ReviewNature protocols2024
High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities.
Review in Nature protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed, 36 citations in OpenAlex.
- Synergy between Enterobacteriaceae and diet mediates competition between dominant Bacteroidales in the human gut.Nature microbiology · 2026Article
- Drug-microbiome-host interactions: antimicrobial effects of non-antibiotic compounds.Nature reviews. Gastroenterology & hepatology · 2026Review
- Common xenobiotics modulate gut microbial responses to low‑calorie sweeteners in vitro.Molecular systems biology · 2026Article
- Reconsidering the Use of Dimethyl Sulfoxide for Xenobiotic-Gut Microbiota Interaction Studies.bioRxiv : the preprint server for biology · 2026Article
- Probiotics mitigate non-antibiotic drug-induced dysbiosis via protein homology-driven competitive binding.Nature communications · 2026Article
- 8-azido-3,8-dideoxy-D-manno-octulosonic acid-mediated metabolic oligosaccharide engineering for specific labeling of diverseiScience · 2026Article
- Widespread effects of catecholamines on growth of human gut bacteria.NPJ biofilms and microbiomes · 2026Article
- A Functional Metabolomics Framework to Track Microbiome Drug Metabolism.bioRxiv : the preprint server for biology · 2026Article
- maldipickr dereplicates microbial MALDI-TOF spectra to facilitate multiplexed isolation.Bioinformatics advances · 2026Article
- Volume electron microscopy in axon regeneration research: insights into mitochondria, endoplasmic reticulum, and membrane contacts.Frontiers in neural circuits · 2026Review
- Antagonistic drug interactions protect commensalGut microbes · 2025Article
- Proton-pump inhibitors increaseGut microbes · 2025Article
- Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro.Nature microbiology · 2025Article
- CFTR modulator therapy drives microbiome restructuring through improved host physiology in cystic fibrosis: the IMMProveCF phase IV trial.Nature communications · 2025Article
- Growth stage and interspecies interactions shape the cell biology and cell cycle characteristics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis.Communications biology · 2025Article
- Article
- Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances.Nature microbiology · 2025Article
- Enabling next-generation anaerobic cultivation through biotechnology to advance functional microbiome research.Nature biotechnology · 2025Review
- Pre-trained molecular representations enable antimicrobial discovery.Nature communications · 2025Article
- A high-throughput anaerobic method for viability assays.Microbiology spectrum · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 7 institutions in 4 countries.
Funding
Abstract
The human gut microbiome is a key contributor to health, and its perturbations are linked to many diseases. Small-molecule xenobiotics such as drugs, chemical pollutants and food additives can alter the microbiota composition and are now recognized as one of the main factors underlying microbiome diversity. Mapping the effects of such compounds on the gut microbiome is challenging because of the complexity of the community, anaerobic growth requirements of individual species and the large number of interactions that need to be quantitatively assessed. High-throughput screening setups offer a promising solution for probing the direct inhibitory effects of hundreds of xenobiotics on tens of anaerobic gut bacteria. When automated, such assays enable the cost-effective investigation of a wide range of compound-microbe combinations. We have developed an experimental setup and protocol that enables testing of up to 5,000 compounds on a target gut species under strict anaerobic conditions within 5 d. In addition, with minor modifications to the protocol, drug effects can be tested on microbial communities either assembled from isolates or obtained from stool samples. Experience in working in an anaerobic chamber, especially in performing delicate work with thick chamber gloves, is required for implementing this protocol. We anticipate that this protocol will accelerate the study of interactions between small molecules and the gut microbiome and provide a deeper understanding of this microbial ecosystem, which is intimately intertwined with human health.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.