Complete Genome Sequence of blaCTX-M-27-Encoding Escherichia coli Strain H105 of Sequence Type 131 Lineage C1/H30R

Escherichia coli sequence type 131 (ST131) is the most frequent antimicrobial-resistant lineage of E. coli, propagating extended-spectrum ß-lactamases (ESBL) worldwide. Recently, an alarming rate of increase in isolates of the sublineage C1/H30R-blaCTX-M-27 of ST131 in geographically distant countries was reported. Here, we present the complete genome sequence of the ST131 sublineage C1/H30R E. coli isolate harboring blaCTX-M-27 from Germany

Thermococcus bergensis sp. nov., a Novel Hyperthermophilic Starch-Degrading Archaeon

A novel hyperthermophilic archaeon, termed strain T7324T, was isolated from a mixed sulfate-reducing consortium recovered from hot water produced from a deep North Sea oil reservoir. The isolate is a strict anaerobic chemo-organotroph able to utilize yeast extract or starch as a carbon source. The genes for a number of sugar degradation enzymes and glutamate dehydrogenase previously attributed to the sulfate reducing strain of the consortium (Archaeoglobus fulgidus strain 7324) were identified in the nearly completed genome sequence. Sequence analysis of the 16S rRNA gene placed the strain in the Thermococcus genus, but with an average nucleotide identity that is less than 90% to its closest relatives. Phylogenomic treeing reconstructions placed the strain on a distinct lineage clearly separated from other Thermococcus spp. The results indicate that the strain T7324T represents a novel species, for which the name Thermococcus bergensis sp. nov. is proposed. The type strain is T7324T (=DSM 27149T = KCTC 15808T)

Actinopolyspora saharensis sp. nov., a novel halophilic actinomycete isolated from a Saharan soil of Algeria

A novel halophilic actinomycete, strain H32T,was isolated froma Saharan soil sample collected in El-Oued province, south Algeria. The isolate was characterized by means of polyphasic taxonomy. Optimal growth was determined to occur at 28–32°C, pH 6.0–7.0 and in the presence of 15–25 %(w/v) NaCl. The strain was observed to produce abundant aerial mycelium, which formed long chains of rod-shaped spores at maturity, and fragmented substrate mycelium. The cell wall was determined to contain meso-diaminopimelic acid and the characteristic whole-cell sugars were arabinose and galactose. The predominant menaquinoneswere found to beMK-10(H4) andMK-9(H4). The predominant cellular fatty acids were determined to be anteiso C17:0, iso-C15:0 and iso-C16:0. The diagnostic phospholipid detected was phosphatidylcholine. Phylogenetic analyses based on the 16S rRNA gene sequence showed that this strain formed a distinct phyletic line within the radiation of the genus Actinopolyspora. The 16S rRNAgene sequence similarity indicated that strain H32T was most closely related to ‘Actinopolyspora algeriensis’ DSM 45476T (98.8 %) and Actinopolyspora halophila DSM 43834T (98.5 %). Furthermore, the result of DNA–DNA hybridization between strain H32T and the type strains ‘A. algeriensis’ DSM45476T, A. halophila DSM 43834T and Actinopolyspora mortivallis DSM 44261T demonstrated that this isolate represents a different genomic species in the genus Actinopolyspora. Moreover, the physiological and biochemical data allowed the differentiation of strain H32T from its closest phylogenetic neighbours. Therefore, it is proposed that strain H32T represents a novel species of the genus Actinopolyspora, for which the name Actinopolyspora saharensis sp. nov. is proposed. The type strain is H32T (=DSM 45459T=CCUG 62966T)

Actinopolyspora righensis sp. nov., a novel halophilic actinomycete isolated from Saharan soil in Algeria

