Lecture 7: Prokaryotic diversity Flashcards
What are 2 ways to describe microbial diversity?
- Phylogenetic diversity
2. Functional diversity
Phylogenetic diversity
- Microbes are grouped into PHYLA based on evolutionary relationships
- Most often based on 16S rRNA gene sequence
basically:
- analyze 16S rRNA DNA sequence & est. a % homology
- take multiple species (multiple genera) & putting them into 1 phylogenetic group based on what similarity they may have (NOT >97% within the gene)
- focused on similarities that are much less but still lets them be placed into a single group
The RED DOTS represent the…
phyla only known from metagenome sequencing from diverse environmental samples (intersperced with the ones we can grow in each subcategory)
- meaning, never seen (or grown) these organisms in a lab
- don’t have much info, other than their genetics, that they exist
How many bacterial archaeal phyla and eukaryotic supergroups are on the tree?
The tree includes 92 named bacterial phyla phyla, 26 archaeal phyla and all five of the Eukaryotic super groups
This tree represents microbial diversity based on 16S rRNA as of 2016
What does…
The tree includes 92 named bacterial phyla, 26 archaeal phyla and all five of the Eukaryotic super groups
show us?
bacteria are MORE diverse - req’s us to put them in more groups to be able to keep them organized b/c that diversity will be rich
- Functional diversity
- Groups microbes based on the activities they carry out
* Some functions appear to be performed in a single phylum only
Functional diversity
Groups microbes based on the activities they carry out (with ex)
hink: grouping ppl who are vegetarian or like meat
- if 2 ppl are vegetarian it doesn’t mean same intellect, hobbies, ethnicity, hair colour etc.
Ex. Anoxygenic phototrophs: dispersed through several Phyla (formulate same coencentric circle)
- like photosynthesis that doesn’t produce O2
- just b/c they do this metabolism doesn’t mean anything abt their genetics
- doesn’t make sense to put them in groups based off this, makes more sense to put them in groups based on genetics
Where does O2 in photosyn. come from, what do you split?
If something is anoxygenic, what do you think about the e- donor?
SPLIT H20
not H20
- H2S - produce S compound rather than O2
Some functions appear to be performed in a single phylum only (with ex)
Ex) oxygenic phototrophy
- splitting of H20, in order to generate e-‘s, & molecular O2
Simply by nature of where they sit on the phylogenetic tree, it’ll be a lil more representative of the genetic characteristics b/c its not anywhere else
- probs b/c req’s a lot of machinery in the cell to do oxygenic photosyn.
- get a bit more cohesiveness since there’s just 1
Dissimilative
poop from metabolism and don’t use it don’t assimilate it
Most prokaryotes cannot be
cultured in the lab (yet)
• Some phyla are well studied in
the lab
• Some are known only from 16S
sequences or metagenomic
studies
Type Species have…
organisms of interest (well studied)
- we grow, study & identify
16S rRNA Gene Sequences have…
NOT been grown (NOT seen)
- only known from METAGENOMIC SEQUENCING ANALYSIS
- take sample & look through genetics in order to identify the 16S rRNA sequences that’re there & realizing its not a species seen before but it exists, so its its own species
Most phyla will contain ____ ___
MULTIPLE GENERA
- meaning not just genus mycobacterium
for ex:
- will be other genera found within the category
To be considered members of same species, you got greater than 97% homology in 16S rRNA gene.
BUT what do you figure within this Bacterial Phyla: Tenericutes, about the genera present? Do you figure closely related to 1 another 97% or no?
NOT REALLY - a lot of variation
- but, still same enough to be put in this category specifically
Bacterial Phyla: Tenericutes
- The Mycoplasmas
- Phylogenetically related to Gram positives, but they don’t have a cell wall (no PD, no lipotycholic acid, etc - lost gram + characteristics)
- Gram stain NEGATIVE
- PINK STAIN much like EUKaryotes b/c ONLY plasma membrane which will lose C.v from alchol destain and take on safranin
- Often PLEOMORPHIC - many diff. shapes (NOT all bacilli, cocci, or spirilla)
Why would we call Tenericutes, pleomorphic?
