The RAST Server: Rapid Annotations using Subsystems Technology

Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.; DeJongh, Matthew; Disz, Terry; Edwards, Robert A.; Formsma, Kevin; Gerdes, Svetlana; Glass, Elizabeth M.; Kubal, Michael; Meyer, Patrick; Olsen, Gary J.; Olson, Robert; Osterman, Andrei L.; Overbeek, Ross; McNeil, Leslie Klis; Paarmann, Daniel; Paczian, Tobias; Parrello, Bruce; Pusch, Gordon D.; Reich, Claudia I.; Stevens, Rick; Vassieva, Olga; Vonstein, Veronika; Wilke, Andreas; Zagnitko, Olga

doi:10.1186/1471-2164-9-75

Cited by 10,177 publications

(8,178 citation statements)

References 22 publications

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“…In a previous study 50 , we retrieved 301 draft reconstructions from Model SEED 14 . Based on lists of human gut microbes reported by Qin et al (2010) 30 and by Rajilić-Stojanović and de Vos (2014) 51 , we obtained 472 additional draft reconstructions from Model SEED and KBase (Department of Energy Systems Biology Knowledgebase, http://kbase.us), both of which use the RAST annotation server 52 to annotate the genomes and build the draft metabolic networks 14 . All reconstructions were downloaded in SBML format and imported into Matlab (Mathworks, Inc., Natick, MA, USA) using the COBRA Toolbox 8 .…”

Section: Methodsmentioning

confidence: 99%

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

et al. 2016

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1 r e s o u r c eChanges in the composition of the human gut microbiota have been associated with the development of chronic diseases including type 2 diabetes, obesity, and colorectal cancer 1 . Gut bacterial functions, such as synthesis of amino acids and vitamins 2 , breakdown of indigestible plant polysaccharides 3 , and production of metabolites involved in energy metabolism 4 , have been linked to human health. The use of 'omics approaches to study human microbiome communities has led to the generation of enormous data sets whose interpretations require systems biology tools to shed light on the functional capacity of gut microbiomes and their interactions with the human host 5 .In order to infer the metabolic repertoire of a gut metagenome data set, researchers usually map sequenced genes or organisms onto metabolic networks derived from the Kyoto Encyclopedia of Genes and Genomes (KEGG) 6 , and functional annotations from KEGG ontologies 7 . However, this approach cannot identify the contribution of each bacterial species to the metabolic repertoire of the whole gut microbiome, nor can it infer the effects of different gut microbial communities on host metabolism.A technique that can bridge this gap is constraint-based reconstruction and analysis (COBRA) 8 using genome-scale metabolic reconstructions (GENREs) of individual human gut microbes. GENREs are assembled using the genome sequence and experimental information 9 . These reconstructions form the basis for the development of condition-specific metabolic models whose functions are simulated and validated by comparison with experimental results. The models can be used to investigate genotype-phenotype relationships 10 , microbe-microbe interactions 11 , and host-microbe interactions 11 . Numerous tools can be used to automatically generate draft GENREs but such models contain errors 12 and are incomplete.Manual curation of draft reconstructions is time consuming because it involves an extensive literature review and experimental validation of metabolic functions 9 .To provide an extensive resource of GENREs for human gut microbes, we developed a comparative metabolic reconstruction method that enables any refinement to one metabolic reconstruction to be propagated to others. This accelerates reconstruction and improves model quality. We generated AGORA, which includes 773 gut microbes, comprising 205 genera and 605 species. All reconstructions were based on literature-derived experimental data and comparative genomics. The metabolic predictions of two AGORA reconstructions and their derived metabolic models were validated against experimental data. RESULTS Metabolic reconstruction pipelineWe devised a comparative metabolic reconstruction method (Fig. 1a,c), which is analogous to the comparative microbial genome annotation approach 13 that has enabled accelerated annotation by propagation of refinements to one genome to others. First, we downloaded draft GENREs using Model SEED 14 and KBase (US Department of Energy Systems Biology Knowledgebase, http:/...

