Meta-proteomic analysis of the Shandrin mammoth by EVA technology and high-resolution mass spectrometry: what is its gut microbiota telling us?

During the last decade, paleoproteomics allowed us to open a direct window into the biological past, improving our understanding of the phylogenetic relationships of extant and extinct species, past human diseases, and reconstruction of the human diet. In particular, meta-proteomic studies, mainly carried out on ancient human dental calculus, provided insights into past oral microbial communities and ancient diets. On the contrary, very few investigations regard the analysis of ancient gut microbiota, which may enable a greater understanding of how microorganisms and their hosts have co-evolved and spread under the influence of changing diet practices and habitat. In this respect, this paper reports the results of the first-ever meta-proteomic analysis carried out on a gut tissue sample some 40,000 years old. Proteins were extracted by applying EVA (ethylene–vinyl acetate) films to the surface of the gut sample of a woolly mammoth (Mammuthus primigenus), discovered in 1972 close to the Shandrin River (Yakutia, Russia), and then investigated via a shotgun MS-based approach. Proteomic and peptidomic analysis allowed in-depth exploration of its meta-proteome composition. The results were validated through the level of deamidation and other diagenetic chemical modifications of the sample peptides, which were used to discriminate the “original” endogenous peptides from contaminant ones. Overall, the results of the meta-proteomic analysis here reported agreeing with the previous paleobotanical studies and with the reconstructed habitat of the Shandrin mammoth and provided insight into its diet. The data have been deposited to the ProteomeXchange with identifier < PXD025518 > .

Microfluidics for Peptidomics, Proteomics, and Cell Analysis

Microfluidics is the advanced microtechnology of fluid manipulation in channels with at least one dimension in the range of 1–100 microns. Microfluidic technology offers a growing number of tools for manipulating small volumes of fluid to control chemical, biological, and physical processes relevant to separation, analysis, and detection. Currently, microfluidic devices play an important role in many biological, chemical, physical, biotechnological and engineering applications. There are numerous ways to fabricate the necessary microchannels and integrate them into microfluidic platforms. In peptidomics and proteomics, microfluidics is often used in combination with mass spectrometric (MS) analysis. This review provides an overview of using microfluidic systems for peptidomics, proteomics and cell analysis. The application of microfluidics in combination with MS detection and other novel techniques to answer clinical questions is also discussed in the context of disease diagnosis and therapy. Recent developments and applications of capillary and microchip (electro)separation methods in proteomic and peptidomic analysis are summarized. The state of the art of microchip platforms for cell sorting and single-cell analysis is also discussed. Advances in detection methods are reported, and new applications in proteomics and peptidomics, quality control of peptide and protein pharmaceuticals, analysis of proteins and peptides in biomatrices and determination of their physicochemical parameters are highlighted.

Inoculation of Mother’s Own Milk Could Personalize Microbiological, Metataxonomic and Peptidomic Profile of Pasteurized Donor Human Milk Used for Feeding Preterm Infants

Background Human milk is a vehicle of bioactive compounds and beneficial bacteria which promote the establishment of a healthy gut microbiome of newborns, especially of preterm infants. Pasteurized donor human milk (PDHM) is the second-best option when preterm mother’s own milk is unavailable. Since pasteurization affect the quality of donor milk, the effect on bacterial growth, human milk microbiota diversity and proteolytic phenomena in PDHM inoculated with different preterm milk samples, was evaluated. Methods Ten preterm milk samples was used to perform inoculation of PDHM at 10% v/v. Microbiological, metataxonomic and peptidomic analysis, on preterm milk samples at the baseline (T0) and PDHM and inoculated milk (IM) samples at T0, after 2h (T1) and 4h (T2) of incubation at 37°C, were conducted. Results IM samples at T2 showed a Total Bacterial Count not significantly different (p > 0.01) compared to preterm milk samples. Lactic acid bacteria (LAB) level was restored in all IM at T2. After inoculation, metataxonomic analysis showed that Proteobacteria remained the predominant phylum while Firmicutes moved from 3% at T1 to 9.4% at T2 in IM samples. Peptidomic profile of IM resembled that of PDHM incubated for the same time in terms of number and type of peptides. Conclusion The study demonstrated that inoculation with fresh mother’s own milk could restore bacterial growth and personalize human milk microbiome in PDHM. This effect could be beneficial thanks to the presence of maternal probiotic bacteria which make PDHM more similar to mother’s own milk.