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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….
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)….
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…
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….
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…
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…
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…
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…
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,…
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…