Lecture 30 Flashcards
How many phyla?
- 92 bacterial phyla
- 26 archael phyla
Human MICROBIOME AIM
- to characterise microbial communities found at multiple human body sites and to look for correlations between chances in microbiome and human health
- five year project started in 2008
- used culture-independent methods of microbial community characterisation (16s and metagenomics) as well as whole genome sequencing of individual bacterial species
- emphasis on: oral, skin, vagina, gut, and nasal/lung
The HMP goals
- to delvelop a reference of set microbial genome sequences and 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 the microbiome research
How many microbial species in the human microbiome
- 10,000
How many bacterial species in gut
500-1000 bacterial species just in gut
Human microbiome project showed that there was:
- strong niche specialisation both within and among individuals = different sites - different microbes
- diversity and abundance of each habitats signature microbes vary widely even among healthy subjects - unique microbiome between people - same bacteria but different stain
Microbiome diversity
- metabolic pathways of microbiome is consistent across humans
- one individuals gut bacteria have 50 times the genetic diversity of the human genome
- HMP documented 81-99% of the genera, enzyme families and communist configurations occupies by healthy western microbiome
- everyone has about 160 species (57 were really common)
- the community can change but the functions do not
- observed variations in both pathways and microbes changes with clinical metadata along ethnic/racial differences
What does the microbiome do for us?
Competition by commensalism microbes protects from pathogens:
- prevent pathogens form being successful
- blocking colonistation niches
- competing for nutrients
- modifying environment to change virulence factor expression
- making environment actively hostile; producing bacteroicins (anti microbial) + short fatty chain acids
- lowering pH
- cause host to thicken mucus layer
- cause host to up regulate anti microbial peptides (defensin, IgA)
- primes host neutrophils and macrophages
Different sites =
Different bacteria in healthy humans
__ bacterial phyla and __ archaeal phyla exist, but human microbial communities are dominated by _
92
26
4
4 dominating phyla
- firmicutes
- bacteroidetes
- actinobacteria
- proteobacteria
An estimated ____ - ___% of human- associated _____ are thought to have eluded cultivation so far
20-80
Microbes
___ bacteria groups, but ____ different ______ and _____
Few bacterial groups but many different species and strains
The human gut: a densely populated world of microbes (NOT CORE)
- human gut also known as: gastrointestinal tract and digestive tract
- highest density of microbes in human body - huge genetic and metabolic potential, varies in pH and oxygen
From oral cavity to anus - different environments and different conditions as u move down
- colon most densely microbal
- 50% of faecal biomass = bacteria
Different sites = different conditions
Differences in microbes reflect this
Some functions of the gut microbiome
- bacteria in gut breakdown cellulose (plant material) into products which are then used by other microorganisms ending up with further end products
- the gut micro bacteria creates SCFAs that modulate our metabolism and affects out defence against pathogens
Some (more) functions of the gut microbiome (vitamins)
The microbiome can: (normal, commensal bacteria - normally found in body, NORMAL MICROFLORA )
- synthesis vitamins including:
- B vitamins: B1, B6, B5 (pantothenic acid), B7 (biotin), B9 (folic acid), B12 (cocalamin)
- modulate the immune response
- alter drug delivery
Functional foods =
Foods claimed to have a health-promoting or disease - preventing property beyond the basic function of supplying nutrients - does something to our microbiome that helps combat disease
(At least 50% of Japanese functional foods target ‘intestinal health’)
Probiotics =
Live microorganisms (fermented food - yoghurt)
- lactic acid bacteria (LAB) and Bifidobacteria are the most common types of microbes used as probiotics (but no experimental data to support that)
Survive transit through stomach and duodenum
Potential benefits of probiotics
- chromic intestinal inflammatory dieseases
- prevention and treatment of pathogen-induces diarrhoea
- urogenital infections
Prebiotics =
An ingredient that beneficially nourishes the good bacteria already in the large bowel or colon
Probiotics stimulate the growth of
Probiotics
Prebiotics digestion? And function
The body itself does not digest these plant fibres; instead e the fibres act as fertiliser to promote the growth of many of the good bacteria in the gut. These, in turn, provide many digestive and general health benefits
- some target biifidobacteria and lactobacilli (prebiotics stimulate the growth of probiotics)
Prebiotics are mainly obtained from… and good sources of…
They are mostly obtained form a type of carbohydrate fibre called an oligosaccharide
Good sources of prebiotics include whoel grains, bananas, onions, garlic and honey and artichoke
Probiotic is the live organism , Prebiotic is the food nutrients fertiliser
Yeah
Differences between probiotics and prebiotics
We are a…
Colonised ecosystem
Colonising microbes can be:
- good
- bad
- neutral
All are simply extracting carbon and energy
Good and bad bacteria
Good vs bad… C. Difficile vs lactobacillus paracasei
Two gut species: C. Difficile and lactobacillus paracasei
Bad - C. Difficile
Good - lactobacillus paracasei
- both use siallic acids from mucins (the main structural component of the mucus layer in the gut) as carbon/energy source —-> heterotrophs
- speed of growth and presence of accessory genes are the only factors making C. Difficile a pathogen
Fecal matter transplant
Fecal microbiata transplantation (FMT) is a highly successful treatment for multiple recurrences of clostridium Difficile infection (CDI)
