Summary:  WHAT DETERMINES MICROBIOME?  Learn that we truly are what we eat, inhale, and absorb since that is what feeds our microbiome.   70% of the microbiome is very stable and supports basic life function, but 30% is very variable and host manipulable. A 30% change is huge because for the microbiome, 30% of the 39 trillion bacterial cells comprising the microbiome results in nearly 11.7 trillion organisms that can be modulated through diet and lifestyle nudging towards an anti-inflammatory state.  These changes increase immunity; 80% of our immunity comes from our gut microbiome.

Since the 30% is easily influenced, it is the population that is also easily negatively affected by things like antibiotics, diet, shifts in environment, sleep deficiency, etc.  The good news is, it can be changed back with the right therapeutic diet and lifestyle approaches. Even a 2% change is big; that’s just shy of a  trillion organism shift that can have a huge metabolic impact.  Learn here, what factors determines the microbiome.  
“We know how to disturb a community.  What we need to learn is how to coax it back into a healthy state.” – Katherine Lemon, a microbiome researcher at the Forsyth Institute of Cambridge, Massachusetts and a clinician at Boston Children’s Hospital.
Actually, everyone needs to understand how best to modulate the microbiome; I call this aggressive preventative medicine.

Summary added in this update for SEO optimization.

 First, a recap: “What is our microbiome?”

The gut microbiome is a newly discovered organ within an organ (the 21 foot intestinal track).  We acquire our microbiome at birth, and the mode of birth, vaginal or C-Section, instills differing microbiomes.  The mode of feeding (breast milk or formula) further develops that microbiome to maturity at about 27 months.  From there, we have all profoundly changed our microbiome mostly to be more pro-inflammatory as evidenced by the current disease epidemics Westerners now experience.

  • The human body is permanently colonized by microbial organisms on virtually every environmentally exposed surface, and each of these areas has a different microbiome:  skin, mouth, respiratory tracts, genitourinary , and the largest colonizer, the gastrointestinal, aka the gut.  -“Gut Microbiota in Health and Disease.”
  • It is estimated that the human microbiota contains as many as 1014 bacterial cells, a number that is 10 times greater than the number of human cells present in our bodies.   We have 1 trillion human cells, but 100 trillium microbial cells.  Thus, we are 90% bacteria, or 10% human, on a cellular level.  On a gene level, we have only 20,000 human genes.  But, our microbial genes, range from 2 to 20 million; we carry around mostly microbial genes!  – Dr. Rob Knight, Saturday October 18, 2014, UColorado Boulder presentation.

Updated to reflect new microbiome estimates from, How many bacteria vs human cells are in the body:  

A recent study out of the Weizmann Institute in Israel states that the number of bacteria may actually be very similar to the number of human cells in the body. The Weizmann scientists redid the estimate and found that there were about 39 trillion bacterial cells in the body. They also estimated the number of human cells in the body, about 84% of which are red blood cells, finding there to be about 30 trillion human cells in the body.

While this results in about 1.3 bacterial cell per human cell, the numbers may vary significantly from person to person and could change significantly with each defecation. They estimate that the range of bacterial cells goes from about 30 to 50 trillion in each individual. Women may also have a higher ratio of bacterial cells than human cells because they have fewer human cells, specifically red blood cells.

While this study does not take into account fungi, viruses, and archaea which all make up the human microbiome and would increase the ratio of microbes to human cells, the often stated ratio of 10:1 for bacterial cells to human cells is most likely not accurate. While I will no longer be able to use this fun fact in my description of the microbiome, it does not take away from the importance of bacterial cells in human health.

It is more accurate to say we are hosts of our microbiome rather then that we are human.  

