Weekend Long Read: Restoring Our “Second Genome”

If Michael Pollan and the NYTImes are to be trusted, the new hot-topic Frontier of Popular Medicine is the human (mostly intestinal) microbiota:

In sheer numbers, these microbes and their genes dwarf us. It turns out that we are only 10 percent human: for every human cell that is intrinsic to our body, there are about 10 resident microbes — including commensals (generally harmless freeloaders) and mutualists (favor traders) and, in only a tiny number of cases, pathogens. To the extent that we are bearers of genetic information, more than 99 percent of it is microbial. And it appears increasingly likely that this “second genome,” as it is sometimes called, exerts an influence on our health as great and possibly even greater than the genes we inherit from our parents. But while your inherited genes are more or less fixed, it may be possible to reshape, even cultivate, your second genome.

Justin Sonnenburg, a microbiologist at Stanford, suggests that we would do well to begin regarding the human body as “an elaborate vessel optimized for the growth and spread of our microbial inhabitants.” This humbling new way of thinking about the self has large implications for human and microbial health, which turn out to be inextricably linked. Disorders in our internal ecosystem — a loss of diversity, say, or a proliferation of the “wrong” kind of microbes — may predispose us to obesity and a whole range of chronic diseases, as well as some infections… (Researchers use the word “microbiota” to refer to all the microbes in a community and “microbiome” to refer to their collective genes.) We’ve known for a few years that obese mice transplanted with the intestinal community of lean mice lose weight and vice versa. (We don’t know why.) A similar experiment was performed recently on humans by researchers in the Netherlands: when the contents of a lean donor’s microbiota were transferred to the guts of male patients with metabolic syndrome, the researchers found striking improvements in the recipients’ sensitivity to insulin, an important marker for metabolic health. Somehow, the gut microbes were influencing the patients’ metabolisms…

These claims sound extravagant, and in fact many microbiome researchers are careful not to make the mistake that scientists working on the human genome did a decade or so ago, when they promised they were on the trail of cures to many diseases. We’re still waiting. Yet whether any cures emerge from the exploration of the second genome, the implications of what has already been learned — for our sense of self, for our definition of health and for our attitude toward bacteria in general — are difficult to overstate. Human health should now “be thought of as a collective property of the human-associated microbiota,” as one group of researchers recently concluded in a landmark review article on microbial ecology — that is, as a function of the community, not the individual….

Full-service sidebar to the main article includes the following exchange:

Aside from eating fermented foods, and not going nuts with the Purell, is there anything else that you recommend to improve your microbiome?

Garden. The exposure to soil is probably a good thing and, unless you live in a Superfund site, gardening is a good way to safely increase your “microbial pressure” on a daily basis. Having a dog may be a good thing too.

(Of course — and I say this as someone who gardens, with imported soil, on a dual Superfund site — for the urbanized mostly-coastal readers who are the NYTimes‘ target advertising audience, it’s safe to assume that one’s garden is contaminated, at the very least, by lead and other formerly-airborne twentieth-century pollutants. As a civil-engineer friend told us, “At least you have an EPA-certified list of all the poisons in your dirt.”)

71 replies
  1. 1
    Calming Influence says:

    There’s an old farmer’s saying, “you’ll eat a peck of dirt before you die” implying ingesting a little soil won’t kill you. May turn out it’s actually good for you.

  2. 2
    MonkeyBoy says:

    Some docs have shown that poop transplants can be effective cures for certain gastrointestinal problems, though they haven’t been officially approved yet.

    I can’t wait until they DO become approved and coverable by insurance. It will attract the usual questionable medical practitioners who will probably promote “off label” applications.

    And do we really need TV infomercials hawking celebrity poop?

    (does anybody know where I can get a few pounds of frozen Reagan feces? They would be worth 100 x an equivalent amount of gold)

  3. 3
    Yatsuno says:

    Human health should now “be thought of as a collective property of the human-associated microbiota,

    We are Borg. Resistance is futile.

  4. 4
    Baud says:

    Eat shit and live!

  5. 5
    StringOnAStick says:

    You absorb most of your nutrients through the small intestine, which is where a good deal of these bacteria (and other microbiota) are located. IIRC, you must have the right bugs in there in order to create vitamin K2, a really critical vitamin that most of us aren’t getting enough of.

