Critical Assessment of MetaProteome Investigation 2 (CAMPI-2): multi-laboratory assessment of sample processing methods to stabilize fecal microbiome for functional analysis

作者：Alessandro Tanca, Kay Schallert, Lucia Grenga, Samantha L. Peters, Marcello Abbondio, Laura De Diego, Maria Antonietta Deledda, Sven‐Bastiaan Haange, Guylaine Miotello, Johan S. Sáenz, Maximilian Wolf, Felipe Bastida, Simon Devos, Guillermina Hernandez‐Raquet, Jana Seifert, Paul Wilmes, Tim Van Den Bossche, Benoît J. Kunath, Robert Heyer, Nico Jehmlich, Dirk Benndorf, Robert L. Hettich, Jean Armengaud, Sergio Uzzau · 发表于：Microbiome · 年份：2025 · DOI：10.1186/s40168-025-02248-x · 被引用次数：5 · 研究领域：Gut microbiota and health、Probiotics and Fermented Foods、Clostridium difficile and Clostridium perfringens research

BACKGROUND: Fecal samples are widely used as a proxy for studying gut microbiome composition in both human and animal research. Fecal metaproteomics provides valuable insights by tracking changes in the relative abundance of microbial taxa and their protein functions. To ensure reliable results, it is crucial to minimize alterations in the metaproteome occurring from sample collection to protein extraction. Therefore, employing effective stabilization methods is essential to preserve the integrity of the fecal metaproteome from sample collection to laboratory analysis, particularly over long distances or when rapid freezing options are not readily available. In line with these needs, the second edition of the Critical Assessment of MetaProteome Investigation (CAMPI-2) was specifically focused on testing sample stabilization protocols to be applied before metaproteomic analysis. RESULTS: This collaborative multicenter study assessed the ability of five different stabilization methods, based on two commercial devices and three specific reagents (acetone, lithium dodecyl sulfate, and an RNAlater-like buffer), respectively, to stabilize the fecal metaproteome during room-temperature storage (14 days) and shipment to mass spectrometry facilities. The five methods were tested simultaneously by eight different laboratories across Europe, using aliquots from the same fecal sample. After protein extraction and digestion, duplicate aliquots of the resulting peptides were analyzed indep...