Gut bacteria

[ys]

you cannot possibly live without bacteria

well, you are assuming that ALL bacteria in the body is beneficial, i highly doubt that.  i don't think there is any benefit of bacteria that's under fingernails.

[yuli]

But the fact that not all bacteria are beneficial is another good reason why we need the good bacteria...

[PaleoPhil]

well, you are assuming that ALL bacteria in the body is beneficial, i highly doubt that.  i don't think there is any benefit of bacteria that's under fingernails.

Actually, you're assuming that I'm making that assumption, which I'm not. On the contrary, I'm fully aware that there are neutral (or their benefit is as yet undiscovered) and pathogenic bacteria, including lethal ones, and I have written about them in this very forum (and they are also discussed in some of the links I provided here and in other threads). We can live without lethal bacteria, but we cannot live without the good ones and we cannot avoid having some bacteria and other microbiota in and on our bodies. It's impossible to avoid them.

As a matter of fact, some scientists have lately started referring to us humans as "[amalgamations] of human and microbial parts":

"We think that there are 10 times more microbial cells on and in our bodies than there are human cells. That means that we're 90 percent microbial and 10 percent human. There's also an estimated 100 times more microbial genes than the genes in our human genome. So we're really a compendium [and] an amalgamation of human and microbial parts."

Gordon's research shows that these microbes living in our bodies aren't just there for the ride — they're actively contributing to the normal physiology of the human body. He points to the trillions of microbes that live in our gut, doing everything from encoding enzymes to serving as pathways for vitamin production to digesting the parts of food we can't digest on our own.

"We're trying to understand how these compendia of microbes operate as a community — how they are shaped by the habitats in which they live and, in turn, how they shape us," he says.

....

Gordon has also looked at the role microbes in the gut play in combating diseases.

He points to an example of a patient infected with the Clostridium difficile bacteria, which causes severe diarrhea and can frequently return, even when treated with antibiotics. The patient was treated with a transfusion of gut microbials from a healthy individual's fecal material to restore the bacterial flora in the intestinal tract — and symptoms improved.

"Most people have this view of our encounters with microbes from the perspective of disease. But that couldn't be farther from the truth," Gordon says. "Most of our interactions with microbes are beneficial and are healthy. And here you have an example of a transplantation of a microbial community ... to help cure this reoccurring and relapsing and severe disease."

--Jeffrey Gordon, Director of the Center for Genome Sciences at Washington University in St. Louis, Bacterial Bonanza: Microbes Keep Us Alive, http://www.npr.org/templates/story/story.php?storyId=129862107

But the fact that not all bacteria are beneficial is another good reason why we need the good bacteria...

correct

[sabertooth]

Life is a never ending biological war being waged by the countless forms of DNA against each other, for the right to live another generation. Fungal life forms have developed the ability to produce antibiotic poisons in order to subdue bacteria that would otherwise eat them, and bacteria have formed chemical defenses as well, both types of life forms are savagely trying to eat us every minuet of every day. Our body's have been designed  to seek out and maintain a healthy balance of these organisms so that one pathogen cannot over take the whole shebang. If something is out of balance and if one harmfull organism becomes over populated then the immune system will purge it out, as long as the body is health and well nourished.  

Some forms of bacteria and fungus are capable of producing poison and causing infection, but perhaps even the toxic strains may have some beneficial effects in small amounts. Low levels of poisonous excretions in the gut could have immune stimulating property's that function to regulate the overall bacteria profile of the gut. I still have doubts whether gut fungus or molds are really essential or if they are  just an invasive enemy that only cause harm if they are allowed to grow unchecked. The antibiotic properties of molds and fungus can be very poisonous to humans and bacteria alike, and I am absolutely appalled by the way antibiotics are used by the medical field.

