Articles tagged with Metagenomics
Comprehensive exploration of living organisms, biological systems, and life processes across all scales from molecules to ecosystems. Encompasses cutting-edge research in biology, genetics, molecular biology, ecology, biochemistry, microbiology, botany, zoology, evolutionary biology, genomics, and biotechnology. Investigates cellular mechanisms, organism development, genetic inheritance, biodiversity conservation, metabolic processes, protein synthesis, DNA sequencing, CRISPR gene editing, stem cell research, and the fundamental principles governing all forms of life on Earth.
Comprehensive medical research, clinical studies, and healthcare sciences focused on disease prevention, diagnosis, and treatment. Encompasses clinical medicine, public health, pharmacology, epidemiology, medical specialties, disease mechanisms, therapeutic interventions, healthcare innovation, precision medicine, telemedicine, medical devices, drug development, clinical trials, patient care, mental health, nutrition science, health policy, and the application of medical science to improve human health, wellbeing, and quality of life across diverse populations.
Comprehensive investigation of human society, behavior, relationships, and social structures through systematic research and analysis. Encompasses psychology, sociology, anthropology, economics, political science, linguistics, education, demography, communications, and social research methodologies. Examines human cognition, social interactions, cultural phenomena, economic systems, political institutions, language and communication, educational processes, population dynamics, and the complex social, cultural, economic, and political forces shaping human societies, communities, and civilizations throughout history and across the contemporary world.
Fundamental study of the non-living natural world, matter, energy, and physical phenomena governing the universe. Encompasses physics, chemistry, earth sciences, atmospheric sciences, oceanography, materials science, and the investigation of physical laws, chemical reactions, geological processes, climate systems, and planetary dynamics. Explores everything from subatomic particles and quantum mechanics to planetary systems and cosmic phenomena, including energy transformations, molecular interactions, elemental properties, weather patterns, tectonic activity, and the fundamental forces and principles underlying the physical nature of reality.
Practical application of scientific knowledge and engineering principles to solve real-world problems and develop innovative technologies. Encompasses all engineering disciplines, technology development, computer science, artificial intelligence, environmental sciences, agriculture, materials applications, energy systems, and industrial innovation. Bridges theoretical research with tangible solutions for infrastructure, manufacturing, computing, communications, transportation, construction, sustainable development, and emerging technologies that advance human capabilities, improve quality of life, and address societal challenges through scientific innovation and technological progress.
Study of the practice, culture, infrastructure, and social dimensions of science itself. Addresses how science is conducted, organized, communicated, and integrated into society. Encompasses research funding mechanisms, scientific publishing systems, peer review processes, academic ethics, science policy, research institutions, scientific collaboration networks, science education, career development, research programs, scientific methods, science communication, and the sociology of scientific discovery. Examines the human, institutional, and cultural aspects of scientific enterprise, knowledge production, and the translation of research into societal benefit.
Comprehensive study of the universe beyond Earth, encompassing celestial objects, cosmic phenomena, and space exploration. Includes astronomy, astrophysics, planetary science, cosmology, space physics, astrobiology, and space technology. Investigates stars, galaxies, planets, moons, asteroids, comets, black holes, nebulae, exoplanets, dark matter, dark energy, cosmic microwave background, stellar evolution, planetary formation, space weather, solar system dynamics, the search for extraterrestrial life, and humanity's efforts to explore, understand, and unlock the mysteries of the cosmos through observation, theory, and space missions.
Comprehensive examination of tools, techniques, methodologies, and approaches used across scientific disciplines to conduct research, collect data, and analyze results. Encompasses experimental procedures, analytical methods, measurement techniques, instrumentation, imaging technologies, spectroscopic methods, laboratory protocols, observational studies, statistical analysis, computational methods, data visualization, quality control, and methodological innovations. Addresses the practical techniques and theoretical frameworks enabling scientists to investigate phenomena, test hypotheses, gather evidence, ensure reproducibility, and generate reliable knowledge through systematic, rigorous investigation across all areas of scientific inquiry.
Study of abstract structures, patterns, quantities, relationships, and logical reasoning through pure and applied mathematical disciplines. Encompasses algebra, calculus, geometry, topology, number theory, analysis, discrete mathematics, mathematical logic, set theory, probability, statistics, and computational mathematics. Investigates mathematical structures, theorems, proofs, algorithms, functions, equations, and the rigorous logical frameworks underlying quantitative reasoning. Provides the foundational language and tools for all scientific fields, enabling precise description of natural phenomena, modeling of complex systems, and the development of technologies across physics, engineering, computer science, economics, and all quantitative sciences.
Researchers are using advanced DNA sequencing technologies to monitor environmental reservoirs of antibiotic resistance genes and assess their impact on human health. The study highlights the importance of integrating gene detection, host identification, and quantitative analysis to evaluate environmental antibiotic resistance.
