RapidAIM: A culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs

Abstract

13Background: Human-targeted drugs may exert off-target effects on the gut microbiota. 14 However, our understanding of such effects is limited due to a lack of rapid and scalable assay to 15 comprehensively assess microbiome responses to drugs. Drugs can drastically change the overall 16 microbiome abundance, microbial composition and functions of a gut microbiome. Although we 17 could comprehensively observe these microbiome responses using a series of tests, for the 18 purpose of a drug screening, it is important to decrease the number of analytical tools used. 19 Results: Here, we developed an approach to screen compounds against individual microbiomes 20 in vitro using metaproteomics adapted for both absolute bacterial abundances and functional 21 profiling of the microbiome. Our approach was evaluated by testing 43 compounds (including 22 four antibiotics) against five individual microbiomes. The method generated technically highly 23 reproducible readouts, including changes of overall microbiome abundance, microbiome 24 composition and functional pathways. Results show that besides the antibiotics, compounds 25 berberine and ibuprofen inhibited the accumulation of biomass during in vitro growth of the 26 microbiome. By comparing genus and species level-biomass contributions, selective 27 antibacterial-like activities were found with 36 of the 39 non-antibiotic compounds. Seven of our 28 compounds led to a global alteration of the metaproteome, with apparent compound-specific 29 patterns of functional responses. The taxonomic distributions of responded proteins varied 30 among drugs, i.e. different drugs affect functions of different members of the microbiome. We 31 also showed that bacterial function can shift in response to drugs without a change in the 32 abundance of the bacteria.33Conclusions: Current drug-microbiome interaction studies largely focus on relative microbiome 34 composition and microbial drug metabolism. In contrast, our workflow enables multiple insights 35 into microbiome absolute abundance and functional responses to drugs using metaproteomics as 36 the one-stop screening tool. The workflow is robust, reproducible and quantitative, and is 37 scalable for personalized high-throughput drug screening applications. 38

Metaproteomic responses ofin vitrogut microbiomes to resistant starches: the role of resistant starch type and inter-individual variations

“…There are numerous types of marketed RS products, which are derived from various plant sources and are processed in to RS in different ways. Our study suggested the importance of individualized screening of dietary RS, using high-throughput approaches like RapidAIM assay [42], for improving health or for their utilization as personalized intervention for human diseases. shift the in vitro gut microbiome [22,23], was used as the positive control.…”

Examining the effects of an anti-Salmonella bacteriophage preparation, BAFASAL, on ex vivo human gut microbiome composition and function using a multi-omics approach

“…Fecal inocula were thawed at 37°C and inoculated at a concentration of 2% (w/v) into a 96-well deep-well plate containing 1 mL MiPro optimized sterile and pre-reduced culture medium (2.0 g L 1 peptone water, 2.0 gL -1 yeast extract, 0.5 g L -1 L-cysteine hydrochloride, 2 mL L -1 Tween 80, 5 mg L -1 hemin, 10 μL L -1 vitamin K1, 1.0 g L -1 NaCl, 0.4 g L -1 K 2 HPO 4 , 0.4 g L -1 KH 2 PO 4 , 0.1 g L -1 MgSO 4 ·7H 2 O, 0.1 g L -1 CaCl 2 ·2H 2 O, 4.0 g L -1 NaHCO 3 , 4.0 g L -1 porcine gastric mucin, 0.25 g L -1 sodium cholate, and 0.25 g L -1 sodium chenodeoxycholate) as per Li et al . in an anaerobic workstation [20, 21]. BAF and IBAF were added at 2% (v/v) and 5% (v/v) to the media.…”

“…We have developed an in vitro microbiome culturing system (MiPro) coupled to a downstream bioinformatics toolbox collectively called RapidAIM (or rapid assay of an individual microbiome) that measures compositional and functional changes in the gut microbiome in response to dietary and therapeutic interventions [20, 21]. RapidAIM can measure the impact of products on the microbiota and can be used to stratify people in clinical studies.…”

Reshaping the Gut Microbiome in An Apc-Mutant Genetic Background: Mechanistic Insights From Integrated Multi-Omics

“…This resulted in 5946 differential features for further analysis. Signi cant features were subjected to clustering and correlation by MetaboAnalyst 4.0 [69][70][71][72].…”