Tag: Metagenome

Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat Microbiol. 2016;1:16048. Article  PubMed  Google Scholar  Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, et al. Genomic expansion of domain archaea highlights roles…

Miyakawa, T., Matsuzawa, H., Matsuhashi, M. & Sugino, Y. Cell wall peptidoglycan mutants of Escherichia coli K-12: existence of two clusters of genes, mra and mrb, for cell wall peptidoglycan biosynthesis. J. Bacteriol. 112, 950–958 (1972). Article  CAS  PubMed  PubMed Central  Google Scholar  Ayala, J. A., Garrido, T., De Pedro,…

Spiro, T. G., Bargar, J. R., Sposito, G. & Tebo, B. M. Bacteriogenic manganese oxides. Acc. Chem. Res. 43, 2–9. doi.org/10.1021/ar800232a (2010). Article  CAS  PubMed  Google Scholar  Roitz, J. S., Flegal, A. R. & Bruland, K. W. The biogeochemical cycling of manganese in San Francisco Bay: Temporal and spatial variations…

Ilyas, M. et al. Environmental and health impacts of industrial wastewater effluents in Pakistan: A review. Rev. Environ. Health 34, 171–186 (2019). MathSciNet  PubMed  CAS  Google Scholar  Roy, M. A. et al. A Metagenomic approach to evaluating surface water quality in Haiti. Int. J. Environ. Res. Public Health 15, 2211…

This volume provides up-to-date and novel techniques for various screening technologies currently used in metagenomics and related areas. Starting with DNA/RNA isolation from environmental samples, the book continues by delving into areas such as current methods used to isolate DNA and construct metagenomic libraries, establishment of metagenome libraries in non-E….

doi: 10.1007/978-1-0716-2795-2_14. Affiliations Expand Affiliations 1 Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany. ines.friedrich@uni-goettingen.de. 2 Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany. rhertel@gwdg.de. 3 Institute of Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany. rhertel@gwdg.de. Item in Clipboard Ines Friedrich et al. Methods Mol Biol. 2023….

Smid, E. J. et al. Practical implications of the microbial group construction of undefined mesophilic starter cultures. Microb. Cell Factories 13, S2. doi.org/10.1186/1475-2859-13-S1-S2 (2014). Article  Google Scholar  Stadhouders, J. & Leenders, G. J. M. Spontaneously developed mixed-strain cheese starters. Their behaviour in direction of phages and their use within the…

Currently, the incidence of infectious diseases has increased globally, and the pathogens show a trend of diversification and complexity. Rapid and accurate pathogenic diagnosis, which enables early selection of sensitive anti-infective drugs or effective and targeted preventive and control measures, is the core of accurate prevention and treatment of infectious…

Building a Simulated Metagenomic Dataset – HackMD       Published Linked with GitHub — tags: ‘JPL: Genetic Inventory Project’ — # Building a Simulated Metagenomic Dataset Here we’ll create a simulated metagenomic datasets for controlled testing. This dataset was used to determine the Kraken 2 confidence score that best…

Data collection The study was performed according to the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) statement20. To attain an exhaustive review of the published literature on the microbiome diversity by NGS in field-collected ticks, a literature search was conducted on Chinese and English databases using a set…

Merlino, C. P. Bartolomeo Bizio’s letter to the most eminent priest, Angelo Bellani, concerning the phenomenon of the red-colored polenta [translated from the Italian]. J. Bacteriol. 9, 527–543 (1924). Grimont, P. A. D. & Dulong de Rosnay, H. L. C. Numerical study of 60 strains of Serratia. J. Gen. Microbiol….

Distribution of nitrogen-cycling pathways in groundwater Differences in nitrogen-cycling processes based on oxygen and nitrate concentrations Sixteen metagenomes (Table S4) were obtained from duplicate wells at four sites (A–D) from two unconfined alluvial aquifers (Canterbury, Fig. S1). These sites encompassed varied nitrate (0.45–12.6 g/m3), DO (0.37–7.5 mg/L), and dissolved organic carbon (DOC) (0–26 g/m3)…

Generally speaking, longer contigs mean better assembly. It is much better to have a small number of long contigs than a large number of short contigs, even if the number of bases is identical between the two. Longer contigs can be binned more reliably because they have stronger signal. Consider…

A study demonstrating the use of long-read Oxford Nanopore sequencing to generate near-finished bacterial genomes from isolates or metagenomes, without short-read or reference polishing, is presented in Nature Methods this week. Oxford Nanopore sequencing has enabled the recovery of highly contiguous microbial genomes from isolates or metagenome but obtaining near-finished…

Salje, J. Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle. Nat. Rev. Microbiol. 19, 375–390 (2021). CAS  PubMed  Article  Google Scholar  Wang, S. & Luo, H. Dating Alphaproteobacteria evolution with eukaryotic fossils. Nat. Commun. 12, 3324 (2021). CAS  PubMed  PubMed Central  Article  Google Scholar  Strassert, J. F. H.,…

Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017). CAS  PubMed  Article  Google Scholar  Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J. & Embley, T. M. Phylogenomics provides robust support for a two-domains tree of life. Nat. Ecol….

