BIOL236 Microbes

Symbiosis

Two organisms that live together and encompasses a spectrum of relationships

Commensalism

one organism benefits, the other neither benefits or is harmed

Mutualism

Both organisms benefit

Parasitism

One organism (The parasite) benefits, the other (The host) is harmed

E.coli in the large intestine is an example of what type of symbiosis

Mutualism (Bacteria release beneficial vitamin K, while getting a favourable environment to live)

Normal microbiome (Normal microbiota)

Refers to organisms that live on or in the body but do not cause disease.

Resident microbiota

Includes microbes that are always present on or in the human body.

Each persons microbiome is...

Unique and highly personalised

Human microbiome is relatively constant but fluctuates with... (4)

Diet, age, geography, drug use

Microbiome primarily comes from...

Your mother and other primary caregivers (Exposure occurs during birth or shortly thereafter)

Bifidobacterium longum subsp. infantis

Short version - ( B. longum subsp. infantis )

Bacteria that are adapted to colonisation of a baby's intestine

Lowers the pH of the intestine, which inhibits pathogen colonisation. It also aids in immune development.

What B.longum subsp. infantis does

Oligosaccharides in human milk..

They feed certain bacteria in the baby's intestine.

Pets, house dust, rural/farm life, siblings

Factors that can shape the developing microbiome

Early antibiotic exposure, mode of delivery, infectious disease, formula feeding

Factors that can shape the developing microbiome

Probiotics

Live cultures of beneficial bacteria

Prebiotics

Nutrients that feed the microbiota

- Skin and conjunctiva (eye)

- Mouth, nose, throat

- Large intestine

- Urinary and reproductive systems

Are examples of...

Areas that inhabit resident microbiota

Transient microbiota

Organisms that are only present under certain conditions

Transient microbiota are found in what body sites...

Found in the same sites as resident microbiota

Opportunists

Species among resident and transient microflora, that do not usually cause disease but can do so under certain conditions.

Conditions that provide opportunity for disease (3)

1. Failure of hosts normal defences, 2. Introduction of organisms into unusual body sites, 3. Disturbances in the normal microbiota

Louis Pasteur (1800's)

He suggested the normal microbiota of humans and animals would be essential for life

Are most of the microbes associated with humans anaerobic or aerobic?

Anaerobic

Establishing germ-free animals involves what...

Birth by sterile caesarian section, and raised in completely sterile conditions

What bacterial phyla make up the vast majority of the human gut microbiota? (3)

Bacteroidetes, Firmicutes, and Proteobacteria

(Bacteroidetes and Firmicutes dominate)

The ratio of Bacteroidetes and Firmicutes...

May influence aspects of health e.g. obesity vs leanness

Short chain fatty acids (SCFA) are...

The end products of the gut bacteria fermentation of indigestible fibre.

Butyrate, acetate, and propionate are examples of what?

Short chain fatty acids (SCFA)

SCFA's help with what? (3)

Reducing inflammation, aiding in gut motility, and wound healing.

Mouse model

Experimental colonisation of germ-free mice by faecal transplant, using paired identical twins a the source of gut microbes, where both mice received the same diet.

What did the mouse model experiment show?

That the gut microbiome can change the energy that can be acquired from the diet.

Regular consumption of probiotics appears to...

Reduce anxiety and depression

MIA

Maternal immune stimulation

Reduced levels of vocalisation and exploration

MIA offspring

Coprococcus and Dialister

Reduced groups of bacteria in people with depression

Periodontal disease

Major cause of gum disease and tooth loss in adults

Commensals that adhere to teeth and feed on food debris that sticks to it.

Dental bacteria

Streptococcus mutans and Streptococcus salivarius

Gram positive bacteria that carry out acidic fermentation that destroys tooth enamel and leads to tooth decay.

Microbiome recovery time after antibiotics

Up to 2 years

C. difficile

Opportunistic antibiotic resistant pathogen in the intestine - faecal transplant cures infection 90% of the time

Helicobacter pylori

Commensal turned pathogen in the stomach, present in 50% of the population

Genetic exchange between bacteria can occur via

bacteriophage, conjugation, or natural transformation

Can unrelated bacteria share genes?

