Draft Whole-genome Sequence Research Articles

Draft Genome Sequence of Streptococcus suis S10, a Virulent Strain Used in Experimental Pig Infections.

Here, we report the draft whole-genome sequence of Streptococcus suis strain S10, isolated from the tonsils of a healthy pig. S. suis S10 belongs to the highly virulent serotype 2, which includes isolates that cause infectious diseases, including meningitis, in pigs and human. The genome contains a complete prophage that encodes a candidate virulence gene.

Whole-Genome Sequences of Salmonella enterica Serovar I 4,[5],12:i:- Isolates from Swine.

Salmonella enterica (non-Typhi) is one of the top five pathogens causing enteric infections worldwide. Draft whole-genome sequences of multidrug-resistant (MDR) Salmonella enterica serovar I 4,[5],12:i:- isolates from swine tissue samples collected at slaughter were evaluated for antimicrobial resistance genotypes. In recent years, Salmonella enterica serovar I 4,[5],12:i:- has increased in prevalence in humans and animals and has been linked to the consumption of contaminated pork.

Draft Whole-Genome Sequences of Three Isolates of a Novel Strain of a Campylobacter sp. Isolated from New Zealand Birds and Water.

Campylobacter spp. are frequently found associated with the avian intestinal tract. Most are commensals, but some can cause human campylobacteriosis. Here, we report the draft genome sequences of three strains of a novel Campylobacter sp. isolated from urban birds and a rural river in New Zealand.

Draft Genome Sequence of Bacillus lehensis M136, Isolated from the Manleluag Hyperalkaline Spring in Pangasinan, Philippines.

Here, we report the draft whole-genome sequence of Bacillus lehensis M136, isolated from a hyperalkaline spring located in Pangasinan, Philippines. From 24 scaffolds, the total genome assembly length is 3,985,437 bp. Industrially important genes like cyclodextrin glycosyltransferase (CGTase) and proteases were detected in this draft genome.

Draft Whole-Genome Sequence of the Green Sulfur Photosynthetic Bacterium Chlorobaculum sp. Strain 24CR, Isolated from the Carmel River.

Green sulfur bacteria are in the family Chlorobiaceae, which is composed of four distinct genera, namely, Chlorobaculum, Chlorobium, Prosthecochloris, and Chloroherpeton, with Chlorobium species being the most commonly represented in genome studies. We have now sequenced only the fourth species of Chlorobaculum, which established Chlorobaculum sp. 24CR as a separate species and should help characterize the genus.

Characterisation of the microbiome for two hexactinellid sponges and purification of associated antimicrobial agents from their resident microbes

The imminent threat of antimicrobial resistance has necessitated that the search for novel antimicrobials be widened to lesser-explored environments. Marine and freshwater sponges have emerged as the most prolific source of such compounds over the last decade, representing the most widely sampled phyla in the hunt for novel biologics over the last 45 years. Most of the work however has focused on sponges from shallow waters, with the deep-sea sponge microbiome highlighted as a major source of untapped antimicrobial potential. Optimisation of bacterial recovery was carried out for two previously unstudied species of deep-sea Hexactinellid sponge species (Pheronema carpenteri and Rhabdodictyum delicatum recovered from the Rockall Trough, North Atlantic), using a variety of culture media, supplementation and environmental conditions. This optimisation was carried out in parallel with 16S rDNA metagenomic sequencing in order to determine community composition for both sponge species (IonTorrent, Life Technologies). All recovered isolates were assayed for antimicrobial activity, forming a panel of ‘active’ organisms. Two isolates (Ph16-28; A11) were selected for downstream purification and characterisation of the responsible antimicrobial agent via column chromatography. Isolate identities are currently being confirmed via draft whole-genome sequencing (MinION, Oxford Nanopore), and are suspected to be members of the Bacillus and Streptomyces genera. Current data provides a working axiom for the cultivation of deep-sea sponge microbes and suggests the deep-sea sponge microbiome to be a promising source for novel antimicrobials.

Draft Genome Sequence of a Clostridium botulinum Isolate from Thailand Harboring the Subtype bont/B8 Gene.

