Lecture 3 Flashcards
What are all viruses?
obligate intracellular parasites. they only grow (ie replicate) in appropriate host cells.
what is a virion? how can they be seen?
the name given to a purified virus particle. can be seen using EM.
what do phages infect?
bacteria and archaea.
what is the structure of a virus?
all virus particles contain nucleic acid genome and capsid proteins; many are enveloped with membranes. Viral genomes can either be RNA or DNA, single or double stranded.
are many genes shared between major groups of viruses?
few/no genes shared.
how do you study viral diversity in the microbiota?
direct sequencing of viral genomes
what is the human viriome?
the entire collection of viral genomes isolated from human tissues
what is the common type of virus identified from human samples?
bacteriophages
what are eukaryotic viruses derived from?
food- e.g. plant viruses- the most common RNA virus isolated from the digestive tract.
what can eukaryotic viruses infect?
microbial eukaryotes (e.g. Giardia and Trichomonas), can modulate mucosal inflammation. viruses infecting human cells: pathogenic viruses and potential mutualistic viruses.
what is the most widely used phylogenic marker?
small submit ribosomal RNA (SSUrRNA) gene.
what SSUrRNA gene is found in each life form?
16SrRNA in prokaryotes, 18SrRNA in eukaryotes and 12SrRNA in mitochondria and plasmids.
why is SSUrRNA the most used phylogenic marker?
its functionally constant- part of the ribosome.
sufficiently conserved, allowing cloning with degenerate primers (PCR) and information alignments to profile taxonomic composition of microbiota.
Why can’t SSUrRNA be used for viruses?
they have no ribosomes.
what has SSUrRNA sequencing told us?
its revealed key features of microbial communities’ structure and microbial interactions.
what is Metagenomics and the meta genome?
Metagenomics sequences an entire population, and the meta genome is a mix of microbial clones and species of a given habitat.
what is the unit of study in Metagenomics?
the microbial community in a specific niche.
what does genome sequencing look like in practice?
extract DNA from faecal material, fragment the genome, large scale random “shotgun” sequencing, >1 billion reads of ~300bp, complete genome sequences of >100 bacteria in one run.
why can’t the majority of micro-organisms not be cultured?
they’re anaerobic for example Bacteroides.
what can Metagenomics be used for in practice?
to see how the features of microbiota change between healthy and diseased states.
what happens if you only focus on DNA in Metagenomics?
you’ll completely miss any RNA viruses.
what were the goals of the human microbiome project?
- determening whether individuals share a core human microbiome.
- understanding whether changes in the human microbiome can be correlated with changes in human health.
- developing the new technological and bioinformatic tools needed to support these goals.
- addressing the ethical, legal and social implications raised by the human microbiome research.
what are cross-sectional studies of the human microbiota?
observation of all members of a population, or a representative subset, at one specific point in time.
what are longitudinal studies of the human microbiota?
studies that involve repeated observations of the same variables over long periods of time- often many decades, for example, how microbiome changes as we age.
what are case-control studies of the microbiota?
observational study in two existing groups with different features are compared on the basis of some supported casual attribute. (e.g. healthy vs diseased state: smoker vs non-smoker, IBD vs healthy.)
what % of the faecal material is made of bacteria and microbes?
60%
why is the lowest amount of microorganisms in the stomach? and how do some microbes survive there?
due to the low stomach ph, some organisms survive by sticking under the mucosal surface.
which mucosal surface has the greatest variety of microbiota?
the GIT is very distinct from the others.
what are the major bacteria phyla in the gut?
Bacteroides and Firmicutes.
what are CAZymes?
carbohydrate active enzymes
what are the four major types of cazyme categories?
- Glycoside hydrolases (GH): 130 families.
- Polysaccharide lyase (LH): 22 families.
- Carbohydrate estherases (facilitate the activities of GH and LHs)
- Glycosyl transferases (not degrading).
what kind of bacteria are Bacteroides and Firmicutes?
Bacteroides gram negative, firmicutes gram positive.
what phyla of bacteria contain the most CAZymes?
Bacteroides and firmicutes.
which phyla of bacteria evidently increases in dysbioitic states in the lung microbiome?
Proteobacteria
what can SCFAs do?
they can dampen down inflammatory pathways in the gut macrophages and DCs, promoting the development of Treg cells and maintain gut epithelial integrity and health.
in a mouse model, SCFAs were shown to do what?
circulating SCFAs can modulate the properties of DC leading to reduces Th2 proinflammatory responses in the lungs.
