Real-world evaluation of vascular complications and comorbidities in Portuguese patients with Type 2 diabetes: Results from the cMORE study.

INTRODUCTION AND OBJECTIVES: Type 2 diabetes poses a significant health challenge in Portugal, increasing the susceptibility to complications/comorbidities such as hypertension, obesity, and cardiovascular (CV) disease. This study aimed to evaluate the prevalence of type 2 diabetes-related vascular complications/comorbidities and their pharmacological management in Portugal. METHODS: cMORE was a non-interventional, cross-sectional, multicenter study conducted in 32 Portuguese primary healthcare units between October 2020 and 2022. Secondary data, including sociodemographic, anthropometric, clinical information, cardiometabolic comorbidities, HbA1c levels, lipid parameters and medication, were collected from electronic medical records. RESULTS: 780 adult patients with type 2 diabetes were included, predominantly male (55.5%), with an average age of 67.7 years and a mean disease duration of 10.5 years. Family history of type 2 diabetes (43.1%) and CV disease (32.1%) was prevalent. Mean HbA1c was 7.0%, progressively increasing with disease duration (p<0.001). Microvascular and macrovascular complications occurred in 38.1% and 19.6% of patients, respectively. The most prevalent comorbidities included overweight/obesity (85.5%), dyslipidemia (85.4%), and hypertension (82.6%). Multimorbidity burden was significant (99.3%) and positively correlated with older age, larger waist circumference, and overweight/obesity. Longer type 2 diabetes duration was associated with higher odds of diabetic retinopathy and CV disease/procedures, while dyslipidemia and hypertension were linked with older age, regardless of disease duration. Most patients received oral antidiabetic medications (94.6%), primarily biguanides (92.4%), followed by DPP-4 (39.1%) and SGLT2 inhibitors (34.2%). CONCLUSIONS: The cMORE study reveals a substantial burden of vascular complications/comorbidities among Portuguese type 2 diabetes patients. Despite the high multimorbidity rates, effective TYPE 2 DIABETES management is observed, emphasizing the country's commitment to personalized care.

Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages.

The majority of bacteriophage diversity remains uncharacterized, and new intriguing mechanisms of their biology are being continually described. Members of some phage lineages, such as the Crassvirales, repurpose stop codons to encode an amino acid by using alternate genetic codes. Here, we investigated the prevalence of stop codon reassignment in phage genomes and its subsequent impacts on functional annotation. We predicted 76 genomes within INPHARED and 712 vOTUs from the Unified Human Gut Virome Catalogue (UHGV) that repurpose a stop codon to encode an amino acid. We re-annotated these sequences with modified versions of Pharokka and Prokka, called Pharokka-gv and Prokka-gv, to automatically predict stop codon reassignment prior to annotation. Both tools significantly improved the quality of annotations, with Pharokka-gv performing best. For sequences predicted to repurpose TAG to glutamine (translation table 15), Pharokka-gv increased the median gene length (median of per genome median) from 287 to 481 bp for UHGV sequences (67.8% increase) and from 318 to 550 bp for INPHARED sequences (72.9% increase). The re-annotation increased median coding capacity from 66.8% to 90.0% and from 69.0% to 89.8% for UHGV and INPHARED sequences predicted to use translation table 15. Furthermore, the proportion of genes that could be assigned functional annotation increased, including an increase in the number of major capsid proteins that could be identified. We propose that automatic prediction of stop codon reassignment before annotation is beneficial to downstream viral genomic and metagenomic analyses.

A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts.

Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.

Effect of hydroxyapatite nanoparticles coating of titanium surface on biofilm adhesion: An in vitro study.

