Week 1 Flashcards
(41 cards)
Definition and difference between microbiome and microbiota.
microbiome: a multi-species system where organism live together in a contiguous environment
microbiota: the microorganisms in the microbiome
definition and characteristics of isolate
A population of microbial cells in pure culture derived from a single colony on an isolation plate and identified to the species level.
definitions and characteristics of strain
An isolate or group of isolates exhibiting phenotypic and/or genotypic traits belonging to the same lineage, distinct from those of other isolates of the same species.
definition and characteristics of clones
An isolate or group of isolates descending from a common precursor strain by nonsexual reproduction exhibiting phenotypic and/or genotypic traits characterized by a strain-typing method to belong to the same group
Definition of species with respect to 16S sequence identity
Typical cut off is 97% Identity in 16S = belong to same species
taxonomic levels of Firmicutes Streptococcus mutans UA159
- Kingdom:
- phylum
- class
- order
- family
- genus
- species
- strain
- Kingdom: bacteria
- phylum: firmicutes
- class: bacilli
- order: lactobacillales
- family: streptococcaceae
- genus: streptococcus
- species: mutans
- strain: UA159
Definition of dysbiosis
shift from healthy homeostasis to disease state
what makes oral diseases so complicated?
1) Polymicrobial diseases (not a single lone etiological agent)
-Even periopathogens can be detected in healthy subjects
- Can have Caries without Streptococcus mutans present
2) Everyone Harbors Variations in Their Microbial Composition
-Same disease but do not carry the same bacterial species
-Species can be same in two oral samples but also in different amounts.
central dogma
DNA–> mRNA –> Protein –> metabolites
which omic technique is used to investigate DNA?
genomics
which omic technique is used to investigate mRNA?
transcriptomics
which omic technique is used to investigate protein?
proteomics
which omic technique is used to investigate metabolites?
metabolomics
Limitations of 16S rRNA gene sequencing (identifies and places an organism in relation to other known groups) with respect to virulence
does not tell you what genes the bacteria has (ex: antibiotic resistance or toxin producing?)
definition of genome
total genetic complement of an organism
role of mutation in bacterial genetics
mutations can greatly impact virulence factors
3 modes of acquisition or transferring of genes in bacteria
transformation: donor cell releases DNA into the recipient cell
transduction: phage from infected donor cell releases DNA into the recipient cell
conjugation: donor cell connects to recipient cell and releases plasmid
Dentition of annotation with respect to bacterial genetics and the first 2 steps
this process tells us?
annotation: the process of attaching biological information to sequences. It consists of three main steps:
1) identifying elements on the sequence, a process called gene prediction
2) Assigning biological information to these predicted genes.
-does the gene look like something that has been seen before (homology based prediction)
tells us what species are present and the genes (functions)
3 mechanisms that can result in the alteration of a gene and the outcome from this type of mutation
deletion: loss of function
duplication: additional copy of a gene
shuffling: change of position on a chromosome
–> Above events may lead to increase or decrease gene expression (upregulation/downregulation)
what is the Ecological Plaque Hypothesis?
shifts in the amounts of organisms can lead to the development of disease
these population shifts can be caused by a change in environemntal conditions (like diet or immune status)
reporting methods:
__________ by taxonomic classification
________ indices
cluster analyses of species comparisons (___________)
statistical ________ between subjects/samples/populations
abundances
diversity
sample comparisons
methods to determine differences
Each site in the oral cavity contains different proportions of ________ with lots of overlap
genera
taxonomic classification largest to smallest and acronym
Dear King Philip Came Over For Good Soup
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
consequences of bacteria evolving to bind to a partner species (4)
mutually beneficial
parasitic
antagonistic
virulence changes (dentirmental to human host)
