ReviewNature protocols2026
Establishing and analyzing the Simplified Human Intestinal Microbiota (SIHUMI) as a versatile in vitro gut microbiome model with qPCR-based strain-level tracking.
Review in Nature protocols, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 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
2 citing papers in PubMed.
- Engineering human Gut-on-a-Chip culturomics for predictive pharmacomicrobiomics of first-pass metabolism.npj biomedical innovations · 2026Review
- Precision microbiome medicine and therapeutics: the enabling role of in vitro gut models.FEMS microbiology reviews · 2026Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
A major challenge in microbiome research is the inherent complexity and inter-individual variability of the human gut microbiota. To address this, we have developed a detailed protocol for establishing and analyzing a Simplified Human Intestinal Microbiota (SIHUMI)-a defined, in vitro bacterial consortium composed of seven fully sequenced and anaerobically culturable human gut commensals. This model enables highly reproducible and controlled experiments, in which the individual growth of each member can be quantitatively tracked over time (up to 48 h) via species-specific qPCR. The protocol outlines optimized and standardized steps, including consortium setup, time-resolved sample collection, DNA extraction and qPCR analysis. It can be used to evaluate community dynamics in response to interventions such as nutrients, antimicrobials or other xenobiotics. The system is readily adaptable: additional strains can be incorporated, including pathogens (e.g., Clostridioides difficile), to transform it into an infectious disease model. In addition, we describe two optional rapid methods for assessing interspecies interactions and provide an open-source web app for generating interaction network plots. This enables exploration of ecological mechanisms and potential off-target effects. The entire workflow-from setup to data acquisition-can be completed within 1 week. This qPCR-based protocol offers a validated and accessible platform for gut microbiome research, providing a standardized, strain-level and time-resolved alternative to 16S- or fluorescence-based workflows and enabling quantitative, scalable analysis of defined microbial communities.
Indexed as
Identifiers
41857249What 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.