Module 18- Microbiome Flashcards
Microbiota
Microbes that live in an established environment
Microbiome
Full complement of microbes, their genes, and genomes in a particular environment
Number of cells in the gut microbiota
200 Trillion
Number of species in gut microbiota
> 1000
Why do we not know how many species of microbes are in the gut microbiota?
Varies between individuals and most cannot be cultured
Ratio of human cells to microbies
10 microbes per human cell
How much larger is the gut microbiome than the human genome?
150X
Least to most microbes in organs of gut
Stomach –> Duodenum –> Jejunum/ileum –> Colon (tolerable environment)
Microbes are aerobic
In duodenum
Microbes are anaerobes
In colon
Stomach and duodenum Microbe Number
10 ^ 1 or 3
Jejunum/ileum Microbe Number
10^ 4 to 7
Colon Microbe Number
10 ^11 or 12
Microbiota 2
Ecological community of commensal, symbiotic, and pathogenic microbes within a body space or other environment
There is at least this many microbes in human microbiota
10 ^ 11
Microbiota % body mass
1-3%
In utero
State of embryo of fetus
Germ free
In Utero but found some in palcenta and babies
Normal microbiota
Microbes that establish permanent colonies inside or on the body without producing disease
Normal microbiota examples
Staphylococcus on skin and MM and E. coli in colon
Transient microbiota
Microbes present for various periods and then disappear but might colonise host and reproduce briefly
Why transient microbiota is transient
Immune defense do not allow permanence or other members of microbiota do not allow them to establish themselves
Living together
Symbiosis
Symbiosis
Long term interaction between two or more different biological species
Exist in symbiosis
Host and normal microbiota
Three types of symbiosis
Commensalism, mutualism , parasitism
Commensalism
One benefits and other is unaffected
Mutualism
Both benefit
Parasitism
One benefits at expense of another
Commensalism exampole
Mycobacterium in the ear (eat secretions)
Mutualism example
E. coli in colon (Vitamin K and protection)
Parasitism example
Disease causing bacteria
Opportunistic pathogen
Do not cause disease under normal conditions in their normal habitat but cause disease under special conditions
Opportunistic pathogens are usually
Members of normal microbiota but change when environment, food, or defenses do
Examples of opportunistic pathogens
E. coli and S. pneumoniae
System for complete absence of bacteria in gut
Gnotic mouse model
Gnotic mouse models have
Defective gut associated/mesenteric lymphoid tissue and low IgA levels
Mutualistic relationships between host and microbes led to…
Immune maturation, immune balance, and specific functions of macrobiotic
7 functions of microbiota
- Seal body spaces
- Mitigate intestinal pathogens
- Maintain tissue homeostasis
- Facilitate fermentation of dietary fiber
- Critical energy yield
- Metabolic end products and therapeutic drug processing
- Signalling among cells and organ systems
Mitigate intestinal pathogens by
Exclusion
Facilitate fermentation of dietary fibers
Inulin and pectin degraded by microbes so enterocytes can uptake them
Metabolic end products
Secrete end products and can activate prodrugs
Microbiota role in signalling
Molecules they secrete as products of fermentation act as signalling molecules among cells
Butyrate
Energy for gut epithelial cells + signal DCs to get anti-inflammatory response
Acetate and propionate
Lipogenesis and glyconeogeneis
Energy to intestinal cells and signal DCs
Butyrate
Specific marker on epithelial cells and a similar effect on ICs
Propionate
Acetate
Broad spectrum on epi cells and immune cells and also a distant effect
Acetate has distant effect on
Lungs, brain, pancreas, liver, BM (5)
Provides hematoposis to DCs in BM to reduce asthma
Acetate
Number of prokaryotes in gut microbiota
10 million with 1800 in 1980 and 14000 in 2016
Make up microbiome
Bacteria, Archie, fungi, intestinal protozoa, DNA and RNA viruses, giant viruses
All unique sequences that cannot be matches to known species
Operational Taxonomic Units (OTUs)
Many gut mirobiome only known as
OTUs
16s rRNA genes present in
All Bacteria and Archaea
16s rRNA genes contains
Highly conserved and more variable regions
How to sequence 16s rRNA
Amplify using primers directed toward conserved regions but flanking variable regions
The conserved and variable regions of 16s rRNA allows you to…
Align gene sequences and resolve phylogenetic relationships at different depths
Usually variable regions of 16s rRNA
V2 and V6 which are specific for species
Complex unit of ribosomes
16s rRNA
OTU purpose
Classify groups of closely related individuals because most 16s rRNA sequences are from undescribed microbes
Cluster OTUs based on
Similarity to each other
Similarity Threshold
OTUs defined by this
OTU Similarity Threshold %
97% similarity
Limitations of 16s rRNA based analysis (6)
1) Genome has multiple and nearly identical copies of operons
2) Can’t always normalize data
3) Can’t always accurately estimate diversity and abundance
4) Can’t always resolve at strain level
5) Strains can have different phenotypes and functional capabilities
6) Conservation can mask sequence diversity of rest of genome
16s of different strains of same species having different phenotypes or functional capabilities –>
Inability to infer or reconstruct functional or metabolic capabilities
Strains of same species with different phenotypes or functions means
They have different regulatory networks that activate and repress genes and behave different
Multiple copies of 16s rRNA
Allow to grow fast because they can translate at multiple promoters
Other techniques to understand microbial communities
(1) Single cell genomics
(2) Metabolomics and metatransciptomics
(3) Imaging of intestines to see spaces and how crowded they are and what interacts with what
(4) All together or single cell gene expression
(5) Phylogenetic diversity and activity
(6) Reference genomes
Single Cell Genomics
Het one cell and do whole sequencing and gene expression
Gene expression
Get for one cell or the entire community to determine which genes are expressed at a given time
Metabolomics
Looks at metabolism of community as whole to see metabolic capability
4 Ways to Understand Microbial Communities
(1) 16s rRNA sequencing
(2) Metagenomic Sequencing
(3) Metatranscriptomic sequencing
(4) Other omics (proteome and glycome, lipidomics…)
16S rRNA sequencing –>
Taxonomic Content
Metagenomic Sequencing leads to
Functional Predictions based on gene content
Metatranscriptomics sequencing leads to
Functional Predictions based on gene expression
Who’s there?
Taxonomic composition + Accurate strain level resolution and abundance estimates for looking at whole genome
What are they doing?
Functional composition and metabolic potential/network
Microbiome is
Body site specific with unique fingerprint of microbes
Who are we?
Individual genetic material + Microbiome (microbial phenotype) + What we eat (diet) –> The triangle
Microbiome is affected by
What we eat
Homeostasis of triangle
Health with low allergy risk and infection resistance
Perturbation of triangle
Disease: Allergies, Metabolic syndrome, obesity, and infections