Yes

Type VI Secretion System:

spring-loaded, poisoned dagger that targets other bacteria

T6SS are essential for several gut pathogens to…

overcome the resident microbiota and establish infections

A measure of a microbe’s ability to cause disease

Virulence

The first person to directly observe bacteria was

Antonie van Leeuwenhoek (1600’s)

The prevailing theory about how infectious disease was acquired, prior to the acceptance of the germ theory, was known as:

Miasma theory

Who disproved spontaneous generation

Louis Pasteur

Koch’s postulates

a set of criteria used to establish a microbe-disease connection ( Still in use today )

Biofilms

aggregates of bacterial communities that attach to surfaces

Endospores

bacterial forms highly resistant to extreme temperatures, dessication, UV, chemicals, extreme pH

The terms “run” and “tumble” are generally associated with:

Chemotaxis

is essential for colonisation by certain bacteria

Chemotaxis

Adhesins

Receptors on the pathogen surface

Bacterial surface structures that aid in attachment or form pellicles

Pili and Fimbriae

Pili

… also facilitate genetic exchange between cells (conjugation)

Capsules

Protect bacteria from phagocytes (e.g., macrophages and neutrophils)

Its membership and gene content can change over time, partly through horizontal gene transfer

The honey bee microbiome

In marine food webs, microbes function as what?

Consumers, decomposers, and producers

Which group of marine microbes is chiefly responsible for nitrogen fixation in the ocean?

Cyanobacteria

What are the primary ecological roles of marine phytoplankton in ocean ecosystems?

Carbon fixation and primary production

In the Hawaiian bobtail squid–Aliivibrio fischeri symbiosis, what does quorum sensing allow the bacteria to do?

Synchronise gene expression ( such at bioluminescence ) based on cell population density

parasitism in microbes

The parasite must coexist with the host long enough to reproduce and spread

What is the leading explanation for how myrtle rust reached NZ

Urediniospores blown 2,000km from eastern Australia on westerly winds

What is a key characteristic of indoor air microbiomes compared to outdoor air microbiomes?

indoor air microbes often reflect the microbial communities of the buildings occupants

What does bray curtis dissimilarity measure?

How different two samples are, based on which species are present and how abundant they are

In the ocean is there more producers or consumers?

consumers

(?)% of all oxygen is produced in the ocean

40%

What is productivity?

Synthesis of biomass

what is the Redfield Ratio?

106C : 16N: 1P : 0.0075Fe (sometimes included Si, K, S)

What limits productivity?

The need for Nitrogen followed by Iron (at upwellings)

Consider an ocean area with strong upwelling of deep, nutrient-rich water to the surface. What level of primary productivity would you expect there, and which nutrient is most likely to limit phytoplankton growth?

High productivity, iron limitation

What is iron necessary for?

chlorophyll biosynthesis

Chloroplast All cells require ___________ to synthesise protein.

Nitrogen

The taking of carbon from the atmosphere and land runoff to the deep ocean

The biological pump

Driven by microbial activity and results in long-term CO₂ removal from atmosphere

The biological pump

Biological debris that falls through the water column - Important source of nutrients which are very important at bottom of water column.

Marine snow

What is marine snow made of?

dead/decaying algae and animals, fecal material

Microbes can show _______ towards marine snow.

chemotaxis

vast, flat region of the deep ocean floor that is dark, cold, and low in oxygen

The abyssal plain

The microscale environment immediately surrounding a phytoplankton cell.

phycosphere

~1mm thick layer of water around an object with limited water movement

Diffusive boundary layer

Diffusive boundary layers (~1 mm thick) surround objects in the ocean. Which environmental parameters typically change across these gradients?

Oxygen and nutrients

Cyanobacteria is (?)-(?)% of primary production

25 - 50%

Autotrophic (producers) seperate carbon into what?

DOC and POC ( or DOM and POM )

The coral symbiont provides what for the coral?

photosynthetic products, Sugars, lipids, amino acids

The coral provides what for the coral symbiont?

inorganic C, N, P and a stable position in water column

the loss of dark colour resulting from expulsion of corals’ endosymbiotic algae

Coral bleaching

Organism located on surface of another organism

Ectosymbiont

Organism located within another organism

Endosymbiont

hosts that have more than one associated symbiont – relationships can be intermittent and cyclic or permanent

Consortium

How do juvenile Hawaiian bobtail squid acquire their Aliivibrio fischeri symbionts?

Horizontally from seawater soon after hatching

How does Wolbachia infection help reduce dengue virus transmission by Aedes aegypti mosquitoes?

blocks virus replication and spreads maternally through the population.

A high-fibre diet is beneficial because

The fibre is fermented by intestinal microbes, yielding beneficial by-products

one organism harmed, other organism unaffected (−/0).

Amensalism

Which type of sequencing method would you use for identifying a single isolate species?

Sanger sequencing

What is the main purpose of an Operational Taxonomic Unit (OTU) in microbiome analysis?

To group sequences based on similarity as a proxy for species.

Why is it important to barcode DNA samples during sequencing?

To distinguish which sample a sequence originated from.