Tim Steele Vegetable Pharm Wisdom

Just popped over to Tim’s place (you remember ‘Tatertot,’ right?) to catch up and had to share these three bits of wisdom, which I agree with wholeheartedly:

Gut Microbiome – I have been quite disappointed that the research and discussion still revolves around identifying the bacteria responsible for different diseases and less emphasis is placed on the diet. I think it is becoming apparent to all that each person is unique and carries a unique set of gut microbes. Fecal transplants get little mention anymore, despite the great promise shown. For each of us, I think all we can do is experiment with the foods we eat and try to find a great mixture of fruits, veggies, fungi, nuts, seeds, grains, etc… foods that keeps our digestive system working well. I have not lost my passion for using potato starch and inulin as a supplement when fiber intake is low, but they should not be a sole source of fiber. I keep trying to expand my repertoire of fibrous foods as I come across new sources (my latest is spelt).

Yep. You are either feeling good, sleeping well, performing well and pooping well…or you’re not. All this fixation on special “boutique” strains some people stress, is pure bunk. BTW, two of three of my American Gut test results came back and I have significant AngelAkkermansia! So there! You can click the image for the readable version.

Screen Shot 2016-01-03 at 8.10.10 AM

Fine print: “Your sample contained 90 rare taxa, including the following: Unclassified Class ABS-6, Unclassified Order iii1-15, Unclassi- fied Family Acidobacteriaceae, Genus Edaphobacter, Unclassified Family Koribacteraceae.”

Speaking of gut tests…

Gut Testing – The various companies offering gut tests have been the biggest let-down of 2015 for me. I’ve spent a lot of time in the black box of bioinformatics this year, and I’ve looked at hundreds of gut reports. I’m afraid there are simply too many variables both in the tests themselves and in the individuality of the guts to use these tests for anything more than amusement value. Now I see that some of these companies are even offering health predictions based on your sample. I stand firmly that a gut test generated using 16s rRNA profiling is in no way useful as a diagnostic tool. For one thing, I do not trust any of the results or percentages generated by 16s rRNA sampling, and for another, the gut biome changes so rapidly after a single meal that a snap-shot of your flora based on a simple swab of poo is meaningless in the grand scheme of gut health. While it is fun to see the species/genera named in a report, they are not worth the paper they are printed on in terms of diagnostic potential. Culture-based sampling is more reliable, but cannot be used to identify an entire microbiome, only certain species. If I suspected a pathogen, I would have a real doctor use a culture-based platform to discover if it exists. Additionally, the bacteria in your gut is only half the story. The fungal/yeast inhabitants are quite likely just as responsible for maintaining good gut (and overall) health as the bacteria identified through standard gut tests.

Absolutely. Worthless. Waste. Of. Money. Plus, American Gut, or Human Food Project, or whatever the hell, has literally the worst process and signup design I have ever seen. You have to sign up by means of a fundraiser donation, then you get a kit, then you have to sign into some website via a printed URL that I’ll be dammed if I can remember (and don’t have the paper), then to get results, you have to go to the same URL, but I can’t find a fucking link to it on any of their pages, nor the email they sent, because it’s not coming from American Gut… They suck.

That’s neither here nor there, though, if the results mean anything and unless it happens to identify some serious pathogen problem, not useful. Mine were all over the map, and Tim spent significant time going through them all just to basically say, “yep, you’ve got a gut.”

The only thing I want to do further is compare the AG and uBiome results that were from the exact same piece of poop. Soon as I can find the damn login and see if the third test set has come in.

So, bottom line, think about food, maybe some probiotic and prebiotic supplementation, and get cultured by a medical facility if you have serious problems.

Dieting Trends – I think the tide has shifted away from low carb diets and more towards vegetables and grains. At present, “”paleo” just seems to be a keyword to direct internet searches and sell diet books. How anyone ever thought that crispy bacon strips emulate ancestral eating is beyond me. Potatoes are “bags of sugar” and all grains are evil. The reality is, almost any whole plant food is healthy for us. Refined grains are not whole foods. We do not require pounds of meat per day. In my mind’s eye, the biggest dangers in eating are the over-processed, refined foods we choose for convenience. In that respect, “”paleo” steered us away from the worst offenders, but never really taught us to eat a human-appropriate diet. I’m hoping that the diet fads of 2016 and beyond all include plenty of whole grains, beans, potatoes, and heavy-hitter fibers.

Yep again. Absolutely need those animal foods, as far as I’m concerned, but they really go a long way, especially if you get in some liver (pate is easy), oysters, clams, and mussels. And this is one area where even canned is fine. I eat lots of smoked oysters in olive oil. I also get then fresh at an Asian market not 3 miles away, $4 per dozen, shuck ’em yourself.