In 2010, a Clostridium botulinum type B isolate was recovered from fermented soybeans during a foodborne botulism investigation. Molecular investigation of the botulinum neurotoxin (bont) gene operon determined that the sequence was a new subtype, denoted B8. Here, we describe the draft whole-genome sequence of the organism.

Draft Whole-Genome Sequences of 10 Atypical Enteropathogenic Escherichia coli Strains Isolated in Brazil.

The number of diarrhea cases caused by atypical enteropathogenic Escherichia coli (aEPEC) has been increasing worldwide. Here, we report the draft whole-genome sequences of 10 aEPEC strains isolated in Brazil. These sequences will provide an important source for future studies concerning aEPEC pathogenicity and genetic markers of potentially virulent strains.

Draft Whole-Genome Sequences of Five Klebsiella pneumoniae Isolates from the Subantarctic Islands of New Zealand.

Klebsiella pneumoniae is a Gram-negative bacterium that can be found in the environment, as well as on mucosal surfaces of humans and animals. Here, we report the genome sequence of five K. pneumoniae isolates from substrate samples and bird feces collected in the Subantarctic Islands of New Zealand.

Draft Whole-Genome Sequences of Seven Isolates of Klebsiella pneumoniae from New Zealand Sea Lions.

Klebsiella pneumoniae is a Gram-negative bacterium that may cause infection in a broad range of hosts. We report here the genome sequences of seven K. pneumoniae isolates from New Zealand sea lions.

Draft Genome Assembly of a Potentially Zoonotic Cryptosporidium parvum Isolate, UKP1.

Cryptosporidium parvum is a zoonotic protozoan parasite that causes food and waterborne gastrointestinal disease and whose major animal reservoirs are cattle and small ruminants. We report here on a draft whole-genome sequence of a zoonotic isolate of C. parvum isolated from a person with cryptosporidiosis.

Genome mining of 2-phenylethanol biosynthetic genes from Enterobacter sp. CGMCC 5087 and heterologous overproduction in Escherichia coli

Background2-Phenylethanol (2-PE) is a higher aromatic alcohol that is widely used in the perfumery, cosmetics, and food industries and is also a potentially valuable next-generation biofuel. In our previous study, a new strain Enterobacter sp. CGMCC 5087 was isolated to produce 2-PE from glucose through the phenylpyruvate pathway.ResultsIn this study, candidate genes for 2-PE biosynthesis were identified from Enterobacter sp. CGMCC 5087 by draft whole-genome sequence, metabolic engineering, and shake flask fermentation. Subsequently, the identified genes encoding the 2-keto acid decarboxylase (Kdc) and alcohol dehydrogenase (Adh) enzymes from Enterobacter sp. CGMCC 5087 were introduced into E. coli BL21(DE3) to construct a high-efficiency microbial cell factory for 2-PE production using the prokaryotic phenylpyruvate pathway. The enzymes Kdc4427 and Adh4428 from Enterobacter sp. CGMCC 5087 showed higher performances than did the corresponding enzymes ARO10 and ADH2 from Saccharomyces cerevisiae, respectively. The E. coli cell factory was further improved by overexpressing two upstream shikimate pathway genes, aroF/aroG/aroH and pheA, to enhance the metabolic flux of the phenylpyruvate pathway, which resulted in 2-PE production of 260 mg/L. The combined overexpression of tktA and ppsA increased the precursor supply of erythrose-4-phosphate and phosphoenolpyruvate, which resulted in 2-PE production of 320 mg/L, with a productivity of 13.3 mg/L/h.ConclusionsThe present study achieved the highest titer of de novo 2-PE production of in a recombinant E. coli system. This study describes a new, efficient 2-PE producer that lays foundation for the industrial-scale production of 2-PE and its derivatives in the future.

