Comparative genomic analysis reveals metabolic diversity of different Paenibacillus groups
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GENOMICS, TRANSCRIPTOMICS, PROTEOMICS
Comparative genomic analysis reveals metabolic diversity of different Paenibacillus groups Wen-Cong Huang 1 & Yilun Hu 2,3 & Gengxin Zhang 2,3 & Meng Li 1 Received: 19 June 2020 / Revised: 13 October 2020 / Accepted: 26 October 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract The genus Paenibacillus was originally recognized based on the 16S rRNA gene phylogeny. Recently, a standardized bacterial taxonomy approach based on a genome phylogeny has substantially revised the classification of Paenibacillus, dividing it into 23 genera. However, the metabolic differences among these groups remain undescribed. Here, genomes of 41 Paenibacillus strains comprising 25 species were sequenced, and a comparative genomic analysis was performed considering these and 187 publicly available Paenibacillus genomes to understand their phylogeny and metabolic differences. Phylogenetic analysis indicated that Paenibacillus clustered into 10 subgroups. Core genome and pan-genome analyses revealed similar functional categories among the different Paenibacillus subgroups; however, each group tended to harbor specific gene families. A large proportion of genes in the subgroups A, E, and G are related to carbohydrate metabolism. Among them, genes related to the glycoside hydrolase family were most abundant. Metabolic reconstruction of the newly sequenced genomes showed that the Embden–Meyerhof– Parnas pathway, pentose phosphate pathway, and citric acid cycle are central pathways of carbohydrate metabolism in Paenibacillus. Further, the genomes of the subgroups A and G lack genes involved in glyoxylate cycle and D-galacturonate degradation, respectively. The current study revealed the metabolic diversity of Paenibacillus subgroups assigned based on a genomic phylogeny and could inform the taxonomy of Paenibacillus. Key points • Paenibacillus clustered into 10 subgroups. • Genomic content variation and metabolic diversity in the subgroup A, E, and G were described. • Carbohydrate transport and metabolism is important for Paenibacillus survival. Keywords Paenibacillus . Phylogeny . Pan-genome . Metabolism . CAZymes Supplementary Information The online version contains supplementary material available at https://doi.org/10.1007/s00253-02010984-3. * Gengxin Zhang [email protected] * Meng Li [email protected] 1
Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People’s Republic of China
2
Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
3
Key Laboratory of Alpine Ecology, CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
Introduction Paenibacillus is a genus comprising facultative anaerobic and endospore-forming bacteria. Members of the Paenibacillus genus are found in various env
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