• I employ a range of meta-omics approaches including: meta-barcoding of microbiomes to assess microbial diversity coupled with the use of comparative meta-genomics and meta-transcriptomics in the frame of interdisciplinary and integrated research projects to link structural and functional diversity of microbes with diversity and community composition of plant communities. (ufz.de)
  • Shotgun metagenomics and comparative isolate genomics were used to understand the impact of oral vancomycin on the microbiome and environmental contamination. (cdc.gov)
  • Currently I am working on a comparative metagenomic analysis to characterize biogeography, diversity and evolutionary origin of keystone soda lake microorganisms and to estimate the communities' contribution to the global carbon budget. (slu.se)
  • The group also uses comparative genomics to extend the discoveries throughout the green algal lineage. (berkeley.edu)
  • Comparative genomics and metagenomics indicate widespread utilization of these economies in nature. (berkeley.edu)
  • Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)
  • Comparative genomics demonstrated that these and other Ca. Nanohaloarchaeota inhabiting saline habitats use a "salt-in" strategy to maintain osmotic pressure based on the high proportion of acidic amino acids. (biomedcentral.com)
  • We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes. (bvsalud.org)
  • Now, the metagenomics approach is used widely in different research areas, including marine ecological research, plant and agriculture, human genetics and diagnosis of human diseases [ 10 ]. (biomedcentral.com)
  • We examine the role of miRNAs in nodule development using a number of different approaches including genetics, genomics, molecular and cellular biology and microscopy. (sdstate.edu)
  • We utilize genetics, metagenomics and molecular microbiology to answer questions related to this research area. (sdstate.edu)
  • A rapidly developing research area focuses on understanding how genetic variation influences organisms, populations, communities and ecosystems and specifically the connections between genetics, gene regulation, species diversity, and ecological and biogeochemical processes. (umces.edu)
  • A discipline within the field of genetics, genomics is the study of the composition of DNA and often includes many other disciplines. (foodincanada.com)
  • We are looking for a highly motivated and curiosity-driven PhD candidate with an interest in microbiology, specifically on the integration of various 'omics' approaches (metagenomics, transcriptomics, proteomics) to study the microbial physiology of prokaryotes in anoxic marine and hot spring sediments. (fems-microbiology.org)
  • Many of the names assigned to these methods end in "omics" and include genomics, metagenomics, transcriptomics, proteomics and metabelomics. (foodincanada.com)
  • New Zealand needs more bioinformatics skills for data analysis to derive maximum meaning from environmental samples and metagenomics information now coming through. (genomics-aotearoa.org.nz)
  • The biggest bottleneck broadly for us is bioinformatics, but metagenomics more specifically, because our bioinformatics person is busy with WGS, and while he has done a lot of 16S, he's done less shotgun sequencing, so we need more in the team to get started and upskill. (genomics-aotearoa.org.nz)
  • The Centre for Infectious Disease Genomics and One Health at SFU is an interdisciplinary group of researchers interested in solving practical health problems using multidisciplinary approaches and in a One Health framework. (sfu.ca)
  • These populations and features may be successfully captured by single-virus genomics and fosmid-based approaches, at least in abundant taxa, but at considerable cost and technical expertise. (peerj.com)
  • For the first time in New Zealand, researchers and students across a diverse range of disciplines and institutes came together at a Genomics Aotearoa Summer School at the University of Auckland in December 2019 to upskill in fundamental metagenomics approaches, building on basic data carpentry skills taught by Genomics Aotearoa and NeSI. (genomics-aotearoa.org.nz)
  • Diversity of Psychrophilic Bacteria in Sea and Glacier Ice Environments-Insights Through Genomics, Metagenomics, and Proteomics Approaches. (uw.edu)
  • We also describe the unusual enzymes discovered via metagenomics approaches, and discuss the future prospects for metagenome technologies. (biomedcentral.com)
  • With experience in both experimental and computational biology, Tian is well-versed in studying microbial diversity and function using genomics, metagenomics, and metatranscriptomics approaches. (iit.edu)
  • Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. (uibk.ac.at)
  • Meta genomics refers to the study of genetic material collected directly from environmental samples. (nature.com)
  • Meta genomics bypasses this issue by sequencing all the DNA in a given sample, capturing a more comprehensive view of the microbial community. (nature.com)
  • The adoption of AI in meta genomics has been a game-changer, offering a powerful means to manage, process, and interpret the colossal amount of data generated. (nature.com)
  • In meta genomics, machine learning can be used to identify patterns and correlations in large datasets, helping us to understand the structure and function of microbial communities. (nature.com)
  • In the context of meta genomics, deep learning algorithms can identify features and patterns that are not immediately apparent or that humans might miss. (nature.com)
