(Part 2) Top products from r/Microbiome

Also if you're into reading, you might enjoy this book to get a clearer picture of how your stomach works:

• Gut: The Inside Story of Our Body's Most Underrated Organ
  
  Another interesting one on longevity is this one:
  
  
• The Blue Zones, Second Edition: 9 Lessons for Living Longer From the People Who've Lived the Longest
  
  The author of Blue Zones has a really good TED Talk here:
  
  
• https://www.youtube.com/watch?v=ff40YiMmVkU
  
  Learning how your body works, as well as what we really actually truly know about managing our bodies, is a really great little hobby to get into. For example, this TED Talk explains how your body actually "burns" fat:
  
  
• https://www.youtube.com/watch?v=vuIlsN32WaE
  
  I think the microbiome is a really exciting field. It took us years to figure out (publicly, at least) that smoking was bad for us. Who knows what the future holds? Maybe GMO's are bad, maybe they're good! Maybe we're all gonna turn into zombies from the Walking Dead from glyphosate, lol. Maybe kale gives you cancer long-term...who knows? My friend's cancer doctor (at one of the top hospitals in the country) swears that chocolate causes cancer & sees recurrences based on the re-inclusion of it in the diet.
  
  Science vs. data vs. hard facts is difficult, because like I linked to in the other post, that lady who's 116 years old eats bacon every day. Common knowledge says that should kill you, but that's not really how our bodies work, once you understand the whole stomach/small intestine/large intestine deal.
  
  Who decided that every single fruit & vegetable were perfectly fine, and that Snickers bars were somehow magically bad? I bought into the "clean eating" myth for a long time, but I've gotten far better results eating against my macros - obviously, not eating a non-stop diet of junk food, but you don't have to feel guilty about a cheat meal or cheat day because you can eat whatever you want - if it fits your macros.
  
  Everyone has a different gut, and there are certain universal rules that affect everyone. If you eat nothing but fried food & salty, preservative-laced fast food & junk food all the time, that's not going to make you feel good or be very healthy for your body long-term, obviously. But, you're going to diet anyway at some point, so the question is: how do you want to experience the ride? What does your personal body tell you & what does science know for sure?
  
  Those are things you have to find out for yourself - for example, pomegranate juice gives me severe acid reflux. I don't know why, but it does, so it's just not something I include in my diet, even though it's pretty tasty! And I eat Whoppers like twice a week sometimes & still hit my macros & still know that I'm feeding my body the correct macro-nutrient balance I need to feel good & have high energy. Now, if fried grease hurts your stomach, or gluten hurts your stomach, then obviously you should not include those things in your diet.
  
  Learning about how food works & how your gut really works & how your own particular body actually works are really big stepping stones for taking control of your health. No one knows your body but you know, and you have a responsibility to care for it & to enable yourself to open up the gates to high energy & being at an ideal weight for health reason through how you choose to eat.
  
  I've tried just about every diet & way of eating you can imagine...juicing, vegan, raw vegan, fruitarian, vegetarian, keto, paleo, you name it (and can give you great recipes from all of them!). Macros has worked the best for me. I do a majority of homemade food from mostly real food sources (I use sugar & flour all the time though), but still enjoy a McFlurry & other stuff as party of my regular diet.
  
  It was really hard to get over the conversational programming we all have about what is good & bad for us. Macros has worked amazing for me, with a majority of it being real, actual food - meat, veggies, grains, fruits, nuts, seeds, and so on. I don't eat ridiculously healthy, I eat primarily for taste, against my macros. I feel great all the time, I look so much better than I did when I was 50 pounds overweight, I have way more energy, all of my blood numbers are awesome, I don't have energy dips mid-morning & mid-afternoon, I don't take 20 minutes to become awake in the morning, etc. Raw diet aside, Chris Califano really nails the energy thing here:
  
  
• https://www.youtube.com/watch?v=U12nMyPLX5Q
  
  If you don't feel like what he says - and if you want to feel like that - then a diet change is a a great starting point! I'd suggest looking into IIFYM (read through my posts here) & if things are severe, doing an elimination diet. Or seeing your GP & a GI doc & a food allergist. Lots of routes to go to begin your journey to better health, energy, and happiness! That's not fluff talk, that's all real stuff - having great bloodwork, being at your ideal weight, feeling good & energetic, feeling driven because of that energy, feeling happy because your stomach system is operating properly!

I want to debunk a couple of points in this article. This will be a long post, but I will provide light at the tunnel at the end. Please standby.

