Lecture 7 - Microbiota Flashcards
number of microbial genes vs human genes
significance?
2-20 million microbial genes vs 20,000 human genes
therefore the bacteria have genes for things we cannot do
3 functions of bacteria in the microbiome
- maturation of immune system and gut physiology
- synthesis of vitamins and metabolites
- digesting of complex glycans derived from food (fibre)
when does the microbiota contribute to disease?
when the gut microbiome is IMBALANCED –> disease
why are we just discovering the involvement of microbiome in disease now?
genetic tools have helped us understand the complexity of the microbiome
3 general methods for studying structure and function of microbiota
- STRUCTURE (ex. 16S rRNA gene sequencing)
- FUNCTIONAL POTENTIAL (what can they do? ex. single cell genome sequencing)
- IN SITU FUNCTION (what are they doing? ex. metabolomics/proteomics/transcriptomics)
why do we look at 16S rDNA?
phylogenetic marker found in all species to identify bacteria
describe the 16S rDNA gene
some regions are conserved, some regions are more variable so can identify specific bacteria
bioinformatic methods for human microbiome profiling
whole genome sequencing –> looking at all DNA in a sample and compare to reference genome or find general functions of genes to see role of bacteria
how do we acquire our gut microbiota?
food, environment, at birth
what is an issue with microbial studies?
if you use PCR, will always see something but may not be truly there
does environment or genetics play a bigger factor in shaping the human gut microbiota?
environment
2 types of diversity we can look at
- alpha
- beta
alpha diversity
within 1 sample, how diverse the bacteria are
beta diversity
compare diff samples
what is Bray-Curtis dissimilarity?
non-phylogenic (does not consider taxonomy) beta diversity which takes into account the abundance
what is the UniFrac distance between a pair of samples?
fraction of unique branch length –> ratio of unique branch length that only leads to OTUs in sample A or B VERSUS total branch length in either sample
purpose of UniFrac
to compare differences based on phylogeny and genetic background
what does UniFrac show if samples are IDENTICAL?
unique branch length is 0 so UniFrac distanc is 0 btwn samples
what does UniFrac show if samples are COMPLETELY DIFFERENT?
UniFrac distance is 1 btwn samples
what does UniFrac show if samples are INTERMEDIATELY SIMILAR?
UniFrac distance is 0.5 btwn samples
Unweighted vs weighted UniFrac
unweighted is qualitative measure of diversity that does not consider the abundances of OTUs
describe Principle Component Analysis
extracts the most important information to reduce the size and complexity of the data set
computes new variables called PRINCIPLE COMPONENTS which are linear COMBINATIONS of the original variable
2 components in PCA
- required to have the largest possible variance to explain/extract the largest part of variance from the data
- orthogonal to the first component and to have the largest possible inertia
describe the microbiome throughout life
becomes more diverse and stable
