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  • 1.
    Baichoo, Shakuntala
    et al.
    University of Mauritius, Mauritius.
    Botha, Gerrit
    University of Cape Town, South Africa.
    Jaufeerally-Fakim, Yasmina
    University of Mauritius, Mauritius.
    Mungloo-Dilmohamud, Zahra
    University of Mauritius, Mauritius.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Stockholm University.
    Mulder, Nicola
    University of Cape Town, South Africa.
    Promponas, Vasilis J.
    University of Cyprus, Cyprus.
    Ouzounis, Christos A.
    Centre for Research & Technology (CERTH), Greece.
    H3ABioNet computational metagenomics workshop in Mauritius: training to analyse microbial diversity for Africa2015In: Standards in Genomic Sciences, ISSN 1944-3277, E-ISSN 1944-3277, Vol. 10, article id 115Article in journal (Refereed)
    Abstract [en]

    In the context of recent international initiatives to bolster genomics research for Africa, and more specifically to develop bioinformatics expertise and networks across the continent, a workshop on computational metagenomics was organized during the end of 2014 at the University of Mauritius. The workshop offered background on various aspects of computational biology, including databases and algorithms, sequence analysis fundamentals, metagenomics concepts and tools, practical exercises, journal club activities and research seminars. We have discovered a strong interest in metagenomics research across Africa, to advance practical applications both for human health and the environment. We have also realized the great potential to develop genomics and bioinformatics through collaborative efforts across the continent, and the need for further reinforcing the untapped human potential and exploring the natural resources for stronger engagement of local scientific communities, with a view to contributing towards the improvement of human health and well-being for the citizens of Africa.

  • 2. Engel, Katja
    et al.
    Ashby, Deborah
    Brady, Sean F.
    Cowan, Don A.
    Doemer, John
    Edwards, Elizabeth A.
    Fiebig, Klaus
    Martens, Eric C.
    McCormac, Dennis
    Mead, David A.
    Miyazaki, Kentaro
    Moreno-Hagelsieb, Gabriel
    O'Gara, Fergal
    Reid, Alexandra
    Rose, David R.
    Simonet, Pascal
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Smalla, Kornelia
    Streit, Wolfgang R.
    Tedman-Jones, Jennifer
    Valla, Svein
    Wellington, Elizabeth M. H.
    Wu, Cheng-Cang
    Liles, Mark R.
    Neufeld, Josh D.
    Sessitsch, Angela
    Charles, Trevor C.
    Meeting Report: 1st International Functional Metagenomics Workshop May 7-8, 2012, St. Jacobs, Ontario, Canada2013In: Standards in Genomic Sciences, ISSN 1944-3277, E-ISSN 1944-3277, Vol. 8, no 1, p. 106-111Article in journal (Other academic)
    Abstract [en]

    This report summarizes the events of the 1st International Functional Metagenomics Workshop. The workshop was held on May 7 and 8, 2012, in St. Jacobs, Ontario, Canada and was focused on building an international functional metagenomics community, exploring strategic research areas, and identifying opportunities for future collaboration and funding. The workshop was initiated by researchers at the University of Waterloo with support from the Ontario Genomics Institute (OGI), Natural Sciences and Engineering Research Council of Canada (NSERC) and the University of Waterloo.

  • 3. Holm, Kare Olav
    et al.
    Nilsson, Kristina
    Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Hjerde, Erik
    Willassen, Nils-Peder
    Milton, Debra L.
    Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Complete genome sequence of Vibrio anguillarum strain NB10, a virulent isolate from the Gulf of Bothnia2015In: Standards in Genomic Sciences, ISSN 1944-3277, E-ISSN 1944-3277, Vol. 10, article id 60Article in journal (Refereed)
    Abstract [en]

    Vibrio anguillarum causes a fatal hemorrhagic septicemia in marine fish that leads to great economical losses in aquaculture world-wide. Vibrio anguillarum strain NB10 serotype O1 is a Gram-negative, motile, curved rod-shaped bacterium, isolated from a diseased fish on the Swedish coast of the Gulf of Bothnia, and is slightly halophilic. Strain NB10 is a virulent isolate that readily colonizes fish skin and intestinal tissues. Here, the features of this bacterium are described and the annotation and analysis of its complete genome sequence is presented. The genome is 4,373,835 bp in size, consists of two circular chromosomes and one plasmid, and contains 3,783 protein-coding genes and 129 RNA genes.