    This almost seems like “master of the bleedin’ obvious” stuff to me; anyone who has had a big intestinal die-off thanks to a round of antibiotics knows that messing with the gut bacteria can cause problems. Some recent studies have shown that as long as 6 months after a course of anitbiotics, the normal gut bacteria have yet to recover, and some bad actors are having a party. Just one more reason why antibiotics shouldn’t be as over-prescribed as they are today….

  6. 6
    p.a. says:

    Speaking of gardens, I recently spread a national brand of cedar mulch bought at a big box ‘hardware’ store. Did the planting several days later, and the mulch was ‘crawling’ with some kind of winged insect I’ve never seen before. Ant-like but not ants, to my eye at least. Anyone have this type of thing happen to them?

  7. 7
    Susan S says:

    Let me throw this in..a family I know.. Carolynn lives to be 96; her husband Clem died at 96 [he was pruning his trees at 90]; their son’s mother in law is still alive at 101; their daughter’s mother in law lived to be 97..and all grew up poor, living and working in Tacoma, WA..breathing daily the fumes of the Tacoma smelter..which has been shut down due to lead and arsenic traces..which still linger in the soils of Puget Sound.

    So far their children are an active 83 and 81..was it the dirt gardens that offset the poisons? Don’t know..just always thought it a fascinating story. And yes, I got to go to Clem and Carolynn’s 50th Golden Anniversary celebration..and shared their 75th with Carolynn..we ate shrimp salad and cake because Clem had to go to the hospital that day.

    .They had a truly great marriage..she smoked till she was 70..Clem never did. They quibbled at each other all day on their 50th, which shocked me, because I didn’t know happily married couples ever quibbled..[my parents were not happy..]..they led an extraordinary life on modest means..and my last vivid image of the two of them together is of Clem, with his arm around Carolynn, describing each slide to her [she was blind at the end of her life] at their son Gene’s 50th wedding anniversary! I never found that kind of love..but I digress. This is supposed to be about bugs and dirt. So I ask again, do you think the early Puget Sound life style was sufficient to offset the arsenic in the smelter?

  8. 8
    cathyx says:

    @p.a.: Carpenter ants? They have a winged stage.

  9. 9
    p.a. says:

    No, I unfortunately have first hand experience with carpenter ants, and these aren’t them. Speaking of carpenter ants, NEVER plant peonies near your house: they love the nectar. I’ll have to wait and see if the unknown critters affect my plants

  10. 10
    Yatsuno says:

    @cathyx: I thought that was only the queens, although many can be born at one time.

  11. 11
    cathyx says:

    @p.a.: earwigs?

  12. 12
    Violet says:

    I’m currently working on increasing my intestinal microbes by eating a lot of fermented foods. My goodness I know when I’ve had some of sauerkraut or kefir. Gut is all gurgly.

    As for gardening, I’m a big gardener and am working as hard on increasing microbial strength in the garden as in me. Tons of compost–everything green that doesn’t get used gets composted or mulched–and lots of additional goodies like molasses and organic fertilizers. This is the third year and we can tell a huge difference. Lizards are back, butterflies are in abundance, pests are down, and the worms are FINALLY back.

    Heavy metals in the soil–mustard greens remove them, especially lead.

  13. 13
    cathyx says:

    @Yatsuno: That’s possible, I don’t remember very well from learning about them so long ago.

  14. 14
    quannlace says:

    So I both garden and I have a dog. Does that mean I’ll live forever?

  15. 15

    The large intestine … the final frontier…. to boldly go where, well, you know the rest….

    Sorry. Just saw the Star Trek movie. Couldn’t help myself.

  16. 16
    quannlace says:

    Heavy metals in the soil–mustard greens remove them, especially lead.

    I take it then, that you cant eat them.

  17. 17
    cyntax says:

    OT, and I’m no birder, but LGM linked to this and it is a pretty amusing take on state birds and what they should be but rarely are.

  18. 18
    Liberty60 says:

    So I constantly work in my vegetable garden, and let my dogs lick my face to wake me up.

    Gawd, I will live to be 100 yet.

  19. 19
    nancydarling says:

    @cyntax: True story, or so my brother says who lived in Alaska for 10 years. The town of Chicken, Alaska was originally to be named Ptarmigan when it was incorporated in the early 1900’s. No one knew how to spell it so they decided to call it Chicken.

