Microbiota Flashcards
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