  • The Centre for Infectious Disease Genomics and One Health at SFU is an interdisciplinary group of researchers with backgrounds in microbiology, molecular biology, computer science, cognitive science, statistics, public health, and genomics. (sfu.ca)
  • Given the diversity of microorganisms (bacteria, viruses, parasites) and the complex of biological phenomena that we seek to understand, data-driven research in microbiology requires researchers to collaborate and to share data. (sfu.ca)
  • The Metagenomics Summer School was a great opportunity for faculty and students from a range of institutions to upskill in metagenomics, an area of microbiology that is moving quickly and requires access to a set of computational resources that many of us have shied away from. (genomics-aotearoa.org.nz)
  • Traditional microbiology relies on isolating and culturing individual species, a method that cannot capture the full diversity of microbial life since many microbes are impossible to culture in the lab. (nature.com)
  • Artificial Intelligence and metagenomics are two rapidly evolving fields, and their intersection is creating a new, exciting frontier in microbiology. (nature.com)
  • My scientific research focused on unravelling the mechanisms of plant-microbe interactions with a particular emphasis on the effect of drivers of global change such as land use intensity, climate change, as well as plant species identity and genetic diversity on the plant associated and rhizosphere soil microbiomes. (ufz.de)
  • This method thus opens the way for addressing important questions about the genetic diversity, gene flow, adaptation, dispersal, and biogeography of hitherto unexplored species. (lu.se)
  • In this study, we used both genome mining and PCR-based screening to explore the genetic diversity of CylC homologs and their distribution in bacteria. (biomedcentral.com)
  • We performed whole-genome sequencing to determine the genetic diversity and phylogenetic relationships of 2 familial clusters of B. gilchristii infections identified in Minnesota. (cdc.gov)
  • To investigate genetic diversity between strains, we performed whole-genome single-nucleotide polymorphism (SNP) analysis using the MycoSNP version 0.19 analytical workflow ( https://github.com/CDCgov/mycosnp ). (cdc.gov)
  • Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. (biomedcentral.com)
  • However, as an endosymbiotic bacterium, Wolbachia does not grow outside the host cell environment, and large-scale recovery of the bacteria required mass rearing of their host, preferably clones of a single individual to avoid strain genetic diversity, or amplification of cell cultures infected with a single Wolbachia strain. (bvsalud.org)
  • BACKGROUND: While genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies of short-reads often result in incomplete and/or highly fragmented metagenome-assembled genomes (MAGs), hampering in-depth genomics. (bvsalud.org)
  • There is nothing short of a revolution underway in methods used to identify the vast number of microbial life forms in our foods and to learn about their genetic diversity. (foodincanada.com)
  • Throughout immeasurable time, microorganisms evolved and accumulated remarkable physiological and functional heterogeneity, and now constitute the major reserve for genetic diversity on earth. (biomedcentral.com)
  • Being the oldest life form, prokaryotic microorganisms have evolved and accumulated remarkable physiological and functional diversity, thereby constituting the world's major reserve of genetic diversity. (biomedcentral.com)
  • Our present-day genetic diversity was shaped by biological and demographic events that marked their signatures in the genome. (lu.se)
  • Shifts in taxonomic and functional diversity, community composition and distribution patterns of soil microbiomes with main focus on general fungi, mycorrhizal fungi and bacteria along land use and simulated drought senarios. (ufz.de)
  • Junge, K., J.F. Imhoff, J.T. Staley and J.W. Deming, "Phylogenetic diversity of numerically important Arctic sea-ice bacteria cultured at subzero temperature", Microb. (uw.edu)
  • This attribute of WGS has led to development of the field of metagenomics, which attempts to identify bacteria from mixed cultures recovered from a sample and sequenced together without enrichment. (foodincanada.com)
  • Along the way, she played an integral part in developing the scientific field of viral metagenomics, and her lab continues to expand the application of this technique to new environments and research questions. (usf.edu)
  • Here, we explored the diversity, ecological distribution, and expression of opsin genes that encode the apoproteins of Type I r. (researchgate.net)
  • Here, we explored Type I opsin gene diversity, ecological distribution, and expression in lakes with contrasting physicochemi. (researchgate.net)
  • Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics. (ku.dk)
  • This increase in the body of data on virophage not only revealed the diversity of the virophage group, but also the relevant ecological impact of these small viruses and their potential role in the dynamics of the microbial network. (mdpi.com)
  • WGS, metagenomics and the other "omics" are now providing our industry with a means of improving food safety and better understanding the ecological changes that take place on food products. (foodincanada.com)
  • This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. (uibk.ac.at)
  • The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome. (uibk.ac.at)