  • 4.
    Olsson, Björn E.
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Korsakova, Ekaterina S.
    Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia.
    Anan'ina, Lyudmila N.
    Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia.
    Pyankova, Anna A.
    Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia.
    Mavrodi, Olga V.
    Department of Biological Sciences, The University of Southern Mississippi, USA.
    Plotnikova, Elena G.
    Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia.
    Mavrodi, Dmitri V.
    Department of Biological Sciences, The University of Southern Mississippi, USA.
    Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3–1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region of Russia2017In: Standards in Genomic Sciences, ISSN 1944-3277, E-ISSN 1944-3277, Vol. 12, no 39, p. 1-13Article in journal (Refereed)
    Abstract [en]

    Halomonads are moderately halophilic bacteria that are studied as models of prokaryotic osmoadaptation and sources of enzymes and chemicals for biotechnological applications. Despite the progress in understanding the diversity of these organisms, our ability to explain ecological, metabolic, and biochemical traits of halomonads at the genomic sequence level remains limited. This study addresses this gap by presenting draft genomes of Salinicola socius SMB35T, Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17, which were isolated from potash mine tailings in the Verkhnekamsk salt deposit area of Russia. The analysis of these genomes confirmed the importance of ectoines and quaternary amines to the capacity of halomonads to tolerate osmotic stress and adapt to hypersaline environments. The study also revealed that Chromohalobacter and Salinicola share 75-90% of the predicted proteome, but also harbor a set of genus-specific genes, which in Salinicola amounted to approximately 0.5 Mbp. These genus-specific genome segments may contribute to the phenotypic diversity of the Halomonadaceae and the ability of these organisms to adapt to changing environmental conditions and colonize new ecological niches.

  • 5.
    Zubair, Saima
    et al.
    Swedish Univ Agr Sci, SLU Global Bioinformat Ctr, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Fischer, Anne
    Int Livestock Res Inst, Nairobi, Kenya.;Int Ctr Insect Physiol & Ecol, Nairobi, Kenya..
    Liljander, Anne
    Int Livestock Res Inst, Nairobi, Kenya..
    Meens, Jochen
    Univ Vet Med Hannover, Inst Microbiol, Dept Infect Dis, Hannover, Germany..
    Hegerman, Jan
    Hannover Med Sch, Inst Funct & Appl Anat, Hannover, Germany.;Biomed Res Endstage & Obstruct Lung Dis Hannover, Hannover, Germany.;REBIRTH Cluster Excellence, Hannover, Germany..
    Gourle, Hadrien
    Swedish Univ Agr Sci, SLU Global Bioinformat Ctr, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Bishop, Richard P.
    Int Livestock Res Inst, Nairobi, Kenya..
    Roebbelen, Ina
    Int Livestock Res Inst, Nairobi, Kenya..
    Younan, Mario
    Vet Sans Frontieres Germany, Nairobi, Kenya..
    Mustafa, Mudassir Imran
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Informatics and Media. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences, Clinical Psychology in Healthcare.
    Mushtaq, Mamoona
    Swedish Univ Agr Sci, SLU Global Bioinformat Ctr, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Bongcam-Rudloff, Erik
    Swedish Univ Agr Sci, SLU Global Bioinformat Ctr, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Jores, Joerg
    Int Livestock Res Inst, Nairobi, Kenya..
    Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel2015In: Standards in Genomic Sciences, ISSN 1944-3277, E-ISSN 1944-3277, Vol. 10, article id 109Article in journal (Refereed)
    Abstract [en]

    We report the genome of a Staphylococcus aureus strain (ILRI_Eymole1/1) isolated from a nasal swab of a dromedary camel (Camelus dromedarius) in North Kenya. The complete genome sequence of this strain consists of a circular chromosome of 2,874,302 bp with a GC-content of 32.88 %. In silico annotation predicted 2755 protein-encoding genes and 76 non-coding genes. This isolate belongs to MLST sequence type 30 (ST30). Phylogenetic analysis based on a subset of 283 core genes revealed that it falls within the human clonal complex 30 (CC30) S. aureus isolate cluster but is genetically distinct. About 79 % of the protein encoding genes are part of the CC30 core genome (genes common to all CC30 S. aureus isolates), similar to 18 % were within the variable genome (shared among multiple but not all isolates) and similar to 3 % were found only in the genome of the camel isolate. Among the 85 isolate-specific genes, 79 were located within putative phages and pathogenicity islands. Protein encoding genes associated with bacterial adhesion, and secretory proteins that are essential components of the type VII secretion system were also identified. The complete genome sequence of S. aureus strain ILRI_Eymole1/1 has been deposited in the European Nucleotide Archive under the accession no LN626917.1.

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