Articles tagged with Metagenomics
Researchers created Knomics-Biota to analyze metagenomic data, identifying bacteria types, proportions, and beneficial substances. The platform allows users to visualize results and compare data with thousands of other samples, facilitating international collaborations in microbiome analysis.
New research from North Carolina State University and the University of Copenhagen finds that most bacterioplankton are B1 auxotrophs, meaning they have to glean the vitamin or pieces of it from their environment. The study also reveals fluctuations in genes responsible for making and/or using environmental B1 and precursors over time.
Bacterioplankton's reliance on vitamin B1 and its precursors has been found to be more significant than previously thought. This study highlights the crucial role of exogenous nutrient availability in supporting growth and nutrient cycling in aquatic ecosystems.
Researchers have discovered a new family of enzymes in the human gut microbiome that can remove red blood cell antigens, enabling the conversion of type A and B blood into universal O-type blood. These enzymes are 30 times more effective than previously studied candidates, paving the way for potential clinical trials.
Researchers analyzed preschool-age children's supragingival microbiomes to understand early childhood caries (ECC) development. Notable differences in bacterial species abundance were found among caries-free, restored disease, and untreated disease groups, suggesting that restorative care alone may not reverse ECC-associated dysbiosis.
A study by international scientists found that viruses cluster in genetically similar organisms and agricultural land, leading to a higher prevalence of viral infections. The research also reveals a vast number of viruses in the natural compartment, which can inform the emergence of plant diseases.
The CAMI challenge ranked metagenome interpretation tools to provide a roadmap for biologists. Biologists face challenges due to the high number of tools and limited accuracy assessments.
The Critical Assessment of Metagenome Interpretation (CAMI) Challenge evaluated computational tools for metagenomes, assessing assemblers, binners, and taxonomic profilers. The benchmarking results provide performance overviews for developers and applied scientists, informing the selection of suitable software for research questions.
Scientists evaluated metagenomics software using international competition benchmarks to assemble, classify, and analyze complex pools of bacterial DNA. The results showed that different algorithms perform better in various contexts, highlighting the need for researchers to choose software based on specific questions.
A team led by David Baker used metagenomic sequences to generate structural models for 614 proteins, including those from neglected families. The collaboration between the Baker lab and DOE JGI enabled a powerful way of predicting structures, increasing coverage of known protein families.
A new metagenomics methodology can quickly diagnose foodborne bacterial outbreaks by analyzing DNA sequencing data. This approach identified Salmonella pathogen variants and detected co-infections with Staphylococcus aureus, revolutionizing disease surveillance.
Scientists developed MetaFast, a software tool that rapidly analyzes metagenomes to identify previously unknown pathogens and develop personalized medicine. The algorithm can work with unknown environments and detect microorganisms like viruses.
Researchers have created a robust method for comparing metagenome-coupled DNA sequences from all organisms in a sample, allowing for more effective and quick comparison of samples. This approach, based on k-mer frequencies, can detect previously unknown segments of DNA and improve the analysis of intestinal bacteria.
A team of researchers has identified a completely new bacterial phylum, dubbed 'Kryptonia', in geothermal springs using metagenomics and single-cell genomics. The novel phylum was found to have unique metabolic pathways and potential biotechnological applications.
Advances in statistics are helping to understand the complex roles microbes play in human biology. The study found no significant association between BMI and bacterial species abundance in the gut microbiome.
Researchers used longer-read sequencing technology to reconstruct microbial communities, revealing over 400 previously unknown species and improving understanding of environmental processes.
Los Alamos scientists have developed a new tool for analyzing microbial communities, GOTTCHA, which can identify co-infections in medical samples. The tool uses a database of reference genomes to classify individual metagenome sequences and provide relative abundance profiles of organisms found within a sample.
MaxBin facilitates genomic analysis of uncultivated microbial populations by automatically sorting their genomes from metagenomic sequences. The software uses an expectation-maximization algorithm to classify metagenomic sequences into discrete bins representing individual microbial species.
Researchers have developed a new DNA sequencing method that can detect and characterize the bacteria causing tuberculosis in a matter of days, without the need for time-consuming laboratory culture. The technique, known as metagenomics, uses high-throughput sequencing technologies to analyze DNA extracted from sputum samples.
Researchers used shotgun metagenomics to sequence DNA from a calcified nodule in a 700-year-old skeleton, recovering the genome of Brucella melitensis, a disease causing fevers and arthritis. The ancient strain was closely related to recent strains found in Italy, providing insights into medieval infections.
Researchers have developed a cost-competitive way to extract fermentable sugars from lignocellulosic biomass using thermophilic microbes. The most active populations in the switchgrass-deconstructing consortium were identified as Gemmatimonadetes and Paenibacillus, which show potential for biofuel production.
Researchers successfully recovered TB genomes from a 215-year-old mummy using metagenomics, revealing mixed-strain infections and strain lineages circulating in Europe for centuries. The study highlights the significance of mixed-strain infections and the effectiveness of metagenomics in tracking microbial evolution.
A study published in Nature found that patients with type 2 diabetes have an altered gut microbiota, which can predict the risk of developing diabetes. The researchers developed a new model to analyze the metagenome and distinguish between patients with type 2 diabetes and healthy women.
Researchers used metagenomics to reconstruct genome sequence of Shiga-toxigenic E. coli outbreak strain, identifying pathogens without laboratory culture. The approach showed potential for rapid identification and characterization of bacterial pathogens in clinical specimens.
