to contact me there for more details.

This is something that I've been thinking about lately.

Last ~May, I spontaneously developed rashes exactly in the middle of the back of my hands at the same time. This lead to skin sensitivity and ultimately skin rashes across my body.

At this point I've visited my dermatologist what, 20 times? In addition to my general physician, bloodwork, etc. Biopsies and bloodwork and other tests don't show anything abnormal, asides from excessively high IgE - 600 and now about 1,000. I recently started on Dupixent but it's too early to tell if it's helping or not.

There doesn't seem to be any clear indicator, so I'm wondering if I ate something + stress, which affected my gut microbiome. My family has no history of this sort of issue and it seriously started about overnight.

There's almost never harm in trying an elimination diet. Cycle out one major food at a time (eg wheat, eggs, milk, meat, nightshades, seafood), for a couple weeks at a time.

Maybe start gradually introducing fermented "live" foods as a matter of routine.

Worst that happens is you eat more veggies and try out a different diet. And if you find something that helps, all the better.

It's pretty well known now that skin conditions can be related to gut conditions.

So I have done this for major things like coffee, milk, wheat. For about a week or so at a time. I guess I can try each again for 2+ weeks... However I'm not convinced the current issue (itching) is related. The symptoms only really present themself at night when going to bed, as I guess I have no other stimuli to focus on. During the day it's basically not an issue.

I plan on trying longer fasts (3days, 5days), maybe 7days as well.

There are a whole host of possible insensitivities (many people are surprised by nightshades for example: potatoes, tomatoes, bell peppers, eggplant. They all share a plant family). Pay attention also to any products you’re directly applying to your skin as there might be ingredients in there that are being absorbed.

Just a couple of random thoughts:

A food and symptom journal can be helpful for trying to connect the dots.

High IgE levels can be due to parasitic infections and these have something of a tendency to go underdiagnosed in the US because they get seen as "third world problems."

"A food and symptom journal can be helpful for trying to connect the dots."

This is a good idea, I will try this once I start cutting out foods again.

"High IgE levels can be due to parasitic infections and these have something of a tendency to go underdiagnosed in the US because they get seen as "third world problems."

How does one go about testing this? I visited my gp multiple times and a bunch of tests were taken. Aside from the general itching and rashes, I don't really have other symptoms. Maybe a little fatigue occasionally.

"A food and symptom journal can be helpful for trying to connect the dots."

This is a good idea, I will try this once I start cutting out foods again.

You should start the journal now. You need to establish a baseline to compare things to. Start it well before you start making changes and don't make more than one change per week. Reactions to changes can be delayed and it's pretty complicated stuff.

How does one go about testing this?

Sorry, I don't know. I never figured out the secret handshake or whatever to get the medical system to give me the right test to actually identify my infection.

I looked up my symptoms online, drew my own conclusions and I've gradually gotten healthier, though I get treated extremely abusively for trying to talk about it online so I got nothing more for you than the two tidbits above.

Best of luck.

>>The symptoms only really present themself at night when going to bed, as I guess I have no other stimuli to focus on. During the day it's basically not an issue.

Do you take night showers? If your house has hard water or your water dept. adds excessive chlorine, then either of those could be the culprit.

This could be ringworm. Have you see any particular patterns on your spots ?

The initial tests looked for fungal infections, and I took anti-fungal pills for about a month as well. After the biopsy at the dermatologist, they told me it was atopic dermatitis / eczema.

On the flip side of what I posted, if it doesn't help then go enjoy your damn food. But good luck figuring it out all the same.

I've had similar problems and I've concluded the main driver was stress after all.

It definitely doesn't help! I've decided to eliminate coffee completely as even if it doesn't trigger itching symptoms, it absolutely makes me more stressed. I like non-caffeinated tea more anyway, but it's hard to turn down family members making lattes...

Sulphites are worth cutting out to test too.

I'm going through something similar, but I haven't visited a doctor ... yet. But its getting out of control. I was reading that itching from eczema drives people to suicide, just like dry eyes ... things one would only assume as minor discomforts, until you realize you can't sleep any more, causing a downward spiral.

Just recently, I found this in medicalXpress https://medicalxpress.com/news/2021-01-acute-eczema-patients...

Which you may want to check out because of IgE. It goes into how typical antihistamines don't work because the itch signal is from a different pathway, etc.

Also this week I found out about this book https://www.penguinrandomhouse.com/books/588965/clean-by-jam...

from this article


"James Hamblin, physician, staff writer for The Atlantic and author of Clean: The New Science of Skin; and Jack Gilbert, a renowned microbial ecology professor at the University of California, San Diego and co-author of Dirt Is Good: The Advantage of Germs for Your Child’s Developing Immune System."

One of them recommends using soap only for "pits and bits" :) But as runners both, thats hard to do when covered in sweat and salt.

"One of them recommends using soap only for "pits and bits" :) But as runners both, that's hard to do when covered in sweat and salt."

I switched to natural soap bars a while ago, as I like those anyways more than typical body washes one gets from e.g. cvs or walmart. For hair, shampoo every time is simply not necessary. I use that 1x a week, but some people don't use it at all- check out nopoo. I don't have issues with my scalp but my dermatologist did mention that Head and Shoulders can make eczema issues worse because it's abrasive.