A novel halophilic actinomycete strain, H23T, was isolated from a Saharan soil sample collected in Djamaˆa (Oued Righ region), El-Oued province, South Algeria. Strain H23T was identified as a member of the genus Actinopolyspora by a polyphasic approach. Phylogenetic analysis showed that strain H23T had 16S rRNA gene sequence similarities ranging from 97.8 % (Actinopolyspora xinjiangensis TRM 40136T) to 94.8 % (Actinopolyspora mortivallis DSM 44261T). The strain grew optimally at pH 6.0–7.0, 28–32°C and in the presence of 15–25 % (w/v) NaCl. The substrate mycelium was well developed and fragmented with age. The aerialmyceliumproduced long, straight or flexuous spore chains with non-motile, smooth-surfaced and rod-shaped spores. Strain H23T had MK-10 (H4) and MK-9 (H4) as the predominant menaquinones. The whole microorganism hydrolysates mainly consisted of meso-diaminopimelic acid, galactose and arabinose. The diagnostic phospholipid detected was phosphatidylcholine. The major cellular fatty acids were anteiso-C17:0 (37.4 %), iso-C17:0 (14.8 %), iso-C15:0 (14.2 %), and iso-C16:0 (13.9 %). The genotypic and phenotypic data show that the strain represents a novel species of the genus Actinopolyspora, for which the name Actinopolyspora righensis sp. nov. is proposed, with the type strain H23T (=DSM 45501T = CCUG 63368T = MTCC 11562T)

Complete Genome Sequence of Raoultella electrica 1GB (DSM 102253T), Isolated from Anodic Biofilms of a Glucose-Fed Microbial Fuel Cell

The type strain Raoultella electrica 1GB (DSM 102253T) was isolated from anodic biofilms of glucose-fed microbial fuel cells. The fully assembled, closed, circular 5.27-Mb genome and corresponding 0.52-Mb plasmid DNA sequences were elucidated. Potential electron transfer and pathogenicity mechanisms were deduced

Actinomadura algeriensis sp. nov., an actinobacterium isolated from Saharan soil

In this study, a hydrophobic synthetic zeolite, namely ZSM-5 is chosen as an adsorbent/catalyst for toluene removal. Experimental results showed that toluene adsorption onto ZSM-5 was favourable, following a Langmuir adsorption isotherm model. ZSM-5 zeolite was regenerated using gaseous ozone at low temperature. Adsorbed toluene was oxidised, releasing mainly CO2 and H2O. Traces of oxidation by-products such as acetic acid and acetaldehyde were formed and remained adsorbed after the oxidativate regeneration with ozone. After four successive cycles of adsorption/ozonation, the adsorption efficiency was not affected (92%–99%). These results showed that volatile organic compound (VOC) removal by adsorption onto ZSM-5 zeolite followed by ozone regeneration could be used as a promising hybrid process for the control of VOC emissions in terms of efficiency

The novel oligopeptide utilizing species Anaeropeptidivorans aminofermentans M3/9T, its role in anaerobic digestion and occurrence as deduced from large-scale fragment recruitment analyses

Research on biogas-producing microbial communities aims at elucidation of correlations and dependencies between the anaerobic digestion (AD) process and the corresponding microbiome composition in order to optimize the performance of the process and the biogas output. Previously, Lachnospiraceae species were frequently detected in mesophilic to moderately thermophilic biogas reactors. To analyze adaptive genome features of a representative Lachnospiraceae strain, Anaeropeptidivorans aminofermentans M3/9T was isolated from a mesophilic laboratory-scale biogas plant and its genome was sequenced and analyzed in detail. Strain M3/9T possesses a number of genes encoding enzymes for degradation of proteins, oligo- and dipeptides. Moreover, genes encoding enzymes participating in fermentation of amino acids released from peptide hydrolysis were also identified. Based on further findings obtained from metabolic pathway reconstruction, M3/9T was predicted to participate in acidogenesis within the AD process. To understand the genomic diversity between the biogas isolate M3/9T and closely related Anaerotignum type strains, genome sequence comparisons were performed. M3/9T harbors 1,693 strain-specific genes among others encoding different peptidases, a phosphotransferase system (PTS) for sugar uptake, but also proteins involved in extracellular solute binding and import, sporulation and flagellar biosynthesis. In order to determine the occurrence of M3/9T in other environments, large-scale fragment recruitments with the M3/9T genome as a template and publicly available metagenomes representing different environments was performed. The strain was detected in the intestine of mammals, being most abundant in goat feces, occasionally used as a substrate for biogas production.Peer Reviewe

Genomic and transcriptomic characterization of Pseudomonas aeruginosa small colony variants derived from a chronic infection model

