Articles tagged with Bacterial Genomes
Researchers identified a novel L-fucose metabolic pathway in Veillonella ratti, which encodes enzymes for a previously unknown non-phosphorylating L-fucose pathway. The study also discovered another L-2-keto-3-deoxyfuconate aldolase involved in the same pathway in Campylobacter jejuni.
The Pangaia project at Bielefeld University is developing new algorithms to analyze genomic data for biomedicine, enabling faster detection of infectious strains and hereditary diseases. Researchers can compare a single genome with thousands of others in a single step, highlighting similarities and differences.
Researchers are developing new algorithms to quickly compare genetic data from viruses, bacteria, and other organisms to identify pathogenic genes. This project, Pangaia, aims to make computer-assisted pangenomics faster and more user-friendly for biomedicine applications.
Researchers created a gene catalog called VIRGO, comprising nearly 1 million genes from the human vagina. This comprehensive resource facilitates deeper understanding of the vaginal microbiome's function and potential treatments for gynecologic conditions.
Researchers sequenced the genomes of 24 strains of Burkholderia bacteria from the ISS water dispenser and found them highly similar to Earth-based strains. The bacteria are susceptible to common antibiotics, making them treatable in the event of an infection.
The Christen Lab has successfully produced a fully artificial genome, the Caulobacter ethensis-2.0, with over 580 functional genes. This breakthrough demonstrates the promise of synthetic biology in producing designer genomes for industrial and health applications.
Researchers found over 350 huge phages with genomes four times larger than average, including the largest bacteriophage to date. These viruses carry genes normally found in bacteria and use them against their hosts, bridging the gap between non-living and living organisms.
Researchers identified 351 large phages carrying bacterial genes, including CRISPR and ribosomal proteins, which blur the line between life and non-life. These enormous phages use these genes against their bacterial hosts and have the potential to provide new tools for genome engineering.
A novel technique called SAG-gel allows for the simultaneous analysis of multiple draft genomes from raw data, identifying bacteria that respond to dietary fiber without reference genomes. The study reveals specific gene clusters and metabolic pathways involved in breaking down inulin.
Bacterial autoimmunity occurs when the CRISPR-Cas system targets viral DNA incorporated into the host genome, leading to damaging autoimmunity. The absence of this key immune system can be beneficial for bacterial survival and proliferation. Anti-CRISPR proteins also provide protection for the host by disabling its immune system.
Researchers have developed a new functional genomics system, MAGIC, which allows them to modulate the activity of multiple genes in concert. By combining individual gene edits with custom DNA sequences, scientists can explore synergistic effects and better understand complex traits.
A new method called ON-rep-seq enables the precise identification of bacteria using selective, strain-specific fragments of the bacterial genome. This approach reduces analysis time and costs to less than $2 per bacterium, increasing accuracy to over 99%.
Research team around Dr Thomas Böttcher studies phage-host interactions to understand the transition from latent to active states, with potential applications for developing alternative antibiotics. The team aims to uncover molecular signals controlling dormant phages and their impact on the human microbiome.
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 developed a novel genomic analysis method for classifying Yersinia strains, revealing unexpected biodiversity and new species. The tool enables accurate identification of pathogenicity, guiding patient monitoring and public health initiatives.
Researchers at the University of California, Davis have successfully genome-edited a dairy bull to prevent it from growing horns, and their findings show that none of its offspring developed horns. The study also highlights the need for screening and selection to address plasmid integration when using genome-editing in livestock.
Vibrio cholerae uses its type VI secretion system (T6SS) to compete with other bacteria and acquire new genetic material, leading to rapid evolution and pathogen emergence. The bacterium can steal up to 150,000 nucleic acid base pairs, or roughly 150 genes, in a single attack.
Researchers at Oak Ridge National Laboratory developed a method to isolate specific microbes from complex human oral microbiome samples using antibody engineering. They successfully isolated three different species of TM7 and another uncultivated bacterial group, SR1.
A team of scientists discovered a giant virus genome in choanoflagellates, unicellular predators that eat bacteria and small algae. The virus encodes genes for microbial rhodopsin proteins, which are also found in vertebrates and help detect light.
A study by Vincent Richards and colleagues found that antibiotic-resistant genes are being transmitted from humans into animal species, including livestock, companion animals, and wildlife. This reverse zoonosis is facilitated by high bacterial genome plasticity, allowing bacteria to adapt quickly to environmental changes.
A new study published in PLOS ONE suggests that many volatile compounds from a male cat's anal sacs are produced by a community of bacteria, rather than the cat itself. This discovery challenges traditional views on scent marking and communication in cats.