  • “We share a functional core microbiome but not a core microbiota [which] can be related to macroecosystems.  For instance, rainforests that look the same and have many of the same functions can be composed of different species that have independently evolved. -“Diversity, stability and resilience of the human gut microbiota”
  • “The microbiome keeps us healthy. It breaks down some of our food into digestible molecules, it detoxifies poisons, it serves as a shield on our skin and internal linings to keep out pathogens, and it nurtures our immune systems, instructing them in the proper balance between vigilance and tolerance”  – Carl Zimmer, “When You Swallow A Grenade,” National Geographic, Dec 2012.
  • “For the most part, the microbes inhabiting our bodies are either beneficial ones or unobtrusive freeloaders.  They help us digest our food and absorb nutrients.  The manufacture vital vitamins and anti-inflammatory proteins that our own genes cannot produce, and they train our immune systems to combat infectious intruders.  Resident bacteria on our skin secrete a sort of natural moisturizer, preventing cracks that could allow pathogens to penetrate.  We get our first dose of these microbial co-conspriators as we pass through our mother’s vaginal canal, where the bacterial population changes dramatically during pregnancy.”  – Nathan Wolfe, “Small, Small World.”
  • The host gains products from microbial fermentation conversion of host indigestible components (dietary fibres) into short-chain fatty acids (SCFA; mainly acetate, propionate and butyrate) contributing to an estimated 10% of our energy requirement [4], vitamin K and B12 production [5, 6], and protection against potential pathogens through competitive exclusion [7, 8].  ~ “The first thousand days – intestinal microbiology of early life: establishing a symbiosis,” June 2014
  • Indeed, “It is precisely due to our microbiome, and the micobiota that it contains, that we are able to even live as they give us all the genes and proteins our human genome does not encode.  You can think of it as:  humans are actually the bystanders; it is the microbiota that does all of the work.”– ” Animated Life: Seeing the Invisible.”
  • The microbiome is determined at birth and differs not only in total diversity but also in altered prevalence of particular bacterial species depending on:  mode of delivery (vaginal or C-Section), how the newborn is fed (breast-milk or not), and even how long the newborn is breast-fed.  See this post for details.
  • Differences in the microbiota and the microbiome could help to explain the variation in the gut metabolic processes of individuals, including the metabolism of drugs and food11, 36.  Many of these metabolic pathways are outside the common functional core, so they can underlie host-specific responses. For example, the health benefits of diets rich in soya, such as improvements in vasomotor symptoms, osteoporosis, prostate cancer and cardiovascular disease, have been attributed to (S)-equol produced from the soya isoflavone daidzein by bacterial rather than human enzymes37. Only 25–30% of the adult population of Western countries produce (S)-equol with a diet of soya-rich foods, compared with 50–60% of adults from Japan, Korea or China38. The cancer-protective effects of soya beans that have been described in Asian populations may therefore not be true of Western populations. -“Diversity, stability and resilience of the human gut microbiota”
  • The Western gut has a very different microbiome from that of non-Westerners as detailed in this study, out of Dr. Rob Knight’s lab, “Diversity, stability and resilience of the human gut microbiota.”  Links to many diseases now known to have altered microbiomes and considered to be a Western epidemic are also provided in this study.  
  • Studies now show that the community of bacteria (along with gut infections, viruses, fungi, and parasites) that occupies the ecosytem of the gut microbiome affects: inflammation, chronic disease, allergies, arthritis, skin disorders including acne, psoriasis and eczema, autism, insulin resistance, overall adiposity, dyslipidemia, gastrointestinal and digestive disorders, autoimmunity, gut-brain interactions such as mood, depression, dementia, eating disorders, obesity, cancer, and more (the list literally grows daily).  This makes sense since 80 to 85 percent of our immune cells reside here.  We’ve only recently learned that this virtual organ even exists due to new gene sequencing technology.  The slew of disorders is epidemic for Western culture:
Disease Epidemic_PNG file
Slide source:

Our microbiome changes by what we feed it.  Species decrease and others increase for it is an ecosystem; changes happen  VERY quickly.  Diet changes must be LONG TERM for changes to stabilize.

