An article published in the journal “Nature” presents a meta-analysis of microbial samples collected by hundreds of researchers from the Earth Microbiome Project (EMP), which pursues a systematic globally attempt to classify microbes. The researchers established protocols and new analytical methods to manage the results of genetic sequencing of bacteria and archaea in multiple studies. Our knowledge of these microorganisms remains limited but this project will allow to expand them and better understand their impact on the ecosystems they’re part of.
There are only very approximate estimates concerning the microbiome, the set of extremely diverse microorganisms existing on Earth. Progress in genetic analysis techniques is expanding the tree of life in new ways, for example with the large branch indicated vaguely with the expression “candidate phyla radiation” described in an article published in the journal “Nature Microbiology” in April 2016.
EMP’s efforts aim exactly to increase our knowledge and thus our understanding of the microbiome. This study involving over 500 researchers from over 160 institutions in 43 nations is the largest ever conducted in this field. 25,751 samples were collected around the world for this meta-analysis and the information gathered were already useful for a hundred more studies, half of which have already been described in articles published in scientific journals.
The project members analyzed the diversity in bacteria in various environments, geographies and chemistries sequencing a genetic marker called 16S rRNA specific for bacteria and archaea. The unique mutations of that gene were used as a sort of barcode and allow to group the bacteria of different samples according to their similarities. About 300,000 unique sequences of that gene were collected and almost 90% of them don’t have exact correspondence in existing databases.
This analysis showed differences in the 16S rRNA gene in the various environments. For example, microbes living in cetacean and fish skin are more similar among them than to those living in water. Similarly, microbes living in salt water are different from those living in fresh water but are more similar to each other than to those living in the skin of aquatic animals.
Precisely because of these differences, the samples were taken in very different environments. The picture shows some of those environments: from the top left there are the Belize rainforest (photo courtesy Krista McGuire, University of Oregon), Colobine monkeys in China whose samples of facial microbes were taken (photo courtesy Kefeng Niu), a bat in Belize whose samples of faecal microbes were taken (photo courtesy Angelique Corthals and Liliana Davalos), Alaska waters (photo courtesy Byron Crump), bird eggs in Spain (photo courtesy Juan Peralta-Sanchez) and a geothermal source in Antarctica (photo courtesy S. Craig Cary, Univ. of Waikato, New Zealand).
This tremendous work will be very useful but it’s far from over. There’s still a lot to be understood about the microbiome and the study of microbial changes along with the ecosystems they live in is another phase of this type of research. In all of this, the Earth Microbiome Project is a reference point for researchers.