With an apple cider vinegar & shallot mignonette.

On the whole grain front I’ve learned a lot. Have tried lots of various breads, emailed some companies, etc. Basically, almost nobody uses true whole grain, with both bran and germ. Usually, it’s just bran and often enough, it’s added back into refined flour, so the whole thing is a mess.

My touchstone is that provided no alcohol is involved, does it give me heartburn or not. Generally speaking, it’s the whole grain sourdough breads that do the best on that score. Hit & miss, otherwise.

Until I found Whole Grain Natural Bread Company at a local market styled after WF. This is a local company over in Santa Cruz, and they mill their grain fresh and whole every baking day. And you can literally feel the difference. The bread has a distinct moist quality that’s feels of slightly oily. Yep, that’s the nutritious germ, there.

And guess what. Through about 1 loaf of simple Mark 1, Mod A whole wheat bread in about a week, not one instance of even an adverse burp, much less heartburn.

Look, as I’ve said before, I begrudge no one their grain free deal if that’s what feels right for them. But Paleos really ought to at least be honest enough to admit that when they blanket condemn grains, they are not making a distinction between true whole grain and refined, bleached, and often “fortified” crap.

Alright, can I have a round of applause for Tim Steele?

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Richard Nikoley

I started writing Free The Animal in late 2003 as just a little thing to try. 20 years later, turns out I've written over 5,000 posts. I blog what I wish...from diet, health, lifestyle...to philosophy, politics, social antagonism, adventure travel, expat living, location and time independent—while you sleep— income by geoarbitrage, and food pics. I intended to travel the world "homeless," but the Covidiocy Panicdemic squashed that. I became an American expat living in Thailand. I celebrate the audacity and hubris to live by your own exclusive authority and take your own chances. ... I leave the toilet seat up. Read More


  1. Craig on January 3, 2016 at 15:26

    ” true whole grain, with both bran and germ. Usually, it’s just bran and often enough, it’s added back into refined flour, so the whole thing is a mess”

    Have you try grounding your own flour from wheat berries and making your own bread?

    • Richard Nikoley on January 4, 2016 at 07:13

      Not yet, but once this off grid experiment is done, I’ll be getting a mill. Motors and heating elements demand too much power and it cuts into Netfix time.

      • Mycroft Jones on January 4, 2016 at 13:19

        Richard, you don’t have to wait. I bought a CS Bell “grist mill”. I ground a pound of wheat into flour in one minute, by hand. These things are rugged and HEAVY. But they aren’t heavy to turn; the counterweight powers through the grain like soft butter. These units are built to be used in a professional farm environment; they aren’t dinky little afterthoughts to the powered mills. The cast iron design hasn’t been changed in 50 years. I liked mine so much I bought more for friends.

      • Richard Nikoley on January 5, 2016 at 07:48

        Cool. Looks like the grinding stones are not cast iron though, which of course you don’t want.

        Crazy they don’t have an order form, that you have to contact them, not on Amazon. What’s the price?

        BTW, Bob’s has whole ground flour, both a general purpose and pastry. I’ve been experimenting with popovers and yorkshire pudding.

  2. Harriet on January 3, 2016 at 18:04

    Yes a round of applause for Tim, and one for your too, Richard. I like it that both of you keep it real. Life is one ongoing experiment, n=1.

    I have had a difficult 6 months since I took a trip of a lifetime away to the US and Canada. The trip didn’t work for me and it was a real struggle to be well enough and fit enough to get my brown belt at karate last month. But I did it and am pleased – not bad at the age of 65 after a life time of being ill.

    So basically its a matter of never giving up. Day after day of doing what one can to improve things even if some things don’t work and doing as much as one can close to nature as possible – natural food, natural exercise, cultivating relationships.

    And as a past colleague once said, “You can’t medicate your way out of an illness that you behave yourself into.”

    So all the best to everyone and keep your personal experiments going.

  3. Tim on January 3, 2016 at 19:18

    Haha, your AmGut report proves my point. According to what they’ve given you, almost half (47%) of your entire gut microbiome is a single genus: Oceanobacillus.

    Oceanobacillus has only a few species, none are normal inhabitants of the human gut. ( http://www.bacterio.net/oceanobacillus.html )

    I’ll be willing to wager that uBiome does not show your gut dominated by this genus, if it sees it at all. This is a predominantly deep-sea bacteria, though sometimes found in kimchee and fish paste, but none of the species are described as being isolated from humans.