If you are so ill and have such a week immune system that you need an antibiotic in order to keep a mild infection under control , then there are some other serious health issues that need to be addressed. Most children where I live are never allowed to even try to fight off the mild infections that come with childhood and I honestly believe that many have had their immune system weakened and gut ecology destroyed by the use of antibiotics. I was put on antibiotics at six months old, two weeks after my 6 month vaccinations, for an ear infection(often after a vaccination the immune system becomes exhausted and leaves the body open to infection, I have seen it happen countless times)and once you are dosed with the stuff you end up even more damaged and less able to fight off future infection on your own. At a year old I had another major infection and had to be dosed again, and again at 18 months(many infections occurred within weeks of a vaccination(perhaps coincidence?)and after three years old I stopped fussing about ear pain and eventually the infections went away, I remember through my childhood that I would still get occasional infections but they would always go away on their own without antibiotics and I stayed fairly health through my teenage years. Almost every other member of my family in this generation has had to endure the same chronic ear and respiratory infection, but I have learned how to break the cycle and none of my kids has been vaccinated and have never had an infection that required antibiotics.(coincidence Perhaps?)  

I just don't think most people are aware of how dangerous these synthetic variants of fungal poison are, My grandfather was allergic to penicillin and so was my father, I had an allergic reaction the last time I took antibiotics about 6 years ago when I first got real sick(hives from head to toe)My gut was never the same afterward. Does anyone else realize that many antibiotics contain the preservative Thimerisol (Mercury). I took agumentin which contains thimerisol, my father had a recent allergy test that showed he was allergic to thimerisol(allergic to mercury, Really?)perhaps many peoples immune reactions to antibiotics are exacerbated by other substances laced into the drug itself.      

 

[majormark]

and second false statement, you do not find bacteria within human body, ONLY IN THE COLON, the rest of human body is sterile.

ys, where did get that info?

Have a look here:

"Strictly by the numbers, the vast majority — estimated by many scientists at 90 percent — of
 the cells in what you think of as your body are actually bacteria, not human cells."

http://www.miller-mccune.com/science-environment/bacteria-r-us-23628/

[ys]

good article, but a little vague.

can you elaborate this one?
P. aeruginosa and C. difficile are common residents of human bodies and under normal circumstances are benign.

where in human body?  Organs?  Blood?  Muscles?

from the searches I concluded that bacteria is present only in the digestive tract, most of it in the colon, small percentage in stomach (h.pylori) for about 50% of population, some in small intestines, and some in the mouth cavity (i highly doubt that bacteria that lives on our teeth is beneficial).
my understanding is bones, muscles, blood, brain, all non-digestive internal organs and cavities are sterile unless they get bacterial infection as a result of injury.

it is also my understanding that newborns are completely sterile including the digestive tract.  http://www.gentlebirth.org/archives/colonization.html

if you can find reputable source that shows there is non-pathogenic bacteria in human cavity besides digestive tract and skin surface i'll gladly change my mind.

[miles]

I didn't read that whole article majormark, but it looked to me like they were just talking about bacteria on the outside of us(digestive tract).

[PaleoPhil]

YS, this is a new wording you're using, different from that in your original statements:

...if you can find reputable source that shows there is non-pathogenic bacteria in human cavity besides digestive tract and skin surface i'll gladly change my mind.

You've correctly expanded beyond your original claim of bacteria being limited to the colon (quoting you: "...you do not find bacteria within human body, ONLY IN THE COLON, the rest of human body is sterile"), but you have still failed to include the vaginal and nasal cavities that Tyler and I mentioned. So your statements and questions are getting closer to the truth, but are not quite there yet.

[sabertooth]

I have had a nutritional blood analysis, A fancy title for looking at a drop of my blood through a high powered microscope and I saw it filled with what the technician referred to as respiratory bacteria, as well as blood parasites. I saw with my own eyes bacteria swimming in my bloodstream.
http://shangrilabiospa.com/livebloodcellanalysis.htm
Bacteria in the blood is a sign of a weak immune system.

[ys]

yes, i have corrected myself to include the whole digestive tract as well as body surface which obviously has contact with foreign objects including bacteria, viruses, and other organisms.  vaginal and nasal cavity is considered part of the body surface http://www.textbookofbacteriology.net/normalflora.html
very detailed article, explains a lot.

conclusion:  the closed loop cavities such as muscles, organs, blood, etc. in the healthy body do not have bacteria present.  Organs and cavities that have contact or openings to the outside harbor both beneficial and harmful bacteria.

