The pangenome of the genus Clostridium

Abstract

The pangenome for the genus Clostridium sensu stricto, which was obtained using highly curated and annotated genomes from 16 species is presented; some of these cause disease, while others are used for the production of added-value chemicals. Multilocus sequencing analysis revealed that species of this genus group into at least two clades that include non-pathogenic and pathogenic strains, suggesting that pathogenicity is dispersed across the phylogenetic tree. The core genome of the genus includes 546 protein families, which mainly comprise those involved in protein translation and DNA repair. The GS-GOGAT may represent the central pathway for generating organic nitrogen from inorganic nitrogen sources. Glycerol and glucose metabolism genes are well represented in the core genome together with a set of energy conservation systems. A metabolic network comprising proteins/enzymes, RNAs and metabolites, whose topological structure is a non-random and scale-free network with hierarchically structured modules was built. These modules shed light on the interactions between RNAs, proteins and metabolites, revealing biological features of transcription and translation, cell wall biosynthesis, C1 metabolism and N metabolism. Network analysis identified four nodes that function as hubs and bottlenecks, namely, coenzyme A, HPr kinases, S-adenosylmethionine and the ribonuclease P-protein, suggesting pivotal roles for them in Clostridium.

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence ofblaCTX-M-55,blaNDM-5andblaIMI-1, along with sophisticated iron acquisition strategies

“…We used the strains listed above (Table 1) to build the E. bugandensis pangenome. Our results support a high genetic diversity and an open pangenome (Figure 1a), features that are often associated with the ability to colonize multiple environments [23]. The E. bugandensis pangenome is composed by 11,682 genes families: 3,167 are common to all strains (core genome); 3,785 are present in more than one (but not all) strains (accessory genome) and; 4,730 are unique to any given strain (Figure 1b).…”

Revisiting the evolution and taxonomy of Clostridia, a phylogenomic update

“…Furthermore, within group I, arguably the authentic Clostridium genus, further taxonomic inconsistencies exist due to the use of BotA for taxonomic classification as a taxonomic marker. This has previously been observed by others (Yutin and Galperin, 2013;Lawson 2016a;Lawson, 2016b;Weigand et al, 2015;Udaondo et al, 2017) but to the best of our knowledge, clostridial taxonomy and evolution has not been revisited using the opportunity offered by next generation sequencing for phylogenomic reclassification until now. Given the pervasiveness of the misclassification in clostridial species, we wonder whether the current system of classification should be kept, or if it should be revisited and simplified using genomic data.…”

Diversity, Function, and Application of Clostridium in Chinese Strong Flavor Baijiu Ecosystem: A Review

“…With the development of sequencing technology and other omics technology, more Clostridium from the SFB ecosystem will be sequenced and analyzed. The pangenome and core-genome of Clostridium from the SFB ecosystem can be studied (Udaondo, Duque, & Ramos, 2017). To build the link between genotype and phenotype, genome-scale metabolic model (GSMM) which contains all the metabolic information of a single organism can be reconstructed (Durot, Bourguignon, & Schachter, 2009;Feist, Herrgard, Thiele, Reed, & Palsson, 2009).…”