Articles tagged with Metagenomics
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.
A recent study published in Nature Communications has found a significant imbalance in the gut microbiome of individuals with Parkinson's disease. The researchers discovered that over 30% of micro-organisms and bacterial genes tested had altered abundances, indicating a widespread imbalance in the microbiome.
A study analyzed the potential of a bacterium to combat coffee rust, a major challenge for Brazilian coffee growers. The researchers found that the bacterium produces antibacterial and antifungal compounds, as well as proteins associated with protection against water stress, making it a promising candidate for biological control.
Researchers uncovered distinct DNA methylation profiles in ocean microbes, shedding light on population dynamics and interactions. The study's findings have significant implications for understanding pathogenicity and developing new approaches to monitoring environmental health.
A new study maps the global landscape of antimicrobial resistance, revealing surprising transmissions in Sub-Saharan Africa and highlighting the need for tailored strategies to combat resistance. The research, which analyzed sewage samples from 243 cities in 101 countries, found that resistance genes are more frequently transmitted acr...
A new study explores the value of 'trash data' from cancer genome sequencing, identifying new strategies to uncover previously unexplored information. The researchers found that genomic and transcriptomic data contain relevant information that can help elucidate carcinogenesis and discover putative biomarkers with clinical applications.
Researchers developed a machine learning-based diagnostic method that combines genomic sequencing and analysis of patients' immune response for remarkable accuracy. The approach identifies and predicts sepsis cases with high accuracy, potentially exceeding current diagnostic capabilities.
A new study by Johns Hopkins Medicine researchers reveals a promising genetic method for identifying hundreds of disease agents using next-generation sequencing. The Respiratory Pathogen Infectious Diseases/Antimicrobial Resistance Panel (RPIP) system shows near-comparability to traditional diagnostics in identifying pathogens.
New research finds that plants with shorter-lived flowers produce more fruits due to reduced microbial growth. Microbes on flowers can negatively impact plant yields.
A new study uses machine learning models to predict cancer patients' responses to immunotherapy based on their gut microbiome features. The research identifies common gut bacterial taxa associated with responders versus non-responders, providing a potential tool for distinguishing and predicting immunotherapy responders.
Researchers sequenced the whole genomes of three species of carpenter bees, gaining insights into their gut microbiome, diet, and viral load. They found beneficial bacteria, including Lactobacillus, which protect against fungal pathogens and boost the immune system.
Researchers developed a comprehensive regional diagnostic method using DNA testing, allowing for precise identification of microorganisms and estimation of their abundance. The technique has the potential to revolutionize our understanding of the ocean's food web and its role in removing greenhouse gases.
Researchers develop a refined microbiome fingerprint method to track sub-strain variations in key gut bacteria species. The study found differences in sub-strain dynamics between healthy individuals and hospitalized COVID-19 patients, suggesting an impending shift in the dominant strains of the gut microbiome.
Researchers have found that preterm infants with certain viral signatures in their gut are at risk of developing necrotizing enterocolitis (NEC), a serious and often fatal disease. The study highlights the potential for early warning signals to alert clinicians, allowing emergency action to be taken.
A new technique called Operational Genomic Units (OGU) allows for improved resolution and simplicity in analyzing microbiome samples. By using individual genomes as basic units, researchers can pinpoint biologically relevant characteristics such as age and sex with greater accuracy.
A study reveals that changes in gut microbiota and metabolome are associated with cardiovascular disease development, particularly coronary heart disease. The research found that alterations in the gut microbiome occur long before the onset of heart disease, suggesting a potential role for the microbiome in its early pathogenesis.
A comprehensive 'vertical map' of airborne microorganisms has been created, showing that temperature is the single most important factor influencing their composition. As global temperatures rise, this could lead to significant changes in the air microbiome, affecting human health and food security.
Researchers at the Earlham Institute developed a new approach to analyze metagenomic samples, combining advanced sampling techniques with mathematical models, to reveal crucial details of low-abundance species. This method, called adaptive sampling, offers a potential solution to enrich species of interest in metagenomic samples.
A new sequencing technique called 2bRAD-M has been developed to accurately identify species-level information from low-biomass and degraded microbiome samples. The method uses restriction site-associated DNA sequencing (RADseq) to produce high-resolution profiles of bacteria, archaea, and fungi down to the level of species.
The Microbiome and Metagenomics Center at UC San Diego will analyze stool samples from 10,000 All of Us Research Program participants to develop algorithms predicting individual responses to food. This will enable personalized nutrition recommendations based on an individual's genetics, gut microbes, and lifestyle factors.
Research reveals Japanese macaques in Kamikochi feed on aquatic insects and molluscs, supplementing their winter diet with high-nutritional value food sources. The unique behavior is attributed to the region's topography and hydrological environment, providing a stable food source for the macaques.
Researchers have identified specific skin microbiome bacteria and their pathways as contributing to ageing skin. The study, published in PLOS ONE, used a novel approach to chart host-microbe co-metabolism in skin aging.