 

I saw with my own eyes bacteria swimming in my bloodstream.

bacteria in the blood may indicate some kind of infection
http://en.wikipedia.org/wiki/Bacteremia

[B.Money]

So I don't quite understand. If say, meat (muscle) has no bacteria present, why do people always say raw meats have "good bacteria"?

Same with raw milk?

[TylerDurden]

Bacteria in the oral cavity cannot really be considered dangerous as it is actually one's diet that determines how well the teeth do. For example, when I consumed dairy or went in for raw vegan diets, my teeth almost fell out despite using antibacterial toothpastes etc. much of the time, whereas a rawpalaeodiet helped my teeth become and stay strong without the use of toothpaste.

[djr_81]

So I don't quite understand. If say, meat (muscle) has no bacteria present, why do people always say raw meats have "good bacteria"?

Same with raw milk?

The meat has good bacteria on the outside digesting it since the animal was slaughtered. That's why searing the outside kills the bacteria.

I'm not sure on the mechanics of the milk. I assume since it's a liquid the bacteria that is in contact with the surface of the milk can pass into the core of the container easier and proliferate in the environment.

[PaleoPhil]

Humans as Ecosystems Old Friends Hypothesis

vaginal and nasal cavity is considered part of the body surface

Yes, as is the colon and rest of the GI tract and all areas that normally contain bacteria, exactly as I wrote:

Bacteria and other microbiota are found on all internal and external surfaces of human beings that are exposed to the environment--the skin, eyes, nose, and the entire GI tract from the mouth to the anus--not just the colon.

conclusion:  the closed loop cavities such as muscles, organs, blood, etc. in the healthy body do not have bacteria present.  

That's correct for healthy individuals. In infected individuals, the bacteria penetrate these areas, such as in the case of an infected wound and sinusitis infection in the normally sterile sinus cavities.

You're not claiming that anyone said that muscles, organs or blood normally contain bacteria in healthy individuals are you?

Organs and cavities that have contact or openings to the outside harbor both beneficial and harmful bacteria.

Correct, and recent science suggests that even "harmful bacteria" may play positive roles in certain limited circumstances (see Valerie Brown on this below) and some microbiota may be effectively neutral (though many of the ones currently regarded as neutral may have beneficial or harmful effects that are simply as yet unknown).

It's also not practical to kill all the bacteria everywhere on and in an adult human. It would require extraordinary bubble-boy type measures. Life-giving air, water and food all contain bacteria. So another conclusion is that while a human could live as a "bubble boy" for years and you can remove the colon from humans without killing them, you cannot remove all the bacteria from a human in a natural environment. To do so using artificial bubble-boy measures would likely produce sub-optimal results anyway, as indicated in the following sources (emphases mine):

Bacterial Bonanza: Microbes Keep Us Alive, Jeffrey Gordon, Director of the Center for Genome Sciences at Washington University in St. Louis
"humans should start thinking of themselves as ecosystems, rather than discrete individuals"

Bacteria 'R Us, Valerie Brown
"pathogens and beneficial bacteria are not necessarily mutually exclusive organisms. A microbe’s effects on the human body can depend on conditions. And if you approach the human body as an ecosystem, some researchers are finding, it may be possible to tune that system and prevent many diseases — from acute infections to chronic debilitating conditions — and even to foster mental health, through bacteria."

Helminthic therapy (incorrectly referred to as worm therapy): the reason for this site
Jaspar Lawrence on the Old Friends Hypothesis (OFH) (a refinement of the Hygiene Hypothesis)--the idea that humans evolved to naturally have wider varieties and larger quantities of bacteria, worms and protozoa than what modern humans have and that this contributes to the diseases of civilization. The OFH makes the mistake of ignoring the contributing factor of diet in the development of the diseases of civilization, but I think the OFH likely explains another contributing factor and the OFH and dietary discordance are both part of the larger model of biological discordance.

