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

Journal: Pharmaceutics

Article Title: In Vitro Stability and Pharmacokinetic Study of Pedunculoside and Its Beta-CD Polymer Inclusion Complex

doi: 10.3390/pharmaceutics16050591

Figure Lengend Snippet: In vitro stability study of pedunculoside and pedunculoside–CDP in the gastrointestinal environment of ( a , b ) simulated gastric and intestinal fluids, ( c , d ) sterilized GAM broth, ( e , f ) Bifidobacterium adolescentis , and ( g , h ) Bifidobacterium breve (n = 3) (PE: pedunculoside, PE–βCDP: pedunculoside–βCDP, RA: rotundic acid).

Article Snippet: General anaerobic medium (GAM) broth was purchased from Beijing Solarbio Science and Technology Co., Ltd.; standard strains of Bifidobacterium adolescentis (CGMCC 1.2190) and Bifidobacterium breve (CGMCC 1.2213) were purchased from the China General Microbiological Culture Collection Center (CGMCC, Beijing, China).

Techniques: In Vitro