lectures 1-3 Flashcards
Checklist for mutualism:
1) Removal of one partner leads to death or reduced growth of the other
2) The genomes of each species show advanced degeneration
3) Products produced by one partner are utilized by the other – often both ways
Mutualism example
fungus + alga
Synergism example
cow rumen microbiome
Checklist for synergism:
1) Each partner benefits from the other
2) Partners can be easily (?) separated and grown independently of each other
Commensalism example
Beggiatoa and other sulfur spring microbes
Checklist for commensalism:
1) One species benefits
2) The other species is neither harmed nor benefitted by
the interaction
Amensalism example
Streptomyces and other soil bacteria
Checklist for amensalism:
1) One species benefits
2) The other species is harmed by the
interaction
3) The interaction is non-specific
Parasitism example
amebas and human lung macrophages
Checklist for parasitism:
1) One species benefits
2) The other species is harmed by the
interaction
3) The interaction is specific, and
usually obligatory for the parasite
Mammalian macrophages and Acanthamoeba display striking
similarities in the molecular mechanisms involved in (5):
- Directional motility
- Recognition
- Binding
- Engulfment
- Phagolysosome processing of bacteria
insect species that are infected by
intracellular bacteria are called…
endosymbionts
In nature, microbes are almost never found as…
single species ecosystems
microbiomes (2)
- Microbial collectives
- Can contain bacteria, archaea, fungi, protists and viruses; often contain members of all of these.
3 main questions of the microbiomes
- 1) Who is there?
- 2) What are they doing?
- 3) How do they respond to different conditions?
Who is there?
* We can determine this using several methods (3):
1) Culture
2) DNA sequencing
3) RNA sequencing
High-throughput culture or ‘culturomics’:
- Reduces labour intensity by using AI & robots
- Allows culture under hundreds of different conditions
- Allows picking of thousands of colonies into multi-well plates
two types of DNA sequencing
A) Amplicon sequencing
B) Metagenomic (‘shotgun’) sequencing
Amplicon sequencing (2)
- A target gene is amplified, barcoded and sequenced
- Most common method amplifies regions from the 16S rRNA gene from bacteria,
a taxonomic marker
Metagenomic (‘shotgun’) sequencing
- The extracted gDNA is broken up into bits (or not, depending on sequencing
method), barcoded and directly sequenced - A computer is used to pull out signature genes from the sequenced pool
Both methods can reveal _____, or the species richness, evenness and _____ in the sample
‘alpha diversity’, ‘dominance’
RNA sequencing/ ‘RNA-seq’ (4)
- Extract the RNA (mRNA) from a community
- Transcribe to DNA (using a viral reverse transcriptase enzyme)
- (or not, depending on the sequence method)
- Barcode and sequence
- Match transcripts to known genomes
what techniques are used to answer: What are the microbes able to do/actually doing in the community? (2)
1) Predictive
2) direct
Predictive
- Use a (powerful!) computer to assemble the MAGs.
- Use software to annotate genes and predict possible function
MAGs
Metagenome-Associated Genomes
Direct (I)
Proteomics
* Extract all the proteins in the sample
* sequence peptide fragments using mass-spectrometry
* Use a (powerful!) computer to match peptides to proteins, and then proteins to genes (metagenome)
direct (II)
- Metabolomics (or, more correctly, metabonomics)
- Extract all the molecules in the sample
- Subject directly to mass-spectrometry or NMR spectroscopy
- Use a (powerful!) computer to match compound signatures from
obtained spectra to standards
Direct (III)
- Metatranscriptomics (RNA-Seq, again!)
- mRNA content reflects active transcription – what the cells are doing/making in response to their environment
Lipidome:
all of the lipid molecules from a given sample
Secretome:
all of the secreted products from cells of a given sample
Resistome:
all of the antimicrobial resistance genes within a given sample
henome:
all of the phenotypic data from species within a given sample
How do microbiomes vary under different
conditions?
