Categories
Tag: Metagenome
What Metagenomics is and Its Applications in Healthcare and Biotechnology – Magazines Weekly
Metagenomics is simply the study of microbes in the natural living environment that involves complex microbial communities where they exist. The study helps examine an organism’s genomic composition, including all its microbes. Rather than considering the concept of an organism and microbes as separate entities, regard them as a community…
GenomeFace: a deep learning-based metagenome binner trained on 43,000 microbial genomes
Abstract Metagenomic binning, the process of grouping DNA sequences into taxonomic units, is critical for understanding the functions, interactions, and evolutionary dynamics of microbial communities. We propose a deep learning approach to binning using two neural networks, one based on composition and another on environmental abundance, dynamically weighting the contribution…
KEGG T30512: 29135
KEGG T30512: 29135 T30512 (Metagenome): 29135 Help Entry 29135 CDS T30512 Symbol fbp Name fructose-1,6-bisphosphatase class 1 KO Best hit Taxonomy Gammaproteobacteria – Others [GN:hin]Taxonomy Pathway 00010 Glycolysis / Gluconeogenesis 00030 Pentose phosphate pathway 00051 Fructose and mannose metabolism 00680 Methane metabolism 00710 Carbon fixation in photosynthetic organisms 01100 Metabolic pathways…
A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing
Introduction Short-read metagenomic sequencing is the technique most widely used to explore the natural habitat of millions of bacteria. In comparison with 16S rRNA sequencing, shotgun metagenomic sequencing (MGS) provides sequence information of the whole genomes, which can be used to identify different genes present in an individual bacterium and…
KEGG T30512: 12494
KEGG T30512: 12494 T30512 (Metagenome): 12494 Help Entry 12494 CDS T30512 Name pyruvate dehydrogenase subunit E1 KO Best hit Taxonomy Actinobacteria [GN:acq]Taxonomy Pathway 00010 Glycolysis / Gluconeogenesis 00020 Citrate cycle (TCA cycle) 00620 Pyruvate metabolism 01100 Metabolic pathways 01110 Biosynthesis of secondary metabolites 01120 Microbial metabolism in diverse environments 01200 Carbon…
Ubuntu Manpage: mash – fast genome and metagenome distance estimation using MinHash
Provided by: mash_2.3+dfsg-1build2_amd64 NAME mash – fast genome and metagenome distance estimation using MinHash SYNOPSIS mash <command> [options] [arguments …] DESCRIPTION mash is the main executable for the Mash software. The actual functionality is provided by the subtools (‘commands’): Commands bounds Print a table of Mash error bounds. dist Estimate…
Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing
Review doi: 10.1111/1751-7915.14396. Online ahead of print. Affiliations Expand Affiliations 1 Quadram Institute Bioscience, Norwich, UK. 2 Earlham Institute, Norwich, UK. 3 Inria, University of Bordeaux, INRAE, Talence, France. 4 University of Bordeaux, CNRS, Bordeaux INP, LaBRI, UMR 5800, Talence, France. 5 INRAE STLO¸University of Rennes, Rennes, France. 6 INRAE,…
LS7C Week 7 Pre-Class Reading Guide (pdf)
Name: Kevin Munguia Fill out this worksheet as you complete your pre-class assignments. Be sure to watch the “The Human Microbiome Part 1-3″ videos before class. Bring your completed worksheet to class to use as a reference for in-class activities. After completing your pre-class assignments, you should be able to:…
Boosting microbiome science worldwide could save millions of children’s lives
Less than 15% of the global population lives in Europe or North America. Yet more than 70% of published human microbiome data — on the collections of bacteria, fungi and viruses that live on and in our bodies — comes from European and North American populations1. Around 85% of the…
Multiple Job openings at Gujarat Biotechnology Research Centre
Government of Gujarat has established Gujarat State Biotechnology Mission (GSBTM) as a nodal agency to develop overall development of biotechnology in the state in 2004. Major activities of GSBTM is promoting research and development in the field of biotechnology and supporting the development of biotechnology industries in the state. Besides…
Metagenomics and the development of viral water quality tools
Abstract Human exposure to pathogenic viruses in environmental waters results in a significant global disease burden. Current microbial water quality monitoring approaches, mainly based on fecal indicator bacteria, insufficiently capture human health impacts posed by pathogenic viruses in water. The emergence of the ‘microbiome era’ and high-throughput metagenome sequencing has…
Building the taxonomic profile of the Riniaie Marwah hot spring of Kishtwar in Jammu and Kashmir: the first high-throughput sequencing-based metagenome study
