Wednesday 12 April 2023

New understanding of microbial niches leads to the first map of the ‘microverse’


From hot springs to the human intestine, and to the deep sea - microorganisms colonise almost every place on Earth, often under extreme conditions. How organisms have adapt to a particular environmental condition makes them "generalists" or "specialists." 



What defines the habitat -- the ecological niche -- of a microorganism? The text-book answer is this is a combination of environmental factors such as temperature, moisture, and nutrient content. However, the exact contribution of each of these factors is difficult to predict.


A step forward has come from Friedrich-Schiller-Universitaet Jena who have sought to redefine microbial niches by determining which microorganisms live together. This has led to the notion of the ‘microverse’.


Using bioinformatician, researchers have described microbial niches, in which the species community itself is considered the decisive environmental factor instead of external habitat conditions. This works because microbial communities adapt rapidly to their environment, so their composition reflects the sum of all environmental factors.


This was drawn from an analysis of thousands of metagenomic data sets from different microbial samples from all over the world.


This revealed that in in most habitats, generalists are dominant. This is because competing generalists could grow much faster and thus gain dominance in the niche over specialists.


However, for the generalists there is a ‘hit-or-miss’ element. Either these organisms make it or they do not. This makes them quite variable in their presence. Specialists are more stable in their niche, albeit at low abundance.



The genomes of the generalists were found not to be particularly large. This contradicted earlier thinking as it was assumed because metabolic flexibility was thought to generally require a larger genome. The correlation between niche range and genome size is more complex.


In habitats with relatively low local biodiversity, such as animal-associated microbiomes, the specialists have a relatively small genome. In highly biodiverse habitats such as soils, the genome of the specialists is significantly larger.


Hence, the genomes of generalists are more variable than those of specialists, with genes coming and going during evolution. This allows them to integrate genetic information from other organisms through horizontal gene transfer and thus to adapt rapidly to the local niche. The functions associated with specialists are much more diverse, often related to very specific metabolic processes. The genomes of specialists are evolutionarily stable, unlike those of generalists.


The research reference is:


F. A. Bastiaan von Meijenfeldt, Paulien Hogeweg, Bas E. Dutilh. A social niche breadth score reveals niche range strategies of generalists and specialists. Nature Ecology & Evolution, 2023; DOI: 10.1038/s41559-023-02027-7


Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (

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