Lutgarde Raskin

Bio: Lutgarde Raskin is an academic researcher from University of Michigan. The author has contributed to research in topics: Bioreactor & Population. The author has an hindex of 58, co-authored 183 publications receiving 13224 citations. Previous affiliations of Lutgarde Raskin include University of Illinois at Urbana–Champaign.

Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens

Abstract: Eight oligonucleotides which are complementary to conserved tracts of 16S rRNA from phylogenetically defined groups of methanogens were designed and characterized for use as hybridization probes for studies in environmental and determinative microbiology. The target-group specificity and temperature of dissociation for each probe were characterized. In general, the probes were very specific for the target methanogens and did not hybridize to the rRNAs of nontarget methanogens. Together, the eight probes circumscribe methanogens now represented in pure culture (with the exception of members of the family Methanothermaceae). Three probes are order specific; two identify members of the order Methanobacteriales, and one is specific for the order Methanococcales. The fourth probe encompasses three families belonging to the order Methanomicrobiales, the third order within the current classification. The fifth probe is specific for the remaining family within this order (Methanosarcinaceae). Three additional probes encompass different genera within the Methanosarcinaceae.

The oligonucleotide probe database.

Abstract: The use of oligonucleotide hybridization probes and PCR primers has become widespread in microbial ecology and environmental microbiology (for reviews, see references 3, 5, 7, 17, and 21), and descriptions of probe applications are abundant in the literature. We have encountered, however, a number of difficulties when relying on the literature for information on probes and primers: (i) probe design, characterization, and application data are scattered throughout the literature and therefore are not easily available; (ii) probe nomenclature is not standardized, making it difficult to recognize a particular probe and evaluate results obtained with that probe; (iii) probes are often designed empirically and used without thorough experimental characterization, making it difficult to interpret experimental results; and (iv) information on the application of individual probes is often not published in detail in the original probe description since the value of some data becomes apparent only as a result of observations made subsequent to publication (e.g., hybridization buffer composition, formamide concentration, membrane supplier and lot number, target group specificity). We designed the Oligonucleotide Probe Database (OPD) to address these concerns. The OPD centralizes information related to the design and use of oligonucleotide probes and PCR primers. The database was originally designed in Microsoft Access Version 2.0 and then converted to Hypertext Transfer Markup Language with PERL scripts. The current data set contains 96 hybridization probes and PCR primers used in microbial ecology and environmental microbiology, published by the authors as well as from direct on-line submissions to OPD. The majority of the probes in the current data set target rRNA, but the database is designed to accommodate probes targeting other gene families. For each probe or primer, the information in the OPD includes design and characterization data important for probe and primer use, including a standardized name, probe sequence, nucleotide position within the target gene, optimal hybridization and wash conditions (or annealing conditions for PCR primers), intended target group, experimentally validated target group specificity, and original citations. Much of the experimental data available in the database were not included in the original publications describing the probes. Standardization of oligonucleotide probe nomenclature. A source of much confusion and frustration during the use of probes or PCR primers designed and characterized in different laboratories has been the absence of a standardized probe nomenclature. Stahl and Amann (18) have previously attempted to address this problem for phylogenetic probes with a nomenclature consisting of three to five letters representing phylogenetic specificity, followed by a number indicating the 59 position on the rRNA complementary to the 39 end of an antisense probe or PCR primer or identical to the 59 end of a sense primer. Limitations to this nomenclature system are apparent when several versions of a probe that have the same target specificity and nucleotide position exist. We modified the nomenclature originally utilized by Stahl and Amann to include multiple probe versions and also to provide additional identifying information. We suggest a method of standardizing the nomenclature for oligonucleotide probes and PCR primers that is both unambiguous and informative. The name for an oligonucleotide probe consists of seven components combined sequentially. These components are discussed below. An example demonstrating construction of probe nomenclature for a small-subunit rRNA-targeted probe is given in parentheses.

A new planning and design paradigm to achieve sustainable resource recovery from wastewater

Abstract: To employ technologies that sustainably harvest resources from wastewater (for example struvite granules shown here), new perceptions and infrastructure planning and design processes are required.

phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.

Abstract: Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

Abstract: 16S ribosomal RNA gene (rDNA) amplicon analysis remains the standard approach for the cultivation-independent investigation of microbial diversity. The accuracy of these analyses depends strongly on the choice of primers. The overall coverage and phylum spectrum of 175 primers and 512 primer pairs were evaluated in silico with respect to the SILVA 16S/18S rDNA non-redundant reference dataset (SSURef 108 NR). Based on this evaluation a selection of 'best available' primer pairs for Bacteria and Archaea for three amplicon size classes (100-400, 400-1000, ≥ 1000 bp) is provided. The most promising bacterial primer pair (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21), with an amplicon size of 464 bp, was experimentally evaluated by comparing the taxonomic distribution of the 16S rDNA amplicons with 16S rDNA fragments from directly sequenced metagenomes. The results of this study may be used as a guideline for selecting primer pairs with the best overall coverage and phylum spectrum for specific applications, therefore reducing the bias in PCR-based microbial diversity studies.

Host-Bacterial Mutualism in the Human Intestine

Abstract: The distal human intestine represents an anaerobic bioreactor programmed with an enormous population of bacteria, dominated by relatively few divisions that are highly diverse at the strain/subspecies level. This microbiota and its collective genomes (microbiome) provide us with genetic and metabolic attributes we have not been required to evolve on our own, including the ability to harvest otherwise inaccessible nutrients. New studies are revealing how the gut microbiota has coevolved with us and how it manipulates and complements our biology in ways that are mutually beneficial. We are also starting to understand how certain keystone members of the microbiota operate to maintain the stability and functional adaptability of this microbial organ.