Markowitz VM, Chen I-MA, Chu K, Szeto E, Palaniappan K, Grechkin Y et al. IMG/M: the integrated metagenome data management and comparative analysis system. Nucl Acids Res 40: D123-D129

Biological Data Management and Technology Center, Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California, CA 94702, USA.
Nucleic Acids Research (Impact Factor: 9.11). 11/2011; 40(Database issue):D123-9. DOI: 10.1093/nar/gkr975
Source: PubMed


The integrated microbial genomes and metagenomes (IMG/M) system provides support for comparative analysis of microbial community
aggregate genomes (metagenomes) in a comprehensive integrated context. IMG/M integrates metagenome data sets with isolate
microbial genomes from the IMG system. IMG/M's data content and analytical capabilities have been extended through regular
updates since its first release in 2007. IMG/M is available at A companion IMG/M systems provide support for annotation and expert review of unpublished metagenomic data sets (IMG/M ER:

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    • "All available (as of 4 February 2013; 1236 metagenomes covering a wide range of environments) metagenomes on the JGI IMG/M server (Markowitz et al., 2012b) were screened for the presence of vanI homologues. We performed an initial BLASTP using the strictest possible cut-off, E < e-50, against the entire img/m database using VanI (dsy_3690) from Desulfitobacterium hafniense Y51 as query. "
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    ABSTRACT: The glycopeptide vancomycin was until recently considered a drug of last resort against Gram-positive bacteria. Increasing numbers of bacteria, however, are found to carry genes that confer resistance to this antibiotic. So far, 10 different vancomycin resistance clusters have been described. A chromosomal vancomycin resistance gene cluster was previously described for the anaerobic Desulfitobacterium hafniense Y51. We demonstrate that this gene cluster, characterized by its d-Ala-d-Lac ligase-encoding vanI gene, is present in all strains of D. hafniense, D. chlororespirans and some strains of Desulfosporosinus spp. This gene cluster was not found in vancomycin-sensitive Desulfitobacterium or Desulfosporosinus spp., and we show that this antibiotic resistance can be exploited as an intrinsic selection marker for Desulfitobacterium hafniense and D. chlororespirans. The gene cluster containing vanI is phylogenetically only distantly related with those described from soil and gut bacteria, but clusters instead with vancomycin resistance genes found within the phylum Actinobacteria that include several vancomycin-producing bacteria. It lacks a vanH homologue, encoding a D-lactate dehydrogenase, previously thought to always be present within vancomycin resistance gene clusters. The location of vanH outside the resistance gene cluster likely hinders horizontal gene transfer. Hence, the vancomycin resistance cluster in D. hafniense should be regarded a novel one that we here designated vanI after its unique d-Ala-d-Lac ligase.
    Full-text · Article · Jul 2014 · Microbial Biotechnology
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    • "In addition to antibiotics and vaccines, restoration of a stable and healthy microbiome is another strategy that should be considered in infection control and anti-infective therapy, since the microbiome plays a direct role in fighting pathogenic infection . This strategy capitalizes on the protective roles of intact microbiomes, as described in both large-scale pangenomic [40] and metagenomic [41] studies. To reinforce host defense during infection, methods for evaluating the stability and imbalances of the microbiomes are needed to identify the infection-prone status and the species that should be replenished as recently reported [42]. "
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    ABSTRACT: The human pharyngeal microbiome, which resides at the juncture of digestive and respiratory tracts, may have an active role in the prevention of respiratory tract infections, similar to the actions of the intestinal microbiome against enteric infections. Recent studies have demonstrated that the pharyngeal microbiome comprises an abundance of bacterial species that interact with the local epithelial and immune cells, and together, they form a unique micro-ecological system. Most of the microbial species in microbiomes are obligate symbionts constantly adapting to their unique surroundings. Indigenous commensal species are capable of both maintaining dominance and evoking host immune responses to eliminate invading species. Temporary damage to the pharyngeal microbiome due to the impaired local epithelia is also considered an important predisposing risk factor for infections. Therefore, reinforcement of microbiome homeostasis to prevent invasion of infection-prone species would provide a novel treatment strategy in addition to antibiotic treatment and vaccination. Hence continued research efforts on evaluating probiotic treatment and developing appropriate procedures are necessary to both prevent and treat respiratory infections.
    Full-text · Article · Jun 2014 · Genomics Proteomics & Bioinformatics
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    • "To estimate the authenticity and completeness of the genome bin, the six neighboring finished genome sequences were extracted from the IMG/M database (Markowitz et al. 2012) (Table S2) and used as the pan-genome. A set of common core COGs shared by the pan-genome contributed to a core-gene set and the genes that occurred only once in each of the genomes contributed to the conserved single copy genes (CSCGs) (Wang et al. 2012). "
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    ABSTRACT: Here, shotgun metagenomic sequencing was conducted to reveal the hydrogen-oxidizing autotrophic-denitrifying metabolism in an enriched Thauera-dominated consortium. A draft genome named Thauera R4 of over 90 % completeness (3.8 Mb) was retrieved mainly by a coverage-defined binning method from 3.5 Gb paired-end Illumina reads. We identified 1,263 genes (accounting for 33 % of total genes in the finished genome of Thauera aminoaromatica MZ1T) with average nucleotide identity of 87.6 % shared between Thauera R4 and T. aminoaromatica MZ1T. Although Thauera R4 and T. aminoaromatica shared quite similar nitrogen metabolism and a high nucleotide similarity (98.8 %) in their 16S ribosomal RNA genes, they showed different functional potentials in several important environmentally relevant processes. Unlike T. aminoaromatica MZ1T, Thauera R4 carries an operon of [NiFe]-hydrogenase (EC catalyzing molecular hydrogen oxidation in nitrate-rich solution. Moreover, Thauera R4 is a mixtrophic bacterium possessing key enzymes for autotrophic CO2-fixation and heterotrophic acetate assimilation metabolism. This Thauera R4 bin provides another genetic reference to better understand the niches of Thauera and demonstrates a model pipeline to reveal functional profiles and reconstruct novel and dominant genomes from a simplified mixed culture in environmental studies.
    Full-text · Article · Apr 2014 · Applied Microbiology and Biotechnology
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