microbes lecture 5- gut feeling Flashcards
what is microbiota and where is it found?
-Tens of trillions of microbes (1014)
-Mostly in colon
-Also SI, lungs, skin, teeth, everywhere…
-80% non-culturable
what is the problem with microbiota?
many bacteria is still not culturable so we use
-16s sequencing
-whole genome sequencing + metagenomics
-computation
what is 16s sequencing
16S sequencing is a molecular technique used to identify and classify bacteria and archaea by analyzing the 16S ribosomal RNA (rRNA) gene, which is highly conserved across prokaryotic species. This gene contains variable regions that are unique to different species, making it a reliable marker for microbial identification.
Key steps include:
DNA Extraction: Microbial DNA is isolated from a sample (e.g., soil, water, or a biological specimen).
PCR Amplification: The 16S rRNA gene is amplified using primers targeting conserved regions.
Sequencing: The amplified gene is sequenced using platforms like Illumina or PacBio.
Bioinformatics Analysis: Sequences are compared to databases (e.g., SILVA, Greengenes) to determine the taxonomy and relative abundance of microbes in the sample.
compare 16s sequencing to whole genome sequencing
16s= identify species and relative frequencies and also give a phylogenetic view of community composition
total dna sequencing= also gives a phylogenetic view of community composition but it also gives functional information and identifies variants and polymorphisms
when would you use 16s or WGS
16S sequencing: Limited to bacterial/archaeal identification; cost-effective for microbiome studies.
WGS: Provides a comprehensive view of any organism’s genome; more expensive but more detailed.
what are bacterial communities?
-Colonise all body surfaces, especially mucosa
-Communities differ at different sites
-Bacteriodes is the most common genus in the colon
-Communities are complex, stable, and interdependent
-Affected by many factors, especially diet
what does this mean for human health?
Metabolise complex carbohydrates from plants —> Short Chain Fatty Acids
Synthesis of micronutrients- vit. B3, B5, B6, B12, biotin, tetrahydrofolate, vit K.
Limit pathogen colonisation
what are short chain fatty acids?
Include butyrate (most abundant), acetate and propionate
Produced by bacterial fermentation of dietary fibre, mostly in colon
Main energy source for epithelial cells
Butyrate has anti-inflammatory effect on intestinal epithelial cells
Involved in differentiation of colonic Tregs and ameliorates colitis in mice*
There are other important bacterial metabolites!
when do you take probiotics?
Live Lactobacillus casei shirota strain, 6.5 billion per 65 mL bottle.
Global market $6970 M in 2021
How many survive stomach acid and colonise?
Limited evidence for efficacy. But little harm.
what is inflammatory bowel disease?
Includes Ulcerative Colitis, Crohn’s disease
Interplay between:
-Host genetic factors
-Innate and adaptive immune response
-The microbiota!
Infiltration of bacteria drives inflammation
Lesions generated by immune response against microbes.
Abnormal microbial colonisation might contribute to disease.
what is the intestinal immune system for?
it is specialised to deal with the food and bacteria in the gut
what is C difficile infection?
1) spread through contaminated surfaces and hands of hospital staff
2) enters the body and multiplies in gastrointestinal tract
3) psedomembrane formation within the colon
4) c difficile realises toxins that damage the colon and may lead to pseudomembrane formation
what is faecal transplants used for?
Transplanting faecal matter from one person to another - the thought might turn your stomach, but it could be lifesaving.
Some doctors are using the procedure to repopulate the gut with healthy bacteria, which can become unbalanced in some diseases.
Faecal microbiota transplantation (FMT)
Full spectrum of microbial components
Used by Ge Hong 2000 years ago in China
90% success via colonoscopy for C. difficile
Much less success for other conditions
Risks?
Exposure to unknown pathogens
May transfer other illness…
