Recent experimental and bioinformatic advances enable the recovery of genomes belonging to yet-uncultured microbial lineages directly from environmental samples. Here, we report on the recovery and characterization of single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) representing candidate phylum LCP-89, previously defined based on 16S rRNA gene sequences. Analysis of LCP-89 genomes recovered from Zodletone Spring, an anoxic spring in Oklahoma, predicts slow-growing, rod-shaped organisms. LCP-89 genomes contain genes for cell wall lipopolysaccharide (LPS) production but lack the entire machinery for peptidoglycan biosynthesis, suggesting an atypical cell wall structure. The genomes, however, encode S-layer homology domain-containing proteins, as well as machinery for the biosynthesis of CMP-legionaminate, inferring the possession of an S-layer glycoprotein. A nearly complete chemotaxis machinery coupled to the absence of flagellar synthesis and assembly genes argues for the utilization of alternative types of motility. A strict anaerobic lifestyle is predicted, with dual respiratory (nitrite ammonification) and fermentative capacities. Predicted substrates include a wide range of sugars and sugar alcohols and a few amino acids. The capability of rhamnose metabolism is confirmed by the identification of bacterial microcompartment genes to sequester the toxic intermediates generated. Comparative genomic analysis identified differences in oxygen sensitivities, respiratory capabilities, substrate utilization preferences, and fermentation end products between LCP-89 genomes and those belonging to its four sister phyla (Calditrichota, SM32-31, AABM5-125-24, and KSB1) within the broader FCB (Fibrobacteres-Chlorobi-Bacteroidetes) superphylum. Our results provide a detailed characterization of members of the candidate division LCP-89 and highlight the importance of reconciling 16S rRNA-based and genomebased phylogenies. IMPORTANCE Our understanding of the metabolic capacities, physiological preferences, and ecological roles of yet-uncultured microbial phyla is expanding rapidly. Two distinct approaches are currently being utilized for characterizing microbial communities in nature: amplicon-based 16S rRNA gene surveys for community characterization and metagenomics/single-cell genomics for detailed metabolic reconstruction. The occurrence of multiple yet-uncultured bacterial phyla has been documented using 16S rRNA surveys, and obtaining genome representatives of these yet-Woyke T, Elshahed M. 2019.Genomic characterization of candidate division LCP-89 reveals an atypical cell wall structure, microcompartment production, and dual respiratory and fermentative capacities. Appl Environ Microbiol 85:e00110-19. https://doi .on July 11, 2020 by guest http://aem.asm.org/ Downloaded from Ͻ50% completion and Ͻ10% contamination; MQD, medium-quality draft (SAG/MAG) with Ն50 completion and Ͻ10% contamination; HQD, high-quality draft (SAG/MAG) with Ͼ90% completion, Ͻ5% contamination, and the presence of rRNA opero...

Background The American Urological Association White Paper on Implementation of Shared Decision Making (SDM) into Urological Practice suggested SDM represents the state of the art in counseling for patients who are faced with difficult or uncertain medical decisions. The Michigan Urological Surgery Improvement Collaborative (MUSIC) implemented a decision aid, Personal Patient Profile-Prostate (P3P), in 2018 to help newly diagnosed prostate cancer patients make shared decisions with their clinicians. We conducted a qualitative study to assess statewide implementation of P3P throughout MUSIC. Methods We recruited urologists and staff from 17 MUSIC practices (8 implementation and 9 comparator practices) to understand how practices engaged patients on treatment discussions and to assess facilitators and barriers to implementing P3P. Interview guides were developed based on the Tailored Interventions for Chronic Disease (TICD) Framework. Interviews were transcribed for analysis and coded independently by two investigators in NVivo, PRO 12. Additionally, quantitative program data were integrated into thematic analyses. Results We interviewed 15 urologists and 11 staff from 16 practices. Thematic analysis of interview transcripts indicated three key themes including the following: (i) P3P is compatible as a SDM tool as over 80% of implementation urologists asked patients to complete the P3P questionnaire routinely and used P3P reports during treatment discussions; (ii) patient receptivity was demonstrated by 370 (50%) of newly diagnosed patients (n = 737) from 8 practices enrolled in P3P with 78% completion rate, which accounts for 39% of all newly diagnosed patients in these practices; and (iii) urologists’ attitudes towards SDM varied. Over a third of urologists stated they did not rely on a decision aid. Comparator practices indicated habit, inertia, or concerns about clinic flow as reasons for not adopting P3P and some were unconvinced a decision aid is needed in their practice. Conclusion Urologists and staff affiliated with MUSIC implementation sites indicated that P3P focuses the treatment discussion on items that are important to patients. Experiences of implementation practices indicate that once initiated, there were no negative effects on clinic flow and urologists indicated P3P saves time during patient counseling, as patients were better prepared for focused discussions. Lack of awareness, personal habits, and inertia are reasons for not implementing P3P among the comparator practices.