Researchers found altered gut microbiota in healthy subjects compared to stroke patients, with increased carotenoid-producing genes and higher blood levels. The study suggests a potential role for probiotics in preventing cardiovascular disease.
A new study by European Molecular Biology Laboratory researchers found that each person's gut metagenome is unique and remains stable over time. The analysis of 207 individuals revealed a high resolution of individual mutations in gut microbes, with potential applications for identifying gut diseases and developing personalized therapies.
Scientists sequenced nearly all genes in an underground microbe community at a contaminated uranium mill site, assigning them to 80 different microbes. The findings could help improve clean-up methods for heavy metal contamination, including arsenic and mercury.
Researchers identify 60,000 T2D-associated metagenomic markers in Chinese patients and develop a new classification system using metagenomic linkage groups. Healthy individuals have higher butyrate-producing bacteria, while T2D patients show an increase in opportunistic pathogens.
Researchers mapped the normal microbial make-up of healthy humans, shedding light on vital tasks such as immune system support and food digestion. The study reveals a unique personal microbiome for each individual, with over 10,000 species occupying the human ecosystem.
The Human Microbiome Project identified a diverse and abundant microbiota in healthy humans, with varying composition across body sites and individuals. Ethnic/racial background was found to be the strongest association for diversity in the Western human microbiome.
Researchers sequenced the microbial communities inside a Tammar wallaby's gut, identifying a bacterium that could help reduce methane emissions in livestock. The study provides insights into the unique gut microbiome of macropods and may lead to strategies for modifying fermentation to produce less methane.
Susannah Tringe, DOE JGI scientist, awarded grant to study microbial communities in restored wetlands and their impact on long-term carbon sequestration from a genomic perspective. Her research aims to understand the role of belowground microbial communities in carbon storage and recycling.
The Human Microbiome Project has launched a centralized database for sequencing microbial genomes, providing a unique resource for future investigations. The HMP has cataloged over 1,400 individual human microbiome projects, enabling researchers to study the interactions between human and microbial cells.
Researchers identified a mysterious microbe, SUP05, that plays a crucial role in shaping the ecology of oxygen-deficient zones. The microbe helps remove toxic sulfides and fixes carbon dioxide, but also produces greenhouse gases, making it a paradoxical organism.
Scientists used novel DNA sequencing technology to analyze bug splatters on car windshields, estimating insect diversity in the region. The study's metagenomic pipeline accurately identified sequences corresponding to various insect taxa, including significant differences between two trips.
Undergrads are enlisted by lecturers to tackle DNA annotation challenge using innovative Annotathon approach. This teaching method trains students as apprentice bioinformaticians to analyze unknown metagenomic DNA fragments and gain confidence in bioinformatics.
The metagenomics field is gaining traction, allowing researchers to reconstruct metabolic profiles of microbes from environmental samples. DOE JGI's advancements in this area are crucial for understanding microbial diversity, as they have characterized many metagenomes across various ecosystems, including acid mine drainage and gut env...
The U.S. Department of Energy Joint Genome Institute has updated the Integrated Microbial Genome System with new microbial genomes, improving its capabilities for analyzing metagenomic data. The system now includes tools for exploring gene cassettes conservation and examining functional annotation of genomes.
A novel approach extracts single genomes and discerns specific microbial capabilities from mixed community sequence data. The research team characterized biochemical pathways associated with nitrogen cycling and methane utilization in Lake Washington sediments, revealing novel versions of metabolism.
Researchers developed a bioinformatics technology that analyzed more than 14 million microbial and viral sequences, revealing distinctive metabolic profiles among viral metagenomes. This discovery has the potential to answer questions about viral dynamics in diseases like cystic fibrosis.
The U.S. Department of Energy Joint Genome Institute has released an upgraded version of its IMG/M metagenome data management and analysis system, featuring five new metagenome datasets from recent studies on termite hindgut microbiota and TM7 microbe. The new system now contains 2,953 reference genomes.
A recent study using metagenomics reveals a surprising high number of quorum sensing genes in the deep Mediterranean, indicating microbes associate with detritus particles. These bacteria have been found to be luminescent, possibly to attract prey in the food-scarce environment.
The DOE JGI has established a gold standard for metagenomic data analysis, enabling accurate classification of sequence fragments into species populations. The method involves simulating metagenomes with known sample genomes, allowing researchers to evaluate the predictive accuracy of existing tools and identify potential pitfalls.
The DOE JGI has released the latest upgrade of its metagenomics data management and analysis system, IMG/M. The enhanced version provides aggregate genome data from recent studies on biological phosphorus removing sludge, human distal gut, a gutless marine worm, and obese and lean mouse gut.
The DOE Joint Genome Institute has released a new tool for analyzing metagenomic data, IMG/M, which integrates aggregate genome data from diverse microbial communities with isolate genome data. The system allows for the examination of functional annotation profiles and strain-level heterogeneity within species populations.
The UC San Diego-Venter Institute partnership aims to create a community resource for metagenomic data, facilitating advances in marine microbial ecology and evolutionary biology. The project will develop a novel cyberinfrastructure to store, analyze, and draw conclusions from large-scale microbial genomic sequence data.
The NIDCR-launched study aims to detect unique patterns of gene expression in oral bacterial communities that predict periodontal diseases. The researchers will store biological information in a searchable online database, allowing for more precise diagnosis and treatment.