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6 results for “auxotrophy”
MAGs and gapseq models for auxotrophy predictions in the human gut microbiome
<p>This dataset contains MAGs, their DNA sequence, genome statistics, quantification per sample, and their metabolic model reconstructions from two human population cohorts from northern Germany.</p>
gapseq reconstruction for 36 human gut bacterial strains with known amino acid auxotrophy status
<p>The data set contains genome-scale metabolic network reconstructions for 36 bacterial genomes, for which the auxotrophy/prototrophy status for amino acids has been reported in scientific literature based on laboratory experiments. Auxotrophy/Prototrophy information and the respective PubMed-IDs (PMID) are summarized in "Validation_models_Metadata.csv". Network reconstructions were made using gapseq (development version: 1.2 commit 2dfa8c80 ; Sequence DB md5sum: bf8ba98 (2023-02-15, Bacteria).</p> <p>The models were reconstructed using the following workflow.</p> <pre><code># Reaction & Pathway prediction ./gapseq find -b 200 -v 1 -p all -k -t Bacteria <genomeID>.fna.gz # Transporter prediction ./gapseq find-transport -b 200 -k <genomeID>.fna.gz # Draft network reconstruction ./gapseq draft -r <genomeID>-all-Reactions.tbl -t <genomeID>-Transporter.tbl -b Bacteria -c <genomeID>.fna.gz -p <genomeID>-all-Pathways.tbl -u 200 -l 100 # gapfill/growth medium prediction ./gapseq medium -m <genomeID>-draft.RDS -p <genomeID>-all-Pathways.tbl -c "cpd00007:0" # Gap-filling # (If H2 is part of the medium) ./gapseq fill -m <genomeID>-draft.RDS -n <genomeID>-medium.csv -c <genomeID>-rxnWeights.RDS -g <genomeID>-rxnXgenes.RDS -b 100 -e highH2 # (If H2 is not part of the medium) ./gapseq fill -m <genomeID>-draft.RDS -n <genomeID>-medium.csv -c <genomeID>-rxnWeights.RDS -g <genomeID>-rxnXgenes.RDS -b 100</code></pre> <p> </p>
Data from: Auxotrophy and intra-population complementary in the 'interactome' of a cultivated freshwater model community
Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin- and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage-based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to 'social' interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring 'interactomes' and to overcome our inability to isolate and grow the microbes dominating in nature.
Data from: Auxotrophy and intra-population complementary in the 'interactome' of a cultivated freshwater model community
Open the record for dataset details and reuse information.
Small molecule activation of PKM in cancer cells induces serine auxotrophy
GEO Series GSE40191. Homo sapiens. 50 samples. Type: Expression profiling by array.
Oncogenic KRAS induces arginine auxotrophy in non-small cell lung cancer and confers a therapeutic vulnerability to SLC7A1 inhibition
GEO Series GSE253688. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
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