Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing.

Human gut microbiota is associated with human health and disease, and is known to have the second-largest genome in the human body. The microbiota genome is important for their functions and metabolites; however, accurate genomic access to the microbiota of the human gut is hindered due to the difficulty of cultivating and the shortcomings of sequencing technology. Therefore, we applied the stLFR library construction method to assemble the microbiota genomes and demonstrated that assembly property outperformed standard metagenome sequencing. Using the assembled genomes as references, SNP, INDEL, and HGT gene analyses were performed. The results demonstrated significant differences in the number of SNPs and INDELs among different individuals. The individual displayed a unique species variation spectrum, and the similarity of strains within individuals decreased over time. In addition, the coverage depth analysis of the stLFR method shows that a sequencing depth of 60X is sufficient for SNP calling. HGT analysis revealed that the genes involved in replication, recombination and repair, mobilome prophages, and transposons were the most transferred genes among different bacterial species in individuals. A preliminary framework for human gut microbiome studies was established using the stLFR library construction method.

The Potential Role of the Methionine Aminopeptidase Gene PxMetAP1 in a Cosmopolitan Pest for Bacillus thuringiensis Toxin Tolerance.

Methionine aminopeptidases (MetAPs) catalyze the cleavage of the N-terminal initiator methionine (iMet) in new peptide chains and arylamides, which is essential for protein and peptide synthesis. MetAP is differentially expressed in two diamondback moth (DBM; Plutella xylostella) strains: the G88 susceptible strain and the Cry1S1000 strain, which are resistant to the Bt toxin Cry1Ac, implicating that MetAP expression might be associated with Bt resistance. In this study, we identified and cloned a MetAP gene from DBMs, named PxMetAP1, which has a CDS of 1140 bp and encodes a 379 amino acid protein. The relative expression of PxMetAP1 was found to be ~2.2-fold lower in the Cry1S1000 strain compared to that in the G88 strain. PxMetAP1 presents a stage- and tissue-specific expression pattern, with higher levels in the eggs, adults, integument, and fatbody of DBMs. The linkage between PxMetAP1 and Cry1Ac resistance is verified by genetic linkage analysis. The knockout of PxMetAP1 in G88 by CRISPR/Cas9 leads to a ~5.6-fold decrease in sensitivity to the Cry1Ac toxin, further supporting the association between the PxMetAP1 gene and Bt tolerance. Our research sheds light on the role of MetAP genes in the development of Bt tolerance in P. xylostella and enriches the knowledge for the management of such a cosmopolitan pest.

Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models.

Common intestinal diseases such as Crohn's disease (CD), ulcerative colitis (UC), and colorectal cancer (CRC) share clinical symptoms and altered gut microbes, necessitating cross-disease comparisons and the use of multidisease models. Here, we performed meta-analyses on 13 fecal metagenome data sets of the three diseases. We identified 87 species and 65 pathway markers that were consistently changed in multiple data sets of the same diseases. According to their overall trends, we grouped the disease-enriched marker species into disease-specific and disease-common clusters and revealed their distinct phylogenetic relationships; species in the CD-specific cluster were phylogenetically related, while those in the CRC-specific cluster were more distant. Strikingly, UC-specific species were phylogenetically closer to CRC, likely because UC patients have higher risk of CRC. Consistent with their phylogenetic relationships, marker species had similar within-cluster and different between-cluster metabolic preferences. A portion of marker species and pathways correlated with an indicator of leaky gut, suggesting a link between gut dysbiosis and human-derived contents. Marker species showed more coordinated changes and tighter inner-connections in cases than the controls, suggesting that the diseased gut may represent a stressed environment and pose stronger selection on gut microbes. With the marker species and pathways, we constructed four high-performance (including multidisease) models with an area under the receiver operating characteristic curve (AUROC) of 0.87 and true-positive rates up to 90%, and explained their putative clinical applications. We identified consistent microbial alterations in common intestinal diseases, revealed metabolic capacities and the relationships among marker bacteria in distinct states, and supported the feasibility of metagenome-derived multidisease diagnosis.IMPORTANCE Gut microbes have been identified as potential markers in distinguishing patients from controls in colorectal cancer, ulcerative colitis, and Crohn's disease individually, whereas there lacks a systematic analysis to investigate the exclusive microbial shifts of these enteropathies with similar clinical symptoms. Our meta-analysis and cross-disease comparisons identified consistent microbial alterations in each enteropathy, revealed microbial ecosystems among marker bacteria in distinct states, and demonstrated the necessity and feasibility of metagenome-based multidisease classifications. To the best of our knowledge, this is the first study to construct multiclass models for these common intestinal diseases.

Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes.

Coding regions have complex interactions among multiple selective forces, which are manifested as biases in nucleotide composition. Previous studies have revealed a decreasing GC gradient from the 5'-end to 3'-end of coding regions in various organisms. We confirmed that this gradient is universal in eukaryotic genes, but the decrease only starts from the ∼ 25th codon. This trend is mostly found in nonsynonymous (ns) sites at which the GC gradient is universal across the eukaryotic genome. Increased GC contents at ns sites result in cheaper amino acids, indicating a universal selection for energy efficiency toward the N-termini of encoded proteins. Within a genome, the decreasing GC gradient is intensified from lowly to highly expressed genes (more and more protein products), further supporting this hypothesis. This reveals a conserved selective constraint for cheaper amino acids at the translation start that drives the increased GC contents at ns sites. Elevated GC contents can facilitate transcription but result in a more stable local secondary structure around the start codon and subsequently impede translation initiation. Conversely, the GC gradients at four-fold and two-fold synonymous sites vary across species. They could decrease or increase, suggesting different constraints acting at the GC contents of different codon sites in different species. This study reveals that the overall GC contents at the translation start are consequences of complex interactions among several major biological processes that shape the nucleotide sequences, especially efficient energy usage.

Treatment regimens may compromise gut-microbiome-derived signatures for liver cirrhosis.

Many of the gut-microbiome-derived signatures for liver cirrhosis, especially the important ones, were likely under the influence of proton pump inhibitors (PPIs). Wu et al. suggest that drug usage is a confounding factor in metagenomics analysis that should be controlled for.

OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.

OGEE is an Online GEne Essentiality database. Gene essentiality is not a static and binary property, rather a context-dependent and evolvable property in all forms of life. In OGEE we collect not only experimentally tested essential and non-essential genes, but also associated gene properties that contributes to gene essentiality. We tagged conditionally essential genes that show variable essentiality statuses across datasets to highlight complex interplays between gene functions and environmental/experimental perturbations. OGEE v3 contains gene essentiality datasets for 91 species; almost doubled from 48 species in previous version. To accommodate recent advances on human cancer essential genes (as known as tumor dependency genes) that could serve as targets for cancer treatment and/or drug development, we expanded the collection of human essential genes from 16 cell lines in previous to 581. These human cancer cell lines were tested with high-throughput experiments such as CRISPR-Cas9 and RNAi; in total, 150 of which were tested by both techniques. We also included factors known to contribute to gene essentiality for these cell lines, such as genomic mutation, methylation and gene expression, along with extensive graphical visualizations for ease of understanding of these factors. OGEE v3 can be accessible freely at https://v3.ogee.info.

Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment.

BACKGROUND: Compromised intestinal barrier (CIB) has been associated with many enteropathies, including colorectal cancer (CRC) and inflammatory bowel disease (IBD). We hypothesized that CIB could lead to increased host-derived contents including epithelial cells into the gut, change its physio-metabolic properties, and globally alter microbial community and metabolic capacities. RESULTS: Consistently, we found host DNA contents (HDCs), calculated as the percentage of metagenomic sequencing reads mapped to the host genome, were significantly elevated in patients of CRC and Crohn's disease (CD). Consistent with our hypothesis, we found that HDC correlated with microbial- and metabolic-biomarkers of these diseases, contributed significantly to machine-learning models for patient stratification and was consequently ranked as a top contributor. CD patients with treatment could partially reverse the changes of many CD-signature species over time, with reduced HDC and fecal calprotectin (FCP) levels. Strikingly, HDC showed stronger correlations with the reversing changes of the CD-related species than FCP, and contributed greatly in classifying treatment responses, suggesting that it was also a biomarker for effective treatment. CONCLUSIONS: Together, we revealed that association between HDCs and gut dysbiosis, and identified HDC as a novel biomarker from fecal metagenomics for diagnosis and effective treatment of intestinal diseases; our results also suggested that host-derived contents may have greater impact on gut microbiota than previously anticipated.