  20. 20
    Violet says:

    @quannlace: You can, but you could increase your lead exposure.

  21. 21
    Sister Rail Gun of Warm Humanitarianism says:

    I’ve also seen reports that multi-grain diets encourage a more varied bacterial population than the long-time mono-culture of the US diet. (Wheat, wheat, and more wheat.) Which makes me wonder if the anti-wheat people aren’t right that wheat is causing a lot of our health problems, just not by the mechanism they think.

  22. 22
    normal liberal says:

    Quannlace asked the question I’ve always had about plants that leech heavy metals out of the soil, but I’m still not sure what you can do with them once they’re all leaded up. Can’t compost, can’t incinerate, and you obviously don’t want to eat them.

    I was thinking of encouraging my extended local skunk family to feast on them – I wonder how much lead a skunk can handle. But then I’m stuck with leaded skunk poop and carcasses, and the latter might damage some of the birds.

    Damn. So what can I do with the plants?

  23. 23
    A Ghost To Most says:


    Could it have been termites? Our last house had termites when we moved in, and before we got rid of them, we got a bloom of flyers (thousands).

    My Terminix guy called mulch fast food for termites. We pulled it all out and put down stones.

  24. 24
    Omnes Omnibus says:

    @normal liberal:

    I was thinking of encouraging my extended local skunk family to feast on them

    Do you really want lead-poisoned and violent skunks?

  25. 25
    gene108 says:

    I’ll take my Purell, anti-biotics and everything else that nukes germs, thank you very much.

    The olden days, where cuts could kill and it wasn’t uncommon for kids to not reach adulthood is worth some mess up to my microbiome

  26. 26
    A Ghost To Most says:


    Those days are coming back, thanks to overuse of antibiotics.

  27. 27
    Shakezula says:

    Does beer count as a fermented food?

    Never mind, I have decided that it does.

  28. 28
    normal liberal says:

    @Omnes Omnibus: I was sort of hoping the skunks would die, but I can see that the less drastic lead impacts might produce bad skunk behavior, and perhaps the development of rodent gangs.

    Sadly, the skunks are ever with us. They drove out a groundhog settlement, and then moved into the tunnels, some of which lead under our deck – so pleasant for cooking and eating outdoors. Some years ago we hired a genius varmint hunter, who quickly trapped and dispatched more than a dozen skunks. ( He baited the traps with Cheetos, which I found…odd. But it worked.). The skunks have regrouped and returned.

    I hates them, I do. Enough to give them lead poisoning, no matter the consequences.

  29. 29
    Sister Rail Gun of Warm Humanitarianism says:

    @gene108: Just anecdotally, kids raised in relatively sterile surroundings seem to have more health problems than kids allowed to get out and get dirty. There’s a happy medium there, somewhere.

  30. 30
    FlyingToaster says:

    We had to have the top 18″ of our yard replaced. It was full of metals and building materials; being two blocks off of the Charles means that our neighborhood was probably a dump for the mills along the river.

    “At least you have an EPA-certified list of all the poisons in your dirt.”

    We have a composty front 2/3 of the yard; the back is still poisonous and we only grown things in pots or at the top of the hill (where testing didn’t find anything interesting).

    About six inches down in most of the back is boulders, so I’m thinking that I can probably get away with a raised bed. I’ve got the stakes for it, I just need landscaping timber and a cubic yard of topsoil :)

  31. 31
    cyntax says:


    That’s awesome. I wouldn’t know a ptarmigan if it crapped on me. I hae to say I was bit shocked that the flamingo is not Florida’s state bird but it’s not we’re doing any better here in California. Though to be fair, I see quail all the time but condors–not so much.

  32. 32
    gene108 says:

    @A Ghost To Most:

    I think it depends on what you mean by “those days are coming back”.

    I doubt we’ll see cholera or typhus out breaks, because of superior sanitation (at least in the U.S.).

    If you go outside the U.S., the rule of “don’t drink the (tap) water” applies, because you can end up with a nasty case of food poisoning/dysentery because other places don’t treat their water in the way our bodies can handle.

    I’m not sure where the drug resistant bacteria trend will wind up. I don’t think we’ll end up going back to 19th century mortality rates though.