    If uBiome does not agree, there is an obvious glaring error, and AmGut apparently has no filter for “obvious, glaring errors.” It seems to me the companies who take your money in return for a full gut bacteria report should have a QC system in place to identify obvious mistakes.

    • Richard Nikoley on January 3, 2016 at 20:21

      Well, Tim, once the third one comes in I’ll get you the data on all three. You already have the five uBiome, and three of those were literally the same swab. I held the one uBiome and 2 Amgut swabs togeter and ran them through a pile of poop together.

      • tatertot on January 4, 2016 at 15:31

        Just looked at the uBiome raw data – no Oceanobacillus in any of them. Yet AmGut says you have almost 50% of total biome made of this rare human inhabitant.

        It will be fun to look at the 3-way swab deal. Let me know when you get the data.

      • Richard Nikoley on January 4, 2016 at 16:39


        Just emailed the AmGut data I have. For now, only the Oct 07 set is head-to-head. It’s explained in the email.

        Once AmGut processes the Sep 24 sample, we’ll have a second head-to-head to compare.

    • Allan Folz on January 3, 2016 at 21:22

      Happy New Year, Richard, Tim, et al.

      I completely agree gut biome tests are among my biggest disappointments for 2015. After seeing Richard’s test results I felt bad for being one of the primary instigators. Seemed like a good idea at the time. I think about all we learned was that the tests themselves are useless. That’s something I guess… lemons from lemon-aide, but sheesh.

      As to the abundant Akkermansia, hehe, well… someone somewhere certainly has my kind of sense of humor.

      Finally, thank you both for all that you do. I don’t comment much, but I do catch every post.

      • Richard Nikoley on January 4, 2016 at 07:31

        Hey Allan.

        The other thing is to look back in your mind’s eye and take account of how bright eyed you were.

        Thing is, that’s not altogether a bad thing. It’s good to get excited or energized about something, enough to give the ‘ole College Try.

        The problem is when people don’t get the results they were looking for, or it turns out to be rubbish, just shake your head and move on. Too many try to justify it all. Well, it is just to try, but it’s not just to ignore whatever the results may be.

  4. Mycroft Jones on January 3, 2016 at 19:52

    Happy New Year Tim. How did your bees fare? My hives are tucked away for winter, and I have lots of ideas for springtime.

  5. Bacchal on January 4, 2016 at 08:10

    Have you had bread from Tartine in San Francisco? They use a lot of heirloom whole grains. Not sure if they grind their own, but all their stuff looks damn good. Looking forward to trying it when I’m out there next week.

  6. CL on January 4, 2016 at 10:32

    What about those sprouted grain breads, such as Ezekiel? What do you think?

    • Richard Nikoley on January 4, 2016 at 11:57

      Completely unsure. Haven’t looked into them. They are in freezers all over, so maybe I will.

      So, this bread? When frozen, still soft and very pliable. That’s evidence of the germ, i.e., the whole thing.

  7. Clare on January 4, 2016 at 14:35

    Erm, I only came across this thread becaus I was trying to find out something about the oceanobacillus the British gut project found in my sample. But regarding the comment above, “That’s neither here nor there, though, if the results mean anything and unless it happens to identify some serious pathogen problem, not useful.” : what do you do if you do in fact get results that seem to list our high number of pathogen type bacteria in your “most enriched microbes” section?? If I take it to a doctor, will he know what to do with it …!?

    • Tim on January 4, 2016 at 16:30

      The entire gut microbiome testing “industry” is simply an exercise in gathering information. What AmGut/BritGut is doing is simply matching what their machine picks up with a database. It could be that Oceanobacillus was recently added to their database and is a closer match than anything else, so the reports are showing high levels, when in fact, it may be non-existent.

      These reports are in no way suitable for diagnosing any gut problem. A doctor would just scratch his head, and maybe run some tests if you are having gut problems. I can guarantee 100% (OK, 98%) that Oceanobacillus is not overtaking anyone’s gut.

      Did you notice when you sent in your sample, you simply put the “sticky” swab in a tube and mailed it off? The bacteria on that swab continued to grow, and they used a series of formulas to reduce the presence of bacteria known to bloom in transit. Other gut testing companies have you insert the swab into a liquid that kills and preserves the bacteria on the swab, a much better approach in my opinion.

      The past year has shown me that a private commercial endeavor to accurately sequence gut microbes is a long way off.

