Taxonomical composition and functional analysis of biofilms sampled from a nuclear storage pool

Sampling small amounts of biofilm from harsh environments such as the biofilm present on the walls of a radioactive material storage pool offers few analytical options if taxonomic characterization and estimation of the different biomass contributions are the objectives. Although 16S/18S rRNA amplification on extracted DNA and sequencing is the most widely applied method, its reliability in terms of quantitation has been questioned as yields can be species-dependent. Here, we propose a tandem-mass spectrometry proteotyping approach consisting of acquiring peptide data and interpreting then against a generalist database without any a priori. The peptide sequence information is transformed into useful taxonomical information that allows to obtain the different biomass contributions at different taxonomical ranks. This new methodology is applied for the first time to analyze the composition of biofilms from minute quantities of material collected from a pool used to store radioactive sources in a nuclear facility. For these biofilms, we report the identification of three genera, namely Sphingomonas, Caulobacter, and Acidovorax, and their functional characterization by metaproteomics which shows that these organisms are metabolic active. Differential expression of Gene Ontology GOslim terms between the two main microorganisms highlights their metabolic specialization

De <i>novo </i>transcriptomes of 14 gammarid individuals for proteogenomic analysis of seven taxonomic groups

Gammarids are amphipods found worldwide distributed in fresh and marine waters. They play an important role in aquatic ecosystems and are well established sentinel species in ecotoxicology. In this study, we sequenced the transcriptomes of a male individual and a female individual for seven different taxonomic groups belonging to the two genera Gammarus and Echinogammarus: Gammarus fossarum A, G. fossarum B, G. fossarum C, Gammarus wautieri, Gammarus pulex, Echinogammarus berilloni, and Echinogammarus marinus. These taxa were chosen to explore the molecular diversity of transcribed genes of genotyped individuals from these groups. Transcriptomes were de novo assembled and annotated. High-quality assembly was confirmed by BUSCO comparison against the Arthropod dataset. The 14 RNA-Seq-derived protein sequence databases proposed here will be a significant resource for proteogenomics studies of these ecotoxicologically relevant non-model organisms. These transcriptomes represent reliable reference sequences for whole-transcriptome and proteome studies on other gammarids, for primer design to clone specific genes or monitor their specific expression, and for analyses of molecular differences between gammarid species

Proteomics in food: Quality, safety, microbes, and allergens

Food safety and quality and their associated risks pose a major concern worldwide regarding not only the relative economical losses but also the potential danger to consumer's health. Customer's confidence in the integrity of the food supply could be hampered by inappropriate food safety measures. A lack of measures and reliable assays to evaluate and maintain a good control of food characteristics may affect the food industry economy and shatter consumer confidence. It is imperative to create and to establish fast and reliable analytical methods that allow a good and rapid analysis of food products during the whole food chain. Proteomics can represent a powerful tool to address this issue, due to its proven excellent quantitative and qualitative drawbacks in protein analysis. This review illustrates the applications of proteomics in the past few years in food science focusing on food of animal origin with some brief hints on other types. Aim of this review is to highlight the importance of this science as a valuable tool to assess food quality and safety. Emphasis is also posed in food processing, allergies, and possible contaminants like bacteria, fungi, and other pathogens

Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences

Advances in the technologies and informatics used to generate and process large biological data sets (omics data) are promoting a critical shift in the study of biomedical sciences. While genomics, transcriptomics and proteinomics, coupled with bioinformatics and biostatistics, are gaining momentum, they are still, for the most part, assessed individually with distinct approaches generating monothematic rather than integrated knowledge. As other areas of biomedical sciences, including metabolomics, epigenomics and pharmacogenomics, are moving towards the omics scale, we are witnessing the rise of inter-disciplinary data integration strategies to support a better understanding of biological systems and eventually the development of successful precision medicine. This review cuts across the boundaries between genomics, transcriptomics and proteomics, summarizing how omics data are generated, analysed and shared, and provides an overview of the current strengths and weaknesses of this global approach. This work intends to target students and researchers seeking knowledge outside of their field of expertise and fosters a leap from the reductionist to the global-integrative analytical approach in research

Pathogen proteotyping: A rapidly developing application of mass spectrometry to address clinical concerns

For the rapid and reliable differentiation of clinically-relevant bacterial species, mass spectrometry-based methods have emerged in recent years as valid alternatives to existing techniques. Mass profiles generated by whole-cell Matrix-Assisted Laser Desorption Ionization-Time of Flight mass spectrometry have revolutionized microorganism identification and proven their potential for proteotyping at the species level. Indeed, the methodology has been widely deployed in clinical settings. However, the low resolution and dynamic range of the methodology has limited its capacity to distinguish between subspecies. This discrimination capacity is pivotal in cases where certain strains display virulence or antibiotic resistance, and for epidemiologic analyses. Moreover, sensitivity and specificity are both key parameters when attempting to discriminate between microorganisms present in complex multi-pathogenic samples. These two parameters are also essential to meet the growing interest in the characterization of microorganisms contained within even more complex samples, such as the human microbiome. Tandem mass spectrometry, with its high resolution, holds great potential for use in the real-time direct analysis of pathogens at the most relevant taxonomic rank in routine clinical practice. This review explores the numerous benefits and challenges of implementing advanced proteotyping methods, based on tandem mass spectrometry, in clinical laboratories. We provide an overview of the current applications and methodologies, while also discussing recent improvements and potential new approaches for typing, as well as their future applications

Leipzig contest @Li2D

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Metaproteomics for deciphering biomass contributions and functions of complex aquatic microbiota

International audienceMetaproteomics aims at comprehensively identifying the preeminent metabolic pathways for gaining insight into the functions of microbiota. This large scale molecular phenotypic analysis is highly complementary to 16S rRNA metabarcoding and metagenomics. We have developed a new method for exploiting metaproteomic datasets and defining the biomass contribution of the organisms present in the sample. The phylopeptidomics concept is based on a signature describing the number of peptide sequences shared with all other organisms calculated by mathematical modeling and phylogenetic relationships. Its efficiency was exemplified with artificial mixtures, as well as with more complex microbiota models. This methodology was applied on aquatic microbiota such as those discovered within the water used to cool a nuclear reactor core. We highlighted in a nuclear reactor at shutdown the predominance of two phyla: Proteobacteria with the genus Methylobacterium (50% of the signal) and Actinobacteria with two genera Asanoa (25%) and Streptomyces (25%). This approach proved to be highly complementary to the metabarcoding analysis of the same samples. We also successfully applied the method to biofilms sampled from the walls of a pool used to store radioactive sources. These examples applied to aquatic microbial communities pave the way to new discoveries regarding novel microorganisms of biotechnological interest

Challenges and solutions for exploring taxonomical and functional changes of microbiota along a soil core

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