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.

/pdf/analysis-of-1-000-type-strain-genomes-improves-taxonomic-345doatvi9.pdf

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes .

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.

/pdf/genome-based-taxonomic-classification-of-bacteroidetes-5y671uumne.pdf

Genome-Based Taxonomic Classification of Bacteroidetes.

Calcium precipitate induced aerobic granulation.

A Gram-stain-negative, rod-shaped, non-motile and yellow-pigmented bacterial strain, designated strain JJ013T, was isolated from an artificial lake in Jeollabuk-do, South Korea, and characterized using a polyphasic approach. The 16S rRNA gene sequence of strain JJ013T indicated that the isolate belonged to the family 
Flavobacteriaceae
and exhibited similarity levels of 96.6 % to the type strains of 
Flavobacterium cheonanense
and 
Flavobacterium koreense
and 96.5 % to the type strain of 
Flavobacterium chungnamense
. Growth was observed at 20–30 °C and pH 5.0–7.0. The major cellular fatty acids of the novel strain were iso-C15 : 0 (27.5 %), iso-C15 : 1 G (17.8 %), iso-C17 : 0 3-OH (9.4 %) and iso-C15 : 0 3-OH (9.2 %). Flexirubin-type pigments were present. The DNA G+C content of strain JJ013T was 33.9 mol%, the major respiratory quinone was menaquinone-6 (MK-6) and the major polyamine was sym-homospermidine. The polar lipid profile of the strain JJ013T consisted of a phosphatidylethanolamine (PE), two unknown aminolipids (AL1–2), three unidentified lipid (L1–3) and an unknown glycolipid (GL). On the basis of the morphological and physiological properties and biochemical evidence presented, it is concluded that strain JJ013T represents a novel species of the genus 
Flavobacterium
, for which the name Flavobacterium aciduliphilum sp. nov. is proposed; the type strain is JJ013T ( = KACC 16594T = JCM 18211T). Since C15 : 0, which is known as a predominant fatty acid of the genus 
Flavobacterium
was not detected in the novel strain and other reference strains, we propose an emended description of the genus 
Flavobacterium
.

Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium

On the Gram-Differentiation of Bacteria by the Simplest Method. III. The Sulfuric Acid Methods.

A Gram-negative, strictly aerobic, yellow-pigmented rod, designated DK69T, was isolated from soil collected from the waste liquid treatment facility of Bafeng Pharmaceutical Company in the city of Enshi, Hubei Province, China. Phylogenetic analysis based on 16S rRNA gene sequences placed strain DK69T in the genus 
Flavobacterium
of the family 
Flavobacteriaceae
. The highest 16S rRNA gene sequence similarities were found with 
Flavobacterium cauense
R2A-7T (96.9 %), 
Flavobacterium saliperosum
AS 1.3801T (96.3 %) and 
Flavobacterium suncheonense
GH29-5T (95.7 %). The major fatty acids (≥5 %) were iso-C15 : 0, iso-C17 : 1ω9c, C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The major respiratory quinone was menaquinone-6. The genomic DNA G+C content was 34.4 mol%. Strain DK69T represents a novel species of the genus 
Flavobacterium
, for which the name Flavobacterium enshiense sp. nov. is proposed. The type strain is DK69T ( = CCTCC AB 2011144T  = KCTC 23775T). Emended descriptions of the genus 
Flavobacterium
and 
Flavobacterium cauense
, 
Flavobacterium saliperosum
and 
Flavobacterium suncheonense
are also proposed.

Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense, Flavobacterium saliperosum and Flavobacterium suncheonense

A strictly aerobic, Gram-staining-negative, rod-shaped, non-motile, yellow-pigmented bacterial strain, designated BX12T, was isolated from soil collected from the peak area of Wudang Mountain in the city of Shiyan, Hubei province, China. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain BX12T was most closely related to 
Flavobacterium subsaxonicum
WB 4.1-42T (95.9 % 16S rRNA gene sequence similarity), followed by 
Flavobacterium beibuense
F44-8T (95.6 %) and 
Flavobacterium rivuli
WB 3.3-2T (94.1 %). The major fatty acids (≥5 %) of strain BX12T were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0, C16 : 0, iso-C17 : 0 3-OH, and C16 : 0 3-OH. The major polar lipid was phosphatidylethanolamine, and the major respiratory quinone was menaquinone-6. The genomic DNA G+C content was 43.9 mol%. On the basis of a high number of phenotypic differentiating properties and phylogenetic uniqueness, strain BX12T represents a novel species of the genus 
Flavobacterium
for which the name 
Flavobacterium
hauense sp. nov. is proposed. The type strain is BX12T ( = CCTCC AB 2012197T = KCTC 32147T). Emended descriptions of 
Flavobacterium subsaxonicum
, 
Flavobacterium beibuense
and 
Flavobacterium rivuli
are also proposed.

Flavobacterium hauense sp. nov., isolated from soil and emended descriptions of Flavobacterium subsaxonicum, Flavobacterium beibuense and Flavobacterium rivuli

A Gram-stain-positive, aerobic, non-motile, rod-shaped bacterium, designated strain CF5-4(T), was isolated from iron mining powder. 16S rRNA gene sequence analysis grouped strain CF5-4(T) in a single cluster with Actinotalea fermentans DSM 3133(T) (97.6% similarity). The major fatty acids (>5%) of strain CF5-4(T) were anteiso-C(15:0), anteiso-C(15:1) A, C(16:0), iso-C(16:0), iso-C(15:0) and anteiso-C(17:0). The predominant respiratory quinone was MK-10(H₄) and the genomic DNA G+C content was 74.7 mol%. The major polar lipids were diphosphatidylglycerol and one unidentified phosphoglycolipid. The peptidoglycan type of strain CF5-4(T) was A4β, containing L-Orn-D-Ser-D-Asp. The cell-wall sugars were rhamnose, fucose, mannose and galactose. The results of DNA-DNA hybridization in combination with the comparison of phenotypic and phylogenetic characteristics among strain CF5-4(T) and related micro-organisms revealed that the isolate represents a novel species of the genus Actinotalea, for which the name Actinotalea ferrariae sp. nov. is proposed. The type strain is CF5-4(T) ( =KCTC 29134(T) =CCTCC AB2012198(T)).

Actinotalea ferrariae sp. nov., isolated from an iron mine, and emended description of the genus Actinotalea

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Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense, Flavobacterium saliperosum and Flavobacterium suncheonense

Flavobacterium hauense sp. nov., isolated from soil and emended descriptions of Flavobacterium subsaxonicum, Flavobacterium beibuense and Flavobacterium rivuli

Actinotalea ferrariae sp. nov., isolated from an iron mine, and emended description of the genus Actinotalea