I will check that book out.

"But its getting out of control. I was reading that itching from eczema drives people to suicide, just like dry eyes"

While I don't have those thoughts, I completely understand it. I'm not sure if people who've never had this kinda of eczema before can understand it. But the constant itching (which is both physical and mental) and the mess afterwards from scratching is brutal after a while. Scratching at 3am (after sitting in bed and trying to concentrate on anything other than the immense signal to scratch) brings a brief bout of euphoric relief, then regret and depending on the size of the scab, blood/sticky fluid. I basically had to wash my sheets and blanket daily because there would be residue all over.

For a while, the backs of my thumbs both kept on weeping. So imagine sticky fluid getting on your keyboard, guitar, etc and constantly having to wipe it. The same happened to the entire back of my right hand as it had gotten a bit infected, so I had to go to the ER and get a corticosteroid (dexamethasone) shot to calm the situation enough that it could get back to "normal"- scabs and immense itching urges.

"Which you may want to check out because of IgE. It goes into how typical antihistamines don't work because the itch signal is from a different pathway, etc."

This is something that I have been noticing too. I took benydryl occasionally and it seemed to have no real effect other than maybe placebo. Same with hydroxyzine- I've taken at max 100mg (4 25mg tablets) about 30 mins before bed, and the only thing it did was make me real sluggish the next morning / sleep through alarms.

I'm a daily runner/rucker who gets completely covered in sweat and grime every day, I've had success only wiping myself off with my hands in the shower followed by washing my hands. Unless I've specifically gotten muddy or poopy, I don't think there's much benefit to soaping up the whole body all the time.

I also stopped using shampoo years ago, and a daily rinse keeps it fairly clean. When I can't shower for several days, like hiking, I do use soap everywhere, because I'm dirty enough that a rinse isn't sufficient.

Try cold showering - hot showers strip the natural oils from your skin and leave it dry.

Ensure you're changing your bedsheets every 5 days, and wash them with 70degree+ water.

All of my showers since last ~April have been coldish/lukewarm. Bedsheets, blankets and pillowcases get changed/washed almost daily. In addition to switching to gentle detergents.

Are you losing weight? I had some rash appeared spontaneously after start losing weight and it took almost a year to clear out

Yes, actually. In that period I was doing intermittent fasting in addition to running 5k daily. I started at ~210/215 lbs and dropped down to around ~190 or so. Once I started taking meds and winter hit I stopped running so I'm back to around 210.

My only theory is bro science tier idea that fat accumulate some toxins and then it released during weight loss.

Anecdotal evidence says this is a valid theory. I personally caused a shingles infection when I was breaking up intramuscular tissues with a lacrosse ball. As well, most massage therapists will have stories about “toxins coming to the surface” for clients after being worked on (especially in first-time clients) (Source: I’ve talked to about a dozen massage therapists about this).

They may say that, but it's unsupported by science. The red flag is that nobody says anything more specific than "toxin".

Personally I feel that “toxin” is appropriate language in the massage industry: the actual individual effects can be widely varied, clients understand it, and it prepares them for potential symptoms without planting any negative biases that would affect their actual experience through placebo effect.

I'm no expert, but something similar happened to me a few years back. The conclusion was an allergic reaction to the sun...

Did it go away on its own?

I can't confirm today because it's very overcast, but as of a few days ago the sun had still not gone away.

I know you're joking, but this is a horrible condition. While researching I've seen some anecdotal stories about the condition just... clearing up after a while for some people, so hence my question.

I’m suspicious that your reply may also have a joke embedded in it...

Addendum: the downvote is totally fair

For what it's worth (very little, since it's a medical anecdote shared online), my wife had a nasty case of hives for the first time in her life after trying a sarecycline treatment. Took us quite a while to connect the dots, though, and to this day we don't know if it was really what caused it (or stress, or the fact that she took 3 different vaccines on the same day, or everything combined)

All of that is to suggest that you think about what you have changed about your diet, medication or anything else either in May or shortly before that

> what you have changed about your diet, medication or anything else either in May or shortly before that

Well, there are only 2 things I can think of. Firstly, due to covid I had been working at home from March to May. Before covid I would still go out a lot to cafes/social workspaces and get sunlight. And around mid-march I started running. By May I was running about 5k-7k daily throughout my neighborhood.

So we initially thought it was a bug related thing, but everything came back clean. We tried eliminating food, but nothing really seemed to have an effect after a week or two.

I spoke to my immunologist and he believes it's not food related as I already have food related allergies (peanuts), so eating something else should give me quick reactions like peanuts do. Also, he said it's rare for adults to spontaneously develop something like that. Bloodwork has been inconclusive because my IgE is so high that it's causing false positives. I did a diff of my allergy bloodwork from and back in October, and multiple values did increase.

I have tried basically everything- getting more sunlight, using sensitive detergent (3 different brands), cutting out coffee/gluten etc. Hell, we even replaced the carpet in my parents house with hardwood, and once I moved into my house we cut out the carpet as well.

Tick borne disease?

It was ruled out early on, along with fungal infections, HIV, etc in an array of tests. Basically every test I've had has come out clean, minus occasionally a little high blood pressure. And the IgE levels in orbit as mentioned above.

Could it be mcas?