Background and objectives: Rinaie Marwah hot spring Kishtwar (RMHSK) is one of the geothermal springs located at 33°51’51″N 75°32’07″E with an elevation of 2134 meters above sea level in Jammu and Kashmir, India. We aimed to study the microbial diversity of this geothermal spring using metagenomics. Materials and methods: In…
The Science Behind It: Metagenomics 101
If microorganisms are invisible to the naked eye, how do we know anything about them? Generally, there are 3 common ways to identify microbes living in a given environment. The first is microscopy – looking at microbes under a microscope. There are only a few different shapes that microbes can…
4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs
Abstract Microbial communities usually harbor a mix of bacteria, archaea, plasmids, viruses, and microeukaryotes. Within these communities, viruses, plasmids, and microeukaryotes coexist in relatively low abundance, yet they engage in intricate interactions with bacteria. Moreover, viruses and plasmids, as mobile genetic elements, play important roles in horizontal gene transfer and…
Senior Bioinformatics Scientist in Chicago, IL for University of Chicago (UC)
Details Posted: 19-Dec-23 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Chicago, IL Job Description: Development of an integrated data warehouse for symbiote including clinical, microbiome sequence, and metabolomic data. Management of DFI Biobank, MMF, and HMMF data within the Symbiote platform. Functional analysis of…
First animal source metagenome assembly of Lawsonella clevelandensis from canine external otitis
Abstract External otitis is one of the most common conditions in dogs to be presented to the veterinarian. Moreover, the disorder is often difficult to manage. The range and role of microorganisms involved in the pathogenesis are currently not fully understood. Therefore, the condition has been studied using third-generation sequencing…
Research Scientist Position – Genomic Basis of Marine Sponge Symbioses – GEOMAR
Research Scientist Position – Genomic Basis of Marine Sponge Symbioses GEOMAR – Helmholtz Centre for Ocean Research Kiel, Germany Project Description: The Hentschel lab at GEOMAR seeks to elucidate the physiological and metabolic functioning and mechanisms of interaction between marine sponges and their symbiotic microbial consortia. Our research covers fundamental…
Senior Bioinformatics Scientist @ University of Chicago
Department BSD DFI – Translational Informatics About the Department The Duchossois Family Institute focuses on the role of commensal bacteria in enhancing disease resistance and is using genomic and metabolomic platforms to characterize the microbiome and its metabolites. Computational and bioinformatic expertise is required to understand how commensal bacteria impact…
Gut Microbiome and Bifidobacterium Research in Zimbabwe
Introduction The Infant Gut Microbiome Untangling what constitutes a healthy gut microbiome is timely, particularly in low- and middle-income (LMIC) settings where problems of infant nutrition, chronic diarrhea, and failure to thrive are high priority.1,2 Studying the infant gut microbiome is also crucial as many of the events capable of…
Binning the rare biosphere
Hello everyone. I would like to start a discussion here. Recently, I responded to a question on Seqanswers regarding the binning of rare microbes from shotgun metagenomes (www.seqanswers.com/forum/applications-forums/metagenomics/324515-software-recommendation-for-metagenome-assembly-for-low-abundance-bacteria). I suggested an idea for an appropriate pipeline for this task, but unfortunately, it did not gain much attention. Nevertheless, I tried…
Metagenome analyses identify human endogenous retrovirus-K113 (HML-2) subtype in glioblastoma
. 2023 Dec 15;133(24):e173959. doi: 10.1172/JCI173959. Item in Clipboard Amanda Macamo et al. J Clin Invest. 2023. Show details Display options Display options Format AbstractPubMedPMID . 2023 Dec 15;133(24):e173959. doi: 10.1172/JCI173959. Item in Clipboard Cite Display options Display options Format AbstractPubMedPMID No abstract available Keywords: Brain cancer; Oncology; Virology. PubMed Disclaimer…
Metagenome analyses identify human endogenous retrovirus-K113 (HML-2) subtype in glioblastoma. Reply
. 2023 Dec 15;133(24):e176406. doi: 10.1172/JCI176406. Affiliations Expand Affiliations 1 Miller School of Medicine, Department of Neurological Surgery, University of Miami, Coral Gables, Florida, USA. 2 National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA. Item in Clipboard Vaidya Govindarajan et al. J Clin Invest. 2023. Show details Display…
Challenges in Estimating Effective Population Sizes from Metagenome-Assembled Genomes
1Shenzhen Research Institute, The Chinese University of Hong Kong, China 2State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology (CAS), China The final, formatted version of the article will be published soon. Notify me Receive an email when…