Liu, Y. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593, 553–557 (2021). CAS  PubMed  Google Scholar  Dombrowski, N., Teske, A. P. & Baker, B. J. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat. Commun. 9, 4999 (2018). PubMed  PubMed…

Article Highlight | 15-Jun-2022 Researchers leverage viruses identified from worldwide environmental samples to expand knowledge of viral taxa and their role in tree microbiomes DOE/US Department of Energy image: Analysis of metatranscriptome samples with novel viral taxa in Populus. (Top) Graphical abstract of the pipeline. (Bottom) Percentage read classification with novel…

RPKM, how to normalize for library size 1 Hi everybody! I’m working on several metagenomes (so not trascriptomes), and I mapped high quality reads to a database made of nucleotide sequences through bowtie2. I want to convert raw mapping counts of each gene in RPKM. I know this method might…

How to normalize biom table from qiime2 to edgeR on Rstudio? 0 Hi, I’m new in this of bioinformatics, I’m making a metagenome analysis of ITS region, then, I want to normalize my data, so i exported a biom table from qiime2 with taxonomic annotations, and then I converted that…

Microbial communities are usually highly diverse and often involve multiple strains from the participating species due to the rapid evolution of microorganisms. In such a complex microecosystem, different strains may show different biological functions. While reconstruction of individual genomes at the strain level is vital for accurately deciphering the composition…

Get reference genome from Kraken2 taxID 0 I have a ~10Gb ONT metagenome from citrus psyllid that I am trying to extract bacterial contigs from to assemble. My current thought for a pipeline is broadly as follows: Tentative ID of each contig with Kraken2, then QC to only take assignments…

MGI HotMps High-Throughput Sequencing Kit BGI Group affiliate MGI has launched new commercial sequencing chemistry called HotMps for its DnbSeq-G400 sequencer. Built upon the combinatorial Probe Anchor Synthesis technology proprietary to MGI, HotMps can achieve low error rates, low duplication rates, and low index hopping while being compatible with commonly…

16S is a very conserved sequence, which is why it’s used for targeted phylogenetic analysis; it makes it easy to amplify and analyse. Unfortunately that conservation is an issue with minimap2, which is built around the idea that matching scattered subsequences within a sequence is good enough for identifying matches…

A large number of microorganisms in nature cannot be cultivated under laboratory conditions by pure culture methods, and the technical methods of traditional microbiology limit the research on environmental microorganisms. The rapid development of high-throughput omics technology has enabled humans to have an unprecedented understanding of the complex microbial communities…

1Week 8Metagenomic study focusing on antibiotic resistance genes from foodMetagenomics?The term “metagenomics” was first used byJo Handelsman,Jon Clardy,Robert M. Goodman, Sean F.Brady, and others, and first appeared in publication in 1998. The term metagenome referenced the ideathat a collection of genessequenced from the environment could be analyzed in a way…

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known…

Hello.I performed metagenome analysis using humann3 with the full UniRef90 database (20.7GB). I found many UniRef100-IDs in the file analyzed with UniRef90 database. Why are UniRef100-IDs included in Uniref90 database? Do I mistake anywhere?Thank you. Do you mean 1) that you saw IDs that looked like UniRef100_XYZ or 2) that…

Hi, I am working with annotating my metagenomes through the MG-RAST pipeline, annotating them with taxonomy and function. For this study we are interested in understanding phosphorus metabolism. To summarise, MG-RAST has a filtering option where you can filter by different levels in subsystems or refseq. When I use the…

File No. of MG-RAST 0 Does anyone know what kind of data ‘File 299.1’ in MG-RAST? While I was downloading raw data by specifying ‘File 050.1’, some came out with error {“ERROR”:”requested file (050.1) is suppressed; try file=299.1″} Can’t find out what kind of data 299.1 would be. MG-RAST Metagenome…

Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…

Steen AD, Crits-Christoph A, Carini P, DeAngelis KM, Fierer N, Lloyd KG, Cameron TJ. High proportions of bacteria and archaea across most biomes remain uncultured. ISME J. 2019;13:3126–30. PubMed  PubMed Central  Google Scholar  Goh KM, Shahar S, Chan K-G, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current…

Wu, W. et al. NDM metallo-β-lactamases and their bacterial producers in health care settings. Clin. Microbiol. Rev. 32, e00115–18 (2019). Yong, D. et al. Characterization of a new metallo-β-lactamase gene, bla NDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14…

doi: 10.1186/s13059-022-02626-w. Affiliations Expand Affiliations 1 Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA. 2 Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA. fsun@usc.edu. Item in Clipboard Yuxuan Du et al. Genome Biol. 2022. Show details Display options Display options Format…

INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…

1 Microbial Life: Origin And Discovery2 Observing The Microbial Cell3 Cell Structure And Function4 Bacterial Culture, Growth, And Development5 Environmental Influences And Control Of Microbial Growth6 Viruses7 Genomes And Chromosomes8 Transcription, Translation, And Bioinformatics9 Gene Transfer, Mutations, And Genome Evolution10 Molecular Regulation11 Viral Molecular Biology12 Biotechniques And Synthetic Biology13 Energetics…

New method and model address blindspot towards uncommon species in mixed samples For higher accuracy and more effective microbial diagnostics, researchers at the Earlham Institute have evaluated a new approach to analyse metagenomic samples that may contain low numbers of certain species – helping to prevent crucial genomic information from…

Abstract Background: Large scale metagenome assembly and binning to generate metagenome-assembled genomes (MAGs) has become possible in the past five years. As a result, millions of MAGs have been produced and increasingly included in pan-genomics workflow. However, pan-genome analyses of MAGs may suffer from the known issues with MAGs: fragmentation,…

FastQC analysis 0 Hii, Could anyone please tell me if I can carry out the FastQC analysis using data available online and not in my system? The sequence data that I want to check is huge so was wondering if there was any way to access them online through FastQC?…

Job title: Assistant Professor of bioinformatics and metagenomics at Novo Nordisk Foundation Center for Protein Research Company: Workscout Job description Job beskrivelse We are looking for a highly motivated and dynamic Assistant Professor for a 4-year position to commence on the 1st of April 2022 or soon hereafter. The position…

The University of Copenhagen invites applications for an Assistant Professor position will be in the Human Proteome Variation group at The Novo Nordisk Foundation Center for Protein Research, Denmark – Jan 2022 Qualification Details Six overall criteria apply for Assistant Professor appointments at the University of Copenhagen. The six criteria…

metagenome low alignment rate 1 I have 20 metagenome samples which need to be analyzed. I started with one sample for the time being with the below tools/pipelines. After assembling first sample I mapped its reads back to contigs but the alignment rate is pretty low, What could be the…

Data representing a variety of microorganisms found in the human skin microflora. Credits: Karen Arnott / EMBL Researchers and colleagues at EMBL’s European Bioinformatics Institute (EMBL-EBI), National Institutes of Health (NIH) National Institute for Human Genome (NHGRI), NIH National Institute for Arthritis, Musculoskeletal and Skin Diseases are new bacteria and…

1. Wang, J. & Jia, H. Metagenome-wide association studies: fine-mining the microbiome. Nat. Rev. Microbiol. 14, 508–522 (2016). CAS  PubMed  Google Scholar  2. Moschen, A. R. et al. Lipocalin 2 protects from inflammation and tumorigenesis associated with gut microbiota alterations. Cell Host Microbe 19, 455–469 (2016). CAS  PubMed  Google Scholar …

1. Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59–64 (2014). 2. Byrd, A. L., Belkaid, Y. & Segre, J. A. The human skin microbiome. Nat. Rev. Microbiol. 16, 143–155 (2018). CAS  PubMed  Google Scholar  3. Oh, J. et al. Temporal stability…

Long read de novo phylogenetic tree for metagenome 0 What tools are available to create de novo phylogenetic trees for long read metagenome datasets? phyloT seems to construct one based on taxonomy and NCBI/GTDb information rather than read alignment. Is MAFFT commonly used? What is the standard methodology? (For reference,…

About Short intro Further reading How to cite Brief project history Authors Funding License and Terms of use Short intro QUAST evaluates genome assemblies by computing various metrics, including N50, length for which the collection of all contigs of that length or longer covers at least 50% of assembly length…

