Articles tagged with Bacterial Genomes
Researchers have made significant breakthroughs in understanding the human gut microbiome by focusing on bacterial strains rather than species. By using a new computational method, scientists can analyze the strains of bacteria present in a microbiome sample more quickly and affordably.
Researchers identified 'pre-resistance' signs in bacteria, predicting future resistance to antibiotics. This discovery allows doctors to select the best treatments for bacterial infections and paves the way for personalized genomic therapy.
A study of Edo-era Japanese skeletons reveals a prevalence of periodontal disease similar to modern times, with distinct bacterial species. Researchers analyzed dental calculus from 12 human skeletons and compared their oral microbiomes to modern samples, shedding light on the evolution of the oral microbiome.
A recent study uses machine learning to rapidly discover bacterial isolates with antifungal properties, identifying promising new compounds for crop protection. The approach analyzes thousands of microbial genomes at once, allowing researchers to identify novel beneficial microbes and bypass traditional screening tactics.
Researchers developed a kinetic hypothesis governing the evolution of the Last Universal Common Ancestor (LUCA) based on simulation experiments. They discovered a kinetic factor that governs the flow of chemical reactions in the TCA cycle, validating their hypothesis for deep-branching bacteria and archaea.
A rapid same-day test has been developed to identify secondary infections in COVID-19 patients on intensive care, allowing for targeted antibiotic treatment and reduced risk of antimicrobial resistance. The test uses nanopore sequencing technology to analyze bacterial and fungal pathogens present in patient samples.
A new computer program called Codetta can analyze the genome sequences of over 250,000 bacteria and archaea to identify alternative genetic codes. This could help scientists understand how genetic codes evolve and change.
Scientists found ancient bacteria in permafrost resistant to streptomycin, spectinomycin, chloramphenicol, and tetracycline. Genome analysis revealed limited differences between ancient and modern strains, suggesting a potential threat to human health due to global warming.
Researchers at Cornell University used machine learning to predict the spread of antibiotic resistance genes among bacteria, identifying potential networks of exchange and driving factors. The approach could help control the spread of antibiotic resistance and develop new targets for novel antibiotics.
Researchers found that Pseudomonas aeruginosa populations in CF patients' sinuses vary widely, with evolution following two stages: pathoadaptive community formation and fragmentation. This discovery may inform new therapeutic approaches by focusing on strongest evolutionary pressures.
Researchers found that DNA tangles create mutational hotspots in bacterial genomes, influencing evolution. By altering the sequence to prevent hairpin tangles, they can predict how microbes might mutate under selective pressure.
Researchers uncovered a remarkable diversity of bacteria associated with fungi, detected in 88% of examined fungal isolates, shedding light on the complexity of the fungal bacteriome. This discovery opens up possibilities for studying bacterial-fungal interactions and their impact on ecosystem functioning and climate change.
Researchers discovered two defence systems in bacteria that work together to protect against modified DNA bacteriophages. BrxU has the potential to be a biotechnological tool for mapping the human epigenome, which alters in cancer and neurodegenerative diseases.
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.
Researchers are sequencing genomes of 700 Bacilli bacteria to enhance CDC's capacity for detecting novel infectious disease agents. The goal is to create a large database of Bacilli to support rapid laboratory methods for detecting emerging biothreats.
Researchers at MIT and Institut Pasteur have created an efficient method for assembling entire genomes, including the human genome, in minutes using personal computers. This approach uses minimizer-space de Bruijn graphs to store only a small fraction of nucleotides while preserving overall genome structure, enabling faster processing ...
A new genomic and geological mapping tool helps track listeria found in ingredients, processing facilities and finished products by pinpointing sources of contamination. The nationwide atlas reveals the natural distribution of listeria across the US, aiding in the identification of risk areas.
Researchers have mapped the structure of CRISPR-Cas12j3 from bacteriophages, a discovery that reveals how it works and solves packaging problems for genome editing. The new system has vast potential for precise genome editing with improved efficiencies and alternative targeting mechanisms.
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.
MIT researchers have created a new DNA writing technique called HiSCRIBE that can record interactions between cells and store spatial information. This approach offers a way to edit genes in the human microbiome, potentially revolutionizing the field of genome editing.