Hadley C (2004) Should auld acquaintance be forgot. EMBO Rep 5:1122-1124
"What we're talking about really is fundamental changes in lifestyle, it's not just the trivial matters of everyday domestic hygiene. It's the fact that we no longer drink water from the stream and we no longer have worms." --Graham Rook, a professor at the Centre for Infectious Diseases and International Health, London, main developer of the OFH

The Gut and Psychology Syndrome, Natasha Campbell-McBride


There's even a hypothesis that the mitochondria that exist within human cells and that are essential for human life evolved from bacteria:

Evolutionary Origin of Mitochondria
http://www.ruf.rice.edu/~bioslabs/studies/mitochondria/mitorigin.html

The endosymbiotic hypothesis for the origin of mitochondria (and chloroplasts) suggests that mitochondria are descended from specialized bacteria (probably purple nonsulfur bacteria) that somehow survived endocytosis by another species of prokaryote or some other cell type, and became incorporated into the cytoplasm. The ability of symbiont bacteria to conduct cellular respiration in host cells that relied on glycosis and fermentation would have provided a considerable evolutionary advantage. Similarly, host cells with symbiont bacteria capable of photosynthesis would also have an advantage. In both cases, the number of environments in which the cells could survive would have been greatly expanded.

So overall, bacteria and microbiota in general are crucially important for humans.

[PaleoPhil]

Review series on helminths, immune modulation and the hygiene hypothesis: the broader implications of the hygiene hypothesis.
Graham A W Rook
Immunology. 2009 Jan;126(1):3-11.
Centre for Infectious Diseases and International Health, London
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632706/

Abstract
Man has moved rapidly from the hunter-gatherer environment to the living conditions of the rich industrialized countries. The hygiene hypothesis suggests that the resulting changed and reduced pattern of exposure to microorganisms has led to disordered regulation of the immune system, and hence to increases in certain inflammatory disorders. The concept began with the allergic disorders, but there are now good reasons for extending it to autoimmunity, inflammatory bowel disease, neuroinflammatory disorders, atherosclerosis, depression associated with raised inflammatory cytokines, and some cancers. This review discusses these possibilities in the context of Darwinian medicine, which uses knowledge of evolution to cast light on human diseases. The Darwinian approach enables one to correctly identify some of the organisms that are important for the 'Hygiene' or 'Old Friends' hypothesis, and to point to the potential exploitation of these organisms or their components in novel types of prophylaxis with applications in several branches of medicine.

Conclusion: ...in relation to allergic disorders the hypothesis is supported by epidemiology, experimental models and therapeutic trials, and backed up by the identification of relevant pathways and gene–environment interactions. Therefore, in view of man's unique ability to adapt to novel environments by means of culture and technology, faster than he can adapt by genetic change, it is logical to anticipate manifestations of gene–environment misfit in other disease contexts. ...

[PaleoPhil]

it is also my understanding that newborns are completely sterile including the digestive tract.  http://www.gentlebirth.org/archives/colonization.html

It's looking like the role of bacteria has been underestimated by even the most ardent proponents of the Old Friends Hypothesis and that fetuses may not be completely sterile after all. Some researchers now believe that fetuses have bacteria even before they are inoculated in the birth canal during natural childbirth. The sterile fetus notion apparently comes from an out-of-date assumption in 1900.

The New York Times: Human Microbiome May Be Seeded Before Birth
http://www.nytimes.com/2013/08/29/science/human-microbiome-may-be-seeded-before-birth.html?smid=pl-share
 
We are each home to about 100 trillion bacteria, which we carry with us from birth till death. But when Juliette C. Madan was trained as a neonatologist in the mid-2000s, her teachers told her in no uncertain terms that we only acquire those bacteria after we are born. “It was clear as day, we were told, that fetuses were sterile,” she said.
 
Dr. Madan is now an assistant professor of pediatrics at the Geisel School of Medicine at Dartmouth, and she’s come to a decidedly different view on the matter. “I think that the tenet that healthy fetuses are sterile is insane,” she said.
 