1. Prescript assist has 2 papers published from it. The total amount of people in both studies was 50. It doesnt say if that means 50 unique people or at worst case, 25 of the same people twice. As a researcher, the fact that the last paper was published on prescript assist was 2007 makes me skeptical.
   
   
2. Most probiotics get really good reviews on amazon. I have read hundreds of reviews. I also reviewed the reports on labdoor.com regarding the efficacy of many of these probiotics. There are several probiotics which are essentially placebo pills because they have a really low CFU, yet they have really good reviews on amazon. I believe this is related to the placebo affect.
   
   For example, Pearls have only 320 million CFU (most researchers agree you need at least 1 billion for a therapeutic dose) when tested via labdoor. Yet, they have a 4.5 star rating on amazon with 80+% being of a 4 star rating or better (over 1300 reviews). All of these people cannot be lying. My guess is its placebo effect. For comparison, Prescript assist has 80% of its users rating it more than 4 stars or better and a total of 377 reviews.
   
   sources:
   https://labdoor.com/review/enzymatic-therapy-acidophilus-pearls
   
   http://www.amazon.com/Enzymatic-Therapy-Acidophilus-Pearls-30/dp/B0013OOIOQ/ref=sr_1_fkmr0_2_a_it?ie=UTF8&qid=1458839257&sr=8-2-fkmr0&keywords=1++%2B+Like++-+Dislike++2+Enzymatic+Therapy+Acidophilus+Pearls
   
   http://www.amazon.com/Prescript-Assist-Probiotic-B0049NW9UI-Prescript-Assist/dp/B00JB2GOFI/ref=sr_1_1_s_it?s=hpc&ie=UTF8&qid=1458839414&sr=1-1&keywords=prescript+assist
   
   
3. The papers cited regarding acne, ABX, and IBD are presented much stronger in this article that the authors of the studies claim. For example, in one of hte papers, the authors explicitly say this:
   
   "We do not have a direct explanation as to why the exposure to tetracycline antibiotics might increase the risk of IBD nor do we have an explanation more specifically why exposure to doxycycline might increase the risk of CD. Clinical and bench science evidence does exist implicating a role of bacteria and/or previous antibiotic exposure in the pathogenesis of IBD and CD"
   
   Another paper says this:
   
   "The effect of ciprofloxacin on the gut microbiota was profound and rapid, with a loss of diversity and a shift in community composition
   occurring within 3–4 d of drug initiation. By 1 wk after the end of each course, communities began to return to their initial state, but the
   return was often incomplete. Although broadly similar, community changes after ciprofloxacin varied among subjects and between the
   two courseswithin subjects. In all subjects, the composition of the gut microbiota stabilized by the end of the experiment but was altered
   from its initial state. As with other ecosystems, the human distal gut microbiome at baseline is a dynamic regimen with a stable average
   state. Antibiotic perturbation may cause a shift to an alternative stable state, the full consequences of which remain unknown."
   
   In this paper here (http://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-7-r89), they argue, and reasonable well since they collected stools samples of 2 people daily for an entire year, that it doesnt matter so much the type of bacteria, but moreso the function, AND, several different populations of bacteria can have the same function. Therefore, you can't conclude that when your biome changes, it is permanently wrecked. It may not be wrecked at all. It might 2 sides of the same coin.
   
   The Silver Lining
   
   It would be unfruitful of me to simply point out all the things wrong with this article but not point you to good science so you have something to hang your hat on.
   
   Here is a great paper that done by some researchers at MIT. These guys submitted their stool daily for a year (over 700 samples) and kept a daily log of what they were doing. They were not shown their biome results until the study was over so they could not influence them.
   
   here is a great article telling the narrative of the paper:
   
   http://www.theatlantic.com/technology/archive/2014/09/these-two-guys-studied-their-feces-for-a-year/378862/
   
   Their scientific paper is here:
   
   http://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-7-r89
   
   The data they used for this study is also publicly available.
   
   Here is another great paper from Lawerence David's group: http://www.ncbi.nlm.nih.gov/pubmed/24336217
   
   They show that diet can change biome rapidly and predictably. They also examined a few other biomarkers.

