Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices

Over 3000 microbial (bacterial and archaeal) genomes have been made publically available to date, providing an unprecedented opportunity to examine evolutionary genomic trends and offering valuable reference data for a variety of other studies such as metagenomics. The utility of these genome sequences is greatly enhanced when we have an understanding of how they are phylogenetically related to each other. Therefore, we here describe our efforts to reconstruct the phylogeny of all available bacterial and archaeal genomes. We identified 24, single-copy, ubiquitous genes suitable for this phylogenetic analysis. We used two approaches to combine the data for the 24 genes. First, we concatenated alignments of all genes into a single alignment from which a Maximum Likelihood (ML) tree was inferred using RAxML. Second, we used a relatively new approach to combining gene data, Bayesian Concordance Analysis (BCA), as implemented in the BUCKy software, in which the results of 24 single-gene phylogenetic analyses are used to generate a "primary concordance" tree. A comparison of the concatenated ML tree and the primary concordance (BUCKy) tree reveals that the two approaches give similar results, relative to a phylogenetic tree inferred from the 16S rRNA gene. After comparing the results and the methods used, we conclude that the current best approach for generating a single phylogenetic tree, suitable for use as a reference phylogeny for comparative analyses, is to perform a maximum likelihood analysis of a concatenated alignment of conserved, single-copy genes. © 2013

Detecting Consensus Emergence in Organizational Multilevel Data: Power Simulations

This is the author accepted manuscript. The final version is available from SAGE Publications via the DOI in this recordTheories suggest that groups within organizations often develop shared values, beliefs, affect, behaviors or agreed-upon routines; however, researchers rarely study predictors of consensus emergence over time. Recently, a multilevel-methods approach for detecting and studying emergence in organizational field data has been described. This approach—the consensus emergence model—builds on an extended three-level multilevel model. Researchers planning future studies based on the consensus emergence model need to consider (a) sample size characteristics required to detect emergence effects with satisfactory statistical power, and (b) how the distribution of the overall sample size across the levels of the multilevel model influences power. We systematically address both issues by conducting a power simulation for detecting main and moderating effects involving consensus emergence under a variety of typical research scenarios, and provide an R-based tool that readers can use to estimate power. Our discussion focuses on the future use and development of multilevel methods for studying emergence in organizational research

Draft genome sequence of Kocuria sp. strain UCD-OTCP (phylum Actinobacteria)

© 2013 Coil et al. Here, we present the draft genome of Kocuria sp. strain UCD-OTCP, a member of the phylum Actinobacteria, isolated from a restaurant chair cushion. The assembly contains 3,791,485 bp (G+C content of 73%) and is contained in 68 scaffolds

Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge

© 2017 Ettinger et al. Background. Zostera marina (also known as eelgrass) is a foundation species in coastal and marine ecosystems worldwide and is a model for studies of seagrasses (a paraphyletic group in the order Alismatales) that include all the known fully submerged marine angiosperms. In recent years, there has been a growing appreciation of the potential importance of the microbial communities (i.e., microbiomes) associated with various plant species. Here we report a study of variation in Z. marina microbiomes from a field site in Bodega Bay, CA. Methods. We characterized and then compared the microbial communities of root, leaf and sediment samples (using 16S ribosomal RNA gene PCR and sequencing) and associated environmental parameters from the inside, edge and outside of a single subtidal Z. marina patch. Multiple comparative approaches were used to examine associations between microbiome features (e.g., diversity, taxonomic composition) and environmental parameters and to compare sample types and sites. Results. Microbial communities differed significantly between sample types (root, leaf and sediment) and in sediments from different sites (inside, edge, outside). Carbon:Nitrogen ratio and eelgrass density were both significantly correlated to sediment community composition. Enrichment of certain taxonomic groups in each sample type was detected and analyzed in regard to possible functional implications (especially regarding sulfur metabolism). Discussion. Our results are mostly consistent with prior work on seagrass associated microbiomes with a few differences and additional findings. From a functional point of view, the most significant finding is that many of the taxa that differ significantly between sample types and sites are closely related to ones commonly associated with various aspects of sulfur and nitrogen metabolism. Though not a traditional model organism, we believe that Z. marina can become a model for studies of marine plantmicrobiome interactions

Draft genome sequence of an actinobacterium, Brachybacterium muris strain UCD-AY4

© 2013 Lo et al. Here we present the draft genome of an actinobacterium, Brachybacterium muris UCD-AY4. The assembly contains 3,257,338 bp and has a GC content of 70%. This strain was isolated from a residential bath towel and has a 16S rRNA gene 99.7% identical to that of the original B. muris strain, C3H-21

Draft genome sequence of Microbacterium sp. strain UCD-TDU (phylum Actinobacteria)

© 2013 Bendiks et al. Here, we present the draft genome sequence of Microbacterium sp. strain UCD-TDU, a member of the phylum Actinobacteria. The assembly contains 3,746,321 bp (in 8 scaffolds). This strain was isolated from a residential toilet as part of an undergraduate student research project to sequence reference genomes of microbes from the built environment

Draft genome sequence of Dietzia sp. strain UCD-THP (phylum Actinobacteria)

© 2013 Diep et al. Here, we present the draft genome sequence of an actinobacterium, Dietzia sp. strain UCD-THP, isolated from a residential toilet handle. The assembly contains 3,915,613 bp. The genome sequences of only two other Dietzia species have been published, those of Dietzia alimentaria and Dietzia cinnamea

Draft genome sequence of Curtobacterium flaccumfaciens strain UCD-AKU (phylum Actinobacteria)

© 2013 Flanagan et al. Here we present the draft genome of an actinobacterium, Curtobacterium flaccumfaciens strain UCD-AKU, isolated from a residential carpet. The genome assembly contains 3,692,614 bp in 130 contigs. This is the first member of the Curtobacterium genus to be sequenced

Case-finding in clinical practice: An appropriate strategy for dementia identification?

This is the final version. Available from Elsevier via the DOI in this record.Earlier diagnosis of dementia is increasingly being recognized as a public health priority. As screening is not generally recommended, case-finding in clinical practice is encouraged as an alternative dementia identification strategy. The approaches of screening and case-finding are often confused, with uncertainty about what case-finding should involve and under what circumstances it is appropriate. We propose a formal definition of dementia case-finding with a clear distinction from screening. We critically examine case-finding policy and practice and propose evidence requirements for implementation in clinical practice. Finally, we present a case-finding pathway and discuss the available evidence for best practice at each stage, with recommendations for research and practice. In conclusion, dementia case-finding is a promising strategy but currently not appropriate due to the substantial gaps in the evidence base for several components of this approach.This work was supported by the Halpin Trust (J.M.R., D.J.L., and E.K.), Mary Kinross Charitable Trust (D.J.L. and E.K.), and National Institute for Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care (CLAHRC) for the South West Peninsula (D.J.L. and I.L.)

Swabs to genomes: A comprehensive workflow

© 2015 Dunitz et al. The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to performit