A new study published in Genome Biology found that the ability of gut bacteria to produce spores is associated with their adaptation to humans. Bacteria that can produce spores have larger genomes and are less abundant in the gut, while those that cannot have smaller genomes and are more adapted to human hosts.
Researchers at Washington University in St. Louis used comparative metabologenomics to study the genomes of Streptomyces bacteria and identify key factors that influence drug production. The study found that fine-tuning of specific nucleotides can control antibiotic production, offering new insights for next-generation drug discovery.
Researchers at the University of Cologne discovered a rare tripartite symbiosis between a ciliate, a green alga and a previously unknown purple bacterium. The genome of the purple bacterium is greatly reduced, suggesting it relies on photosynthesis for survival.
Researchers have developed cells that can construct artificial polymers from building blocks not found in nature, while also making them resistant to viral infections. This breakthrough could lead to the development of new polymers and more reliable manufacturing of certain drugs using bacteria.
Scientists have created a new instrument that can sort and sequence the genome of individual soil bacteria while identifying their functions. The RACS-Seq technique uses laser tweezers and gravity to analyze each bacterium one by one.
Researchers have discovered a novel formaldehyde sensor in bacteria that helps them detect and respond to elevated levels of the toxic chemical. The EfgA protein directly senses formaldehyde and stops bacterial growth to protect cells.
Researchers have shown that CRISPR-Cas components are physically linked, enabling efficient updates of immune memory when infected by mutant viruses. This link allows bacteria to efficiently adapt and interfere with viral infections.
Researchers have successfully split the E. coli genome into tripartite-genome of 1 million base pairs per genome, allowing for stable proliferation and paving the way for artificial life forms with designed functions.
The Yap hadal snailfish genome contains extra genes that help stabilize proteins and DNA under high pressures, enabling it to survive in the deepest parts of the ocean. The fish has lost genes involved in vision, taste, and smell, which are likely unnecessary in its dark environment.
Researchers found that glyphosate inhibits the symbiotic bacteria of the saw-toothed grain beetle, preventing it from forming its exoskeleton. The study suggests that this can make insects more vulnerable to stress and death.
A recent study uses phylogenetic methods to integrate vertical and horizontal gene transmission, revealing that genes travel vertically two-thirds of the time. This analysis predicts a root between two major clades, Terrabacteria and Gracilicutes, shedding light on early bacterial evolution.
Researchers discovered a new species of bacteria, Sphingobacterium phlebotomi, in sand fly rearing substrates that attracts pregnant females, offering a potential tool for reducing sand fly populations and preventing diseases like Leishmaniasis. The bacterium's volatile chemicals can be used to create ecologically safe baits or traps.
Researchers developed a genetic material-based catalogue to predict antibiotic resistance in MDR-TB, enabling accelerated treatment development. The study found that 99% of predicted drug combinations were effective in traditional microbiological testing.
Researchers created Retron Library Recombineering (RLR) to generate up to millions of mutations simultaneously and screen mutant cells efficiently. RLR eliminates the toxicity observed with CRISPR and improves genome-level exploration of mutations.
Researchers at the University of Cologne discovered two previously undescribed genera and one new species of bacteria related to Legionella, which live in amoebae. The findings suggest a wider range of host organisms than previously thought, potentially leading to more cases of disease.
Researchers studying the symbiotic bacteria of beewolves found signs of genome erosion and metabolic streamlining for antibiotic production. The bacteria's genome is being reduced as it focuses on its defensive symbiosis with the host insects, suggesting an adaptation to their mutual benefit.
Researchers have developed a new search engine, DIAMOND, that enables fast and accurate comparison of protein sequences across species. With an 80- to 360-fold computational speedup compared to BLAST, DIAMOND is poised to revolutionize comparative genomics research and enable the analysis of millions of eukaryotic genomes.
Researchers used biochemical metabolic networks and evolutionary trees to analyze 1,089 bacterial genomes, predicting the biochemistry of LBCA. The analysis reveals that LBCA was likely rod-shaped and had the acetyl-CoA pathway for carbon fixation, similar to LUCA.
A study by HKBU scientists reveals symbiotic relationship between clams and bacteria, enabling them to adapt to deep-sea conditions. The research found 28 genes transferred from ancestral chemoautotrophic bacteria to the clam, facilitating chemosynthesis and energy production.
