The First Insights into the Phylogeny, Genomics, and Ecology of the Novel Bacterial Phylum Armatimonadetes
type: CreativeWork
description: Currently, a large proportion of novel microbial evolutionary lineages is poorly understood due to limited coverage of representative species. These “candidate” lineages represent significant gaps in our understanding of microbial function and ecology. This study focused on Chthonomonas calidirosea, the earliest isolated species within Armatimonadetes, the most recently-recognised bacterial phylum. The overall aim of this research was to start to understand the ecology and phylogeny of Armatimonadetes, and provide a foundation for future research into the phylum, with the benefit of narrowing the current knowledge gaps on microbial diversity. This was achieved by integrating multiple data types (phylogenetics, genomics, and community profiling metagenomics). The initial stage of this research aimed to address and clarify conflicts in reported phylogeny of the phylum Armatimonadetes. This study generated a comprehensive reference phylogenetic tree of 16S rRNA genes for the phylum, so that the phylogenetic position of newly-identified phylotypes can be reliably associated across studies. Multiple robust statistical methods were used to arrive at a consensus on the partitioning of classes and neighbouring phyla. The process also helped to identify and exclude candidate phyla previously misattributed to Armatimonadetes, thus better defining the phylum for future studies. The deeply-branching phylogenetic relationship of Armatimonadetes with other bacterial phyla was resolved by the sequencing of C. calidirosea T49T genome and analysing concatenated amino acid sequences of conserved genes against homologs in other prokaryotic genomes. The phylogenomic analysis showed Chloroflexi to be the most closely related formal phylum to Armatimonadetes. This publication was the first analysis of a genome from the phylum Armatimonadetes, and provided evolutionarily- and genetically-distinct insights to the overall knowledge of microbial genetic diversity. Analysis of the genome show…
abstract: Currently, a large proportion of novel microbial evolutionary lineages is poorly understood due to limited coverage of representative species. These “candidate” lineages represent significant gaps in our understanding of microbial function and ecology. This study focused on Chthonomonas calidirosea, the earliest isolated species within Armatimonadetes, the most recently-recognised bacterial phylum. The overall aim of this research was to start to understand the ecology and phylogeny of Armatimonadetes, and provide a foundation for future research into the phylum, with the benefit of narrowing the current knowledge gaps on microbial diversity. This was achieved by integrating multiple data types (phylogenetics, genomics, and community profiling metagenomics). The initial stage of this research aimed to address and clarify conflicts in reported phylogeny of the phylum Armatimonadetes. This study generated a comprehensive reference phylogenetic tree of 16S rRNA genes for the phylum, so that the phylogenetic position of newly-identified phylotypes can be reliably associated across studies. Multiple robust statistical methods were used to arrive at a consensus on the partitioning of classes and neighbouring phyla. The process also helped to identify and exclude candidate phyla previously misattributed to Armatimonadetes, thus better defining the phylum for future studies. The deeply-branching phylogenetic relationship of Armatimonadetes with other bacterial phyla was resolved by the sequencing of C. calidirosea T49T genome and analysing concatenated amino acid sequences of conserved genes against homologs in other prokaryotic genomes. The phylogenomic analysis showed Chloroflexi to be the most closely related formal phylum to Armatimonadetes. This publication was the first analysis of a genome from the phylum Armatimonadetes, and provided evolutionarily- and genetically-distinct insights to the overall knowledge of microbial genetic diversity. Analysis of the genome show…
author: Lee, Chien-Yu Kevin
keywords: Microbiology, Microbial Ecology, Candidate Division, Genomics, Comparative Genomics, Phylogeny, Armatimonadetes, OP10, Chthonomonas calidirosea, Chthonomonadetes
license: https://researchcommons.waikato.ac.nz/bitstreams/a2688808-8867-47ca-89b9-892eaf3a1358/download
date published: 2015
date modified: 2026-07-24T05:57:46Z
provider: University Waikato
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: University of Waikato