AIM: To evaluate the adhesion of mono and duospecies biofilm on a commercially available dental implant surface coated with hydroxyapatite nanoparticles (nanoHA). MATERIAL AND METHODS: Titanium discs were divided into two groups: double acid-etched (AE) and AE coated with nanoHA (NanoHA). Surface characteristics evaluated were morphology, topography, and wettability. Mono and duospecies biofilms of Streptococcus sanguinis (S. sanguinis) and Candida albicans (C. albicans) were formed. Discs were exposed to fetal bovine serum (FBS) to form the pellicle. Biofilm was growth in RPMI1640 medium with 10% FBS and 10% BHI medium for 6 h. Microbial viability was evaluated using colony-forming unit and metabolic activity by a colorimetric assay of the tetrazolium salt XTT. Biofilm architecture and organization were evaluated by confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM). RESULTS: AE surface had more pores, while NanoHA had even nanoHA crystals distribution. Roughness was similar (AE: 0.59 ± 0.07 µm, NanoHA: 0.69 ± 0.18 µm), but wettability was different (AE: Θw= 81.79 ± 8.55°, NanoHA: Θw= 53.26 ± 11.86°; P = 0.01). NanoHA had lower S. sanguinis viability in monospecies biofilm (P = 0.007). Metabolic activity was similar among all biofilms. In SEM both surfaces on C. albicans biofilm show a similar distribution of hyphae in mono and duospecies biofilms. AE surface has more S. sanguinis than the NanoHA surface in the duospecies biofilm. CLSM showed a large proportion of live cells in all groups. CONCLUSIONS: The nanoHA surface reduced the adhesion of S. sanguinis biofilm but did not alter the adhesion of C. albicans or the biofilm formed by both species.

Biochemical properties of a Flavobacterium johnsoniae dextranase and its biotechnological potential for Streptococcus mutans biofilm degradation.

Cariogenic biofilms have a matrix rich in exopolysaccharides (EPS), mutans and dextrans, that contribute to caries development. Although several physical and chemical treatments can be employed to remove oral biofilms, those are only partly efficient and use of biofilm-degrading enzymes represents an exciting opportunity to improve the performance of oral hygiene products. In the present study, a member of a glycosyl hydrolase family 66 from Flavobacterium johnsoniae (FjGH66) was heterologously expressed and biochemically characterized. The recombinant FjGH66 showed a hydrolytic activity against an early EPS-containing S. mutans biofilm, and, when associated with a α-(1,3)-glucosyl hydrolase (mutanase) from GH87 family, displayed outstanding performance, removing more than 80% of the plate-adhered biofilm. The mixture containing FjGH66 and Prevotella melaninogenica GH87 α-1,3-mutanase was added to a commercial mouthwash liquid to synergistically remove the biofilm. Dental floss and polyethylene disks coated with biofilm-degrading enzymes also degraded plate-adhered biofilm with a high efficiency. The results presented in this study might be valuable for future development of novel oral hygiene products.

Kaplan-Meier Survival Analysis: Practical Insights for Clinicians.

This article aims to provide a guide that will help healthcare professionals and clinical researchers from all fields that deal with Kaplan-Meier curves. Survival analysis methods are among the most frequently used in the medical sciences and in clinical research. Overall survival, progression free survival, time to recurrence, or any other clinically relevant parameter represented by a Kaplan-Meier curve will be discussed. We will present a practical and straightforward interpretation of these curves, setting aside intricate mathematical considerations. Our focus will be on essential concepts that interface with biological sciences and medicine in order to guarantee proficiency in one of the most popular yet frequently misunderstood methods in clinical research. Being familiar with these concepts is not only essential for designing new clinical studies but also for critically assessing and interpreting published data.

Ingestion and depuration of polyester microfibers by Crassostrea gasar (Adanson, 1757).