I had a look at the symptoms and I don't think it matches what I have. I believe my urine and stool test would have ruled out high mediators, although I can ask my GP next time if they were checking for that or not.

Ultimately I think my solution will be to go to a tertiary/quaternary center like Duke.

Check out Dr. John Sarno's works. It's mostly about back pain but he covers other manifestations of the condition he calls TMS. He talks about a personality type which you seem to fit.

It's interesting to see more and more articles lately reporting a strong connection between ilnesses (or lack) and one's microbiome health. What I noticed from my experience, is that kombucha and kimchi make me feel great if I consume these regularly (once or twice a week). Sometimes I will indulge in some crap food like pizzas and noodles, which make me feel unwell, but kombucha and kimchi work as a reset :)

pizza and noodles are also high on the "glycemic index" whatever that means, and probably should be avoided. I don't think all noodles are, but probably most of the noodles in america should be avoided?

Kombucha, especially if you brew your own and can adjust the tea used to make the perfect taste, is probably not doing any harm, and if any of the health benefits are true (i'm not sure, i never researched it, i just like the flavor) then awesome.

I don't want to comment more than a couple times in these threads, so i'll just put this here: I've been saying that the gut bacteria are probably more "us" than our brains are; i read a study about 16 or 17 years ago that showed that wheat and sugar (two grasses) when digested in human guts release agonists/antagonist/whatever for opioids which your brain takes up. So when you go on a diet that restricts sugar or wheat, you actually literally mentally and physically suffer withdrawal symptoms. This can make massive cravings take hold, which might lead to over-indulgence in, say, chocolate chip cookies or cake, which cause the dwindling gut fauna to bloom like crazy, making you feel great even though you broke your diet, and making it even harder to attempt to get your plan back on the rails again.

they're linking everything to gut biome now, alzheimers and a slew of other mental issues. I was so enraptured by the research and papers i read that i actually swore i'd have a farm before i was 45, producing excess food for anyone that wanted it. Nothing since then has contradicted the prior research, and as i said, there's new "traced to gut flora/fauna" papers being published what seems like biweekly.

Mouth and gut health are directly related to physical health AND mental health.

The gut is often called the second brain, and lots of mental health issues like anxiety, depression, stress, etc can be greatly helped by improving diet and healthy gut.

It’s criminal that medical establishments are controlled by pharmaceutical companies and establishment media spreads prescription drug propaganda.

Everyone needs to do their own research about gut health and direct impacts to physical and mental health.

> The gut is often called the second brain, and lots of mental health issues like anxiety, depression, stress, etc can be greatly helped by improving diet and healthy gut.

Who calls it that? I've seen a comment or two before, but certainly not "everyone" calling it that. It's a nice analogy that probably could be stretched way too far, as these things go.

Are the causal links clearly _known_ or correlation shows that the link may be identifiable?

> It’s criminal that medical establishments are controlled by pharmaceutical companies and establishment media spreads prescription drug propaganda.

Hmm... this sounds like conspiratorial thinking. Do you have evidence of this, and if it is the case, a reason why this status quo is worse than other alternatives?

> Everyone needs to do their own research about gut health and direct impacts to physical and mental health.

Why? Wouldn't it be more reasonable for scientists to research, work towards consensus, then report findings, rather than duplicating the fixed costs of setting up laboratories and health testing facilities in our garages? Considering I did this, what is the likelihood I find a stronger connection or novel fact about certain microbiota that inhabit my or my families' bodies? Or perhaps you're being less precise in your terminology, and you're advocating that people study scientists' research rather than conducting wetlab studies. Could you clarify?

Analogously, we should also all study the universe, but few advocate for all to build radio telescopes on their available rooftops.

>Who calls it that?

It comes from some studies[1] that show a large number of neurons in the gut which control subsystems, which number about as much as a cat brain. This is interesting and makes things more complicated than initially thought, but is a bit apples to oranges; just having as many neurons as a cat brain doesn't mean they operate like you hacked a brain into your gut.

Spitballing here, but this probably started as an analogy to show the number of neurons, and people started thinking it was an actual brain.


(Maybe not the best source, but google "human gut cat brain" and you'll see this view all over the place.)

Makes sense. So the neurons themselves are not an analogy, but their operational status perhaps is. I appreciate you humoring me.

I don’t have anything to add to this brilliant response but I’d like to say how much I appreciate it.

I’m curious as to why you think it’s brilliant response?

Was it the lack of initiative to do simple google search on gut brain physiological connections? The common phrases gut feeling, gut check, gut intuition are related to the gut brain connection.

Was it the lack of insight into the hundreds of billions of dollars spent on prescription drug propaganda? Google how pharma company marketed Oxicontin, which was huge part of opioid addiction crisis.

Was it the lack of clarity in the scientific community reproducibility crisis? Especially in the drug development fields, where Big Pharma has big incentives to push through dangerous drugs on people? Please Google prescription drug called Vioxx.

Programming and software fields are full of people with steep disregard for culturally established theories and truisms.

Until some VC backed tech company builds a product around a 1000+ year old theory, it seems to hold no water in this community.

"Analogously, we should also all study the universe, but few advocate for all to build radio telescopes on their available rooftops. "

But the conditions of the stars are not linked to our well being (unless you are into astrology).

But the condition of our gut microbiome is.