Researchers successfully grew Candidatus Liberibacter asiaticus, the bacterium causing Citrus Greening Disease, in a laboratory for the first time. This breakthrough enables studies on the disease and potential treatments.
Researchers at Technical University of Denmark have developed a method to quickly couple enzymes with specific methylation patterns, revealing which enzymes are responsible for certain patterns. This discovery holds great promise for improving DNA transformation and introducing foreign DNA into host organisms.
Researchers at Penn State have discovered that the genomes of luminescent bacteria contain two copies of a gene required for the type VI secretion system (T6SS), which is used to kill neighboring cells. Disabling either copy of the gene still allows the T6SS system to function, but not both, revealing functional redundancy.
Scientists at the Wyss Institute successfully manipulated four bacterial strains to exhibit beneficial interactions and balance in complex environments. By modifying their genomes, they encouraged the bacteria to adopt a live-and-let-live approach, promoting resilience and diversity within the consortia.
Researchers discovered that Clostridium difficile is evolving into two separate species, with one group highly adapted to spread in hospitals. The emerging species, named Clade A, has evolved genes that metabolize simple sugars, allowing it to thrive on Western sugar-rich diets and evade common hospital disinfectants.
A new genus of bacteria has been identified as a major contributor to coral decline, siphoning energy from corals and making them more susceptible to disease. The study found that the bacterial genus is globally associated with many different coral hosts and has genes that enable it to parasitize its hosts for amino acids and ATP.
Researchers developed a simple measurement of gene flow to define microbe populations, separating co-existing microbes in genetically and ecologically distinct groups. This approach identifies parts of the genome that show different adaptations, enabling pinpointing of populations associated with health conditions like Crohn's disease.
A University of Maryland Center for Environmental Science-led research cruise is exploring the marine carbon cycle in the deep Atlantic Ocean. Scientists are analyzing bacterial diversity and function to better understand how cyanobacteria contribute to the process.
Researchers at UCI have sequenced the genome of the white-footed mouse, which carries the bacteria causing Lyme disease. The study provides a roadmap for fresh approaches to preventing disease transmission, including developing an environmentally-safe vaccine method.
Researchers developed an algorithm that can identify a certain type of bacterial viruses called inoviruses, significantly expanding their known diversity. The tool was trained on a reference dataset and combed through over 70,000 microbial and metagenome datasets, ultimately identifying more than 10,000 inovirus-like sequences.
Researchers found that red algae stole approximately 1% of their genes from bacteria to adapt to toxic metals and salt stress in hot springs. The study suggests that this genetic adaptation could be used to develop novel genetic engineering methods to produce fuels and clean up polluted sites.
Researchers developed a novel computational approach to assign functions to unknown genes, revealing transporters play a critical role. The study highlights the importance of environmental conditions shaping minimal genomes and paves the way for focused research on essential and facilitator gene sets.
Researchers discovered hundreds of previously unknown protein interactions through a new statistical model applied to the human genome. These findings may open new routes to develop drugs against deadly pathogens like M. tuberculosis.
Researchers developed a bacterial memory circuit that can detect and report disease signals in the gut, enabling non-invasive diagnosis. The system uses E. coli bacteria with synthetic trigger elements to identify potential biosensors, showing promise for long-term digestive health monitoring and treatment.
Researchers found 87 genes in E. coli bacteria that protect against plasma treatment, including a heat shock protein Hsp33. The study suggests that genetic changes can increase plasma resistance in bacteria.
Researchers have developed a new gene editing tool called INTEGRATE that harnesses bacterial jumping genes to insert any DNA sequence into the genome without cutting DNA. This technology offers a precise and reliable alternative to current gene-editing tools, which can lead to errors.
The study reveals 621 genetic strains of Streptococcus pneumoniae worldwide, showing evolutionary changes that lead to vaccine evasion. It provides crucial information for future vaccine strategy and helps save lives by identifying important strains for new vaccines.
Researchers discovered that bacteria employ Cas13 to counter viral attacks, employing a dormancy strategy to hinder virus replication. This approach offers superior protection against viral mutations and phage escape.
Researchers found large numbers of errors in publicly available genomic data, including mistakes in gene annotation that resulted in truncated or missing sequences. The errors are due to human and technological factors, such as imperfect DNA sequencing technology and confusion about protein function.
Three Rochester Prep High School seniors, working in the RIT Genomics Lab, isolated and genetically sequenced a Yimella bacterium that produces antibiotic compounds against Escherichia coli and Bacillus subtilis. The discovery is significant in addressing antibiotic resistance, a growing concern worldwide.
