Animal Microbiology

• 1. a role in the origin of animals
• 2. a role in the subsequent diversification and the shaping of animal life
• 3. influenced the evolution of animal development

4500. (Speculated 3 million)

The environment.

Bacteria, Archaea and Eucarya

Layered groups or communities of microbial populations.

• -Hypersaline bodies of water
• -hot springs
• -dry temperate deserts
• -cold dry enviro of Antarctica

• 1. Relevance to study of life on Earth
• 2. Relevance to the study of the co-evolution of life and Earth
• 3. Relevance to the study of the possibility of life elsewhere
• 4. Finding life outside our own solar system

Laminated organo-sedimentary structures formed by the trapping and binding, and/or precipitation of minerals by microorganims by a cyanobacterial microbial mat community. 

(can be 1300 million years old!!)

The ocean

Microbial symbiosis

Symbiotic incorporation of bacterial chloroplasts and mitochondria

3.5 billion years

~500 million years

A group of different species of microorganisms inhabiting a specific environment and performs some functions

The use of microorganisms metabolism to remove pollutants

Petroleum degradation

• -multiple pollutant biodegradation
• -waste water treatment

a condition where two dissimilar organisms live together in an intimate associate that sees both organisms benefit.

co-existence of two or more microorganisms- supply nutrients to host in return for a place to live. 

• symbiotic- rely on each other
• commensal- share, but don`t rely on each other 
• pathogenic- cause disease

• True residents: long term association with host.
• Ex. Stable population in a particular region of the gut

Passing through: Do not persist in ecosystem, only detectable for a limited time. (can find niche and become autochthonous)

• Planktonic
• Adherent 
• Colonized

• drug discovery
• nanoparticles
• bioremediation

More than 99.9%

• Free bacteria
• Hot spots
• marine snow
• phytoplankton

• Distal tips- lowest amount of bacteria (usually require oxygen to survive)
• Middle Thallus- moderate amount of bacteria
• Base- greatest amount of bacteria (usually convert nitrogen to nitrates to survive)

The MARINE SPONGE- originated over a billion years ago. 

They rely on the associate bacteria to survive. 

• Bacteria
• Archaea
• Microalgae
• Fungi

40%

• Photosynthesis
• Nitrogen Fixation

Fermenters

cyanobacteria- serve as barrier and are involved in colouration

• Proteobacteria- Nitrification, dehalogenation
• Actinobacteria- prolific secondary metabolite producers (metabolites prevent viral infections)
• Archaea 
• Cyanobacteria

600 Million years

Used as a model system to unravel workings of the human immune system

• Prolific marine producers- more than 200 new metabolites reported each year
• Sponge/ microbe derived compounds- terpenoids, alkaloids, peptides and polyketides
• sponge derived compounds are in medical trials such as anticancer,antibacterial, antiviral, anti-inflammatory, & antifouling

• Bacteria obtain nutrient supply from coral, protected from protozoan or bacteriophage
• Coral- protective barrier from pathogens

any organism (animal or plant) and all of its associated symbiotic microbes

the sum of the genetic info of the host and its microbiota

• the holoboint is a unit of selection in evolution
• - natural selection happens on all levels
• - microbiota are selected: host enviro and microenviro
• - the genome being selected by hologenome
• - diverse microbiota associated with host as part of the evolving holobiont

• 1. all animals and plants establish symbiotic relationships with microorganims
• 2. symbiotic microorganims are transmitted between generations
• 3. The association between host and symbionts affects the fitness of the holobiont within its environment
• 4. Variation in the hologenome can be brought about by change in host or microbiota genomes; under enviro stress; the symbiotic microbial community can change rapidly. 

Microbial symbionts can aid host adaptation and evolution

• -genetic variation passed to offspring
• - genetic variation gained through amplification of existing strains and gaining new strains from enviro
• - inheritance of acquired characteristics- (use and disuse)
• - cooperation and competition effect evolution (natural selection)

16SrRNA

18SrRNA

• - understand different ecological processes particularly the interactions among individuals and populations
• - understand how above changes influence the evolution of the diversity (richness and abundance of species or genotypes) and function of ecosystem

the number of species (diversity)

the number of individuals of a particular species

• Adaptive radiation
• ecological parameters
• connections

the members of a community recognizing a niche causing adaptation and evolution

the regular structure of a microbial community

how the individual members interact within and between communities

• Physical- temp, pressure, oxygen
• Chemical- pH, nutrients, peptides, carbs, ion strength
• Biological- host, species, genetics of host

Competition or interaction involving: predation, parasitism, disturbance and productivity

the diversification of nutrients

the ability to sense chemical gradients and direct motility accordingly (causes bacterial accumulation in ocean enviros)

• Microbial evolution. 
• Ex. fast swimming bacteria will find food source

A small representative system having analogies to a larger system in constitution, configuration or development. 

