The fasta files (Genome_Set01.zip) contain the reference-assisted de novo assemblies (as contigs) of seven Legionella pneumophila subps. pneumophila isolates. The table contains rows as isolates (yellow) and columns as attributes (green) for each individual genome. This dataset is associated with the following publication: Gomez-Alvarez, V., L. Boczek, D. King, A. Pemberton, S. Pfaller, M. Rodgers, J. Santodomingo, and R. Revetta. Draft Genome Sequences of Seven Legionella pneumophila Isolates from a Hot Water System of a Large Building. Microbiology Resource Announcements. American Society for Microbiology, Washington, DC, USA, 8(18): e00384-19, (2019).

The fasta files (Genome_Set01.zip) contain the reference-assisted de novo assemblies (as contigs) of three Escherichia coli isolates. The table contains rows as isolates (yellow) and columns as attributes (green) for each individual genome. This dataset is associated with the following publication: Gomez-Alvarez, V., and J. Hoelle-Schwalbach. Draft Genome Sequences of Antibiotic-Resistant Escherichia coli Isolates from U.S. Wastewater Treatment Plants. Microbiology Resource Announcements. American Society for Microbiology, Washington, DC, USA, 8(23): e00351-19, (2019).

The fasta files (Genome_Set01.zip) contain the reference-assisted de novo assemblies (as contigs) of four Campylobacter spp. isolates. The table contains rows as isolates (yellow) and columns as attributes (green) for each individual genome. This dataset is associated with the following publication: Gomez-Alvarez, V., N. Ashbolt, J. Griffith, J. Santo Domingo, and J. Lu. Whole-Genome Sequencing of Four Campylobacter strains Isolated from Gull Excreta collected from Hobie Beach (Oxnard, CA, USA). Microbiology Resource Announcements. American Society for Microbiology, Washington, DC, USA, 8(32): e00560-19, (2019).

This dataset contains the molecular occurrence and concentration of Legionella pneumophila, M. avium, M. intracellulare and M. abscessus by structure type. Portions of this dataset are inaccessible because: This data set will have a second paper that is not written yet. Please hold off publishing the data set until the second paper is published. They can be accessed through the following means: This data will be accessible via Science Hub at a later date. Format: Molecular Data. This dataset is associated with the following publication: Donohue, M., J. Mistry, N. Tucker, and S. Vesper. Hot Water in Residences and Office Buildings Have Distinctive Legionella pneumophila Contamination Risk. . (ed.), INTERNATIONAL JOURNAL OF HYGIENE AND ENVIRONMENTAL HEALTH. Elsevier B.V., Amsterdam, NETHERLANDS, 245: 114023, (2022).

These are raw data/image files from the Malvern Zetasizer Instrument. This dataset is associated with the following publication: Buse, H., J. Hoelle, C. Muhlen, and D. Lytle. Electrophoretic mobility of Legionella pneumophila serogroups 1 to 14. FEMS MICROBIOLOGY LETTERS. Elsevier Science Ltd, New York, NY, USA, 1, (2018).

PS_GenBank.fasta file contain the sequences of the bacterial 16S rRNA-encoding gene for each representative sequence. The sequence containing four hypervariable regions was amplified using the primer set Eub-8f and 787. PS_GenBank.xlsx file contains rows as sample and columns as entries representing the accession number (NCBI) deposited in GenBank for each representative sequence (i.e. unique sequences). PS_OTU.fasta file contain the sequences of the bacterial 16S rRNA-encoding gene for each Operational Taxonomic Unit (OTU). The sequence containing four hypervariable regions was amplified using the primer set Eub-8f and 787. This dataset is associated with the following publication: Revetta , R., V. Gomez-Alvarez, T. Gerke, J. Santodomingo , and N. Ashbolt. CHANGES IN BACTERIAL COMPOSITION OF BIOFILM IN A METROPOLITAN DRINKING WATER DISTRIBUTION SYSTEM. JOURNAL OF APPLIED MICROBIOLOGY. Blackwell Publishing, Malden, MA, USA, 121(1): 294-305, (2016).