The study aimed to obtain environmentally relevant microfibers (MFs) from polyester fabric and assess their impact on the oyster Crassostrea gasar. MFs were obtained by grinding the fabric, and their accumulation in oysters gills and digestive glands was analyzed after exposure to 0.5 mg/L for 2 and 24 h. Additionally, a 48 h depuration was conducted on the oysters exposed for 24 h. Sublethal effects were assessed in oysters exposed for 24 h and depurated for 48 h, using biomarkers like Catalase (CAT), Glutathione S-transferase (GST), and Glutathione Peroxidase (GPx), along with histological analyses. Polyester fabric grinding produced significant MFs (average length: 570 µm) with degraded surface and increased malleability. Oysters showed increased MF accumulation in digestive glands post-exposure, with no impact on antioxidant enzymes. Depuration decreased MFs accumulation. Histological analysis revealed accumulation in the stomach and brown cells, possibly indicating inflammation. This raises concerns about MFs bioaccumulation in marine organisms, impacting the food chain and safety.

An animal model of trait anxiety: Carioca high freezing rats as a model of generalized anxiety disorder.

Despite being one of the main components of anxiety and playing a pivotal role in how an individual perceives and copes with anxiogenic situations or responds to a given treatment, trait anxiety is paradoxically omitted in most animal models of anxiety. This is problematic and particularly more concerning in models that are used to screen drugs and other treatments for specific anxiety disorders and to investigate their neurobiological mechanisms. Our group has been engaged in the search for specific anxiety-related traits in animal models of anxiety. We developed two new lines of rats with strong phenotypic divergence for high (Carioca High-conditioned Freezing [CHF]) and low (Carioca Low-conditioned Freezing [CLF]) trait anxiety as expressed in the contextual fear conditioning paradigm. Here, we summarize key behavioral, pharmacological, physiological, and neurobiological differences in one these lines, the CHF rat line, relative to randomized-cross controls and discuss how far they represent a valid and reliable animal model of generalized anxiety disorder and so high trait anxiety.

Factors influencing the first and the fifth years adherence to adjuvant endocrine therapy in breast cancer patients in a low income country.

PURPOSE: Breast cancer is the leading cause of cancer death in Brazil and in many countries around the world. In order to minimize the risk of recurrence and death, adjuvant endocrine therapy (AET) is used in women whose tumors express hormone receptors; however, the therapy is associated with low rates of compliance. Therefore, we sought to evaluate the proportion of patients who are adherent/non-adherent to AET at the beginning of the therapy (1st year) and at its end (5th year). METHODS: Cross-sectional study assessing adherence through the Brief Medication Questionnaire. RESULTS: It was identified that eventual failures in maintaining the correct adherence to the treatment have risen from 23% of patients in the 1st year of treatment to 35% of patients in the 5th year (p = 0.005). In both groups, use of aromatase inhibitors, polypharmacy of at least 3 mediations and the previous diagnosis of diabetes mellitus (DM) or systemic arterial hypertension (SAH) have contributed to low adherence among patients. CONCLUSION: The proportion of patients who are not adherent to AET was high in both cohorts, and the rate of non-adherent patients rises over time. It is essential to incorporate screening methods for lack of compliance to AET, as well as measures to try to reduce non-persistence to the treatment, such as educating the patients on the benefits of the treatment, managing comorbidities through lifestyle changes and, therefore, reducing polypharmacy and, above all, detecting and treating very early the adverse effects of AET that might interfere with its correct use.

A decade-long journey shed light on chemical composition and field determination of acid mine drainage in Brazil.

Regular monitoring of Acid Mine Drainage (AMD) is essential for understanding its extent and impact on water resources. Traditional manual sampling methods have limitations, such as limited representativeness and delayed lab analysis. High-frequency monitoring offers an alternative, enabling real-time analysis of AMD fluctuations and determination of constituents in the field. This study assessed a decade-long environmental monitoring database from watersheds impacted by coal mining in Brazil to analyze the relationships between physical properties and constituents from different water sources affected by AMD. Samples were grouped into four categories based on location and contamination levels. Results revealed that water samples from the two groups not affected by AMD exhibited near-neutral pH, low metal and sulfate concentrations, and a large portion of samples below the quantification limit for Mn and Al. In contrast, samples from groups affected by AMD displayed high metal and sulfate concentrations and acidic pH, with the highest contamination observed in the underground mine discharges group (AMD UMD). Spearman correlation analyzes between field (pH and electrical conductivity (EC)) and lab (SO42-, Fe, Mn, and Al) parameters showed no significant correlations in non-AMD-affected groups, but significant correlations in AMD-affected groups, particularly the Streams group. A regression model between sulfate and EC was identified as the best predictor for AMD, enabling continuous, low-cost monitoring of contaminated streams and providing insight into previously unobserved AMD processes, such as variations in contamination during storm events and river flushing.

