Tag: TIGRFAMs

Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008). Article  ADS  CAS  PubMed  Google Scholar  Yu, X. J., Walker, D. H., Liu, Y. & Zhang, L. Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts. Infect. Genet. Evol….

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Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil | Microbiome | Full Text

Soil free Agricultural soil samples were collected out a long-term soil experimental range (ZOFE, Zurich Biological Fertilization Experiment), found into an pastoral area surrounding Zurich (Agroscope, Reckenholz, Switzerland). Soil consisted of 56% sand, 28% silt and 14% clay (in mass %: 0.6 soil organic charcoal, 1.1 soil humus, pH ~ 5.7)….

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Genome-resolved carbon processing potential of tropical peat microbiomes from an oil palm plantation

Dargie, G. C. et al. Age, extent and carbon storage of the central Congo Basin peatland complex. Nature 542, 86–90 (2017). Article  ADS  CAS  PubMed  Google Scholar  Page, S. E., Rieley, J. O. & Banks, C. J. Global and regional importance of the tropical peatland carbon pool. Global Change Biology…

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Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution

Manrique, P., Dills, M. & Young, M. J. The human gut phage community and its implications for health and disease. Viruses 9, 141 (2017). Article  PubMed  PubMed Central  Google Scholar  Li, Z. et al. Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. ISME J….

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Expanding known viral diversity in the healthy infant gut

Moeller, A. H. et al. Cospeciation of gut microbiota with hominids. Science 353, 380–382 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Milani, C. et al. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol. Mol. Biol. Rev. 81, e00036-17…

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A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics | Environmental Microbiome

Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J-F, et al. Insights into the phylogeny and coding potential of microbial dark matter nature. Nat Publ Group. 2013;499:431–7. CAS  Google Scholar  Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, et al. Unusual biology across…

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Prokka Annotation or NCBI Annotation

Prokka Annotation or NCBI Annotation 1 Dear All, I have two sets of annotation files for 15 Bacterial genomes. One set from NCBI annotations (from RefSeq) and the other from Prokka (I have run it in my local machine). Which one is advisable to use between the two for all…

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Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis

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…

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How are the HMM cutoff scores in TIGRFAMs determined?

How are the HMM cutoff scores in TIGRFAMs determined? 0 Hello everyone, As indicated in the title, I am wondering how are the HMM cutoff scores in TIGRFAMs determined? Where did I find the score? (If you search a TIGRFAM accession in the NCBI protein family model database, e.g. TIGR02064.1,…

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Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance

1. Lee, M.-R. et al. Mycobacterium abscessus complex infections in humans. Emerg. Infect. Dis. 21, 1638–1646 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Prince, D. S. et al. Infection with Mycobacterium avium complex in patients without predisposing conditions. N. Engl. J. Med. 321, 863–868 (1989). CAS  PubMed  Article  Google…

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