Phenotypic change is a hallmark of bacterial adaptation during chronic infection. In the case of chronic Pseudomonas aeruginosa lung infection in patients with cystic fibrosis, well-characterized phenotypic variants include mucoid and small colony variants (SCVs). It has previously been shown that SCVs can be reproducibly isolated from the murine lung following the establishment of chronic infection with mucoid P. aeruginosa strain NH57388A. Using a combination of single-molecule real-time (PacBio) and Illumina sequencing we identify a large genomic inversion in the SCV through recombination between homologous regions of two rRNA operons and an associated truncation of one of the 16S rRNA genes and suggest this may be the genetic switch for conversion to the SCV phenotype. This phenotypic conversion is associated with large-scale transcriptional changes distributed throughout the genome. This global rewiring of the cellular transcriptomic output results in changes to normally differentially regulated genes that modulate resistance to oxidative stress, central metabolism and virulence. These changes are of clinical relevance because the appearance of SCVs during chronic infection is associated with declining lung function

Actinomadura adrarensis sp. nov., an actinobacterium isolated from Saharan soil

A novel actinobacterial strain, designated ACD12T, was isolated from a Saharan soil sample collected from Adrar province, southern Algeria. A polyphasic study was carried out to establish the taxonomic position of this strain. Strain ACD12T was observed to form extensively branched substrate mycelia. Aerial mycelium was absent or was weakly produced on all media tested, while spore chains were short with a hooked and irregular spiral form (2–3 turns). The dominant diaminopimelic acid isomer in the cell wall was meso-diaminopimelic acid. Glucose, ribose, galactose, mannose and madurose occured in whole-cell hydrolysates. The major phospholipid was diphosphatidylglycerol and phosphatidylinositol. The predominant menaquinone was MK-9(H6). The fatty acid profile was characterized by the presence of C16 : 0, C17 : 0, C15 : 0, C18 : 0, C18 : 1 cis9 and iso-C16 : 0. Results of 16S rRNA gene sequence comparisons revealed that strain ACD12T shared the highest degree of 16S rRNA gene sequence similarity with Actinomadura sputi DSM 45233T (98.3 %) and Actinomadura hallensis DSM 45043T (97.8 %). All tree-making algorithms used also supported strain ACD12T forming a distinct clade with its most closely related species. In addition, DNA–DNA hybridization indicated only 39.8 % relatedness with A. sputi DSM 45233T and 18.7 % relatedness with A. hallensis DSM 45043T. The combined phenotypic and genotypic data show that the novel isolate represents a novel species of the genus Actinomadura , for which the name Actinomadura adrarensis sp. nov., is proposed, with the type strain ACD12T (=DSM 46745T =CECT 8842T)

Next Generation DNA-Seq and Differential RNA-Seq Allow Re-annotation of the Pyrococcus furiosus DSM 3638 Genome and Provide Insights Into Archaeal Antisense Transcription

Pyrococcus furiosus DSM 3638 is a model organism for hyperthermophilic archaea with an optimal growth temperature near 100 degrees C. The genome was sequenced about 18 years ago. However, some publications suggest that in contrast to other Pyrococcus species, the genome of P. furiosus DSM 3638 is prone to genomic rearrangements. Therefore, we re-sequenced the genome using third generation sequencing techniques. The new de novo assembled genome is 1,889,914 bp in size and exhibits high sequence identity to the published sequence. However, two major deviations were detected: (1) The genome is 18,342 bp smaller than the NCBI reference genome due to a recently described deletion. (2) The region between PF0349 and PF0388 is inverted most likely due an assembly problem for the original sequence. In addition, numerous minor variations, ranging from single nucleotide exchanges, deletions or insertions were identified. The total number of insertion sequence (IS) elements is also reduced from 30 to 24 in the new sequence. Re-sequencing of a 2-year-old "lab culture" using Nanopore sequencing confirmed the overall stability of the P furiosus DSM 3638 genome even under normal lab conditions without taking any special care. To improve genome annotation, the updated DNA sequence was combined with an RNA sequencing approach. Here, RNAs from eight different growth conditions were pooled to increase the number of detected transcripts. Furthermore, a differential RNA-Seq approach was employed for the identification of transcription start sites (TSSs). In total, 2515 TSSs were detected and classified into 834 primary (pTSS), 797 antisense (aTSS), 739 internal and 145 secondary TSSs. Our analysis of the upstream regions revealed a well conserved archaeal promoter structure. Interrogation of the distances between pTSSs and aTSSs revealed a significant number of antisense transcripts, which are a result of bidirectional transcription from the same TATA box. This mechanism of antisense transcript production could be further confirmed by in vitro transcription experiments. We assume that bidirectional transcription gives rise to non-functional antisense RNAs and that this is a widespread phenomenon in archaea due to the architecture of the TATA element and the symmetric structure of the TATA-binding protein