This study found differences in fecal microbiome and bile acid content between preterm infants with parenteral nutrition-associated cholestasis (PNAC) and those without PNAC. PNAC development was associated with higher abundance of Proteobacteria, Fusobacteriota, and lower Bacteroidota in cholestatic infants.
Scientists successfully sequenced a woolly rhinoceros genome from a 14,400-year-old tissue sample found in an ancient wolf's stomach. The study reveals that the species likely died out due to rapid population collapse rather than gradual decline.
Researchers discover that excess hydrogen disrupts microbial balance, triggering major shifts in metabolism and viral dynamics. This study provides molecular-level evidence on the effects of hydrogen oversupply on methane production, highlighting the need for gas-ratio control in industrial reactors.
A team of HSE researchers has created a comprehensive map of quadruplexes, unstable DNA structures involved in gene regulation. The study reveals that quadruplexes function in pairs, regulating tissue-specific genes in healthy tissues and cell growth and division in cancerous tissues.
Researchers at Arizona State University introduce powerful tools to analyze microbial family trees and biological data, strengthening microbiome research, disease tracking and environmental monitoring. The new software library scikit-bio provides a foundation for analyzing large biological datasets.
Researchers have successfully isolated and sequenced RNA molecules from Ice Age woolly mammoths, providing new insights into the biology of extinct species. The study reveals that RNA can be preserved for nearly 40,000 years, offering a glimpse into the final moments of life.
MARTi enables rapid taxonomic classification and abundance analysis of microorganisms in various settings, including agriculture, environmental monitoring, and clinical environments. The tool provides immediate analysis results, allowing for quick identification and targeted treatments of pathogen infections.
The Global Pathogen Analysis Platform (GPAP) will enable low- and middle-income countries to conduct research and surveillance of infectious diseases independently. The platform aims to prevent disease outbreaks from developing into pandemics by detecting genetic sequences of potential pathogens.
Dr. Amin's transformative insights reshape international understanding of depression genetics, identifying novel therapeutic targets and biomarkers for diagnosis and treatment. Her systemic disease model challenges traditional views of depression as a brain disorder.
Scientists developed a method to isolate genes from tiny amounts of microbial DNA, revealing previously unknown antibiotic resistance genes. The researchers discovered new types of efflux pumps and an entirely new family of streptothricin resistance proteins in bacterial DNA isolated from human stool and aquarium samples.
Researchers found that children with stable gut microbiomes tend to have better growth outcomes. The study created the first-ever pediatric undernutrition microbial genome catalog, which can predict and prevent malnutrition. This discovery opens the door to new diagnostics and therapeutics for addressing global child stunting issues.
A recent study found that individuals with a specific type of gut bacteria (Firmicutes) had higher bone mineral density and better metabolic health. The researchers suggest that promoting the growth of butyrate-producing bacteria could be an effective strategy for maintaining bone mass and preventing osteoporosis.
Researchers have found new organisms that can capture carbon dioxide and clean pollutants from the environment. By exploring extremophiles in homes, scientists can gain insights into their unique characteristics and develop sustainable solutions.
Researchers discovered that sulfur bacteria from the Desulfobacteraceae family work together like a team to break down diverse organic compounds. By analyzing six strains, they found similar molecular strategies and a highly energy-efficient central metabolism pathway, enabling them to thrive in oxygen-free environments.
A new method for detecting antibiotic resistance genes (ARGs) in wastewater has been developed by researchers, which uses CRISPR-Cas9 technology to enrich ARG fragments and increase detection sensitivity. This enhanced method was found to detect 1189 more ARGs and 61 more ARG families compared to standard metagenomics methods.
Researchers at the Institute for Systems Biology (ISB) have developed a breakthrough method to track diet using stool metagenomic data. The MEDI approach detects food-derived DNA in stool samples to estimate dietary intake, offering a convenient alternative to traditional methods that suffer from misreporting and compliance issues.
A large-scale study analyzed the gut microbiomes of over 21,500 individuals and found that vegan diets had the healthiest microbiomes, followed by vegetarians and omnivores. The researchers discovered unique microbial signatures for each dietary pattern, with vegans having more beneficial bacteria associated with fiber fermentation.
A new study reveals that bacteria species in Lake Mendota rapidly evolve over time, responding to changing seasonal conditions. The researchers found that hundreds of separate species would return almost fully to near copies of their genetic predecessors after a thousand or so generations of evolutionary pressures.
Joe DeRisi, Chan Zuckerberg Biohub San Francisco President and UC San Francisco Professor, received the Arthur Kornberg and Paul Berg Lifetime Achievement Award in Biomedical Sciences. His work has significantly impacted pathogen discovery, disease tracking, and clinical diagnostics through metagenomic sequencing.