NO CELL WALL - no thick rigid barrier that’ll confer a morphological det to outside of cell
- therefore, A LOT of FLEXibility in the structure
Provide an example of an organism part of the phyla Tenericutes and explain key characteristics
Mycoplasma genitalium (sexually transmitted infection - STI; bacteria anywhere in reproductive tract) - can be asymptomatic, should be tested (chlamydia, gonerila all cause STI's)
- Common cause of urethritis (inflammation of urethra) and pelvic inflammatory disease (PID)
- First free-living bacterium to have it’s genome sequenced
• One of the smallest genomes known at 500 kbp (vs E. coli has million base pairs)
- think: pick 30 page recipe book to recopy & understand entire vs. 500 pages
explain how pelvic inflammatory disease is caused?
When you get an STI, the organism gets deposited in vagina (normally mucus plug blocks opening to uterus in cervix - but in periods where ovulation is about to happen, the MUCUS PLUG IS SHED), so bacterium comes into uterus & then enters in FT
OUTCOME: immune system activates (v. aggressive)
- sees what shouldn’t be there & goes after organism, which does a lot of damage to wall of FT
- replace damage tissue with scar tissue inside body
- egg ovulates from FT & sperm can still come & do fertilization, but egg can’t fit b/c has become so narrow & inflexible b/c of scar tissue
- if you get fertilization in FT (diploid cell), starts cleavage division (becomes blastula) - (ampulla - where sperm & egg unite, egg starts dividing since its fertilized & diploid)
- wanted to implant in uterus where its flexible & has nutrients & blood supply, but natural tendency is to implant in FT - called ectopic pregnany (FT will NOT be hospitable to host baby so BURTS & that bacteria gets released in pelvic cavity & is often a lethal condition (bacteria in sterile sites, haemorrhage)
Bacterial Phyla: Actinobacteria
Gram POSITIVE bacteria – HIGH GC Gram positives
- meaning, within its genetic material, it’ll have a lot of C & G
- triple H-bonding – if heated, will be more resistant (stable) based on DNA sequence
- BUT, still have to have stability of PL bilayer & of protein structure
- just b/c DNA is thermostable, it doesn’t mean much of how rest of cell can cope when faced with heat
- Includes CORYNEFORM BACTERIA
- Club-shaped morphology
Provide an example of an organism part of the phyla Actinobacteria and explain key characteristics; 1 st one studied
Corynebacterium diphtheriae
- club shaped
• Produces an EXOTOXIN that INHIBITS PROTEIN SYNTHESIS
- toxins that are proteins (built inside) secreted to the outside of a bug, to do whatever its specific for
- protein syn is a BIG DEAL - so inability to make proteins will be lethal to the cell
• Causes tissue death in the respiratory tract - diphtheria
- as respiratory cells become parasitized in this way, they start to die & get replaced by (scar tissue), PSEUDOMEMBRANE FORMATION - impedes breathing - difficulty doing gas exchange
• Can lead to death by suffocation
What would we describe the effects of exotoxin as? (seen in Corynebacterium diphtheriae)
BACTERIOCIDAL - b/c cell can’t survive
Produces an EXOTOXIN that INHIBITS PROTEIN SYNTHESIS
- toxins that are proteins (built inside) secreted to the outside of a bug, to do whatever its specific for
- protein syn is a BIG DEAL - so inability to make proteins will be lethal to the cell
DPT (Diptheria DPT (Diptheria Pertussis Tetanus) Tetanus) vs. DTaPertussis
DPT (Diptheria Pertussis Tetanus)
- petusssis, this component created a lot of side effect –> led to ppl not wanting to get vaccine
*3 toxoid vaccines (look like a bacterial toxin, but NOT)
- priming immune system against multiple things all @ same time
- produce an immune response against toxoid
- then works against toxin
(LESS PPL GET, MORE EFFECTIVE)
DTaPertussis
- acellular
(MORE PPL GET, LESS EFFECTIVE AS A VACCINE (DOESN’T WORK AS WELL))
Mycobacteria
PHYLUM; ACTINOBACTERIA
Mycobacteria have a modified Gram POSITIVE cell wall
• Layer of MYCOLIC ACIDS outside the peptidoglycan layer
• Makes them ACID-FAST
- need another way to get gram stain
- treatment will also have to be diff. (diff. antibiotic)
acid fast stain result:
- pink = carbol fuschin
- blue = methylene blue
Provide an example of a member part of the mycobacteria
Mycobacterium tuberculosis
• SLOW growing (~ 24 hr/gen)
- can get a test (swab of sputum) but won’t see growth for a long period of time on a petri dish
- but would do genetic analysis, chest X-ray, manto test etc., in meantime in order to make a (+) diagnosis
• Colonies can take weeks to form on agar
medium (for conclusive (+) diagnosis)
• Cause of tuberculosis – slow, fatal respiratory disease
* in active cases vs. latent infection (substantial amount of ppl can become active cases)
Bacterial Phyla: Filamentous Actinobacteria
• Genus of filamentous (long and thin) Gram positives