Dr. Rob Knight just gave a talk, October 18, 2014, that explained what the American Gut project has shown to date, as most affecting the microbiome.  You can catch  details at my post, “Optimal Microbiome Diet From American Gut Data.”   You’ll want to understand the Eleven Factors that Dr. Knight relayed as it is  FOOD FOR THOUGHT most definitely:

  • Eat lots of  plants:  5 to 30 different varieties each week preferably.  See MY NOTES below for more explanation.  
  • Aging increases microbiome diversity:  Microbiomes are more diverse at age 50 to 60 then populations in their twenties  (see below slides).
  • Having an IBD diagnosis means your microbiome is altered.  NOTE:  Many chronic and autoimmune diseases are also following suit.
  • The time of year alters the microbiome with a more diverse microbiome being with sun and outdoor exposure.
  • Antibiotics wipe the microbiome with some folks recovering relatively soon whereas others do not recover the pre-antibiotic microbiome even one year later.
  • Males vs females:  The sex for a  given microbiome can now be accurately predicted.
  • Sleep 8 hours for a more diverse microbiome.  Less than 6 hours yields a less diverse microbiome.
  • BMI but it only subtly affects the microbiome.
  • Plants: eating 6 to 10 each week is good, but eating 30 plus different varieties is best.  (See further discussion below.)
  • Alcohol: one drink is helpful, more than one reduces diversity.
  • Frequent exercisers have a more diverse microbiome and it is best if exercise is outdoors rather than indoors.

This post details the healing affects of dietary protocols and identifies the state of the art studies, with a focus on autism and IBD, that demonstrate how changing up the microbiome alters health by bringing remission or management to chronic disease.

This post explains:  Consuming a carbohydrate- or fat-restricted low-calorie diet for a year6, or a high-fat and a low-fibre, or low-fat and high-fibre diet for 10 days32 can induce statistically significant changes in the gut microbiota. However, these changes in species and gene content are small compared with the baseline variations that occur between individuals. Long-term dietary surveys and cross-cultural comparisons suggest that changes to diet might lead to regime changes over longer periods of time4, 32, perhaps by eroding the landscape of alternative stable states to allow changes that short-term ‘nudges’ cannot.”

This study addresses the impact of meat versus plant based diet on microbiome and concludes:  “Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut12345, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term 5 day consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression.  Subjects’ gut microbiota reverted to their original structure 2 days after the animal-based diet ended.

The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila  and  Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale  and  Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals2, reflecting trade-offs between carbohydrate and protein fermentation…  

The ‘plant-based diet’ consisted of grains, legumes, fruits and vegetables; the ‘animal-based diet’ was composed entirely of meats, eggs and cheeses.

[Sidenote emphasizing the survival of the fermentation bacteria consumed by the animal diet through the digestive tract:]  The cheese and cured meats included in the animal-based diet were dominated by lactic acid bacteria:  Lactococcus lactis, Pediococcus acidilactici and Streptococcus thermophilus (Fig. 4a), which is commonly used as starter cultures for fermented foods22, 23:  During the animal-based diet, three of the bacteria associated with cheese and cured meats (L. lactis, P. acidilactici and Staphylococcus) became significantly more prevalent in faecal samples indicating that bacteria found in common fermented foods can reach the gut at abundances above the detection limit of our sequencing experiments.”  The gut healing diets include fermented foods as a staple due to anti-inflammatory and microbiome modulating effects; see this post for SCD/GAPS homemade lactose free yogurt details.


The following is a complete excerpt from this study as I cannot say it any better:

Antibiotic administration can move the microbiota to alternative stable states. In healthy volunteers who were given two courses of ciprofloxacin in a 10-month period, the faecal microbiota reached a stable state similar to, yet distinct from, the pretreatment state41. However, the magnitude of disturbance that occurred after ciprofloxacin treatment, and the speed and extent of recovery to the pre-ciprofloxacin state, suggested that resilience of the microbiota varies across individuals and between ciprofloxacin treatments in the same individual41.

