Detecting microbial niches in Metagenomic data

Microbes colonising the surface of grass.
The image was taken using a Hitachi S-4700 FESEM scanning electron microscope by Alan Cookson 
at the IBERS Advanced Microscopy and Bio-Imaging Laboratory, Edward Llwyd building, Penglais.
In collaboration with the Agriculture and Food Development Authority in Ireland (Teagasc) we recently published a new way of identifying how different types of microbes can survive when competing for resources in the same environment.

The paper by former PhD student in the group, Dr Francesco Rubino, identifies what is known as ‘niche specialisation’  and is published in the Nature Publishing Group (NPG) ‘Multidisciplinary Journal of Microbial Ecology’: The ISME Journal.

Niche specialisation is the process by which, through natural selection, a species becomes better adapted to the specific characteristics of a particular habitat.
These organisms can be the principal drivers of important processes in the community and therefore are prime targets for researchers looking to engineer microbial communities to achieve desired outcomes.

It has long been thought that ecological principles developed for the study of large organisms should also be applicable to micro-organisms and while processes such as successional change and competition are known to occur in microbial communities, identifying signatures of niche specialisation remains a challenge.

Despite the large numbers of microbiome studies that have been generated from the microbial populations found in the gut, the soil, the sea and human skin, we still lack a clear understanding of the ecology of the micro-organisms that have an essential role to play in everything from human health to earth system processes.

We were looking to identify what resources different micro-organisms compete over when they are present in the same environment. Developing such an understanding is essential to meet many of the major challenges facing human society today, such as management of natural ecosystems and mitigation of climate change.

This study examined the signatures of niche specialisation between some of the most abundant organisms in the rumen microbiome of cattle, a major source of methane – the second most significant greenhouse gas in the UK.

We used a novel computational biology approach implemented in MGKit and based on evolutionary methods to identify the genes and functions that play an important role in maintaining niche specialisation.

The results identified the specific functions important for each organism within the microbial community to maintain its niche in the rumen of cattle and represent novel targets for engineering this microbiome for desirable outputs (such as reducing greenhouse gasses).
This represents the first use of evolutionary approaches in this context and will open avenues of further research to both identify niche specialisation in any microbiome and to identify the organisms important for specific functions in any microbial community.

This work was funded by the Biotechnology and Biological Sciences Research Council (BBSRC), EU Seventh Framework Programme and Science Foundation Ireland.