PrOgnosis in Pulmonary Embolism (PoPE): 30-Day mortality risk score based on five admission parameters.

INTRODUCTION AND OBJECTIVE: Several scoring systems have been developed for risk stratification in patients with acute pulmonary embolism (PE). The Pulmonary Embolism Severity Index (PESI) and its simplified version (sPESI) are among the most used, however the high number of variables hinder its application. Our aim was to derive an easy-to-perform score based on simple parameters obtained at admission to predict 30-day mortality in acute PE patients. METHODS: Retrospective study in 1115 patients with acute PE from two institutions (derivation cohort n=835, validation cohort n=280). The primary endpoint was all-cause mortality at 30 days. Statistically and clinically relevant variables were selected for multivariable Cox regression analysis. We derived and validated a multivariable risk score model and compared to other established scores. RESULTS: The primary endpoint occurred in 207 patients (18.6%). Our model included five variables weighted as follows: modified shock index ≥1.1 (hazard ratio [HR] 2.57, 1.68-3.92, p<0.001), active cancer (HR 2.27, 1.45-3.56, p<0.001), altered mental state (HR 3.82, 2.50-5.83, p<0.001), serum lactate concentration ≥2.50 mmol/L (HR 5.01, 3.25-7.72, p<0.001), and age ≥80 years (HR 1.95, 1.26-3.03, p=0.003). The prognostic ability was superior to other scores (area under curve [AUC] 0.83 [0.79-0.87] vs 0.72 [0.67-0.79] in PESI and 0.70 [0.62-0.75] in sPESI, p<0.001) and its performance in the validation cohort was deemed good (73 events in 280 patients, 26.1%, AUC=0.76, 0.71-0.82, p<0.0001) and superior to other scores (p<0.05). CONCLUSIONS: The PoPE score (https://tinyurl.com/ybsnka8s) is an easy tool with superior performance to predict early mortality in patients admitted for PE with non-high-risk PE.

IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.

Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.

Generalized global solar radiation forecasting model via cyber-secure deep federated learning.

Recently, the increasing prevalence of solar energy in power and energy systems around the world has dramatically increased the importance of accurately predicting solar irradiance. However, the lack of access to data in many regions and the privacy concerns that can arise when collecting and transmitting data from distributed points to a central server pose challenges to current predictive techniques. This study proposes a global solar radiation forecasting approach based on federated learning (FL) and convolutional neural network (CNN). In addition to maintaining input data privacy, the proposed procedure can also be used as a global supermodel. In this paper, data related to eight regions of Iran with different climatic features are considered as CNN input for network training in each client. To test the effectiveness of the global supermodel, data related to three new regions of Iran named Abadeh, Jarqavieh, and Arak are used. It can be seen that the global forecasting supermodel was able to forecast solar radiation for Abadeh, Jarqavieh, and Arak regions with 95%, 92%, and 90% accuracy coefficients, respectively. Finally, in a comparative scenario, various conventional machine learning and deep learning models are employed to forecast solar radiation in each of the study regions. The results of the above approaches are compared and evaluated with the results of the proposed FL-based method. The results show that, since no training data were available from regions of Abadeh, Jarqavieh, and Arak, the conventional methods were not able to forecast solar radiation in these regions. This evaluation confirms the high ability of the presented FL approach to make acceptable predictions while preserving privacy and eliminating model reliance on training data.

Biological and phytochemical potential of Baccharis trimera (Less.) DC leaf extract on swine clinical isolates.