  • Further, high-throughput sequencing (HTS) is also used to study the relationship between host and surrounding environment (using eNA) during a disease event, to understand how environmental microbial diversity influences animal health, and to understand the host pathobiome. (cefas.co.uk)
  • Faster and more accessible DNA sequencing technologies have enabled, in the past decade, a large number of genomics and metagenomics projects focused on the microbial world [ 3 ]. (biomedcentral.com)
  • However, metagenomics based on next-generation sequencing (NGS) technique is a target-independent assay that enables simultaneous detection and genomic characterisation of all microorganisms present in a sample. (biomedcentral.com)
  • Recently, traditional isolation methods, complemented by high-throughput sequencing metagenomics technology, have greatly increased our understanding of the diversity of bacteriophages. (biomedcentral.com)
  • The PhD candidate will obtain sediment samples and isolate DNA to determine the microbial community composition using 16S rRNA amplicon sequencing and genome-resolved metagenomics analyses. (fems-microbiology.org)
  • Although Nanopore sequencing has increasingly been used in microbial metagenomics as long reads greatly improve the assembly quality of MAGs, the recommended DNA quantity usually exceeds the recoverable amount of DNA of environmental samples. (bvsalud.org)
  • The 'VirION' (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. (peerj.com)
  • Some were planning a sequencing project, several needed more analytical skills to make the most of existing plant or animal datasets, while others were getting into metagenomics research. (genomics-aotearoa.org.nz)
  • Our team has a lot of interest in whole genome sequencing (WGS) and metagenomics. (genomics-aotearoa.org.nz)
  • Genomics Aotearoa has assembled a crack team of instructors who were able to patiently walk us through the use of the NeSI servers and data analysis pipelines for analysing complex populations in our DNA sequencing projects. (genomics-aotearoa.org.nz)
  • The Microbial Genomics and Metagenomics Laboratory (MGML) provides metagenomic sequencing and analysis support to the Cincinnati Children's, University of Cincinnati and surrounding communities. (cincinnatichildrens.org)
  • The MGML is staffed and equipped to provide services ranging from 16S ribosomal RNA sequencing (16S rRNA), shotgun metagenomics and RNA sequencing. (cincinnatichildrens.org)
  • However, since most marine communities are far richer in species diversity than the AMD biofilm, on the order of 100 to 200 species per milliliter of water [ 13 , 14 ], this further complicated their sequencing and assembly. (biomedcentral.com)
  • According to the Genomes OnLine Database (GOLD) [ 17 ] until January 2009, 137 metagenomics projects were in various stages of sequencing, 72% of which were derived from environmental samples, 23% from endobiotic samples, along with 5% synthetic metagenomes. (biomedcentral.com)
  • He takes advantage of state-of-the-art technologies in microbial genomics studies, such as third generation sequencing (e.g. (iit.edu)
  • Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution, but their assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. (peerj.com)
  • We routinely use metagenomics to characterize and obtain multi-gene data for such pathogens, and to reconstruct whole genomes of novel pathogens. (cefas.co.uk)
  • These communities consist of individual microorganisms across the continuum of phylogenetic diversity, ranging from coexisting members of different domains of life and phyla to multiple strains with only a handful of single nucleotide variant. (researchgate.net)
  • With extensive experience in studying and understanding the incredible diversity of microorganisms, I am dedicated to unraveling the mysteries of these tiny, yet powerful, life forms. (nature.com)
  • We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. (bvsalud.org)
  • Candidatus Nanohaloarchaeota, an archaeal phylum within the DPANN superphylum, is characterized by limited metabolic capabilities and limited phylogenetic diversity and until recently has been considered to exclusively inhabit hypersaline environments due to an obligate association with Halobacteria . (biomedcentral.com)
  • Thus, the diversity, metabolic potential, symbiotic lifestyles, and evolutionary adaptations to multiple extreme environments of the Ca. Nanohaloarchaeota are not completely understood. (biomedcentral.com)
  • Final Round of 2022 CSP Functional Genomics Awardees Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call. (doe.gov)
  • vB_OliS_GJ44 showed synteny with six uncultured phages, which supports its representation in uncultured environmental viral contigs from metagenomics. (biomedcentral.com)
  • Combined with the eight environmental viral contigs from metagenomics, this study helps fill the gap in our understanding of the isolation, genomic and evolutionary development of Oceanospirillum bacteriophages and provides new insights into the interactions between hosts and bacteriophages for these important marine hydrocarbon-degrading microbial populations. (biomedcentral.com)
  • A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity. (doe.gov)
  • Metagenomics, the study of genetic material recovered directly from environmental samples, is giving microbial ecologists a much more detailed look at the previously hidden diversity of microscopic life, significantly adding to our understanding of the living world. (genomics-aotearoa.org.nz)
  • Such processes expand the potential uses of valuable environmental or host associated data, unlocking potential new ways to explore and maintain microbial diversity, identify microbial contributions to environment and animal health, and manage precious water resources in an era of climate change. (genomics-aotearoa.org.nz)
