SUMMARY: This post discusses the effect of birth mode on the microbiome, the effect of chronic disease on the microbiome, and ends with summarizing how food can alter disease status.
The gut microbiome begins at the beginning with the birthing process: Vaginal or C-Section.
A vaginal delivery inoculates the baby with a gut microbiome that studies today indicate set a life trajectory for immunity and health. C-Section delivery on the other hand, yields a gut flora that more closely resembles oral flora.
Population studies have found there are increased risk of disease for C-Section babies compared to vaginally delivered babies. The post, “MICROBIRTH” EVERY PARENT NEEDS TO VIEW, which actually discusses a film, “Microbirth,“ details links between C-section and disease. The film has a cast of characters (researchers) that reads like a who’s who list. You are familiar with most if you read my work. Not to be missed is the Downloads section of the “Microbirth“ website as it contains FAQ, some of which I excerpted:
- 20% increased risk of developing asthma,
- 20% increased risk of developing type 1 diabetes,
- 20% increased risk of obesity,
- slightly smaller increases with gastro-intestinal conditions like Crohn’s disease or coeliac disease, and
- These conditions are all linked to the immune system.
Studies are underway to learn if the C-Section baby can be innoculated with a microbiome that more closely resembles the vaginal delivery. Read the post, “Delivery & Breastfeed Studies & Microbiome Manipulation,” to learn more on swabbing the baby with gauze inserted into the mother one hour prior to delivery to attempt to achieve a microbiome that is more like that of a vaginal delivery.
In 27 months, a vaginally delivered baby’s gut “matures” to that of adulthood. Check it out at: “The Assembly of an Infant Gut Microbiome Framed Against Healthy Human Adults”, University of Colorado Boulder, 2:45 minute YouTube.
Mode of FEEDING impacts the microbiome!
ANY breastmilk (exclusive OR partial) protects the infant microbiome and gives it TIME to properly develop the immune system.
The microbiome differences found for breastfed vs formula have been independently linked to the risk of later life diseases such as obesity, asthma and allergy.
A 2024 study looked at 903 infant microbiomes (both community and its function) from age 3 to 46 months. The cohort came from from three European countries (Germany, Sweden and Finland) and three U.S. states (Colorado, Georgia and Washington). Some of the findings:
- Microbiome development progressed through three distinct phases: a developmental phase (months 3–14), a transitional phase (months 15–30), and a stable phase (months 31–46).
- The first year of life (months 3 to 14) was a KEY phase for the development of the microbiome. The receipt of any breast milk (partial or exclusive) was the main factor that influenced microbiome development. After month 14, only 10% of infants received any breast milk.
- Breastfeeding was associated with higher levels of beneficial Bifidobacterium species and suppressed Firmicutes. Infants having dominance of Bifidobacterium had significantly lower diversity when compared with infants no longer receiving breast milk across all phases.
- The cessation of breast milk resulted in faster maturation of the gut microbiome as marked by the bloom of phylum Firmicutes. The maturation of the gut microbiome is driven by the cessation of breast milk (rather than the introduction of solid foods), hallmarked by increased levels of Firmicutes.
- The metabolic function of the microbiome differed between breastfed and formula. For breastfed, genes increased for ‘carbohydrate and lipid metabolism’ pathway. Formula fed microbiomes had increased genes for rapid turnover of the metabolic capacity, and the ‘dicarboxylate-hydroxybutyrate cycle’ and ‘reductive acetyl-CoA pathways as well as vitamins B7 amino acid metabolism’ pathway which is associated with an adult microbiome.
- The mode of delivery also left an imprint. Vaginally born babies had higher levels of Bacteroides which is associated with increased gut diversity.
- Environmental factors including geographical location and household exposures also represented important covariates. Infants living with siblings and/or with furry pets showed accelerated rates of maturation of the microbiome.
-[Stewart et al 2024] Temporal development of the gut microbiome in early childhood from the TEDDY study
Why do Westerners have epidemic chronic disease?
Increased microbiome diversity means stronger immunity.
Westerners have less microbiome diversity. This can result in increased bacterial strains that cause inflammation. representative of obesity, Type2 Diabetes, cardiovascular disease and more:
The study, “Diversity, stability and resilience of the human gut microbiota,” notes “Disruptions to the normal balance between the gut microbiota and the host have been associated with obesity6, 7, malnutrition8, inflammatory bowel disease (IBD)9, 10, neurological disorders11 and cancer12.”
Dr. Maria Gloria Dominguez-Bello estimated that 1/3 of the population has reduced microbiome in the interview for the film “Microbirth.”