Phytochemical studies have shown extracts obtained from the aerial parts of Baccharis trimera (Less.) DC has antioxidant and antimicrobial activities and the potential to treat some diseases. This study investigated the phenolic compounds, antioxidant and antimicrobial activity, and phytochemical potential of B. trimera leaf extract obtained by decoction on ATCC standard bacterial strains and 23 swine clinical isolates. Water was used as an extraction solvent based on the principles of green chemistry and at a low cost. The decoction process resulted in an extract rich in phenolic compounds and a high capacity for scavenging DPPH and ABTS radicals. Phytochemical analysis of aqueous extracts was performed using HPLC-DAD, and high concentrations of chlorogenic, ferulic, caffeic, and cinnamic phenolic acids were found. Antimicrobial activity was observed against gram-negative bacteria. B. trimera aqueous extract may be a promising low-cost agent for prophylactic treatment against swine enteropathogens and contribute to reducing production costs.

A Challenging Case Of Pulmonary Arterial Hypertension: Never Judge By Appearances

Abstract We report the case of a patient with symptomatic pulmonary hypertension (PH) associated with diffuse systemic sclerosis (SSc) whose initial assessment suggested a group 3 (clinical classification) PH. The patient had a history of drugs/toxins consumption, which contributed to the development of intrinsic pulmonary vascular disease. This changed the panorama towards the diagnosis of pulmonary arterial hypertension (PAH), with important therapeutic and prognostic implications. In fact, the excellent clinical, laboratory and hemodynamic response to therapy confirmed the hypothesis of a case of drug-associated PAH (DPAH) in a patient with diffuse SSc and lung disease. Considering the presence of DPAH, it was deemed necessary to assess acute vasoreactivity during right heart catheterization (RHC). If criteria were met, the clinical scenario may change towards a favorable and sustained clinical and hemodynamic response with oral calcium channel blockers. However, the response to inhaled nitric oxide was negative in our patient and the therapeutic strategy with dual oral combination therapy with tadalafil and ambrisentan was continued. After six-months of therapy the patient significantly improved, from a high to a low risk of one-year mortality.

Situational diagnosis of policies in Latin American and Caribbean countries for the use of fluoride and reduction of sugar consumption.

Policy evaluation and guidance on fluoride use and sugar consumption in Latin American and Caribbean countries (LACC) may provide a scientific evidence basis for policymakers, dental professionals, civil society organizations and individuals committed to improving public oral health. A cross-sectional study was conducted to evaluate the extent of implementation of policies/guidelines on fluoride use, and sugar consumption in LACC. The study had two stages. First a questionnaire covering four major areas was developed: fluoridation of public water supplies; salt fluoridation; fluoride dentifrices, and sugar consumption. Then, the questionnaire was applied to collect data among representative participants in public oral health from LACC. Ninety-six participants from 18 LACC answered the questionnaire. One-hundred seventy documents were attached, and 285 links of websites were provided by the respondents. Implementation of policies and guidelines on water and table salt fluoridation and processed and ultra-processed food consumption were found in most countries, with some issues in the consensus and coverage. Thus, differences were identified in the extent of implementation of public oral health strategies on sugar consumption and fluoridation among the countries. There is no consensus on the policies in LACC to reduce sugar consumption and for the use of fluoride. A few policies and guidelines were applied in isolated countries, with a variety of strategies and standards. For future actions, it will be important to encourage the development of strategies and public policies within countries, and to evaluate the effectiveness of existing policies in reducing dental caries and in improving oral health in LACC.

Association between the number of altered late potential criteria and increased arrhythmic risk in Brugada syndrome patients.

