Paraneptunicella aestuarii gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from seawater in East China Sea

An aerobic Gram-stain-negative, curved rod-shaped and non-spore-forming bacterial strain (NBU2194T) was isolated from seawater collected in an intertidal zone in Ningbo, Zhejiang Province, PR China. It was motile though a single polar flagellum and grew at 20–42 °C (optimum, 30 °C), in 0–2.0 % NaCl (0 %, w/v) and at pH 5.0–9.0 (pH 6.0–7.0). The sole respiratory quinone was ubiquinone-8. The major cellular fatty acids were C16 : 0, C16 : 1 ω7c and/or C16 : 1 ω6c. The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid and two unidentified aminophosphoglycolipids. A phylogenetic analysis based on 16S rRNA gene sequences and 65 genomic core genes showed that strain NBU2194T formed a distinct lineage in the family Alteromonadaceae . The genome of strain NBU2194T was 4 913 533 bp with a DNA G+C content of 43.9 mol% and coded 3895 genes, 12 rRNA genes and 47 tRNA genes. The average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values between strain NBU2194T and related species of Alteromonadaceae were below the threshold limit for prokaryotic species delineation. NBU2194T could be distinguished from other genera in the family Alteromonadaceae based on phenotypic, chemotaxonomic and genomic characteristics. On the basis of the polyphasic taxonomic evidence collected in this study, strain NBU2194T is considered to represent a novel genus and species in the family Alteromonadaceae , for which the name Paraneptunicella aestuarii is proposed. The type strain is NBU2194T (=KCTC 82442T=GDMCC 1.2217T).

The Thermosynechococcus genus: wide environmental distribution, but a highly conserved genomic core

Cyanobacteria thrive in very diverse environments. In Earth history however, delayed oxygenation has raised questions of growth limitation in ancient environmental conditions. As a single genus, the Thermosynechococcus are known to be cosmopolitan and live in chemically diverse habitats. To understand the genetic basis for this, we compared the protein coding component of Thermosynechococcus genomes. Supplementing the known genetic diversity of Thermosynechococcus, we report draft metagenome-assembled genomes of two Thermosynechococcus recovered from ferrous carbonate hot springs in Japan. We find that as a genus, Thermosynechococcus is genomically conserved, having a small pan-genome with few accessory genes per individual strain and only 18 protein clusters appearing in all Thermosynechococcus but not in any other cyanobacteria in our analysis. Furthermore, by comparing orthologous protein groups, including an analysis of genes encoding proteins with an iron related function (uptake, storage or utilization), no clear differences in genetic content, or adaptive mechanisms could be detected between genus members, despite the range of environments they inhabit. Overall, our results highlight a seemingly innate ability for Thermosynechococcus to inhabit diverse habitats without having undergone substantial genomic adaptation to accommodate this. The finding of Thermosynechococcus in both hot and high iron environments without adaptation recognizable from the perspective of protein coding genes has implications for understanding the basis of thermophily within this clade, and also suggests that ferrous iron in ancient oceans may not have inhibited the proliferation of Cyanobacteria on Earth. The conserved core genome may be indicative of an allopatric lifestyle – or reduced genetic complexity of hot spring habitats relative to other environments.

Abstract TP281: Transcriptome Analysis of the Human Brain Microvascular Endothelial Cells During and After Oxygen-Glucose Deprivation Stress as a Tool to Identify Novel Targets

Background: The blood-brain barrier (BBB) constitutes an important component of the neurovascular unit (NVU) by providing a physical and a chemical barrier critical for the brain homeostasis. The disruption of the BBB during cerebral ischemia constitutes a key event of the disease, resulting in its opening and ultimately the formation of cerebral edema. Therefore, targeting such BBB disruption by restoring the barrier function could mitigate such insult. In this study, we investigated change in gene expression profile of the human BBB in vitro using an induced pluripotent stem cell (iPSC) based model. Methods: BMECs derived from two human iPSC lines (CTR90F and CTR65M) were exposed to acute OGD stress (1% O2, no glucose) for 6h, followed by reoxygenation (21% O2, 1g/L glucose) for 18h and compared to control (21% O2, 1g/L glucose, 24h) Total RNA was extracted for cDNA microarray analysis to the University of Texas Southwestern Genomic Core Facility using a ClariomD® chip. Fold-change >2 was considered statistically significant (P<0.05). Results: OGD/reoxygenation resulted in almost 3700 genes differentially expressed, including over 600 coding genes. Most of such differential expression occurred during the OGD phase. Reoxygenation yielded to quasi-similar expression profile than controls. Several original pathways have been identified and include nuclear receptors, PI3K/Akt signaling pathways, microRNAs, and adhesion signaling pathways. Conclusions: Our preliminary findings suggest that our iPSC-derived model of the BBB based on BMECs showed an overlap of several genes commonly identified as hypoxic/ischemic responsive genes, but also highlighted novel signaling pathways that have little or no literature on their function at the BBB. We are currently refining our list of genes and focusing our attention on genes that have shown the highest enrichment or depletion.

