Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota.

The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics.

Phyllosticta paracitricarpa is synonymous with the EU quarantine fungus P. citricarpa based on phylogenomic analyses.

Phyllosticta citricarpa is an important citrus-pathogen and a quarantine organism in the European Union. Its recently described relative, P. paracitricarpa, is very closely related and not listed as a quarantine organism. P. paracitricarpa is very difficult to distinguish from P. citricarpa, since its morphological features overlap and the barcoding gene sequences that were originally used to delimit them as distinct species have a low number of species-specific polymorphisms that have subsequently been shown to overlap between the two clades. Therefore, we performed extensive genomic analyses to determine whether the genetic variation between P. citricarpa and P. paracitricarpa strains should be considered to represent infraspecific variation within P. citricarpa, or whether it is indicative of distinct species. Using a phylogenomic analysis with 3,000 single copy ortholog genes and whole-genome comparisons, we determined that the variation between P. citricarpa and P. paracitricarpa can be considered as infraspecies variation within P. citricarpa. We also determined the level of variation in mitochondrial assemblies of several Phyllosticta species and concluded there are only minimal differences between the assemblies of P. citricarpa and P. paracitricarpa. Thus, using several orthogonal approaches, we here demonstrate that variation within the nuclear and mitochondrial genomes of other Phyllosticta species is larger than variation between genomes obtained from P. citricarpa and P. paracitricarpa strains. Thus, P. citricarpa and P. paracitricarpa should be considered as conspecific.

Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses.

Thermophily is a trait scattered across the fungal tree of life, with its highest prevalence within three fungal families (Chaetomiaceae, Thermoascaceae, and Trichocomaceae), as well as some members of the phylum Mucoromycota. We examined 37 thermophilic and thermotolerant species and 42 mesophilic species for this study and identified thermophily as the ancestral state of all three prominent families of thermophilic fungi. Thermophilic fungal genomes were found to encode various thermostable enzymes, including carbohydrate-active enzymes such as endoxylanases, which are useful for many industrial applications. At the same time, the overall gene counts, especially in gene families responsible for microbial defense such as secondary metabolism, are reduced in thermophiles compared to mesophiles. We also found a reduction in the core genome size of thermophiles in both the Chaetomiaceae family and the Eurotiomycetes class. The Gene Ontology terms lost in thermophilic fungi include primary metabolism, transporters, UV response, and O-methyltransferases. Comparative genomics analysis also revealed higher GC content in the third base of codons (GC3) and a lower effective number of codons in fungal thermophiles than in both thermotolerant and mesophilic fungi. Furthermore, using the Support Vector Machine classifier, we identified several Pfam domains capable of discriminating between genomes of thermophiles and mesophiles with 94% accuracy. Using AlphaFold2 to predict protein structures of endoxylanases (GH10), we built a similarity network based on the structures. We found that the number of disulfide bonds appears important for protein structure, and the network clusters based on protein structures correlate with the optimal activity temperature. Thus, comparative genomics offers new insights into the biology, adaptation, and evolutionary history of thermophilic fungi while providing a parts list for bioengineering applications.

Neurospora intermedia from a traditional fermented food enables waste-to-food conversion.

Fungal fermentation of food and agricultural by-products holds promise for improving food sustainability and security. However, the molecular basis of fungal waste-to-food upcycling remains poorly understood. Here we use a multi-omics approach to characterize oncom, a fermented food traditionally produced from soymilk by-products in Java, Indonesia. Metagenomic sequencing of samples from small-scale producers in Western Java indicated that the fungus Neurospora intermedia dominates oncom. Further transcriptomic, metabolomic and phylogenomic analysis revealed that oncom-derived N. intermedia utilizes pectin and cellulose degradation during fermentation and belongs to a genetically distinct subpopulation associated with human-generated by-products. Finally, we found that N. intermedia grew on diverse by-products such as fruit and vegetable pomace and plant-based milk waste, did not encode mycotoxins, and could create foods that were positively perceived by consumers outside Indonesia. These results showcase the traditional significance and future potential of fungal fermentation for creating delicious and nutritious foods from readily available by-products.

