Manipulation of Microbiome Flashcards
HMP Goal
Define composition and complete functionality of normal microbiota in healthy individuals
Challenge with research on microbial composition (4)
1) Depends on location of subject
2) Dynamic community of microbes that change in days
3) Affected by diet, illness, travel, chemicals, antibiotics
4) Intimately related to host physiology
Known and unknown about microbiota and disease
Know certain phenotypes are linked to composition but not if they cause disease or modulate it –> Know microbiome is different but not if it causes
Diseases linked to different microbiomes
Fibromyalgia, cardiac function
The microbiota shows high
Plasticity
High plasticity of microbiota
Antimicrobials and diet cause metagenomic changes in hours and metatranscriptomic changes in minutes
Prebiotics
Nutrients promoting the growth of beneficial microbes
Modulate microbiota positively with
Prebiotics, probiotics, and pharmaceuticals
Microbes in stomach
Helicobacter, Lactobacillus, Veillonella
Microbes in duodenum, jejunum, Ileum
Bacilli, Actinobacteria, Streptococcus, Actinomycinae, Corynebacterium
Bacteria in colon
Lachnospiraceae, Bacteriodetes
As you go down GI tract there is an increase in
Diversity and number of microbes
Longitudinal variation of intestinal tract
Epithelium, mucus layer, lumen
In epithelium and mucus layer
Clostridium, Lactobacillus, Enterococcus
In intestinal lumen (8)
Bacteroides, Bifido, Clostridium, Enterococcus, Enterobacteria, Lactobacillus, Streptococcus, Rumincoccus
Temporal changes in microbiome
Increase number and diversity in first year and then numbers maintained while composition changes until death
Very few studies on
Impact of probiotics on microbiome
Most studies show … on probiotics and changes in microbiome
No change in overall population for Lactobacillus or Bifido but significant health effects + probiotics dominate (see new microbe you introduced but no shift)
Need more studies to understand interface between
Probiotic, host, and microbiota mechanism
The ___ of probiotic strain is an important factor for its impact on the gut microbiome
Origin
Strains of LAB isolated from human intestine classified as…
Autochthonous or Allochthonous
Autochthonous
Bacteria naturally occurring in the GI system
Allochthonous
Bacteria transiently passing in the human GI tract but cannot colonize
Autochthonous bacteria and colonization
Long-term association with particular host and stable populations with characteristic size in particular region of gut
Allochthonous bacteria might be
From a proximal region as auto that has dislodged or form ingested food and water
Why it was believed Lactobaillus was dominant in the human GI tract
Culturable because of oxygen tolerance and Metchinkoff findings
Bacteria with higher oxygen tolerance (4)
Lactobacilli, Clostridium, Enterococcus, E. coli
Lactobacillus not dominant genera based on
Anaerobic culturing, Fluoresent in situ hybridization (FISH), High throughput analysis of 16S rRNA sequences
Lactobacillus concentration…
Depends on isolation technique and really variable
Anaerobic culturing showed
10^6-10^8/g of stool with 0.01% lactobacillus; not detectable in 25% of samples
FISH results
10^6g/stoll with 0.01% lacto
Animals that have Lactobacillus as dominant species
Pigs (16%) chicken (35%), rats (22%), mice (11%)
Lactobacillus commonly detected in
Feces, Oral cavity, and Good
Species in feces and oral cavity but not food
L. acidiophilus
Species found in feces and food
L. johnsonii
Recovery of allochthonous lactobacilli in human feces
Big decrease in survival when they make their way through the GI tract
Example of most re-isolation allochthonous bacteria
L. rhamnosus GG
Autochthonous and Immune System
Characterized by tolerance with no strong IR
Allochthonous and Immune system
Characterized by stronger immune response
Auto vs Allo?
Depends on objective of probiotic and one type is not perfect for every treatment