• Form branching hyphae and mycelia
- sounds like gungi, extracellular digestion and absorption
• Hyphae produce reproductive spores for
dispersal – conidia
• DO NOT PRODUCE endospores
- OBLIGATE AEROBES
Live in well aerated soils;in well mixed soils, O2 at top is mixed into layers below
• Give soil its earthy smell: geosmins
• Also produce substances that kill or
inhibit the growth of other microbes -
antibiotics; organism tries to kill off competitors
Provide an example of an organism part of the phyla Filamentous Actinobacteria and explain key characteristics
• Produces streptomycin: BROAD spectrum protein synthesis INHIBITOR active AGAINST Gram NEGATIVE bacteria
- widely used antibiotic
- not just targeting 1 partic. species (ex: Mycobacterium tuberculus only targets 1 partic. species (v. narrow spectrum)
- narrow spectrum in the sense that its active against gram - bacteria NOT gram +
Which of the following are true (thioglycolyte broth)?
Obligate aerobe (growing at top)
a) Streptomyces griseus
b) a member of the bacteriodetes phylum such as Bacteriodes spp.
c) using fermentation to produce ATP
d) cannot produce enzymes to remove ROS
a) Streptomyces griseus CORRECT
- an ex of obligate aerobes
b) a member of the bacteriodetes phylum such as Bacteriodes spp.
- obligate ANAEROBES - tube would have it down at bottom (far from O2)
c) using fermentation to produce ATP
- organism in q is engaging with aerobic respiration - using O2 & cellular respiration
- NOT fermentation b/c it would’ve been far away from O2 & this is close to O2 so means it must be using O2
d) cannot produce enzymes to remove ROS
- can tolerate O2, therefore means you must be able to deal with the toxic forms that accumulate
- so would need enzymes
(only obligate anaerobes or microaerophiles don’t produce them - steer clear of O2)
Bacterial Phyla: Bacteroidetes
• Large, heterogeneous phylum of Gram NEGATIVE bacteria
• Aerobes and anaerobes
- diversity with respect to O2 utilization
• FEW unifying characteristics
- genetically makes sense to put them here, but aside from that, diff. to group based on physical features or phenotypes
Provide an example of an organism part of the phyla Bacteroidetes and explain key characteristics
Bacteroides (genus) thetaiotaomicron
• STRICT ANAEROBE - poisoned by presence of O2 (can’t tolerate it)
• NUMERICALLY DOMINANT microbe in the human large intestine
- even if you got a lot of species diversity (lot of diff. organisms present within large intestine that collectively create your community within environment)
- these organisms will still be most abundant numerically
• PRODUCES ENZYMES to DEGRADE POLYSACCHARIDES, greatly increasing the variety of plant polymers that can be digested in the human gut
- expansion of what is able to be digested
Explain what role Bacteroides thetaiotaomicron play in the human gut?
• PRODUCES ENZYMES to DEGRADE POLYSACCHARIDES; we haven’t digested it, it went straight thru small intestine which is location for absorption and digestion but in this case we didn’t do anything with it but this organism has enzymes allowing for it to be digested
greatly increasing the variety of plant polymers that can be digested in the human gut
- expansion of what is able to be digested
- if it wasn’t present we wouldn’t be able to digest it
*we aren’t specialized for absorption in LI that means simple sugars produced by this will only be used to sustain local microbial growth, whatever organism doesn’t take if its hydrophobic and small it can cross wall of LI and into blood stream
Bacterial Phyla: Chlamydiae
• Gram negative cell wall type, but lack peptidoglycan
• Obligate intracellular parasites; obligation to live inside and parasit= +/-
similar to viruses in this way, small like them
- cant be grown in the lab
- most relevant STI can casue PID
Describe the life cycle of chlamydiae
• Unique life-cycle with two types of cells:
- Elementary body
• Small dense cell, resists drying
• Allows infection of new host cells
* INFECTIOUS FORM
naive cell= uninfected
- Reticulate body
- large vegetative cell (metabolically active, making proteins)
- multiplying in host cell
- not infective
Provide an example of an organism part of the phyla Chlamydiae and explain key characteristics
Example: Chlamydia trachomatis
• Trachoma: infection of the eye
• Causes scarring and blindness
in certain places in the world this is more common among children bc of closeness and can be spread from person to person bc of close interactions
-WOMEN will have higher chance of getting this bc mother is in contact with kids more
the infection can be gotten and then cleared so isnt a problem but problem is with recurrent infection which leads to scar tissue formation
* eyelashes rub on surface of eye everytime you blink bad bc it can scar the surface and make it difficult to see
What would be a key characteristic for treatment for chlamydiae?