Comprehensive Shielding System Enhances Radiation Protection for Structural Heart Procedures.

Background: This study of radiation exposure (RE) to physicians performing structural heart procedures evaluated the efficacy of a novel comprehensive radiation shield compared to those of traditional shielding methods. A novel comprehensive shielding system (Protego, Image Diagnostics Inc) has been documented to provide superior RE protection during coronary procedures compared to that provided by a standard "drop down" shield. The purpose of this study was to assess the efficacy of this shield in transcatheter aortic valve replacement (TAVR) procedures, which are associated with disproportionate RE to operators. Methods: This single-center, 2-group cohort, observational analysis compared RE to the primary physician operator performing TAVR using the Protego shield (n = 25) with that using a standard drop-down shield with personal leaded apparel (n = 25). RE was measured at both thyroid and waist levels with a real-time dosimetry system (RaySafe i3, RaySafe) and was calculated on a mean per case basis. Data were collected on additional procedural parameters, including access site(s) for device implantation, per case fluoroscopy time, air kerma, and patient factors, including body mass index. Between-group comparisons were conducted to evaluate RE by group and measurement sites. Results: The Protego system reduced operator RE by 99% compared to that using standard protection. RE was significantly lower at both the thyroid level (0.08 ± 0.27 vs 79.2 ± 62.4 µSv; P < .001) and the waist level (0.70 ± 1.50 vs 162.0 ± 91.0 µSv, P < .001). "Zero" total RE was documented by RaySafe in 60% (n = 15) of TAVR cases using Protego. In contrast, standard protection did not achieve zero exposure in a single case. Conclusions: The Protego shield system provides superior operator RE protection during TAVR procedures. This shield allows operators to work without the need for personal lead aprons and has potential to reduce catheterization laboratory occupational health hazards.

SCAI Expert Consensus Statement on the Management of Calcified Coronary Lesions.

The prevalence of calcification in obstructive coronary artery disease is on the rise. Percutaneous coronary intervention of these calcified lesions is associated with increased short-term and long-term risks. To optimize percutaneous coronary intervention results, there is an expanding array of treatment modalities geared toward calcium modification prior to stent implantation. The Society for Cardiovascular Angiography and Interventions, herein, puts forth an expert consensus document regarding methods to identify types of calcified coronary lesions, a central algorithm to help guide use of the various calcium modification strategies, tips for when using each treatment modality, and a look at future studies and trials for treating this challenging lesion subset.

Retrospective Multicenter Analysis of Intravascular Lithotripsy Use During Calcified Left Main Coronary Artery Percutaneous Coronary Interventions.

Background: Intravascular lithotripsy (IVL) safely and effectively modifies calcified coronary lesions during percutaneous coronary interventions (PCI). Data regarding its utility in modifying calcified left main coronary artery (LMCA) disease are limited. This study aimed to evaluate short-term outcomes of IVL-assisted LMCA PCI. Methods: This retrospective multicenter all-comers study analyzed patients who underwent intravascular imaging-guided, IVL-assisted PCI for calcified LMCA disease. Clinical and procedural characteristics were obtained, including intravascular imaging measurements. Technical success was defined as successful stent deployment with <30% residual diameter stenosis. Major adverse cardiac events (MACE) was a composite of all-cause death, myocardial infarction, and target vessel revascularization evaluated immediately postprocedure and at 30-day follow-up. Results: Among 184 patients treated at 7 centers from 2019-2023, IVL-assisted LMCA PCI achieved 99.4% technical success. Calcium fracture was identified in 136/165 cases (82.4%) on post-IVL imaging. Pretreatment minimal luminal area increased significantly compared to post-PCI minimal stent area (MSA) (4.1 ± 1.3 to 9.3 ± 2.5 mm2, respectively; P < .001). There was a direct correlation between IVL balloon size and the final MSA (P = .002). In-hospital MACE was 4.4% and 30-day MACE was 8.8%. In multivariate logistic regression, presentation with troponin-positive myocardial infarction was the sole predictor of 30-day MACE. Conclusions: IVL-assisted PCI for calcified LMCA lesions was safe and resulted in high technical success rates, confirming its utility as an effective treatment in this challenging lesion subset.

