Metagenomics and Antibiotics Quiz

Study Notes

Hemolysin is a bacterial toxin that punctures holes in cell membranes, causing cell death.
Hemolysin lyses red blood cells, creating a clear zone around bacterial colonies on blood agar plates.

Two novel antibiotics, turbomycin A and B, were discovered while screening a metagenomic library.
These antibiotics were found in E. coli clones with dark red or orange colors.

Novel biodegradation pathways have been identified in bacteria inhabiting contaminated sites.
These bacteria utilize pollutants as an energy source, containing enzymes that reduce the toxic effects of oil and petroleum-based contaminants.

Enrichment strategies are essential for metagenomics research, maximizing the quality of a metagenomic library.
Several enrichment strategies include stable isotope probing (SIP), BrdU enrichment, and suppressive subtraction hybridization (SSH).

SIP was initially developed to trace single carbon compounds during the metabolism of cultured methylotrophs.
Labeled precursor carbons were traced into fatty acids during bacterial growth.
The method was adapted for environmental samples, allowing identification of organisms metabolizing labeled substrates.
Environmental samples are mixed with a labeled precursor (e.g., methanol, phenol, carbonate, or ammonia) with stable isotopes (e.g., ^15^N, ^13^C, or ^18^O).
Organisms metabolizing the precursor incorporate the stable isotope into their genome.
During centrifugation, the heavier labeled DNA migrates further than unlabeled DNA, allowing for separation.
This technique is particularly useful for identifying organisms that degrade contaminants, such as phenol.

The environment is a vast source of novel products and technologies.
Hidden life forms, including bacteria and viruses, are present in air, water, and soil.
These organisms often display unique metabolisms and abilities not seen in other organisms.
The virosphere, with an estimated 10^31^ to 10^32^ viral particles, is a potential source of novel genes.
Less than 1% of microorganisms have been cultured.
Environmental biotechnology revolutionized the study of these previously hidden life forms and DNA.

Culture enrichment techniques are used to enhance the starting material for metagenomics research.
Suppressive subtraction hybridization (SSH) utilizes genetic differences between samples from two different areas.
SSH compares the mRNA from two different samples, identifying mRNA that is unique to each sample.
For example, SSH can compare contaminated and uncontaminated soil samples to identify microorganisms specifically enriched in the contaminated site.
The contaminated soil serves as the "tester" DNA, while the uncontaminated soil is the "driver" DNA.
Linkers are added to the tester DNA, and the hybridized DNA is amplified using PCR.
This technique is particularly helpful for identifying microorganisms involved in the biodegradation of specific contaminants.

Metagenomics can be used to study biogeochemical processes, such as natural attenuation of pollutants.

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