Abstract：
:Antibiotic-induced microbial perturbations alter host metabolism and affect host physiology. In this study, we aimed to investigate the effects of vancomycin (Vanc) and ciprofloxacin/metronidazole (CiMe) exposures on the gut microbiome and metabolome in the colonic content and tissue samples from advanced-stage type 1 diabetic (AST1D) rats and age-matched controls (AMCs) using 16S ribosomal RNA gene sequencing and nuclear magnetic resonance-based metabolomics. The results show that antibiotic effects on the gut microbiota were stronger in AMC rats relative to AST1D rats. These microbial alterations were accompanied by a series of metabolic changes, including energy metabolism, short-chain fatty acid metabolism, and amino acid metabolism. We found that AMC rats had a more notable metabolic response to antibiotic exposure than AST1D rats. Additionally, Vanc had a stronger impact on the gut microbiota and host metabolic phenotype versus CiMe. Therefore, our results reveal that antibiotic-induced shifts in the gut microbiome and metabolome are different between AST1D and AMC rats. If confirmed in human studies, these findings suggest that diabetic patients may need a specific strategy for antibiotic use in clinical practice.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Zheng H,Fan K,Ji H,Jiang Q,Ning J,Xu P,Li C,Gao Hdoi
10.1021/acs.jproteome.9b00402subject
Has Abstractpub_date
2019-11-01 00:00:00pages
3944-3954issue
11eissn
1535-3893issn
1535-3907journal_volume
18pub_type
杂志文章abstract：:As a potential tool for proteomics and protein characterization, in-gel cysteine- and arginine-specific cleavage is demonstrated by means of trypsin or endoproteinase Lys-C for six model proteins (lysozyme, alpha-lactalbumin, beta-lactoglobulin, ribonuclease A, albumin, and transferrin), ranging in size from 14 kDa to...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr025568g
更新日期：2003-03-01 00:00:00
abstract：:Tryptic digestion of biotinylated Lys-C peptides followed by affinity chromatography allows the selective isolation of lysine-free tryptic peptides delimited by arginine residues (RRnK peptides). In silico analysis revealed that RRnK peptides represent 87% of the whole proteomes and their specific isolation simplifies...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060003w
更新日期：2006-05-01 00:00:00
abstract：:Tandem mass spectrometry has become the method of choice for high-throughput, quantitative analysis in proteomics. Peptide spectrum matching algorithms score the concordance between the experimental and the theoretical spectra of candidate peptides by evaluating the number (or proportion) of theoretically possible fra...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00499
更新日期：2019-06-07 00:00:00
abstract：:Protein post-translational modification by ubiquitin-fold modifier 1, UFM1, regulates many biological processes such as response to endoplasmic reticulum stress and regulation of tumor progression. A recent study has indicated that the UFM1-binding and PCI domain-containing protein 1 (UFBP1) is required for the conjug...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00843
更新日期：2018-04-06 00:00:00
abstract：:The abundant proteins in human milk have been well characterized and are known to provide nutritional, protective, and developmental advantages to both term and preterm infants. However, relatively little is known about the expression of the low abundance proteins that are present in human milk because of the technica...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr2008797
更新日期：2012-03-02 00:00:00
abstract：:Kalirin-7 (Kal7), a multifunctional Rho GDP/GTP exchange factor (GEF) for Rac1 and RhoG, is embedded in the postsynaptic density at excitatory synapses, where it participates in the formation and maintenance of dendritic spines. Kal7 has been implicated in long-term potentiation, fear memories, and addiction-like beha...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200088w
更新日期：2011-06-03 00:00:00
abstract：:There are three quantitative phosphoproteomic strategies most commonly used to study receptor tyrosine kinase (RTK) signaling. These strategies quantify changes in: (1) all three forms of phosphosites (phosphoserine, phosphothreonine and phosphotyrosine) following enrichment of phosphopeptides by titanium dioxide or i...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200697x
更新日期：2011-12-02 00:00:00
abstract：:Acute kidney injury (AKI) is a frequent complication after cardiopulmonary bypass, but early detection of postoperative AKI remains challenging. Protein biomarkers predict AKI excellently in homogeneous cohorts but are less reliable in patients suffering from various comorbidities. We employed nuclear magnetic resonan...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00219
