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Daniel B. Oerther

Bio: Daniel B. Oerther is an academic researcher from Missouri University of Science and Technology. The author has contributed to research in topics: Activated sludge & Population. The author has an hindex of 23, co-authored 133 publications receiving 3011 citations. Previous affiliations of Daniel B. Oerther include University of Illinois at Urbana–Champaign & University of South Florida.


Papers
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Journal ArticleDOI
TL;DR: The Oligonucleotide Probe Database (OPD) is designed and modified to include multiple probe versions and also to provide additional identifying information, and a method of standardizing the nomenclature for oligon nucleotide probes and PCR primers that is both unambiguous and informative is suggested.
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.

608 citations

Journal ArticleDOI
TL;DR: The results from this metagenomic survey demonstrated the presence of genes associated with resistance to antibiotics and carbohydrate metabolism suggesting that the swine gut microbiome may be shaped by husbandry practices.
Abstract: Background Uncovering the taxonomic composition and functional capacity within the swine gut microbial consortia is of great importance to animal physiology and health as well as to food and water safety due to the presence of human pathogens in pig feces. Nonetheless, limited information on the functional diversity of the swine gut microbiome is available.

327 citations

Journal ArticleDOI
TL;DR: In this paper, the effect of tangential flow and crossflow on membrane fouling was analyzed by the resistance-in-series model where the reason for flux decline was subdivided into adsorption, concentration polarization, and reversible and irreversible fouling.

221 citations

Journal ArticleDOI
TL;DR: In this paper, the influence of cross-flow velocity on the formation of fouling layer during microfiltration and ultrafiltration of biological suspension with 5 g/l of mixed liquor suspended solids was studied.

187 citations

Journal ArticleDOI
TL;DR: Terminal restriction fragment length polymorphism analysis of 16S rRNA genes was used to investigate the reproducibility and stability in the bacterial community structure of laboratory-scale sequencing batch bioreactors and to assess the impact of solids retention time (SRT) on bacterial diversity.
Abstract: Terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes was used to investigate the reproducibility and stability in the bacterial community structure of laboratory-scale sequencing batch bioreactors (SBR) and to assess the impact of solids retention time (SRT) on bacterial diversity. Two experiments were performed. In each experiment two sets of replicate SBRs were operated for a periods of three times the SRT. One set was operated at an SRT of 2 days and another set was operated at an SRT of 8 days. Samples for T-RFLP analysis were collected from the two sets of replicate reactors. HhaI, MspI, and RsaI T-RFLP profiles were analyzed using cluster analysis and diversity statistics. Cluster analysis with Ward's method using Jaccard distance and Hellinger distance showed that the bacterial community structure in both sets of reactors from both experimental runs was dynamic and that replicate reactors were clustered together and evolved similarly from startup. Richness (S), evenness (E), the Shannon-Weaver index (H), and the reciprocal of Simpson's index (1/D) were calculated, and the values were compared between the two sets of reactors. Evenness values were higher for reactors operated at an SRT of 2 days. Statistically significant differences in diversity (H and D) between the two sets of reactors were tested using a randomization procedure, and the results showed that reactors from both experimental runs that were operated at an SRT of 2 days had higher diversity (H and D) at the 5% level. T-RFLP analysis with diversity indices proved to be a powerful tool to analyze changes in the bacterial community diversity in response to changes in the operational parameters of activated-sludge systems.

159 citations


Cited by
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Journal ArticleDOI
TL;DR: 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.
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.

5,346 citations

Journal ArticleDOI
TL;DR: In this paper, a review of more than 300 publications on membrane bioreactor fouling is presented, and the authors propose updated definitions of key parameters such as critical and sustainable flux, along with standard methods to determine and measure the different fractions of the biomass.

2,113 citations

Journal ArticleDOI
TL;DR: In this article, the technical applicability of various physico-chemical treatments for the removal of heavy metals such as Cd(II), Cr(III, Cr(VI), Cu(II, Ni(II) and Zn(II).

1,732 citations

Journal ArticleDOI
TL;DR: The fouling behaviour, fouling factors and fouling control strategies were discussed, and recent developments in membrane materials including low-cost filters, membrane modification and dynamic membranes were reviewed.

1,708 citations

Journal ArticleDOI
TL;DR: PCR primers 63f and 1387r were found to be more useful for 16S rRNA gene amplification in ecological and systematic studies than PCR amplimers that are currently more generally used.
Abstract: We report the design and evaluation of PCR primers 63f and 1387r for amplification of 16S rRNA genes from bacteria. Their specificity and efficacy were tested systematically with a variety of bacterial species and environmental samples. They were found to be more useful for 16S rRNA gene amplification in ecological and systematic studies than PCR amplimers that are currently more generally used.

1,582 citations