- Microbiomes are dynamic systems – they change in response to
their environment and/or what you do to them experimentally
multi-omics integration
- Carry out multiple ‘omics studies on a given sample, longitudinally if possible
- Integrate ‘metadata’ into the analysis
- Use a computer to combine the datasets
Most ocean microbes are
oligotrophic
Holger Jannasch (1927-1998) discovered:
- unculturable marine bacteria
- Demonstrated that decomposition of material in the depths of the ocean takes up to 100 times longer than on land
In a single drop (one millilitre) of seawater, there are ____
viruses, _____ bacteria and about ____ small protist
10 million, 1 million, 1,000
In the upper ocean layers, _____ is the main determinant of microbiome composition
temperature
Open ocean floor:
- Extreme pressure – barophiles
- Extreme cold – psychrophiles
- Extreme nutrient depletion - oligotrophs
The microbes on the ocean floor have: (2)
- extremely slow
metabolic rates - high concentrations of heavy metal resistance genes
What is soil? (2)
– Complex mixture of decaying organic and mineral matter
– Life support for microbes and terrestrial plants
Each particle of soil
supports: (3)
- miniature colonies
- biofilms and
filaments of bacteria - fungi
Streptomyces:
a major genus of soil bacteria, notable for the diversity of antibiotics they make
Microbes in the
_____ help to protect plants from Pathogens
rhizosphere
Ectomycorrhizae
- Colonize the rhizoplane
- Form a thick, protective mantle around the root
- Extend outwards to absorb nutrients
Endomycorrhizae (5)
- Grow inside plant cells
- Dependent on their
hosts - Lack sexual cycles
- Exist entirely
underground - Relatively small
number of
endomycorrhizae
species – but they are
extremely important to the ecosystem
Plant endophytic communities
- grow within plant tissues
- Can be bacterial or fungal
- One specialist endophytic relationship is that of plant roots and rhizobia
The human body microbiome
- Majority (other than bacteriophage) are bacterial
- Most are harmless
- Many are beneficial to their host
human body barriers for microbial invaders (2):
- Non-specific defences
- Adaptive and non-adaptive immune defences
Microbes normally found at various non-sterile body sites are called:
commensal organisms
The consortium of colonizing microbes has been given the name ____ or ______
human microbiota, microbiome
indicates the cell consortium
Microbiota
indicates the genetic potential of the consortium
Microbiome
approximately _____ bacterial species per person
200
skin: (3)
- 10 12 microbes in moist areas
- Mostly Gram positive bacteria
- More resistant to salt and dryness
a human infant’s mouth is colonized by:
- Non-pathogenic Neisseria spp. (gram-negative cocci)
- Streptococcus (gram-positive cocci), Lactobacillus spp. (gram-positive rods)
As teeth emerge, other bacteria start
growing: (2)
- E.g. Prevotella and Fusobacterium spp.: between gums and teeth
- E.g. Streptococcus mutans: tooth enamel
Nostrils and nasopharynx are dominated by:
Bacillota and
Actinomycetota
Nasopharynx is populated by:
Staphylococcus aureus and Staph.
epidermidis
Urogenital tract
- The urethra contains S. epidermidis and some members of the
Enterobacteriaceae - Lactobacillus spp. protects from STIs and improve reproductive success
Stomach
- low pH
- few microbes survive
- Helicobacter pylori burrows into protective mucus and can cause gastric ulcers
Intestine (3)
- The lower intestine contains 10 9 -10 11 per gm
of feces - Ratio of 1000 anaerobes to 1 facultative anaerobe
- most important microbial ecosystem in the human body lives in the colon
It’s not the species that you have in your gut but their _____ that is important!
metabolic potential
What do our gut microbes do for us? (6)
- Regulate the immune system
- Helps extract energy from foods
- Control potential pathogens
- Make some essential metabolites, including vitamins and cofactors
- Improve intestinal function
- Remove toxins and carcinogen
how do we acquire our microbes? (3)
- vaginal delivery
- breastfeeding
- interactions with environment
how do we lose our microbes? (6)
*C-section delivery
* maternal antibiotics
* formula breastfeeding
* indoor living
* excessive sanitation
* chemical preservation of food
High diversity of species: (4)
*Healthy ecosystem
*Balance
*Functional redundancy (High gene count)
*Resistance to damage
Low diversity of species: (4)
*Sick ecosystem
*Imbalance
*Functional disability (Low gene count)
*Susceptibility to damage
Missing microbiota hypothesis
Loss of microbiota generally compounds over generations, and recent changes in lifestyle have greatly exacerbated this loss
How is the microbiota protective?
- Competitive exclusion
- Environment modification
- Host stimulation
- Direct pacification
Competitive exclusion
Colonization of a niche to prevent pathogen from growing there
What happens when microbial balance is compromised?
- Containment breaches
- Niche disturbance
- Extinction events
obesity is associated with a:
less diverse microbiome
Obesity is also associated with:
low-grade intestinal inflammation
Gnotobiotic animals
An animal where the associated microbiota is known and defined
germ-free animals have abnormal physiology (6)
- Poorly developed immune systems
- Lower cardiac output
- Requirement for more calories to maintain body
weight - poorly developed intestinal walls (stunted villi)
- enlarged ceca
- Misshapen mitochondria