更新日期：2015-07-02 00:00:00
abstract：:Mitosis is a highly regulated process in which errors can lead to genomic instability, a hallmark of cancer. During this phase of the cell cycle, transcription is silent and RNA translation is inhibited. Thus, mitosis is largely driven by post-translational modification of proteins, including phosphorylation, methylat...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100281h
更新日期：2010-09-03 00:00:00
abstract：:Increased throughput as well as increased multiplexing of liquid chromatography coupled to selected reaction monitoring mass spectrometry (LC-SRM-MS) assays for protein quantification challenges routine data analysis. Despite the measurement of multiple transitions from multiple peptides, for clinical applications a s...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00854
更新日期：2020-06-05 00:00:00
abstract：:Two-dimensional differential gel electrophoresis (2-D DIGE) was used to analyze human serum following the removal of albumin and five other high-abundant serum proteins. After protein removal, serum was analyzed by SDS-PAGE as a preliminary screen, and significant differences between four high-abundant protein removal...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr049921p
更新日期：2004-11-01 00:00:00
abstract：:S-Nitrosylation is a redox-based post-translational modification of a protein in response to nitric oxide (NO) signaling, and it participates in a variety of processes in diverse biological systems. The significance of this type of protein modification in health and diseases is increasingly recognized. In the central ...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/acs.jproteome.5b00857
更新日期：2016-01-04 00:00:00
abstract：:In Ralstonia eutropha H16, seven genes encoding proteins being involved in the phosphoenolpyruvate-carbohydrate phosphotransferase system (PEP-PTS) were identified. In order to provide more insights into the poly(3-hydroxybutyrate) (PHB)-leaky phenotype of the HPr/EI deletion mutants H16ΔptsH, H16ΔptsI, and H16ΔptsHI ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300042f
更新日期：2012-07-06 00:00:00
abstract：:Target-decoy approach (TDA) is the dominant strategy for false discovery rate (FDR) estimation in mass-spectrometry-based proteomics. One of its main applications is direct FDR estimation based on counting of decoy matches above a certain score threshold. The corresponding equations are widely employed for filtering o...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00144
更新日期：2017-02-03 00:00:00
abstract：:When analyzing proteins in complex samples using tandem mass spectrometry of peptides generated by proteolysis, the inference of proteins can be ambiguous, even with well-validated peptides. Unresolved questions include whether to show all possible proteins vs a minimal list, what to do when proteins are inferred ambi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200039p
更新日期：2011-07-01 00:00:00
abstract：:The Esx/WXG-100 (ESAT-6/Wss) exporters are multiprotein complexes that promote protein translocation across the cytoplasmic membrane in a diverse range of pathogenic and nonpathogenic bacterial species. The Esx-1 (ESAT-6 System-1) system mediates virulence factor translocation in mycobacterial pathogens, including the...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500484w
更新日期：2014-11-07 00:00:00
abstract：:The use of combinatorial peptide ligand libraries, containing hexapeptides terminating with a primary amine, or modified with a terminal carboxyl group, allowed discovering and identifying a large number of previously unreported proteins in cow's whey. Whereas comprehensive whey protein lists progressively increased i...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900221x
更新日期：2009-08-01 00:00:00
abstract：:Salt stress is a major abiotic factor limiting maize yield. To characterize the mechanism underlying maize salt tolerance, we compared the seedling root proteomes of salt-tolerant Jing724 and salt-sensitive D9H. The germination rate and growth parameter values (weight and length) were higher for Jing724 than for D9H u...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00455
更新日期：2018-01-05 00:00:00
abstract：:Phosphorylation is an essential post-translational modification for regulating protein function and cellular signal transduction. Mass spectrometry (MS) combined with isobaric tandem mass tags (TMTs) has become a powerful platform for simultaneous, large-scale phospho-proteome site identification and quantitation. To ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00610
