The Human Microbiome Flashcards
What is a micro biome
The complete collection of microorganisms, and their genes, within a particular environment
What is a microbiota
Individual microbial species in a biome - bacteria, fungi, archaea, and viruses
How many bacterial, and how many archaea phylum/phyla
92 bacterial
26 archaeal
Outline the human micro biome project
Five year project started in 2008
Used culture independent methods of microbial community characterisation (16s ribosomal metagenomics) as well as whole genome sequencing of individual bacterial species
Emphasis on: oral, skin, vaginal, gut, and nasal/lung
How many microbial species in the human micro biome. How many in just the gut
10,000 microbial species in human micro biome.
500-1000 bacterial species just in gut
What where the human micro biome project goals
To develop a reference set of microbial genome sequences and to perform preliminary characterisation of human micro biome.
To explore the relationship between disease and changes in the human micro biome.
To develop new technologies and tools for computational analysis.
To establish a resource repository.
To study the ethical, legal, and social implications of human micro biome research.
Outline niche specialisation of human microbiome
Strong niche specialisation both within and among individuals - different sites different microbes
Outline diversity of multiple individuals microbiomes
Diversity and abundance of each habitats signature microbes may vary widely even among healthy subjects = your microbiome is not my microbiome. Strains are different between individuals
What are the 4 take homes regarding individual microbiome diversity
One individuals gut bacteria has 50 times the genetic diversity of the human genome
HMP documented 81-99% of the genera, enzyme families, and community configurations occupied in healthy western microbiome.
Everyone has -160 species (57 very common)
The community can change, but the functions do not change ( observed variations in both pathways and microbes changed with clinical metadata along ethnic/racial differences)
What does the microbiome do for us
Preventing pathogens form being successful
Block colonising niches
Competitions for nutrients
Modifying environment to change virulence factor expression
Making environment actively hostile (bacteroicins and short fatty acid production)
Lowering pH
cause host to thicken mucus layer
cause host to upregulated anti microbial peptides (definesin, IgA)
Primes host neutrophils and macrophages
Outline the relationship between commensal microbes and pathogens
Competition by commensal microbes protects from pathogens
Outline the effect of a broad spectrum antibiotic on the microbiome
Broad spectrum antibiotic kills natural microbiome, foreign microbe now has no competition
More than 92 bacterial and more than 26 archaeal groups exist, but what 4 dominate human microbiome
Firmicutes
Bacteroidetes
Actinobacteria
Proteobacteria
What are the take homes about the human gut in terms of microbes
Human gut, also known as gastrointestinal/digestive tract, has the highest density of microbes within the human body.
Different sites - different conditions, which is reflected in the species of microbes that inhabit these microbes.
50% faecal biomass = bacteria
Microbe density increases as you go down, minimum at stomach and maximum at gut
What is the functions of the gut microbiome
The gut microbiota creates SCFA (short chain fatty acids) that modulate our metabolism and affect our Defense against pathogens
Microbiome can synthesise vitamins, (pathogenic acid B1, B5, B6, biotin B7, folic acid B9, cobalamin B12)
Can modulate the immune response and alter drug delivery
