Rokubacteria (六)

Introduction

Rokubacteria is a bacterial phylum that is found in diverse environment such as:

• Groundwater (Hug et al., 2015)
• Soil (Becraft et al., 2017; Crits-Cristoph et al., 2018)
• Hydrothermal sediments (Zhou et al., 2020)

Aim

To better understand the ecology and diversity of Rokubacteria, we attempt to apply metapangenomics and phylogenomics using publically-available metadata.

Disclaimer

This analysis was meant as a practice. In the case if we are considering of publishing results using these data, we will inform the data providers beforehand.

The flow of the analysis

• Obtain genomes and metadata
• Phylogenomics analysis
• Pangenomics + metabolism estimation analysis using anvio
• Metapangenome analysis using anvio
  • This will require a number of metagenome data

• some ideas
  • find codon/amino acid bias
  • explore unknown genes using agnostos
  • find defense genes
  • find bacterial microcompartment genes
  • find biosynthetic gene clusters

TODO

• Attempt genome annotation using bakta
• Try alternative genetic codes
  • Use prodigal for gene calling
  • Using genetic code 4, 11 and 15
  • Write script to count gene density: calculate sum length of genes over total contig length
• Try detecting bacterial defense mechanisms
  • Might not be the best on MAGs, but we'll see
• Compare anvio-estimate-metabolism with DRAM output

Citations

Becraft, E. D., Woyke, T., Jarett, J., Ivanova, N., Godoy-Vitorino, F., Poulton, N., Brown, J. M., Brown, J., Lau, M. C. Y., Onstott, T., Eisen, J. A., Moser, D., & Stepanauskas, R. (2017). Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla . In Frontiers in Microbiology (Vol. 8, p. 2264). https://www.frontiersin.org/article/10.3389/fmicb.2017.02264

Crits-Christoph A, Diamond S, Butterfield CN, Thomas BC, Banfield JF. 2018. Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis. Nature 558:440–444. https://10.1038/s41586-018-0207-y

Hug, L.A., Thomas, B.C., Sharon, I., Brown, C.T., Sharma, R., Hettich, R.L., Wilkins, M.J., Williams, K.H., Singh, A. and Banfield, J.F. (2016), N- and C-cycling organisms in the subsurface. Environ Microbiol, 18: 159-173. https://doi.org/10.1111/1462-2920.12930

Zhou Z, Liu Y, Xu W, Pan J, Luo ZH, Li M. Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment. mSystems. 2020 Jan 7;5(1):e00795-19. https://10.1128/mSystems.00795-19