  • Currently funded by an NSF Assembling the Tree of Life grant, the Breitbart lab is now focusing on exploring the diversity and ecology of single-stranded DNA viruses, whose widespread environmental distribution has only recently been recognized. (usf.edu)
  • Using metagenomics, namely genetic material recovered directly from environmental samples, this biogenetic diversification can be accessed without the need to cultivate cells. (biomedcentral.com)
  • Soil fungal diversity and community composition of grassland and forest ecosystems along land use gradients in three German Biodiversity Exploratories. (ufz.de)
  • Advance the use of genomics and metagenomics for detecting fungal pathogens and antifungal drug resistance. (cdc.gov)
  • Genomics is a Big Data field now, and we develop tools to automate analyses. (ezlab.org)
  • Metagenomics analysis revealed an average of 280,768 reads in which 5% of the reads were derived from viruses. (biomedcentral.com)
  • Despite the difficulties in sample preparation and analysis process, we showed that metagenomics approach is a powerful and promising tool for the detection and characterisation of different viruses in clinical samples. (biomedcentral.com)
  • The first application of metagenomics study in virus discovery was the analysis of virus particles in soil samples from marine sites in San Diego [ 9 ]. (biomedcentral.com)
  • Genomics Aotearoa, in partnership with NeSI , has upped its training on analysis methods to build national capabilities, linking researchers working in the field to create much-needed networks. (genomics-aotearoa.org.nz)
  • As part of the Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium of over 100 cities worldwide, we collaborate with experts across many fields, including genomics, data analysis, engineering, public health, and architecture. (lu.se)
  • Still, little is known regarding the diversity and distribution of these enzymes. (biomedcentral.com)
  • The remarkable diversity of natural products (NPs) results from a similarly diverse pool of biosynthetic enzymes [ 2 ]. (biomedcentral.com)
  • However, despite the contributions from metagenomics technologies consequent upon the discovery of novel enzymes, this relatively new enterprise requires major improvements. (biomedcentral.com)
  • Taxonomic Diversity of the Microbial Biofilms Collected along the Thermal Streams on Kunashir Island. (uibk.ac.at)
  • In this study, we aimed to develop a metagenomics approach using NGS to identify and characterise viruses in stool samples from infants and children with Acute Gastroenteritis (AGE) in Kuwait. (biomedcentral.com)
  • A metagenomics approach using NGS to characterise viruses in clinical samples was used. (biomedcentral.com)
  • Our results showed 71% agreement (k = 0.445, P = 0.000) between multiplex Real-Time PCR, which is used as a routine diagnostic test and metagenomics approach in the detection of viruses causing gastroenteritis in clinical samples. (biomedcentral.com)
  • Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. (nature.com)
  • Research at the intersection of biological and microbial oceanography and functional genomics. (ucsd.edu)
  • The Genomics and Systematics team is also central to the operation of the WOAH Collaborating Centre for Emerging and Aquatic Animal Diseases and to the description of emerging/novel disease agents. (cefas.co.uk)
  • Microbial ecology, metagenomics and prokaryotic genomics. (slu.se)
  • Metagenomics has made it possible for us to analyze the entire ecology of our foods and the environments in which they are prepared in a level of detail that we could only dream about a decade ago. (foodincanada.com)
  • Although WGS and metagenomics are game-changing advances in our quest for improving food safety, this technology is not without its issues - something anyone contemplating using these methods needs to keep in mind. (foodincanada.com)
  • Advances in metagenomics and single-cell genomics have significantly extended our understanding of the diversity and potential functions of uncultured archaea [ 4 ]. (biomedcentral.com)
  • Dr. Breitbart has spent over a decade studying oceanic viral abundance, diversity, and biogeography. (usf.edu)
  • I know, my research tends to be expensive as I work on deep sea organisms and do genomics and such. (blogspot.com)
  • SAGO statement on newly released SARS-CoV-2 metagenomics data from China CDC on GISAID. (who.int)
  • The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. (lu.se)
  • The aim of the current project is to employ various genomics strategies to gain insight in the physiology and metabolism of selected Asgard archaeal lineages that reside in anoxic environments. (fems-microbiology.org)
  • Metagenomics is a rapidly expanding field and has been a useful tool in examining alternative causes and treatments for diseases. (cincinnatichildrens.org)
  • We are also interested in determining plant mechanisms that influence the microbial diversity in the rhizosphere and plant intercellular spaces. (sdstate.edu)
  • We examine the diversity and activity of microbial life in the deep sea , including within the deepest ocean trenches. (ucsd.edu)
  • Junglen, S. & Drosten, C. Virus discovery and recent insights into virus diversity in arthropods. (nature.com)
  • Over the years I have participated in diverse research projects involving metagenomics and prokaryotic genomics but my main focus has always been on aquatic systems, especially on soda lakes. (slu.se)