I simply read the comment as a urge to investigate about your own biome. What works and what helps you individually, with the methods you have avaiable. Like checking what you eat, your medicines ... and how that affects your well being. Good indicator for health is .. a good shit so to say. But yeah, if you have a lab avaiable, or know a competent one, why not also professionally investigate your digestion outcome.

Perhaps you missed the big pharma conspiracy.

I ignored that part mostly ...

But that big pharma does things, that strenghten peoples believe in conspiracy is sadly not far off:

For example about Sanofi, a french pharma company. On the german Wiki page is a section criticsm, stating various bad things, like not telling about side effects of drugs and trying to suppress that knowledge in various cases and testing in poor countries with lax standards, etc.


(one english link: https://techcrunch.com/2015/04/14/big-pharma-small-startup)

But nothing to be seen on the english version for example. And I heard countless other stories, of which most were surely crackpot realm, but not at all everything, so I am also not really a fan of big pharma.

Excited for more research in gut health.

I know HN hates to entertain any lay science, but I wonder if scraping my tongue, as I do with a copper scraper, is good or bad for your oral biome?

FWIW, the reason I use a copper scraper is simply that copper, as I understand it, has antimicrobial properties, and consequently I would be able to get by with a less thorough cleaning of the scraper than something plastic or wood that's not single-use. I basically rinse it under heavy water and give it a rub with my thumb.

My wife and I can both objectively report that bad breath has gone WAY down with the scraper. There's almost no morning breath now, as a matter of fact, with a scrape before bed.

Dentists (ones I have) usually recommend brushing your tongue as part of your tooth brushing routine. This helps prevent bad breath I think, which is correlated with oral hygiene.

in the morning, even scraping with your hand is good since you're removing the dead stuff thats accumulated on your tongue during sleep. eating this stuff has no nutritional value and is considered a 'toxin' in yogic traditions.

lot of those online sites are just trying to 'sell something' to make a living so they mandate you 'need' a metallic scraper.

Below is an interesting bit of research which gets quite close to tackling your curiosity, or at least stimulating it. It specifically concerns oral hygiene and blood pressure, with a focus on nitric oxide. Tongue scraping seems beneficial, though there's no mention of copper. However, chlorhexidine (mouthwash ingredient) seems a disruptor of NO and may contribute to higher BP. I need to read the article myself, but a brief skim left a big impression.




Edit: I deleted and reposted this comment because I found the article was abridged and might not be the one I remember. I think I've got it right this time, but if not, follow the "full text links". Should be interesting either way.

I found that my bad breath was the result of eating highly processed food and wheat based products, once i stopped eating these, my bad breath vanished.

No tongue scraping or brushing required.



It really seems like some decades in the future we'll look back at the results of gut microbiome research as akin to the discoveries of bacteria and viruses. Before those discoveries it was known that people got sick, and that developing sickness was correlated with various things, like proximity to sick people, or poor hygiene, but the mechanisms behind those correlations weren't known. (Or they were suspected, but with some misconceptions or lack of detail.)

I expect and certainly hope that as this system is better understood, it will unlock numerous significant advances in medical science. Would just be nice if that process could happen faster!

Besides the gut flora being capable of some neurological effects it has demonstrated to be psychoactive. Professor Robert Sapolsky[1] has an amazing course on Behavorial Evolution. The toxoplasmic gondii comes from the rat -> cat -> gut -> brain, it is profound that side effects in the brain are chemically constructed from the stomach. Considering that most animals do not even have a brain,but usually have a stomach, it is evident that the gut is underestimated in the evolutionary tree.

[1] https://www.youtube.com/watch?v=Y0Oa4Lp5fLE

Someone please enlighten me as to why in 2021 DOCTORS and DENTISTS are still completely separate in the healthcare system?

Danny I sincerely hope your team's efforts will accelerate the bridging of this divide.

Where I come from, you'll find orthodontists in hospitals along with all the other doctors. If you're referring to the dentists whose job is to clean you up regularly and tell you to floss more often, I guess they're a distinct profession from GPs because that part of the body benefits from regular specific maintenance by a trained professional, but they're still doctors.

Here in the US they offer health insurance and dental insurance as two completely separate programs. They are separated enough that it strikes me as remarkable.

Insurance companies pushing a narrative to avoid paying for it? Complete guess.

so they can milk people's £$€

As a layman, this is so exciting! It feels as though we may be getting closer to finding a cause for a diverse set of neurodegenerative disorders. Alzheimer's, Parkinson's, etc.

Gut and oral microbiota having influence across the blood-brain barrier seems so plausible. If they get into the nervous system and migrate, they could cause inflammation in the brain leading to damage over time.

The immune system is incredible, and we'll no doubt find it a fertile ground for progress against a lot of diseases.

Do we know whether these microbes are cause or effect? On the bright side I'd say even if they're [only] an effect of those illnesses, we'd have an excellent opportunity for earlier diagnosis.

I can only wish these researchers good luck; we don't even understand the gut's microbial ecosystem as it relates to gut diseases.

I, unfortunately, have first hand experience here. The short version of my story is that I started out 2020 with an acid reflux diagnosis and ended 2020 laid out in bed 24/7 eating nothing but rice and potatoes with doctors shrugging over a mystery GI issue.