Research Biologist (Computational/Bioinformatics)/Microbiologist (Research Associate) Job in Columbia, MO
Summary The Agricultural Research Service (ARS) is the United States Department of Agriculture’s chief scientific research agency and one of the world’s premiere scientific organizations. ARS Postdoctoral Research Associates are hired to supplement a lead scientist’s research on agricultural problems of high national priority affecting American agriculture. **ANNOUNCEMENT IS OPEN…
Solved Question 57 (2 points) A small, circular piece of DNA
Transcribed image text: Question 57 (2 points) A small, circular piece of DNA that replicates independently of the main chromosome in bacteria, and is commonly used for molecular cloning, is called a … plasmid metagenome GMO complement Question 60 (2 points) A mutation in the gene “tan” in fruit flies…
Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles
Rignot, E., Jacobs, S., Mouginot, J. & Scheuchl, B. Ice-shelf melting around antarctica. Science (80-) 341, 266–270 (2013). Article ADS CAS Google Scholar Wadham, J. L. et al. Ice sheets matter for the global carbon cycle. Nat. Commun. 10, 1–17 (2019). Google Scholar Adusumilli, S., Fricker, H. A., Medley, B.,…
A standalone pipeline to assess the quality of metagenome-assembled genomes
%PDF-1.7 % 1 0 obj <>/Metadata 5 0 R/Outlines 2 0 R/Pages 3 0 R/StructTreeRoot 4 0 R/Type/Catalog/ViewerPreferences 6 0 R>> endobj 5 0 obj <>stream Microsoft Word 2023-12-13T16:44:22Z 2023-12-14T05:22:09-08:00 2023-12-14T05:22:09-08:00 uuid:867F3424-7E46-4F8D-87B3-27DFE027E5CC uuid:e4adc279-1dd1-11b2-0a00-900000000000 application/pdf MAGqual: A standalone pipeline to assess the quality of metagenome-assembled genomes endstream endobj 2 0 obj <>…
MAGqual: A standalone pipeline to assess the quality of metagenome-assembled genomes
Abstract Metagenomics, the whole genome sequencing of microbial communities, has provided insight into complex ecosystems. It has facilitated the discovery of novel microorganisms, explained community interactions, and found applications in various fields. Advances in high-throughput and third-generation sequencing technologies have further fuelled its popularity. Nevertheless, managing the vast data produced…
Postdoc on Gut Microbiome and Metagenome
Your job Are you the enthusiastic scientist with a PhD, who is experienced with metagenomics data and wants to focus on understanding the function of our microbiome? Are you interested in how microbes can improve the health of babies? We at Wageningen University and Research have a vacancy for a…
total 30,851 single-cell genomes, 51 metagenomes, and 1,544 metagenome-assembled genomes from the human oral/gut microbiota
README This is the large single amplified genome calatog (bbsag20) corresponding to the publication below: Title: “Single Amplified Genome Catalog Reveals the Dynamics of Mobilome and Resistome in the Human Microbiome” (preprint: 10.1101/2023.12.06.570492) Authors: Tetsuro Kawano-Sugaya, Koji Arikawa, Tatsuya Saeki, Taruho Endoh, Kazuma Kamata, Ayumi Matsuhashi, and Masahito Hosokawa Research…
CEDARS-SINAI Research Bioinformatician II – Human Microbiome Research Institute in Beverly Hills, CA | 889550076
Cedars-Sinai has established a new Human Microbiome Research Institute that will support investigators studying how the microbiome plays a role in human health and disease with key focus areas in: Cancer, Metabolism, Early Life, GI & Liver, and Autoimmunity. The Human Microbiome Research Institute (HMRI) is an innovation hub and…
A laboratory ice machine as a cold oligotrophic artificial microbial niche for biodiscovery
Flemming, H.-C. & Wuertz, S. Bacteria and archaea on earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019). Article CAS PubMed Google Scholar Flemming, H.-C., Neu, T. R. & Wozniak, D. J. The EPS matrix: The “house of biofilm cells”. J. Bacteriol. 189, 7945–7947 (2007). Article CAS …
Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes
Steffen, W. et al. Planetary boundaries: guiding human development on a changing planet. Science 347, 1259855 (2015). Article PubMed Google Scholar Kanter, D. R. et al. Nitrogen pollution policy beyond the farm. Nat. Food 1, 27–32 (2020). Article ADS Google Scholar Tian, H. et al. A comprehensive quantification of global…
Disease signatures in the gut metagenome of a prospective family cohort of inflammatory bowel disease
Abstract Inflammatory bowel disease (IBD) is associated with dysbiotic microbiomes. However, whether microbiomes of family members of IBD patients harbour microbial disease signatures of IBD is unknown. Here, we generate shotgun metagenomic data of an IBD family cohort and treatment-naive IBD cases, which we combine with published IBD metagenomes, to…
How does sequencing depth affect the identification of bacteria, fungi and viruses?