organism is living inside of the cell; nto free living so antibiotic needs to have good tissue penetration
What do DRs know abt STI?
STI travel in groups just based on mode of spread
; if person has one they could have others
want to give treatment that’ll have good coverage against more than 1
Planktomycete
Neither Gram + or -; protein cell wall similar to archea
- No PD
- Protein stalk for attachment
- Appendaged bacteria and Budding bacteria
- membrane bound compartments
Example: Gemmata obscuriglobus
• Nuceoid is surrounded by a
true unit membrane
Cyanobacteria
Impressive morphological diversity, generally larger than other bacteria: pleomorphic
• Unicellular, filamentous, or branching filamentous
- Some form heterocysts
- Specialized nitrogen fixing cells ( anoxic environment; low o2 environment) bc poisined by O2
arry out oxygenic photosynthesis
• Harvest energy from light, and produce oxygen
• All are autotrophs
• Fix CO2 to build cell material- Calvin cycle
• Like chloroplasts they carry out photosynthesis in specialized
membranes called thylakoids
- Unlike chloroplasts they have cell walls
- Contain peptidoglycan
- Gram negative cell wall type
Ex
Proteobacteria
- Most abundant and encountered
- contain medically relevant bacteria
- diverse metabolic styles
- Facultative; can switch metabolic styles depending on what is present or not
Alpha Gamma Beta; well studied
Delta-, Epsilon- are smaller
classes but with a broad range of
phenotypes
• Zetaproteobacteria has barely
been studied with only one
known species: Mariprofundus
ferrooxydans
Alphaproteobacteria
includes path/ non pathogens
ex; non path
Rhizobium leguminosarum • Forms root nodules on legume plants • Symbiotic relationship • Bacterium fixes nitrogen into a bioavailable form n2--> 2 NH3 • Plant provides nutrients and a home for the bacteria
pathogen ex; Rickettsia rickettsii • Obligate intracellular pathogen • Carried by insects and transmitted by insect bites; vector based transmission • Causes Rocky Mountain spotted fever • Phylogenetically Rickettsia is the closest relative to the eukaryotic mitochondrion
Beta proteobactreia
Metabolically diverse; shows that we shouldn’t use functional diversity
• Some are pathogens and some are non-
pathogens
• Examples:
• Neisseria mucosa
• Non-pathogenic commensal
of the human body: lives on
mucous membranes
- lives on mucosal sites and has modes of attachment so it doesn’t get flushed
- microbial antagonism and competitive exclusion
• Neisseria gonorrhoeae
• Pathogenic: causes
gonorrhea
Gammaproteobacteria
Metabolically and ecologically diverse
• Many grow well in the lab and have become
important research models
• Examples:
• Escherichia coli
• Gram negative, rod shaped, facultative
aerobes
• Motile by means of peritrichous flagella
• Ferments lactose to a mixture of acids and alcohols
• Resident of the large intestine of warm-blooded animals
• Serves as an important indicator of fecal contamination
Pseudomonas aeruginosa
• Gram negative, rod shaped, motile by means of polar flagella
• Does not ferment sugars
• Naturally resistant to many antibiotics and disinfectantsl; grows in contact lens solutions
• Opportunistic pathogen – causes infections in immunocompromised
patients
* coward- looking for organisms that cant fight back
• Ex) Respiratory tract infections in cystic fibrosis patients
Opportunistic pathogen
causes infections in immunocompromised
patients
