lecture 6 microbiota Flashcards
How does S. aureus cause infections and intoxication?
Causes infection due to the bacteria and intoxication due to toxins secreted by the bacteria.
How is most microbiota present?
as a mixed species biofilm
Bacteria colonizes surfaces such as:
mucosal (nares, surfaces, GI, vagina), skin, are highly variable from person to person, many bacteria present in the microbiota cannot be cultured**
What is the microbiota?
the bacteria present , many cannot be cultured, is a mixed species biofilm, highly variable from person to person
Microbiome
genetic analysis of the genomes present
What varies throughout the biofilm
nutrients and oxygen concentration
What varies depending on the location of the biofilm?
metabolic cooperativity and cell-cell signaling (quorum sensing) The availability of metabolites and quorum sensing are different throughout the biofilm
Why do phenotypes in the biofilm differ?
mutation and selection , and biophasic switches . Differences also lead to transcriptional regulation
What is 16S rRNA sequencing? “phylogeny”
Method used to compare the evolutionary relatedness of bacteria. Present in ALL cells, non-transferable, large, appropriate conservation, variable regions allow distinguish closely related bacteria, highly conserved to distinguish distantly related bacteria, functional stability so under the same selective pressure in all bacteria.
What are the three kingdoms of life?
bacteria, archaea, eucaryota archaea are single celled organisms originally considered bacteria, but on the basis of evol relatedness and key differences in structure, they are now considered a distinct kingdom.
How are bacteria referred to?
by their genus and species. strep pyogenes. Occasionally pathogens are referred to by subspecies . Bacterial names are always in italics. When analyzing the microbiota, bacteria are often grouped by phylum/families.
How can one characterize the microbiome and microbiota?
various samples including: tissues-animal models, surgically removed/post-mortem, swab- mucosal surfaces, fecal samples can be used to study GI microbiota. Fecal specimens will have bacteria shed from the surface usually pieces of biofilms, may or may not fully represent the entire microbiota
Why is the use of culture to characterize microbiota limited?
only a small percent of the bacteria can be cultured and many different kinds of growth medium are used. Yields only culturable bacteria. **Culture tech. are USEFUL for screening for carriage of pathogens as part of the microbiota (MRSA)
How does the DNA get characterized?
After specimen is obtained, PCR reactions can be performed directly on sample or purified DNA. DNA has to be extracted for whole genome sequencing. (WGS)
What does processing of DNA include?
disrupting the tissue, lysing the bac cells, removing lip/pro, removing proteins from DNA -proteases, concentration of the DNA by precipitation or using affinity chromatography.
What is pyrosequencing?
single fragments of DNA are attached to beads, PCR amplified and sequenced. This also can be used to determine relative abundance of genes.
How are phylogenic trees sequenced?
16S rRNA sequences can be used to group the organisms. Often organisms are identified that have not been studied and they are assigned OTU numbers.
How do bacteria get cultured?
many bacteria cannot be cultured because bacteria are adopted to live in a mixed species environment many species cannot be cultured in pure culture using current techniques.
What techniques are used to culture bacteria?
conditions are often hard to establish. New tech involve the use of co-culture since many organisms are adapted to live in mixed species biofilms. special req. for culture of the bacteria can be determined and the new species can be grown and characterized. Culture allows for characterization of new pathogens and use of consortia of microbiota
How are populations compared?
relative abundance of different bacteria and diversity of the population
What is KEGG and other metabolic pathway programs?
metabolic pathways can be assesed using KEGG. reverse transcriptase can monitor quantitative PCR . Relative abundance of the genes can be determined by number of hits. The number of different bacteria can be assessed by the number of homologs present. The genes are not associated with a specific bacterium unless they have already been sequenced.
Can bacteria use multiple carbon sources?
YES
Discuss bacteria within the colon
colon has large numbers of bacteria 10 11 - 10 12. By the time food reaches the colon, it does not have any sugars in it. Bacteroidetes (phylum) and Bacteriodes (genera) are generally associated with intestinal health
Bacteria in the colon produce what?
hydrolases , esterases, and lyases to degrade complex polysaccharides (starch , inulin, pectin, cellulose) into fermentable sugars.
