Complete Genome Sequence of Achromobacter denitrificans PR1

Reis, Ana C.; Kroll, Kevin J.; Gomila, Margarita; Kolvenbach, Boris A.; Corvini, Philippe F.-X.; Nunes, Olga C.

doi:10.1128/genomea.00762-17

Cited by 12 publications

(5 citation statements)

References 22 publications

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“…The reconstruction of strain GP’s genome from whole-consortium sequencing generated a metagenome-assembled genome (MAG) consisting of 11 contigs, with 3.84 Mb, 3621 coding sequences (CDS), 69.68% in G + C and a total mapped coverage of 61x (Table 1). In spite of an enrichment step with 2-phenylethanol, only 18.5% of the total of reads obtained with Oxford Nanopore (ONT) and Illumina technologies were mapped to strain’s GP MAG, while the remaining reads mapped to the complete genome of A. denitrificans PR1 (148x coverage in the consortium, see Additional file 2 Table S1), previously determined [35]. The MAG of strain GP encoded a complete rRNA operon and harbored two copies of the 5S and one copy of the 16S and 23S rRNA subunits, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…The metagenome was aligned to the complete genome of strain PR1 (Genbank accession no. CP020917) [35] with BLASTn v2.7.1+ to remove contigs affiliated to the proteobacterium [108] (e-value, identity and hit length threshold cutoffs set to 1e-10, 80 and 30%, respectively). Contigs without significant hits were retrieved from the metagenome and used to construct the new taxonomic bin corresponding to strain GP.…”

Section: Methodsmentioning

confidence: 99%

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Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader ‘Candidatus Leucobacter sulfamidivorax’ strain GP

et al. 2019

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BackgroundMicrobial communities recurrently establish metabolic associations resulting in increased fitness and ability to perform complex tasks, such as xenobiotic degradation. In a previous study, we have described a sulfonamide-degrading consortium consisting of a novel low-abundant actinobacterium, named strain GP, and Achromobacter denitrificans PR1. However, we found that strain GP was unable to grow independently and could not be further purified.ResultsPrevious studies suggested that strain GP might represent a new putative species within the Leucobacter genus (16S rRNA gene similarity < 97%). In this study, we found that average nucleotide identity (ANI) with other Leucobacter spp. ranged between 76.8 and 82.1%, further corroborating the affiliation of strain GP to a new provisional species. The average amino acid identity (AAI) and percentage of conserved genes (POCP) values were near the lower edge of the genus delimitation thresholds (65 and 55%, respectively). Phylogenetic analysis of core genes between strain GP and Leucobacter spp. corroborated these findings. Comparative genomic analysis indicates that strain GP may have lost genes related to tetrapyrrole biosynthesis and thiol transporters, both crucial for the correct assembly of cytochromes and aerobic growth. However, supplying exogenous heme and catalase was insufficient to abolish the dependent phenotype. The actinobacterium harbors at least two copies of a novel genetic element containing a sulfonamide monooxygenase (sadA) flanked by a single IS1380 family transposase. Additionally, two homologs of sadB (4-aminophenol monooxygenase) were identified in the metagenome-assembled draft genome of strain GP, but these were not located in the vicinity of sadA nor of mobile or integrative elements.ConclusionsComparative genomics of the genus Leucobacter suggested the absence of some genes encoding for important metabolic traits in strain GP. Nevertheless, although media and culture conditions were tailored to supply its potential metabolic needs, these conditions were insufficient to isolate the PR1-dependent actinobacterium further. This study gives important insights regarding strain GP metabolism; however, gene expression and functional studies are necessary to characterize and further isolate strain GP. Based on our data, we propose to classify strain GP in a provisional new species within the genus Leucobacter, ‘Candidatus Leucobacter sulfamidivorax‘.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader ‘Candidatus Leucobacter sulfamidivorax’ strain GP

et al. 2019

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“…Not to forget fundamental applications for long-read sequencing studies, such as de novo genome assembly, improvement of existing genome assemblies, and discovery of structural variants and long repeats [13–16]. ONT sequencing is favorable for microbiology research as small-sized bacterial genomes can be covered in just one MinION read [17, 18], thus providing high resolution in genome architecture.…”

Section: Introductionmentioning

confidence: 99%

NanoPipe—a web server for nanopore MinION sequencing data analysis

et al. 2019

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Background The fast-moving progress of the third-generation long-read sequencing technologies will soon bring the biological and medical sciences to a new era of research. Altogether, the technique and experimental procedures are becoming more straightforward and available to biologists from diverse fields, even without any profound experience in DNA sequencing. Thus, the introduction of the MinION device by Oxford Nanopore Technologies promises to “bring sequencing technology to the masses” and also allows quick and operative analysis in field studies. However, the convenience of this sequencing technology dramatically contrasts with the available analysis tools, which may significantly reduce enthusiasm of a “regular” user. To really bring the sequencing technology to every biologist, we need a set of user-friendly tools that can perform a powerful analysis in an automatic manner. Findings NanoPipe was developed in consideration of the specifics of the MinION sequencing technologies, providing accordingly adjusted alignment parameters. The range of the target species/sequences for the alignment is not limited, and the descriptive usage page of NanoPipe helps a user to succeed with NanoPipe analysis. The results contain alignment statistics, consensus sequence, polymorphisms data, and visualization of the alignment. Several test cases are used to demonstrate the efficiency of the tool. Conclusions Freely available NanoPipe software allows effortless and reliable analysis of MinION sequencing data for experienced bioinformaticians, as well for wet-lab biologists with minimum bioinformatics knowledge. Moreover, for the latter group, we describe the basic algorithm necessary for MinION sequencing analysis from the first to last step.

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“…Achromobacter denitrificans is a ubiquitous gram-negative bacterium. [ 1 ] Metabolically, it is a strictly aerobic, non-fermenting, mobile, catalase-positive and oxidase-positive bacterium. [ 2 ] A. denitrificans inhabit soils and aquatic environments, including well water, intravenous fluids and water in humidifiers, occasionally being part of the normal flora of some parts of the body and rarely a causal agent of human infections.…”

mentioning

confidence: 99%

“…[ 2 ] A. denitrificans inhabit soils and aquatic environments, including well water, intravenous fluids and water in humidifiers, occasionally being part of the normal flora of some parts of the body and rarely a causal agent of human infections. [ 1 2 ] Here, we present the first case of central venous catheter-related bacteraemia on hemodialysis due to A. denitrificans .…”

mentioning

confidence: 99%