SIFR® Technology: Closing the Gap Between Preclinical and Clinical Prebiotics Research

New research has found a way to predict the impact of prebiotics on the human gut microbiota within days, using an ex vivo, reactor-based, high-throughput SIFR® (Systemic Intestinal Fermentation Research) technology. 


In this article, we’ll take a closer look at the research, its method, and what it means for the future of prebiotic research. We’ll also look at the core role that the CosmosID-HUB played in enabling this study to be conducted with success.


The study, which assessed three different prebiotics – inulin, resistant dextrin, and 2′-fucosyllactose – found that specific types of prebiotics stimulated the growth of certain microbes, which in turn produced particular types of short-chain fatty acids (SCFA). In vivo studies have found that these SCFA can have particular health benefits.


The SIFR® technology is a bioreactor-based method that relies on anaerobic bioreactors with supplements that promote bacterial growth. 


SIFR® bioreactors that were inputted with 6 distinct fecal inoculums and SIFR® medium were capable to predict the impact of the prebiotics on the fecal microbiota within days, whereas conventional human intervention studies would have required weeks or even months. 


The study has compared microbiome samples post-incubation at the bioreactor to illustrate the impact of different prebiotics in microbiome composition. To do that, DNA was extracted from fecal inoculums, and short-read shotgun metagenomics sequenced. 


The sequenced reads were than analyzed using CosmosID-HUB microbiome platform. The findings from the CosmosID-HUB illustrated that inulin stimulated Bifidobacteriaceae, resistant dextrin increased Parabacteroides distasonis and 2’fucosyllactose promoted Bifidobacterium adolescentis and Anaerobutyricum hallii. 


These correlations illustrated by the study may indicate mechanistic insights, thanks to the usage of six individual fecal microbiota inoculums, instead of a single or pooled fecal microbiota. It also found that the technology’s high technical reproducibility and sustained similarity between the ex vivo and in vivo microbiota made it a promising tool for product development. 


Moreover, the capacity of SIFR® to capture short-chain fatty acid output of microbes, that would have been otherwise rapidly absorbed in vivo, is another strong suit of the technology.


The study also highlights the importance of considering interpersonal differences in the gut microbiota when evaluating the efficacy of prebiotic treatments. 


Given the large intrinsic variability between humans and the inaccessibility of the site of fermentation where metabolites are rapidly absorbed, clinical trials may not be the best way to elucidate the impact of prebiotics on microbial activity and composition.


Instead, the SIFR® technology offers a promising alternative for preclinical studies.


The research is significant, as it offers a better understanding of how prebiotics can be used to modulate the human gut microbiota for better health. By identifying which prebiotics stimulate which types of microbes, scientists can potentially create targeted prebiotic treatments for different health conditions.


In conclusion, the SIFR® technology offers an exciting new avenue for studying the impact of prebiotics on the human gut microbiota. 


By enabling accurate predictions of results within days, the technology could potentially increase the success rate of microbiome modulating clinical trials, and help scientists create targeted prebiotic treatments for different health conditions.

How did CosmosID support this research?

The CosmosID-HUB enabled researchers to analyze sequencing data with great accuracy and speed, revealing the effects of different prebiotics on the gut microbiota.


The platform was able to identify correlations between prebiotics and specific strains of bacteria, offering new insights into how prebiotics can be used to modulate the human gut microbiota for better health. The technology also enabled rapid predictions of results, speeding up preclinical studies and increasing the success rates of clinical trials.


Overall, CosmosID-HUB proved to be a powerful tool for studying the impact of prebiotics on the human gut microbiota. It allowed researchers to gain valuable insights into how prebiotic treatments can be used to better health outcomes.


If you’d like to learn more about how CosmosID can be used to support research and clinical applications, don’t hesitate to get in touch today.

Unlock the power of the microbiome. Get started with the CosmosID-HUB now.





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Barış Özdinç

Barış Özdinç analyzes microbiome research with his educational background in genetics and evolution. As a research analyst for CosmosID, he combines metagenomics and data analyses to identify microbial biomarkers in disease cohorts and evaluate microbiome research tools. His work involves curating microbiome data and creating interesting microbiome content for newsletters and blog posts. Barış Özdinç received his bachelor’s degree in genetics and master’s degree in biodiversity, evolution, and conservation from University College London (UCL). Currently, he lives in Istanbul, Turkey, where he lives with his cat, Delight, and mentors female students in their STEM career pursuits.