  33. 33
    Omnes Omnibus says:

    @normal liberal: My brother had raccoons nesting in the detached garage at his last house. He does not find them cute.

    ETA: Once, while sleeping outdoors at Fort Sill, I woke up with a skunk standing on my stomach and staring me in the face. Luckily, my rigorous training as an army officer prevented me from panicking. I just stayed very still until the little fucker went away.

  34. 34
    LevelB says:

    You are correct about the soil in urban areas. I have spent 30 years working on Superfund sites. Be sure to wash your hands…

  35. 35

    @Sister Rail Gun of Warm Humanitarianism: my cousin lived in a rubbish tip of a home but she moved everything every day to wipe all surfaces with Dettol. Her doctor told her that her immune system was so compromised that if they ever stopped making Dettol she and her entire family would be goners.

  36. 36
    FlyingToaster says:

    @gene108: You’d actually be better off to use some plain old plant-based soap (we use Sun&Earth for liquid, and Shea Butter or Olive Oil bar soaps) than the Purell. My daughter’s school replaced the hand sanitizers with liquid soap in the bathrooms and the illnesses went down (she hasn’t missed a day from illness this past school year).

    Right now, what we’re seeing in preschool is that vaccination and simple hygiene are doing more for illness prevention and transmission than anything else. One of WarriorGirl’s schoolmates got pinkeye; the only person she managed to infect was her twin brother. The one girl who wasn’t vaccinated for varicella came down with Chicken Pox; nobody got the flu in her class at all.

  37. 37
    normal liberal says:

    @Omnes Omnibus: I’m not surprised. While the skunks are annoying and can be a rabies vector, they’ve got nothing on raccoons for destructive capacity and general random mayhem.

    One night a raccoon got caught in one of our skunk traps. By the next morning when I idiotically released the raccoon, he had dug about two inches under each square in the trap mesh in an amazingly patient attempt to escape. This was years ago, and there’s still a trap-sized depression in the lawn.

    Did the raccoons dismantle the garage and sell the components? I wouldn’t put it past them.

  38. 38
    TheMightyTrowel says:

    Archaeology:bad for the wallet and live, fucking ace for the gut flora.

  39. 39
    TheMightyTrowel says:

    Archaeology:bad for the wallet and liver, fucking ace for the gut flora.

  40. 40
    gene108 says:

    @Sister Rail Gun of Warm Humanitarianism:

    I think my whole concern about the “let the germs back into your life” mindset is it sort of reminds me of the anti-vaccination rhetoric.

    The scientists studying this stuff are just doing their job, but in the hands of a sage pop-culture figure, like Jenny McCarthy, who the hell knows what crazy ass crap misguided people will start doing.

    Also, there’s a difference between antibiotics and sanitizers, such as anti-bacterial soap or Purell or Lysol or bleach. The sanitizers kill surface germs on our hands or on surfaces.

    What impact sanitizers will have on our gut bacteria is in large part what the current research is studying, versus places where you don’t get antibacterial soap or hygiene and sanitation aren’t as good, such as poor Ecuadorian villages (saw something about this on the Smithsonian Channel this morning).

    Anyway, given the fact indoor plumbing has probably done as much or more to change the sort of germ-ridden world our ancestors lived in compared to the recent development of portable sanitizers – bleach having been available for some time, and even Lysol being around for decades, but you weren’t taking containers of either of these in your pocket – I really have to see if this research goes anywhere in actually identifying causes and effects cause by different environmental conditions, before ditching my hand sanitizers and antibacterial soaps.

  41. 41
    Omnes Omnibus says:

    @normal liberal:

    Did the raccoons dismantle the garage and sell the components? I wouldn’t put it past them.

    He got someone to live trap them and help them self-deport.

  42. 42
    Sister Rail Gun of Warm Humanitarianism says:

    @Litlebritdifrnt: Ayup. I know lots of such stories, but haven’t heard of any studies to back them up as a general case.

    There are appropriate times to use antibiotics. I just had one of them. I love my kitties, but cat scratches are dangerous. The scratch site is now cleaned with alcohol and under a layer of ointment.

  43. 43
    Anon says:

    “dual Superfund”

    Toms River?

  44. 44
    AnnaN says:

    Man in service to microbe? Excommunicate the scientist!