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Section: Methodsmentioning

confidence: 99%

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

et al. 2016

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“…The NGS tool kit (Patel and Jain, 2012) was used for quality control of the sequence read data. High‐quality reads were de novo assembled into contiguous sequences using CLC Genomics Workbench 8.0 (CLC bio, Aarhus, Denmark), and annotation of draft genomes was performed with RAST server (Aziz et al ., 2008). …”

Section: Methodsmentioning

confidence: 99%

Environmental adaptation and vertical dissemination of ESBL‐/pAmpC‐producing Escherichia coli in an integrated broiler production chain in the absence of an antibiotic treatment

Projahn

Daehre

Semmler

et al. 2018

Microbial Biotechnology

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SummaryHigh prevalence numbers of extended‐spectrum beta‐lactamase‐ (ESBL‐)/plasmid‐mediated AmpC beta‐lactamase‐ (pAmpC‐) producing Escherichia coli in broiler chicken and their distribution along the broiler production chain is an ongoing problem in food production. We, therefore, investigated resistant isolates along the broiler production chain to determine whether there is a constantly occurring direct vertical transmission of the ESBL‐/pAmpC‐producing E. coli from the parent flocks to their offspring or not. We, furthermore, analysed the isolates concerning the occurrence of virulence factors and their ability to form biofilms to estimate their potential to effectively colonize broiler chickens and/or persist and survive in the environment of the broiler production facilities. Using whole genome sequencing, we could show that ESBL‐/pAmpC‐producing E. coli were likely transferred in a step‐wise process along the broiler production chain but not directly from the parent flock to the fattening flock with every single batch of offspring chickens. Additionally, resistant E. coli strains showing an extraintestinal pathogenic genotype as well as high numbers of virulence‐associated genes including the production of curli fibres and cellulose have high capabilities to persist and spread in the broiler production chain.

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“…The resultant alignments were parsed with aid of the samtools package ) using custom Python scripts to determine the number of paired-end fragments aligned to each annotated ORF in the sense orientation. The NATL2A gene calls and annotations used were made by the RAST pipeline (Aziz et al, 2008) and previously described (Biller et al, 2014); the A. macleodii MIT1002 genome was annotated in the same way for consistency (data available from GEO). In some cases, RAST predicted NATL2A coding sequences not present in the GenBank entry for the genome, and these are listed solely by chromosomal location (Supplementary Table S2).…”

Section: Sequence Analysismentioning

confidence: 99%

Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus

2016

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Microbial interactions, whether direct or indirect, profoundly affect the physiology of individual cells and ultimately have the potential to shape the biogeochemistry of the Earth. For example, the growth of Prochlorococcus, the numerically dominant cyanobacterium in the oceans, can be improved by the activity of co-occurring heterotrophs. This effect has been largely attributed to the role of heterotrophs in detoxifying reactive oxygen species that Prochlorococcus, which lacks catalase, cannot. Here, we explore this phenomenon further by examining how the entire transcriptome of Prochlorococcus NATL2A changes in the presence of a naturally co-occurring heterotroph, Alteromonas macleodii MIT1002, with which it was co-cultured for years, separated and then reunited. Significant changes in the Prochlorococcus transcriptome were evident within 6 h of initiating co-culture, with groups of transcripts changing in different temporal waves. Many transcriptional changes persisted throughout the 48 h experiment, suggesting that the presence of the heterotroph affected a stable shift in Prochlorococcus physiology. These initial transcriptome changes largely corresponded to reduced stress conditions for Prochlorococcus, as inferred from the depletion of transcripts encoding DNA repair enzymes and many members of the 'high light inducible' family of stress-response proteins. Later, notable changes were seen in transcripts encoding components of the photosynthetic apparatus (particularly, an increase in PSI subunits and chlorophyll synthesis enzymes), ribosomal proteins and biosynthetic enzymes, suggesting that the introduction of the heterotroph may have induced increased production of reduced carbon compounds for export. Changes in secretion-related proteins and transporters also highlight the potential for metabolic exchange between the two strains.

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The RAST Server: Rapid Annotations using Subsystems Technology

Abstract: Background: The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them.

Cited by 10,177 publications

References 22 publications

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

Environmental adaptation and vertical dissemination of ESBL‐/pAmpC‐producing Escherichia coli in an integrated broiler production chain in the absence of an antibiotic treatment

Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus

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