PMI02-2004 Flashcards
What is taxonomy?
Branch of science concerned with classification
What is a eukaryote?
Organism with cell/cells where the genetic material is contained within a distinct nucleus and has membrane-bound organelles
What is a prokaryote?
Single cell micro-organism that lacks a distinct nucleus and membrane-bound organelles
Which kingdoms are eukaryotic?
Animalia
Plantae
Protista
Fungi
Which kingdoms are prokaryotic?
Bacteria
Archaea
What is a habitat?
Specific site of organism growth
What is a microbial community?
The micro-organisms present in a given habitat
What is the microbiota?
Total collection of micro-organisms in a microbial community
What is the microbiome?
Microbiota and all associated genes
What is a metagenome?
Total genomic DNA of all organisms within a community
What is a biofilm?
Structured aggregate of micro-organisms adhered to each other and/or a defined substrate
What is a super-/holo-organism?
Assembly of a host and numerous mutually interdependent smaller organisms and their genomes
What is the ratio of microbial cells to human cells in the body?
~10:1
About how many genes are in the human gut microbiome?
~3.3mil
Why is the human microbiome important?
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
What were the aims of the Human Microbiome Project (2008-2013)? (4)
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
What is the traditional culture approach?
Growing microbes directly from a sample
Phenotypic identification of isolates
What is the new molecular approach?
Identification of organisms by gene sequence homology after extraction of DNA from samples
Uses either targeted sequencing (16S rRNA) or shotgun metagenomic sequencing
What are the main advantages and disadvantages of the traditional culture approach?
+ Cheap
- Labour-intensive
- Cannot tell apart strains and you need to know what to expect
- Some species cannot grow in lab
What are the main advantages and disadvantages of the new molecular approach?
+ Identifies all species present and genes => higher discriminatory power
- Sequence bias if using primers
- Expensive
- Time-consuming to analyse
What is the 16S rRNA gene?
Highly conserved and specific 1542bp sequence found in all bacteria and archaea
Encodes small subunit of ribosomal complex
How do we use the 16S rRNA gene to identify different species?
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
What is the benefit of shotgun metagenomics over 16S rRNA sequencing?
Can sequence whole genes other than 16S rRNA
Covers all kingdoms, not just bacteria and archaea
Gives functional and taxonomic info (bioinformatics)
Which database is used with 16S rRNA sequencing?
Green Genes
What are the limitations of databases?
Can only identify sequences already present in the database
Need to sequence more organisms to increase info available in databases
Need to annotate sequences
What is the importance of sequence annotation?
Makes sense of the A/T/G/C sequence
Identifies ORFs
Predicts putative functions for genes
What are the limitations of annotation?
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
What are virulence genes? Give an example of what they could code for.
Contribute to pathogenicity of an organism
Endotoxin, fimbriae, cell wall proteins, adhesion
What are resistance genes? Give an example.
Induce antibiotic resistance
Erm genes, MecA genes
What are diagnostic markers?
Genes which aid in rapid diagnosis of a disease (eg Hepatitis antibodies for Hep. C)
When does microbial colonisation of the body start?
At birth
During what time period does the microbiome change the most dramatically?
First 3 years of life
What can influence the microbiome generally?
Diet
Lifestyle
Environment
Why aren’t all the microbiomes the same in one body at different sites?
Different habitats affect type of microbes that can grow
What organism can colonise the stomach and is associated with gastritis, ulcers and stomach cancer?
Helicobacter pylori
What micro-organisms are commonly found in the small intestine?
Streptococci
Lactobacilli
Yeasts
Which of the small and large intestine has more micro-organisms present?
Large intestine
Describe the microbiome of the large intestine.
Heavily populated with varied genera (10^12 species)
Anaerobic microbes greatly outnumber aerobic and facultative microbes
Describe the skin microbiome.
Large variation between different sites
Low numbers on exposed surfaces but larger numbers in protected areas (eg axilla, groin) and around orifices
What skin condition is Propioibacterium acnes associated with?
Acne
What skin condition is Malassezi furfur (yeast) associated with?
Dandruff
How many microbes are there in saliva?
10^8/ml
What are the early oral colonisers (Gram-positive)?
Streptococcus
Actinomyces
Which Gram-negative bacillus is associated with gingivitis?
Fusobacterium
Which Gram-negative bacilli are associated with periodontitis?
Prevotella
Porphyromonas
Why is the normal microbiota essential for health?
Required for development of gut structures and immune system
Protects against colonisation by pathogens (colonisation resistance)
What non-infectious diseases are associated with altered microbiomes?
Obesity
Type II diabetes
Ulcerative colitis
Asthma
COPD
What is dysbiosis?
Imbalance in host microbiota