Dr. Madan and a number of other researchers are now convinced mothers seed their fetuses with microbes during pregnancy. They argue that this early inoculation may be important to the long-term health of babies. And manipulating these fetal microbes could open up new ways to treat medical conditions ranging from pre-term labor to allergies. They argue that this early inoculation may be important to the long-term health of babies. And manipulating these fetal microbes could open up new ways to treat medical conditions ranging from pre-term labor to allergies.

In 1900, the French pediatrician Henry Tissier declared unborn babies bacteria-free. Only when they started their journey down through the birth canal did they begin to get covered with microbes. The newborns then acquired more as they were handled and nursed.

“This was considered a kind of scientific dogma,” said Esther Jiménez Quintana of Complutense University of Madrid.

This dogma gained strength from studies on babies born prematurely. Infections are a major risk factor in early labor. Many researchers saw this as evidence that the only bacteria in the uterus were dangerous ones.

But scientists came to this conclusion without finding out whether healthy fetuses had bacteria, too. “It became a self-fulfilling prophecy,” said Dr. Madan.

That has started to change in the past few years. ....

[cherimoya_kid]

Interesting, Phil.  Good find.

[PaleoPhil]

Thanks Cheri.

WARNING: THIS GUT BACTERIA STUFF IS TURNING OUT TO BE HUGELY MORE IMPORTANT THAN ALMOST ANYONE REALIZED!!!

Please, think twice about staying on a chronic ketogenic diet, especially one that is low in resistant starch and that you rarely or never come out of ketosis on and especially if you are not obese or have issues like:

- high fasting blood glucose
- cold fingers/hands/extremities/body, low body temperature in the early morning
- dry eyes
- chronic constipation or diarrhea
- history of antibiotic treatment
- history of autoimmune symptoms
(there are others)

Remember Aajonus saying that body fat was protective in some ways? That's one of the few things I think he probably got right.

More info to come. For now, please read Spanish Caravan's warnings at http://freetheanimal.com/2014/01/carbing-this-beast.html and whatever he writes in the future.

I have some comments there too, but his are especially important. Or if you don't want to read a cooked food blog for some bizarre reason, I guess you could check out my posts on resistant starch here and maybe search for info on raw foods high in resistant starch, and notice how they are all believed to be super healthy by the peoples that eat them. And also check for info here and elsewhere on the Old Friends Hypothesis.

[Iguana]

Very interesting indeed, thanks Phil. I hadn’t read that thread: I only read this page 2 just now.

This confirms what I’ve always thought and said. Low carb and zero carb diets have nothing to do with a paleo nutrition.

[PaleoPhil]

Agreed, you were right Iguana. It's no wonder you've managed to stay on raw Paleo so long. If you had been ZC I think you would likely have been seriously ill by now, maybe even dead.

GCB was right to suspect that a raw diet too heavy in meat is problematic and may have contributed to his wife's cancer and death, probably not so much because it contained so much meat as because of what it probably didn't contain enough of to offset the mild stress from lots of lean meat and feed the gut bacteria--resistant starch and other prebiotics.

I know I asked for this before and it was voted down, but I hope it's becoming clearer now that it's time to bury ZC and completely disassociate this forum from it. Ban the term from any forum sub-heading. It's a nightmare. It's that serious. This is not hysterics, please believe me. I tried ZC for a few months myself out of curiosity, so it's not like I'm just blindly against it for no reason. It can actually improve symptoms in the short-term, which makes it misleading and therefore especially dangerous.

It kills off many of the good bacteria. Some even said that they eventually excrete almost no feces and they don't flatulate anymore. If that's true, that's horrific, not good. It would mean very little bacteria left, thus opening the way for extremely pathogenic bacteria to step in and take over later on. Once they take hold, it may be too late. The only hope I've seen for when the problem reaches that point is a fecal transplant and maybe raw honey, one of the last remaining therapeutics that can fight the super-germs of today.

I've said it before and now I'm even more convinced--humans cannot survive without bacteria. Bacteria are an essential part of what makes us human and keeps us alive.