Researchers analyzed over 850 drug-resistant E. coli genomes to identify survival strategies, finding that clones use niche separation and NFDS to evolve and succeed in the host environment. The study's findings highlight the importance of understanding bacterial ecology to develop effective prevention methods.
Researchers at Arizona State University have developed a method to render the CRISPR-Cas9 gene editing tool 'immunsilent', allowing for reliable and stealthy gene repair. This breakthrough brings CRISPR closer to safe clinical application, addressing key safety concerns.
Researchers at the Wellcome Sanger Institute have sequenced the genome of a non-toxigenic strain of Vibrio cholerae from WWI, showing it is distantly related to strains causing modern pandemics. The strain lacked a flagellum and possessed genes for ampicillin resistance.
A single bacterium supplies the gutless Paracatenula worm with lipids, proteins, sugars, fatty acids, vitamins, and other substances for energy and biomass production. The bacteria use chemosynthesis to convert carbon dioxide into organic compounds, which are then delivered to the host in small droplet-like vesicles.
Researchers discovered a unique symbiotic relationship between a marine flatworm and its bacterial partner, Candidatus Riegeria santandreae. The bacteria store chemical energy, which is then secreted to the host, bypassing digestion.
Researchers at ETH Zurich develop a computer-generated genome for Caulobacter ethensis, which is based on the genome of a harmless freshwater bacterium. The new genome contains over 800,000 DNA letters and was generated using an algorithm that simplifies genetic information to facilitate production.
Researchers identified a novel mobile genetic element, pWCP, in the Wolbachia bacterium of Culex pipiens mosquitoes. This discovery opens up new avenues for understanding interactions between the bacterium and its host, as well as its role in pathogen transmission.
Researchers reconstruct nearly 61,000 microbial genomes from human gut metagenomes, uncovering 2,058 previously unknown species and shedding light on the metabolic capabilities of uncultivated microbes. The study improves genomic resources for global populations, especially in regions with limited data.
Researchers from the Center for Genomic Regulation developed a method to predict and classify these tiny proteins using bioinformatics tools, discovering they account for 16% of bacterial genomes. The small proteins play a crucial role in antimicrobial responses, microbiota balance, and may be overlooked in complex organisms.
A new study reveals a promising therapeutic target for tuberculosis (TB) using the toxin-antitoxin system in M. tuberculosis bacteria. Activating this system can trigger cell death and slow down bacterial growth, offering hope for developing new treatments.
Researchers identified nearly 2000 novel bacterial species in the human gut using computational methods, revealing significant geographical diversity and underscoring the importance of collecting data from underrepresented populations to achieve a comprehensive understanding of the human microbiome.
Researchers use genetic analysis to determine when certain groups of bacteria evolved, providing insight into early environments and animal life. They found that three major groups of soil bacteria diversified around 450-350 million years ago, likely in response to changes in the environment.
Researchers have identified a new group of massive viruses, known as megaphages, that target specific bacteria found in the guts of individuals eating non-Western, high-fiber diets. These phages, which are 10 times larger than average phages, can carry genes that exacerbate human illnesses and may move between humans and animals.
Researchers developed PopPUNK, a computational tool that analyzes tens of thousands of bacterial genomes in a single run, up to 200-fold faster than previous methods. This enables the efficient estimation of population structure and easy identification of emerging strains.
Researchers found that lethal disease can occur without viral replication in EHEC-infected mice. The study suggests potential novel treatments for EHEC and life-threatening kidney complications in children.
A recent study sequenced the genome of the Hawaiian bobtail squid, revealing unique evolutionary footprints in symbiotic organs that house beneficial bacteria. The research provides clues about how these partnerships are maintained and lays the groundwork for furthering knowledge of human microbiome relationships.
A promising compound discovered by Swiss TPH researchers is highly effective against Buruli ulcer, both in vitro and in vivo. The study found that compound Q203 has an activity level exceeding the current most active antibiotic rifampicin, potentially leading to a shorter treatment regimen with fewer adverse side effects.
Researchers found strains of Enterobacter bugandensis on the ISS with antimicrobial resistance patterns similar to those on Earth. The strains included genes involved in virulence and disease, raising concerns about potential health implications for future missions.
Researchers discovered genetic retroelements copying into and harming bacterial genomes, indicating a potential role in eukaryotic cell emergence. The study suggests an interplay between DNA repair mechanisms and retroelements may have driven evolutionary pressures.