Researchers developed an integrated framework combining single-cell and metagenomics to characterize microbes. The approach showed higher accuracy and precise binning, revealing more bacterial genera and intra-species diversity.
A novel metagenome assembler called MetaPlatanus has been developed to improve DNA sequence accuracy, including those of uncultured organisms. The tool uses accurate short DNA sequence reads to assemble contigs and scaffold larger chromosome-scale structures.
Researchers analyzed fecal metagenomic DNA sequencing data to see if specific donor strains correlated with successful treatment outcomes. They found no correlation between donor strains and response to anti-PD-1 therapy in melanoma patients.
The Verrucomicrobiota group of bacteria plays a crucial role in degrading polysaccharides released by algae during spring blooms in the North Sea. These specialized bacteria consume hard-to-degrade sugars, including those containing sulfate and fucose, using unique pathways and organelle-like structures to avoid toxic compounds.
Researchers successfully detected local mammals and birds by collecting 18 litres of water from a two-kilometre stretch along the river Mulde. The team identified 50% of fish species, 22% of mammal species, and 7.4% of breeding bird species in the region.
Researchers at Rice University are developing novel computational approaches to track environmental microbiome dynamics over time, across species and after perturbations. The team will use biofilm-based 'species abundance networks' on scaffolds to observe how they form their own genome-exchange networks.
The KAUST Metagenomic Analysis Platform (KMAP) enables researchers worldwide to analyze massive microbial data, eliminating the need for advanced bioinformatics skills. KMAP allows scientists to identify proteins and enzymes with potential applications in various industries, such as agriculture and pharmaceuticals.
A global study found that each city has a distinct microbial signature, with over 4,246 known species identified. The research also revealed a core set of 31 species found in 97% of samples across urban areas.
The conference aims to share experience in developing and applying bioinformatics algorithms, with topics including sequencing technologies, molecular sequence analysis, and genome assembly. Selected abstracts will be published as part of the BiATA 2021 BMC Bioinformatics supplement.
The study found that spinal cord injury-dependent effects on bacteria and viruses were observed, with beneficial bacteria decreasing and potentially pathogenic bacteria increasing. Functional microbial genes encoding essential pathways for central nervous system function were also reduced after spinal cord injury.
A public repository of 52,515 microbial draft genomes has been made available, revealing 44% new bacterial and archaeal diversity. The GEM catalog provides a valuable resource for understanding the biology and diversity of uncultivated microbes.
Researchers developed phyloFlash to analyze SSU rRNA from raw metagenome data, overcoming limitations of traditional methods. The user-friendly software identifies organisms in simple communities with high reliability.
Researchers have developed metaFlye, a new assembler for decoding microbial genomes from diverse environmental samples. The tool allows for the assembly of metagenomes, providing insights into the types and quantities of organisms present, their interactions, and substances synthesized.
MetaviralSPAdes is a new assembler for virus genomes, enabling biologists to reconstruct complete viral genomes from metagenome sequencing results. This tool tackles the challenge of identifying and stitching together viral sequences from thousands of bacterial genomes.
The new metadata-database helps researchers incorporate data on terrestrial microbiological communities into their work, making it easier to compare findings and avoid repeating experiments. With 15,022 metagenome datasets from forests or grasslands, the database enables global-scale analyses of microbiological communities.
A team of researchers in China has developed a new algorithm to compare metagenomes, allowing for more accurate understanding of microbiome diversity. The Dynamic Meta-Storms (DMS) algorithm compares metagenomes at the species level, considering physical and genetic details, as well as evolutionary relationships.
A recent study published in Annals of the Rheumatic Diseases reveals a novel link between the gut microbiome and host genome in the pathology of rheumatoid arthritis. The research found that bacteria belonging to the genus Prevotella were abundant in the gut microbiota of Japanese patients with rheumatoid arthritis.
Researchers report the discovery of a giant marine virus genome in predatory unicellular flagellates, encoding three rhodopsin photosensitive proteins. The findings suggest these viruses may confer phototrophic abilities on their hosts.
A recent study found that seaweed can travel up to 5000 kilometers beyond coastal areas and sequester significant amounts of carbon. This discovery has significant implications for the global carbon budget and highlights the importance of macroalgae in blue carbon assessments.
The OmCyn cyanobacterium has been found to have a worldwide distribution, hidden by its symbiotic relationship with a dinoflagellate. The discovery represents an ecologically important group of cyanobacteria and suggests that other undiscovered cryptic cyanobacterial lineages may exist.
Researchers have made an important advance in understanding the role of gut bacteria in human health, including diagnostic methods and therapies. The study found that patients with certain diseases had a smaller number of protein families in their microbiome compared to healthy individuals.
A new computational method called CATCH enables scientists to design molecular probes that can capture genetic material of various microbes, including viruses. This approach has been successfully tested in detecting low-abundance viruses like Zika, improving the detection of viral content in clinical samples.
Research on gut metagenome of patients with Crohn's disease shows a decrease in beneficial microbes and increased abundance of pathogenic Escherichia coli. The analysis identifies diverse strains of E. coli that can coexist in the human gut, influencing treatment efficacy.
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.