They finally gave me a specially designed, brand name, and expensive as hell antibiotic that specifically targets the gut microbiota. The drug and its effect is the medical equivalent of the old IT adage: "Have you tried turning it off and on again?" The idea is to rain hell down upon your gut and hope it resets to a better balanced microbiota.

So yeah, that's the current state of modern medicine when it comes to GI issues; bludgeon it to death and hope for the best. So God have mercy on this researcher attempting to identify links between the GI microbiota and other illnesses.

P.S. I was somewhat inclined to go into more details on my journey, cause finding information on GI issues is so hard, but it would be a stupidly long comment. Suffice it to say, I learned a lot about the gut, but mostly about what we don't know. For all those people with IBS-*, SIBO, and NCGI out there, you have my deepest commiserations. Science can take the FODMAP diet and shove it up its poorly understood rectum.

EDIT: I think in my revisions of this comment I forgot an important bit: the treatment seems to have worked. My symptoms are continuing to improve after the round of antibiotics. So as crude as the science may be, at least it worked.

I've being suffering IBS for the past ten years. I also had that nuke all treatment and then try to colonize the gut.

It was antibiotics for x days, I don't remember how many, and then pre and probiotics for x days. Rinse and repeat.

It didn't work.

I only can speak for myself but the FODMAP diet is the only relief I've had experienced in ten years, and for the first time (pardon my french) my shit is not watery.

P.S. I agree science has a lot to learn about this topic.

> for the first time (pardon my french) my shit is not watery

Yeah. If I could impart advice on anyone, it's that if your shit isn't "good" (a nice, clean Type 3 or Type 4), you need to sort your shit out. In retrospect, my BMs were never "great" in the past couple years and ... I clearly should have done something about that a long time ago. It's likely whatever was wrong with me was brewing for awhile, and just triggered into something severe when something pushed it over the edge.

Right, the Bristol Stool chart. What a fun when doctors ask you to keep a stool record.

> It's likely whatever was wrong with me was brewing for awhile, and just triggered into something severe when something pushed it over the edge.

I can't back it up with any evidence but my feeling is that a combo of stress and too healthy food (for me) triggered my gut crisis.

What I mean is that I started to eat food that was too rich in GOS, and also fructose, just before my problems started.

> I can't back it up with any evidence but my feeling is that a combo of stress and too healthy food (for me) triggered my gut crisis.

Similar. I'd been trying to eat healthier for the past couple years, slowly cutting back on dessert/sweet foods, eating more vegetables and fruits. Even started doing green and fruit smoothies this year. But yeah, under the FODMAP theory a lot of fruits could ferment in the gut, some vegetables too, and beans, a staple of a healthy diet, are probably the prototypical high-FODMAP food.

I'm not sure what the moral of that is ... I guess ... don't eat healthier because it might kill you? shrug The gut is a weird beast.

Was there a re-colonization process? If so what kind/brand/bacteria types?

The treatment is just 14-days of the antibiotic, there's nothing specifically done to recolonize your gut. The "off-and-on" again thing is really just a theory, if you can even call it that. Like a lot of medicine, it's something a drug they developed with an idea in mind, found that it worked and that's about the extent of our understanding of it. It may or may not do what we think it does, because all the manufacturer cared about is whether it works.

I did do my own research on whether taking probiotics would be helpful, to recolonize my gut as you say. Of all the studies I read, none found any benefit. Both during treatment and after. So it's unlikely that a manual recolonization process is even needed.

My personal pet theory is that the antibiotic doesn't wipe everything out, but instead works by making the gut a much, much more competitive environment. Beneficial flora tend to be better survivors in our guts (for various reasons), so they are more likely to survive the assault and the bad bugs are less likely. Once the good bugs have the advantage again they can outcompete and take over. There's also your gut's immune system which, based on my reading, has the potential to "farm" the flora in your gut. It too will be working to rid the bad bugs and promote the good ones. It seems like in the case of GI issues a bad bug gets a beachhead for one reason or the other and then your immune system can't naturally correct. The antibiotic gives it the chance to do that.

Hence why probiotics are unlikely to do anything. It isn't a total elimination, so there's nothing to reseed. And your immune system is going to favor the same microbiota it grew accustomed to when you were born. Not to mention the appendix which is suspected as being a safe-harbor for your natural gut flora.

I did take probiotics myself, since they don't seem to do any harm. I took them during and after treatment. Probiotic pills, Yakult, and yogurt. But there's no science backing that action.

It seems reasonable. It's been said, even if we cloned a Mammoth, it would quickly die if we didn't colonize its gut carefully. It had adapted to eating what was growing forty thousand years ago. It would need different flora to digest hay today. Even then, there might be no solution compatible with its intestinal biochemistry. We are all products of our environment.

Several people I know have some seemingly disjoint food allergies, some of the attributed to lack of certain enzymes, some without any explanations.

I'm wondering if some of the effects could be mitigated with sufficiently smart microbiome engineering.

I'm on antibiotics for an infection right now, how badly have I disrupted my microbiome? How will this effect me down the line?

You can work to repopulate the gut through diet. Fermented foods like sauerkraut and kimchi, for example, the odd bit of green banana every now and then to reach the intestines as a prebiotic, and avoiding junk food, obviously. There’s lots you can do.

