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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
Q

Exist in symbiosis

A

Host and normal microbiota

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26
Q

Three types of symbiosis

A

Commensalism, mutualism , parasitism

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27
Q

Commensalism

A

One benefits and other is unaffected

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28
Q

Mutualism

A

Both benefit

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29
Q

Parasitism

A

One benefits at expense of another

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30
Q

Commensalism exampole

A

Mycobacterium in the ear (eat secretions)

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31
Q

Mutualism example

A

E. coli in colon (Vitamin K and protection)

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32
Q

Parasitism example

A

Disease causing bacteria

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33
Q

Opportunistic pathogen

A

Do not cause disease under normal conditions in their normal habitat but cause disease under special conditions

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34
Q

Opportunistic pathogens are usually

A

Members of normal microbiota but change when environment, food, or defenses do

35
Q

Examples of opportunistic pathogens

A

E. coli and S. pneumoniae

36
Q

System for complete absence of bacteria in gut

A

Gnotic mouse model

37
Q

Gnotic mouse models have

A

Defective gut associated/mesenteric lymphoid tissue and low IgA levels

38
Q

Mutualistic relationships between host and microbes led to…

A

Immune maturation, immune balance, and specific functions of macrobiotic

39
Q

7 functions of microbiota

A
  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
Q

Mitigate intestinal pathogens by

A

Exclusion

41
Q

Facilitate fermentation of dietary fibers

A

Inulin and pectin degraded by microbes so enterocytes can uptake them

42
Q

Metabolic end products

A

Secrete end products and can activate prodrugs

43
Q

Microbiota role in signalling

A

Molecules they secrete as products of fermentation act as signalling molecules among cells

44
Q

Butyrate

A

Energy for gut epithelial cells + signal DCs to get anti-inflammatory response

45
Q

Acetate and propionate

A

Lipogenesis and glyconeogeneis

46
Q

Energy to intestinal cells and signal DCs

A

Butyrate

47
Q

Specific marker on epithelial cells and a similar effect on ICs

A

Propionate

48
Q

Acetate

A

Broad spectrum on epi cells and immune cells and also a distant effect

49
Q

Acetate has distant effect on

A

Lungs, brain, pancreas, liver, BM (5)

50
Q

Provides hematoposis to DCs in BM to reduce asthma

A

Acetate

51
Q

Number of prokaryotes in gut microbiota

A

10 million with 1800 in 1980 and 14000 in 2016

52
Q

Make up microbiome

A

Bacteria, Archie, fungi, intestinal protozoa, DNA and RNA viruses, giant viruses

53
Q

All unique sequences that cannot be matches to known species

A

Operational Taxonomic Units (OTUs)

54
Q

Many gut mirobiome only known as

A

OTUs

55
Q

16s rRNA genes present in

A

All Bacteria and Archaea

56
Q

16s rRNA genes contains

A

Highly conserved and more variable regions

57
Q

How to sequence 16s rRNA

A

Amplify using primers directed toward conserved regions but flanking variable regions

58
Q

The conserved and variable regions of 16s rRNA allows you to…

A

Align gene sequences and resolve phylogenetic relationships at different depths

59
Q

Usually variable regions of 16s rRNA

A

V2 and V6 which are specific for species

60
Q

Complex unit of ribosomes

A

16s rRNA

61
Q

OTU purpose

A

Classify groups of closely related individuals because most 16s rRNA sequences are from undescribed microbes

62
Q

Cluster OTUs based on

A

Similarity to each other

63
Q

Similarity Threshold

A

OTUs defined by this

64
Q

OTU Similarity Threshold %

A

97% similarity

65
Q

Limitations of 16s rRNA based analysis (6)

A

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
Q

16s of different strains of same species having different phenotypes or functional capabilities –>

A

Inability to infer or reconstruct functional or metabolic capabilities

67
Q

Strains of same species with different phenotypes or functions means

A

They have different regulatory networks that activate and repress genes and behave different

68
Q

Multiple copies of 16s rRNA

A

Allow to grow fast because they can translate at multiple promoters

69
Q

Other techniques to understand microbial communities

A

(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
Q

Single Cell Genomics

A

Het one cell and do whole sequencing and gene expression

71
Q

Gene expression

A

Get for one cell or the entire community to determine which genes are expressed at a given time

72
Q

Metabolomics

A

Looks at metabolism of community as whole to see metabolic capability

73
Q

4 Ways to Understand Microbial Communities

A

(1) 16s rRNA sequencing
(2) Metagenomic Sequencing
(3) Metatranscriptomic sequencing
(4) Other omics (proteome and glycome, lipidomics…)

74
Q

16S rRNA sequencing –>

A

Taxonomic Content

75
Q

Metagenomic Sequencing leads to

A

Functional Predictions based on gene content

76
Q

Metatranscriptomics sequencing leads to

A

Functional Predictions based on gene expression

77
Q

Who’s there?

A

Taxonomic composition + Accurate strain level resolution and abundance estimates for looking at whole genome

78
Q

What are they doing?

A

Functional composition and metabolic potential/network

79
Q

Microbiome is

A

Body site specific with unique fingerprint of microbes

80
Q

Who are we?

A

Individual genetic material + Microbiome (microbial phenotype) + What we eat (diet) –> The triangle

81
Q

Microbiome is affected by

A

What we eat

82
Q

Homeostasis of triangle

A

Health with low allergy risk and infection resistance

83
Q

Perturbation of triangle

A

Disease: Allergies, Metabolic syndrome, obesity, and infections

84
Q
A

Probiotics 2 (9 decks)

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