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Probiotics 2 > Module 18- Microbiome > Flashcards

Module 18- Microbiome Flashcards

1
Q

Microbiota

A

Microbes that live in an established environment

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2
Q

Microbiome

A

Full complement of microbes, their genes, and genomes in a particular environment

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3
Q

Number of cells in the gut microbiota

A

200 Trillion

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4
Q

Number of species in gut microbiota

A

> 1000

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5
Q

Why do we not know how many species of microbes are in the gut microbiota?

A

Varies between individuals and most cannot be cultured

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6
Q

Ratio of human cells to microbies

A

10 microbes per human cell

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7
Q

How much larger is the gut microbiome than the human genome?

A

150X

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8
Q

Least to most microbes in organs of gut

A

Stomach –> Duodenum –> Jejunum/ileum –> Colon (tolerable environment)

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9
Q

Microbes are aerobic

A

In duodenum

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10
Q

Microbes are anaerobes

A

In colon

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11
Q

Stomach and duodenum Microbe Number

A

10 ^ 1 or 3

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12
Q

Jejunum/ileum Microbe Number

A

10^ 4 to 7

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13
Q

Colon Microbe Number

A

10 ^11 or 12

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14
Q

Microbiota 2

A

Ecological community of commensal, symbiotic, and pathogenic microbes within a body space or other environment

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15
Q

There is at least this many microbes in human microbiota

A

10 ^ 11

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16
Q

Microbiota % body mass

A

1-3%

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17
Q

In utero

A

State of embryo of fetus

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18
Q

Germ free

A

In Utero but found some in palcenta and babies

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19
Q

Normal microbiota

A

Microbes that establish permanent colonies inside or on the body without producing disease

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20
Q

Normal microbiota examples

A

Staphylococcus on skin and MM and E. coli in colon

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21
Q

Transient microbiota

A

Microbes present for various periods and then disappear but might colonise host and reproduce briefly

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22
Q

Why transient microbiota is transient

A

Immune defense do not allow permanence or other members of microbiota do not allow them to establish themselves

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23
Q

Living together

A

Symbiosis

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24
Q

Symbiosis

A

Long term interaction between two or more different biological species

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25
Exist in symbiosis
Host and normal microbiota
26
Three types of symbiosis
Commensalism, mutualism , parasitism
27
Commensalism
One benefits and other is unaffected
28
Mutualism
Both benefit
29
Parasitism
One benefits at expense of another
30
Commensalism exampole
Mycobacterium in the ear (eat secretions)
31
Mutualism example
E. coli in colon (Vitamin K and protection)
32
Parasitism example
Disease causing bacteria
33
Opportunistic pathogen
Do not cause disease under normal conditions in their normal habitat but cause disease under special conditions
34
Opportunistic pathogens are usually
Members of normal microbiota but change when environment, food, or defenses do
35
Examples of opportunistic pathogens
E. coli and S. pneumoniae
36
System for complete absence of bacteria in gut
Gnotic mouse model
37
Gnotic mouse models have
Defective gut associated/mesenteric lymphoid tissue and low IgA levels
38
Mutualistic relationships between host and microbes led to...
Immune maturation, immune balance, and specific functions of macrobiotic
39
7 functions of microbiota
1. Seal body spaces 2. Mitigate intestinal pathogens 3. Maintain tissue homeostasis 4. Facilitate fermentation of dietary fiber 5. Critical energy yield 6. Metabolic end products and therapeutic drug processing 7. Signalling among cells and organ systems
40
Mitigate intestinal pathogens by
Exclusion
41
Facilitate fermentation of dietary fibers
Inulin and pectin degraded by microbes so enterocytes can uptake them
42
Metabolic end products
Secrete end products and can activate prodrugs
43
Microbiota role in signalling
Molecules they secrete as products of fermentation act as signalling molecules among cells
44
Butyrate
Energy for gut epithelial cells + signal DCs to get anti-inflammatory response
45
Acetate and propionate
Lipogenesis and glyconeogeneis
46
Energy to intestinal cells and signal DCs
Butyrate
47
Specific marker on epithelial cells and a similar effect on ICs
Propionate
48
Acetate
Broad spectrum on epi cells and immune cells and also a distant effect
49
Acetate has distant effect on
Lungs, brain, pancreas, liver, BM (5)
50
Provides hematoposis to DCs in BM to reduce asthma
Acetate
51
Number of prokaryotes in gut microbiota
10 million with 1800 in 1980 and 14000 in 2016
52
Make up microbiome
Bacteria, Archie, fungi, intestinal protozoa, DNA and RNA viruses, giant viruses
53
All unique sequences that cannot be matches to known species
Operational Taxonomic Units (OTUs)
54
Many gut mirobiome only known as
OTUs
55
16s rRNA genes present in
All Bacteria and Archaea
56
16s rRNA genes contains
Highly conserved and more variable regions
57
How to sequence 16s rRNA
Amplify using primers directed toward conserved regions but flanking variable regions
58
The conserved and variable regions of 16s rRNA allows you to...
Align gene sequences and resolve phylogenetic relationships at different depths
59
Usually variable regions of 16s rRNA
V2 and V6 which are specific for species
60
Complex unit of ribosomes
16s rRNA
61
OTU purpose
Classify groups of closely related individuals because most 16s rRNA sequences are from undescribed microbes
62
Cluster OTUs based on
Similarity to each other
63
Similarity Threshold
OTUs defined by this
64
OTU Similarity Threshold %
97% similarity
65
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
66
16s of different strains of same species having different phenotypes or functional capabilities -->
Inability to infer or reconstruct functional or metabolic capabilities
67
Strains of same species with different phenotypes or functions means
They have different regulatory networks that activate and repress genes and behave different
68
Multiple copies of 16s rRNA
Allow to grow fast because they can translate at multiple promoters
69
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
70
Single Cell Genomics
Het one cell and do whole sequencing and gene expression
71
Gene expression
Get for one cell or the entire community to determine which genes are expressed at a given time
72
Metabolomics
Looks at metabolism of community as whole to see metabolic capability
73
4 Ways to Understand Microbial Communities
(1) 16s rRNA sequencing (2) Metagenomic Sequencing (3) Metatranscriptomic sequencing (4) Other omics (proteome and glycome, lipidomics...)
74
16S rRNA sequencing -->
Taxonomic Content
75
Metagenomic Sequencing leads to
Functional Predictions based on gene content
76
Metatranscriptomics sequencing leads to
Functional Predictions based on gene expression
77
Who's there?
Taxonomic composition + Accurate strain level resolution and abundance estimates for looking at whole genome
78
What are they doing?
Functional composition and metabolic potential/network
79
Microbiome is
Body site specific with unique fingerprint of microbes
80
Who are we?
Individual genetic material + Microbiome (microbial phenotype) + What we eat (diet) --> The triangle
81
Microbiome is affected by
What we eat
82
Homeostasis of triangle
Health with low allergy risk and infection resistance
83
Perturbation of triangle
Disease: Allergies, Metabolic syndrome, obesity, and infections
84

Probiotics 2 (9 decks)

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