Permanent draft genome sequence of Comamonas testosteroni KF-1

Weiss, Michael J.; Kesberg, Anna-Isabella; LaButti, Kurt; Pitluck, Sam; Bruce, David; Hauser, Loren; Copeland, Alex; Woyke, Tanja; Lowry, Stephen R.; Lucas, Susan; Land, Miriam; Goodwin, Lynne; Kjelleberg, Staffan; Cook, Alasdair M.; Buhmann, Matthias T.; Thomas, Torsten; Schleheck, David

doi:10.4056/sigs.3847890

Cited by 14 publications

(27 citation statements)

References 98 publications

(119 reference statements)

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“…They found that the glycolysis is incomplete due to lack of the hexokinase and glucokinase genes so that the strain cannot utilize most types of sugars. Studies on the genomes of C. testosteroni strains ATCC 11996 [ 22 ] and KF-1 [ 23 ] showed the same results. We built metabolic pathway maps of 14 strains of C. testosteroni (including above strains) and showed that all genes for hexose phosphorylation were missed in all genomes of this species (Figure 6 ).…”

Section: Discussionmentioning

confidence: 68%

“…The draft sequences were submitted to GenBank Whole Genome Shotgun (WGS) database [ 27 ] and the accession numbers are shown in Table 1 . Genome sequences of four other C. testoteroni strains, CNB-2 [ 5 ], ATCC 11996 [ 22 ], KF-1 [ 23 ] and S44 [ 6 ] (Table 1 ) were obtained from the NCBI database. Genome sequences of eight strains of the Comamonadaceae family were also obtained from the NCBI database (Additional file 2 : Table S2).…”

Section: Methodsmentioning

confidence: 99%

“…Gong et al [ 22 ] sequenced the genome of the type strain of C. testosteroni ATCC 11996. Weiss et al [ 23 ] sequenced the genome of strain KF-1, and found genes for degradation of aromatic compounds such as a gene cluster for PCA 4,5-cleavage and a gene cluster for isophthalate degradation. In our previous study, a multiple heavy-metal resistant strain named C. testosteroni S44 was isolated and its genome was sequenced [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

“…Recently, we have identified ten C. testosteroni strains from different mining soils [ 24 , 25 ] according to the 16S rRNA gene and physiological and biochemical analysis . In order to gain a comprehensive genotypic and phonotypic understanding, we sequenced the ten C. testosteroni strains and analyzed them together with the four published C. testosteroni genomes [ 5 , 6 , 22 , 23 ]. This study is a first comparative genomic analysis for C. testosteroni strains.…”

Section: Introductionmentioning

confidence: 99%

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High correlation between genotypes and phenotypes of environmental bacteria Comamonas testosteroni strains

et al. 2015

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BackgroundMembers of Comamonas testosteroni are environmental microorganisms that are usually found in polluted environment samples. They utilize steroids and aromatic compounds but rarely sugars, and show resistance to multiple heavy metals and multiple drugs. However, comprehensive genomic analysis among the C. testosteroni strains is lacked.ResultsTo understand the genome bases of the features of C. testosteroni, we sequenced 10 strains of this species and analyzed them together with other related published genome sequences. The results revealed that: 1) the strains of C. testosteroni have genome sizes ranging from 5.1 to 6.0 Mb and G + C contents ranging from 61.1% to 61.8%. The pan-genome contained 10,165 gene families and the core genome contained 3,599 gene families. Heap’s law analysis indicated that the pan-genome of C. testosteroni may be open (α = 0.639); 2) by analyzing 31 phenotypes of 11 available C. testosteroni strains, 99.4% of the genotypes (putative genes) were found to be correlated to the phenotypes, indicating a high correlation between phenotypes and genotypes; 3) gene clusters for nitrate reduction, steroids degradation and metal and multi-drug resistance were found and were highly conserved among all the genomes of this species; 4) the genome similarity of C. testosteroni may be related to the geographical distances.ConclusionsThis work provided an overview on the genomes of C. testosteroni and new genome resources that would accelerate the further investigations of this species. Importantly, this work focused on the analysis of potential genetic determinants for the typical characters and found high correlation between the phenotypes and their corresponding genotypes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1314-x) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 68%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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High correlation between genotypes and phenotypes of environmental bacteria Comamonas testosteroni strains

et al. 2015

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“…A taxonomic study using a polyphasic approach placed B. chironomi strain AIMA4 T in the genus Brachymonas within the family Comamonadaceae (Figure 1 ). The family Comamonadaceae comprises a larger number of genera (as shown in Figure 1 ) and a larger variety of species and phenotypes [ 15 ],[ 16 ].…”

Section: Organism Informationmentioning

confidence: 99%

High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass

Laviad

Lapidus

Han

et al. 2015

Stand in Genomic Sci

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Brachymonas chironomi strain AIMA4T (Halpern et al., 2009) is a Gram-negative, non-motile, aerobic, chemoorganotroph bacterium. B. chironomi is a member of the Comamonadaceae, a family within the class Betaproteobacteria. This species was isolated from a chironomid (Diptera; Chironomidae) egg mass, sampled from a waste stabilization pond in northern Israel. Phylogenetic analysis based on the 16S rRNA gene sequences placed strain AIMA4T in the genus Brachymonas. Here we describe the features of this organism, together with the complete genome sequence and annotation. The DNA GC content is 63.5%. The chromosome length is 2,509,395 bp. It encodes 2,382 proteins and 68 RNA genes. Brachymonas chironomi genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

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Mechanisms and high-value applications of phthalate isomers degradation pathways in bacteria

Lequan,

Yanan,

Xianda

et al. 2024

World J Microbiol Biotechnol

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Permanent draft genome sequence of Comamonas testosteroni KF-1

Cited by 14 publications

References 98 publications

High correlation between genotypes and phenotypes of environmental bacteria Comamonas testosteroni strains

High correlation between genotypes and phenotypes of environmental bacteria Comamonas testosteroni strains

High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass

Mechanisms and high-value applications of phthalate isomers degradation pathways in bacteria

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