Hey there. I am new at making this yogurt too, after reading /u/resistingdopamine 's threads on BB536. I got one of these yogurt makers: https://www.amazon.com/gp/product/B002BQ98EU/ref=od_aui_detailpages00?ie=UTF8&psc=1

I boiled a pot of milk (42 oz or 7 cups) to 180 degrees, let it cool to 110 degrees, poured the milk into the 7 cups that came with the yogurt maker, broke open 1 pill for each cup of milk and emptied into the 7 containers with the milk, stirred it around, turned on the yogurt maker and covered with the transparent lid.

It took around 24 hours for the yogurt to become solid, but once it was, I put it in the fridge, took it out a few hours later, and it tastes great.

I save 1 of the 7 cups of yogurt in the first batch to inoculate the next 42 oz/7 cups. I think you can repeat this a couple times, so you don't have to use new pills for each batch. After a couple times using previously made yogurt to inoculate a new batch of yogurt, the probiotic stops growing, so then you'd need to use a fresh set of pills.

I'm just sort of learning as I go, but having the yogurt maker to keep it at that sweet spot of 110 degrees for 24 hours is key. Hope it helps a little. I'm only on day 2, so hoping for good results soon! Eating 2 cups a day. :)

Is it? Hm, I never noticed. I mean: I do have a significant interest in the current state (and direction) of agriculture so it shouldn't be that much of a surprise. >shrug<

Pretty cool to share your rationale for why you subbed to this sub.

Have you read Mycorrhizal Planet by Michael Phillips yet? It was a nice late winter read for me; marked my copy up pretty good with notes for later reference.

I did Elaine Ingham's "Life in Soil Class" recently too; and while I didn't agree with her position on a couple of things, I found it to be very interesting and have some different approaches I'll be implementing on my acreage.

I've also done significant soil-biology testing this spring with A&L Canada (think: Solvita test on steroids), to develop a baseline for levels/populations of my soil life. I'm taking bi-weekly tests of the same type now that I've applied my glyphosate/atrazine/isoxaflutole so that I can see soil population response and recovery. It's going to be a pretty cool experiment. The same fields will be getting randomized cover crops (some that will over-winter and some that will not); and we'll see how my soil life (along with farm ROI) changes.

Thanks for showing an interest, too bad you banned me from /r/Organic; because we could have had some great discussions in that sub as well.

Awesome! Good for you. (I wasn’t talking to you)

Have you read this. This is interesting

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672390/


Let me clarify re: TMAO. I’m talking about TMAO,
LDL, saturated fat from red meat as a package. There’s no back and forth.

Here’s a book Dr Allen just wrote.

https://www.amazon.com/Oversaturated-Guide-Conversations-about-Patients-ebook/dp/B07VR28YRJ

Very interesting re: organ meats.

Humans have eaten 100g of fiber for 100’s of thousands of years. Many of us are in uncharted territory with our 0-15g daily for generations

I wish you luck.

Carnivore clearly not a long term answer as far as real evidence is concerned. Not sure how that’s know it all. I don’t know anything

Show me the evidence

And I’m not sure what you’re saying about misguided appeals to authority. I just mentioned Wahls as someone who reversed her condition with diet expertly

Mikhalia Peterson did exactly the same thing - she also reversed her chronic depression and RA with a carnivore diet.

They’re in the same category - diet healed them

But now what for Mikhalia is the question.

So I’m not pointing to either of them as an answer. Just examples of what’s possible with diet.

Carnivore until she’s 90 rears old? What does that gut microbiome profile look like?

Completely uncharted/ undocumented territory

The gut microbiome is a central player in all this. Without routine metagenomic sequencing and a team of dietary experts you just aren’t going to figure it all out on your own. 39 trillion microbes with 150x genetic of the human

I don’t know shit. Let’s make that perfectly clear.

You're on the right track. Other things to consider:

1. Cutting down on carbohydrates to something like 50g or less a day (or even better, go fully ketogenic 30g or less).
   
2. Upping your dark leafy green vegetables.
   
3. Look into a probiotic as a temporary helper in your transition to your new diet. (I like this one)
   
4. Exercise has effects on your biome as well. So do something. Anything. Even 50 jumping jacks a day..
   
5. Sleep and stress. Make sure you're paying them enough respect.
   

I'm not sure of your level of education but as a beginner I'd suggest going to university and studying microbiology. If that is not possible, reading a few relevant textbooks like Mims medical microbiology and The Human Microbiota and Microbiome will give you the basic knowledge required to spot wild or impossible claims such as getting arthritis from a probiotic. These are available for free digitally on websites I am unable to link to on reddit.

Beyond that, simply not commenting and not linking to unproven studies is a better option than doing so. It only muddies the water.

