Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Sep 17;23(18):10884.
doi: 10.3390/ijms231810884.

Comparative Genomic Analysis of Agarolytic Flavobacterium faecale WV33T

Affiliations

Comparative Genomic Analysis of Agarolytic Flavobacterium faecale WV33T

Jun Ho Lee et al. Int J Mol Sci. .

Abstract

Flavobacteria are widely dispersed in a variety of environments and produce various polysaccharide-degrading enzymes. Here, we report the complete genome of Flavobacterium faecale WV33T, an agar-degrading bacterium isolated from the stools of Antarctic penguins. The sequenced genome of F. faecale WV33T represents a single circular chromosome (4,621,116 bp, 35.2% G + C content), containing 3984 coding DNA sequences and 85 RNA-coding genes. The genome of F. faecale WV33T contains 154 genes that encode carbohydrate-active enzymes (CAZymes). Among the CAZymes, seven putative genes encoding agarases have been identified in the genome. Transcriptional analysis revealed that the expression of these putative agarases was significantly enhanced by the presence of agar in the culture medium, suggesting that these proteins are involved in agar hydrolysis. Pangenome analysis revealed that the genomes of the 27 Flavobacterium type strains, including F. faecale WV33T, tend to be very plastic, and Flavobacterium strains are unique species with a tiny core genome and a large non-core region. The average nucleotide identity and phylogenomic analysis of the 27 Flavobacterium-type strains showed that F. faecale WV33T was positioned in a unique clade in the evolutionary tree.

Keywords: CAZymes; Flavobacterium faecale; agarase; comparative genomics.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Circular representation of the genome of F. faecale WV33T. From the outer to inner circle: predicted protein-coding sequences (colored by COG categories) on the plus strand, predicted protein-coding sequences (colored by COG categories) on the minus strand, RNA genes (tRNAs, blue; rRNAs, red), GC content (blue/black), and GC skew (red/black). NC in color codes of COG represents no classified category.
Figure 2
Figure 2
Phylogenetic tree of the seven putative agarases encoded in F. faecale WV33T genome and mRNA expression analysis of five of them. (A) A multiple alignment performed with ClustalW was used for the construction of a phylogenetic tree through the neighbor-joining method using MEGA-X. Scale bar indicates 0.2 amino acid substitutions per site. Numbers at nodes indicate bootstrap percentages (from 1000 bootstrap replicates). Beta-xylanase of F. faecale WV33T (AWG23231.1) was used as an outgroup to root the tree. (B) After F. faecale WV33T was grown in 100 mL flasks containing 1 g/L sliced solidified agar as carbon source, mRNA expression levels of five putative agarase genes were determined via RT-qPCR. Relative mRNA expression was normalized based on that of the housekeeping gyrB gene (as a control). Bars represent the mean, whereas the error bars represent the standard deviation. Experiments were performed in biological triplicates (n = 3).
Figure 3
Figure 3
Average nucleotide identity (ANI) analysis of the 27 representative genomes of Flavobacterium strains including F. faecale WV33T. ANI analysis was performed using pyani with ANIm (A), ANIb (B), ANIblastall (C), and TETRA (D) algorithms. ANI similarities with 1 being identical are indicated in the heatmaps. Scale of similarity values are represented by a continuous color gradient. A similarity value is presented in each cell. Green box represents F. faecale WV33T (GCF 003076455.1).
Figure 4
Figure 4
Pangenome analysis of 27 Flavobacterium strains including F. faecale WV33T. (A) Box-Whisker plot of pangenome as a function of the number of genomes (1–27) of Flavobacterium strains. (B) Box-Whisker plot of core genome as a function of the number of genomes (1–27) of Flavobacterium strains. Outliers are shown as open circles. (C) Phylogenetic tree and a gene presence/absence matrix plot generated using Roary. Green box represents F. faecale WV33T (GCF 003076455.1). In the matrix a blue line represents gene presence. The numbers on the right represent the total number of core and unique genes of each Flavobacterium strain.
Figure 5
Figure 5
Phylogenomic analysis of 27 Flavobacterium strains including F. faecale WV33T. Phylogenetic tree was generated using GToTree and the red triangle represents the presence of predicted agarase (Pfam:PF00722). The numbers on the right represent abundance of Pfam:PF00722 (=GH16) in genomes of 27 Flavobacterium strains. Green box represents F. faecale WV33T (GCF 003076455.1). Psychrobacillus glaciei (GCA_008973485.1) was used as an outgroup to root the tree.

Similar articles

Cited by

References

    1. Bernardet J.F., Bowman J.P., Genus I. Flavobacterium. In: Krieg N.R., Ludwig W., Whitman W., Hedlund B.P., Paster B.J., Staley J.T., Ward N., Brown D., Parte A., editors. Bergey’s Manual of Systematic Bacteriology. 2nd ed. Volume 4. Springer; New York, NY, USA: 2011. pp. 112–154.
    1. Touchon M., Barbier P., Bernardet J.F., Loux V., Vacherie B., Barbe V., Rocha E.P.C., Duchaud E. Complete genome sequence of the fish pathogen Flavobacterium branchiophilum. Appl. Environ. Microbiol. 2011;77:7656–7662. doi: 10.1128/AEM.05625-11. - DOI - PMC - PubMed
    1. Huang L., Zhou J., Li X., Peng Q., Lu H., Du Y. Characterization of a new alginate lyase from newly isolated Flavobacterium sp. S20. J. Ind. Microbiol. Biotechnol. 2013;40:113–122. doi: 10.1007/s10295-012-1210-1. - DOI - PubMed
    1. Bernardet J.F., Nakagawa Y. An introduction to the family Flavobacteriaceae. In: Dworkin M., Falkow S., Rosenberg E., Schleifer K., Stackebrandt E., editors. The Prokaryotes, a Handbook on the Biology of Bacteria. 3rd ed. Volume 7. Springer; New York, NY, USA: 2006. pp. 455–480.
    1. Herrera L.M., Braña V., Franco Fraguas L., Castro-Sowinski S. Characterization of the cellulase-secretome produced by the Antarctic bacterium Flavobacterium sp. AUG42. Microbiol. Res. 2019;223–225:13–21. doi: 10.1016/j.micres.2019.03.009. - DOI - PubMed

Supplementary concepts

LinkOut - more resources