Pathogenesis of colorectal cancer (CRC) is associated with alterations in gut microbiome. Previous studies have focused on the changes of taxonomic abundances by metagenomics. Variations of the function of intestinal bacteria in CRC patients compared to healthy crowds remain largely unknown. Here we collected fecal samples from CRC patients and healthy volunteers and characterized their microbiome using quantitative metaproteomic method. We have identified and quantified 91,902 peptides, 30,062 gut microbial protein groups, and 195 genera of microbes. Among the proteins, 341 were found significantly different in abundance between the CRC patients and the healthy volunteers. Microbial proteins related to iron intake/transport; oxidative stress; and DNA replication, recombination, and repair were significantly alternated in abundance as a result of high local concentration of iron and high oxidative stress in the large intestine of CRC patients. Our study shows that metaproteomics can provide functional information on intestinal microflora that is of great value for pathogenesis research, and can help guide clinical diagnosis in the future.

Red blood cell distribution width (RDW) is increased in liver disease. Its clinical significance, however, remains largely unknown. The aim of this study was to identify whether RDW was a prognostic index for liver disease. We studied, retrospectively, 33 patients with non-cirrhotic HBV chronic hepatitis, 125 patients with liver cirrhosis after HBV infection, 81 newly diagnosed primary hepatocellular carcinoma (pHCC) patients, 17 alcoholic liver cirrhosis patients and 42 patients with primary biliary cirrhosis (PBC). Sixty-six healthy individuals represented the control cohort. We analyzed the relationship between RDW on admission and clinical features. The association between RDW and hospitalization outcome was estimated by receiver operating curve (ROC) analysis and a multivariable logistic regression model. Increased RDW was observed in liver disease patients. RDW was positively correlated with serum bilirubin and creatinine levels, prothrombin time, and negatively correlated with platelet counts and serum albumin concentration. A subgroup analysis, considering the different etiologies, revealed similar findings. Among the patients with liver cirrhosis, RDW increased with worsening of Child-Pugh grade. In patients with PBC, RDW positively correlated with Mayo risk score. Increased RDW was associated with worse hospital outcome, as shown by the AUC [95% confidence interval (CI)] of 0.76 (0.67-0.84). RDW above 15.15% was independently associated with poor hospital outcome after adjustment for serum bilirubin, platelet count, prothrombin time, albumin and age, with the odds ratio (95% CI) of 13.29 (1.67-105.68). RDW is a potential prognostic index for liver disease.

Metaproteomics can provide valuable insights into the functions of human gut microbiota (GM), but is challenging due to the extreme complexity and heterogeneity of GM. Data-independent acquisition (DIA) mass spectrometry (MS) has been an emerging quantitative technique in conventional proteomics, but is still at the early stage of development in the field of metaproteomics. Herein, we applied library-free DIA (directDIA)-based metaproteomics and compared the directDIA with other MS-based quantification techniques for metaproteomics on simulated microbial communities and feces samples spiked with bacteria with known ratios, demonstrating the superior performance of directDIA by a comprehensive consideration of proteome coverage in identification as well as accuracy and precision in quantification. We characterized human GM in two cohorts of clinical fecal samples of pancreatic cancer (PC) and mild cognitive impairment (MCI). About 70,000 microbial proteins were quantified in each cohort and annotated to profile the taxonomic and functional characteristics of GM in different diseases. Our work demonstrated the utility of directDIA in quantitative metaproteomics for investigating intestinal microbiota and its related disease pathogenesis.

Introduction. Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) is an emerging pathogen associated with severe clinical outcomes, prompting an urgent investigation into its genomic characteristics and pathogenic potential. Hypothesis/Gap Statement. We hypothesize that CR-hvKP strains exhibit high-level resistance and high virulence, leading to their rapid spread in clinical settings and posing a serious threat to clinical treatment. Aim. The aim of the study was to investigate the phenotype and genotype of CR-hvKP strains, reveal their resistance- and virulence-related genomic characteristics and elucidate the biological characteristics of high-virulence and high-resistance strains to provide molecular epidemiological data for clinical use. Methodology. Carbapenem-resistant K. pneumoniae (CRKP) strains were obtained from clinical samples, from January 2013 to December 2018. PCR amplification was conducted to screen for carbapenem genes. To evaluate the virulence potential of the isolates, we conducted various tests, including a string test, Galleria mellonella larvae infection test, capsular polysaccharide synthesis genotyping and genetic sequencing analyses. We used PFGE, multilocus sequence typing and next-generation sequencing to detect the genetic relationship and homology of the strains. Results. In this study, we obtained 500 strains of CRKP, among which 18 strains were identified as CR-hvKP. All CR-hvKP strains were multidrug-resistant, exhibiting high-level resistance to most β-lactam antibiotics, including carbapenems. All CR-hvKP strains except N5 were positive for blaKPC-2, of which 14 isolates belonged to capsular serotype K64. Ten unrelated PFGE types were identified by PFGE analysis. Based on the results of PFGE, a total of 12 CR-hvKP isolates were selected from the 18 isolates for further testing, and 9 isolates had high homology with pLVPK virulence-related plasmids. All CR-hvKP strains showed high virulence in the Galleria mellonella infection model. Conclusions. The study revealed the resistance- and virulence-related genomic characteristics of CR-hvKP strains and confirmed the high virulence of these strains. These results are of great significance for understanding the epidemiological characteristics and clinical treatment of CR-hvKP and provide basic data for the formulation of corresponding prevention and control strategies.