gut microbiota
What is a microbiome vs a microbiota vs microflora?
Microbiome = the collection of microbes in a space
Microbiota = the lists of what microbes are in that space
Microflora = historically microorganisms were classified as "micro" plants and in this respect the term microflora was born
What are the major gut phyla?
Firmicutes - 80-95% of species, gram positive, over 300 genre
Bacteriodetes - 5-20%, gram negative
what is the chao equation
Chao1 = Sobs + f12 / 2f2
Sobs = # of species observed
f1 = # of species seen exactly once
f2 = # of species seen exactly twice
Who invented the first microscope and what did they use it for?
Anton von larenhook
to see Animocules
What does the healthy stage look like?
Normal mood fluctuations
Take things in stride
Normal sleep patterns
Physically and socially active
Usual self-confidence
consistent performance
engaged in studies
What are the host implications on why to study the microbiome?
Exclusion of pathogens and stimulation of immunity
Synthesis or degradation of harmful compounds
ability to break down otherwise indigestible plant polysaccharides
Synthesis and competition for nutrients between host and microbiota
Etiology proposed obesity, inflammatory bowel disease, cancer, gut-brain exis
What are the microbial colonization factors?
Age - intestine is sterile at birth/hatch = inoculation occurs at or within hours of birth, increased diversity until adult
Diet - diet provides substrates for microbial fermentation
Anti-microbial components - fat
environment, location and genetics
What is beta diversity?
The diversity between samples
How many prokaryotic cells on earth?
How many cells are we comprised of?
how many microbes on or in you?
How many genes are in your microbiome?
Estimated that there are 1030 prokaryotic cells on earth
You are comprised on 1013 cells
There are 1013-1014 single celled microbes on or in you
million genes
What does the reacting stage look like?
Irritable, impatient
Nervousness, sadness
Increased worrying
difficulty relaxing
Trouble sleeping
Lowered energy
Procrastination, forgetfulness
decreased social activity
Pressure by academic demands
What are the general features of the gut microbiome
A couple thousand species
99% of abundance is a small number of species
Millions of genes to provide differential functions
aggregate biomass of 1.5kg
great plate count anomaly
What is gut microbial ecology? what questions do you ask
viewing the microbes as a community
Trying to explore how the microbes function as a whole community as opposed to solitary bugs
question 1 - who is there
question 2 - how many of each type are there
What is DNA barcoding and what does it require?
Established in eukaryotes to identify and catalogue biodiversity
Barcode framework requires - universality, vouchered specimen data, distance (intraspecific < innterspecific)
What are things you can do after PCR to determine microbial profile
TRFLP
DNA sequencing
What does the injured stage look like?
Frequent anger, anxiety
lingering sadness, tearfulness, worthlessness, hopelessness
Significantly disturbed sleep
Difficulty listening, processing and problem solving
Avoidance of social situations, withdrawal
Decreased academic performance
missed deadlines, requests for extensions
What are the 3 phylum classes?
Archaea
Eukaryota
Bacteria
What is abundance, richness and diversity?
Abundance = number of animals
richness = number of species
diversity = what portion of the species are there
What are the key genes used for barcoding? whats important about them?
16S rRNA- structural RNA gene, part of the 30S ribosomal subunit, widely used in microbial profiling, many possible targets for PCR
cpn60/groEL/hsp60 - protein coding gene, assists in structural confirmation of proteins, established for microbial profiling, a single PCR target, conserved in eukaryotes
What is PCR-restriction fragment length polymorphism?
Restriction endonucleases cut DNA at specific sites creating fragments of DNA with blunt ends or overhangs
SNP may alter a restriction endonuclease recognition site
Gel electrophoresis shows different lengths based on the restriction fragment
What does the ill stage look like?
Angry outbursts
excessive anxiety
persistent depressed mood
suicidal thoughts, intent behaviour
constant fatigue and feeling overwhelmed
significant disturbances in thinking
not going out or answering emails/phones
Significant difficulty with academic functioning
What are the different classifications of intestinal microbiota? (Hint 6)
Commensal - normal microbes, non-pathogens
Symbiotic - mutually beneficial
probiotic - live microorganism which when administered in adequate amounts confer a health benefit on the host
pathogenic - disease causing
autochthonous - normal residents; present in all individuals
allochthonous - just visiting
What is alpha diversity?
the diversity within a sample
richness - the number of taxa
What are the four stages on the mental health continuum?
healthy
reacting
injured
ill
What is molecular diagnostics?
Transition from a microbial profile of every microbe to a diagnostic for a specific microbe
Instead of having a technique that can identify all microbes we want to track an individual microbe
What do you need for PCR to work?
DNA template
Priming oligo nucleotide (3'-end)
DNA dependent DNA polymerase (Taq)
dNTPs