      • Clare on January 5, 2016 at 14:00

        Ok thanks for your thoughts. Oceanobacillus wasn’t actually the numerous pathogens I was referring to, but not to worry. I’ll dwell on it some more, cl

  8. marie on January 5, 2016 at 10:44

    Richard, thank you for the pointer to Tim’s latest post. More than that, since I haven’t been able to drop-in here or anywhere for a long while, thank you for always updating your careful, well-researched synthesis of nutrition information and understanding, it’s making it easy for me to catch up. Even when you don’t do the research yourself, you foster the work of people who prove they do their homework and with all the references I can follow-through on my own in whatever I’m most interested.
    As a celiac, I don’t do wheat myself, but in preparing traditional dishes for the family (spanakopita, baklava!) it’s good to know I’m not promoting diabesity.

    Though I always figured that regular fasting corrects for any dietary transgressions that might have cumulative effects, yes?

    Even so, seeing as how the US does not have a traditional fasting culture, perhaps Low-Carb should not be roundly discarded yet, considering that a majority of the population is already insulin resistant, pre-diabetic or diabetic? Having a broken system, it’s reasonable to think they’ll need more than elimination of added sugars/processed foods in order just to come back to baseline.
    Nor is it clear whether they can successfully repopulate their gut biome, if starches remain a major food source?

    Though, looking at the fasting work of Dr.Jason Fung and his recent popularity with big LCers like Eenfeldt, maybe everyone should just skip the LC and just adopt fasting already!

    In any case, for all you do, bisous bisous! (même si je ne comprends pas du tout ta politique ces derniers temps).

    • Richard Nikoley on January 5, 2016 at 14:31

      Amour, long temps. 🙂

      “même si je ne comprends pas du tout ta politique ces derniers temps”

      Les données modifiées, Marie.

      Please don’t tell me that in our petty little micro blink of an eye in time, that you’re one of those people who don’t always evaluate new data.

      People killed French in Paris in multiple places, out partying, explicityly. Then people killed people at a Christams party in San Bernardino.

      …And supposedly smart people keep saying, 20+ years and running now, “it’s our fault.”

      Bullshit and I’m fucking tired of it and I care less who thinks otherwise. What, you all just want more?


      Anyway, shifting to something else, this is interesting. I know we had a discussion on IQ way back, but check this out, and go through the comments. I initially posted it it kinda tongue in cheek. but it’s certainly not an obvious test, but I’ve been blown away by how many readers offer up big scores. I know people who, whom I respect, even, who would never even score very near 100.

      I don’t think it matters a great deal, in terms of societal evolution. That will always turn on lowest common denominator and the rare communicator who can’t energize dumb fucks.

      Anyway, there you go. Check it out.


  9. Hegemon on January 6, 2016 at 19:53

    Richard, I’m glad to hear that the bread thing is going well for you. I experimented a bit and wanted to bounce it off of you and any other commenters.

    Was diagnosed with celiac years ago and have done well with no grain. Having it usually gives instant heartburn, also crazy dreams that night.

    Around Thanksgiving I found a local bread company that sells a bread that is made from Fresh stone-ground whole wheat flour sweetened with pure clover honey. It has the purest ingredient list I’ve found locally available so far – just the above, with an egg wash, salt, and yeast. I warmed a slice and put butter on it, and about 5 minutes after eating it my head felt like it was floating off my shoulders. I haven’t felt like that since my college experimentation days. There were people over for dinner and I felt so high I couldn’t keep up with the conversation. It was not pleasant at all. Needless to say I have been a little gunshy to try again.

    Ever experience that with your recent foray into wheat? Reading over what I just typed, I know I sound like an idiot, a liar, or both; but that’s really what happened. I would love to add bread back in, but not sure where to go from here. I’d appreciate any words of wisdom you have.

    • Richard Nikoley on January 7, 2016 at 07:08

      Well, first, I’ve always said this isn’t for celiacs, may not be for those not clinical but somewhere on the spectrum.

      It’s a big I don’t know, from me.

      If you were insistent, thouh, I’d definitely do it under the supervision of a celiac specialist.

      So far as I know, the only evidence pointing to weirdness is that you don’t see the celiac rates in France. We’ve covered this, but of course that sort of thing never applies to any particular individual.

      Did you get any gut distress? Weird that you would experience it as a mind buzz, like auto-brewery syndrome.

      • Hegemon on January 7, 2016 at 07:32

        Thanks for the reply. As to gut distress, I recall a bit of loose stool. If I eat out and get a bit of gluten, I normally see some reflux, maybe loose stool, but almost always I will have crazy vivid dreams (and sometimes night terrors from what the wife unit says, but I never rememeber them). But never the high I experienced. I wonder if it’s because it was such a pure form – not anything like the refined or denuded forms I would normally get from commercially processed food.

