Microbiota
The microorganisms that typically inhabit a specific environment
Microbiome
The totality of microbes, their genomes and environmental interactions in a defined environment
Dysbiosis
Microbiome imbalance
Gut microbes
Involved in immune system regulation, remove toxins and carcinogens, crowd out pathogens, improve intestinal functions and gut brain links
HMP
- Determine whether individuals share a core human microbiome
- Can changes in the human microbiome be correlated with changes in human health
- Develop new technological + bioinformative tools needed to support the HMP
- Address the ethical, legal and social implications raised by human microbiome research
Microbiome analysis
- 16S rRNA sequencing
All bacteria have a 16S subunit of ribosomes
It contains both highly conserved and highly variable regions, that can be used to identify taxonomic groups
Useful for defining the composition of the microbiota - Metagenome sequencing
Whole genome shotgun sequencing of the microbiome
Identify the repertoire of functions and pathogens present within the microbiome
Microbial diversity in the human microbiome
178 HMP-sequenced genomes present
- 2 kingdoms
- 9 phyla
- 18 classes
- 24 orders
The gut microbiome
- The most heavily colonised organ in the human body is the GI tract
- Strict anaerobes outnumber faculatative aerobes and aerobes
The gut microbiota is dominated by 2 phyla
- Bacteroidetes
- Firmicutes
- It is estimated that the human gut contains ~ 500 - 1000 bacterial species
- Bacterial abundance increases as we progress from the stomach to the colon
Obesity and gut microbiome
- Obesity was associated with a large shift in the relative abundance of the taxa present
- A 50% reduction in Bacteroidetes + a significant increase in Firmicutes
- Obese = more Firmicutes
Better at harvesting energy - An ‘obese microbiome’ promoted weight gain when transplanted to a germ-free mouse
IBD
Crohn’s disease
- Nod2 is an intracellular sensor for bacterial peptidoglycan
It is trying to find the microbes in you to upregulate the innate immune system - Nod2 function is required for optimal defensin expression which is an important antimicrobial peptide, a critical component of the innate immune system
- Nod2 is a function which is required for optimum defensin expression in individuals
- Defensins are important antimicrobial peptides, a critical part of the innate immune system
- 3 polymorphisms of Nod2 associated with CD, each polymorphism results in reduced activation of NF-kB in response to bacterial peptidoglycan
There is a higher incidence of adhesive or invasive E.Coli in patients with dysfuntion in Nod2
CD vs healthy
DNA from faecal samples of healthy individuals and CD individuals have been looked at
A change in microbiome
Is there a function of the microbes which is inducing or reducing an individuals likelihood of having CD?
- Faecalibacterium is an anti-inflammatory commensal bacterium
It is promoting anti-inflammatory cytokines and inhibiting pro-inflammatory conditions
Decreasing inflammation in CD individuals
Not found in not CD patients
An anti-inflammatory gut organism such as Faecalibacterium might be an effective probiotic treatment of CD
Eradication therapy targeted against ‘harmful’ components of the microbiota Eg. H. pylori
Disease
A condition that impairs normal tissue function
Infection
An infection results when a pathogen invades and begins growing within a host
Disease results only if and when, as a consequence of the invasion and growth of a pathogen, tissue function is impaired
Pathogen
An organism that is capable of causing disease
It is a disease causing agent in a susceptible host
A true pathogen is an infectious agent that causes disease in virtually any susceptible host
Pathogenicity
Pathogenicity is defined by the capacity of a microbe to cause damage in a susceptible host
It is a discontinuous variable
It is dependent on host variables
Virulence
It is a continuous variable that is defined by the amount of damage or disease that is manifest
Median infective dose (ID50)- the amount of pathogenic microorganisms that will produce a 50% infection of the test subjects
Median lethal dose (LD50)- the quantity of an agent that will kill 50% of the test subjects
What can influence the ID50 and LD50 of a pathogen
- Host
- Immunological status
- Physiological status
- Route of infection
Koch’s molecular postulates
- Gene under investigation should be associated with pathogenic members of a pathogenic spcies
The gene in question should be found in all pathogenic strains of teh species but be absent in non-pathogenic strains - The gene which causes virulence must be expressed during infection
- Specific inactivation of the gene associated with teh suspected virulence trait should lead to a measurable loss in pathogenicity of virulence
Virulence of the microorganism with the inactivated gene must be less than that of the microorganism with the inactivated gene must be lesss than that of the unaltered microorganism in an appropriate animal model - Allelic replacement of the mutated gene should lead to restoration of pathogenicity
Incidence
The number of new cases of a disease in a given area or population
Prevelance
The total number, new and already existing
Major adherence factors
Capsule layer: E.Coli
Adherence proteins: Streptococcus pyogenes, M protein
Neisseria gonorrhoeae, Opa protein
Lipoteichoic acid: Streptococcus pyogenes
Fimbrae/ pili: Neisseria gonorrohoeae, pili
Salmonella, type I fimbriae
E.Coli, fimbriae
Type of exotoxins
- Cytolytic enzymes- they work by attacking cell constituents, causing lysis
- A-B toxins- Unit B binds to the cell receptor and allows A to cross the membrane
Type of exotoxins
Cytolytic enzymes
- Toxins that lyse red blood cells are called hemolysins
- Staphylococcal a-toxin kills nucleated cells and lyses erythrocytes
Type of exotoxins
A B toxins
Eg. Diptheria toxin, tetanus toxin, botulinum toxin and shiga toxin
