ChipFilter: Microfluidic-Based Comprehensive Sample Preparation Methodology for Microbial Consortia.

The metaproteomic approach is an attractive way to describe a microbiome at the functional level, allowing the identification and quantification of proteins across a broad dynamic range as well as the detection of post-translational modifications. However, it remains relatively underutilized, mainly due to technical challenges that should be addressed, including the complexity of extracting proteins from heterogeneous microbial communities. Here, we show that a ChipFilter microfluidic device coupled to a liquid chromatography tandem mass spectrometry (LC-MS/MS) setup can be successfully used for the identification of microbial proteins. Using cultures of Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae, we have shown that it is possible to directly lyse the cells and digest the proteins in the ChipFilter to allow the identification of a higher number of proteins and peptides than that by standard protocols, even at low cell density. The peptides produced are overall longer after ChipFilter digestion but show no change in their degree of hydrophobicity. Analysis of a more complex mixture of 17 species from the gut microbiome showed that the ChipFilter preparation was able to identify and estimate the amounts of 16 of these species. These results show that ChipFilter can be used for the proteomic study of microbiomes, particularly in the case of a low volume or cell density. The mass spectrometry data have been deposited on the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD039581.

Selective solid phase extraction of lanthanides from tap and river waters with ion imprinted polymers.

For the first time, an ion imprinted polymer (IIP) able to selectively extract simultaneously all the lanthanide ions was successfully synthesized in acetonitrile using Nd3+ as a template ion, methacrylic acid as a complexing monomer, and ethylene glycol dimethacrylate as a cross-linker. A non-imprinted polymer (NIP) was synthesized under the same conditions as those of the IIP, but in the absence of the template ion. After the removal of the template ions, grounding and sieving, the IIP particles were packed in solid phase extraction (SPE) cartridges. The selectivity of the IIP was evaluated by comparing its behavior with the one of the NIP. Each SPE step (percolation, washing, and elution) was optimized in order to find the best compromise between the selectivity and the extraction recoveries. Using the optimized SPE conditions, the extraction recoveries of eight lanthanide ions representative of the lanthanide family were higher than 77% with an average value of 83% with the IIP, whereas, in the case of the NIP, they ranged between 14 and 36% and they were below 3% for the interfering ions from alkali, transition, and post-transition metal families with the IIP. A first evaluation of the reproducibility of the SPE profiles was carried out by performing statistical tests on the data obtained with several cartridges filled with particles obtained from two different IIP and NIP syntheses. Promising results were obtained. The specific capacity, i. e. the adsorption capacity of Nd3+ ions by the specific cavities of the imprinted polymer, was about 9 mg of Nd3+ per gram of IIP (60 µmol g-1), which is more than enough for the extraction of the lanthanide ions at trace levels. The breakthrough volume was about 1 mL per mg of IIP, leading to an enrichment factor of 15, which allows not only to selectively extract the lanthanides but also to concentrate them. Finally, the imprinted polymer was successfully used to selectively extract lanthanides from tap and river waters spiked at 1 µg L-1.