I found a possible new species of bacteria.
For the ITS DNA sequence, similarity to other bacteria of the genus ranges from 80 to 91%. Making a Neighboor-Joining tree with the ITS sequence, my samples form a unique clade.
By analyzing its genomic sequence (the 7 contigs formed), they have 80 to 91% similarity with other species of the genus. What tool can I use to make a phylogenetic tree from comparison of complete genomic sequences?
I also analyzed the predicted proteins for rpoB (and other proteins in the rpo family) as well as the predicted proteins gyrA and gyrB (using spades + prokka). All these comparisons have 80 to 91% similarity. I also made trees for these proteins, and in all my samples form a single clade.
What more do I need to prove it's a new species?
For new species characterization of bacteria you have to follow polyphasic taxonomic approach i.e. phyogenetics, 16S rRNA gene characterization, chemotaxonomy, complete genome sequencing: dDDH, ANI etc. you should read the article on IJSEM: Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.002516
Best wishes,
Mohinder
In addition to all what Mohinder Pal has mentioned in his answer: it could be useful to make a phylogenomic tree based on conserved single-copy genes in the genomes of your possibly novel bacteria as well as closely-related bacteria taxa (from public databases). A convenient tool to make such a genome-level phylogenetic tree is GToTree (https://github.com/AstrobioMike/GToTree)
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