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BDS2 PMI > PMI02-2004 > Flashcards

PMI02-2004 Flashcards

1
Q

What is taxonomy?

A

Branch of science concerned with classification

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2
Q

What is a eukaryote?

A

Organism with cell/cells where the genetic material is contained within a distinct nucleus and has membrane-bound organelles

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3
Q

What is a prokaryote?

A

Single cell micro-organism that lacks a distinct nucleus and membrane-bound organelles

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4
Q

Which kingdoms are eukaryotic?

A

Animalia

Plantae

Protista

Fungi

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5
Q

Which kingdoms are prokaryotic?

A

Bacteria

Archaea

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6
Q

What is a habitat?

A

Specific site of organism growth

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7
Q

What is a microbial community?

A

The micro-organisms present in a given habitat

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8
Q

What is the microbiota?

A

Total collection of micro-organisms in a microbial community

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9
Q

What is the microbiome?

A

Microbiota and all associated genes

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10
Q

What is a metagenome?

A

Total genomic DNA of all organisms within a community

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11
Q

What is a biofilm?

A

Structured aggregate of micro-organisms adhered to each other and/or a defined substrate

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12
Q

What is a super-/holo-organism?

A

Assembly of a host and numerous mutually interdependent smaller organisms and their genomes

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13
Q

What is the ratio of microbial cells to human cells in the body?

A

~10:1

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14
Q

About how many genes are in the human gut microbiome?

A

~3.3mil

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15
Q

Why is the human microbiome important?

A

Some micro-organisms are protective against disease and pathogenic species

Changes in the microbiome composition is associated with disease

Microbial genes modulate fundamental human physiological processes

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16
Q

What were the aims of the Human Microbiome Project (2008-2013)? (4)

A

Generate resources to help study human microbiome

Characterise microbiome associated with human health and disease

Determine whether individuals share a common core microbiome

Understand whether changes in the human microbiome result in changes to human health

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17
Q

What is the traditional culture approach?

A

Growing microbes directly from a sample

Phenotypic identification of isolates

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18
Q

What is the new molecular approach?

A

Identification of organisms by gene sequence homology after extraction of DNA from samples

Uses either targeted sequencing (16S rRNA) or shotgun metagenomic sequencing

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19
Q

What are the main advantages and disadvantages of the traditional culture approach?

A

+ Cheap

  • Labour-intensive
  • Cannot tell apart strains and you need to know what to expect
  • Some species cannot grow in lab
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20
Q

What are the main advantages and disadvantages of the new molecular approach?

A

+ Identifies all species present and genes => higher discriminatory power

  • Sequence bias if using primers
  • Expensive
  • Time-consuming to analyse
21
Q

What is the 16S rRNA gene?

A

Highly conserved and specific 1542bp sequence found in all bacteria and archaea

Encodes small subunit of ribosomal complex

22
Q

How do we use the 16S rRNA gene to identify different species?

A

Between conserved regions, there are variable regions which act as “molecular clocks”

Create primers for the conserved regions and amplify across variable regions with PCR

DNA sequence similarities correlate with “evolutionary relatedness” and there is little evidence of horizontal gene transfer

23
Q

What is the benefit of shotgun metagenomics over 16S rRNA sequencing?

A

Can sequence whole genes other than 16S rRNA

Covers all kingdoms, not just bacteria and archaea

Gives functional and taxonomic info (bioinformatics)

24
Q

Which database is used with 16S rRNA sequencing?

A

Green Genes

25
Q

What are the limitations of databases?

A

Can only identify sequences already present in the database

Need to sequence more organisms to increase info available in databases

Need to annotate sequences

26
Q

What is the importance of sequence annotation?

A

Makes sense of the A/T/G/C sequence

Identifies ORFs

Predicts putative functions for genes

27
Q

What are the limitations of annotation?

A

They are only predictions and require experimental confirmation

Time-consuming (~100hrs/genome)

Mistakes can be made

Genes are shared between species but their functions may vary

28
Q

What are virulence genes? Give an example of what they could code for.

A

Contribute to pathogenicity of an organism

Endotoxin, fimbriae, cell wall proteins, adhesion

29
Q

What are resistance genes? Give an example.

A

Induce antibiotic resistance

Erm genes, MecA genes

30
Q

What are diagnostic markers?

A

Genes which aid in rapid diagnosis of a disease (eg Hepatitis antibodies for Hep. C)

31
Q

When does microbial colonisation of the body start?

A

At birth

32
Q

During what time period does the microbiome change the most dramatically?

A

First 3 years of life

33
Q

What can influence the microbiome generally?

A

Diet

Lifestyle

Environment

34
Q

Why aren’t all the microbiomes the same in one body at different sites?

A

Different habitats affect type of microbes that can grow

35
Q

What organism can colonise the stomach and is associated with gastritis, ulcers and stomach cancer?

A

Helicobacter pylori

36
Q

What micro-organisms are commonly found in the small intestine?

A

Streptococci

Lactobacilli

Yeasts

37
Q

Which of the small and large intestine has more micro-organisms present?

A

Large intestine

38
Q

Describe the microbiome of the large intestine.

A

Heavily populated with varied genera (10^12 species)

Anaerobic microbes greatly outnumber aerobic and facultative microbes

39
Q

Describe the skin microbiome.

A

Large variation between different sites

Low numbers on exposed surfaces but larger numbers in protected areas (eg axilla, groin) and around orifices

40
Q

What skin condition is Propioibacterium acnes associated with?

A

Acne

41
Q

What skin condition is Malassezi furfur (yeast) associated with?

A

Dandruff

42
Q

How many microbes are there in saliva?

A

10^8/ml

43
Q

What are the early oral colonisers (Gram-positive)?

A

Streptococcus

Actinomyces

44
Q

Which Gram-negative bacillus is associated with gingivitis?

A

Fusobacterium

45
Q

Which Gram-negative bacilli are associated with periodontitis?

A

Prevotella

Porphyromonas

46
Q

Why is the normal microbiota essential for health?

A

Required for development of gut structures and immune system

Protects against colonisation by pathogens (colonisation resistance)

47
Q

What non-infectious diseases are associated with altered microbiomes?

A

Obesity

Type II diabetes

Ulcerative colitis

Asthma

COPD

48
Q

What is dysbiosis?

A

Imbalance in host microbiota

BDS2 PMI (21 decks)

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