The pan-genome of Treponema pallidum reveals differences in genome plasticity between subspecies related to venereal and non-venereal syphilis

Background Spirochetal organisms of the Treponema genus are responsible for causing Treponematoses. Pathogenic treponemes is a Gram-negative, motile, spirochete pathogen that causes syphilis in human. Treponema pallidum subsp. endemicum (TEN) causes endemic syphilis (bejel); T. pallidum subsp. pallidum (TPA) causes venereal syphilis; T. pallidum subsp. pertenue (TPE) causes yaws; and T. pallidum subsp. Ccarateum causes pinta. Out of these four high morbidity diseases, venereal syphilis is mediated by sexual contact; the other three diseases are transmitted by close personal contact. The global distribution of syphilis is alarming and there is an increasing need of proper treatment and preventive measures. Unfortunately, effective measures are limited. Results Here, the genome sequences of 53 T. pallidum strains isolated from different parts of the world and a diverse range of hosts were comparatively analysed using pan-genomic strategy. Phylogenomic, pan-genomic, core genomic and singleton analysis disclosed the close connection among all strains of the pathogen T. pallidum, its clonal behaviour and showed increases in the sizes of the pan-genome. Based on the genome plasticity analysis of the subsets containing the subspecies T pallidum subsp. pallidum, T. pallidum subsp. endemicum and T. pallidum subsp. pertenue, we found differences in the presence/absence of pathogenicity islands (PAIs) and genomic islands (GIs) on subsp.-based study. Conclusions In summary, we identified four pathogenicity islands (PAIs), eight genomic islands (GIs) in subsp. pallidum, whereas subsp. endemicum has three PAIs and seven GIs and subsp. pertenue harbours three PAIs and eight GIs. Concerning the presence of genes in PAIs and GIs, we found some genes related to lipid and amino acid biosynthesis that were only present in the subsp. of T. pallidum, compared to T. pallidum subsp. endemicum and T. pallidum subsp. pertenue.

CYP4 and CYP6 gene variability in genome of Aphis fabae mordvilkoi Börner & Janisch, 1922

Aim. To estimate the variability of genes of 4th and 6th families of CYP450, which were extracted from the whole genome data of Aphis fabae mordvilkoi collected from Philadelphus coronaries L. in Belarus. Methods. The whole genome sequencing was carried out in the University of Utah DNA Sequencing and Genomic Core Facilities (USA). CYP4 and CYP6 gene sequences were extracted from the whole genome data by sequential mapping the whole genome reads to CYP4 and CYP6 CDSs of three reference genomes (Acyrthosiphon pisum Harris, 1776, Myzus persicae (Sulžer, 1776) и Diuraphis noxia (MordvilkoexKurdjumov, 1913)). All found uniqueversion of assembling were taken as a single gene. Results. In A. fabae mordvilkoi genome we found out 31 CYP4 genes and 24 from them were copies of CYP4C1s. We also found out 19 CYP6 gene sand 8 from them were identified as CYP6A13s. Variability of nucleotide an damino acid sequences of CYP4 and CYP6 CDSs were high. Conclusions. In A. fabae mordvilkoi genome most CYP4genes were identified as CYP4C1 and most CYP6 genes were CYP6A13s. Other CYP4 and CYP6 were mostly presented as single copies of different genes.Keywords: aphids, cytochrome p450, Aphis fabae, trophic specialization, gene copies.

A Comparative Genomic Analysis of Diverse Clonal Types of EnterotoxigenicEscherichia coliReveals Pathovar-Specific Conservation

ABSTRACTEnterotoxigenicEscherichia coli(ETEC) is a major cause of diarrheal illness in children less than 5 years of age in low- and middle-income nations, whereas it is an emerging enteric pathogen in industrialized nations. Despite being an important cause of diarrhea, little is known about the genomic composition of ETEC. To address this, we sequenced the genomes of five ETEC isolates obtained from children in Guinea-Bissau with diarrhea. These five isolates represent distinct and globally dominant ETEC clonal groups. Comparative genomic analyses utilizing a gene-independent whole-genome alignment method demonstrated that sequenced ETEC strains share approximately 2.7 million bases of genomic sequence. Phylogenetic analysis of this “core genome” confirmed the diverse history of the ETEC pathovar and provides a finer resolution of theE. colirelationships than multilocus sequence typing. No identified genomic regions were conserved exclusively in all ETEC genomes; however, we identified more genomic content conserved among ETEC genomes than among non-ETECE. coligenomes, suggesting that ETEC isolates share a genomic core. Comparisons of known virulence and of surface-exposed and colonization factor genes across all sequenced ETEC genomes not only identified variability but also indicated that some antigens are restricted to the ETEC pathovar. Overall, the generation of these five genome sequences, in addition to the two previously generated ETEC genomes, highlights the genomic diversity of ETEC. These studies increase our understanding of ETEC evolution, as well as provide insight into virulence factors and conserved proteins, which may be targets for vaccine development.

Genomic Lessons from Biomining Organisms: Case Study of the Acidithiobacillus Genus

Advances in DNA sequencing technologies have promoted the use of genome information as a key component in most of biological studies. In the case of biomining microorganisms, partial and complete genome information has provided critical clues for unraveling their physiology. This information has also provided genetic material for the generation of functional and biodiversity directed markers. In this work, we present a compilation of the most relevant findings based on genomic analysis of the model organism Acidithiobacillus ferrooxidans ATCC23270 that were extended and compared to the recently sequenced genomes of Acithiobacillus thiooxidans and Acidithiobacillus caldus. The phylogenetic relatedness of these three microorganisms has permitted the identification of a shared genomic core that encodes the common metabolic and regulatory functions critical for survival and proliferation in extremely acidic environments. We also identified microorganism-specific genomic components that are predicted to be responsible for the metabolic speciation of these microorganisms. Finally, we evaluated the impact of lateral gene transfer on these genomes in order to determine the functional contribution of this phenomenon to the fitness of these microbial representatives. The information gathered by genomic analyses in the Acidithiobacillus genus will be presented in conjunction with other biomining genomic and metagenomic information in order to generate a more comprehensive picture of the biodiversity, metabolism and ecophysiology of the bioleaching niche.