I made my first kimchi a couple of months and I’ve been making sauerkraut for a few years now. Even if they weren’t healthy I’d continue, the taste is worth it! (And so much better than what you can buy in the shops)

Most of all, don’t let news like this stress you out, let it inspire you to a more fulfilling diet instead. Stress isn’t going to help.

Only some antibiotics will cause issues. If you have to take alternatives to any of the "cillin" family, the medical community at large recommends no more than 2 full treatments within 18 months. Anything more than that can lead to things like C. Diff and may require a fecal transplant or needing to take probiotics that a pharmacy will carry in a refrigerator up on their deck.

I forget what the terminology is, but broad spectrum antibiotics are generally worse for your gut than something targeted, iirc.

Adding to the anecdotes:

Around summer 2014, I began to focus very heavily on "bulking" for strength training. This was about a year after I'd developed very obvious symptoms of lactose intolerance and had had to cut uncultured dairy out of my diet. My meals were not diverse: fruit and Greek yogurt in the morning; chicken cooked in Indian sauces, roasted potatoes, and some green (usually broccoli or spinach) for lunch and dinner, along with protein shakes and a pre-workout carb load (such as PB+J). Drinks were water, orange juice, and kefir.

That winter, my health collapsed. I started developing skin abscesses, and the antibiotics I received for a particularly bad episode caused me to develop a C diff infection. I had to severely limit my food intake, as too much or certain kinds would cause me to develop cramps, listlessness, and diarrhea, and lost about 40 pounds in 3 months. My body could not hold onto food long enough to process it correctly and I developed symptoms of incomplete digestion, and especially of fat indigestion (symptoms improved with anti-diarrheals).

The next 3 years were a long battle to try to get back to normal. Store-bought probiotics didn't help; digestive enzymes did. Things didn't improve noticeably until after I began eating homemade sauerkraut, and especially after I began taking enzymes on an empty stomach (I was told that this might help to break down some structure that might harbor unhelpful bacteria).

Eventually, I was able to return to most foods without issue, until last year, when a prediabetes scare prompted to try a ketogenic diet (this also seemed to solve a lingering issue, of multiple daily and urgent movements).

All this to say... I don't really know what's going on. I've found some things that seem to work, but I could only guess at why, based on the timing of my downturns and upturns and of my interventions.

I've spent literal days over this period trying to understand why my body is acting and reacting the way that it does, and following the (often slapdash) advice of people who target the microbiome as the source of ill or good health has sadly seemed to be the most efficacious route. However, I'm still not able to achieve the level of well-being I'd like to, and I attribute that largely to the dearth of hard facts available relating to diet and the human microbiome. Over the course of this journey, I've seen more and more professionals begin to take the issue seriously, but not nearly the level or quality of research we'd hope to see with such a fundamental topic. Here's to seeing that corrected before I have to punch whatever card this adulthood of gut trouble has been leading to.

Seems like a good plug for a startup I used to work for. I'm no longer associated with them aside from my personal friendships but they're creating a pretty cool oral health product: https://freshhealth.com/

I say this all the time. There is a lot to say about this but anti-biotics aren't a silver bullet. There is a drawback to them bigger than any of us have really imagined.

There are a whole slew of mysterious illnesses probably caused by imbalances in the gut.

The evidence is weak to non-existent. I wish popular magazines would stop publishing these non-sense stories. At least they went with "linked" which is clearly saying correlation (which is not causation).

Or many ills affect the body in more extensive ways than thought. Constipation could be an early warning sign of Parkinson's and other problems, for example, not that you'd be able to tell.

I'm pretty "natural", never had antibiotics and stuff. But I can tell you I've got plenty of problems that can never be fixed by gut bacteria.

Besides, modern lives are anything but natural.

Interestingly, this is what holistic practitioners and naturopaths have been trying to say for a long time

They’ve just substituted the scientific method with no method at all and devoid of all peer review or capability of it

As technology improves I expect individualized and therefore holistic treatments to be at the forefront

A while back I read that people with root canal are far more likely to get cancer. The reasoning being that the empty root canal provides a pathway for bacteria/viruses to enter into the body. Causing chronic infections. Which leads to cancer.

solid read


A long time ago, our ancestors were single-celled.

Then, some cells decided to live together, form a slime, division of labor, organs, etc. And today, voila, we have humans.

However, the single-celled never went away. We have been living together, co-evolving together, all this time.

No human has ever lived without a microbiome. We have been in symbiosis all this time. The immune system picks off the baddies, while the goodies get to stick around, serving all sorts of useful functions. Not only that, but the goodies actually edge out the baddies, because they consume most of the resources available to microbes. Combined with help from immune system police, a balance is reached.

That's the way it works until you introduce various ways to harm the microbiome. Preservatives in the food. Substances which indiscriminately kill bacteria on the skin and elsewhere. Antibiotics. Then the balance is thrown off, the baddies get to proliferate unchecked, the immune system can no longer cope with their scale.

I've stopped using any products which harm my microbiome. It's not easy, and it's not a one-day or one-month or one-year transition, but it's paid off in ways I didn't even imagine possible when I started out.

Edit: When I post about this stuff, I often get asked about specifics. For reasons of privacy, and several others, I would rather not get into them. Do your own research, find your own way. Don't wait for everything to be handed to you on a plate. I've provided more than enough information in this comment.

