Person:
Konstantinidis,
Kostas T.
Konstantinidis,
Kostas T.
Permanent Link
Associated Organization(s)
Organizational Unit
ORCID
ArchiveSpace Name Record
Publication Search Results
Now showing
1 - 10 of 15
-
ItemMetagenomic evaluation of the performance of passive Moore swabs for sewage monitoring relative to composite sampling over time resolved deployments(Georgia Institute of Technology, 2024-01) Cha, Gyuhyon ; Zhu, Kevin J. ; Fisher, Jamie M. ; Flores, Camryn I. ; Brown, Joe ; Pinto, Ameet ; Hatt, Janet K. ; Konstantinos, Kostas T. ; Graham, Katherine E.Moore swabs have re-emerged as a versatile tool in the field of wastewater-based epidemiology during the COVID-19 pandemic and offer unique advantages for monitoring pathogens in sewer systems, especially at the neighborhood-level. However, whether Moore swabs provide comparable results to more commonly used composite samples remains to be rigorously tested including the optimal duration of Moore swab deployment. This study provides new insights into these issues by comparing the results from Moore swab samples to those of paired composite samples collected from the same sewer lines continuously over six to seventy-two hours post-deployment, during low COVID-19 prevalence periods. Our results show that Moore swabs accumulated approximately 10-fold higher PMMoV concentrations (on a basis of mL of Moore swab squeezed filtrate to mL of composite sewage) and showed comparable trends in terms of bacterial species abundance when compared to composite samples. Moore swabs also generally captured higher SARS-CoV-2 N1/N2 RNA concentrations than composite samples. Moore swabs showed comparable trends in terms of abundance dynamics of the sewage microbiome to composite samples and variable signs of saturation over time that were site and/or microbial population-specific. Based on our dual ddRT-PCR and shotgun metagenomic approach, we find that Moore swabs at our sites were optimally deployed for 6 hours at a time at two sites.
-
ItemLow Richness -- Set 1(Georgia Institute of Technology, 2014-02-03) Konstantinidis, Kostas T. ; Rodriguez, Luis M.Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.
-
ItemAll Complete Bacterial and Archeal Genomes -- Set 6(Georgia Institute of Technology, 2014-02-03) Konstantinidis, Kostas T. ; Rodriguez, Luis M.Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.
-
ItemAll Complete Bacterial and Archeal Genomes -- Set 3(Georgia Institute of Technology, 2014-02-03) Konstantinidis, Kostas T. ; Rodriguez, Luis M.Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.
-
ItemEscherichia Genomes -- Set 2(Georgia Institute of Technology, 2014-02-03) Konstantinidis, Kostas T. ; Rodriguez, Luis M.Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.
-
ItemAll Complete Bacterial and Archeal Genomes -- Set 7(Georgia Institute of Technology, 2014-02-03) Konstantinidis, Kostas T. ; Rodriguez, Luis M.Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.
-
ItemLow Richness -- Set 2(Georgia Institute of Technology, 2014-02-03) Konstantinidis, Kostas T. ; Rodriguez, Luis M.Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.
-
ItemEscherichia Genomes -- Set 1(Georgia Institute of Technology, 2014-01-31) Konstantinidis, Kostas T. ; Rodriguez, Luis M.Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.
-
ItemEscherichia Genomes -- Set 6(Georgia Institute of Technology, 2014-01-31) Konstantinidis, Kostas T. ; Rodriguez, Luis M.Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.
-
ItemAll Complete Bacterial and Archeal Genomes -- Set 5(Georgia Institute of Technology, 2014-01-31) Konstantinidis, Kostas T. ; Rodriguez, Luis M.Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.