Insight into the draft whole-genome sequence of the dermatophyte Arthroderma vanbreuseghemii

Next-generation technologies have prompted efforts towards generating a large repertoire of whole-genome sequences. The dermatophyte Arthroderma vanbreuseghemii has been considered as a good model in which to conduct molecular biological studies on this fungal group. Despite the considerable repertoire of molecular tools developed for this fungus, the lack of genomic data has represented a major limitation, preventing effective implementation of those tools. Herein, the authors report the first draft whole-genome sequence of this dermatophytic species. The size of the draft genome was 23 Mb, exhibiting a GC content of 48.1%. Given the significance of secreted proteases in tissue invasion, a comparative analysis of genes encoding extracellular proteases was performed between A. vanbreuseghemii and other dermatophytes. Furthermore, genes that might be involved in DNA repair also were compared among dermatophytes. Moreover, the complete mitochondrial genome of A. vanbreuseghemii was obtained and shown to consist of 24,287 bp with a GC content of 24%. In conclusion, the availability of genomic data for A. vanbreuseghemii is expected to facilitate the implementation of the molecular tools established for this fungus, enhancing our understanding of the biology of dermatophytes.

Draft Whole-Genome Sequences of Seven Listeria monocytogenes Strains with Variations in Virulence and Stress Responses.

Listeria monocytogenes is an important foodborne pathogen that causes listeriosis. Here, we report the draft genome sequences of seven L. monocytogenes strains isolated from food, environmental, and clinical sources. Sequence differences at the genome level may help in understanding why these strains displayed different virulence and stress response characteristics.

Draft Whole-Genome Sequence of Leishmania (Viannia) braziliensis Presenting Leishmania RNA Virus 1, from Western Amazon, Brazil.

Leishmania (Viannia) braziliensis is the main etiological agent of tegumentary leishmaniasis in the neotropics. Here, we report a draft genome sequence (31.2 Mb) of an L. braziliensis strain from the western Amazon region of Brazil. This genome sequence will complement those available for other Leishmania species and contribute to further studies focusing on this parasite and the neglected diseases associated with it.

Draft Genome Sequences of Two Carbapenemase-Producing Klebsiella pneumoniae Strains Isolated from Blood Cultures.

Carbapenemase-producing Klebsiella pneumoniae represents an emerging public health issue. Here, we present the draft whole-genome sequences of K. pneumoniae clinical strains KPL0.1 (OXA-48 carbapenemase) and KPL0.2 (NDM-1 carbapenemase). These genome sequences should help in investigating pathophysiological mechanisms of digestive colonization or infection with these highly resistant bacteria.

Arcobacter haliotis Tanaka et al. 2017 is a later heterotypic synonym of Arcobacter lekithochrous Diéguez et al. 2017.

The draft whole-genome sequence of Arcobacter haliotis strain LMG 28652T was obtained and compared against the type strain of Arcobacter lekithochrous LFT 1.7T. High similarity was found between the two strains, showing average nucleotide identity and in silico DNA-DNA hybridization values of 98.40 and 86.10 %, respectively. These values indicated that both genomes belonged to the same species, confirming the evidences derived from the phylogenetic analysis performed with the 16S rRNA gene and the concatenated sequences of five housekeeping genes. In addition, the metabolic, physiological and chemotaxonomic features of A. haliotis LMG 28652T were shown to be congruent with those of A. lekithochrous. We conclude that Arcobacter haliotis Tanaka et al. 2017 is a later heterotypic synonym of Arcobacter lekithochrousDiéguez et al. 2017.

Draft Whole-Genome Sequence of "Candidatus Liberibacter asiaticus" Strain TX1712 from Citrus in Texas.

The draft genome sequence of "Candidatus Liberibacter asiaticus" strain TX1712, obtained from a Texas citrus tree, is reported here. Strain TX1712 has a draft genome size of 1,203,333 bp, a G+C content of 36.4%, 1,230 predicted open reading frames, and 41 RNAs and comprises 97.4% of the psy62 reference genome.

Draft Genome Sequence of a Clinical Isolate of Fusarium fujikuroi Isolated from a Male Patient with Acute Myeloid Leukemia.

ABSTRACTHere, we present the draft whole-genome sequence of a clinical isolate of Fusarium fujikuroi cultured from a patient undergoing chemotherapy for refractory acute myeloid leukemia.

Draft Genome Sequence of n-Alkane-Utilizing Acinetobacter sp. Strain BS1, Isolated from Ethane Oxidation Culture.

ABSTRACTHere, we report the draft whole-genome sequence of a bacterial strain, Acinetobacter sp. strain BS1, isolated from black soil during ethane oxidation culture. Medium- or long-chain alkane oxidation-related genes were identified; however, the short-chain alkane monooxygenase was not detected.