Oncological and surgical outcomes of radical surgery in elderly colorectal cancer patients with intestinal obstruction

BackgroundThe treatment strategy for elderly colorectal cancer patients with intestinal obstruction remains controversial. The choice of reasonable treatment and surgical method directly affects perioperative safety and prognosis. This study investigated the safety and long-term efficacy of radical surgery in elderly colorectal cancer patients over 80 years old with intestinal obstruction.MethodsThe clinicopathological data of elderly patients over 80 years old with intestinal obstruction who underwent colorectal cancer surgery from January 2012 to December 2021 were retrospectively collected and analysed. Patients were assigned to a radical group and a palliative group according to the surgical method. Propensity score matching (PSM) was performed to match patients in the radical group 1:1 with those in the palliative group. The perioperative-related indexes and prognosis were compared between the two groups.ResultsA total of 187 patients were enrolled in this study. After PSM, 58 matched pairs were selected, and the radical and palliative groups were well balanced in terms of the clinical and surgical characteristics (P > 0.05). The proportion of patients transferred to the ICU after surgery in the radical group was significantly higher than that in the palliative group (17.2% vs. 5.2%, P = 0.039). In terms of postoperative complications, the incidence of grade 1–5 complications in the radical group was significantly higher than that in the palliative group (37.9% vs. 15.5%, P = 0.006); however, there was no significant difference in the incidence of grade 3–5 complications between the two groups (6.9% vs. 1.7%, P = 0.364). In addition, the complications were subclassified, and it was found that the incidence of gastrointestinal disorders (20.7% vs. 6.9%, P = 0.031) after surgery was significantly higher in the radical group. The 3-year OS rates were 55.2% and 22.6% in the radical and palliative groups, respectively (P < 0.001). Multivariate analysis revealed that radical surgery was an independent prognostic factor for OS (HR: 4.32; 95% CI, 1.93–12.45; P < 0.001).ConclusionAlthough elderly colorectal cancer patients over 80 years of age with intestinal obstruction are more likely to be admitted to the ICU and develop more postoperative complications after radical surgery, long-term survival benefits can be achieved

Metagenomic Insights Into a Cellulose-Rich Niche Reveal Microbial Cooperation in Cellulose Degradation

BackgroundCellulose is the most abundant organic polymer mainly produced by plants in nature. It is insoluble and highly resistant to enzymatic hydrolysis. Cellulolytic microorganisms that are capable of producing a battery of related enzymes play an important role in recycling cellulose-rich plant biomass. Effective cellulose degradation by multiple synergic microorganisms has been observed within a defined microbial consortium in the lab culture. Metagenomic analysis may enable us to understand how microbes cooperate in cellulose degradation in a more complex microbial free-living ecosystem in nature.ResultsHere we investigated a typical cellulose-rich and alkaline niche where constituent microbes survive through inter-genera cooperation in cellulose utilization. The niche has been generated in an ancient paper-making plant, which has served as an isolated habitat for over 7 centuries. Combined amplicon-based sequencing of 16S rRNA genes and metagenomic sequencing, our analyses showed a microbial composition with 6 dominant genera including Cloacibacterium, Paludibacter, Exiguobacterium, Acetivibrio, Tolumonas, and Clostridium in this cellulose-rich niche; the composition is distinct from other cellulose-rich niches including a modern paper mill, bamboo soil, wild giant panda guts, and termite hindguts. In total, 11,676 genes of 96 glucoside hydrolase (GH) families, as well as 1,744 genes of carbohydrate transporters were identified, and modeling analysis of two representative genes suggested that these glucoside hydrolases likely evolved to adapt to alkaline environments. Further reconstruction of the microbial draft genomes by binning the assembled contigs predicted a mutualistic interaction between the dominant microbes regarding the cellulolytic process in the niche, with Paludibacter and Clostridium acting as helpers that produce endoglucanases, and Cloacibacterium, Exiguobacterium, Acetivibrio, and Tolumonas being beneficiaries that cross-feed on the cellodextrins by oligosaccharide uptake.ConclusionThe analysis of the key genes involved in cellulose degradation and reconstruction of the microbial draft genomes by binning the assembled contigs predicted a mutualistic interaction based on public goods regarding the cellulolytic process in the niche, suggesting that in the studied microbial consortium, free-living bacteria likely survive on each other by acquisition and exchange of metabolites. Knowledge gained from this study will facilitate the design of complex microbial communities with a better performance in industrial bioprocesses

Impact of the COVID-19 Pandemic on Mental Health and Quality of Life among Local Residents in Liaoning Province, China: A Cross-Sectional Study

Our study aimed to investigate the immediate impact of the COVID-19 pandemic on mental health and quality of life among local Chinese residents aged ≥18 years in Liaoning Province, mainland China. An online survey was distributed through a social media platform between January and February 2020. Participants completed a modified validated questionnaire that assessed the Impact of Event Scale (IES), indicators of negative mental health impacts, social and family support, and mental health-related lifestyle changes. A total of 263 participants (106 males and 157 females) completed the study. The mean age of the participants was 37.7 ± 14.0 years, and 74.9% had a high level of education. The mean IES score in the participants was 13.6 ± 7.7, reflecting a mild stressful impact. Only 7.6% of participants had an IES score ≥26. The majority of participants (53.3%) did not feel helpless due to the pandemic. On the other hand, 52.1% of participants felt horrified and apprehensive due to the pandemic. Additionally, the majority of participants (57.8–77.9%) received increased support from friends and family members, increased shared feeling and caring with family members and others. In conclusion, the COVID-19 pandemic was associated with mild stressful impact in our sample, even though the COVID-19 pandemic is still ongoing. These findings would need to be verified in larger population studies