My wife had terrible acne for years - she tried every product under the sun, visited dermatologists, all of it.

About nine months ago I persuaded her to try absolutely nothing. Just wash her face with mild soap and water when she showers or after exercise. It was a hard sell. A really hard sell. It looked sinfully angry for the first few weeks, and then, bit by bit, started to fade.

Now... her skin is perfect, the scars are subsiding, and she hasn’t had even a hint of acne or so much as a zit in four months.

The crux of my hypothesis was that she was eradicating her skin microbiome over and over, and possibly breeding incredibly resistant bacteria with no competition.

I take a similar approach with oral hygiene - I don’t brush, I don’t use toothpaste or mouthwash, I just use a wooden toothpick to get anything stuck out. I started this in my teens at boarding school, as toothbrushes were often “borrowed” for cleaning rugby boots, and then replaced in the rack. At the time, I figured not brushing was better than god only knows what being rubbed into my gums. I had appalling breath and swollen gums for several months - but both just disappeared after adaptation.

I go to see a dentist every few years, mostly out of a sense of obligation, and have never had a carie, cavity, periodontal disease, or anything - I’m pushing 40. The most they’ve ever done is polish them. By my age my mother had lost half her molars, my father had a gobful of crowns and fillings, so it’s not genetics.

Maybe I’m talking crap, but I think we significantly underestimate our bodies abilities to maintain themselves, and buy into the idea that we require products to keep them working.

Unfortunately, weaning yourself off this stuff usually involves some degree of disruption, be it honking breath, or skin so angry you don’t want to be seen in public.

I've heard that some people do indeed have better bacterial biomes than others, some will be fine without brushing or flossing, and others will have problems. Saliva has a large part to play in preventing caries and bad breath, dry mouth can cause a lot of the issues you describe. Also, water fluoridation has made quite a big impact in public dental health. Remember that most people used to lose teeth regularly before the advent of fluoride toothpaste, often very early in their lives. Do you think that these people's teeth were maintaining themselves? Looking at old WW2 videos made me realize this, where many soldiers in their 20s had completely black teeth or massive gaps.


I can’t find the name now, but there was a researcher who looked at crooked teeth and tooth decay in modern society, then started flying around the globe to see if the issue was the same in tribes. Turned out it wasn’t.

What do you have to say to that?

I'm not a dentist, but I do know that bacteria feed on sugar and carbohydrates. There's some info that says refined carbs are just as bad as candy. If all you eat is meat, vegetables, and some fruit, you're probably not gonna get as many cavities as a refined grain-based diet with more refined sugar.

The beasties that make plaque thrive on sugar. Turns out refined sugar and processed foods made with sweeteners like high fructose corn syrup are really hard to come by out in the sticks.

Yeah, I'd say don't apply that thinking to everything.

For what it's worth, I've done the same, but it only worked because I wasn't eating a bunch of sugary garbage. Definitely nobody should try it who eats that sort of stuff even somewhat often.


A close friend of mine had horrible dental hygiene, rarely brushing, drank soda and beer as his water, and only went to the dentist after developing intolerable pain something like a decade into this mode.

When he came to work the day after his dentist visit, he said the dentist told him "this is what we call mountain dew mouth" when examining his teeth.

If you don't eat stuff that makes plaque thrive, the consequences of ignoring it are less severe.

A similar, and perhaps better option: https://en.wikipedia.org/wiki/Miswak

Did you have your wisdom teeth out? Are your teeth straight? That makes a huge difference.

Knowing that what you eat - more fiber, less fiber, more carbs, less carbs, etc, how do you optimize your microbiome when there is so much variety among humans? Which is the right biome?

You can start at blood type.

Is it that why now more people live on earth than ever since?

Probably because of reduced all-cause mortality, increased food production, and the relative peace of the 20th century.

Relative peace of the 20th century? At least 108M have died in war. I believe it to be one of the biggest on record, and certainly not one of the peaceful times. So relative peace compared to what?

> So relative peace compared to what?

Total world population.


Well, I meant the latter part of the 20th century. Population has more than tripled since then. The crazy thing is that the 108M that died in WW2 really only slowed, or paused world population growth. It was not a devastating depopulation event like the Bubonic plague that killed 1/3rd of Europe.

When you say peace, I don’t think about plagues, natural disasters, or anything of the sort. I think of war. And there’s been war every decade (I believe) of the 20th century.

Your comment has nothing to do with the comment you are replying to. It's about quality of life and individual health.

You could breed humans like we do with industrial agriculture and factory farms, but you would have a difficult time arguing this is good for the health of the animals (or people) involved.

how did you start?

Starting in around 2013 or so, I stopped using any kind of soap or cleaner on my body, with a couple of exceptions. I still wash my hands regularly, and I use a tiny little bit of fairly bland, unscented soap between my legs in the shower. Note that my head hair is quite long, naturally coming down to my mid/lower back.

How do I get my body/face clean in the shower? Very hot water and very vigorous scrubbing/rubbing.

After doing that for a week, my body odor virtually disappeared, even when I was hot and sweaty. While my overall skin and hair condition had always been ok, it improved noticeably.

I did this after reading a number of articles online about it and figured it would be worth trying.

