Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities.

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 genome-based 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-uncultured lineages is critical to our understanding of the role of yet-uncultured organisms in nature. This study provides a genomics-based analysis highlighting the structural features and metabolic capacities of a yet-uncultured bacterial phylum (LCP-89) previously identified in 16S rRNA surveys for which no prior genomes have been described. Our analysis identifies several interesting structural features for members of this phylum, e.g., lack of peptidoglycan biosynthetic machinery and the ability to form bacterial microcompartments. Predicted metabolic capabilities include degradation of a wide range of sugars, anaerobic respiratory capacity, and fermentative capacities. In addition to the detailed structural and metabolic analysis provided for candidate division LCP-89, this effort represents an additional step toward a unified scheme for microbial taxonomy by reconciling 16S rRNA gene-based and genomics-based taxonomic outlines.

Association between author conflicts of interest and industry-sponsorship with the favorability of outcomes of systematic reviews focusing on treatments of erectile dysfunction.

BACKGROUND: Authors' conflicts of interest and industry sponsorship have been shown to influence study outcomes. OBJECTIVE: We aimed to determine whether author conflicts of interest and industry sponsorship influenced the nature of results and conclusions of systematic reviews focusing on treatment interventions for erectile dysfunction. MATERIALS AND METHODS: We searched PubMed and Embase for systematic reviews and meta-analyses focusing on erectile dysfunction treatments published between September 1, 2016, and June 2, 2020. Authors' conflicts of interest were collected from the systematic reviews' disclosure statements. These disclosures were verified using the information provided by the Open Payments, Dollars for Profs, Google Patents, and US Patent and Trademark Office databases and from previously published disclosure statements. RESULTS: Our study included 24 systematic reviews authored by 138 authors. Nineteen authors (13.8%) were found to have conflicts of interest (disclosed, undisclosed, or both). No authors completely disclosed all conflicts. Nine reviews (37.5%) contained at least one author with conflicts of interest; of which eight reported narrative results favoring the treatment group, and seven reported conclusions favoring the treatment group. Of the 15 (62.5%) reviews without a conflicted author, 11 reported results favoring the treatment group, and 12 reported conclusions favoring the treatment group. DISCUSSION: The results and conclusions of systematic reviews for erectile dysfunction treatments did not appear to be influenced by authors who reported conflicts of interest. However, our search algorithm relied on the US-based Open Payments database and a large percentage of reviews in our study were produced by authors with international affiliations. Our study results underscore the difficulties in conducting such analyses. CONCLUSION: Although we found that undisclosed conflicts of interest (COI) were problematic among systematic reviews of erectile dysfunction treatment, only 14% of authors in our sample possessed them and these COI did not appear to influence the favorability of systematic review outcomes.