What are some latest advances in clinical metagenomic diagnostics for pathogen detection using shirt and long read sequencing?5 answersClinical metagenomic diagnostics for pathogen detection using short and long read sequencing have seen several recent advances. Traditional pathogenic diagnosis methods have limitations such as low positivity rates and inability to identify…
MetaSPAdes genome assembly (shotgun metagenome singleend) – usegalaxy.org support
Busrak December 11, 2023, 3:31pm 1 Hi friends, Metagenomic single end raw data with cut adapt‘Maximum error rate 0.3’Match times: 1Minimum overlap length:3minimum lenght: 15Max N: 0.3Max expected errors: 30 parameters.Then I aligned the host genome with gallus gallus with BBmap tool. I want to Assembly unmapped read. However, MetaSPAdes…
Using Metagenome Samples for HNSCC analysis
Using Metagenome Samples for HNSCC analysis 0 So I’m trying to analyze the floor-of-mouth HNSCC(Head and Neck Squamous Cell Carcinoma) and controls. I’m going to be using SRA files. The issue I’ve encountered is that I could only find 2 controls. The 2 controls were tumor-adjacent normals. For floor-of-mouth, there…
Week 7 Microbiome Immune System.pdf – The Human Microbiome The Human Microbiome Learning Goal: Understand how hosts can influence their microbiome and
1The Human Microbiome The Human Microbiome Learning Goal:Understand how hosts can influence their microbiome and how the microbiome can influence its host. After completing the pre-class assignments, students will be able to… •Define and differentiate between the terms microbiome, microbiota, metagenome, and holobiont •Explain how and when the human microbiome…
Carbohydrates and carbohydrate degradation gene abundance and transcription in Atlantic waters of the Arctic
Seawater samples were collected from surface waters (SRF) and the bottom of the surface mixed layer (BML) in the Eastern Fram Strait region to investigate the distribution of carbohydrates and their utilisation by microbial communities. The ten sites were grouped into three categories based on the underlying seafloor topography (above-slope,…
An article on how to quickly, efficiently and robustly screen metagenomic-derived enzymes
Over the past few decades, the use of metagenomics to mine genomes from non-cultured microorganisms has been a powerful tool for discovering new proteins and other valuable biomolecules. The vast amounts of sequencing data generated by metagenomics provide a glimpse into the biosynthetic potential of uncultured microorganisms. However, functional characterization…
Resin acids play key roles in shaping microbial communities during degradation of spruce bark
Bark preparation Spruce bark was obtained from the Iggesund pulp and paper mill (Iggesund, Holmen AB, Sweden), from a bark pile resulting from stripping of spruce logs at the mill after harvest, with the average age of trees at harvest being ~70 years. The bark was left to dry at…
In situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day
doi: 10.1111/1755-0998.13909. Online ahead of print. Affiliations Expand Affiliations 1 Microbiome Analysis Laboratory, Systems Biology Department, CNB-CSIC, Madrid, Spain. 2 Departamento de Ecoloxía e Bioloxía Animal, Centro de Investigación Mariña, Universidade de Vigo, Vigo, Spain. 3 Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN-CSIC), Madrid, Spain….
Refinement of the “ Candidatus Accumulibacter” Genus Based on a Metagenomic Analysis of Biological Nutrient Removal (BNR) Pilot-Scale Plants Operated with Reduced Aeration
Abstract Members of the “ Candidatus Accumulibacter” genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 “ Ca . Accumulibacter” species, which have been proposed based on the phylogenetic divergence of the polyphosphate…
Freshwater Viral Metagenome Analyses Targeting dsDNA Viruses
doi: 10.1007/978-1-0716-3515-5_3. Affiliations Expand Affiliations 1 Division of Environmental Materials, Honam National Institute of Biological Resources, Mokpo, Republic of Korea. 2 Department of Biological Sciences and Bioengineering, Inha University, Incheon, Republic of Korea. chojc@inha.ac.kr. Item in Clipboard Kira Moon et al. Methods Mol Biol. 2024. Show details Display options Display options…
Metagenomics reveals effects of fluctuating water conditions on functional pathways in plant litter microbial community
Keller, J. K. Wetlands and the global carbon cycle: what might the simulated past tell us about the future?. New Phytol. 192, 789–792 (2011). Article CAS PubMed Google Scholar Dolinar, N., Rudolf, M., Šraj, N. & Gaberščik, A. Environmental changes affect ecosystem services of the intermittent Lake Cerknica. Ecol. Complex….
Metagenome-assembled genomes of three Hepatoplasmataceae provide insights into isopod-mollicute symbiosis
Metagenome-assembled genomes of three Hepatoplasmataceae provide insights into isopod-mollicute symbiosis | Microbiology Society 1887 This is a required field Please enter a valid email address Approval was a Success Invalid data An Error Occurred Approval was partially successful, following selected items could not be processed due to error…
What are the factors that influence the bias of 16S rRNA gene ampicon sequencing?
What are the factors that contribute to coverage bias in amplicon sequencing?4 answersCoverage bias in amplicon sequencing can be influenced by several factors. These include differences in 3′-end stability, primer Tm, amplicon length, amplicon GC content, and GC content of amplicon flanking regions. The presence of a highly dominant taxon…
Metagenome Sequencing – SeqCenter, LLC