Long-term studies of the microbiota after antibiotic treatment indicate that post-antibiotic equilibrium states are themselves resilient. For example, clindamycin treatment affected Bacteroides in the gut for up to 2 years after treatment had finished60. Similarly, three individuals with dyspepsia treated for 1 week with a combination of metronidazole, clarithromycin and omeprazole had a shift in their microbiota state that persisted for up to 4 years without additional antibiotic treatment42. In both cases, a significant increase in the antibiotic-resistance genes persisted for years42, 60, suggesting that the post-disturbance state would probably be more resilient to the same disturbance again because a greater proportion of the microbiota would be resistant. This is consistent with a case from the study of healthy volunteers given the two courses of ciprofloxacin41. Initial recovery of the microbiota was slow and incomplete, stabilizing in a different interim state, but after a second treatment, recovery was relatively quick. But in the same study, a different case had the opposite response, in which an essentially complete recovery occurred after the first ciprofloxacin treatment, but stabilized to a distinct state after the second treatment, suggesting that the initial antibiotic treatment decreased resilience41, and that the resilience of the microbiota to future antibiotic treatments can vary considerably between individuals.


Our microbiome changes by the air that we breath when we travel internationally. See this post.

Our biome is the source for 80 to 85% of our immunity,  ~1st International Symposium on the Microbiome in Health and Disease with a Special Focus on Autism as well as Wise Traditions London 2010 – Natasha Campbell McBride (creator of the GAPS diet used by so many autistic children).

“Tending the Body’s Microbial Garden”, by Carl Zimmer, NY Times, June 2012 is an incredible read that easily explains the microbiome if you aren’t there yet.  In summary, our body is comprised of many different microbiomes in many different locations (skin, oral cavity, stomach, gut, colon, genitals, nose…) and our microbiome affects 80 to 85% of our immunity.

All researchers acknowledge that there is much we don’t know about the microbiome.  

Well.. here’s a mind bender: In addition to that which we know we don’t know… consider that there is another 40% of matter that the sequencers haven’t a clue what it is, and  that is above and beyond that which we already know we know little about.  Whoa…  Come again…

Every microbiome is a community of many (trillions actually) of bacteria, viruses, fungi and much more yet to be discovered.  About 40% to be exact  and the gene sequencers call this substrate “DARK MATTER.”  check it out: Dr. Nathan Wolfe’s incredible TED talk:

If you doubt the truth about how truly little we know about the form and function of our microbiome, check out the below slide:

Summed nicely:  “They’re invisible.  They’re everywhere.  And they rule.”    – Nathan Wolfe, “Small, Small World.”
Our microbiome, manipulable through diet and lifestyle, affects gene expression.

Despite our genome being more or less fixed, our microbiota affects our epigenome.  One such example is DNA methylation and histone modification mechanisms regulating gene expression, which we are only now beginning to understand.  This is called epigenetics.  ~ “The first thousand days – intestinal microbiology of early life: establishing a symbiosis,” June 2014

Slide source
In total, all the microbes on your body outnumbers human cells by ten to one.
Updated to reflect new microbiome estimates:  A recent study out of the Weizmann Institute in Israel states that the number of bacteria may actually be very similar to the number of human cells in the body. The Weizmann scientists redid the estimate and found that there were about 39 trillion bacterial cells in the body. They also estimated the number of human cells in the body, about 84% of which are red blood cells, finding there to be about 30 trillion human cells in the body.  This results in about 1.3 bacterial cell per human cell

We are more bacterial than human and truth be told, the bacteria rules.  It has been said the gut is the second brain, some in the know suggest perhaps it really is the first brain, that is how much it is in control of our body’s functioning.

The microbiome weighs 3 to 5 pounds, and it is about the size of your brain, or larger.  When I tell that to doctors, most answer, “I didn’t know it was that large and heavy,” and they truly don’t know much about the microbiome.  This is all new science, not taught in medical schools until very recently (hopefully).

Sequencing centers

Sequencing centers are busy collecting samples from around the world to analyze the composition of the gut microbiome of all peoples.  Some sequencing centers areThe American Gut project“, “Ubiome“, and “23AndMe“; you can pay these centers to have your own or your children’s microbiome sequenced.

