Microbiomes Flashcards
microbiome
entire habitat including the microorganisms, their genomes, and the surrounding environmental conditions
microbiota
assembly of microorganisms present in a defined environment established using marker genes (16S or 18S ribosomal NA or other) and genomic regions, amplified and sequenced from biological samples
metagenome
collection of genomes and genes from members of a microbiota which is obtained via shotgun sequencing (followed by assembly or mapping to a knowledge database)
How are microbiomes related to everything around it?
Major Factors which Shape the Microbiome
diet, antibiotic use, host genetics, age, sex
also environmental conditions, xenobiotics, and stress
Are microbiomes unique?
yes, to the species, to the individual, to specific body sites within the individual
Diseases which can affect the Microbiome
autism spectrum disorder, infectious diseases, Type 2 diabetes, atherosclerosis, liver cirrhosis, depression, asthma, obesity, cancer, IBD
5 Major Functions of the Microbiome
- Immune Stimulation
- Production of Micronutrients
- Digestion
- Defense
- Detox
4 Components of Microbiome Defense Against Incoming Pathogens
- Competitive Exclusion
- Physical Barrier
- Chemical Warfare
- Biologic Warfare
competitive exclusion
microbes “win” and prevent colonization by pathogens
physical barrier defense
tightens tight junctions, but also increasing mucus thickness (especially in the gut) to prevent colonization of pathogens
chemical warfare
microbes can secrete AMPs, or toxins, or secondary bile acids
bacteriophage
virus that infects bacteria
primary bile acids
from the host; emulsify fat
secondary bile acids
from microbes
What species depend on microbiome for digestion?
ruminants
cellulase
enzyme that vertebrates don’t have, so depend on microbial metabolism to breakdown plant matter
short chain fatty acids
fermentation products [of microbes] that provides nutrients and energy for gut cells which promote the balance between inflammatory and anti-inflammatory signals, particularly at high concentrations
examples of short chain fatty acids
acetate, propionate, butyrate
How does the microbiome of the gut affect the rest of the body?
short chain fatty acids and other microbial metabolites can extend the reach outside the gut via endocrine signaling, behavior, immune development, etc.
What vitamins can be synthesized by microbes?
Vitamin B12, other B vitamins, Vitamin K
What percent of the daily requirement of vitamin K can be produced by your microbiome?
0.002 - 15%
What vitamin can ONLY be synthesized by microbes?
vitamin B12
How does the microbiome affect the immune system?
stimulates development of mucosally-associated lymphoid tissues (like GALT)
also increases barrier function, increases AMP secretion, provides tolerogenic environment