Microbiomes contain diverse microbial communities whose interactions not only impact the system residents, but also have profound effects on the ecology, chemistry, and health of their shared host or environment. Capturing the interactions among microbes is essential as we expand our understanding of host-microbe dynamics, evaluate environmental degradation or remediation,…
KEGG T30512: 26705
KEGG T30512: 26705 T30512 (Metagenome): 26705 Help Entry 26705 CDS T30512 Name KO Best hit Taxonomy Actinobacteria [GN:acq]Taxonomy Pathway 00230 Purine metabolism 01100 Metabolic pathways 05340 Primary immunodeficiency Other DBs LinkDB All DBs Position C1167575:complement(3..554) AA seq 184 aa AA seqDB searchRLAVRYAGDQPGEVIGFGLSNDERAGQTSSWERAFAIARRGGLASMPHGGELLGPDHLREVVSCLGPTRLGHGVRAGEDPALLDAIVASGISLEVCPASNVSLGVYHSPDDVPLRRLMSHGAQIALSADDPLLFQSRLVDQYEIARTLGCDDAELAELARGSIRACLASPTAKQTWLAEVDAWL T30512 (Metagenome): 26591 Help Entry 26591 CDS T30512 Name KO…
KEGG T30376: 31478
KEGG T30376: 31478 T30376 (Metagenome): 31478 Help Entry 31478 CDS T30376 Name succinate dehydrogenase subunit A KO Best hit Taxonomy Bacteroidetes [GN:afd]Taxonomy Pathway 00020 Citrate cycle (TCA cycle) 00190 Oxidative phosphorylation 00650 Butanoate metabolism 00720 Carbon fixation pathways in prokaryotes 01100 Metabolic pathways 01110 Biosynthesis of secondary metabolites 01120 Microbial metabolism…
Metagenomic next-gene sequencing for respiratory infections
Introduction Respiratory tract infections are common and occur frequently. Rapid and accurate microbial detection is essential for timely and appropriate treatment. Traditional microbial detection methods have some limitations such as dependence on morphology, long duration, low sensitivity, and high variability.1,2 Metagenomic next-generation sequencing (mNGS) is a new detection technology characterized…
KEGG T30201: 12043
KEGG T30201: 12043 T30201 (Metagenome): 12043 Help Entry 12043 CDS T30201 Name probable aspartate aminotransferase KO K00816 kynurenine—oxoglutarate transaminase / cysteine-S-conjugate beta-lyase / glutamine—phenylpyruvate transaminase [EC:2.6.1.7 4.4.1.13 2.6.1.64] Best hit Pathway 00270 Cysteine and methionine metabolism 00380 Tryptophan metabolism 00450 Selenocompound metabolism 01100 Metabolic pathways 01110 Biosynthesis of secondary metabolites 05204 …
Host DNA depletion methods and genome-centric metagenomics of bovine hindmilk microbiome
doi: 10.1128/msphere.00470-23. Online ahead of print. Affiliations Expand Affiliation 1 Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway. Item in Clipboard Vinícius da Silva Duarte et al. mSphere. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1128/msphere.00470-23. Online ahead of print. Affiliation 1…
Metagenome-based microbial community analysis of urine-derived fertilizer
%PDF-1.4 % 60 0 obj <> endobj 77 0 obj <>stream PyPDF2 application/pdf Metagenome-based microbial community analysis of urine-derived fertilizer 2023-12-07T08:58:22-08:00 2023-12-07T08:58:22-08:00 2023-12-07T08:58:22-08:00 uuid:1d1cb7eb-1dd2-11b2-0a00-4e09278d5b00 uuid:1d1cb7ee-1dd2-11b2-0a00-1e0000000000 endstream endobj 1 0 obj <> endobj 2 0 obj <>/MediaBox[0 0 595.29999 841.90002]/Parent 1 0 R/Resources<>/ProcSet[/PDF/Text]>>/Type/Page>> endobj 3 0 obj <>/MediaBox[0 0 595.29999 841.90002]/Parent 1…
KEGG T30641: 73770
KEGG T30641: 73770 T30641 (Metagenome): 73770 Help Entry 73770 CDS T30641 Symbol glk Name KO Best hit Pathway 00010 Glycolysis / Gluconeogenesis 00052 Galactose metabolism 00500 Starch and sucrose metabolism 00520 Amino sugar and nucleotide sugar metabolism 00521 Streptomycin biosynthesis 00524 Neomycin, kanamycin and gentamicin biosynthesis 01100 Metabolic pathways 01110 Biosynthesis…
Advancements in Non-human Forensic DNA Analysis
Alahi MEE, Mukhopadhyay SC (2017) Detection methodologies for pathogen and toxins: a review. Sensors 1885:17 Google Scholar Aly SM, Sabri DM (2015) Next generation sequencing (NGS): a golden tool in forensic toolkit. Archiwum Medycyny Sądowej i Kryminologii/Archives of Forensic Medicine and Criminology 65(4):260–271 Google Scholar Amendt J, Richards CS, Campobasso…
Zea mays genotype influences microbial and viral rhizobiome community structure
Oburger E, Schmidt H. New methods to unravel rhizosphere processes. Trends Plant Sci. 2016;21:243–55. Article CAS PubMed Google Scholar Rout ME, Southworth D. The root microbiome influences scales from molecules to ecosystems: the unseen majority. Am J Bot. 2013;100:1689–91. Article PubMed Google Scholar Pratama AA, Terpstra J, de Oliveria ALM,…
BF23 bacteriophage study reveals that viruses can cope with bacterial restriction and modification
Model of BF23 virion with depicted positions of proteins identified by mass spectrometry analysis of phage virion. Credit: Mikhail Skutel and coauthors Bacteriophages are natural “predators” and enemies of bacteria. They are able to recognize specific types of bacteria and are considered safe for humans. Due to the increasing resistance…
Comparing 16S rRNA (culture) sequences with metagenome
Comparing 16S rRNA (culture) sequences with metagenome 0 I have 8 metagenome from a sample and also other team extracted several bacteria from the same sample and did 16S rRNA sequencing for them. Approximately 400 and isolation is still progressing. Now, I wanted to match the 16S rRNA data to…
Accessing the Soil Metagenome | 4 | Soil Metagenomics
Direct cultivation or indirect molecular approaches can be used to explore and exploit the microbial diversity present in soil. Cultivation and isolation of microorganisms is the traditional method but, as only 0.1% to 1.0% of the soil bacteria are culturable using standard cultivation methods. Methods described for metagenomic DNA isolation…