AKA a tiny, often microscopic segment of an ecosystem represented by a specialized community of organisms. 

community functions

Diversification

• DNA sequences
• DNA maintenance
• Copying mechanisms

• Horizontal gene transfer: adaptation, speciation, evolution
• Random mutagenesis and selection on genome evolution

• Long-term- millions of years
• Short-term- a hundred years or shorter

• Mutations & horizontal gene transfer
• evolution of cellular proteins
• conserved protein sequences

• Human association with microbes in health and the environment
• Bacterial evolution of recalcitrance to xenobiotics and industrial pollutants in the environment

short term

E.coli and its diversification under different hosts. 

In the feces from a child in 1885.

• clinically, based on epidemiology
• signs and symptoms
• microscopic observations and interactions with host cells
• biotypes
• unique gene markers

• natural occurrence with the evolution of different mammalian hosts
• Horizontal gene transfer- far more extensively anticipated

Horizontal gene transfer

All the hereditary information of an organism encoded in the DNA (or RNA for some viruses)

The study of an organisms entire genome. Includes intensive efforts to determine the entire DNA sequence of organisms.

all genomics of microorganisms

All genomes of viruses in a specific community.

Modification of the genetic material of a cell.

~30,000

~24,000 to 25,000

~20,000 to 23,000

• Absorbance levels at 260nm. 
• Double strand = 50 ug/ml
• Single strand = 40 ug/ml

• Method to produce many copies of a specific DNA sequence using a heat resistant enzyme
• Allows researchers to target a specific gene or sequence within a genome

Kary Mullis 1983- recieved Nobel prize in Chemistry in 1993

• Decreasing- in 2003 human genome sequence completed after 13 years and $3 billion
• now it take approx. 2 weeks for $10 000

guinea pig, chinese hamster, lab mouse, rat, dog, cat, horse, pig, cow, sheep, etc.

The creation of a genetic map assigning DNA fragments to chromosomes. 

A gene or DNA sequence with a known location on a chromosome- may have a variation (mutation or alteration)

Single Nucleotide Polymorphism- is DNA sequence variation when a single nucleotide differs between members of a species. (ex. mutation of base guanine to thymine)

the process of determining the genotype of an individual using biological assays.

Because bacteria are so small.

• 1. Library construction
• 2. Random sequencing phase
• 3. Closure phase
• 4. Complete genome sequence

Insights into all genes; prediction and explanation of phenotypic traits

Identification of genes from all microorganisms.

In heat resistant bacteria in hotsprings (Yellowstone national park?)

Can help to identify new/ uncultivated microorganisms

• understand the function of total microbial community
• predict the function of unculturable species
• identify function of these species
• discovery of microbial enzymes/proteins/peptides

The science of developing and utilizing computer databases and algorithms to accelerate and enhance biological research

• Host phylogeny
• Gut morphology
• Diet

Any RNA molecule that is not translated into a protein.- Regulator of gene expresssion

98%

• biological development
• cell proliferation and differentiation
• cancer initiation and progression
• disease and immune response

• Enviro changes
• Stress growth conditions

normally on parts of body exposed to or communicate with external environment

• A group of microorganisms present in a specific location
• Ex. bacterial colonies found in human gut

Microorganisms that are normally associated with a particular tissue or organ

All the microbes, their genetic elements (genome) and environmental interactions in a defined environment

• host specific
• differ from surrounding community
• similar microbial population from the same species (geographically separated)
• different microbial population from different species at same location
• different communities often dominate different tissues of the same organism
• large diversity, certain bacterial groups dominate

Prominent in arid ecosystems

They have the ability to breakdown lignocellulose at a rate of 85-90%

4%

foregut, midgut and hindgut

• Higher termites don't have protozoa in their guts whereas lower termites do.
• ANNND higher termites have better social skills

inorganic nitrogen is converted to ammonia and the ammonia is utilized by the host for protein and amino acid production.

anaerobic metabolism pathways that utilize H₂ and CO₂ to synthesize acetate and methane

methanogenesis

Cellulose---> malate--(uses ATP)---> CO_2, H_2, acetate

Acetate

• 1. Bacteria closely associated with protists as symbionts.
• 2. Mutual relationship between Methanogen and protist

