Microbial community profiling and functional inference via 16S rRNA analysis is quickly expanding across various areas of microbiology due to improvements to technology. There are numerous platforms for producing 16S rRNA taxonomic data which often vary in file and sequence formatting, creating a common barrier in microbiome studies. Additionally, many of the methods for analyzing and visualizing this sequencing data each require their own specific formatting. As a result, efficient and reproducible comparative analysis of taxonomic data and corresponding metadata in multiple programs remains a challenge in the investigation of microbial communities. PUMA, the Program for Unifying Microbiome Analysis, alleviates this problem in microbiome studies by allowing users to take advantage of numerous 16S rRNA taxonomic identification platforms and analysis tools in an efficient manner. PUMA accepts sequencing results from several taxonomic identification platforms and then automates 1 configuration of data and file types for analysis and visualization via many popular tools. The protocol accomplishes this by producing a variety of properly configured, annotated, and altered files for both analysis and visualization of taxonomic community profiles and inferred functional profiles. PUMA provides an easy and flexible interface to accommodate for a variety of users to produce all files needed for all-inclusive analysis of targeted amplicon sequencing studies.PUMA is an unprecedented open-source solution for unifying multiple microbiome analysis softwares and uses an adaptable implementation with the potential to improve and consolidate the state of microbiome research.
Bacteriophages exhibit a vast spectrum of relatedness and there is increasing evidence of close genomic relationships independent of host genus. The variability in phage similarity at the nucleotide, amino acid, and gene content levels confounds attempts at quantifying phage relatedness, especially as more novel phages are isolated. This study describes three highly similar novel Arthrobacter globiformis phages–Powerpuff, Lego, and YesChef–which were assigned to Cluster AZ using a nucleotide-based clustering parameter. Phages in Cluster AZ and Microbacterium Cluster EH, as well as the former Microbacterium singleton Zeta1847, exhibited low nucleotide similarity but gene content similarity in excess of the recently adopted Microbacterium clustering parameter, which resulted in the reassignment of Zeta1847 to Cluster EH. Additionally, while Clusters AZ and EH phages lack identifiable repressors or partitioning systems typically required for lysogeny, they encode a shared integrase indicative of a lysogenic life cycle. In the first experimental verification of a Cluster AZ phage’s life cycle, we show that phage Powerpuff is a true temperate phage and forms stable lysogens. Moreover, we provide evidence that Clusters AZ and EH phages exhibit similar genome architectures in addition to their shared integrases, suggesting that these phages may all be temperate and undergo an unknown lysogeny mechanism. Our findings further highlight the importance of using multiple metrics to capture phage relatedness and provide additional evidence of significant shared phage genomic content spanning multiple actinobacterial host genera.
The benziloyl hydrazones of testosterone-17-heptanoate, estrone-3-heptanoate and 17a-hydroxyprogesterone-17-heptanoate gave prolonged hormonal effects after subcutaneous injection into rats when compared to equivalent doses of the parent hormones, their benziloyl hydrazones or their heptanoate esters.
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