Introduction to the Microbiome
Table of Contents
Key take aways
- Understand the size and location of the gut microbiome
- Understand the impact of early life events on the microbiome
- Define what a “germ free” mouse is
- Understand how various lifestyle impacts, namely diet diversity, can impact microbial diversity in the GI tract
- Recognize the difference between causation and correlation
- Understand how germ free mice, colonized with bacteria from humans, can “prove” causation of disease by the microbiome
Summary
• The microbiome, seeded during the birthing process, is almost like an “organ system” unto itself • The impacts of the microbiome reach into almost every aspect of human health and biology • Lifestyle changes, namely industrialization, dramatically alter the microbiome
[Microbiome]
There are 2 to 20 million microbial genes in the human body
100x number of genes within your human cells
99% microbial genes
You can change the genes of the microbiome
How?
Microbiome in your colon processes the nutrients left over from the rest of the digestion of food product.
Microbrial load is increasing as food product is decreasing
Germ-free mice
- decreased mucosal cell regeneration
- digestive enzyme activity
- mucosa-associated lymphoid tissue
- lamina propria cellularity
- muscle layer thickness
- resistance to infection
There are changes in other places too.. bone marrow, less T and B cells
Microbiome - Early Life
- Birthing canal is loaded with microbes
- breast milk is loaded with bacteria
- Microbiome undergoes rapid changes during the first three years of life. then more gradual
- notable changes occur after weaning from breast milk which drives a large expansion in microbial diversity
- C-section vs vaginal delivery
- normal seeding vs abnormal seeding
- there can be downstream consequences of sequencing of microbiomes
Once solid food is introduced, diversification of the microbiome increases
Antibiotic use early in life. linked to health issues later in life through the disruption of the microbiome
The average child in the United States receives ten courses of anIbioIcs by age ten
antibiotics can mess up your gut. If you can avoid using them the better, especially for children
Antibiotic treatment in children has also been associated with an increased risk for: • Obesity • Asthma and allergies • Diabetes • Inflammatory bowel disease
associated with dysbiosis – the screwing up of your microbiome
Microbiome - Later life
The microbiomes of various carnivore, herbivore and omnivores are dras;cally different (le> graph), but the basic func;ons overlap significantly (right graph)Whether your an omnivore,
Carnivores only have enzymes that break protein down Herbivors had enzymes that built amino acids
Lifestyle impacts
The differences in the microbiomes of western and nonwestern populations are profound and likely driven at least partly by diet
- Industrialized diets generally have drastically reduced fiber intake compared to hunter gatherer societies
- [Dietary emulsifiers] and artificial sweeteners can disrupt the gut mucosal barrier, inducing low-grade inflammation and changes in microbial composition
contries that are more industrialized have much less diverse microbiomes There are many diseases (almost all) that have a microbiome link
Causation vs Correlation
An altered microbiome can cause atopic dermatitis VERSUS The altered microbiome in psoriasis may be an effect of the physiological changes of the skin
Use Germ Free Mice to Test Causation.
- Transplant microbiome of a person with a certain disease and put that in a germ-free mouse
This has now been done successfully for multiple diseases and conditions including:
- Obesity
- Malnutrition
- Insulin resistance
- Depression
- Jetlag
- Etc
Microbe induced malnutrition
Proteobacteria - shown to increase inflamation