BACKGROUND: Brugada syndrome (BrS) is associated with abnormal electrophysiological properties at right ventricular epicardium, consisting of fragmented electrograms extending well beyond QRS termination. We aimed to evaluate the utility of signal-averaged electrocardiogram (SA-ECG) for the noninvasive assessment of late potentials (LP) and risk stratification of BrS patients. METHODS: A prospective, observational, single-center study of BrS patients is submitted to SA-ECG with the determination of the total filtered QRS duration (fQRS), root mean square voltage of the 40 ms terminal portion of the QRS (RMS40), and duration of the low-amplitude electric potential component of the terminal portion of the QRS (LAS40). LP were considered positive when above standard cut-offs: fQRS > 114 ms, RMS40 < 20 µV, and LAS40 > 38 ms. The rates of malignant arrhythmic events (MAEs), defined as sudden death or appropriate shocks, were compared in relation to clinical characteristics and SA-ECG findings. RESULTS: A total of 106 BrS patients (mean age, 48 ± 12 years, 67.9% male) were studied, 49% with type-1 spontaneous pattern and 81% asymptomatic. During a median follow up of 4.7 years, 10 patients (7.1%) suffered MAEs, including 4 sudden deaths. The presence of LP was significantly associated with the arrhythmic risk, which increased with the number of altered LP criteria. In comparison to the patients who had none or 1 altered LP criterium, MAE risk was 4.7 times higher in those with 2 altered criteria and 9.4 times higher in those with 3 altered LP criteria. CONCLUSIONS: SA-ECG may be a useful tool for risk stratification in BrS. The presence of 2 or 3 abnormal LP criteria could identify a subset of asymptomatic patients at high risk of arrhythmic events.

Recombinant Prevotella melaninogenica α-1,3 glucanase and Capnocytophaga ochracea α-1,6 glucanase as enzymatic tools for in vitro degradation of S. mutans biofilms.

Dental biofilms represent a serious oral health problem playing a key role in the development of caries and other oral diseases. In the present work, we cloned and expressed in E. coli two glucanases, Prevotella melaninogenica mutanase (PmGH87) and Capnocytophaga ochracea dextranase (CoGH66), and characterized them biochemically and biophysically. Their three-dimensional structures were elucidated and discussed. Furthermore, we tested the capacity of the enzymes to hydrolyze mutan and dextran to prevent formation of Streptococcus mutans biofilms, as well as to degrade pre- formed biofilms in low and abundant sugar conditions. The percentage of residual biofilm was calculated for each treatment group in relation to the control, as well as the degree of synergism. Our results suggest that both PmGH87 and CoGH66 are capable of inhibiting biofilm formation grown under limited or abundant sucrose conditions. Degradation of pre-formed biofilms experiments reveal a time-dependent effect for the treatment with each enzyme alone. In addition, a synergistic and dose-dependent effects of the combined enzymatic treatment with the enzymes were observed. For instance, the highest biomass degradation was 95.5% after 30 min treatment for the biofilm grown in low sucrose concentration, and 93.8% after 2 h treatment for the biofilm grown in sugar abundant condition. Strong synergistic effects were observed, with calculated degree of synergism of 5.54 and 3.18, respectively and their structural basis was discussed. Jointly, these data can pave the ground for the development of biomedical applications of the enzymes for controlling growth and promoting degradation of established oral biofilms.

Unraveling the functional dark matter through global metagenomics.

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.

Identification of mobile genetic elements with geNomad.

Identifying and characterizing mobile genetic elements in sequencing data is essential for understanding their diversity, ecology, biotechnological applications and impact on public health. Here we introduce geNomad, a classification and annotation framework that combines information from gene content and a deep neural network to identify sequences of plasmids and viruses. geNomad uses a dataset of more than 200,000 marker protein profiles to provide functional gene annotation and taxonomic assignment of viral genomes. Using a conditional random field model, geNomad also detects proviruses integrated into host genomes with high precision. In benchmarks, geNomad achieved high classification performance for diverse plasmids and viruses (Matthews correlation coefficient of 77.8% and 95.3%, respectively), substantially outperforming other tools. Leveraging geNomad's speed and scalability, we processed over 2.7 trillion base pairs of sequencing data, leading to the discovery of millions of viruses and plasmids that are available through the IMG/VR and IMG/PR databases. geNomad is available at https://portal.nersc.gov/genomad .