Phylogenomics of the Phylum Proteobacteria: Resolving the Complex Relationships

Phylogenomics of the Phylum Proteobacteria: Resolving the Complex Relationships

Proteobacteria is one of the largest and phenotypically most diverse divisions within the domain bacteria. Due to the economic importance, this phylum demands an urgent need for a clear and scientifically sound classification system to streamline their characterization. The goal of our study was to...

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Published in:Current microbiology Vol. 79; no. 8; p. 224
Main Authors: Sharma, Vaibhav, Vashishtha, Amit, Jos, Arsha Liz M., Khosla, Akshita, Basu, Nirmegh, Yadav, Rishabh, Bhatt, Amit, Gulani, Akshanshi, Singh, Pushpa, Lakhera, Sanidhya, Verma, Mansi
Format: Journal Article
Language:English
Published: New York Springer US 01-08-2022
Springer Nature B.V
Subjects:
Amino acids
Biomedical and Life Sciences
Biotechnology
Classification
Economic importance
Genes
Genomes
Life Sciences
Microbiology
Phylogenetics
Phylogeny
Proteins
Proteobacteria
Reclassification
rRNA 16S
Trees
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Summary:Proteobacteria is one of the largest and phenotypically most diverse divisions within the domain bacteria. Due to the economic importance, this phylum demands an urgent need for a clear and scientifically sound classification system to streamline their characterization. The goal of our study was to carefully reevaluate the current system of classification and suggest changes wherein necessary. Phylogenetic trees of 84 Proteobacteria were constructed using single gene-based phylogeny involving 16S rRNA genes and protein sequences of 85 conserved genes, whole genome-based phylogenetic tree using CVtree3.0, amino acid Identity matrix tree, and concatenated tree with aforementioned conserved genes. The results of our study confirm the polyphyletic relationship between Desulfurella acetivorans, a Deltaproteobacteria with Epsilonproteobacteria. The group Syntrophobacterales was found to be polyphyletic with respect to Desulfarculus baarsii and the group Thiotrichales was found to be splitting in different phylogenetic trees. Placement of phylogenetic groups belonging to Rhodocyclales , Oceonospirilalles , and Chromatiales is controversial and requires further study and revisions. Based on our analysis, we strongly support reclassification of Magnetococcales as a separate class Etaproteobacteria. From our results, we conclude that concatenated trees of conserved proteins are a more accurate method for phylogenetic analysis, as compared to other methods used.
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ISSN:0343-8651
1432-0991
DOI:10.1007/s00284-022-02910-9