Study Need and Importance:There is a lack of realworld evidence on the use of active surveillance (AS) for favorable intermediate-risk prostate cancer (FIRPC) from diverse clinical practice settings. Further, little is known about the short-term oncologic outcomes for men with FIRPC who receive up-front treatment vs those who delay radical prostatectomy (RP). We retrospectively reviewed the Michigan Urological Surgery Improvement Collaborative data to assess the use of AS for men diagnosed with FIRPC and investigated short-term outcomes including adverse pathology and time to biochemical recurrence for those who underwent radical prostatectomy from 2012 to 2020. What We Found: We found considerable variability in the use of AS for men with FIPRC by practice ranging from 8% to 65% (23% to 85% for Grade Group [GG] 1 and 8% to 57% for GG2 disease). The 5-year treatment-free probability for those managed with AS was 63% overall and 73% for GG1 and 57% for GG2 disease. In risk-adjusted models, men with delayed RP had a higher risk of adverse pathology (46% vs 32%) but had similar rates of biochemical recurrence (22% vs 14%) to those who received immediate treatment (see Figure ). Limitations: The present study has limitations that are inherent to observational designs, including selection bias. Since the Michigan Urological Surgery Improvement Collaborative is a relatively new surgical registry, we were limited to reporting shortterm oncologic outcomes for surgical patients only.Other limitations include lack of standardization in AS follow-up care as well as the inconsistent criteria for transition from AS to treatment. Interpretation for Patient Care: Our study shows that men who delayed RP had similar oncologic outcomes to men undergoing up-front treatment suggesting many men with FIRPC can safely avoid radical treatment for years without compromising the survival benefit associated with radical treatment.

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Introduction: Decision aids have been found to improve patients' knowledge of treatments and decrease decisional regrets. Despite these benefits, there is not widespread use of decision aids for newly diagnosed prostate cancer (PCa). This analysis investigates factors that impact men's choice to use a decision aid for newly diagnosed PCa.Methods: This is a retrospective analysis of a PCa registry from the Michigan Urological Surgery Improvement Collaborative. We included data from men with newly diagnosed, clinically localized PCa seen from 2018e2021 at practices offering a PCa decision aid (Personal Patient Profile-Prostate [P3P]). The primary outcome was men's registration to use P3P. We fit a multilevel logistic regression model with patient-level factors and included urologist specific random intercepts. We estimated the intraclass correlation and predicted the probability of P3P registration among urologists.Results: A total of 2,629 men were seen at practices that participated in P3P and 1,174 (45%) registered to use P3P. In all, 41% of the total variance of P3P registration was attributed to clustering of men under a specific urologist's care. In contrast, only 1.5% of the variance of P3P registration was explained by patient factors. Our model did not include data on socioeconomic, literacy or psychosocial factors, which limits the interpretation of the results.Conclusions: These results suggest that urologists' effect far outweighs patient factors in a man's decision to enroll in P3P. Strategies that encourage providers to increase decision aid adoption in their practices are warranted.