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. 2022 Mar 15;23(6):3135.
doi: 10.3390/ijms23063135.

A Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological Applications

Martina Aulitto  1   2 , Laura Martinez-Alvarez  3 , Gabriella Fiorentino  1   4   5 , Danila Limauro  1   4   5 , Xu Peng  3 , Patrizia Contursi  1   4   5
Affiliations

A Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological Applications

Martina Aulitto et al. Int J Mol Sci. .

Abstract

The production of biochemicals requires the use of microbial strains with efficient substrate conversion and excellent environmental robustness, such as Weizmannia coagulans species. So far, the genomes of 47 strains have been sequenced. Herein, we report a comparative genomic analysis of nine strains on the full repertoire of Carbohydrate-Active enZymes (CAZymes), secretion systems, and resistance mechanisms to environmental challenges. Moreover, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) immune system along with CRISPR-associated (Cas) genes, was also analyzed. Overall, this study expands our understanding of the strain's genomic diversity of W. coagulans to fully exploit its potential in biotechnological applications.

Keywords: B. coagulans; CAZymes; CRISPR-Cas systems; bacteriocins.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic tree based on the genome comparison of the nine strains of W. coagulans.
Figure 2
Figure 2
Comparative genomic analysis of W. coagulans MA-13 and the closest eight relatives.
Figure 3
Figure 3
Heat-map of singletons. The depth of color corresponds to the number of proteins. Dark green and light green/white represent the highest and lowest number of proteins.
Figure 4
Figure 4
Heat map showing the genome-wide distribution of CAZymes in the W. coagulans strains. A total of 36 families were identified and obtained with Search with dbCAN2 HMMs of CAZy families. Blue and white represent the highest and lowest number of proteins.
Figure 5
Figure 5
Genetic determinants of bacitracin resistance in MA-13.
Figure 6
Figure 6
Graphical representation of circularin A gene cluster in diverse W. coagulans strains.
Figure 7
Figure 7
Heat map distribution of innate immunity systems in the W. coagulans strains. Green and white represent the highest and lowest number of proteins.
Figure 8
Figure 8
CRISPR-Cas cassettes present in W. coagulans genomes. The cas operons for each strain are depicted: (A) MA-13, (B) DSM1, (C) 2–6, (D) H-1, (E) P38, (F) XZL9, (G) 36D1, and (H) CSIL1. The headers above each operon refer to the type of cas operon, strain, contig, and location. The color of cas genes corresponds to their associated stage of the CRISPR-Cas response: blue—adaptation; yellow—interference; and red—crRNA maturation. CRISPR arrays are depicted as black, vertical lines.
Figure 9
Figure 9
Heat map distribution of cas operon genes among W. coagulans strains. Green and white represent the highest and lowest number of genes.
Figure 10
Figure 10
Graphical representation of interaction networks between spacers and viruses. Nodes represent spacers and virus sequences, with lines representing a match between them. (A) Spacer nodes colored by their strain of origin. (B) Virus nodes are colored by their ecosystem of isolation.
Figure 11
Figure 11
Circular visualization of predicted genomic islands. Blocks are colored according to the prediction method: IslandPath-DIMOB (blue), SIGI-HMM (orange), as well as the integrated results (dark red).
Figure 12
Figure 12
Linear genomic map of prophage phBC6A52 identified with PHASTER from MA-13 genome.
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