Long-Read Genome Assembly of Saccharomyces uvarum Strain CBS 7001

Here, we report a long-read genome assembly for Saccharomyces uvarum strain CBS 7001 based on PacBio whole-genome shotgun sequence data. Our assembly provides an improved reference genome for an important yeast in the Saccharomyces sensu stricto clade.

An integrated approach for synonymization of Rotylenchus rhomboides with R. goodeyi (Nematoda: Hoplolaimidae) reveals high intraspecific mitogenomic variation

Rotylenchus is a widely-distributed economically important plant-parasitic nematode group whose species-level identification relies largely on limited morphological characters including character-based tabular keys and molecular data of ribosomal and mitochondrial genes. In this study, a combined morphological and molecular analysis of three populations of R. goodeyi from Belgium, Poland and the Netherlands revealed important character variations of this species leading to synonymisation of R. rhomboides with R. goodeyi, and a high nucleotide variation within cox1 gene sequences in these populations. Additional Illumina sequencing of DNA from individuals of the Dutch population revealed two variants of mitogenomes each of approximately 23 Kb in size, differing by about 9% and containing eleven protein coding genes, two ribosomal RNA genes and up to 29 transfer RNA genes. In addition to the first representative whole genome shotgun sequence datasets of the genus Rotylenchus, this study also provides the full length mitogenome and the ribosomal DNA sequences of R. goodeyi.

Case report: Detection of aadB and tet (39) on the plasmid of Acinetobacter baumannii TN81 in Vietnam through next-generation sequencing and bioinformatics analysis

Acinetobacter baumannii (A. baumannii) is currently ranked as the frst concern for the development of new antibiotics due to its capacity of resistance to all available families of antibiotics. The most common mechanism of antibiotic resistance development in A. baumannii is through the acquisition of mobile genetic elements such as plasmid, transposon and integrons carrying resistance genes. A. baumannii strain TN81 was isolated from sputum specimen of a 45-year-old man at Thanh Nhan Hospital (Hanoi, Vietnam) and confrmed to be a multidrug resistance strain with high minimum inhibitory concentration value of 8/9 type of antibiotics, especially colistin. De novo assembly of the whole genome shotgun sequence of strain TN81 yielded an estimated genome size of 3,739,193 bp with 593 contigs and N50 is 9,126 bp. MLST analysis showed that TN81 belongs to ST164, which was frst reported as genome assembly in Vietnam. Resistance genes identifcation through database found that TN81 contained 12 genes encoding for antibiotic resistance. Notably, we performed de novo assembly of plasmid through short read sequence and identifed two potential plasmid-encoded antibiotic resistance genes (ant(2’’)-Ia / aadB and tet (39), which were reported for the first time as in ST164 group. This study aimed to investigate the plasmid-containing antibiotic resistance genes from a nosocomial isolate of Acinetobacter baumannii. Conclusively, all of these results would be crucial information on antibiotic resistance in A. baumannii in Vietnam.

Restructuring the Gut Microbiota by Intermittent Fasting Lowers Blood Pressure

Raionale: : In recent years, it has been demonstrated that a pathological change in the gut microbiota, termed gut dysbiosis, can be an underlying factor for the development of hypertension. Prevention of this dysbiosis can attenuate or abolish hypertension. Translational mechanisms to prevent gut dysbiosis as well as understanding of the mechanisms linking gut dysbiosis to hypertension are lacking. Objective: We first examined the efficacy of intermittent fasting (IF) in altering the gut microbiota and lowering blood pressure (BP). Next, we utilized a multi-omics approach to examine microbial influenced metabolites that may serve as the link between the gut microbiota and host BP regulation. Methods and Results: We demonstrate that IF significantly altered the makeup of the gut microbiota, cecal and plasma metabolome, and prevented the development of hypertension in the spontaneously hypertensive stroke-prone rat (SHRSP). The beneficial effects of IF were shown to be due to alterations of the gut microbiota through germ-free (GF) transplantation studies. GF rats receiving microbiota from IF SHRSP had significantly lower BP as compared to GF rats receiving microbiota from ad libitum fed SHRSPs. Through whole genome shotgun sequence analysis of the microbiota and untargeted metabolomics of cecal content and plasma we identified bile acid (BA) metabolism as a potential mediator in BP regulation. Finally, we show supplementation with cholic acid, or activation of the G protein-coupled BA receptor (TGR5), significantly reduced BP of the SHRSP. Conclusions: These studies demonstrate the BP lowering effects of IF involves manipulation of the gut microbiota and metabolome, and implicates disrupted BA signaling as novel mechanisms by which gut dysbiosis contributes to hypertension.

