Recently, Prof. Zhang Zheng and Prof. Li Yuezhong’s group from the State Key Laboratory of Microbial Technology (Institute of Microbial Technology) at Shandong University published a research paper titled "GDPF: a data resource for the distribution of prokaryotic protein families across the global biosphere” in the Nucleic Acids Research (5-Year IF=16.4, Q1). Postdoctor Pan Zhuo from the State Key Laboratory of Microbial Technology and assistant researcher Li Dandan from the Institute of Marine Science and Technology are the joint first authors. Prof. Li Yuezhong and Prof. Zhang Zheng from the State Key Laboratory of Microbial Technology are the joint corresponding authors. Shandong University is the sole institutional affiliation for this research.

Microorganisms are ubiquitous on Earth, hidden on people’s skin, gut and soil, rivers, oceans and other environments, and their functions constitute pivotal factors influencing human health, disease development and global ecological changes. Until now, the vast majority of microbial biogeography research has concentrated on uncovering the phylogenetic diversity of microorganisms in complex environments, disregarding their functional diversity; nevertheless, it is the functions demonstrated by these microorganisms that genuinely propel the relevant ecological processes. Recently,numerous studies have quantified the functional aspects of microbial communities in specific environments (e.g., the human gut) based on families. However, comprehensive data on the distribution of microbial functional families in the global biosphere are still lacking.

Previous research by the authors has revealed that the proportion of sequenced genomes of global microbial communities has reached a high level (Microbiome, 8:134). Building upon this foundation, the present study leveraged data from the Earth Microbiome Project (EMP) along with sequenced genome information, and consolidated functional annotations from classification systems such as KEGG, CDD, PFAM,and COG to construct the GDPF database (global distribution of prokaryotic protein families,http://bioinfo.qd.sdu.edu.cn/GDPF/). GDPF provides global distribution information for 36,334 protein families, 19,734 superfamilies and 12,089 KEGG orthologs from multiple source databases, covering typical environments such as soil, oceans, animals, plants, and sediments. Users can browse, search, and download the distribution data of each entry in 10,000 global microbial communities, as well as conduct a comparative analysis of distribution disparities among multiple entries across various environments. The GDPF data resource contributes to uncovering the geographical distribution patterns, key influencing factors, and macroecological principles of microbial functions at a global level, thereby promoting research in Earth ecology and human health.

Greenhouse gas-induced global warming threatens biological biodiversity, agricultural productivity, and food security. Glycoside hydrolases (GHs) encoded by prokaryotes play a crucial role in the degradation of carbohydrates, which is a key step in the carbon cycle. In this study, we conducted a comprehensive investigation of the global biogeographic patterns of prokaryotic-encoded GHs, providing a panoramic view of the functional potentials for carbohydrate degradation across prokaryotic communities under diverse environmental conditions. The composition of GHs encoded by prokaryotic communities exhibits clear habitat specificity, which is driven by a combination of biotic and abiotic factors and generated through highly deterministic assembly processes. The related paper entitled "Deterministic assembly processes shaping habitat-specific glycoside hydrolase composition" was published in the Global Ecology and Biogeography (5-Year IF=7.4, Q1). Assistant researcher Li Dandan and Prof. Zhang Zheng are the joint first authors. Prof. Zhang Zheng and Prof. Li Yuezhong are the joint corresponding authors, and Shandong University is the sole institutional affiliation.

In recent years, Prof. Zhang Zheng and Prof. Li Yuezhong’s group has made significant strides in the field of microbial community ecology. The findings have been published in international journals, including Nucleic Acids Research (2023 and 2022), Global Ecology and Biogeography(2023),mSystems(2023, 2021, and 2020), Environmental Microbiology (2023 and 2021), Microbiology Spectrum(2021), Applied and Environmental Microbiology(2021), Computational and Structural Biotechnology Journal (2021 and 2020), and Microbiome (2020). These works were supported by the National Key Research and Development Program, the Science & Technology Fundamental Resources Investigation Program, the National Natural Science Foundation of China, the China Postdoctoral Science Foundation, the Shandong Provincial Natural Science Foundation,and the Qilu Young Scholars Program of Shandong University.

Article links:

https://doi.org/10.1093/nar/gkad869

https://doi.org/10.1111/geb.13768