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1x r2a medium  (Teknova)


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    Teknova 1x r2a medium
    1. MiND was performed by measuring TE for import proteins in a 16-member SynCom grown in complex medium and was employed to predict each microbe’s substrate preferences. a , b , and c show TE for ribose, glutathione, and putrescine import proteins, respectively. Organisms with high TE for a substrate’s import protein were predicted to increase in relative abundance upon addition of this substrate as a prebiotic to the culture medium (primary targets); d) 2. Guilds were used to predict competition in the SynCom as described in . Competitors of the organisms that benefit from a prebiotic intervention were predicted to decrease in relative abundance (secondary targets); e- j) 3. Predictions made in a-d) were experimentally validated by supplementing the SynCom culture medium with selected substrates; e-g) linear regression and 99% CI of metagenomic relative abundances (RPKM, log scaled) in <t>0.1x</t> <t>R2A</t> control versus 0.1x R2A + ribose ( e ), glutathione ( f ) or putrescine ( g ). Microorganisms above or below the 99% CI are considered significantly increased or decreased upon metabolite addition (arrows). As predicted, 6/7 organisms that increased in relative abundance had a high TE for the added substrate’s import protein(s), and 9/10 microbes that concomitantly decreased were competitors from a similar guild (see for detailed competition scores). Note: we did not predict Brevibacillus decrease in f) and Chitinophaga increase in g); h-j) boxplots showing RPKM abundance of significantly increased primary targets with increasing concentration of ribose ( h ), glutathione ( i ), or putrescine ( j ). More examples are available in Suppl. Fig S12, S15 and S16.
    1x R2a Medium, supplied by Teknova, used in various techniques. Bioz Stars score: 93/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/1x+r2a+medium/bio_rxiv__2023__05__11__540389-185-11-14?v=Teknova
    Average 93 stars, based on 16 article reviews
    1x r2a medium - by Bioz Stars, 2026-07
    93/100 stars

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    1) Product Images from "Guild and Niche Determination Enable Targeted Alteration of the Microbiome"

    Article Title: Guild and Niche Determination Enable Targeted Alteration of the Microbiome

    Journal: bioRxiv

    doi: 10.1101/2023.05.11.540389

    1. MiND was performed by measuring TE for import proteins in a 16-member SynCom grown in complex medium and was employed to predict each microbe’s substrate preferences. a , b , and c show TE for ribose, glutathione, and putrescine import proteins, respectively. Organisms with high TE for a substrate’s import protein were predicted to increase in relative abundance upon addition of this substrate as a prebiotic to the culture medium (primary targets); d) 2. Guilds were used to predict competition in the SynCom as described in . Competitors of the organisms that benefit from a prebiotic intervention were predicted to decrease in relative abundance (secondary targets); e- j) 3. Predictions made in a-d) were experimentally validated by supplementing the SynCom culture medium with selected substrates; e-g) linear regression and 99% CI of metagenomic relative abundances (RPKM, log scaled) in 0.1x R2A control versus 0.1x R2A + ribose ( e ), glutathione ( f ) or putrescine ( g ). Microorganisms above or below the 99% CI are considered significantly increased or decreased upon metabolite addition (arrows). As predicted, 6/7 organisms that increased in relative abundance had a high TE for the added substrate’s import protein(s), and 9/10 microbes that concomitantly decreased were competitors from a similar guild (see for detailed competition scores). Note: we did not predict Brevibacillus decrease in f) and Chitinophaga increase in g); h-j) boxplots showing RPKM abundance of significantly increased primary targets with increasing concentration of ribose ( h ), glutathione ( i ), or putrescine ( j ). More examples are available in Suppl. Fig S12, S15 and S16.
    Figure Legend Snippet: 1. MiND was performed by measuring TE for import proteins in a 16-member SynCom grown in complex medium and was employed to predict each microbe’s substrate preferences. a , b , and c show TE for ribose, glutathione, and putrescine import proteins, respectively. Organisms with high TE for a substrate’s import protein were predicted to increase in relative abundance upon addition of this substrate as a prebiotic to the culture medium (primary targets); d) 2. Guilds were used to predict competition in the SynCom as described in . Competitors of the organisms that benefit from a prebiotic intervention were predicted to decrease in relative abundance (secondary targets); e- j) 3. Predictions made in a-d) were experimentally validated by supplementing the SynCom culture medium with selected substrates; e-g) linear regression and 99% CI of metagenomic relative abundances (RPKM, log scaled) in 0.1x R2A control versus 0.1x R2A + ribose ( e ), glutathione ( f ) or putrescine ( g ). Microorganisms above or below the 99% CI are considered significantly increased or decreased upon metabolite addition (arrows). As predicted, 6/7 organisms that increased in relative abundance had a high TE for the added substrate’s import protein(s), and 9/10 microbes that concomitantly decreased were competitors from a similar guild (see for detailed competition scores). Note: we did not predict Brevibacillus decrease in f) and Chitinophaga increase in g); h-j) boxplots showing RPKM abundance of significantly increased primary targets with increasing concentration of ribose ( h ), glutathione ( i ), or putrescine ( j ). More examples are available in Suppl. Fig S12, S15 and S16.

