Amazing stuff!
"... a method that can simultaneously identify, through testing a stool sample, all the proteins in the intestine – including those from food, from the person’s own body and from the intestinal microbiome. The method thereby makes it possible to decode the interactions among these proteins with unprecedented accuracy and resolution. ...
The method, dubbed IPHOMED – short for Integrated Proteo-genomics of HOst, MicrobiomE and Diet – makes it possible to decode the entirety of microbiome activity by showing which proteins in a stool sample come from which bacterial strains and in what amounts. In addition, it identifies the proteins secreted by the human gut in response to signals coming from the microbiome. Taken together, proteins from these two sources generate an atlas of the body’s communication with the microbiome, for example, during exposure to disease-causing bacteria or to antibiotics. ...
No more cheating on the diet
When the researchers thought they’d finished developing the method, it could identify 97 percent of the proteins in each stool sample, which was a high rate, but the failure to consistently characterize the remaining 3 percent seemed puzzling. Further research clarified that these originated neither in the microbiome nor in the body tissues: They came from food.
This revelation suggested that the Weizmann method might be able to meet a dire, long-standing need of nutritional science, that of supplying a noninvasive means of revealing the exact details of a person’s diet. To address this challenge, the team created a database of proteins found in hundreds of food products and identified the ones unique to each food item. These developments made it possible to learn with unprecedented precision, from stool samples, what people had eaten. ..."
From the highlights and abstract:
"Highlights
• Metagenome-informed metaproteomics (MIM) concurrently assesses diet, host, and microbiome
• MIM distinguishes compositional from functional dysbiosis in multiple disease contexts
• MIM links host IBD cues to commensal suppression and uncovers trans-kingdom biomarkers
• MIM gauges IBD-related dietary shifts, EEN compliance, and small intestinal malabsorption
Summary
Host-microbiome-dietary interactions play crucial roles in regulating human health, yet their direct functional assessment remains challenging.
We adopted metagenome-informed metaproteomics (MIM), in mice and humans, to non-invasively explore species-level microbiome-host interactions during commensal and pathogen colonization, nutritional modification, and antibiotic-induced perturbation.
Simultaneously, fecal MIM accurately characterized the nutritional exposure landscape in multiple clinical and dietary contexts. Implementation of MIM in murine auto-inflammation and in human inflammatory bowel disease (IBD) characterized a “compositional dysbiosis” and a concomitant species-specific “functional dysbiosis” driven by suppressed commensal responses to inflammatory host signals.
Microbiome transfers unraveled early-onset kinetics of these host-commensal cross-responsive patterns, while predictive analyses identified candidate fecal host-microbiome IBD biomarker protein pairs outperforming S100A8/S100A9 (calprotectin).
Importantly, a simultaneous fecal nutritional MIM assessment enabled the determination of IBD-related consumption patterns, dietary treatment compliance, and small intestinal digestive aberrations. Collectively, a parallelized dietary-bacterial-host MIM assessment functionally uncovers trans-kingdom interactomes shaping gastrointestinal ecology while offering personalized diagnostic and therapeutic insights into microbiome-associated disease."
Graphical abstract:
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