1,720,975 research outputs found
Metaproteogenomic analyses of the gut microbiota in human and animal models: identification of changes induced by special diets in health and disease
Full text linkGut microbiota (GM) is known to have a role in immune system development, metabolism and protection from enteropathogen invasion. Characterizing the health-associated GM is key to formulate targeted interventions in case of dysbiotic states. As diet is one of the main factors with an impact on gut microbes, comprehending how it shapes the GM is also crucial.In view of this, through an integrated multi-omic approach based on 16S and shotgun metagenomics and metaproteomics, several studies were performed to obtain deeply characterized GMs in human, sheep and animal models and to shed light on specifically selected diet-GM interactions.
First, the GM of a human healthy cohort and sheep were in-depth characterized, improving insights on taxonomy, active and taxon-specific functions. Further, butyrogenesis and glutamate degradation were detected as consistently active in all human subjects, becoming potential candidates for biomarkers of intestinal health.Second, the response of GM to caloric restriction (CR), and the GM possible changes at the onset of celiac disease (CD) were evaluated in animal models. Several changes solely due to CR were noted, regarding Lactobacillus spp. abundance and propionogenesis, while microbiota changes clearly related to the onset of CD were not observed.Lastly, preliminary data on two pilot studies on small human populations were reported, the first based on the analysis of different diet habits and the second as an actual dietary intervention
Biofilm production, quorum sensing system and analysis of virulence factors of Staphylococcus epidermidis collected from sheep milk samples
No full textIntramammary infections are a serious problem in dairy sheep farming, and Staphylococcus epidermidis is one of the main etiological agents of ovine mastitis. In this work, 199 S. epidermidis isolates collected in Sardinia (Italy) from sheep milk samples and used for the preparation of inactivated autogenous vaccines were characterized with phenotypic and genotypic methods. The potential for biofilm production was evaluated phenotypically by assessing colony characteristics on Congo Red Agar (CRA), and genotypically by PCR for i) the icaA/D genes coding the polysaccharide intercellular adhesin (PIA) and ii) for the bhp, aap and embp genes coding biofilm accumulation proteins. Isolates were also investigated by PCR for the presence of autolysins (atlE and aae genes), microbial surface components recognizing adhesive matrix molecules (MSCRAMMs, sdrG and sdrF genes), enterotoxins (sea, seb, sec, sed and see genes), and the toxic shock syndrome toxin (tsst genes). In addition, the staphylococcal accessory gene regulator (agr), the most important locus responsible for the regulation of virulence factors, was characterized for the first time. As a result, only two isolates showed biofilm production on CRA and harbored the icaA/D genes. Four isolates, phenotypically classified as non-biofilm producers, possessed the icaA/D genes (n = 3) or only the icaA gene (n = 1). All isolates harbored the atlE, aae, embp and sdrG genes, but none harbored the genes encoding enterotoxins and tsst. Most isolates belonged to the agr-3se group (56.3%), followed by agr-1se (41.2%) and agr-2se (2.5%). All six isolates that harbored ica genes belonged to agr-1se.
In conclusion, this study provides a detailed characterization of the putative virulence genes present in S. epidermidis strains circulating in Sardinian sheep. Because of their role in ovine mastitis pathogenesis, these might represent valuable candidates for vaccine development
Proteomic discovery and immunohistochemical validation of glucose metabolism-related enzymes as biomarkers in canine mammary tumours
No full textMetaproteomic portrait of the healthy human gut microbiota
No full textGut metaproteomics can provide direct evidence of microbial functions actively expressed in the colonic environments, contributing to clarify the role of the gut microbiota in human physiology. In this study, we re-analyzed 10 fecal metaproteomics datasets of healthy individuals from different continents and countries, with the aim of identifying stable and variable gut microbial functions and defining the contribution of specific bacterial taxa to the main metabolic pathways. The "core" metaproteome included 182 microbial functions and 83 pathways that were identified in all individuals analyzed. Several enzymes involved in glucose and pyruvate metabolism, along with glutamate dehydrogenase, acetate kinase, elongation factors G and Tu and DnaK, were the proteins with the lowest abundance variability in the cohorts under study. On the contrary, proteins involved in chemotaxis, response to stress and cell adhesion were among the most variable functions. Random-effect meta-analysis of correlation trends between taxa, functions and pathways revealed key ecological and molecular associations within the gut microbiota. The contribution of specific bacterial taxa to the main biological processes was also investigated, finding that Faecalibacterium is the most stable genus and the top contributor to anti-inflammatory butyrate production in the healthy gut microbiota. Active production of other mucosal immunomodulators facilitating host tolerance was observed, including Roseburia flagellin and lipopolysaccharide biosynthetic enzymes expressed by members of Bacteroidota. Our study provides a detailed picture of the healthy human gut microbiota, contributing to unveil its functional mechanisms and its relationship with nutrition, immunity, and environmental stressors
Meta4P: A User-Friendly Tool to Parse Label-Free Quantitative Metaproteomic Data and Taxonomic/Functional Annotations
No full textWe present Meta4P (MetaProteins-Peptides-PSMs Parser), an easy-to-use bioinformatic application designed to integrate label-free quantitative metaproteomic data with taxonomic and functional annotations. Meta4P can retrieve, filter, and process identification and quantification data from three levels of inputs (proteins, peptides, PSMs) in different file formats. Abundance data can be combined with taxonomic and functional information and aggregated at different and customizable levels, including taxon-specific functions and pathways. Meta4P output tables, available in various formats, are ready to be used as inputs for downstream statistical analyses. This user-friendly tool is expected to provide a useful contribution to the field of metaproteomic data analysis, helping make it more manageable and straightforward