    Techniques Used: Control, Concentration Assay



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    1. MiND was performed by measuring TE for import proteins in a 16-member SynCom grown in complex medium and was employed to predict each microbe’s substrate preferences. a , b , and c show TE for ribose, glutathione, and putrescine import proteins, respectively. Organisms with high TE for a substrate’s import protein were predicted to increase in relative abundance upon addition of this substrate as a prebiotic to the culture medium (primary targets); d) 2. Guilds were used to predict competition in the SynCom as described in . Competitors of the organisms that benefit from a prebiotic intervention were predicted to decrease in relative abundance (secondary targets); e- j) 3. Predictions made in a-d) were experimentally validated by supplementing the SynCom culture medium with selected substrates; e-g) linear regression and 99% CI of metagenomic relative abundances (RPKM, log scaled) in <t>0.1x</t> <t>R2A</t> control versus 0.1x R2A + ribose ( e ), glutathione ( f ) or putrescine ( g ). Microorganisms above or below the 99% CI are considered significantly increased or decreased upon metabolite addition (arrows). As predicted, 6/7 organisms that increased in relative abundance had a high TE for the added substrate’s import protein(s), and 9/10 microbes that concomitantly decreased were competitors from a similar guild (see for detailed competition scores). Note: we did not predict Brevibacillus decrease in f) and Chitinophaga increase in g); h-j) boxplots showing RPKM abundance of significantly increased primary targets with increasing concentration of ribose ( h ), glutathione ( i ), or putrescine ( j ). More examples are available in Suppl. Fig S12, S15 and S16.
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    1. MiND was performed by measuring TE for import proteins in a 16-member SynCom grown in complex medium and was employed to predict each microbe’s substrate preferences. a , b , and c show TE for ribose, glutathione, and putrescine import proteins, respectively. Organisms with high TE for a substrate’s import protein were predicted to increase in relative abundance upon addition of this substrate as a prebiotic to the culture medium (primary targets); d) 2. Guilds were used to predict competition in the SynCom as described in . Competitors of the organisms that benefit from a prebiotic intervention were predicted to decrease in relative abundance (secondary targets); e- j) 3. Predictions made in a-d) were experimentally validated by supplementing the SynCom culture medium with selected substrates; e-g) linear regression and 99% CI of metagenomic relative abundances (RPKM, log scaled) in <t>0.1x</t> <t>R2A</t> control versus 0.1x R2A + ribose ( e ), glutathione ( f ) or putrescine ( g ). Microorganisms above or below the 99% CI are considered significantly increased or decreased upon metabolite addition (arrows). As predicted, 6/7 organisms that increased in relative abundance had a high TE for the added substrate’s import protein(s), and 9/10 microbes that concomitantly decreased were competitors from a similar guild (see for detailed competition scores). Note: we did not predict Brevibacillus decrease in f) and Chitinophaga increase in g); h-j) boxplots showing RPKM abundance of significantly increased primary targets with increasing concentration of ribose ( h ), glutathione ( i ), or putrescine ( j ). More examples are available in Suppl. Fig S12, S15 and S16.
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    Image Search Results


