The Human Microbiome Flashcards
Describe the Human Microbiome Project
The aim of HMP is the characterise microbial communities found at multiple human body sites and to look for correlations between changes in the microbiome and human health.
- Five year project started in 2008 ($150M)
- Used culture-independent methods of microbial community characterisation (16S and meta genomics) as well as whole genome sequencing of individual bacterial species
- Emphasis on: oral, skin, vaginal, gut, and nasal/lung
What were the goals of the Human Microbiome Project?
10,000 microbial species in human microbiome
500-1,000 bacterial species just in the gut
Goals:
- To develop a reference set of microbial genome sequences and to perform preliminary characterisation of the human microbiome
- To explore the relationship between disease and changes in the human microbiome
- To develop new technologies and tools for computational analysis
- To establish a resource repository
- To study the ethical, legal and social implications of human microbiome research
What can we learn from the Human microbiome?
- Strong niche specialisation both within and among individuals = different sites, different microbes
- Diversity and abundance of each habitat’s signature microbes vary widely even among heathy subjects = YOUR microbiome, is not MY microbiome
What can we learn from graphing the different bacteria found in different area’s of our body and comparing it to other individuals?
- One individual’s gut bacteria have 50 times the genetic diversity of the human genome
- HMP documented 80-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome
- Everyone has ~160 species (57 were really common)
- The community can change, but the functions do not (as much)
- Observed variations in both pathways and microbes changed with clinical metadata along ethnic/racial differences
What does the microbiome do for us?
Competition by commensal microbes protects from pathogens
- preventing pathogens from being successful
- block colonisation niches
- competing for nutrients
- modifying environment to change virulence factor expression
- making environment actively hostile: Producing bacteriocins (antimicrobial) & short chain fatty acids (SCFA)
- lowering pH
- cause host to thicken mucus layer
- cause host to up regulate antimicrobial peptides (defensive, IgA)
- primes host neutrophils and macrophages
Describe the human gut microflora
Different sites = different bacteria in healthy humans
> 92 bacterial and 26 archaean groups exist, but human microbial communities are dominated by 4:
- Firmicutes
- Bacteroidetes
- Actinobacteria
- Proteobacteria
An estimated 20-80% of human-associated microbes are thought to have eluded cultivation so far.
Few bacterial groups, but many different species and strains.
Describe some of the functions of the gut microbiome
- The gut microbiota creates short chain fatty acids (SCFAs) that modulate our metabolisms and affects our defence against pathogens
The microbiome can:
- synthesise vitamins including: B vitamins: B1, B6, B5 [pantothenic acid], B7 [biotin], B9 [folic acid], B12 [cobalamin] and Vitamin K
- modulate the immune response
- alter drug delivery
Can we modify our gut microflora for beneficial effects?
Functional foods - food claimed to have an health-promoting or disease-preventing property beyond the basic function of supplying nutrients.
At least 50% of Japanese functional foods target ‘intestinal health’.
Describe probiotics
Probiotics: live microorganisms (fermented foods - yogurt)
Lactic acid bacteria (LAB) and Bifidobacteria are the most common types of microbes used as probiotics
Survive transit through stomach and duodenum (can survive the pH changes and make it to the colon)
Potential benefits: chronic intestinal inflammatory diseases, prevention and treatment of pathogen-induced diarrhoea, urogenital infections.
Describe prebiotics
- Prebiotics = an ingredient that beneficially nourishes the good bacteria already in the large bowel or colon (it is a form of fibre)
- Prebiotics stimulate the growth of probiotics
- The body itself does not digest plant fibres; instead, the fibres act as a ‘fertiliser’ to promote the growth of the good bacteria in the gut. These, in turn, provide many digestive and general health benefits
- Some target Bifidobacteria and Lactobacilli (prebiotics stimulate the growth of probiotics)
- They are mostly obtained from a type of carbohydrate fibre called an oligosaccharide. Good sources of prebiotics include whole grains, bananas, onions, garlic, honey and artichokes.
How does modifying our microbiome influence us?
- We are a colonised ecosystem
- Colonising microbes can be: good, neutral, bad
- All are simply extracting carbon and energy
There are two gut species: C. difficile and lactobacillus. Both use lactic acids from mucins (the main structural component of the mucus layer in the gut) as a carbon/energy source - heterotrophs. Speed of growth and presence of accessory genes are the only factors making C. difficile a pathogen.
- Can’t do anything to prevent getting C. difficile in you because your gut has all the things it needs to grow/stay alive.
Describe focal matter transplants: a growing field
Fecal microbiota transplantation (FMT) is a highly successful treatment for multiple recurrences of Clostridium difficile infection (CDI).