  45. 45
    gene108 says:


    I’m not a serious germphobe. I use liquid handsoap that says it is “antibacterial”. I grew up using bar soap to wash my hands, after going to the bathroom, before liquid soap became common.

    From what I’ve read/seen this research is trying to figure out things about our insides based on our environmental surroundings. The research may come up with something or maybe a big nothing burger.

    Sanitation, which you credit for your daughters good health at school, is one of those relatively recent developments that has totally changed the sort of germs/bacteria we are exposed to compared to our ancestors.

    I just think there are so many factors effecting gut bacteria, such as sanitation conditions, i.e. living with indoor plumbing versus living in a third world slum without adequate access to toilets, that I don’t know how these researchers are going to be able to draw up anything conclusive.

    I think this is a lot of media hype, before any results are in and may cause people to make bad decisions.

  46. 46
    Yatsuno says:


    Man in service to microbe? Excommunicate the scientist BURN THE WITCH!

    Fixteth for moar Teabangelical truthiness.

    (And FYWP.)

  47. 47
    angler says:

    Bummer, another health habit to monitor, improve, sell. Here’s hoping beer improves my second genome.

  48. 48
    Poopyman says:

    Sounds like one of my favorite curses, “eat shit and die”, may just be wishful thinking, eh? Maybe I should start greeting friends with “eat shit and thrive.”

  49. 49
    Jennifer says:

    I wrote about this topic <a href = "http://3weirdsisters.com/?s=no....."here 3 years ago after reading the excellent Good Germs, Bad Germs by Jessica Snyder Sachs. For whatever reason, I find bacteria and viruses fascinating.

    gene108, dump the antibacterial soaps. Plain soap removes just as much bacteria from hands (or other skin) as “antibacterial” soaps do; the problem with the antibacterial ingredients in soaps and many household cleaners is that they function like antibiotics and encourage bacterial resistance to antibiotics as a result. The best bacteria-killing cleaners to use are things like vinegar and hydrogen peroxide, or bleach. Vinegar kills through creating a ph level hostile to germs, to which they cannot develop resistance. Peroxide and bleach both kill via oxidation to which again bacteria cannot become resistant.

    And also, develop some perspective. Bacteria typically don’t thrive on dry surfaces; they may land there and live for a few days, but in the absence of moisture or food they won’t multiply. That having been said, we’re swimming in a sea of bacteria every moment of our lives, and it would be both impossible and dangerous to our health to wipe them out entirely; our best bet is to not be so freaked out about them while still maintaining sensible habits such as frequent hand washing and proper food prep.

  50. 50
    Jennifer says:

    Not being able to edit sucks.

  51. 51
    PsiFighter37 says:

    OT, but I am poolside overlooking the Puget Sound, drinking a well-hoppy Pike IPA here in Seattle. It may not be hella sunny, but this is hard to beat. Devouring a ton of oysters in a couple hours.

    Life is good, and I can forget about why politics infuriates me for a good while.

    PF37 +3

  52. 52
    Omnes Omnibus says:


    Devouring a ton of oysters in a couple hours.

    Do you get a t-shirt for that?

  53. 53
  54. 54
    PsiFighter37 says:

    @Omnes Omnibus: No, but that might be partially awesome?

    Either way, it’s phenomenals

  55. 55
    Yatsuno says:

    @PsiFighter37: Ugh. No shelled sea slugs for me. Though you could challenge CaseyL to an oyster eating contest. Nothong personal, but my money’s on her. I’ve seen her pack those suckers away.

  56. 56
    FlyingToaster says:

    @gene108: I only can go from my own (therefore, anecdotal) experience.

    I’m comparing first world environments forty years and a culture apart. Both with adequate sanitation, both with adequate medical care, and the difference in philosophy on everyday germ exposure.

    My mom (and many members of her generation) were/are both neatniks and germophobes; because of some of their practices, the allergies I inherited are exacerbated. My mom freaks out if you spill anything, because bacteria will grow there. She uses lysol and bleach with abandon.