• bacterial- 10¹⁴
• human cells - 10¹²

• some bacteria are carried only transiently
• most bacteria are fairly permanent
• it is very difficult to alter the microflora of a healthy individual

• GI tract
• Urogenital tract
• skin
• oronasalpharyngeal cavity

Gram-postive

in the nose and ears

behind the knee ( likely not important)

• moisture
• body temp
• pH
• nutrition
• skin type

Dry and moist- oily is the most stable

• weather
• clothes
• chemicals
• hormones
• water balance

propionlbacteria

600

• mostly good- help maintain teeth and gums
• few bad- cause tooth decay and gum disease, some linked to heart disease, stroke and premature birth

Biofilm= dental plaque

lactic acid bacteria

S.mutans produces a polysaccaride adhesive from sucrose and the sugar is used as a substrate to produce organic acids which lower pH.

Xylitol- found in chewing gum!

None. It's usually sterile.

Usually transient and populations are kept low due to acidity. 10³ to 10⁶

sparse 10³

Moderately mixed flora. 10⁶ to 10⁸

Dense! 10⁸ to 10¹¹

sterile

• Breast-fed- Bifidobacterium
• Formula- typical adult gut microbiota

2

Only Japanese people have this microbe, which may be an evolutionary difference due to the consumption of marine foods such as seaweed.

• diet
• phylogeny
• age
• gut morphology
• host genetics
• geography

• digestion of unutilized substrates
• stimulating cell growth
• repressing harmful microorganisms
• protection against epithelial cell injury
• training the immune system to respond only to pathogens
• defending against some diseases
• regulation of host fat storage

age, vaginal pH and hormone levels

transient organisms

sparse mixed flora 10^4.

spontaneous pregnancy loss in 2nd trimester and spontaneous preterm birth

• changes in physiology and development- female genital tract
• When antibiotics select for a resistant microflora
• When new organisms are acquired- ex. pregnancy, diet, environment

most

many

very few

a communication mechanism that enables microorganisms/ bacteria to make collective decisions

The Hawaiian squid- using Vibrio fisheri to for bioluminescence

• 1. small chemical signal molecules are synthesized and secreted into the environment
• 2. using specific detection, systems sense signals and cell density
• 3. When the concentration of a signal molecule reaches a certain threshold gene expression turns on
• 4. behaviour of total population changes

• Gram-negative bacteria - uses lactones (AHL)
• Gram-positive bacteria -autoinducing polypeptides (AIP)
• Both (-) and (+)- AI-2 
• beyond bacterial borders- (AI 3) - communication between host and bacteria

Gram postive bacteria- use autoinducing polypeptides (AIP)

Gram negative bacteria uses lactones (AHL) 

uses Gram negative and Gram positive bacteria. Involves autoinducer 2 (AI-2)

• Biofilm formation
• Virulence adaptation
• Production of antimicrobial substances
• Motility
• Sporulation

yes.

-involves autoinducer 3 (AI-3)- pretty much bugs communicating with the host through compounds.

• 1. Signal molecules as potential biomarkers
• 2. A theraputic tool to regulate pathogenic bacteria

A complex aggregation of microorganisms growing on a solid substrate.

lakes, oceans, sink drainage, waste treatment plants, gut, surface materials, tissues , medical implant materials

microbial cells and EPS (extracellular polymeric substances) EPS may account for 50-90% of carbon in biofilms

• Structural hetergeneity
• genetic diversity
• complex community interactions
• an extracellular matrix of polymeric substances

• Not a uniform structure:
• clusters
• channels
• matrix

Probably not

No, some are dead and some are dormant.

They may or may not be. They could all be a single species

• A) form a dense and protected environment for free-floating microbes to cooperate and interact with eachother
• B) facilitates communication among them through chemical and physical signals
• C) Water channels that help distribute nutrients and signalling molecules

They form on medical products and may cause infection for patients. Ex. biofilms may form on catheters, aritifical hearts, contact lenses, joint replacements, etc. - Expesive to repair/clean/remove

conventional methods of antibiotics and disinfectants are often ineffective. - Cholination doesn't work and using tonns of antibiotics isn't smart for medical or environmental purposes.

• 1. prevent invasion into host epithelial tissue
• 2. environmental- bioremediation and provides biobarriers to soil and groundwater from contamination and Biofiltering of industrial water

80%