[Projectile Vomit]

I completely agree that ZC or VLC is probably detrimental over the long term, but my own experience suggests can be useful for shorter tern stints. For example, I suspect it was common for pre-agricultural peoples to go zero carb for stretches during the winter when carb containing foods weren't available, but once those foods because available again people knew to quickly add them back into their diets. I think there's a lot of gold to mine in seasonality, and exploring how seasonality can push us into dietary extremes for brief periods that deliver certain benefits.

[PaleoPhil]

Probably so, though as you likely know, some trees can provide berries during the winter or early spring. Typically, the berries are bitter in the fall so that birds and animals don't eat them too soon and they are still available when other fruits are gone, per what I've read. These trees could be life-saving and thus tended to be regarded as sacred.

Some Eskimos reportedly even froze berries to make them last through the winter. Sometimes they mixed them with other things like seal oil or pemmican to help preserve them and add flavor, IIRC.

Tyler won't like this bit, but if you believe that Europeans have even some ancient genes that originated in Africa, then the carby seasons were longer there, so presumably there would be a certain amount of adaptation to that, though who knows how much of that would have been canceled out by later Eurasian adaptation and mixing with Neanderthals/Denisovans. No proof one way or the other on how adapted we are to any particular place or time frame, of course, so it will be argued endlessly.

GCB of Instincto eating also thinks that humans originated in a tropical area and recommends tropical fruits in part for that reason, IIRC from his past posts.

Ray Peat, like GCB, claims that tropical fruits are healthier because they tend to contain saturated fats, instead of polyunsaturated, due to the warm climate, and because he also believes that humans originated in a tropical area and ate lots of tree foods in the original homeland.

Even some Tibetan Buddhist monks thought that "tree foods" were particularly good for longevity, which has been posted about before somewhere.

I'm not recommending any of these sources or drawing any conclusions, just sharing that the idea is out there that it may be more optimal to eat carby foods, particularly tropical carby foods, for a longer period than what's available fresh in cold climates. Some tropical fruits are fatty or starchy instead of sugary, so it gets rather complicated.

[eveheart]

WARNING: THIS GUT BACTERIA STUFF IS TURNING OUT TO BE HUGELY MORE IMPORTANT THAN ALMOST ANYONE REALIZED!!!

Please, think twice about staying on a chronic ketogenic diet, especially one that is low in resistant starch and that you rarely or never come out of ketosis on and especially if you are not obese or have issues like:

- high fasting blood glucose
- cold fingers/hands/extremities/body, low body temperature in the early morning
- dry eyes
- chronic constipation or diarrhea
- history of antibiotic treatment
- history of autoimmune symptoms

Phil, you have my undivided attention. I maintain low carb (<50g/day) to maintain good blood sugar control, but I think there is a link between supporting gut bacteria and further healing for me. As I understand the links you posted, a good plan would be to "count" RS using the list of resistant starches in food and aim for 20 - 30g of RS per day. Much of this would replace other carby foods, but I am not averse to exceeding 50g of carbs/day to achieve the RS goal. Does this should like a good plan to you?

Also, I'm wondering about gut bacteria... I already enjoy fermented foods. Should these be enough to "feed" the resistant starch? Or should I consider supplemental probiotics or other measures?

Thanks for your feedback.

[PaleoPhil]

Resistant starch is not a carb. I wish the word "starch" was not in the term, as it doesn't work like starch. It feeds essential gut bugs, not us. It is converted into fat by gut bacteria, so it should be counted as fat. However, it's only nearly pure RS if it's in the form of potato starch. With other foods, there would be both some regular starch and some RS.

[eveheart]

Resistant starch is not a carb. I wish the word "starch" was not in the term, as it doesn't work like starch. It feeds essential gut bugs, not us. It is converted into fat by gut bacteria, so it should be counted as fat. However, it's only nearly pure RS if it's in the form of potato starch. With other foods, there would be both some regular starch and some RS.

Thanks for the clarification. It's an important distinction.