Nucleotide sequences and metadata file of archaeal viruses

The database contained annotated nucleotide sequences (FASTA + GFF), accompanied with a metadata file (Table S6) describing the origin of each contig, taxonomy, including VC, host prediction information, completeness score etc. </p

Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments

Summary: Plasmid diversity is still poorly understood in pelagic marine environments. Metagenomic approaches have the potential to reveal the genetic diversity of microbes actually present in an environment and the contribution of mobile genetic elements such as plasmids. By searching metagenomic datasets from flow cytometry-sorted coastal California seawater samples dominated by cyanobacteria (SynMeta) and from the Global Ocean Survey (GOS) putative marine plasmid sequences were identified as well as their possible hosts in the same samples. Based on conserved plasmid replication protein sequences predicted from the SynMeta metagenomes, PCR primers were designed for amplification of one plasmid family and used to confirm that metagenomic contigs of this family were derived from plasmids. These results suggest that the majority of plasmids in SynMeta metagenomes were small and cryptic, encoding mostly their own replication proteins. In contrast, probable plasmid sequences identified in the GOS dataset showed more complexity, consistent with a much more diverse microbial population, and included genes involved in plasmid transfer, mobilization, stability and partitioning. Phylogenetic trees were constructed based on common replication protein functional domains and, even within one replication domain family, substantial diversity was found within and between different samples. However, some replication protein domain families appear to be rare in the marine environment.14 page(s

Metagenomic analysis reveals unexplored diversity of archaeal virome in the human gut

Human gut archaeal viruses remain largely unknown. Here the authors present a bioinformatic pipeline to identify viruses of human gut archaea, revealing diversity of archaeal viruses, their hosts and their functional gene repertoire in the human gut

A human gut phage catalog correlates the gut phageome with type 2 diabetes

Abstract Background Substantial efforts have been made to link the gut bacterial community to many complex human diseases. Nevertheless, the gut phages are often neglected. Results In this study, we used multiple bioinformatic methods to catalog gut phages from whole-community metagenomic sequencing data of fecal samples collected from both type II diabetes (T2D) patients (n = 71) and normal Chinese adults (n = 74). The definition of phage operational taxonomic units (pOTUs) and identification of large phage scaffolds (n = 2567, ≥ 10 k) revealed a comprehensive human gut phageome with a substantial number of novel sequences encoding genes that were unrelated to those in known phages. Interestingly, we observed a significant increase in the number of gut phages in the T2D group and, in particular, identified 7 pOTUs specific to T2D. This finding was further validated in an independent dataset of 116 T2D and 109 control samples. Co-occurrence/exclusion analysis of the bacterial genera and pOTUs identified a complex core interaction between bacteria and phages in the human gut ecosystem, suggesting that the significant alterations of the gut phageome cannot be explained simply by co-variation with the altered bacterial hosts. Conclusions Alterations in the gut bacterial community have been linked to the chronic disease T2D, but the role of gut phages therein is not well understood. This is the first study to identify a T2D-specific gut phageome, indicating the existence of other mechanisms that might govern the gut phageome in T2D patients. These findings suggest the importance of the phageome in T2D risk, which warrants further investigation

DeephageTP: a convolutional neural network framework for identifying phage-specific proteins from metagenomic sequencing data

Bacteriophages (phages) are the most abundant and diverse biological entity on Earth. Due to the lack of universal gene markers and database representatives, there about 50–90% of genes of phages are unable to assign functions. This makes it a challenge to identify phage genomes and annotate functions of phage genes efficiently by homology search on a large scale, especially for newly phages. Portal (portal protein), TerL (large terminase subunit protein), and TerS (small terminase subunit protein) are three specific proteins of Caudovirales phage. Here, we developed a CNN (convolutional neural network)-based framework, DeephageTP, to identify the three specific proteins from metagenomic data. The framework takes one-hot encoding data of original protein sequences as the input and automatically extracts predictive features in the process of modeling. To overcome the false positive problem, a cutoff-loss-value strategy is introduced based on the distributions of the loss values of protein sequences within the same category. The proposed model with a set of cutoff-loss-values demonstrates high performance in terms of Precision in identifying TerL and Portal sequences (94% and 90%, respectively) from the mimic metagenomic dataset. Finally, we tested the efficacy of the framework using three real metagenomic datasets, and the results shown that compared to the conventional alignment-based methods, our proposed framework had a particular advantage in identifying the novel phage-specific protein sequences of portal and TerL with remote homology to their counterparts in the training datasets. In summary, our study for the first time develops a CNN-based framework for identifying the phage-specific protein sequences with high complexity and low conservation, and this framework will help us find novel phages in metagenomic sequencing data. The DeephageTP is available at https://github.com/chuym726/DeephageTP