Final Exam Flashcards
What is the ratio of our microbiome open reading frames to ours?
150:1
microhabitats
different environments with different physical characteristics
Each microhabitat is NOT homologous. ie. There can be differences in the same microhabitat
Microbiota
describes all of the microbes in a microhabitat
microbiome
the entire collection of microbes living in all of the microhabitats
ie there is a human microbiome and a cat microbiome but there is no gut or skin microbiome (these are microbiota)
Which dominate in most microbiota, Gram - or Gram +?
Gram positive organisms dominate. When gram-negative organisms dominate - it is an indication of a diseased state
Bacteria get increasingly _______ and _______ the deeper we get into the GI system?
anaerobic and neutral in pH
GI microbiota
10 trillion microbial cells
Primarily fermentative Bacteroidetes (Gram-negative), Firmicutes (Gram+), Actinobacteria, Proteobacteria
First two dominate the GI tract
The colon resembles a continuous culture system (environment where they can grow close to exponentially)
We shed 10^11 cells a day (1/3 of fecal mass)
WHere is the diversity of microbes the highest in the GI tract?
Where it is closest to neutral in pH and most anaerobic
What type of bacteria are most microbiota dominated by? What is the exception?
Gram positive
The GI microbiota - about 50/50 dominated by Gram - and Gram + bacteria
What percentage of human nutrition is from short chain fatty acids ?
10% of human nutrition is from short chain fatty acids produced by Bacteroidetes and Firmicutes in the GI tract ex. citrate
microbial fermentation produces SCFA (butyrate, propionate, acetate)
Hygiene hypothesis
Exposure to microbe-associated molecular patterns (MAMPs) early in life is crucial to neonatal gut maturation and immune system development
MAMPs - series of carbs, amino acids, LPS that are specific to bacteria (identify the healthy ones here)
Insufficient exposure to MAMPs can result in reduced colonization resistance and susceptibility to immune-mediated disease (IBD, Type2 Diabetes, obesity, asthma)
- If we are initially not exposed to the right ‘patterns’ our IS has a tough time when exposed to these patterns later on
SCFA
Short chain fatty acids produced by microbial fermentation
ex. citrate, butyrate, propionate, acetate
Important signalling molecules that suppress inflammation, strengthen tight junctions between epithelial cells, promote B-oxidation of fatty acids, and repressed glycolysis
What happens in intestinal bowel disease?
Likely a result of: improper colonization/development of the gut in infancy
Massive changes to diet and lifestyle, changes to environment
Pathogenic species gain access to the gut epithelium altering normal functioning
- immune system responds with an inflammatory response
- immune system learns to view normal bacteria as pathogenic
- gut becomes more aerobic -facilitates the growth of pathogenic bacteria, causing greater inflammatory response - can lead to more serious problems.
How do the gut microbiota differ in obese animals from lean animals?
Obese - fewer Bacteroidetes (gram neg) , more Fermicutes, and WAY more methanogens. usually there is slightly more Bacteroidetes in the gut microbiota
more methanogens in the gut associated with
obesity
How do diet changes in terms of fat and fiber change the type of bacteria in the gut microbiota?
high fat/ low fibre diet –> promote colonization of obese-like microbiota (fewer Bacteroidetes, more Fermicutes, more methanogens)
low fat/high fiber diet –> promote the colonization of lean-like microbiota (More Bacteroidetes, less Firmicutes (50/50ish, less methanogens)
Fecal transplants in Mice GI microbiota experiments
Germ free mice have 40% less body fat than wildtype mice
Transplant poop from WT mice - the germ free mice gain 60% more body fat without changes to diet.
What happened when fecal transplants from obese human were transplanted to a GF mouse?
Mouse acquired comparable GI microbiota
Mouse gained mass, despite no changes in diet
What happened when fecal transplants from lean human were transplanted to a GF mouse?
Mouse acquired comparable GI microbiota. Mouse did not gain mass, and no changes in diet
What is the role of methanogens?