Genomic Analysis of Aspergillus Section Terrei Reveals a High Potential in Secondary Metabolite Production and Plant Biomass Degradation.

Aspergillus terreus has attracted interest due to its application in industrial biotechnology, particularly for the production of itaconic acid and bioactive secondary metabolites. As related species also seem to possess a prosperous secondary metabolism, they are of high interest for genome mining and exploitation. Here, we present draft genome sequences for six species from Aspergillus section Terrei and one species from Aspergillus section Nidulantes. Whole-genome phylogeny confirmed that section Terrei is monophyletic. Genome analyses identified between 70 and 108 key secondary metabolism genes in each of the genomes of section Terrei, the highest rate found in the genus Aspergillus so far. The respective enzymes fall into 167 distinct families with most of them corresponding to potentially unique compounds or compound families. Moreover, 53% of the families were only found in a single species, which supports the suitability of species from section Terrei for further genome mining. Intriguingly, this analysis, combined with heterologous gene expression and metabolite identification, suggested that species from section Terrei use a strategy for UV protection different to other species from the genus Aspergillus. Section Terrei contains a complete plant polysaccharide degrading potential and an even higher cellulolytic potential than other Aspergilli, possibly facilitating additional applications for these species in biotechnology.

Symmetric and asymmetric DNA N6-adenine methylation regulates different biological responses in Mucorales.

DNA N6-adenine methylation (6mA) has recently gained importance as an epigenetic modification in eukaryotes. Its function in lineages with high levels, such as early-diverging fungi (EDF), is of particular interest. Here, we investigated the biological significance and evolutionary implications of 6mA in EDF, which exhibit divergent evolutionary patterns in 6mA usage. The analysis of two Mucorales species displaying extreme 6mA usage reveals that species with high 6mA levels show symmetric methylation enriched in highly expressed genes. In contrast, species with low 6mA levels show mostly asymmetric 6mA. Interestingly, transcriptomic regulation throughout development and in response to environmental cues is associated with changes in the 6mA landscape. Furthermore, we identify an EDF-specific methyltransferase, likely originated from endosymbiotic bacteria, as responsible for asymmetric methylation, while an MTA-70 methylation complex performs symmetric methylation. The distinct phenotypes observed in the corresponding mutants reinforced the critical role of both types of 6mA in EDF.

Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces.

The Lipomyces clade contains oleaginous yeast species with advantageous metabolic features for biochemical and biofuel production. Limited knowledge about the metabolic networks of the species and limited tools for genetic engineering have led to a relatively small amount of research on the microbes. Here, a genome-scale metabolic model (GSM) of Lipomyces starkeyi NRRL Y-11557 was built using orthologous protein mappings to model yeast species. Phenotypic growth assays were used to validate the GSM (66% accuracy) and indicated that NRRL Y-11557 utilized diverse carbohydrates but had more limited catabolism of organic acids. The final GSM contained 2,193 reactions, 1,909 metabolites, and 996 genes and was thus named iLst996. The model contained 96 of the annotated carbohydrate-active enzymes. iLst996 predicted a flux distribution in line with oleaginous yeast measurements and was utilized to predict theoretical lipid yields. Twenty-five other yeasts in the Lipomyces clade were then genome sequenced and annotated. Sixteen of the Lipomyces species had orthologs for more than 97% of the iLst996 genes, demonstrating the usefulness of iLst996 as a broad GSM for Lipomyces metabolism. Pathways that diverged from iLst996 mainly revolved around alternate carbon metabolism, with ortholog groups excluding NRRL Y-11557 annotated to be involved in transport, glycerolipid, and starch metabolism, among others. Overall, this study provides a useful modeling tool and data for analyzing and understanding Lipomyces species metabolism and will assist further engineering efforts in Lipomyces.