Abstract Genome binning has been essential for characterization of bacteria, archaea, and even eukaryotes from metagenomes. Yet, no approach exists for viruses. We developed vRhyme, a fast and precise software for construction of viral metagenome-assembled genomes (vMAGs). vRhyme utilizes single- or multi-sample coverage effect size comparisons between scaffolds and employs…

Lichen fungi live in a symbiotic association with unicellular phototrophs and have no known aposymbiotic stage. A recent study postulated that some of them have lost mitochondrial oxidative phosphorylation and rely on their algal partners for ATP. This claim originated from an apparent lack of ATP9, a gene encoding one subunit…

1. Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015). PubMed  Google Scholar  2. Zou, Y. et al. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. Nat. Biotechnol. 37, 179–185 (2019). CAS  PubMed  PubMed Central  Google Scholar  3. Mohammad,…

Redundancy analysis (RDA) for metagenomic community 0 Hello I want to do Redundancy analysis (RDA) to see variation in my bacterial community samples but I am kinda lost and don’t know where to start. I searched online but couldn’t find any. Is there any R code or tutorial available for…

This article was originally published here Phytopathology. 2021 Dec 10. doi: 10.1094/PHYTO-10-21-0418-RVW. Online ahead of print. ABSTRACT Genomics’ impact on crop production continuously expands. The number of sequenced plant and microbial species and strains representing diverse populations of individual species rapidly increases thanks to the advent of next generation sequencing…

DGAP-News: BRAIN Biotech AG / Key word(s): Miscellaneous/Patent08.12.2021 / 15:00 The issuer is solely responsible for the content of this announcement. Zwingenberg, Germany, December 8th, 2021 Additional Genome Editing Nuclease: BRAIN-Metagenome-Cas 01 (BMC01) BRAIN Biotech AG has successfully extended its proprietary genome editing toolbox with the addition of BRAIN-Metagenome-Cas 01…

Antibiotic discovery rates dramatically declined following the “golden age” of the 1940’s to the 1960’s. The platforms that underpinned that age of discovery rested upon laboratory cultivation of a small clade of bacteria, the actinomycetes, primarily isolated from soil environments. Fermentation extracts of these isolated bacteria have provided the majority…

doi: 10.1128/mSystems.00790-21. Online ahead of print. Affiliations Expand Affiliation 1 Department of Biology, University of Waterloo, Waterloo, Ontario, Canada. Item in Clipboard Angus S Hilts et al. mSystems. 2021. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1128/mSystems.00790-21. Online ahead of print. Affiliation 1 Department of Biology, University of Waterloo,…

DGAP-Ad-hoc: BRAIN Biotech AG / Key word(s): Miscellaneous/PatentBRAIN Biotech AG: Additional Differentiated Genome-Editing Nuclease: BRAIN-Metagenome-Cas 01 (BMC01) 08-Dec-2021 / 14:53 CET/CESTDisclosure of an inside information acc. to Article 17 MAR of the Regulation (EU) No 596/2014, transmitted by DGAP – a…

The oral microbiota contains billions of microbial cells, which could contribute to diseases in many body sites. Challenged by eating, drinking, and dental hygiene on a daily basis, the oral microbiota is regarded as highly dynamic. Here, we report significant human genomic associations with the oral metagenome from more than…

This repository include scripts for analysis of biosynthetic gene clusters (BGCs) in large metagenome assemblies. All scripts were created within the Chernevaya Taiga project funded by the Russian Science Foundation (grant 19-16-00049). The repository also contains results of the scripts application to four hybrid (illumina + ONT) assemblies of various…

how to create a custom database (GTDB) ? 0 Hello I was asked for creating a custom database from GTDB, I just need to incorporate some metagenome assembly genomes (MAGs) to the GTDB database the issue is that I dont know how to do that. the GTDB file “gtdbtk_data.tar.gz” from…

Searching metagenomic datasets for a specific species 1 Hi, There are a vast number of metagenomic datasets available from microbiomes in different environments, such as marine, terrestrial, human, etc. These datasets seem to capture a massive amount of data relating to community composition. As such, I am wondering if there…

Job Portal Postdoc in bioinformatics and metagenomics at Novo Nordisk Foundation Center for Protein Research We are looking for a highly motivated and dynamic researcher for a 2 year position, to commence on 1 January 2022 or soon hereafter. The position will be in the Human Proteome Variation group at The Novo Nordisk…

