Tag Archives: prebiotics

Mushrooms are awesome (P<0.05)

“Without leaves, without buds, without flowers;
Yet they form fruit.
As a Food, as a tonic, as a medicine;
The entire creation is precious.”

-weird mushroom poem of sketchy origin

Mushrooms: They have B12! When exposed to UV light, they make vitamin D2.  Protein, fibre, and selenium.  Shall I go on?

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Animal fibre

Fruits and veggies, fermented or otherwise, aren’t the only source of prebiotics in your diet.  Eat a whole sardine and some of the ligaments, tendons, bones, and cartilage will surely escape digestion to reach the distal intestine where they will be fermented by the resident microbes.  


Salmon skin and the collagen in its flesh, the tendons that hold rib meat to the bone, and maybe even some of the ligaments between chicken bones.  All of these are potential prebiotics or “animal fibres.”  And it may explain why fermented sausages are such good vessels for probiotics.

“Animal prebiotic” may be a more appropriate term because the food matrix is quite different from that of non-digestible plant polysaccharides.  And while I doubt those following carnivorous diets are dining exclusively on steak, these studies suggest it might be particularly important to eat a variety of animal products (as well as greens, nuts, dark chocolate, fermented foods, etc.) in order to optimize gut health.


These studies are about the prebiotics in a cheetah’s diet.  Cheetah’s are carnivores, and as such, they dine on rabbits, not rabbit food.


As somewhat of a proof of concept study, Depauw and colleagues tried fermenting a variety of relatively non-digestible animal parts with cheetah fecal microbes (2012).  Many of the substrates are things that are likely present in our diet (whether we know it or not).


Collagen (tendons, ligaments, skin, cartilage, bones, etc.)

Glucosamine-chondroitin (cartilage)

Glucosamine (chitin from shrimp exoskeleton? exo bars made with cricket flour?)

Rabbit bone, hair, and skin (Chicken McNuggets?)

Depauw ferments

The positive control, fructooligosaccharides (FOS), was clearly the most fermentable substrate; however, glucosamine and chondroitin weren’t too far behind.  Chicken cartilage and collagen were also well above the negative control (cellulose).  Rabbit skin, hair, and bone weren’t particularly good substrates.

As to fermentation products, collagen, glucosamine, and chondroitin were actually on par with FOS in terms of butyrate production:

Depauw SCFAs

Glycosaminoglycans (glucosamine and chondroitin) are found in cartilage and connective tissues (ligaments and tendons) and may have been mediating some of these effects as they’re some of the carbiest parts of animal products.  Duck Dodgers wrote about this in a guest post at FTA and in the comments of Norm Robillard’s article (probably elsewhere, too); very interesting stuff.

The authors also mentioned that the different fermentation rates in the first few hours suggests an adaptive component (some took a while to get going), or that certain substrates induced the proliferation of specific microbes.  “Animal prebiotics.”

Depauw close up

This is particularly noticeable for FOS (solid line), which is a plant fibre that wouldn’t really be present at high levels in a cheetah’s diet, so the microbes necessary to ferment it were probably not very abundant (initially).  Chicken cartilage (long dashes), on the other hand, started immediately rapidly fermenting, perhaps because this is more abundant in the cheetah’s diet.

Depauw took this a step further and fed cheetahs either exclusively beef or whole rabbit for a month (2013). Presumably, the beef had much less animal fibre than whole rabbit.  When they initially examined fecal short chain fatty acids, there were no major differences between the groups:

SCFAs per gram

However, if you take into consideration that the whole rabbit-fed cheetahs produced over 50% more crap than meat-fed cheetahs, then some other differences become apparent.  For example, the concentration of total SCFAs is actually greater in the feces from whole rabbit-fed cheetahs:

updated table

edit: la Frite pointed out that the table in the original manuscript is incorrect; the total SCFA numbers are reversed. The excel table above is corrected.