The flora of the vagina does change in the months prior to parturition (cite: Rosebury's classic Life on Man). However, how these changes come about is unknown. Certainly before the days of hospital births, there was greater exposure to the mother's feces which would result in inoculation. Whether or not the mother's vaginal flora is changed by the ingestion of probiotics via the anus- I don't know. Some women claim their yeast infections may be cleared up with oral yogurt, so perhaps it's possible.

As to whether the 1-2-3 (or as many as 10-15) organisms in encapsulated probiotics- many of which do not survive transit through the acid environment of the stomach- are even healthy for newborns- I doubt there are any good data on that.

I've had a mild sore throat for years. I've noticed that it flares in the morning when I eat late. This suggests silent reflux as a cause. I've read that reflux can be caused by inadequate stomach acid (HCL). I also had very long digestion times (5-7 hours). I frequently noticed ammonia on my breath. I started with a hypothesis that I had H. pylori, which creates ammonia and suppresses stomach acid. I read that Zinc Carnosine can knock out H. pylori, so I gave it a shot.

After a month or two I noticed an occasionally upon waking, I had an extra burst of energy in the morning. Instead of feeling like I had a bungee cord connecting my sternum to my pelvis dragging me down, I felt a sense of internal energy after getting out of bed. It was only occasional, but it was very different, so I kept taking the zinc carnosine.

I watched a talk by Jerry Tennant where he says that you need an acid (such as apple cider vinegar[ACV]), iodine, selenium and thiamine to produce HCL. I was already taking ACV, and doing well with zinc, so I added that other supplements.

Another thing Tennant mentioned was taking boron 6 mg before bed to displace flouride. I tried that and notice an immediate reduction in pains that were making it difficult to sleep.

I read somewhere (maybe Ben Lynch) that you cannot convert glutamate to GABA if you are manganese deficient. I tried Mn 10 mg in the morning and really liked the results.

At this point I found Seeking Health Trace Minerals Complex which has everything I was already taking. They also have a version (II) that omits copper, if it is a problem for you.

I also tried ConenTrace tablets, but I didn't really like it.

I don't think I have h. pylori (the tests are always negative), but I'm pretty sure my stomach acid is low. I really like the results I've had taking minerals, which suggests 1) I'm not absorbing them, 2) I'm excreting them or 3) I have toxic metals interfering with my use of nutritional metals. Still figuring this one out.

If you decide to supplement minerals, take at the end of a meal if you're prone to stomach irritation. Consider pulsing every other day or week to see how you feel with and without.

Oh, and all of my standard bloodwork for minerals has been pretty "normal" (in range).

On a related note, do you know of, or do you think it would be possible to make a guide to strain identifiers?

For example, HA-188 vs SD-5865. These have drastically different affects on me, but I have no idea why. I'm guessing that the strain identifier has something to do with where the microbe was found (such as pigs vs humans), but I have no idea what "HA" or "SD" mean. And knowing more about this would likely really help with identifying patterns of which probiotics are likely to be the most beneficial for me and others.

I only know of the klebsiella pneumonia starvation diet because it's what I need to be on for an autoimmune disease, however, it is supposed to help with a pretty broad range of problems from IBS to crohn's disease, to various autoimmune problems, but it only works in circumstances where the root problem is klebsiella pneumonia, which is not always the case. You have to cut out starch, sugar, and casein protein. This book is the basis for the diet.
https://www.amazon.com/IBS-Low-Starch-Diet-Carol-Sinclair/dp/0091912865

It's worth a try to anyone in my opinion, because if you can stick strictly to the diet for a period of just 5 consecutive days, you can usually tell if its working because your symptoms will have greatly improved. But it's also an extremely strict and hard to stick to diet you cannot cheat on. You cannot eat 1 single gram of starch or it won't work. I've been on it for 18 months and it's helped me get my life back.

Biotics Research FC-Cidal and Biotics Research Dysbiocide are apparently as effective as Rifaximin.

Amazon

Actually... “Eat Dirt: Why Leaky Gut May Be the Root Cause of Your Health Problems and 5 Surprising Steps to Cure It” https://www.amazon.com/dp/0062433679/ref=cm_sw_r_cp_api_i_dL6UDb193RNRZ

I am taking this one.
https://www.amazon.com/gp/product/B000FGXO0W/ref=oh_aui_detailpage_o04_s00?ie=UTF8&psc=1

I try to take it on an empty stomach either first time in the morning and delay breakfast or before I go to bed.