    I don’t own any lysol, and the gallon of bleach I buy lasts for years. When things get spilled, we wipe them up and once a year run the steam cleaner on the carpets. I have a cleaning crew do a deep cleaning on my bathrooms every other week, so that I don’t destroy what’s left of my lungs; and they use “green” cleaners. I do wash my hands when I come back in the house, and so does WarriorGirl (because both home and school has that rule). Wounds are cleaned with 1) wet washcloth 2) peroxide wipe 3)polysporin/neosporin 4)bandage.

    As the genetic counsellor warned, my daughter did inherit the primary condition from which my other allergies sprang. But she has only seasonal hay fever and eczema, and no dietary allergies or contact dermatitis to common substances. No asthma. No hives. Nothing.

    There are times and places I thing antibacterial soap and hand santizers are vital (medical facilities, yes?), but those places aren’t my home.

  57. 57
    normal liberal says:

    @Omnes Omnibus:
    Re your alarm skunk: Good God. Congratulations on your impressive control of your reflexes, no doubt a tribute to the training you received while serving in the military. That was unusual behavior for a skunk; I wonder what he was thinking.

    My father’s training for WWII involved swamps and deserts, and their various slithery and poisonous fauna, which was tremendously useful when he shipped out for three years in northern Europe. I think he preferred dealing with the Germans over snakes and scorpions.

  58. 58
    lojasmo says:

    I don’t wash my fruits or vegetables, and I don’t wash wounds more than just to get any gross mud or sticks out of my skin.

    I have to wash my hands a million times a day at work, as I am a practicioner.

  59. 59
    Sister Rail Gun of Warm Humanitarianism says:

    @gene108: Everything I’ve seen has been focused on diet, not environment. From what I’ve read, this may be at least part of the answer to why some foods are associated with certain disease states. The one that really caught my attention was connection between inflammation and the waste product from the bacteria that dominate when the diet is mostly red meat.

    OTOH, are we really having better results with all the extra antibiotics in everything around us?

  60. 60
    sm*t cl*de says:

    To the extent that we are bearers of genetic information, more than 99 percent of it is microbial

    If 90% of the cells in the body are bacteria, and those bacteria each have a genome an order of magnitude or so smaller than the 10% of eukaryotic cells, then to get from there to “more than 99% of genetic information” requires MM’s calculator.

  61. 61
    Suzanne says:

    I just had the second round of my allergy tests performed. I am pretty much allergic to the entire Sonoran desert. And dogs and cats. And dust mites. Good ing for me that I don’t have any of those things nearby.

    I have given up hand sanitizers except when I visit a hospital. The rest of the time, I just wash my hands well and frequently, and try not to do gross things. Other than my damn allergies, I do pretty well.

    I do want to replace the carpet in my house with tile, however.

  62. 62
    StringOnAStick says:

    @Sister Rail Gun of Warm Humanitarianism: I don’t do evidence by anecdote, but cutting wheat saved me from the knee replacement I was ready to sign up for this spring. According to the genetic test I had done, I have both the genes that are linked to celiac disease; have those 2 bad boys in your DNA and the question of developing celiac disease is more one of “when” not “if” (of course, constant exposure to wheat is necessary in order to cause celiac so I chose to get off the train). A common side effect of gluten intolerance is joint pain, and I had that in spades (please note the word “had”, as in this is no longer the case).

    I quit eating all other grains because of being borderline diabetic with lots of family history; grains are just too concentrated a source of carbohydrates that trigger insulin spikes. I was already showing the signs of insulin resistence, high triglycerides and poor cholesterol numbers; all this on top of a very active exercise regime (20 hours of aerobic exercise per week, sometimes more). No grains has resulted in perfect fasting blood sugar scores), something I didn’t have before.

    Also, there are some real problems with that study linking red meat to TMAO production and increases in heart disease, one being that it was based on 6 people, one of which was a vegan that was convinced to eat a steak for science – the rest of the data came from mouse studies where carnitine was fed, not red meat. Checking the graphs in that publication shows that by far, the greatest increase in TMAO was not from eating red meat, it was from eating Halibut and Cod; wait, haven’t we been told to eat lots of fatty fish and run from red meat like it was poison? Hmm, something isn’t making sense. Further details here: http://chriskresser.com/red-me.....t-the-meat

  63. 63
    Anne Laurie says:

    @Anon: Woburn, where the high school football team are called Tanners.