更新日期：2017-11-03 00:00:00
abstract：:In this Letter, we reanalyze published mass spectrometry data sets of clinical samples with a focus on determining the coinfection status of individuals infected with SARS-CoV-2 coronavirus. We demonstrate the use of ComPIL 2.0 software along with a metaproteomics workflow within the Galaxy platform to detect cohabita...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00822
更新日期：2021-01-04 00:00:00
abstract：:Modeling and simulation of biological networks is an effective and widely used research methodology. The Biological Network Simulator (BioNSi) is a tool for modeling biological networks and simulating their discrete-time dynamics, implemented as a Cytoscape App. BioNSi includes a visual representation of the network t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00278
更新日期：2016-08-05 00:00:00
abstract：:To gain insights into how TGF-beta regulates epithelial-mesenchymal transition (EMT), we assessed the time course of proteins and mRNAs during EMT by multiplex iTRAQ labeling and 2D-LC-MS/MS, and by hybridization, respectively. Temporal iTRAQ analysis identified 66 proteins as differentially expressed during EMT, incl...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr8006478
更新日期：2009-01-01 00:00:00
abstract：:Automated sequencing of unknowns in bottom-up proteomics makes the data produced susceptible to process control errors, which can be propagated into mistakes in analyte identification. Inclusion of an unintrusive internal standard, such as lysozyme, allows monitoring all phases of the proteomics process including samp...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr049819s
更新日期：2005-01-01 00:00:00
abstract：:Hepatocellular carcinoma (HCC) causes more than half a million annual deaths worldwide. Understanding the mechanisms contributing to HCC development is highly desirable for improved surveillance, diagnosis, and treatment. Liver tissue metabolomics has the potential to reflect the physiological changes behind HCC devel...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00185
更新日期：2019-08-02 00:00:00
abstract：:Geobacter sulfurreducens is a dissimilatory metal-reducing bacterium capable of forming thick electron-conducting biofilms on solid electrodes. Here, we employ for the first time comparative proteomics to identify key physiological changes involved in G. sulfurreducens adaptation from fumarate-respiring planktonic cel...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b01019
更新日期：2016-01-01 00:00:00
abstract：:We report the proteomic characterization and biological activities of the venom of the black-speckled palm pitviper, Bothriechis nigroviridis, a neotropical arboreal pitviper from Costa Rica. In marked contrast to other Bothriechis species investigated, the venom of B. nigroviridis does not possess detectable Zn(2+)-d...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100545d
更新日期：2010-08-06 00:00:00
abstract：:Plasma biomarkers of exposure to environmental contaminants play an important role in early detection of disease. The emerging field of proteomics presents an attractive opportunity for candidate biomarker discovery, as it simultaneously measures and analyzes a large number of proteins. This article presents a case st...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070491n
更新日期：2008-01-01 00:00:00
abstract：:Protein microarrays consist of known proteins spotted onto solid substrates and are used to perform highly multivariate assessments of protein-binding interactions. Human protein arrays are routinely applied to pathogen detection, immune response biomarker profiling, and antibody specificity profiling. Here, we descri...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00892
更新日期：2020-07-02 00:00:00
abstract：:We analyzed the whole-cell protein content of gastrocnemius muscles from rats in different thyroid states. Twenty differentially expressed proteins were unambiguously identified. They were involved in substrates and energy metabolism, stress response, cell structure, and gene expression. This study represents the firs...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0701299
更新日期：2007-08-01 00:00:00
abstract：:We performed proteomic analyses of human olfactory epithelial tissue to identify missing proteins using liquid chromatography-tandem mass spectrometry. Using a next-generation proteomic pipeline with a < 1.0% false discovery rate at the peptide and protein levels, we identified 3731 proteins, among which five were mis...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00408
更新日期：2018-12-07 00:00:00