Further, the mere fact that there was 50% more fecal mass per day pretty much confirms way more animal fibre in whole rabbits.  And while neither of these studies were accompanied by microbial analysis, a more recent study on cheetahs fed primarily meat, “randomly interspersed with unsupplemented whole rabbits,” showed low levels of Bacteroidetes and Bifidobacteria, two potentially health-promoting groups of microbes (Becker et al., 2014).  I suspect this may have been at least partially due to a relative lack of animal fibre, compared to the Depauw’s exclusive whole rabbit diet.

Human digestive physiology and gut microbes are certainly far different from that of a cheetah, but maybe we too receive some prebiotic benefits from these animal fibres… just something to think about next time you’re eating sardines or pork ribs.

Consults are open, contact me if you’re interested: drlagakos@gmail.com

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Fermented meat & probiotics

From Slate: “Sausage made with bacteria from baby poop isn’t as gross as it sounds.” 

and my favorite: “Pooperoni? Baby-poop bacteria help make healthy sausages.

Much ado about: Nutritionally enhanced fermented sausages as a vehicle for potential probiotic lactobacilli delivery (Rubio et al., 2014)

The media seems to have missed the ball, but not by far.  They focused on healthy microbes being incorporated into fermented meats, whereas the scientists seemed to want to make a “healthier” low-salt, low-fat sausage.

The low-salt part seems to partially make sense from a fermentation-perspective: using probiotics instead of salt to reduce the potential for pathogenic microbial contamination.  However, I doubt reducing the sodium by 25% will have any appreciable impact on health outcomes.  The effect of adding beneficial microbes, on the other hand, might.

They also mentioned making it lower in fat, but that doesn’t make as much sense; I don’t think there’s a big contamination risk of having a higher fat content.  #lipophobia

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Gut microbiome & short-chain fatty acids: resistant starch vs. prebiotics

Bifidobacteria undoubtedly like resistant starch (RS).  They bind and hold on tight, an effect mediated by cell surface proteins.  Big thanks to Tim Steele for passing along many of the studies cited here.  One of said studies showed that treatment of bifidobacteria with proteases abolished the RS binding; but even dead critters would bind if their cell surface proteins were intact (Crittenden et al., 2007).  

I suspect fermented foods have this all figured out.  The microbes in sauerkraut are going to be embedded in & all around the cabbage polysaccharides; likely protected from digestive enzymes (to a degree) and holding on tight.

Something similar has been shown for galactooligosaccharides (GOS) (Shoaf et al., 2006).  In this study, GOS, but not a variety of other fibres, inhibited the binding of pathogenic gut microbes to intestinal epithelial cells.

These mechanisms are likely not mutually exclusive, and both seem like they could benefit the host (us).

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On resistant starch and blood glucose control

For overall health and well-being, fermented foods like sauerkraut and kefir are great.  Especially when following a low carbohydrate diet which is generally low in the types of foods which feed the gut microbiome.

For those with gastrointestinal problems, the gut microbiota is probably involved.  Whether it is bacterial overgrowth or dysbiosis, gut bugs are usually the culprit.  Treatment options vary widely, ranging from global extermination with vinegar & a low fibre diet (as per Jane Plain), or remodeling the microbiome with a prebiotic like galactooligosaccharides.   Probiotics like bifidobacteria can help, too, if they’re administered with either prebiotics or fermented foods (they need something to nourish them in transit).  Dark chocolate is also an excellent vessel.  Resistant starch is another option, although the question remains as to whether or not this is compatible with a low carbohydrate diet.

Resistant starch has been around for a while, and when I was in school it received about 10 minutes of attention during the fibre lecture.  But Jimmy Moore and Richard Nikolay have been talking about it a lot lately so I decided to freshen up on the topic.  In brief, it can be therapeutic for GI issues, but some studies have shown mixed effects on glucose & insulin metabolism.  The former is virtually unarguable, but I found the latter interesting.  And the impact of resistant starch on ketosis is included as well.

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Ketosis: anti-brain fog. Neurotransmitters, dietary protein, and the gut microbiome.