Researchers discovered a highly stable carbonic anhydrase enzyme CA-KR1, accelerating CO₂ dissolution in water. The enzyme enhances CO₂ capture productivity by 90% under industrial conditions.
A new k-mer sketching metagenomic profiler called sylph has been developed at Carnegie Mellon University, allowing for faster and more precise analysis of genomic data. The method breaks bacterial genomes into smaller subsamples and compares them to the initial sample, enabling the detection of rare genomes present in the sample.
A groundbreaking metagenomic sequencing test has proven effective in rapidly diagnosing almost any kind of pathogen, including viruses, bacteria, fungus or parasite. The test analyzes all nucleic acids present in a sample, replacing multiple tests with a single one and speeding up diagnosis.
The journal has been indexed and archived in over 60 databases and received a Scopus CiteScore of 5.4, placing it in Q1 in several categories. Its inclusion in the Web of Science will further enhance its visibility and impact.
A study found that doxycycline post-exposure prophylaxis (doxy-PEP) did not significantly alter the overall composition of gut bacteria in individuals who took it for six months. However, the researchers noted signs of resistance building against tetracycline, a class of antibiotics to which doxycycline belongs.
A new study from European universities has developed a method to analyze wastewater data from seven major cities, identifying thousands of disease-causing bacteria, viruses, and antimicrobial resistance. This approach can detect potential health threats simultaneously, potentially preventing epidemics from escalating into outbreaks.
Researchers have developed a comprehensive database of the 'food microbiome' by sequencing metagenomes from 2,533 foods, identifying 10,899 food-associated microbes. The study shows that these microbes can influence human health and provide insights into how to improve food quality, safety, and authenticity.
The study evaluated the impact of database choice and confidence score on Kraken2's classification performance. Higher confidence scores generally decreased classification rates in smaller databases, while larger databases maintained higher rates and showed improved precision and F1 scores with increasing confidence.
A new software platform has been developed to investigate viral genomes of the world, revealing unique viruses that may impact human health and exacerbate conditions like irritable bowel disease. The 'Hecatomb' project also provides a robust method for identifying viruses in all animals, plants, and environments.
A deep metagenomic sequencing study in Berlin wastewater reveals common viruses like RSV and flu, seasonal visitors like asparagus-infecting viruses, and astroviruses with potential for gastrointestinal tract infections. The analysis also identifies novel enzymes with biotechnological potential, expanding our knowledge of viral diversity.
Researchers created GraSSRep and rhea, tools that outperform current methods for handling repeats and structural variants in metagenomic data. These methods use self-supervised learning and graph neural networks to analyze microbiome data, offering new insights into biological processes and potential applications in antibiotic resistance.
Researchers at the University of Trento have identified a collection of molecular tools to rewrite DNA, including a compact Cas9 enzyme from the human microbiome. The discovery has potential for gene therapy applications and could speed up the development of therapies for genetic diseases.
A mysterious plasmid, pBI143, found in 90% of human intestines, could be used to identify faecal contamination and offer insights into intestinal diseases. The discovery also highlights the prevalence of 'cryptic' plasmids in human gut microbiota.
Researchers at MBL have found a genetic arrangement that confers antibiotic resistance to the bacterium Bacteroides fragilis, which may help it protect itself from tetracycline. The study highlights the role of transposons in horizontal gene transfer and potential mechanisms for controlling gene expression.
A new metagenomics tool has improved the diagnosis of infections by detecting rare pathogens with high accuracy. The tool was tested on 742 samples from 523 patients and showed a diagnostic yield of over 25% in cases where infection was strongly suspected.
Researchers analyzed DNA sequenced datasets of microbes collected from salt marsh sites to study the relationship between cordgrasses and sulfur-cycling microbes. They found diverse microbial communities with varying combinations of genes for sulfate reduction and sulfur oxidation, allowing them to thrive in salt marsh sediments.
A new study doubles the number of protein families known up until now and identifies many novel structure predictions using a massive analysis of 1.3 billion proteins. The researchers leveraged AI methodologies to unravel the roles of previously unknown protein sequences, expanding the horizons of potential functions.
A study published in eBioMedicine identified 9 sets of biomarkers, both metagenomic and transcriptomic, associated with 30-day mortality in patients with severe community-acquired pneumonia. The biomarkers were validated with an accuracy of 85%, significantly higher than existing clinical prediction models.
The Biodiversity Knowledge Hub (BKH) is a one-stop portal providing access to FAIR biodiversity data and services. It enables researchers to navigate linked data, tools, and services across the entire biodiversity research cycle.
Researchers analyzed dairy cows' uterine microbiota and found significant associations with fertility, including a correlation between microbial diversity and AI frequency. The study suggests that farm-to-farm variations in microbiota can impact fertility, paving the way for new diagnostic approaches to low fertility in dairy farms.