A recent study by biophysicists at the University of Cologne shows that bacteria can easily integrate genetic material from other bacterial strains, producing hybrid organisms with extensive genomic and functional changes. This horizontal gene transfer enables rapid evolution and can drive evolutionary processes efficiently.
Researchers have discovered a dual symbiosis system in deep-sea vent-endemic snails, where they host both sulfur-oxidizing and methane-oxidizing bacteria for nutrient synthesis. This finding provides new insights into how animals thrive in extreme environments and sheds light on the adaptation to microbes.
Researchers identified over 140,000 viral species in the human gut, with more than half never seen before. The discovery opens up new research avenues to understand how viruses living in the gut affect human health and disease.
A recent study published in Genome Biology reveals a high level of site-specificity in bacteria found in the human mouth, with distinct genetic forms associated with specific sites. The researchers used metapangenomics to identify novel bacterial strains and potential habitat-specific genes.
Achromatium oxaliferum is a highly adaptable bacterium that thrives in diverse environments, including hot springs and ice-cold water. Its unique gene expression mechanism allows it to 'archive' unused genes, enabling rapid adaptation to changing conditions.
A study published in Nature Microbiology reveals that drug-resistant E. faecium can spread within hospitals despite deep cleaning, with high rates of infection found in vulnerable patient groups. The bacteria's ability to evade cleaning measures poses a significant challenge to infection control.
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.
A study reveals that re-emergence of yaws, a neglected tropical disease, was caused by at least three distinct lineages of bacteria. The researchers recommend employing strategies to maximize population coverage and intensive post-MDA surveillance to control the spread of new infections.
Researchers from RUDN University discovered that non-pathogenic Xanthomonas bacteria can acquire virulence genes from other species, making them deadly to plants. The study found that the key factor in pathogenicity is the VirE protein, which was likely borrowed through lateral gene transfer.
Scientists at Cold Spring Harbor Laboratory discovered the intricate details of the Origin Recognition Complex (ORC), a crucial protein in human genome replication. ORC changes shape dramatically as it assembles around DNA, with parts twisting and pinching to interact with the molecule.
Researchers analyzed 200 bacterial strains' genomes to determine which ribosomal proteins are essential for a working ribosome. They found that only nine proteins were completely conserved, while 48 were lost in at least one strain, suggesting a non-random pattern of loss.
Researchers have compiled an unparalleled inventory of the human gut ecosystem by sequencing over 200,000 bacterial genomes from more than 4,600 species. The new databases reveal tremendous diversity in human guts and pave the way for microbiome research.
Scientists found that ultra-small, parasitic bacteria from the TM7 phylum are present in humans, moose, dogs, cats, dolphins, and groundwater. Despite their diverse environments, these bacteria have minimally changed genomes, indicating recent acquisition by humans.
A team at Broad Institute of MIT and Harvard developed a new molecular editor that can precisely edit mitochondrial DNA, enabling modeling of disease-associated mutations. The editor, engineered from a bacterial toxin, enables researchers to study genetic changes associated with cancer, aging, and more.
The study mapped bacterial resistance to last-line antibiotics in the Philippines, enabling better tracking of resistant bacteria and controlling outbreaks. The genomic capacity has enhanced national infection control efforts and improved understanding of antimicrobial resistance at local, national, and international scales.
A new genetic engineering method has been developed to improve the efficiency and reach of recombineering, a decades-old technique used to swap DNA pieces in bacteria. The new approach identifies efficient proteins that mediate attachment and placement of short DNA strands, enabling single-spot edits and multiplex editing.
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.
UC Riverside scientists have solved a 20-year-old genetics puzzle, differentiating three particles of Brome Mosaic virus. The discovery could lead to ways to protect wheat, barley, and other crops from the virus.
A new study by Princeton researcher Britt Adamson and colleagues enables direct capture of sgRNA sequences during scRNA-seq, allowing for easier tracking of multiple sgRNAs in individual cells. This breakthrough facilitates the expansion of Perturb-seq experiments to larger scales and with combinatorial perturbations.
Researchers found that syphilis bacteria alter a single gene, called tprK, which provides instructions for a protein on its surface. This change allows the bacterium to evade the immune system and resist eradication, contributing to its ability to hide in the body for decades.
Researchers discovered that bacteria employ a strategy of adding new DNA while shedding unused genes, allowing them to avoid overloading their genomes. This process helps the bacteria outgrow competitors and potentially infect other organisms more easily.