Soil metagenome

Human pursuit has led to cultivation of bacteria from almost all possible habitats on earth for studies related to bacterial diversity, diseases, ecological functions and biotechnological applications. Bacteria were initially isolated from habitats commonly associated with humans, at near neutral pH and ambient temperature. Later these were isolated from even the most hostile environments, like thermal vents, acidic ponds, saturated brine and glaciers. Successful isolation of bacteria from earth’s crust and polar ice has led to the belief that bacterial life may exist even on other planets. Though the search to find bacterial life on other planets is ongoing, we are still far away from understanding the bacterial diversity in even the most common and well-studied niches .Most (more than 99%) of the bacteria present in many environmental samples cannot be cultivated in the laboratory as unculturable and hence remain obscure for their ecological functions, and unexploited for biotechnological applications.

Unculturable bacteria

The great plate count anomaly is the observation that most of the microbes seen in the microscope cannot currently be grown under laboratory conditions, some may actually be nonviable, others are viable but nonculturable (VBNC).

For over a century, microbiologists have been using growth media solidified with agar to culture microbes from environmental samples. Individual cells are easily separated on the solid surface, allowing each cell to grow and divide and form a colony of thousands of clones. We can change the nutrients in the media and physical parameters such as temperature and pH to promote the growth of different microbes. But no matter the trick, we still fall short and can only successfully cultivate in the lab a few microbes of the many that we can see under the microscope in the original sample. Estimates are that we can cultivate roughly one out of every 100 microbes. This is what has been described as The Great Plate Count Anomaly

Need to study?

Accessing this missing diversity is important for two key reasons: it likely plays significant roles in the function of the biosphere, and quite possibly represents an untapped mine of novel bioactive compounds. Not surprisingly, learning the nature of the ‘missing’ diversity and understanding their phylogenetic relationship and ecological significance is widely recognized as one of the most important challenges for microbiologists .

Cultivating unculturables

Abundance and diversity of unculturable bacteria in almost all environmental niches have led to the understanding that the so-called ‘unculturable’ bacteria actually multiply in their natural environment and if suitable culture conditions were provided it should be possible to cultivate them in the laboratory.

• Use of media with very low nutrients.
• By an integrated approach using various growth parameters like low nutrient media, varying oxygen and carbon dioxide concentrations, long incubation period and additives like humic acids and quorum signaling molecules.
• Other innovative and successful approaches considered include, simulation of natural environment, community interactions and cell–cell communication important for the cultivation.
• The isolates did not grow on artificial media alone but formed colonies in presence of other microorganisms indicating that they required specific signals originating from their neighbours that point to the presence of familiar environment.

Specific aims of metagenomics

1. Examining phylogenetic diversity using 16S rRNA,which can be used for monitoring and predicting environmental conditions and change.
2. Examining genes/operons for desirable enzyme candidates (e.g., cellulases, chitinases, lipases, antibiotics, other natural products and these may be exploited for industrial or medical applications )
3. Examining bacteriophage or plasmid sequences. They potentially influence diversity and structure of microbial communities
4. Examining potential lateral gene transfer events.
5. Examining metabolic pathways.
6. Directed approach towards designing culture media for the growth of previously-uncultured microbes.
7. Examining genes that predominate in a given environment compared to others.
8. Finally, metagenomic data and metadata can be leveraged towards designing low and high-throughput experiments focused on defining the roles of genes and microorganisms in the establishment of a dynamic microbial community.

Uses of metagenomics

• To understand the cell structure and function
• To understand the metabolism
• To understand the host interaction
• For genetic engineering
• To Understand the expression of proteins
• For the development of new drugs and vaccines
• To understand the protein-protein interactions

It can be expected that the number of novel genes identified through metagenome technologies will exceed the number of genes identified through sequencing individual microbes .However, the challenge now not only lies in accumulating these sequences but moreover in understanding the function of these novel genes and proteins within the microbial niches and their role in the global cycles.