Microbes carve out a niche for themselves

What is it about?

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. 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. 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.

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Why is it important?

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 and in microbial communities are prime targets for researchers looking to engineer desired outcomes. In this paper we use an evolutionary approach to identify the genes and functions that play an important role in maintaining niche specialisation in microbial communities from metagenomic data. 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 - an important greenhouse gas. 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 allow researchers to both identify niche specialisation in any microbiome and to identify the organisms important for specific functions in any microbial community.