Rethinking Gut Bacteria

[Light]

One of the reasons antibiotics are so popular on this forum is to eliminate, or at least significantly reduce gut bacteria.

There are a few threads about sterilizing the gut, and it's mentioned that babies have sterile guts, and we should all hope to be as healthy as babies.

So I started looking into babies' guts (not literally), and it seems we have it wrong:
from: The composition of the gut microbiota throughout life, with an emphasis on early life

"Since the studies of Tissier (1) concerning the acquisition of the infant gut microbiota, the idea that fetuses are sterile in utero and that microbial colonization of the newborn starts during and after birth has been widely accepted."
"This view arises from the fact that, during decades, microbiological analyses of pregnancy-related biological samples (chorioamnion, amniotic fluid, and meconium) were only performed in cases where an intrauterine infection was evident or suspected."
"In contrast, relatively few studies have examined the uterine microbiota associated with healthy term pregnancies, partly because of the enduring influence of the sterile womb paradigm, and also due to the technical and ethical issues of collecting samples from healthy pregnancies before birth. However, investigations into the potential for bacterial transmission through the placental barrier have detected bacteria in placenta tissue (5), umbilical cord blood (6), amniotic fluid (7–9), and fetal membranes (9, 10) from healthy newborns without any indication of infection or inflammation."

"Meconium is not sterile" (Meconium = baby's first poop)
"A recent study characterized the microbiota of meconium and fecal samples obtained from preterm babies during the first 3 weeks of life using culture-dependent and culture-independent techniques (12). Both approaches provided similar results and showed that spontaneously released meconium of such neonates contains a specific microbiota that differs from those observed in early fecal samples. Firmicutes was the main phylum detected in meconium while Proteobacteria was abundant in feces. Culture-based techniques showed that staphylococci predominated in meconium while enterococci and certain gram-negative bacteria, such as Escherichia coli, Klebsiella pneumoniae, or Serratia marcescens, were more abundant in fecal samples. In addition, 16S rRNA gene-based microarrays revealed the high prevalence of bacteria related to Streptococcus mitis and Lactobacillus plantarum in meconium, whereas those related to E. coli, Enterococcus, and K. pneumoniae predominated in the infant feces"

It really seems to me that it's not a race to clear/sterilize the gut, but a race to colonize the gut with beneficial bugs.

For starters, sterilizing the gut doesn't always help, even with issues that we know are affected by gut bacteria, @haidut gave a few examples of that:
in Sterilizing The Gut Restores Insulin Sensitivity By Reducing Fatty Acid Oxidation :
"Similarly to the human study with aspirin, sterilizing the gut with antibiotics did not reduce the weight in the obese subjects (in this case mice)."

And there's the old chinese "Yellow Soup" and its newer version - fecal transplant, which can do wonders:
from: Regulation of life span by the gut microbiota in the short-lived African turquoise killifish

Abstract
"Gut bacteria occupy the interface between the organism and the external environment, contributing to homeostasis and disease. Yet, the causal role of the gut microbiota during host aging is largely unexplored. Here, using the African turquoise killifish (Nothobranchius furzeri), a naturally short-lived vertebrate, we show that the gut microbiota plays a key role in modulating vertebrate life span. Recolonizing the gut of middle-age individuals with bacteria from young donors resulted in life span extension and delayed behavioral decline. This intervention prevented the decrease in microbial diversity associated with host aging and maintained a young-like gut bacterial community, characterized by overrepresentation of the key genera Exiguobacterium, Planococcus, Propionigenium and Psychrobacter. Our findings demonstrate that the natural microbial gut community of young individuals can causally induce long-lasting beneficial systemic effects that lead to life span extension in a vertebrate model."

Some of the strains that are prevalent in human babies' guts are available in probiotic supplements, like Lactobacillus plantarum that's mentioned above.
I'm definitely gonna give it a closer look.

The whole field of science that investigates the gut microbiota is still very new and there's alot we don't know. We should beware of trying to eliminate this whole universe of microbes that live, and have evolved to live inside us.

