Abstract
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.
Highlights
The Bacteroidetes constitute a cosmopolitan phylum that inhabits a broad array of habitats on Earth
Structural annotation at JGI and DSMZ was done using Prodigal v. 2.6.2 (Hyatt et al, 2010). These annotated genome sequences were processed further as in our previous study using the high-throughput version of the Genome BLAST Distance Phylogeny (GBDP) approach in conjunction with BLAST+ v2.2.30 in blastp mode (Auch et al, 2006; Camacho et al, 2009; Meier-Kolthoff et al, 2014a) and FastME v 2.1.6.1 using the improved neighborjoining algorithm BioNJ for obtaining starting trees followed by branch swapping under the balanced minimum evolution criterion (Desper and Gascuel, 2004) using the subtree-pruningand-regrafting algorithm (Desper and Gascuel, 2006; Lefort et al, 2015)
Since here the 16S rRNA gene is in significant conflict with genome-scale data, which is highly unusual, we propose to include the entire genus Labilibacter in Saccharicrinis in order to allow 16S rRNA gene trees to agree with the taxonomic classification
Summary
The Bacteroidetes constitute a cosmopolitan phylum that inhabits a broad array of habitats on Earth. Bacteroidetes colonize a variety of other natural habitats such as soils, sediments, sea water and freshwater (Thomas et al, 2011), and some even tolerate extreme environmental conditions (Anders et al, 2014). This is reflected in the great metabolic diversity of the phylum, which includes aerobes Striking features of Bacteroidetes are their specialized carbohydrate decomposition machineries, oligosaccharide uptake systems, and storage features that enables them to play a key role in the decomposition of particulate organic matter (Martens et al, 2009; Sonnenburg et al, 2010; Dodd et al, 2011; Fischbach and Sonnenburg, 2011; Thomas et al, 2011; Reintjes et al, 2017; Mathieu et al, 2018)
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