As a bit of an experimental control, I didn't tell my wife that I was doing this. We do regularly brush and braid each other's hair. After about two weeks, she said that my hair was more full and healthy than it's ever been, and she also confirmed the body odor changes.

So this is anecdotal: it was useful for me, and might be useful to some others. However, given everything we're learning about microbiomes in and on the body, it seems to make a lot of sense.

Tried this for months, I really smelled bad. Good friends telling me unprompted etc. YMMV.

I concur.

I've lived in homesteading environments where numerous people go months bathing sparingly using just water, while still actually getting things done involving significant labor, sweating and generally getting dirty.

Everyone reeks in these conditions. They don't realize it, and their intimate partners who are in constant contact also don't quite appreciate the degree of odor, because it's shared.

But from an outsider perspective, it's ripe.

There's probably an evolutionary reason for this, members of a tribe will smell similarly when eating the same food and sharing space/objects in close quarters. I can easily imagine how that would be advantageous. Foreigners will stink.

> bathing sparingly

That could be a difference; I scrub a good long time using quite a bit of hot water.

I used to use hot water + scrub. Was told it's terrible for your skin by my dermatologist, you start developing eczema in some cases in the long run. Warm water, white unscented mild soap and no scrub was his recommendation.

I've been using olive oil based soap and it works great.


can you expand on that? and also what do you mean by ways you couldn't even imagine?

You lost me at antibiotics. Overuse is a problem for certain, but we'd have a lot more death, and possibly worse, disability without them.

You just made up an argument for a point that the OP wasn't making.

He is not wrong... OP did not make this point however you can infer it, from his point of view

Actually in my limited knowledge about biology, both are right, when things are way discompensated, you have to use things to kill bacterias which almost take control of a part of your body (the baddies one) .

That misses the point. It's a trade off. The mindset of saying something is good or bad is ridiculously limiting.

Yes, more people would die. Does that mean the ones who didn't would be worse off? Less healthy?

There is a natural balance to the world order. Pushing the system, even building it up, creates strains that might not be obvious until it is catastrophically so.

> Edit: When I post about this stuff, I often get asked about specifics. For reasons of privacy, and several others, I would rather not get into them. Do your own research, find your own way. Don't wait for everything to be handed to you on a plate. I've provided more than enough information in this comment.

Come on now, are you really going to post about how something "paid off in ways I didn't even imagine possible when I started out" and not name even one example? This lowers your comment to being basically on the same tier of conversation as conspiracy theorists who brush off requests for proof with "DO YOUR RESEARCH, THE TRUTH IS OUT THERE I CAN'T GIVE YOU SPECIFICS".

Haha, that's what he did :D.

Coincidentally I looked OP's profile and found this URL again http://hn:hn@sHiTMyseLf.com/index.html. I had stumbled upon it in a previous thread (don't remember which one, but I only look at profile when I read some specific kind of comments).

I didn't get what the website was about last time and I didn't stay long enough this time either.

That URL was obfuscated to prevent bot abuse.

It will now be replaced with a new one.

unfortunately mentioning any specifics risks transforming the conversation into arguing about such a specific item with the results being projected back onto the main statement. It also risks sounding like one is pushing his/her pseudoscientific stuff. In the area like microbiome with highly individual situations and relatively low level of established science any specifics is just an anecdote not much suitable for rigorous discussion. (i have myself found a couple ways of dealing with my SIBO (test based diagnosed by GE) for example and almost never discuss those specifics. It is really an area of "do you own research" and the useful methods/etc. are really "out there".)

Maybe so but “Don't wait for everything to be handed to you on a plate. I've provided more than enough information in this comment.” is really condescending and not inspiring much trust.

It's also a classic move when you can't backup your claims.

"This worked for me, but might not work for you, because of our specific circumstances," followed by a detailed description, would suffice, and in turn be much less useless and condescending.

Please, discuss specifics (as I have).

with all the caveats of not being a doctor and all the risks known and unknown, "don't try at home", etc. https://news.ycombinator.com/item?id=17139208

while i didn't get totally cured, the condition went down very significantly, a couple orders of magnitude (by subjective feeling and some objective metrics), and since then i've mostly been maintaining the situation by a daily teaspoon of activated charcoal mixed into 2 cups of water (i drink it at least 3 hours after meal and at least 2 hours before meal to minimize charcoal binding on food instead of its intended targets).

This is interesting. I was never diagnosed with anything (too poor to go to the doctor at the time, even with insurance), but I came to the conclusion that I had a similar issue: bad (or overgrown) bacteria housed snugly in biofilm. As mentioned here (https://news.ycombinator.com/item?id=26119265), someone suggested taking digestive enzymes on an empty stomach would help to break down the biofilm and allow healthier bacteria a chance to eatablish themselves.

Two different self-treatments aimed at what seem to be similar issues with anecdotal success. Hm. I really, really do hope that all aspects of our experiences get studied more thoroughly in the future.

Thanks for sharing.

If you aren't willing to post specifics about your own activities, you could at least provide references for the statements you did make, e.g. battle to consume resources, and throwing the microbiome off.

Don't bother to make vague generalizations without being willing to back them up, especially anonymously. It makes the statement nearly information-free. And this is coming from someone who agrees with your assessment.

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