The consensus of experts (as of today) summarizing our microbiome reads as described by Michael Pollan in the “NY Times” article Some of My Best Friends Are Germs dated May 2013:

“Scientists can’t even yet say with confidence exactly what a “healthy” microbiome should look like. But some broad, intriguing patterns are emerging. More diversity is probably better than less, because a diverse ecosystem is generally more resilient — and diversity in the Western gut is significantly lower than in other, less-industrialized populations. The gut microbiota of people in the West looks very different from that of a variety of other geographically dispersed peoples. So, for example, the gut community of rural people in West Africa more closely resembles that of Amerindians in Venezuela than it does an American’s or a European’s.

These rural populations not only harbor a greater diversity of microbes but also a different cast of lead characters. American and European guts contain relatively high levels of bacteroides and firmicutes and low levels of the prevotella that dominate the guts of rural Africans and Amerindians. (It is not clear whether high or low levels of any of these is good or bad.) Why are the microbes different? It could be the diet, which in both rural populations features a considerable amount of whole grains (which prevotella appear to like), plant fiber and very little meat. (Many firmicutes like amino acids, so they proliferate when the diet contains lots of protein; bacteroides metabolize carbohydrates.)

As for the lower biodiversity in the West, this could be a result of our profligate use of antibiotics (in health care as well as the food system), our diet of processed food (which has generally been cleansed of all bacteria, the good and the bad), environmental toxins and generally less “microbial pressure” — i.e., exposure to bacteria — in everyday life. All of this may help explain why, though these rural populations tend to have greater exposures to infectious diseases and lower life expectancies than those in the West, they also have lower rates of chronic disorders like allergies, asthma, Type 2 diabetes and cardiovascular disease.”

Conventional medicine has viewed bacteria as virulent and therefore hunted down to be killed and eradicated before they can spread.  We now know that antibiotics permanently cause a demise in the diversity of our gut microbiome and while antibiotics can and do save lives, we need to use greater care in their use along with targeting probiotic treatments that don’t just temporarily boost the numbers of one microbe or another, but rather that shore up the whole of the community population.  See this post for Eric Alm’s, PhD MIT, one year gene sequencing experiment which included an antibiotic prescription.

We truly are what we eat, inhale, and absorb since that is what feeds our microbiome. Makes sense to me.  You?

Updated to add Summary section for SEO optimization and to reflect new microbiome estimates. Last updated: March 23, 2016 at 5:54 am



  1. I also don’t want to lose sight of this understanding as it gives hope, the below excerpt coming from: “Diversity, stability and resilience of the human gut microbiota,”

    High-throughput sequencing of samples suggests that the microbiota of each person has some resistance to perturbation, but that this resistance can be overcome by diet, drugs, prebiotics or probiotics. Dietary changes may alter the regime in the gut over long time periods. The surprising success of whole community transplants in healthy rats and in humans with CDAD shows that exogenous microbes can colonize the gut even with resistance from an entrenched microbiota. However, which microbes will be the best colonizers is unknown; neither do we know how a particular microbial configuration and its functional attributes change in response to dietary components or exogenous microbes. We need to learn what conditions promote the health of desired species and exclude the undesirable ones, just as a gardener would exclude weeds.

  2. I don’t want to lose sight of these concerns, the below excerpt coming from: “Diversity, stability and resilience of the human gut microbiota,”

    How resilient the microbiota is to diet, disturbance by antibiotics and challenge by exogenous microbes will have important implications for health care. The degree to which repeated applications of broad-spectrum antibiotics degrade the microbiota and its ability to function as a healthy system would need to be studied, especially in children, in whom the development of interactions between the microbiota and host is crucial5.

    Regime change is not always instigated by acute disturbances and can occur gradually, as indicated by studies of resilience to dietary changes. Individuals whose microbiota has been degraded by long-term consumption of a high-fat and high-sugar diet may need long-term dietary changes to restore their microbiota to a healthy state.

    The lower taxonomic diversity in individuals from Western cultures who have a high-fat and high-sugar diet raises the concern that global trends in diet could result in important microbial symbionts being lost from the broader population, possibly leading to the extinction of bacterial species that can provide important health benefits. Maintaining a collection of cultures from individuals in the developing world, and specifically from agrarian cultures, could help to preserve potentially important components of the microbiota.

Now I'd like to hear your thoughts... comments are always welcome!