Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan.

Thermoflexus hugenholtzii JAD2T, the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2T and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2T and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing "Candidatus Thermoflexus japonica," "Candidatus Thermoflexus tengchongensis," and "Candidatus Thermoflexus sinensis." Genomics was integrated with targeted exometabolomics and 13C metabolic probing of T. hugenholtzii. The Thermoflexus genomes each code for complete central carbon metabolic pathways and an unusually high abundance and diversity of peptidases, particularly Metallo- and Serine peptidase families, along with ABC transporters for peptides and some amino acids. The T. hugenholtzii JAD2T exometabolome provided evidence of extracellular proteolytic activity based on the accumulation of free amino acids. However, several neutral and polar amino acids appear not to be utilized, based on their accumulation in the medium and the lack of annotated transporters. Adenine and adenosine were scavenged, and thymine and nicotinic acid were released, suggesting interdependency with other organisms in situ. Metabolic probing of T. hugenholtzii JAD2T using 13C-labeled compounds provided evidence of oxidation of glucose, pyruvate, cysteine, and citrate, and functioning glycolytic, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways (PPPs). However, differential use of position-specific 13C-labeled compounds showed that glycolysis and the TCA cycle were uncoupled. Thus, despite the high abundance of Thermoflexus in sediments of some geothermal systems, they appear to be highly focused on chemoorganotrophy, particularly protein degradation, and may interact extensively with other microorganisms in situ.

Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot.

The rocky, seasonally-dry and nutrient-impoverished soils of the Brazilian campos rupestres impose severe growth-limiting conditions on plants. Species of a dominant plant family, Velloziaceae, are highly specialized to low-nutrient conditions and seasonal water availability of this environment, where phosphorus (P) is the key limiting nutrient. Despite plant-microbe associations playing critical roles in stressful ecosystems, the contribution of these interactions in the campos rupestres remains poorly studied. Here we present the first microbiome data of Velloziaceae spp. thriving in contrasting substrates of campos rupestres. We assessed the microbiomes of Vellozia epidendroides, which occupies shallow patches of soil, and Barbacenia macrantha, growing on exposed rocks. The prokaryotic and fungal profiles were assessed by rRNA barcode sequencing of epiphytic and endophytic compartments of roots, stems, leaves and surrounding soil/rocks. We also generated root and substrate (rock/soil)-associated metagenomes of each plant species. We foresee that these data will contribute to decipher how the microbiome contributes to plant functioning in the campos rupestres, and to unravel new strategies for improved crop productivity in stressful environments.

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community.

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes.

Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic gene clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery.

The impact of bird-beak configuration on aortic remodeling of distal arch pathology after thoracic endovascular aortic repair with the Zenith Pro-Form TX2 thoracic endograft.

OBJECTIVE: Structural changes and incomplete endograft apposition to the aortic arch (bird-beak configuration) after thoracic endovascular aortic repair are poorly understood. The aim of this study was to analyze the morphologic changes, conformability, and angulation factors in patients who underwent stainless steel-based stent graft repair of thoracic aortic pathology. METHODS: From March 2011 to March 2012, the study enrolled 19 patients with aortic pathology requiring proximal fixation in zones 2 and 3 who underwent stent graft repair using Zenith Pro-Form TX2 stent grafts (Cook Medical, Bloomington, Ind). For comparison, another 19 patients who received Zenith Z-Trak stent grafts were selected from December 2009 to February 2011. Chest computed tomography scans were analyzed at baseline, and then at 1, 6, and 12 months postoperatively. Arch angulation and bird-beak configuration were evaluated according to sealing zones of attachment by Aquarius iNtuition software (TeraRecon, San Mateo, Calif). RESULTS: The treated diseases included chronic type B aortic dissection in 17 patients and degenerative aneurysms in 21. Significant arch angle transformation was noted at the zone 2 level between the Pro-Form and Z-Trak treated groups (150° ± 11° vs 158° ± 6°; P = .033) and left subclavian artery level (152° ± 12° vs 160° ± 8°; P = .031) during 1 year of follow-up. The bird-beak configuration was detected in six patients (32%) in the Pro-Form group and in 11 (58%) in the Z-Trak group (P = .096) at 1 month, and in six (32%) in the Pro-Form group and in 14 (74%) in the Z-Trak group (P = .022) at 12 months. The mean bird-beak angle was significantly less in Pro-Form-treated patients at 1 month (5° ± 9° vs 15° ± 13°; P = .019) and at 1 year (6° ± 10° vs 18° ± 15°; P = .033). In the Pro-Form platform, a preoperative zone 2 angle <151.1° was a better estimation of the presence of a postoperative bird-beak configuration, with a sensitivity of 86% and specificity of 83%. CONCLUSIONS: Aortic remodeling after stainless steel stent graft repair of thoracic aortic pathology is a continuous process. Significant arch angle transformation was discovered over the zone 2 and left subclavian artery levels. TX2 Pro-Form stent grafts improved arch conformation after 1 year of follow-up. Furthermore, in the patients with dissection, a preoperative distal arch angle of zone 2 was predictive of postoperative bird-beak configuration, regardless of whether they were treated with a Pro-Form stent graft.