Global microbiome connectivity explored

The Earth contains about a trillion species of microbes, of which only about a tenth have been identified. A single human can harbor 100,000 billion microbes, creating a single microbiome that serves as an ecosystem of microbes.

Microbes connect and transform in multiple ways, again creating, combining and separating microbiomes. How can we begin to analyze how microbiomes differ, how they are similar, how they have evolved, and how they may change in the future?

An international team of researchers could have the answer. They released a fully connected, scaleless research-based network to explore the connectivity of microbiomes across the world on July 13 in mSystems.

“The makeup of the microbiome, a fundamental characteristic of any microbiota – microbes sharing a particular characteristic such as a site or a geological period – is shaped by a plethora of environmental factors,” said co-lead author JING Gongchao, researcher at the Single-Cell Center in Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT) of the Chinese Academy of Sciences (CAS). “However, it remains unclear whether and how changes in composition at the ‘community-to-community’ level between microbiomes relate to the origin and evolution of global microbiome diversity.”

To better understand how the large number of diverse microbial species evolved, JING and ZHANG Yufeng, a graduate student from Qingdao University, built a global “microbiome transition network” (MTN) that connects, according to Their compositional similarities, 177,022 microbiomes from various ecosystems which include the plethora of ecological niches on the human body and in the environment.

They used the Microbiome (MSE) search engine, software developed by the team. MSE can build the global microbiome transition network in less than three hours and return the nearest neighbors of a query microbiome in less than 0.5 seconds.

Interestingly, the global MTN is scaleless, which is similar to the internet or social network among human individuals. In this type of networks, most of the nodes are each connected to a small number of other nodes, but a small part of the nodes are connected to many other nodes. Such a network structure ensures a high degree of tolerance of the network against accidental disturbances.

“We have drawn the first global microbiome transition roadmap to illustrate the potential but most likely pathways to explain the evolutionary process of global microbiomes,” said SU Xiaoquan, professor at Qingdao University and lead author. of the study, noting that the roadmap traces high similarities between microbiomes. “Although the compositions are distinct by habitat, each microbiome is, on average, only six” parents “(or seven” stages “) of any other microbiome on Earth, indicating the inherent homology and common origin of the microbiomes to it. ‘global scale. “

On the other hand, information from the global NTD can indicate important information, such as the evolution or interaction of microbiomes. For example, the roadmap found that the oceans are the microbiomes most likely to interact with beach sand and marine fish, while soil and freshwater are the gateway for microbial exchange between the environment. and plants or humans.

With the rapid change in climate as well as civilization on Earth, many microbiomes are disappearing and emerging every day. Although only a tiny proportion of them have been recorded via metagenome sequencing, building and updating the global MTN can be a “mission impossible” without powerful search engines and standardized databases for microbiomes such as those of the MSE.

“Such research-based global microbiome networks, reconstructed in a matter of hours in a single computer mode via MSE, provide an easily extended reference to trace the origin and evolution of existing microbiomes, and possibly to guide design. new microbiomes, ”said XU Jian, director of Single-Cell Center at QIBEBT and the other lead author of the study.

Reference: Jing G, Zhang Y, Liu L et al. A scaleless and fully connected global transition network underpins the known diversity of the microbiome. mSystems. 0 (0): e00394-21. doi: 10.1128 / mSystems.00394-21

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