Marine toxin domoic acid alters nitrogen cycling in sediments
Effects of DA on potential N transformation rates It was reported that DIN in overlying water is mainly from sediments25, so the variation of DIN concentrations in overlying water was monitored, so as to infer the potential N transformation process in sediments. Generally, it can be observed that the overlying…
Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses
Honegger, R. The lichen symbiosis: What is so spectacular about it?. Lichenologist 30, 193–212 (1998). Article Google Scholar Grube, M. & Berg, G. Microbial consortia of bacteria and fungi with focus on the lichen symbiosis. Fung. Biol. Rev. 23, 72–85 (2009). Article Google Scholar Spribille, T. et al. Basidiomycete yeasts…
Using metagenome assembly and binning to identify and mitigate contamination in a genome
Hi everyone, This may be a silly question, but I am interested if using metagenome assembly and binning is a valid method of determining if a sample contains a mixture of species. Similarly, can metagenomics be used to identify and remove contamination from a single genome? For some background, I…
Quast Genome assembly Quality (Galaxy Version 5.2.0+galaxy1) – usegalaxy.org support
Busrak November 29, 2023, 9:55am 1 Hi dear galaxy family, When I put my metagenome single read Megahit assembly data into Quast, I encounter the following error code. How can I solve this problem? Assembly_with_MEGAHIT_on_data_658 /usr/local/opt/quast-5.2.0/metaquast.py –single /jetstream2/scratch/main/jobs/53997042/inputs/dataset_f68c8b4a-bea0-4985-8324-4c64cdbe4d6d.dat –labels Assembly_with_MEGAHIT_on_data_658 -o outputdir –max-ref-num 50 –m 822: Quast on data 196…
Metagenome Dataset of Maize Rhizosphere for Saline Soil from Mau Region of Uttar Pradesh by Alok Kumar Singh, Alok Kumar Srivastava, Mala Trivedi :: SSRN
Abstract In India, after rice and wheat, maize (Zea mays L.) is most significant food crop. Like others, maize is also influenced by the rhizospheric region’s microbial communities, which are incredibly diverse and unquestionably play a key role in the nutrient cycle and growth productivity. Maize rhizospheric soil samples were…
How to estimate -g genome-size for Flye for de novo genome or for –meta mode when using Metaflye?
How to estimate -g genome-size for Flye for de novo genome or for –meta mode when using Metaflye? 0 A few questions regarding the -g genome-size argument for Flye and MetaFlye: How much does this value influence the performance and output of the assemblies? How can I estimate the genome…
filtering SAM/BAM to remove hits spanning short combined alignment lengths and low counts
filtering SAM/BAM to remove hits spanning short combined alignment lengths and low counts 0 hi folks, apologies if this has been answered elsewhere. I’m using read mapping to quantitate the abundance of viral metagenome assembled genomes (MAGs) across samples and I’d like to do a bit of data cleaning that’s…
Hot Springs Viruses At Yellowstone National Park Have Ancient Origins And Are Adapted To Their Thermophilic Hosts
Taxonomic classification consensus of virus operational taxonomic units (vOTUs). — biorxiv Geothermal springs in areas such as Yellowstone National Park (YNP), USA house unicellular red algae that dominate the microbial biomass. Little is known about the viruses that infect the biota. Here we used metagenomics to characterize the multi-kingdom infecting…
Minimalist Or Maximalist? The Life Of A Microbe A Mile Underground
Prof. Magdalena Osburn removes a sample during a site visit in August. CREDIT Sanford Underground Research Facility If you added up all the microbes living deep below Earth’s surface, the amount of biomass would outweigh all life within our oceans. But because this abundant life is so difficult to reach,…
Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel.
Suarez C, Hackl T, Wilen BM, Persson F, Hagelia P, Jetten MSM, Dalcin Martins P FEMS Microbiol. Lett. 370 (-) – [2023-01-17; online 2023-06-09] The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion…
I made an error when using metawrap to binning
I made an error when using metawrap to binning 1 my code metawrap binning -o bin_out -t 24 -m 200 -a all_contig/all_merge.fasta –metabat2 –maxbin2 –concoct all_fastq/*fastq Error reported as follows sorting the SRR10492802 alignment file [bam_sort_core] merging from 24 files and 24 in-memory blocks… [E::sam_hdr_sanitise] Malformed SAM header at line…
Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface
Sampling sites and depths Metagenomes were produced from sediment samples at drilling sites U1545B to U1549B that follow a northwest-to-southeast transect across the northwestern flanking region of Guaymas Basin (Fig. 1A) and include an off-axis hydrothermal system, the Ringvent site (Fig. 1B). The samples were selected to coordinate with depths used for…
Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster | Microbiome
Diversity of the RCA cluster and genome characteristics The phylogenomic analysis yielded three major clades within the RCA cluster (Fig. 1) Genomes of the three clades were relatively distinct with appr. < 70% average nucleotide identity (ANI), resulting in the proposal of three genera, the known genus Planktomarina, and two new genera without…
Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost
Tarnocai C, Canadell JG, Schuur EA, Kuhry P, Mazhitova G, Zimov S. Soil organic carbon pools in the northern circumpolar permafrost region. Global Biogeochem Cycles. 2009;23:1–11. Article Google Scholar Hugelius G, Strauss J, Zubrzycki S, Harden JW, Schuur EA, Ping CL, et al. Estimated stocks of circumpolar permafrost carbon with…