Benchmarking low- and high-throughput protein cleanup and digestion methods for human fecal metaproteomics
No full textABSTRACT The application of fecal metaproteomics to large-scale studies of the gut microbiota requires high-throughput analysis and standardized experimental protocols. Although high-throughput protein cleanup and digestion methods are increasingly used in shotgun proteomics, no studies have yet critically compared such protocols using human fecal samples. In this study, human fecal protein extracts were processed using several different protocols based on three main approaches: filter-aided sample preparation (FASP), solid-phase-enhanced sample preparation (SP3), and suspension trapping (S-Trap). These protocols were applied in both low-throughput (i.e., microtube-based) and high-throughput (i.e., microplate-based) formats, and the final peptide mixtures were analyzed by liquid chromatography coupled to high-resolution tandem mass spectrometry. The FASP-based methods and the combination of SP3 with in-StageTips (iST) yielded the best results in terms of the number of peptides identified through a database search against gut microbiome and human sequences. The efficiency of protein digestion, the ability to preserve hydrophobic peptides and high molecular weight proteins, and the reproducibility of the methods were also evaluated for the different protocols. Other relevant variables, including interindividual variability of stool, duration of protocols, and total costs, were considered and discussed. In conclusion, the data presented here can significantly contribute to the optimization and standardization of sample preparation protocols in human fecal metaproteomics. Furthermore, the promising results obtained with the high-throughput methods are expected to encourage the development of automated workflows and their application to large-scale gut microbiome studies.IMPORTANCEFecal metaproteomics is an experimental approach that allows the investigation of gut microbial functions, which are involved in many different physiological and pathological processes. Standardization and automation of sample preparation protocols in fecal metaproteomics are essential for its application in large-scale studies. Here, we comparatively evaluated different methods, available also in a high-throughput format, enabling two key steps of the metaproteomics analytical workflow (namely, protein cleanup and digestion). The results of our study provide critical information that may be useful for the optimization of metaproteomics experimental pipelines and their implementation in laboratory automation systems
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Potential and active functions in the gut microbiota of a healthy human cohort
Full text linkAbstract Background The study of the gut microbiota (GM) is rapidly moving towards its functional characterization by means of shotgun meta-omics. In this context, there is still no consensus on which microbial functions are consistently and constitutively expressed in the human gut in physiological conditions. Here, we selected a cohort of 15 healthy subjects from a native and highly monitored Sardinian population and analyzed their GMs using shotgun metaproteomics, with the aim of investigating GM functions actually expressed in a healthy human population. In addition, shotgun metagenomics was employed to reveal GM functional potential and to compare metagenome and metaproteome profiles in a combined taxonomic and functional fashion. Results Metagenomic and metaproteomic data concerning the taxonomic structure of the GM under study were globally comparable. On the contrary, a considerable divergence between genetic potential and functional activity of the human healthy GM was observed, with the metaproteome displaying a higher plasticity, compared to the lower inter-individual variability of metagenome profiles. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several GM members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis, and short-chain fatty acid production). Noteworthy, Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the metabolic activity with the highest expression rate and the lowest inter-individual variability in the study cohort, in line with the previously reported importance of the biosynthesis of this microbial product for the gut homeostasis. Conclusions Our results provide detailed and taxon-specific information regarding functions and pathways actively working in a healthy GM. The reported discrepancy between expressed functions and functional potential suggests that caution should be used before drawing functional conclusions from metagenomic data, further supporting metaproteomics as a fundamental approach to characterize the human GM metabolic functions and activities
Metaproteogenomics Reveals Taxonomic and Functional Changes between Cecal and Fecal Microbiota in Mouse
Full text linkPrevious studies on mouse models report that cecal and fecal microbial communities may differ in the taxonomic structure, but little is known about their respective functional activities. Here, we employed a metaproteogenomic approach, including 16S rRNA gene sequencing, shotgun metagenomics and shotgun metaproteomics, to analyze the microbiota of paired mouse cecal contents (CCs) and feces, with the aim of identifying changes in taxon-specific functions. As a result, Gram-positive anaerobes were observed as considerably higher in CCs, while several key enzymes, involved in oxalate degradation, glutamate/glutamine metabolism, and redox homeostasis, and most actively expressed by Bacteroidetes, were clearly more represented in feces. On the whole, taxon and function abundance appeared to vary consistently with environmental changes expected to occur throughout the transit from the cecum to outside the intestine, especially when considering metaproteomic data. The results of this study indicate that functional and metabolic differences exist between CC and stool samples, paving the way to further metaproteogenomic investigations aimed at elucidating the functional dynamics of the intestinal microbiota.Version of Recor
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