        I hear you on saying it’s not for celiacs. I try it on occassion and when I do, I do everything to eliminate any other variables that might cloud the results. Here’s where I have hope, though. If I am really pounding down the soil probiotics and resistant starch, I can down a couple beers and sleep like a baby. Poops are normal too. A few years back I seem to have developed a problem with nightshades as well, but again, if I am really downing the pro/prebiotics I can eat them with no problem. Leads me to believe it is a function of having the right microbiome to process things. I was a kid that was formula fed and given antibiotics 1-2 times a year growing up. I think the carpet bombing eradicated a lot of gut bugs.

        I may go the sourdough route and see if that makes any difference. I’ll post the results when I do. For now, one of my main “bread” sources is Pão de queijo, made from sour manoic starch. Per your posts on grains, I started doing oatmeal and some other gf grains that I do as hot cereals in the morning. I feel better than ever and sleep like a baby at night now. So thanks for all the research!

      • Richard Nikoley on January 7, 2016 at 08:18

        Unlike many others, nothing I ever write is filled with legal disclaimers. In fact, in the little Paleo book I put out, I specifically forbade it (can’t recall if they put it in anyway).

        I don’t second-guess people and I really don’t care if they kill themselves (while others pretend they do).

        Dose makes the poison and obviously, you have already done your own experimentation on that score, discovering your own tradeoff levels for certain things like beer.

        So, experimenting with true whole grain bread ought be no different. On your own, but I’d go low enough dose where symptoms are non-existent or mild, gradually up it.

        Could be you just freaked your system out. That you have vivid dreams suggests that your gut is doing something with it.

        Be smart, maintain presence of mind always.

      • Hegemon on January 7, 2016 at 15:50

        Thanks for that. Believe me, I understand what you’re saying. At 25 years old, I went to the doctor for an annual checkup, feeling great. I was hit with a diagnosis of leukemia, fatty liver disease, high triglycerides and cholesterol, labeled prediabetic, and left with the realizeation that something had to change. My diet was shit, and had been my whole life.

        I have since turned all that around and eat super clean. I’m to the point where aside from my rare experiment, I do all my own cooking and do no gluten, sugar, or refined foods period. The wife thinks I’m a bit overboard with it, but I really like not having GERD or gross poops. And honestly I just don’t like the taste of chips or snickers bars anymore. I’m still kicking, so I must be doing something right.

        But, point taken.

      • Richard Nikoley on January 8, 2016 at 09:04

        Chalk it up to living in your own private laboratory.

    • Harriet on January 7, 2016 at 16:58

      I am one who gets odd neurological symptoms with different foods. I suspect what happened is you got a sudden growth of a particular bug which had spectacular, if undesirable, results. I remember once a meal of kidney beans making me hear voices telling me to kill myself. Something similar had been reported in the medical literature that I looked up a decade later when I got into the medical industry as a researcher. So what you experienced isn’t unknown.

      Go cautiously if you are celiac. But I don’t go along with once a celiac always celiac. It is probably the case, but I never say always/never. My research has been with outliers who defy usual medical expectations and they are incredibly interesting.

  10. marie on January 6, 2016 at 21:25

    Hegemon, your comment caused me some concern for you. Being celiac, what makes you think you can ‘add bread back in’? I froze when I read that. Celiac is a deadly disease if gluten exposure is not strictly avoided, due to progressive damage to the small intestine. However, in western countries it is difficult to eliminate all gluten exposure since processing with wheat ‘thickeners’ and ‘vegetable protein additives’ is ubiquitous and the gut damage can be silent for many patients until it’s quite advanced, so a celiac diagnosis is always followed by life-long monitoring.

    I am hoping actually that the celiac diagnosis you received years ago was not firm? It takes at least two types of tests to definitively diagnose celiac and today all three available types of tests are usually done : serum Transglutaminase, endoscopic imaging of the small intestine and genetic testing to identify which variant is present (there are two that are prevalent in celiacs). Is it possible you are gluten intolerant in some form but not celiac?

    Otherwise, you had a criminally negligent doctor and I’d urge you to find a gastroenterologist for monitoring of your disease (so as to know how good a job you are doing of avoiding gluten). He’ll probably also refer you to the celiac foundation for more information on management.

    In case it’s not obvious, I am a life-long celiac, scoring on all three tests (transglutaminase should be checked before one stops eating gluten). I also however come from a family where ‘the farina problem’ was known and this helped me deal with it successfully.

    BTW, there is only one candidate for a ‘cure’ of celiac and it is experimental and involves hookworms. If interested, see for example here : http://www.sciencedaily.com/releases/2014/09/140925100929.htm

    • Hegemon on January 7, 2016 at 04:55

      Thanks for the concern. I’m waiting to hear what Richard says.

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