    1. MiND was performed by measuring TE for import proteins in a 16-member SynCom grown in complex medium and was employed to predict each microbe’s substrate preferences. a , b , and c show TE for ribose, glutathione, and putrescine import proteins, respectively. Organisms with high TE for a substrate’s import protein were predicted to increase in relative abundance upon addition of this substrate as a prebiotic to the culture medium (primary targets); d) 2. Guilds were used to predict competition in the SynCom as described in . Competitors of the organisms that benefit from a prebiotic intervention were predicted to decrease in relative abundance (secondary targets); e- j) 3. Predictions made in a-d) were experimentally validated by supplementing the SynCom culture medium with selected substrates; e-g) linear regression and 99% CI of metagenomic relative abundances (RPKM, log scaled) in 0.1x R2A control versus 0.1x R2A + ribose ( e ), glutathione ( f ) or putrescine ( g ). Microorganisms above or below the 99% CI are considered significantly increased or decreased upon metabolite addition (arrows). As predicted, 6/7 organisms that increased in relative abundance had a high TE for the added substrate’s import protein(s), and 9/10 microbes that concomitantly decreased were competitors from a similar guild (see for detailed competition scores). Note: we did not predict Brevibacillus decrease in f) and Chitinophaga increase in g); h-j) boxplots showing RPKM abundance of significantly increased primary targets with increasing concentration of ribose ( h ), glutathione ( i ), or putrescine ( j ). More examples are available in Suppl. Fig S12, S15 and S16.

    Journal: bioRxiv

    Article Title: Guild and Niche Determination Enable Targeted Alteration of the Microbiome

    doi: 10.1101/2023.05.11.540389

    Figure Lengend Snippet: 1. MiND was performed by measuring TE for import proteins in a 16-member SynCom grown in complex medium and was employed to predict each microbe’s substrate preferences. a , b , and c show TE for ribose, glutathione, and putrescine import proteins, respectively. Organisms with high TE for a substrate’s import protein were predicted to increase in relative abundance upon addition of this substrate as a prebiotic to the culture medium (primary targets); d) 2. Guilds were used to predict competition in the SynCom as described in . Competitors of the organisms that benefit from a prebiotic intervention were predicted to decrease in relative abundance (secondary targets); e- j) 3. Predictions made in a-d) were experimentally validated by supplementing the SynCom culture medium with selected substrates; e-g) linear regression and 99% CI of metagenomic relative abundances (RPKM, log scaled) in 0.1x R2A control versus 0.1x R2A + ribose ( e ), glutathione ( f ) or putrescine ( g ). Microorganisms above or below the 99% CI are considered significantly increased or decreased upon metabolite addition (arrows). As predicted, 6/7 organisms that increased in relative abundance had a high TE for the added substrate’s import protein(s), and 9/10 microbes that concomitantly decreased were competitors from a similar guild (see for detailed competition scores). Note: we did not predict Brevibacillus decrease in f) and Chitinophaga increase in g); h-j) boxplots showing RPKM abundance of significantly increased primary targets with increasing concentration of ribose ( h ), glutathione ( i ), or putrescine ( j ). More examples are available in Suppl. Fig S12, S15 and S16.

    Article Snippet: Precultures of individual isolates were generated in 5 mL of liquid 1x R2A medium (Teknova, cat # R0005) under oxic conditions and grown at 30 °C for 7 days without shaking.

    Techniques: Control, Concentration Assay