Improving Species Level-taxonomic Assignment from 16S rRNA Sequencing Technologies
Affiliations Expand Affiliations 1 Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, Barcelona, Catalonia, Spain. 2 ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain. 3 Department of Clinical Sciences, Faculty of Medicine and Health Sciences and Universitat de Barcelona Institute…
A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics
Título: Autor: Haro-Moreno, José M.; Cabello-Yeves, Pedro J.; Garcillán-Barcia, M. Pilar; Zakharenko, Alexandra; Zemskaya, Tamara I.; Rodriguez-Valera, Francisco Palabras clave: Ca. PatescibacteriaLake BaikalLong-read metagenomics16S rRNA Fecha de publicación: 2023 Editor: Springer Nature Citación: Environmental Microbiome 18: 12 (2023) Resumen: [Background]: Lake Baikal, the world’s deepest freshwater lake, contains important numbers…
Metagenome profiling and containment estimation through abundance-corrected k-mer sketching with sylph
Profiling metagenomes against databases allows for the detection and quantification of microbes, even at low abundances where assembly is not possible. We introduce sylph, a metagenome profiler that estimates metagenome-genome average nucleotide identity (ANI) through zero-inflated Poisson k-mer statistics, enabling ANI-based taxa detection. Sylph is the most accurate method on…
Name
<< addMetaGenome.pl – Wrapper script to add a metagenome to a collection in Smash addMetaGenome.pl [options] –collection (required) Name of metagenome collection to which this metagenome is added –title A short title to identity this metagenome. We recommend using something short, like under 8 characters, since this will be used…
Data_Sheet_3_First shotgun metagenomics study of Juan de Fuca deep-sea sediments reveals distinct microbial communities above, within, between, and below sulfate methane transition zones.xlsx
The marine deep subsurface is home to a vast microbial ecosystem, affecting biogeochemical cycles on a global scale. One of the better-studied deep biospheres is the Juan de Fuca (JdF) Ridge, where hydrothermal fluid introduces oxidants into the sediment from below, resulting in two sulfate methane transition zones (SMTZs). In…
Using 16S rDNA and metagenomic sequencing technology to analyze the fecal microbiome of children with avoidant/restrictive food intake disorder
Patient demographics Among the children, 102 were diagnosed with ARFID, and 33 were healthy. There were 50 males and 52 females in the ARFID group and 15 males and 18 females in the healthy control group (HC group). There was no significant difference in age (P = 0.352) or sex composition (P = 0.512)….
Tiny Vesicles Redefine Cell Communication
A new study has uncovered the vital role of extracellular vesicles in horizontal gene transfer among ocean microorganisms. This finding challenges existing beliefs about gene exchange mechanisms and introduces ‘protected extracellular DNA’ (peDNA) as a new term to encompass the diversity of genetic carriers beyond viruses, setting a new direction…
Shotgun metagenomes from productive lakes in an urban region of Sweden
Williamson, C. E., Saros, J. E., Vincent, W. F. & Smol, J. P. Lakes and reservoirs as sentinels, integrators, and regulators of climate change. Limnology and Oceanography 54, 2273–2282, doi.org/10.4319/lo.2009.54.6_part_2.2273 (2009). Article ADS Google Scholar Cavicchioli, R. et al. 2019. Scientists’ warning to humanity: microorganisms and climate change. Nature Reviews…
Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2’-fucosyllactose utilization can be facilitated by coexisting species
Stewart, C. J. et al. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature 562, 583–588 (2018). Article CAS ADS PubMed PubMed Central Google Scholar Tamburini, S., Shen, N., Wu, H. C. & Clemente, J. C. The microbiome in early life: implications for health outcomes….
Study show extracellular vesicles exchange genetic information between cells in the sea
For this study, the researchers from the Max Planck Institute in Bremen also collected water samples off the North Sea Island of Helgoland. Credit: Silvia Vidal, Max Planck Institute for Marine Microbiology Researchers led by Susanne Erdmann from the Max Planck Institute for Marine Microbiology in Bremen have looked at…
Online metagenomics training (free) in April
Free Cloud-SPAN course on METAGENOMICS 11-21 April 2023 Join our experts for this free online module! We welcome environmental scientists who would like to use high performance computing for metagenomics analysis, or anyone with an interest in metagenomics to register. No previous experience of the command line or HPC is…
The expanding range of emerging tick-borne viruses in Eastern Europe and the Black Sea Region
Our pooled and individual metagenome-based tick screening using NS revealed 25 virus taxa including four tick-borne pathogens in samples collected from countries from Eastern Europe and around the Black Sea. Known tick-borne viruses endemic in the region, such as CCHFV or TBEV, were not detected, owing to the low prevalence…
Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide
Murray, C. J. et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629–655 (2022). Article CAS Google Scholar Brito, I. L. et al. Mobile genes in the human microbiome are structured from global to individual scales. Nature 535, 435–439 (2016). Article ADS CAS PubMed …
What are the differences in the metagenome of COVID-19 associated mucormycosis between patients with and without mortality?