Studies now show that the community of bacteria (along with gut infections, viruses, fungi, and parasites) that occupies the ecosystem 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 70 to 80 percent of our immune cells reside in the gut. 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. This study, out of Dr. Rob Knight’s lab, “Diversity, stability and resilience of the human gut microbiota,” summarizes how different the Western gut microbiome is from that of non-Westerners and links to many diseases now known to have altered microbiomes.
“Microbes may be the missing piece of the puzzle that makes personalized medicine work.. [The microbiome] patterns are certainly interesting, and we are hoping that the American Gut data provides other researchers a foundation to further study the effects of diet and lifestyle on the human microbiome… Optimizing the microbes you have may be even more important than optimizing your lifestyle – although in many cases you may be able to optimize your microbes by optimizing your lifestyle.” –Dr. Rob Knight
“Many of these diseases are seemingly unrelated but are actually caused by gut microbiome community problems called dysbiois (inbalance of the community). If you want to fix your health and emotional and mental wellbeing, you must start in your gut. Gut health literally affects your entire body.”
Add to this is the role of diet, medicines (antibiotics and others), and environmental toxin exposures all of which negatively affects the gut microbiome which constantly changes and adjusts, regardless of age. Included here are antibacterial products such as hand soap, chemicals in our topical personal care products, gases emitted from our furnishings – home, school, and office, chemicals in our food that we ingest (plastics, BPA, BPS, PFAS, teflon, ceramic dyes, lead, water containing flouride/chloride/drugs/antibiotics, and heavy metal ingestion and inhalation (arsenic, cadmium, etc), GMOs, etc…)
So what does a gut microbiome protective diet look like?
Dr. Rob Knight gave a talk, October 18, 2014, that explained what the American Gut project had shown to date, as most affecting the microbiome. All that was found in 2014 STILL rings true today! The post, “Optimal Microbiome Diet From American Gut Data” dives into details, but the Eleven Factors Dr. Knight relayed is FOOD FOR THOUGHT:
- Eat lots of plants: 5 to 30 different varieties each week preferably.
- Aging increases microbiome diversity: Microbiomes are more diverse at age 50 to 60 then populations in their twenties.
- Having an IBD diagnosis means your microbiome is altered. NOTE: Many chronic and autoimmune diseases also follow suit.
- The time of year alters the microbiome with a more diverse microbiome being with sun and outdoor exposure. Spikes in microbiome populations seem to occur around holidays in July and in November through January.
- 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.
- 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.
There are a lot of healing diets like the MIND diet, Mediterranean, Bredesen’s Diet, PALEO, SCD, IBD-AID, AIP, WAHLs, etc. These diets are more alike than not and share many common tenets.
My post LEARN 3 KEY BRAIN HEALTHY DIETS. MIND, MEDITERRANEAN, DALE BREDESEN’S PROTOCOL is a great place to start to learn these tenets.
“Actually, the goal of the healing diets, which are nutrient dense, low-toxin, and anti-inflammatory, is to achieve resiliency in a gut microbiome that supports healthy immune function. When the diet and lifestyle is properly individualized, the resultant microbiome immune status often resolves and manages chronic conditions including autoimmunes.” -A great listen is Dr. Amy Shah, double board certified in Internal Medicine and Immunology/Allergy.
Finding out and eliminating what the individual can not tolerate (common intolerances are grains, dairy, eggs, nuts, nightshades…), AND eliminating foods that down-out harms the microbiome (like emulsifers — see this post for the whys), carrageenan, maltodextrin, and polysorbate 80, carbosymethylcellulose, and trans fats (store-bought baked goods, anything containing “partially hydrogenated oil”)), AND eating foods supporting the microbiome diversity and richness (lots of diverse forms of fiber, prebiotics, and probiotics) is a protective microbiome diet.
The diets I’ve listed are all healthy diets. Interestingly, the IBD-AID diet is being used by pregnant women to learn if the vaginal microbiome can be altered using diet to reduce the risk of disease transmission to the newborn! The clinical trail is called the MELODY Trial, ClinicalTrials.gov Identifier: NCT03850600. Learn more about that and the diet here.
Even more amazing is the power of your microbiome to work around your genes! Your genes are not your destiny.
Epigenetics is one mechanism that triggers disease in those predisposed. Disease is rooted in our DNA expression which is hugely influenced by diet (via its whooping impact on microbiome and its consequent metabolites — aka by-products). In addition, other factors impacting DNA expression are environment, sleep, toxin exposures, sun exposure, exercise, and stress (all aspects such as physical, mental, emotional, ongoing inflammation and disease). The process whereby these factors influence gene expression is called “Epigenetics.” Read the post, Learn How Diet Pierces the Disease Epigenetics Process, for details.
The bottom line is: We can STOP and REVERSE the epigenetic changes that trigger disease by IMPLEMENTING diet and lifestyle changes.