 

[Light]

Just saw this too:
from: Germ-free Animals Have Autistic Like Behaviors And No Resistance To Stress

"Germ-free animals, which are bred and raised to be sterile and have no gut microbiota, have distinctly unhuman characteristics: disrupted sociability, autistic like behavior, poor cardiac output, atrophied organs (heart, liver, and brains), constant feeding behavior, and, ironically, poor gain of both lean muscle and body adipose."

From http://www.prescript-assist.com/inte.../commensal-gut-flora/
No references to studies here, but I could find this: Advances in Applied Microbiology

Or Growing up in a Bubble: Using Germ-Free Animals to Assess the Influence of the Gut Microbiota on Brain and Behavior

 

[LeeLemonoil]

I find research on the microbiome-produced SCFAs very interesting. Butyrate especially seems a substance favourable to health in many different tissues.
It’s a product from the gut bacteria as we are aware, dietary sources are dairy, especially butter but the mail portion stems from the microbiome.

 

[somuch4food]

Really interesting. After reading an article about vagina versus cesarean births and gut bacteria composition, I was wondering how the baby could be sterile in the womb if we have more bacteria than cells in our body and that they are everywhere (circulating in the blood, in the gut, on our skin, in our mouth).

I'm guessing the real link they found in the article is that mothers who require C section to give birth have underlying health problems that affects the child's microbiota even before birth.

 

[tankasnowgod]

Just saw this too:
from: Germ-free Animals Have Autistic Like Behaviors And No Resistance To Stress

I think this is the key quote from that study- "However, a germ-free upbringing can induce permanent neurodevelopmental deficits that may deem the model unsuitable for specific scientific queries that do not involve early-life microbial deficiency."

It doesn't necessarily mean that the germs themselves are positive or negative. Take, for example, the only case of a human raised in a 100% sterile environment- David Vetter.



"Life in a Germ-Free World":: Isolating Life from the Laboratory Animal to the Bubble Boy

Physically and Mentally (in terms of cognitive ability), he developed as well as any other child. His development was actually considered superior.

Psychologically, however, he was a wreck. And it's not hard to see why. Essentially, he spent his entire life in a plastic prison. He had loud machines constantly maintaining his environment. He didn't have direct contact via touch with any other human or animal (or likely even plant) for the vast majority of his 14 year life in the bubble. He never felt direct sunlight on his skin. NASA built him a spacesuit so he could go outside. He only used it a few times. He was an astronaut on his own planet.

I'm guessing similar measures are taken to raise germ free mice. I don't know how it would even be possible to raise germ free animals without drastically sacrificing their social development.

 

[Makrosky]

Yeah thanks for bringing this up. I also think completely sterilizing the gut is absolutely non sense and I wonder if Peat himself uses that term more like a metaphor than a real thing. Using daily small ammounts of sterilizing compounds like garlic, onion, cinnamon, cloves etc... is a completely different thing. The key is favouring good bacteria over the bad ones.

And by the way, I don't understand why people take a baby metabolism/gut/whatever as a good thing. Babies are extremely vulnerable and besides that... we are adults, not babies. Life evolves from a seed to a mature tree, from an egg to a mature bird and from a babie to a mature human being. It is stupid to try to mimmick early stages because we are not that anymore.

 

[Rinse & rePeat]

I think Ray Peat is referring to babies in the womb, not once they are out and ingesting disgusting baby formula, dirty pacifiers and god knows what else.

 

[Greyfox]

Really interesting. After reading an article about vagina versus cesarean births and gut bacteria composition, I was wondering how the baby could be sterile in the womb if we have more bacteria than cells in our body and that they are everywhere (circulating in the blood, in the gut, on our skin, in our mouth).

I'm guessing the real link they found in the article is that mothers who require C section to give birth have underlying health problems that affects the child's microbiota even before birth.

Urine is widely known to be sterile and the amniotic fluid is pretty much urine I believe.