Question

One approach to investigate the functional capability of a microbial community is through genomic assignment methods. In these methods, one first determines which microbial species are present in a community (for example, by sequencing the bacterial 16S rRNA gene), and then attempts to assign functional genes to these species by comparing them to a database of fully sequenced microbial genomes

A. For what kind of microbial communities and ecosystems do you think this approach will work well (meaning, give an accurate estimate of the true metagenome)? In what situations do you think it will work poorly? Explain why. (8 points)

B. The value of genomic assignment approaches grows as we continue to add reference genomes to our databases, especially for unculturable species. Describe one way in which scientists can gain full genome sequences from organisms that they cannot grow in culture. (8 points)

Answer 1

Microbial communities are spaces where groups various microorganisms species like archaea, bacteria, fungus,algae, eubacteria, helminth,viruses live together. There may be a symbiotic relationship between them or as prey & predator.

As it is a community,the theory of natural selection and the survival of the fittest applies there.

For identification of the abundance of these communities, different techniques can be applied :-

Microbiological culture techniques, molecular biological genome Sequencing, Next generation Sequencing,etc.

But some species cannot be cultured on artificial media. In such cases genome Sequencing using molecular biology and bioinformatics helps.

A) Human body is an ecosystem for various microbes.

For the communities in human gut, these advanced techniques can be used.

The sample can be taken from the cheeks,throat or stools.The DNA can be extracted and this DNA can be used for genome sequencing.

After the sequencing is complete,the data obtained is matched with already available reference databases followed by annotation of the genes. This is called as Metagenomics.

Metagenomes consist of many short-read sequences obtained from numerous different species, many of which are unknown.

Two highly informative metagenomic traits that reflect ecologica strategies of microorganisms as well as the environmental conditions they inhabit are

• the Average Genome Size (AGS) and
• The 16S rRNA gene Average Copy Number (ACN) .

It is estimated that in the gut,the AGS is 2.5 to 5.8 megabases.

However,these methods does not provide information on ecologically relevant genes involved in various biogeochemical cycles.

B) Metagenomic analyses using high throughput sequencing have been extremely valuable for describing microbial structure and functionality in extreme ecosystems and also for finding novel genes.

Inorder to gain full genome sequence information of the organisms which cannot be cultured scientists can use whole genome shot-gun sequencing technology.

In this method,the DNA extracted from the microbe is broken into small fragments for sequencing.

These fragments are of sizes 2 to 20 kilobases.

Sequencing these fragments gives order of DNA bases A,C,G and T.

The sequenced fragments are assembled clone by clone using computer programs i.e bioinformatics tools where the fragments overlap.

It is a less expensive and much faster method to sequence the whole genome of unculturable microorganisms.