Treatment for dietary protein-induced brain fog: dark chocolate with 3% GOS and 10% MCTs.  Who’s in?

#IntermediaryMetabolism (bear with me here)
Ketosis from liver’s perspective:  increased fatty acid influx & [partial] oxidation causes acetyl-CoA levels to rise dramatically.  Concomitantly, gluconeogenesis redirects oxaloacetate (OAA) away from combining with acetyl-CoA via TCA cycle citrate synthesis and toward gluconeogenesis.  Since the acetyl-CoA doesn’t have much OAA with which to couple, it does itself to make acetoacetate.  Ergo, ketosis, and fortunately liver lacks ketolytic apparatus.



Brain is singing a different tune.  Ketones provide ample acetyl-CoA and are efficiently metabolized in the TCA cycle.  Ketolysis is not ketogenesis in reverse, else liver would consume ketones.keto metabolism

Teleologically speaking (and I don’t really know what that word means), ketones are meant to spare glucose for the brain by replacing glucose as a fuel for peripheral tissues like skeletal muscle and displacing some brain glucose utilization.  The former is vital as one of the few sources of “new” glucose is skeletal muscle amino acids, and they would be exhausted in a short amount of time if skeletal muscle kept burning glucose –> incompatible with survival.  Getting some of that fuel from fatty acids, ie, ketones, is just way better.  Thus, the “glucose sparing effect of fat-derived fuel.”  And by “glucose,” I mean “muscle;” and by “fat-derived fuel,” I mean “ketones.”  There are numerous intracellular signaling events and biochemical pathways pwned, but that’s the gist of it.

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Guts ‘n GOS, Op. 142

Part 1.  Guts

Nice review article about the great diversity of carbohydrate-modified diets used in the treatment of gastroin-testiness.

Short-chain carbohydrates and functional gastrointestinal disorders (Shepherd, Lomer, and Gibson 2013)

this handy table:
handy table

the full version (click to enlarge, print, and use as a cheat sheet):full table

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Non-sequiter nutrition IV. in vino veritas

The French Paradox is neither a paradox nor French, really.  Red wine isn’t saving the French from a saturated-fat induced heart attack epidemic….  Not to take anything away from red wine, however, as the metabolic effects of red wine (and alcohol in general) are rather interesting.

Background info: alcohol (ethanol) metabolism produces NADH (stick with me here, this article doesn’t get all technical on you I promise).

NADH inhibits gluconeogenesis (Krebs et al., 1969); as such, alcohol lowers blood glucose, regardless of whether if it’s pinot, cabernet, or straight moonshine (Harold  R. Murdock, 1971).

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Protein bar takedown, part III (or V)

No more pretense or cute backstory; I just like reviewing ingredient profiles of protein bars.  It’s a hobby of mine:
Candy in disguise, Op. 73 (circa April 2012)
Decepticon Promicor (soluble corn fiber), Op. 81 (June 2012)
Candy in disguise II, Op. 87 (July 2012)
Protein bar round-up, take II (September 2012)


This is a review of Netrition’s “highest rated” bars.  Important notes about this category: these are not necessarily “new” protein bars, or even the bars everyone buy (“best sellers”).  They are the bars everyone who votes like the most.  They’re not the healthiest either… but some come close.   Continue reading


Dark chocolate meets probiotics; the bifidobacteriomance continues

or the next big thing in functional foods, Op. 84

Altered gut bacteria can cause a whole host of problems, anywhere from depression and fatigue to ADHD and heartburn.  Thus, while running my daily search for “bifidobacteria,” I happened across these little goodies: 

The Attune Foods Dark Chocolate Probiotic Bar.  Combining probiotics (e.g., bifidobacteria, acidophilus, etc.) with chocolate?!  And with 68% cocoa, I’d expect this bar to deliver at least some of the benefits of dark chocolate (e.g., improved insulin sensitivity). They’re gluten-free and even contain inulin! (my second favorite bifidogenic prebiotic.)

