Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences

Shotgun metagenomic sequencing reveals the potential in microbial communities. However, lower-cost 16S ribosomal RNA (rRNA) gene sequencing provides taxonomic, not functional, observations. To remedy this, we previously introduced Piphillin, a software package that predicts functional metagenomic content based on the frequency of detected 16S rRNA gene sequences corresponding to genomes in regularly updated, functionally annotated genome databases. Piphillin (and similar tools) have previously been evaluated on 16S rRNA data processed by the clustering of sequences into operational taxonomic units (OTUs). New techniques such as amplicon sequence variant error correction are in increased use, but it is unknown if these techniques perform better in metagenomic content prediction pipelines, or if they should be treated the same as OTU data in respect to optimal pipeline parameters

An IFN-γ-IL-18 Signaling Loop Accelerates Memory CD8+ T Cell Proliferation

Rapid proliferation is one of the important features of memory CD8+ T cells, ensuring rapid clearance of reinfection. Although several cytokines such as IL-15 and IL-7 regulate relatively slow homeostatic proliferation of memory T cells during the maintenance phase, it is unknown how memory T cells can proliferate more quickly than naïve T cells upon antigen stimulation. To examine antigen-specific CD8+ T cell proliferation in recall responses in vivo, we targeted a model antigen, ovalbumin(OVA), to DEC-205+ dendritic cells (DCs) with a CD40 maturation stimulus. This led to the induction of functional memory CD8+ T cells, which showed rapid proliferation and multiple cytokine production (IFN-γ, IL-2, TNF-α) during the secondary challenge to DC-targeted antigen. Upon antigen-presentation, IL-18, an IFN-γ-inducing factor, accumulated at the DC:T cell synapse. Surprisingly, IFN-γ receptors were required to augment IL-18 production from DCs. Mice genetically deficient for IL-18 or IFN-γ-receptor 1 also showed delayed expansion of memory CD8+ T cells in vivo. These results indicate that a positive regulatory loop involving IFN-γ and IL-18 signaling contributes to the accelerated memory CD8+ T cell proliferation during a recall response to antigen presented by DCs

Strain level and comprehensive microbiome analysis in inflammatory bowel disease via multi-technology meta-analysis identifies key bacterial influencers of disease

Inflammatory bowel disease (IBD) is a heterogenous disease in which the microbiome has been shown to play an important role. However, the precise homeostatic or pathological functions played by bacteria remain unclear. Most published studies report taxa-disease associations based on single-technology analysis of a single cohort, potentially biasing results to one clinical protocol, cohort, and molecular analysis technology. To begin to address this key question, precise identification of the bacteria implicated in IBD across cohorts is necessary. We sought to take advantage of the numerous and diverse studies characterizing the microbiome in IBD to develop a multi-technology meta-analysis (MTMA) as a platform for aggregation of independently generated datasets, irrespective of DNA-profiling technique, in order to uncover the consistent microbial modulators of disease. We report the largest strain-level survey of IBD, integrating microbiome profiles from 3,407 samples from 21 datasets spanning 15 cohorts, three of which are presented for the first time in the current study, characterized using three DNA-profiling technologies, mapping all nucleotide data against known, culturable strain reference data. We identify several novel IBD associations with culturable strains that have so far remained elusive, including two genome-sequenced but uncharacterized Lachnospiraceae strains consistently decreased in both the gut luminal and mucosal contents of patients with IBD, and demonstrate that these strains are correlated with inflammation-related pathways that are known mechanisms targeted for treatment. Furthermore, comparative MTMA at the species versus strain level reveals that not all significant strain associations resulted in a corresponding species-level significance and conversely significant species associations are not always re-captured at the strain level. We propose MTMA for uncovering experimentally testable strain-disease associations that, as demonstrated here, are beneficial in discovering mechanisms underpinning microbiome impact on disease or novel targets for therapeutic interventions

Current status of tertiary debulking surgery and prognosis after secondary debulking surgery for recurrent Müllerian epithelial cancer in Japan: a retrospective analysis of 164 patients (KCOG-G1402)