Inhibition of TPL2 by interferon-α suppresses bladder cancer through activation of PDE4D.

BACKGROUND: Drugs that inhibit the MEK/ERK pathway have therapeutic benefit in bladder cancer treatment but responses vary with patients, for reasons that are still not very clear. Interferon-α (IFN-α) is also used as a therapeutic agent for bladder cancer treatment but the response rate is low. It was found that IFN-α could enhance the cytotoxic effect of MEK inhibition. However, the potential mechanisms of that are still unclear. Understanding of the cross-talk between the IFN-α and MEK/ERK pathway will help enhance the efficacy of IFN-α or MEK inhibitors on bladder cancer. METHODS: Immunoprecipitation and pull-down assay were used to reveal the formation of signaling complex. The protein expressions were detected by western blot and immunohistochemistry. The cAMP level, Phosphodiesterase 4D (PDE4D) activity and Prostaglandin E2 (PGE2) concentration in cells, serum and tissues were detected by enzyme-linked immunosorbent assay. The role of PDE4D in bladder tumorigenesis in vivo was examined by the xenograft model. Tissue microarray chips were used to investigate the prognostic roles of PDE4D and tumor progression locus 2 (TPL2) in bladder cancer patients. RESULTS: IFN-α down-regulated the cyclooxygenase-2 (COX-2) expression in bladder cancer cells through the inhibition of TPL2/NF-κB pathway; IFN-α also inhibited COX-2 expression by suppressing cAMP signaling through TPL2-ERK mediated PDE4D activity. Reduction of the intracellular cAMP level by PDE4D potentiated the antitumor effect of IFN-α against bladder cancer in vitro and in vivo. Further analysis of clinical samples indicated that low PDE4D expression and high level of TPL2 phosphorylation were correlated to the development and poor prognosis in bladder cancer patients. CONCLUSIONS: Our data reveal that IFN-α can exert its antitumor effect through a non-canonical JAK-STAT pathway in the bladder cancer cells with low activity of IFN pathway, and the TPL2 inhibition is another function of IFN-α in the context of bladder cancer therapy. The antitumor effects of IFN-α and MEK inhibition also depend on the PDE4D-mediated cAMP level in bladder cancer cells. Suppression of the TPL2 phosphorylation and intracellular cAMP level may be possible therapeutic strategies for enhancing the effectiveness of IFN-α and MEK inhibitors in bladder cancer treatment.

Dissecting complicated viral spreading of enterovirus 71 using in situ bioorthogonal fluorescent labeling.

Enterovirus 71 (EV71), the major pathogen of hand-foot-and-mouth disease (HFDM), can cause severe neurological and respiratory manifestations in young children. Viral spread route and tissue tropism are key factors contributing to different pathogenicity of EV71, however it remains a challenge to dynamically visualize EV71 infection in vivo. The present study applies an in situ bioorthogonal fluorescent labeling strategy to track clinically isolated EV71 strains with different pathogenicity in neonatal mice. The results show that the in situ labeling strategy effectively captures EV71 viruses through in vivo bioorthogonal reaction in multiple infected organs without interfering viral spread and tissue tropism. More importantly, the in situ labeling reveals different viral dynamics, dissemination, and tissue tropism of severe case EV71 (SC-EV71) and mild case EV71 (MC-EV71), consistent with their different pathogenicity in HFDM patients. Compared with MC-EV71, SC-EV71 not only enters the blood circulation and spreads out more quickly, but also shows more significant neuronal and respiratory tropism, which certainly contribute severe neurological complications and clinical manifestations in the patient. Hence, the in situ bioorthogonal fluorescent labeling is a plausible strategy to dissect complicated process of EV71 viral spread in the early stage of infection, thereby offering great opportunities to understand its pathogenesis and develop anti-viral drugs.