And it packs a big, or rather huge, probiotic punch (6.1 billion B. lactis HN019, L. acidophilus NCFM, & L. casei LC-11).  Attune loses a little cred by trying to disguise their sugar as “evaporated cane juice,” like it’s something inherently healthier than plain old sugar… just like all-natural agave syrup, honey, and organic coconut blossom sugar.  just own it for crying out loud.  On the other hand, at only 6 grams, the sugar in Attune’s bar is harmless especially in the context of the high cocoa content, inclusion of inulin, and whopping dose of probiotics.

But, chocolate & probiotics?  Alas, the curiousity bug had bitten.

Apparently, a lot of companies think dark chocolate is a good vehicle for probiotic delivery.

GI Health’s Probiotic Chocolate is gluten-free and contains a half billion L. helveticus R0052 and B. longum R0175 per serving.  A half-billion is low by conventional standards*, but such standards might be irrelevant if the delivery vehicle (i.e., chocolate) is superior.

*Most probiotic products are rated (by me) by the number of live bacteria per serving, or “colony forming units (cfu).”  This is usually in the billions because most die in transit, thus the importance of the delivery method.  Yogurt and apparently now chocolate seem to be good delivery vehicles, however, yogurt and most probiotic pills require refrigeration; these chocolate products do not.  And neither do Nature’s Way Probifia Pearls, although they are the only pill that doesn’t (I suspect alien technology).

gimme Probiotics Dark Chocolate Candies, Youngevity Triple Treat; the list goes on and on.  Apparently, I was late to the game… (expect to see these in your local grocer soon.)

Enough shameless promotion, what about the data?

Possemiers (2010) set out to test how well probiotics survived in a robot gut simulator when mixed in chocolate.  1 billion L. helveticus CNCM I-1722 and B. longum CNCM I-3470 were mixed with either chocolate or milk.  An astounding 85% of the probiotics survived when administered in chocolate compared to only 25% with milk.  FYI the study was funded by Barry Callebaut, a fancy Belgian chocolate maker who is currently developing their own line of probiotic chocolates … it’s not a conflict of interest, it’s what companies should be doing IMO (while an independent third party would be optimal, any data are better than none).  I have no idea how well their robot gut simulator emulates actual human digestion, but these results suggest that chocolate is [at least] potentially a good candidate to deliver probiotics.

An additional benefit of loading probiotics into chocolate is that cocoa itself can function as a prebiotic.  Tzounis (2011) gave real-life live humans cocoa every day for 4 weeks and showed that bifidobacteria increased dramatically.  These findings were confirmed by Fogliano (2011), who showed (via another robotic gut simulator) that water-insoluble cocoa fractions (e.g., cocoa fiber) alone markedly stimulated the growth of bifidobacteria.

So: 1) chocolate is a good vehicle to deliver exogenous bifidobacteria; and 2) cocoa promotes the growth of endogenous bifidobacteria.  win-win.

Why is this relevant?  because probiotics by themselves don’t survive the trip!  They die off somewhere between the factory and your large intestine.  In a study by Prilassnig (2007), 7 people were fed one of 6 different commercially available probiotics for a week.  2 of the products contained bifidobacteria, Omniflora and Infloran.  None of the bifido in Omniflora survived in any of the volunteers, and the bifido in Infloran was detectable in only 1 out of 4.  Feeling lucky?

Thus, chocolate may be not only viable, but an optimal way to administer probiotics.  The bifidobacteria can feed on the cocoa while in transit (from the factory to your cupboard to your bowels), and the cocoa can directly stimulate them along with your native gut flora.

And chocolate with GOS?!  according to Davis (2010), chocolates enriched with 10 grams of GOS increased endogenous bifidobacteria a whopping 3-fold.

Formula for the healthiest chocolate on Earth? >70% cocoa, a billion bifidobacteria, and a few grams of GOS… don’t get your hopes up, however, this won’t likely be made any time soon.  Despite all of the data showing the remarkable health-promoting properties of GOS, it’s still not widely commercially available.  In the meantime, Attune’s use of inulin will have to suffice.



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