BackgroundThis study aimed to evaluate the current status of secondary debulking surgery (SDS) and tertiary debulking surgery (TDS; performed for recurrence after SDS) and to assess the overall survival after recurrence of Müllerian epithelial cancer in Japan. We also evaluated the data of patients who underwent a fourth debulking surgery (i.e., quaternary debulking surgery (QDS)).MethodsWe conducted a retrospective study of 164 patients with recurrent Müllerian epithelial cancers (i.e., ovarian, tubal, and peritoneal cancers). The SDS was performed between January 2000 and September 2014 in 20 Japanese hospitals. Clinicopathological data were collected and analyzed.ResultsOf the 164 patients, 66 patients did not have a recurrence or died after SDS. Ninety-eight patients had a recurrence after SDS. Forty-three of the 98 patients underwent TDS; 55 of the 98 patients did not undergo TDS and were classified into the non-TDS group. The overall survival (OS) after SDS was significantly better in the TDS group than in the non-TDS group. The median OS after SDS was 123 and 42 months in the TDS group and non-TDS group, respectively. Of the 43 patients who received TDS, 11 patients were further treated with QDS. The median OS after SDS was 123 months for patients who underwent QDS.ConclusionsThis multicenter study on the prognosis of post-SDS is apparently the first report on QDS in Japan. Patients undergoing TDS have a good prognosis, compared to patients in the non-TDS group. Novel drugs are being evaluated; however, debulking surgery remains a necessary treatment for recurrence

Factors that Impact Anxiety and Depression in Patients with Chronic Obstructive Pulmonary Disease

[Purpose] There are numerous reports about anxiety and depression in patients with chronic obstructive pulmonary disease (COPD) in the literature. However, the incidence of and the factors that affect anxiety and depression differ depending on cultural backgrounds and assessment methods. In Japan, there is insufficient understanding of the mental and psychological conditions of COPD patients. To examine the comorbidity of anxiety and depression in inpatients and outpatients with COPD and to evaluate the factors affecting anxiety and depression. [Method] Mental and psychological assessments based on medical information, family composition, educational history, occupational history, respiratory function tests and the Hospital Anxiety and Depression Scale (HADS) were conducted with 156 patients with COPD as subject. [Results] The comorbidity of anxiety in all patients with COPD was 26%; moreover, the comorbidity of depression in these patients was 44%. Among inpatients, 42% displayed anxiety and 69% exhibited depression, whereas among outpatients, 18% displayed anxiety and 32% demonstrated depression. Factors causing anxiety included of living alone and hospitalization. Factors causing depression included of hospitalization, low BMI and low education level. [Conclusion] The data suggest that the causes of anxiety and depression in patients with COPD are affected by individual background. Consideration of the factors that cause these effects is important

Personality Traits of Patients with Chronic Obstructive Pulmonary Disease Who Exhibit Depression

[Purpose] The objective of this study was to examine the differences in personality traits based on the presence of depression in chronic obstructive pulmonary disease (COPD) patients. [Subjects and Methods] The current study involved 39 subjects with COPD. Personality traits of subjects were compared with the presence of depression and effectors of depression, including personality traits, were reviewed. [Results] Fourteen subjects (35.9% of the total) were classified as having depression (Center for Epidemiologic Studies Depression Scale (CES-D)≥16). Subjects who exhibited depression also displayed differences in items of the Yatabe-Guilford personality inventory and demonstrated high values for all St. George\u27s Hospital Respiratory Questionnaire (SGRQ) items. Additionally these personality traits and SGRQ items were partially correlated with CES-D score. Effectors for CES-D were "Nervousness" "Sense of cooperation", and "Symptoms" of SGRQ. [Conclusion] Subjects who exhibited depression displayed traits such as a sense of inferiority, nervousness, lack of cooperation, inactivity, thinking introversion, excessive punctuality and unsociability. Therefore, in COPD patients, consideration of personality traits can be linked to early detection and appropriate treatment of depression via methods such as group cognitive behavioral therapy in respiratory rehabilitation