Bacterial associations in the healthy human gut microbiome across populations

In a microbial community, associations between constituent members play an important role in determining the overall structure and function of the community. The human gut microbiome is believed to play an integral role in host health and disease. To understand the nature of bacterial associations at the species level in healthy human gut microbiomes, we analyzed previously published collections of whole-genome shotgun sequence data, totaling over 1.6 Tbp, generated from 606 fecal samples obtained from four different healthy human populations. Using a Random Forest Classifier, we identified 202 signature bacterial species that were prevalent in these populations and whose relative abundances could be used to accurately distinguish between the populations. Bacterial association networks were constructed with these signature species using an approach based on the graphical lasso. Network analysis revealed conserved bacterial associations across populations and a dominance of positive associations over negative associations, with this dominance being driven by associations between species that are closely related either taxonomically or functionally. Bacterial species that form network modules, and species that constitute hubs and bottlenecks, were also identified. Functional analysis using protein families suggests that much of the taxonomic variation across human populations does not foment substantial functional or structural differences.

Whole-Genome Shotgun Sequence of Bacillus mycoides Strain U53, a Psychrotolerant Bacterium Isolated from the Sakhalin Region in Russia

ABSTRACT The shotgun genome sequence of Bacillus mycoides strain U53, a psychrotolerant bacterium that was isolated from soil in Russia, is characterized. The bacterial genome is 5,710,017 bp long and is predicted to have 5,847 genes. The GC content is 35.4%.

Mitochondrial genomes of Columbicola feather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice

Most animals have a conserved mitochondrial genome structure composed of a single chromosome. However, some organisms have their mitochondrial genes separated on several smaller circular or linear chromosomes. Highly fragmented circular chromosomes (“minicircles”) are especially prevalent in parasitic lice (Insecta: Phthiraptera), with 16 species known to have between nine and 20 mitochondrial minicircles per genome. All of these species belong to the same clade (mammalian lice), suggesting a single origin of drastic fragmentation. Nevertheless, other work indicates a lesser degree of fragmentation (2–3 chromosomes/genome) is present in some avian feather lice (Ischnocera: Philopteridae). In this study, we tested for minicircles in four species of the feather louse genus Columbicola (Philopteridae). Using whole genome shotgun sequence data, we applied three different bioinformatic approaches for assembling the Columbicola mitochondrial genome. We further confirmed these approaches by assembling the mitochondrial genome of Pediculus humanus from shotgun sequencing reads, a species known to have minicircles. Columbicola spp. genomes are highly fragmented into 15–17 minicircles between ∼1,100 and ∼3,100 bp in length, with 1–4 genes per minicircle. Subsequent annotation of the minicircles indicated that tRNA arrangements of minicircles varied substantially between species. These mitochondrial minicircles for species of Columbicola represent the first feather lice (Philopteridae) for which minicircles have been found in a full mitochondrial genome assembly. Combined with recent phylogenetic studies of parasitic lice, our results provide strong evidence that highly fragmented mitochondrial genomes, which are otherwise rare across the Tree of Life, evolved multiple times within parasitic lice.

Whole-Genome Shotgun Sequence of Halomonas sp. Strain SBS 10, Isolated from a Hypersaline Lake in India

The whole-genome shotgun sequence of a moderately halophilic bacterium, Halomonas sp. strain SBS 10, was assembled and studied. The assembled genome size was 1.5 Mb, with a G+C content of 63.6%. The genome sequence of this Halomonas sp. SBS 10 isolate will be valuable in understanding gene clusters and functions involved in the adaptability of this bacterium to hypersaline conditions.

Interrogating the Whole-Genome Shotgun Sequence of Escherichia coli Sequence Type 127 Strain 1538RHQ, Which Harbors Virulent Antigenic Factors, Isolated from a Mastitic Cow

We report the whole-genome sequence of Escherichia coli sequence type 127 (ST127) strain 1538RHQ, recovered from a mastitic cow in a dairy herd in Selangor, Malaysia. The objective of this study was to identify the antigenic and virulence properties that can be used as suitable targets for vaccine development against bovine mastitis.