Bioinformatics Scientist – Agricultural DNA Extraction!This Jobot Job is hosted by Drew J. Fibus Are you a fit? Easy Apply now by clicking the “Apply” button and sending us your resume. Salary $75,000 – $130,000 per year A Bit About Us Based in St. Louis, MO with 2 offices across…

1. Hackstein JH, Stumm CK. Methane production in terrestrial arthropods. Proc Natl Acad Sci USA. 1994;91:5441–5. CAS  PubMed  PubMed Central  Article  Google Scholar  2. Hackstein JHP, van Alen TA. Fecal methanogens and vertebrate evolution. Evolution. 1996;50:559–72. PubMed  Article  PubMed Central  Google Scholar  3. Borrel G, McCann A, Deane J, Neto…

Applications are invited for a Postdoctoral Research Scientist to join the Laboratory of Dr Chris Quince in the High-Resolution Microbiomics group at the Earlham Institute, based in Norwich, UK.   Background: The High-resolution Microbiomics group focusses on both theoretical and experimental methods for microbial community analysis. Combining statistical bioinformatics with…

Postdoctoral Fellow in BioinformaticsUNC Charlotte – Charlotte, NC The Department of Bioinformatics and Genomics at the University of North Carolina at Charlotte seeks a post-doctoral fellow to work under the supervision of Dr. Anthony Fodor. The successful applicant will work on NIH supported projects that investigate the role of…

Category Research / Academic Location Wageningen You might share our view that wild plant communities might act as viral reservoirs that are also connected to agricultural plants. Since viruses can spill over from natural to agricultural systems, it is highly relevant to characterize virus diversity in wild plants. Plant virus…

How does MetaProdigal handle metagenomics where different genetic codes are used? 1 I’m wondering how prodigal when using -p meta can handle genes from different genetic codes? For example, if Gracilibacteria/SR1 was in there it would use genetic code 25. Would it catch this? When running in meta mode does…

Postdoctoral researcher Microbiome Bioinformatics 100%, Zurich, fixed-term 100%, Zurich, fixed-term The Food Systems Biotechnology (FSB) group is seeking a postdoctoral researcher with expertise in microbiome metagenomics and bioinformatics to lead efforts for characterization and analysis of global microbial biodiversity as part of the Microbiota Vault initiative’s efforts to preserve our microbial…

How to compute module completion ratio of KEGG modules from KO identifiers? (command line) 0 I was previously using KEGG-MAPLE to compute module completion ratios for metagenome assembled genomes. However, this tool was web only (very frustrating) and also it has been discontinued. Now I’m trying to do something similar…

In der aktuellen Covid-19 Situation laufen die Rekrutierungen weiter. Es kann dabei allerdings zu Verzögerungen kommen. Vielen Dank für Ihr Verständnis. 100%, Zurich, fixed-term The Food Systems Biotechnology (FSB) group is seeking a postdoctoral researcher with expertise in microbiome metagenomics and bioinformatics to lead efforts for characterization and analysis of global…

WGS bacterial metagenomic pipeline – group comparison 0 Hello all, I was wondering what’s the recent state-of-the-art pipeline to do metagenome comparison, with multiple samples and groups? E.g. I have several “patients” and several “controls” in the form of WGS reads, and I want to run a comparison (on some…

Mapping reads and quantifying genes – Metagenomic workshop 0 Hello, I am using the following metagenomic workshop tutorial to analyse my own metagenomic data. metagenomics-workshop.readthedocs.io/en/latest/annotation/quantification.html I performed the following steps: mapped reads with bowtie2 and generated .bam file with samtools sort. Removed duplicates with picard Extracted gene information from prokka…

Genomics Data Scientist – 93419 Organization: JG-Joint Genome Institute Lawrence Berkeley National Lab (LBL, lbl.gov/) Joint Genome Institute (JGI, jgi.doe.gov/) Division has an opening for a Genomics Data Scientist. This is an exciting opportunity for applying your data science expertise in genomics to solve the most challenging energy and environmental…

How to search for species with certain function or pathway in the annotated genome? 0 I’m trying to find bacterial species with certain metabolic pathways. I want to curate a “metagenome” of individual species that each have certain metabolic characteristics. So far, I have found KEGG has information on metabolic…

Job:SRA splitting for each metagenome-assembled genome 0 Hi everybody, we obtained viruses from water and sequenced them with Illumina. we formed different metagenomic-assembled genomes and get a Bioproject number and Biosample numbers (for each of them). Now, i should do SRA submission. But i cannot submit for my all genomes…