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HUMAN HEALTH AND DISEASE > The Human and Oral Microbiomes > Flashcards

The Human and Oral Microbiomes Flashcards

1
Q

what is a habitat?

A

specific site of organism growth

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2
Q

what is a microbial community?

A

the micro-organisms that are present in a given habitat

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2
Q

What is microbiota?

A

the total collection of micro-organisms within a microbial community

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3
Q

what is microbiome?

A

The microbiota and all of its associated genes.

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4
Q

what is the metagenome?

A

the total genomic DNA of all the organisms within a community

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5
Q

what is a biofilm?

A

A physically (often temporally) structured aggregate of micro-organisms, adhered to each other and/or a defined substrate (ie. dental plaque attached to a tooth/gum margin).

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6
Q

What is the human microbiome made up of?

A

“we are an organism made up of numerous mutually interdependent smaller organisms and their genomes ”.
* There are 10X moremicrobial cells in the human bodythan human cells
* 10,000 The number of different species identified to-date within the human body
* ~ 22,000 The number of genes in the human genome
* 3.3 million The number of genes in the human gut microbiome

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7
Q

Why is the human microbiome is important?

A
  • Health: Specific microorganisms are protective against disease, and pathogenic bacterial species
  • Disease: changes in the composition of the microbiome are associated with disease. Examples: Inflammatory Bowel Disease, Obesity, Diabetes, Rheumatoid Arthritis
  • Microbial Genes: Modulate fundamental human physiological processes. Examples: Metabolism, Energy acquisition, Immune modulation, Neurological development
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8
Q

what are two methods to study the microbiome?

A
  1. The Traditional Culture Approach
  2. The New Molecular Approach
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9
Q

how do you carry out a The Traditional Culture Approach?

A

Grow microbes directly from sample
Requires phenotypic identification of isolates:
* Morphology / Motility
* Biochemical
* Antibody / Serological
* Metabolic

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10
Q

how do you carry out the new molecular approach?

A
  • Identifies organisms by gene sequence homology
  • Extract microbial DNA from samples
  • Sequence analysis of DNA by targeted sequencing (16s rRNA) or Shotgun Metagenomics sequencing
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11
Q

what are the positives of the traditional cultivation approach?

A

cheap

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12
Q

what are the negative of the traditional cultivation approach?

A
  • Labour intensive [> 24 hours for org ID]
  • Only gross species discrimination possible
  • Not many species can grow (only 50% of known oral bacteria are currently cultivable in the laboratory)
  • Need to know what species to expect to be able to use the right growth conditions for them.
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13
Q

what are the positives of the new molecular approach?

A
  • Tells you what is present not just what you can grow
  • Can tell you what genes are present able to determine whether a particular bacteria is pathogenic or not
  • Higher discriminatory power for species identification
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14
Q

what are the negatives of the new molecular approaches?

A
  • Sequence bias due to primer specificity
  • Expensive
  • Time consuming and Computational taxing
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15
Q

what is the 16s rRNA gene?

A
  • 1542 bp gene
  • Encodes the small subunit of the ribosomal complex, necessary for protein synthesis
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16
Q

why target the 16s rRNA gene?

A
  • Found in all bacteria and archaea
  • Because the gene has an essential function it also has a highly specific highly conserved regions that do not vary. But between there is a regions that are highly variable which allow for discrimination of bacterial genera.
  • “molecular clock” – rDNA sequence similarities correlated with ‘evolutionary relatedness’. Little evidence of horizontal gene transfer
17
Q

what is shotgun metagenomics?

A
  • Is the study of uncultured microbial communities, typically relying on high-throughput experimental data and bioinformatic techniques
  • Sequences whole genes. (ie. Sequences all genes present in the sample not just 16S rRNA)
18
Q

what are the positives of shotgun metagenomics?

A
  • Covers all kingdoms, not just Bacteria and Archaea (even human genes)
  • Gives both functional and taxonomic information
  • More technical and expensive
19
Q

How to make sense of sequencing data ?

A

Sequence output is a list of A, T, G, C’s
‘ATGCATCGATCGTACTGACTATGCATATAGTTCA’
Comparison of A, T, G, C’s to curated databases for identification:
* 16S rRNA database for taxonomic identification (2011 green genes database contains 1,049,116 aligned 16S rDNA records >1250nt)
* Genome databases for metagenomics (ie. Database of all know genes of interest)

20
Q

what are the limitations of sequencing data?