Diet alters the microbiome community ⇒ this targets the trillions of beasties in the gut microbiome (which is where over 70 percent of our immunity resides) and changes their metabolites (aka by-products). That alters epigenetics (including methylation and histone modification) with consequent change in gene expression. This can change disease status.
Epigentics is at the heart of microbiome manipulation and management of chronic disease. Even though one might be “predisposed” to disease, we can stop the epigenetic changes that trigger disease by implementing lifestyle and diet changes. That is the mission of Biome Onboard Awareness, LLC: to make you aware of “Whole Health Pillars“ so that you can optimize your gut microbiome to preclude triggering disease or if already triggered, to manage chronic disease often with reduction or elimination of medications (always with medical professional support). How empowering!
My hope is that the tools on my website help you find empowerment in realizing and implementing “food can be thy medicine” or put more accurately, “food is Epigenetic Medicine.”
In good health through increased awareness,
Last updated: May 24, 2024 at 15:24 pm to add new header, update post material to include [Stewart et al 2024], and fix the broken Dr. Amy Shah link. Temporal development of the gut microbiome in early childhood from the TEDDY study. Prior update removed and relocated the epigenetic content to a new post so it could be updated. Its link, Learn How Diet Pierces the Disease Epigenetics Process was added to this post. Editorial changes were also made.
Prior update Feb 19, 2017 added in recipe links. Prior update March 26, 2016 was for SEO optimization.
RHR: Is a Disrupted Gut Microbiome at the Root of Modern Disease?—with Dr. Justin Sonnenburg, June 2019, https://chriskresser.com/is-a-disrupted-gut-microbiome-at-the-root-of-modern-disease-with-dr-justin-sonnenburg/
[Sender et al 2016] Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans, https://www.cell.com/cell/fulltext/S0092-8674(16)00053-2
The rario of microbial cells to human cells in the bodywas originally said tobe 10:1. Nature study updated the ratio to 1.3:1, but there are a few things to note there. There were revisions on both sides. The microbes got a little less abundant, and the human cells got a little more abundant. In this revision, they counted our red blood cells, which, by far, are the most numerous type of cell in our body, making up over 80 percent of the cells in the human body. Now, these cells aren’t even really considered cells by a lot of biologists just because they don’t have a nucleus and they don’t conduct a lot of the same biology and signalling that normal other cells, nucleated cells, do. So if you get rid of those cells, we’re back to a 10:1 ratio.
But number isn’t too important. Dwayne Savage who’s one of a previous generation of scientists that really established the foundation for this field, said, “Humans are basically elaborate vessels for the propagation of microorganisms.” I think it really puts into context that the microbes are holding the reins to a lot of what’s going on in and on us, and in our environment. We really are is an ecosystem. We have microbial and human parts that come together to work in a concerted fashion to make us this superorganism, and we can’t forget about the microbes because they’re really an important part of our biology.
Up until recent, what kind of diet is appropriate and other kinds of environmental and lifestyle interventions have all centered around their effect on the human host and not necessarily on their effect on microbes.
The microbes haven’t been a part of the conversation up until very recently. That really needs to change because I think our appreciation of this microbial community has come to the point where we understand that what we put in our mouth is what is driving what this community is doing and, therefore, influencing health and disease. So that’s something that we just need to think about and try to make a bigger part of the conversation.
REGARDING REDUCED DIVERSITY: Less diversity can result in increased bacterial strains that cause inflammation representative of obesity, Type2 Diabetes and cardiovascular disease.
This Danish study, “Richness of human gut microbiome correlates with metabolic markers,” at http://www.nature.com/nature/journal/v500/n7464/pdf/nature12506.pdf (or read the University of Copenhagen scientific article “One in four has alarmingly few intestinal bacteria” at: http://news.ku.dk/all_news/2013/2013.8/one_in_four_has_alarmingly_few_intestinal_bacteria/ ) showed that one in four had 40% less gut bacteria than average. “This is a representative study sample, and the study results can therefore be generalized to people in the Western world,“ says Oluf Pedersen, Professor and Scientific Director at the Faculty of Health and Medical Sciences, University of Copenhagen. This population had reduced bacterial diversity and harbored more bacteria that caused low-grade inflammation of the body that is representative of obesity, Type 2 Diabetes, and some cardiovascular disorders.
Dr. Maria Gloria Dominguez-Bello estimated that 1/3 of the population has reduced microbiome as seen on this interview for the film “Microbirth”: http://microbirth.com/
The study, “Diversity, stability and resilience of the human gut microbiota,” at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577372/ noted some dire consequences and ramifications of the altered and depleted microbiome status such as being associated with obesity6,7, malnutrition8, inflammatory bowel diseases (IBD) 9,10, neurological disorders11, and cancer12. (see article for interacting links).