Metagenomics: Breakthrough in identifying our environment

Our environment has always been a concern and preservation of the living world has been one of the main focal points because of human misadventure. One of the largest offshore oil spills occurred in 2010 when the Deepwater Horizon sank in the Gulf of Mexico disseminating over 210 million gallons of oil into the ocean. Environmentalists, conservationists and the general public were aghast and the damage to the ocean was vast. Yet two years later incredibly over 200,000 tons of oil had been consumed by species of native bacteria that consumed the oil slick.  

These species were later identified as Colwellia (Olivia U Mason, 2015), and Oceanospirillales prevalent in the Gulf of Mexico with the ability to consume and digest oil. Many scientists believe that the microbiome is constantly evolving and the fact that the Gulf of Mexico has oil slick consuming bacteria shows a natural evolution to the surrounding environment. The way that these bacteria can be identified is by sequencing the bacteria and hence identifying their makeup. 

Metagenomics is the study of genetic material by samples acquired from the environment. Why is this important? In the last decade this area of science has yielded a large amount of new findings that has many implications not only to the environment but also to industry, medicine, agriculture and biotechnology in general. A few examples at its application would be to study the presence of microbial and fungal activity in healthcare environments effectively eliminating hospital acquired infections. 

In agriculture, based on the genetic makeup of soil one could decide the best crop to plant in that location. Just as important the environmental and ecological implications of a technology like this would help both in preservation and understanding to both the scientific and public communities. 

The application of this technology does not apply only to the external environment but to our own bodies as well. Recent studies (Sultana, 2013) have revealed hundreds of new gut microbes and all of them are not bad, in fact a good deal of them help in various functions in the body. Again the implications are many fold, the microbiome of the gut would contribute to being lean or obese, digestion of important nutrients especially in infants, and even answers to patients with Crohn’s, or inflammatory bowel disease. As time progresses metagenomics will add a wealth of data to help us understand how we work with our indwelling neighbours and help us to take advantage of their co-existence. 

Going forward the applications are limitless so how can we as a nation benefit from such cutting edge technology. The Global Ocean Sampling project by the renowned Craig Venter identified many unique microbial organisms along the south-western coast of North America in the Pacific Ocean.  Sri Lanka with its rich marine diversity is teaming with an abundance of unique organisms and their analysis could reveal unique advantages to our ecology and environment.  

Furthermore as the country progresses towards healthcare tourism we can see the need for hospitals to have a control on all microbial activity not just as a value addition but also as a standard of excellence. With a large export market of fish, tea, spices, and other goods, metagenomic testing might be the route to go to give value addition. Other industries that would benefit from checking microbial content would be the water industry, food retail, cosmetic, ayurvedic, pharmaceutical, biotech just to name a few. 

A recent metagenomic study on the New York City Subway portrayed microbial diversity (al, 2015). Humans passed these bacteria, as they used the subway system but the microbial diversity allowed both pathogenic and non-pathogenic bacteria to reside in the same ecosystem. If a future outbreak were to occur from the location, the data from the study would be able to localise causative agent and location. 

The community health implications are numerous and metagenomics is already being looked at in identifying public health outbreaks and controlling them. Metagenomics is here to stay and as abundance of organisms are accurately identified so will there be discoveries of new species of bacteria, fungi and viruses. Considering our microenvironment in the future is of incredible importance and the technology is now available to help us achieve this. 

Works Cited

al, A. e. (2015). Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. CELS.

Olivia U Mason, J.H. (2015). Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill. Frontiers in Microbiology, 5 (332).

Sultana, G.N. (2013). The Use of Metagenomic Approaches to Analyze changes in Microbial communities. Microbiology Insights, 37 (48), 43.

(The writer is the CEO/Director at Credence Genomics.)