Emergency coronary artery bypass surgery after chronic total occlusion percutaneous coronary intervention: Insights from the PROGRESS-CTO registry.

BACKGROUND: Emergency coronary artery bypass surgery (eCABG) is a serious complication of chronic total occlusion (CTO) percutaneous coronary artery intervention (PCI). METHODS: We examined the incidence and outcomes eCABG among 14,512 CTO PCIs performed between 2012 and 2023 in a large multicenter registry. RESULTS: The incidence of eCABG was 0.12% (n = 17). Mean age was 68 ± 6 years and 69% of the patients were men. The most common reason for eCABG was coronary perforation (70.6%). eCABG patients had larger target vessel diameter (3.36 ± 0.50 vs. 2.90 ± 0.52; p = 0.003), were more likely to have moderate/severe calcification (85.7% vs. 45.8%; p = 0.006), side branch at the proximal cap (91.7% vs. 55.4%; p = 0.025), and balloon undilatable lesions (50% vs. 7.4%; p = 0.001) and to have undergone retrograde crossing (64.7% vs. 30.8%, p = 0.006). eCABG cases had lower technical (35.3% vs. 86.7%; p < 0.001) and procedural (35.3% vs. 86.7%; p < 0.001) success and higher in-hospital mortality (35.3% vs. 0.4%; p < 0.001), coronary perforation (70.6% vs. 4.6%; p < 0.001), pericardiocentesis (47.1% vs. 0.8%; p < 0.001), and major bleeding (11.8% vs. 0.5%; p < 0.001). CONCLUSIONS: The incidence of eCABG after CTO PCI was 0.12% and associated with high in-hospital mortality (35%). Coronary perforation was the most common reason for eCABG.

On the origin of bird's nest fungi: Phylogenomic analyses of fungi in the Nidulariaceae (Agaricales, Basidiomycota).

Nidulariaceae, also known as bird's nest fungi, is an understudied group of mushroom-forming fungi. The common name is derived from their nest-like morphology. Bird's nest fungi are ubiquitous wood decomposers or saprobes on dung. Recent studies showed that species in the Nidulariaceae form a monophyletic group with five sub-clades. However, phylogenetic relationships among genera and placement of Nidulariaceae are still unclear. We present phylogenomic analyses of bird's nest fungi and related Agaricales fungi to gain insight into the evolution of Nidulariaceae. A species tree with 17 newly generated genomes of bird's nest fungi and representatives from all major clades of Agaricales was constructed using 1044 single-copy genes to explore the intergeneric relationships and pinpoint the placement of Nidulariaceae within Agaricales. We corroborated the hypothesis that bird's nest fungi are sister to Squamanitaceae, which includes mushroom-shaped fungi with a stipe and pileus that are saprobes and mycoparasites. Lastly, stochastic character mapping of discrete traits on phylogenies (SIMMAP) suggests that the ancestor of bird's nest fungi likely possessed an evanescent, globose peridium without strings attaching to the spore packets (funiculi). This analysis suggests that the funiculus was gained twice and that the persistent, cupulate peridium form was gained at least four times and lost once. However, alternative coding schemes and datasets with a wider array of Agaricales produced conflicting results during ancestral state reconstruction, indicating that there is some uncertainty in the number of peridium transitions and that taxon sampling may significantly alter ancestral state reconstructions. Overall, our results suggest that several key morphological characters of Nidulariaceae have been subject to homoplasy.

Draft genome sequence of Yarrowia lipolytica NRRL Y-64008, an oleaginous yeast capable of growing on lignocellulosic hydrolysates.

Yarrowia lipolytica is an oleaginous yeast that produces high titers of fatty acid-derived biofuels and biochemicals. It can grow on hydrophobic carbon sources and lignocellulosic hydrolysates. The genome sequence of Y. lipolytica NRRL Y-64008 is reported to aid in its development as a biotechnological chassis for producing biofuels and bioproducts.

Impact of Calcium Eccentricity on the Safety and Effectiveness of Coronary Intravascular Lithotripsy: Pooled Analysis From the Disrupt CAD Studies.