  64. 64
    Sister Rail Gun of Warm Humanitarianism says:

    @StringOnAStick: If you have the genetic markers for celiac, then of course you’re going to be better off cutting out gluten. That doesn’t mean the rest of us should go paleo. (Which I am intensely skeptical of, BTW.)

    I will admit that the red meat TMAO study and the carnitine study had blended in my memory with the studies on lipopolysaccharides, but it’s clear that the paleo advocate you cite is focusing on what’s important to him, a possible escalation of the anti-meat campaign we’ve been hearing for years.

    What interested me was how they reinforce that varying what you eat is a good thing. An all-American diet of McD burgers and steak-and-potatoes is bad for you because it leads to an overpopulation of a particular gut bacteria that produces a particular toxin. Other studies on these bacterial populations suggest that much of the negative effect can be abated by adding soluble fiber to the meal.

  65. 65
    Sister Rail Gun of Warm Humanitarianism says:

    @StringOnAStick: Cutting out gluten makes sense for celiacs. Not so much for the rest of us. I’m highly skeptical of paleo in general, and the paleo advocate you cited in particular. Is he still an anti-vaxxer?

    The whole body of research both interests me and amuses me because it’s looking more and more like an argument is building for a food combining diet, though not one that looks anything like the fads.

  66. 66
    Sister Rail Gun of Warm Humanitarianism says:

    FYWP. I waited 15 minutes before deciding that my post had been lost to the ether.


  67. 67

    I’ve long been convinced that the calories in your food are just a crude starting point in terms of understanding what the effect on your weight will be.

    Digestion is a very complex process, and they’re modeling that by burning a piece of food to see how much extra heat is produced.

    Maybe the microbiota in your gut break down food into nutrients much more efficiently than the microbiota in mine do. If so, we can eat the same meal, and it will cause you to gain weight while I don’t.

    And then there’s the mechanics of digestion. Maybe certain foods are more prone than others to take a quick trip through the system, in which case they would be absorbed much less efficiently than another food with the same calorie count, thereby being much kinder to your waistline.

    I’ve never outgrown eating (natural) peanut butter straight from the jar, and I’m convinced that this is what happens when I eat a few ounces of it – that it not only moves through the system a bit faster, but pushes everything ahead of it as well, so that my bedtime snack of natural peanut butter somewhat reduces the calories I’m going to absorb from my dinner. At least, that interpretation is consistent with years of observed outcomes.

  68. 68
    Larryb says:

    @p.a.: Er, termites? Reminds me of a scene from John Brunner’s “The Sheep Look Up” where the hippies receive a gift of “earthworms” for their organic garden that aren’t quiet *right* (queue ominous music).

  69. 69
    lojasmo says:


    I had similar results when I gave up grains.

    HDL increased by 17
    LDL decreased by 79
    Triglycerides dereased by 20

    Systolic blood pressure down by 25
    Diastolic down by 15

    Ankle pain…gone.

  70. 70
    EthylEster says:

    @gene108: there is a middle ground.

  71. 71
    PhoenixRising says:

    From what I’ve read/seen this research is trying to figure out things about our insides based on our environmental surroundings. The research may come up with something or maybe a big nothing burger.

    God, I hope it’s not nothing. The toddler actually pictured on the cover of last week’s NYT Mag (and the dog in the study referred to is not her actual dog, BTW) is standing in for my niece.

    As a participant in the Poop Preservation Project, to allow her father to sequence the genetic evolution of gut microbes, I have very high hopes for the results. They have already justified the freezing of each time/date Sharpie’d full diaper, in that the data set didn’t exist before she was a year old.

    It was known that somehow, bacteria colonize the gut and change babies who can only tolerate breast milk (or formula made with sterile water) into toddlers who can mostly digest a McNugget. But because IRBs won’t approve anything using human subjects under 6 months, the exact mechanics of this colonization is now in view of the supercomputer and her handmaidens, as I refer to the scientists described in the article.

    There were other reasons my niece was born, as I plan to assure her when she’s mature enough to understand that she was used as a research subject before she could focus her eyes. They wanted kids before he got tenure…I think.

    Anyhow, as anecdata: The guys and gals who work on this question let their own toddlers drink out of the dog’s bowl, prep a raw chicken in the same sink they wash bottles in, and won’t allow anything with added topical antibiotics in the house. Because they don’t know what your hand soap is killing, despite specializing in the field.

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