Articles tagged with Metagenomics
Researchers developed Metax, a computational tool that accurately identifies and estimates the abundance of microorganisms in complex samples. This improves taxonomic profiling, helping to uncover microbial patterns linked to health and disease.
Researchers discovered a distinctive pattern in DNA polymerase genes from China's Napahai plateau wetland, suggesting the unique geography and environmental conditions of the wetland contribute to the genetic diversity of microbial communities. This finding raises the possibility that DNA polymerase genes could serve as biogeographical...
A new study reports that loading biochar with oxygen nanobubbles can help overcome the problem of rapid oxygen depletion in flooded rice soils, creating a more oxidizing environment around rice roots. This leads to reduced cadmium accumulation in rice plants and improved plant growth.
A new global database has been developed to map pathogens and antibiotic resistance risks in coastal waters, providing a practical tool for assessing biological risks. The Coastal Water Pathogen Database integrates shotgun metagenomic sequencing data from six coastal regions across three continents.
The partnership aims to develop genomic tools addressing large-scale problems in health and the environment, combining research strengths across UC San Diego's departments. The collaboration will accelerate discovery and drive real-world impact, leveraging CRISPR technology and microbiome-editing tools.
A new study reveals that a small group of highly connected microorganisms helps maintain essential ecosystem functions, such as carbon and nitrogen cycling, despite major shifts in the wider microbial community. The research found functional redundancy, where different microorganisms can perform similar ecological roles.
Researchers have developed an iron-modified biochar additive that significantly reduces ammonia and nitrous oxide emissions during pig manure composting. The additive enhances microbial activity, improves nitrogen cycle efficiency, and produces a more toxic-free compost product.
Researchers identified genetic changes in the virus that explain why it wasn't detected by existing tests. The new diagnostic method shows promise for future suspected cases with greater accuracy.
J. Craig Venter's pioneering work in expressed sequence tags revolutionized brain-expressed genes identification, while his synthetic cells paved the way for synthetic biology as a working discipline. His legacy has reshaped our understanding of genomes and their functions.
Researchers have developed a new metagenomic software called nanoMDBG, which enables faster and more accurate analysis of microbial diversity. The software can assemble microbial genomes from nanopore sequencing data, allowing for the tracking of complex microbial communities over time.
A team from Emory University developed a simple method to test the accuracy of protein language models, which are used to analyze complex biological data. By comparing how these models 'embed' natural proteins versus synthetic ones, researchers can estimate their reliability and improve their performance.
A study found that age, biological sex, and human genetic factors determine the quantity and specificity of antibodies produced in response to viral infections. The research has significant implications for vaccine and therapeutic design, as it shows that individual profiles can be tailored to improve treatment effectiveness.
Scientists from the University of Texas at Austin have solved the mystery of how complex life evolved. The discovery suggests that eukaryotes arose when an Asgard archaeon developed a symbiotic relationship with an alphaproteobacterium, which led to the evolution of mitochondria and oxygen-based energy metabolism.
A global study found that a group of bacteria, CAG-170, consistently appeared in high numbers in the gut microbiomes of healthy individuals. This species has the capacity to produce Vitamin B12 and break down carbohydrates, suggesting it plays a crucial role in maintaining human health.
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 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.
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.
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.