What is the canonical pathway? 4 answers What is the effect of increasing the GPA admission requirement on teacher diversity? 5 answers How many people diagnosis and dead by SARS-CoV-2? 3 answers What is the prevalence of Parkinson’s disease by race and ethnicity? 5 answers What are the challenges and…
Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years
Egan, E. S., Fogel, M. A. & Waldor, M. K. Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol. Microbiol. 56, 1129–1138 (2005). Article CAS PubMed Google Scholar Harrison, P. W., Lower, R. P., Kim, N. K. & Young, J. P. Introducing the bacterial ‘chromid’: not a…
Erythroderma combined with deeper dermal dermatophytosis due to Trichophyton rubrum in a patient with myasthenia gravis: first case report and literature review | BMC Infectious Diseases
de Hoog GS, Dukik K, Monod M, Packeu A, Stubbe D, Hendrickx M, et al. Toward a novel multilocus phylogenetic taxonomy for the dermatophytes. Mycopathologia. 2017;182(1–2):5–31. Article PubMed Google Scholar Segal E, Elad D. Human and zoonotic dermatophytoses: epidemiological aspects. Front Microbiol. 2021;12:713532. Article PubMed PubMed Central Google Scholar Burstein…
Case of Spine Infection with Brucella melitensis
Introduction Brucellosis is a common zoonotic infection in most of the developing regions of the world, severely affecting livestock productivity and human health. It caused by a small, nonmotile gram-negative coccobacillus of the genus Brucella. Among reported human brucellosis cases, the pathogenic strain B. melitensis is the most frequently encountered.1,2…
Forecasting the dynamics of a complex microbial community using integrated meta-omics
Characterization of the microbial community From the experimental period between 21 March 2011 and 3 May 2012 (ref. 27), we previously obtained and analysed 51 weekly samples, to which we added 21 samples collected in the month of June during the years 2012–2016. The 72 samples were submitted to the…
Course Catalogue – Metagenomics (BITE11004)
Course Outline School School of Biological Sciences College College of Science and Engineering Credit level (Normal year taken) SCQF Level 11 (Postgraduate) Availability Not available to visiting students SCQF Credits 10 ECTS Credits 5 Summary The course will provide lecture-based instruction in the field of metagenomic analysis, practical instruction in…
A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources
40,039 MAGs reconstructed from large-scale genome-resolved metagenomics To reconstruct previously unexplored bacterial and archaeal genomes, we performed a large-scale single-sample metagenomic assembly on 3304 soil metagenomes across the globe (Fig. 1a), including 363 metagenomes from the in-house dataset and 2941 from publicly available metagenomes. The soil samples were mainly collected from…
Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae
Sheridan, P. O. et al. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat. Commun. 11, 1–12 (2020). Article Google Scholar Sheridan, P. O., Meng, Y., Williams, T. A. & Gubry-Rangin, C. Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat. Commun. 13, 1–13…
Metagenome-assembled genomes from High Arctic glaciers highlight the vulnerability of glacier-associated microbiota and their activities to habitat loss
doi: 10.1099/mgen.0.001131. Affiliations Expand Affiliations 1 Department of Life Sciences (DLS), Aberystwyth University, Wales, UK. 2 Interdisciplinary Centre for Environmental Microbiology (iCEM), Aberystwyth University, Wales, UK. 3 Department of Geography and Earth Sciences (DGES), Aberystwyth University, Wales, UK. 4 Present address: Department of Pathobiology and Population Sciences, The Royal Veterinary…
Analysis of microbial composition and sharing in low-biomass human milk samples: a comparison of DNA isolation and sequencing techniques
Victora CG, Bahl R, Barros AJD, França GVA, Horton S, Krasevec J, et al. Breastfeeding in the 21st century: Epidemiology, mechanisms, and lifelong effect. Lancet. 2016;387:475–90. Article PubMed Google Scholar Bardanzellu F, Fanos V, Strigini FAL, Artini PG, Peroni DG. Human breast milk: Exploring the linking ring among emerging components….
RVFScan predicts virulence factor genes and hypervirulence of the clinical metagenome | Briefings in Bioinformatics
Abstract Bacterial infections often involve virulence factors that play a crucial role in the pathogenicity of bacteria. Accurate detection of virulence factor genes (VFGs) is essential for precise treatment and prognostic management of hypervirulent bacterial infections. However, there is a lack of rapid and accurate methods for VFG identification from…
Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics
Albone, E. S. Mammalian semiochemistry. The investigation of chemical signals between mammals. 2–5 (1984). Wyatt, T. D. Pheromones and Animal Behaviour: Communication by Smell and Taste (Cambridge University Press, 2003). Book Google Scholar Doty, R. L. Odor-guided behavior in mammals. Experientia 42, 257–271 (1986). Article CAS PubMed Google Scholar Brennan,…
Spark-Based Label Diffusion and Label Selection Community Detection Algorithm for Metagenome Sequence Clustering
PLDLS, a parallel community detection algorithm in the spark framework, is designed to address the randomness of label selection during clustering and improve the completeness of metagenome sequence clustering. The algorithm combines four steps of node scoring and core node selection, core node diffusion and fast label selection, improved label…