METAGENOMICS BULLETIN BOARD

Ads related to Microbiology and specifically Genomics and Metagenomics. New positions, calls for grants, fellowships etc. Any brief announcement that can be of interest to the community of genome and metagenome sequencing.

If you are interested in publishing on this space, please contact Professor Francisco Rodríguez Valera at frvalera@umh.es.

• [13/09/2021] Three year posdoc on Metagenomics under the Genome of the Biosphere program at King Abdullah University of Science and Technology with Prof. Carlos M. Duarte
  
  The Computational BioScience Research Center has developed a metagenomic analysis platform, KMAP (1), and developed a large base of metagenomic samples across environments.  Initially rooted in the exploration of the Ocean Genome, the program now encompasses a catalogue of over 1.5 billion genes across domains in the biosphere, aiming at addressing fundamental questions of functionalo genomics, evolution, adaptation and metabolic processes across the biosphere (e.g. 2, 3, 4).A three year postdoctoral position is offered to join this project under the leadership of Prof. Carlos M. Duarte, with the Computational BioScience Research Center  and Red Sea Research Center at King Abdullah University of Science and Technology, a leading postgraduate, research-intensive international university with unparalleled duspport for research. cf.
  
  https://cemse.kaust.edu.sa/cbrc
  https://rsrc.kaust.edu.sa
  https://kaust.edu.sa/en
  https://kaust.edu.sa/visit
  
  Intetrested applicants, please send a letter of motivation, your ideas on what questions to explore with the Genome of the Biosphere program, and a letter of motivation to carlos.duarte@kaust.edu.sa. The position will remain open until a candidate is selected.
  
  1. Alam, I., A.A. Kamau, D. K.Ngugi, T. Gojobori, C.M. Duarte, and V.B. Bajicv. 2021. KAUST Metagenomic Analysis Platform (KMAP), enabling access to massive analytics of re‑annotated metagenomic data. Scientific Reports 11:11511, //doi.org/10.1038/s41598-021-90799-y.
  
  2. Acinas, S., P. Sánchez, G. Salazar, F. M. Cornejo-Castillo, M. Sebastián, R. Logares, M. Royo-Llonch, L. Paoli, S. Sunagawa, P. Hingamp, H. Ogata, G. Lima-Mendez, S. Roux, J. M. González, J.M. Arrieta, I.S. Alam, A. Kamau, C. Bowler, J. Raes, S. Pesant, P. Bork, S. Agustí, T. Gojobori, D. Vaqué, M. B. Sullivan, C. Pedrós-Alió, R. Massana, C. M. Duarte, J. M. Gasol. 2021. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Communications Biology 917.
  
  3. Duarte, C.M., D. K. Ngugi, I. Alam, J. Pearman, A. Kamau, V. M. Eguiluz, T. Gojobori, S.G. Acinas, J.M. Gasol, V. Bajic and X. Irigoien. 2020. Sequencing Effort Dictates Gene Discovery in Marine Microbial Metagenomes. Environmental Microbiology 22: 4589–4603, doi:10.1111/1462-2920.15182.
  
  4. Ngugi, D.K., M. Ziegler, C.M. Duarte and C.R. Voolstra. 2020. Genomic blueprint of glycine betaine metabolism in the coral metaorganisms and their contribution to reef ecosystem nitrogen budgets. eLife iScience 23, 101120, https://doi.org/10.1016/ j.isci.2020.101120
  

• [24/03/2021] 2021 C-DEBI Virtual Meeting Series
  
  The Center for Dark Energy Biosphere Investigations (C-DEBI) has started a series of both science and personal development workshops, starting April 5th. For more information, click here.

• [07/12/2020] Follow-up to Daniel Portik's seminar
  
  What is the best method for DNA fragmentation?
  We recommend the Diagenode Megaruptor with Covaris g-Tubes. Recommendations for metagenomics samples can be found in the shotgun sequencing protocol. Please note there is a section specific to the usage of the Covaris g-Tubes. The protocol is available here.
  
  Is it possible to sequence full-length 16S and ITS?
  Shoreline Biome has just released a new product that targets full-length 16S-ITS-23S amplicons, which are designed to be sequenced on PacBio Sequel II systems. This is part of their StrainID product line. They recently presented a webinar on this topic: Link here
  
  Availability of PacBio metagenomics datasets:
  HiFi data are publicly available for three libraries of a complex mock community dataset. This is ZymoBIOMICS gut microbiome standard D6331, a community containing 21 species that mimic the human gut microbiome. It includes staggered abundances across species (from 14% down to 0.0001%), as well as 5 strains of E. coli, making it a challenging community for methods testing. The NCBI project page is: http://www.ncbi.nlm.nih.gov/bioproject/680590
  
  SRA accessions:
  Standard Input: SRX9569057
  Low Input: SRX9569058
  Ultra-Low Input: SRX9569059
  
  PacBio metagenomics tools:
  We are actively developing and adding tools to our metagenomics repo: https://github.com/PacificBiosciences/pb-metagenomics-tools I always appreciate feedback and proposals for new tools. Please contact me directly at dportik@pacificbiosciences.com to start a discussion.
  
  For additional information, please reach out to me directly at dportik@pacificbiosciences.com, and I can answer your questions or direct you to the best contact at PacBio.