BACKGROUND: Coronary intravascular lithotripsy (IVL) safely facilitates successful stent implantation in severely calcified lesions. This analysis sought to determine the relative impact of lesion calcium eccentricity on the safety and effectiveness of IVL using high-resolution optical coherence tomography imaging. METHODS: Individual patient-level data (n=262) were pooled from 4 distinct international prospective studies (Disrupt CAD I, II, III, and IV) and analyzed by an independent optical coherence tomography core laboratory. IVL performance in eccentric versus concentric calcification was analyzed by dividing calcified lesions into quartiles (≤180° [most eccentric], 181°-270°, 271°-359°, and 360° [concentric]) by maximum continuous calcium arc. RESULTS: In the 230 patients with clear imaging field on optical coherence tomography, there were no differences in preprocedure minimum lumen area, diameter stenosis, or maximum calcium thickness. The calcium length and volume index increased progressively with increasing mean and maximum continuous calcium arc (ie, concentricity). Conversely, the minimum calcium thickness decreased progressively with increasing concentricity. Post-procedure, the number of calcium fractures, fracture depth, and fracture width increased with increasing concentricity, with a 4-fold increase in the number of fractures in lesions with 360° of calcium arc compared with ≤180°. This increase in IVL-induced calcium fracture with increasing calcium burden and concentricity facilitated stent expansion and luminal gain such that there were no significant differences across quartiles. CONCLUSIONS: IVL induced calcium fractures proportional to the magnitude of coronary artery calcium, including in eccentric calcium, leading to consistent improvements in stent expansion and luminal gain in both eccentric and concentric calcified coronary lesions.

Genome-scale phylogeny and comparative genomics of the fungal order Sordariales.

The order Sordariales is taxonomically diverse, and harbours many species with different lifestyles and large economic importance. Despite its importance, a robust genome-scale phylogeny, and associated comparative genomic analysis of the order is lacking. In this study, we examined whole-genome data from 99 Sordariales, including 52 newly sequenced genomes, and seven outgroup taxa. We inferred a comprehensive phylogeny that resolved several contentious relationships amongst families in the order, and cleared-up intrafamily relationships within the Podosporaceae. Extensive comparative genomics showed that genomes from the three largest families in the dataset (Chaetomiaceae, Podosporaceae and Sordariaceae) differ greatly in GC content, genome size, gene number, repeat percentage, evolutionary rate, and genome content affected by repeat-induced point mutations (RIP). All genomic traits showed phylogenetic signal, and ancestral state reconstruction revealed that the variation of the properties stems primarily from within-family evolution. Together, the results provide a thorough framework for understanding genome evolution in this important group of fungi.

Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi.

Diverse members of early-diverging Mucoromycota, including mycorrhizal taxa and soil-associated Mortierellaceae, are known to harbor Mollicutes-related endobacteria (MRE). It has been hypothesized that MRE were acquired by a common ancestor and transmitted vertically. Alternatively, MRE endosymbionts could have invaded after the divergence of Mucoromycota lineages and subsequently spread to new hosts horizontally. To better understand the evolutionary history of MRE symbionts, we generated and analyzed four complete MRE genomes from two Mortierellaceae genera: Linnemannia (MRE-L) and Benniella (MRE-B). These genomes include the smallest known of fungal endosymbionts and showed signals of a tight relationship with hosts including a reduced functional capacity and genes transferred from fungal hosts to MRE. Phylogenetic reconstruction including nine MRE from mycorrhizal fungi revealed that MRE-B genomes are more closely related to MRE from Glomeromycotina than MRE-L from the same host family. We posit that reductions in genome size, GC content, pseudogene content, and repeat content in MRE-L may reflect a longer-term relationship with their fungal hosts. These data indicate Linnemannia and Benniella MRE were likely acquired independently after their fungal hosts diverged from a common ancestor. This work expands upon foundational knowledge on minimal genomes and provides insights into the evolution of bacterial endosymbionts.