A
  • Can only identify sequences present in our databases
  • Need to perform whole genome sequencing of more organisms so this genetic information can be added to the databases
  • Need to annotate the sequences. Ie. What do the ATCG’s code for? What is their function?
21
Q

what is the importance of annotation?

A
  • Makes sense of the A, T, G, C’s
  • Identifies the open reading frame (ORF) of genes
  • Predicts putative functions for genes and gene products
22
Q

what are the issues with annotation?

A
  • Its only a prediction. Need confirmation experiments
  • Takes about 100 hours per genome (1 minute/gene)
  • Mistakes are made
  • Various software available to help predict function of genes. Some are better than others
  • Genes shared and vary between species
23
Q

when does colonisation occur in humans?

A

Colonisation begins at birth. Microbiome changes over time. Most dramatically in the first 3 years of life. Influenced by diet, lifestyle, environment.

24
Q

what is the microbiome like in the stomach?

A

Traditionally always thought to be sterile. Any colonisation in the stomach was thought to be transient as it was due to being brought by food.
Helicobacter pylori is a coloniser:
* Associated with gastritis and ulcers and stomach cancer
* Up to 40% of the population colonised by this bacteria.

25
Q

what is the microbiome like in the small intestine?

A
  • There are a lower numbers of organisms but the number increases closer to the colon
  • Microbes found here are those which have passed through stomach acid without being killed.
  • Include Streptococcus Spp. And Lactobacillus Spp. and yeasts.
  • All are aciduric (acid-tolerating)
26
Q

what is the microbiome like in the colon/large intestine?

A
  • Heavily populated with highly varied bacterial genera
  • Anaerobic microbes greatly outnumber the aerobic and facultative microbes
  • Heavily studied for health and disease assocaitions
27
Q

what is the microbiome like in the skin?

A
  • Varied microbiota - Large variation between different sites
  • Relatively low numbers of microbes on exposed areas because of the fact these areas are continuously abraded.
  • Large numbers present in protected areas e.g. axilla, groin, between toes
  • Large numbers also present around orifices
  • Principal species include those associated with skin conditions such as acne
28
Q

what is the microbiome like in the mouth?

A

High numbers of bacteria in the mouth:
* ~108/ml in saliva
* ~109/mg in plaque
Highly diverse more than 700 species identified in the oral cavity.

29
Q

is the oral microbiome in harmony with its host?

A

no, The oral microbiome is usually associated with oral diseases.

30
Q

why is the oral microbiome not in harmony with its host?

A

may be due to our oral hygiene where we are constantly brushing away oral bacteria so the oral biofilm never settles down to a particular static community.

31
Q

what is the most dominant species in the saliva

A

Streptococcus

32
Q

what bacteria in mouth is considered healthy?

A

Streptococcus and actinomyces

33
Q

what bacteria in the mouth is associated with gingivititis?

A

Fusobacterium*

34
Q

what bacteria in the mouth is associated with periodontitis?

A

Prevotella and Spirochaetes

35
Q

what are the dynamic changes in Plaque Microbiota due to Disease?

A

Aerobic cocci, some aerobic bacilli Mostly healthy

Aerobic cocci, more aerobic bacilli. New cocci genera appearing Mostly healthy

Gram-negative anaerobic species appear – Gingivitis associated

Gram-negative anaerobic species begin to dominate. Gingivitis and Periodontitis associated

36
Q

why is microbiota essential for health?

A
  • Required for development of gut structures and the immune system
  • Protects against colonisation with pathogens – colonisation resistance
  • Disruption of normal microbiota e.g. by antibiotics leads to infection bypathobionts e.g. Candida spp
37
Q

what is dysbiosis?

A

an imbalance in the host microbiota

38
Q

how can dysbiosis occur?

A

Can result in development of both infectious and non-infectious diseases.

39
Q

what are the environmental factors that drive dysbiosis?

A
  • (mal)nutrition
  • antibiotics consumption
  • infection
40
Q

what is the impact of post-genomic microbiology research on dentistry?

A
  • A greater understanding of dental diseases - Prevention and restoration
  • Improved diagnosis, we know what species are present in the saliva could lead to more rapid and accurate diagnosis and maybe earlier intervention, broader range
  • Novel antimicrobial drugs, which can improve our repertoire of antibiotics for use on treating infection

HUMAN HEALTH AND DISEASE (58 decks)

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