Increased in obese animals (have fewer bacteroidetes, more fermicutes)
Methanogens remove hydrogen gas which FAVOURS the growth of Fermicutes (which are moreso present in obese animals compared to lean)
Fewer methanogens also mean less SCFAs are available to the host
Greater Hydrogen concentrations
Restrict fermicute growth
so more hydrogen in the gut in lean-individuals
the methanogens that are more present in obese animal micriobiota… they REMOVE hydogen from the gut, which promotes the present of Fermicutes
probiotics
ingestions of live beneficial bacteria - promote healthy gut bacteria
-ingestions of some Bacillus species can prevent the colonization of pathogenic S. aureus strains
prebiotics
ingestion of nutrients that promote the growth of the beneficial bacteria (probiotics)
synbiotics
A mic of pre- and pro-biotics
Translocate systems moderate the transport of proteins using
ATP, GTP, PMF (proton motive force)
Sec and Tat
Two universal translocases (ie they are in both gram neg and Gram pos bacteria)
Sec
A universal translocase system. Translocase systems moderate the transport of microbial proteins into the membrane or released outside the cell
Sec is a general secretory system that
1. facilitates the co-translation of transmembrane proteins into the cytoplasmic membrane (SRP and GTP mediated)
SRP = signal recognition particle –> will bind the signal sequence on these folded and unfolded molecules
- Transports unfolded extracellular proteins out of the cytosol into the periplasm (SecA and ATP mediated)
Tat
A universal translocase system. Translocase systems moderate the transport of microbial proteins into the membrane or released outside the cell
(twin-arginine transport)
- Transports folded extracellular proteins out of the cytosol: response regulator and proton motive force mediated
Gram-negative secretion systems
These bacteria may require proteins to be embedded in the outer membrane or released on the outside of the cell
- Two-step translocases (Type II and V)
- One Step translocations (Type I, III, IV and VI)
Type II Secretion Systems T2SS
Either Sec or Tat move proteins across the inner membrane
Proteins attach to a secretion pore and are pushed out of the cell by ATP-mediated pseudopolin extension (Type 4 SS)
Common for secretion of AB toxins such as ExoA and CT (cholera toxin)
The translocase machinery of
type II systems includes a secretion pore in the outer membrane that is anchored to the cytoplasmic membrane by proteins that span the periplasm. While the type II system does possess cytoplasmic membrane and periplasmic components, proteins to be
secreted do not translocate through these and are instead delivered to the secretion pore in the outer membrane by either the Sec or Tat system
typically SecA binds to
proteins that are to be exported into the periplasm (or outside)
typically SRP binds to
signal sequences on proteins that are to be inserted into the membrane
What are the two-step translocase systems?
Type II and V
Type V secretion system (T5SS)
A two step translocase
Sec moves autotransporter proteins across the inner membrane
The transporter (AMINO end) domain of the autotransporter forms a pore in the outer membrane for the passenger domain (CARBOXY) to exit the cell.
Autoproteolysis separates the two domains
Common for secretion of exonucleases (IgA protease), adhesins (perlactin), cytotoxins (vacuolating cytotoxin)
The proteins to be moved outside the cell via this system are initially transported in an unfolded state.
T1SS
One-step Translocase
Involve ABC-binding cassettes (use ATP)
ABC transporters that move proteins across both bilayers in one step
An inner membrane ABC transporter delivers proteins to a periplasmic membrane fusion protein via ATP hydrolysis, which pushes the proteins out an outer membrane pore
Common for secretion of bacteriocin, biofilm mediators, RTX toxins
T3SS
One step translocase - Injectisomes
Puncture adjacent cells!
Transports proteins directly from the cytosol of the bacterial cell into the cytosol of the recipient cell (prokaryote or eukaryote) - good for delivery of toxins as it goes directly to the other cell
Found in both pathogens and symbionts
Upon contact, the tip fuses with the host cell membrane and proteins are transported via PMF
Use to transport a variety of proteins
T4SS
A one-step translocase. Most common one, ATP-mediated
Transports proteins/DNA directly from the cytosol of the bacterial cell into the cytosol of a recipient cell (prokaryote or eukaryote)
Conjugation systems
- responsible for the majority of horizontal gene transfer in prokaryotes. Used to transfer F plasmids and Ti plasmids
Protein transport systems
transfers proteins into other cells or into the extracellular space (pertussis toxin)
T6SS
One step-translocase
Transports proteins directly from the cytosol from the bacterial cell into the cytosol of a recipient prokaryotic or eukaryotic cell via an ATP-mediated T4-phage like injection system
When close to a target, contractile sheath proteins under undergo a conformational change that extends a spike out of the donor cell and into the recipient, delivering the exoproteins
Primarily used in microbial warfare and may help maintain stable species composition in complex communities (microbiome)
Modification of the T4 infection mechanism… cells comes closer together – inverted punching mechanism that delivers toxins