Researchers found that viruses can insert genes into bacteria to help them adapt and survive in nutrient-depleted man-made environments. The study also identified novel immune systems against viruses in bacteria and detected antibiotic resistance genes in viruses on human skin and surfaces.
Researchers have discovered that eukaryotes, including plants, animals, and fungi, share a common ancestor among the Asgards. The team identified a newly described order called the Hodarchaeales as the closest microbial relative to all complex life forms on the tree of life.
Researchers investigated how gut bacteria respond to repeated antibiotic disruptions, finding that they evolve antibiotic-resistant variants and adapt through slowing of cell growth. The study reveals the complex response of the microbiome to antibiotics, including ecological effects and induction of prophages.
A new study reveals that previously unknown antibiotic resistance genes are widespread in bacteria across various environments, including the human microbiome. The findings suggest that these genes can pose a significant threat to human health, highlighting the need for enhanced understanding of their development and spread.
Researchers discovered Vibrio pathogens can stick to microplastics, adapting to plastic, and have aggressive behavior, forming biofilms and causing infections. The study highlights the risks of Sargassum-plastic marine debris interactions, with potential for opportunistic pathogens and disease transmission.
Researchers at York University found more pathogens and parasites in urban bee populations, leading to inbreeding and reduced genetic diversity. Conservation efforts focused on green spaces and habitat connectors can help mitigate these effects.
Researchers discovered that certain bacterial species, including lactic acid bacteria, correlate with high levels of Candida yeasts in the gut microbiome. This suggests a complex interaction between these microorganisms, where lactic acid bacteria may favor Candida proliferation while making the fungus less virulent.
Researchers reconstructed ancient bacterial genomes from human and Neanderthal remains to discover previously unknown metabolites, including paleofurans. This breakthrough expands the ability to study microbial natural products, offering insights into the nutrition and health of early hominins.
GPMeta accelerates pathogen detection in metagenomic sequencing (mNGS) tests, achieving higher accuracy while significantly reducing processing time. The approach uses a succinct hash index scheme and multi-GPU support to handle massive data sets.
Rapid metagenomics can provide accurate results within just 6 hours of knowing bacteria are growing in a blood sample, allowing for effective treatment 18-42 hours earlier than conventional laboratory tests. Metagenomic sequencing has the potential to save lives and better manage the use of antibiotics by rapidly identifying antimicrob...
Researchers discovered that viruses that infect bacteria and archaea in deep-sea hydrothermal vents share a common immunological memory, allowing symbiotic microbes to defend against the same virus. This challenges conventional wisdom on virus-host interactions, revealing a more nuanced relationship between these microorganisms.
Researchers at CZ Biohub SF developed a new diagnostic method for LRTI in children, leveraging machine learning and genomics to identify pathogens with high accuracy. The method uses metagenomic sequencing data to analyze gene expression and microbial abundance, providing a more holistic approach to diagnosing the condition.
A German-Dutch research team has created the first map of the Microverse, redefining microbial niches. Generalists, which can cope with a wide range of conditions, dominate most habitats, while specialists have more specific environments and smaller genomes.
A study found that honeybee hive debris contains diverse genetic information from environmental bacteria, fungi, and plants, indicating unique microbial signatures for each city. This could be used to assess the overall health of cities and honeybees.
A study published in the Journal of Infection found that mNGS was significantly more effective at detecting bloodstream infections than conventional microbiological tests (CMTs), identifying 187 infection cases compared to CMTs' 81. Viral infections were the most common type, with CMV being the leading cause.
A study published in Nature Communications reveals that microbes living on the leaves of perennial crops like miscanthus and switchgrass play a crucial role in plant resilience. The research identifies specific microbial functions that could be targeted for future management, promoting crop growth and reducing environmental impact.
Researchers from Hiroshima Shudo University and the University of Tokyo have successfully identified species of deep-sea brittle stars using a novel metabarcoding approach. This method analyzes environmental DNA released from marine invertebrates, enabling efficient and cost-effective monitoring of biodiversity.
A study published in PLOS ONE found that common microbiome analysis techniques can yield erroneous results due to incomplete DNA databases. The researchers used computer simulations to test the consistency of current methods, showing that a large number of detected species are not actually present in the community.
Researchers identified a new type of flagellin in the human gut that binds to Toll-like receptor 5 without inducing an inflammatory response. This discovery provides a mechanism for the immune system to tolerate beneficial microbes while remaining responsive to pathogens.
Researchers have documented cases of Japanese macaques hunting and eating fish in the Kamikochi region of Japan, suggesting an evolutionary adaptation to harsh winter conditions. The behavior appears to be an extension of existing feeding habits on vegetation and aquatic plants, with potential implications for future generations.