The raw sequence reads have been submitted to the NCBI Sequence Read Archive (SRA) under the BioProject PRJNA961987 with the following BioSample numbers: SAMN39596420, SAMN39596421, SAMN39596422, SAMN39596423, SAMN39596424, SAMN39596425, SAMN39596426, SAMN39596427, SAMN39596428, SAMN39596429, SAMN39596430, SAMN39596431, SAMN39596432, SAMN39596433, SAMN39596434, SAMN39596435, SAMN39596436, SAMN39596437, and SAMN39596438. A table (Table_diversity_indices.xlsx) contains rows as samples with ID, columns as distance from top to bottom (cm), sample volume (L), flushed volume (L), diversity indices (Chao and Shannon), and water temperature (°C) for each Set of samples. A table (Table_Legiolert.xlsx) contains rows as samples with ID, columns as distance from top to bottom (cm), sample volume (L), flushed volume (L), abundance of cultured Legionella pneumophila (MPN/100mL), and water temperature (°C) for each Set of samples. A table (Table_qPCR_L_pneumophila.xlsx) contains rows as samples with ID, columns as distance from top to bottom (cm), sample volume (L), flushed volume (L), copy number of L. pneumophila (GCN/100mL), and water temperature (°C) for each Set of samples. A table (Table_qPCR_Legionella.xlsx) contains rows as samples with ID, columns as distance from top to bottom (cm), sample volume (L), flushed volume (L), copy number of Legionella spp. (GCN/100mL), and water temperature (°C) for each Set of samples. A table (Table_qPCR_Mycobacterium.xlsx) contains rows as samples with ID, columns as distance from top to bottom (cm), sample volume (L), flushed volume (L), copy number of Mycobacterium spp. (GCN/100mL), and water temperature (°C) for each Set of samples. A table (Table_qPCR_V_vermiformis.xlsx) contains rows as samples with ID, columns as distance from top to bottom (cm), sample volume (L), flushed volume (L), copy number of V. vermiformis (GCN/100mL), and water temperature (°C) for each Set of samples. An abundance matrix (Table_taxonomy.xlsx) contains rows as taxonomic lineage, columns as samples, and entries representing the abundance of each lineage as a number of reads obtained for each Set of samples. A table (Table_water_temperature.xlsx) contains rows as water samples with ID, columns as temperature (°C and °F) measured from the top, bottom and drain of the water tank for each Set of samples. This dataset is associated with the following publication: Gomez-Alvarez, V., H. Ryu, M. McNeely, C. Muhlen, D. Williams, D. Lytle, and L. Boczek. Vertical Stratification of the Water Microbiome in an Electric Water Heater Tank: implications for premise plumbing opportunistic pathogens. JOURNAL OF WATER AND HEALTH. IWA Publishing, London, UK, 22(12): 2346–2357, (2024).

Background Ribosomal 16S DNA sequences are an essential tool for identifying and classifying microbes. High-throughput DNA sequencing now makes it economically possible to produce very large datasets of 16S rDNA sequences in short time periods, necessitating new computer tools for analyses. Here we describe FastGroup, a Java program designed to dereplicate libraries of 16S rDNA sequences. By dereplication we mean to: 1) compare all the sequences in a data set to each other, 2) group similar sequences together, and 3) output a representative sequence from each group. In this way, duplicate sequences are removed from a library. Results FastGroup was tested using a library of single-pass, bacterial 16S rDNA sequences cloned from coral-associated bacteria. We found that the optimal strategy for dereplicating these sequences was to: 1) trim ambiguous bases from the 5' end of the sequences and all sequence 3' of the conserved Bact517 site, 2) match the sequences from the 3' end, and 3) group sequences >=97% identical to each other. Conclusions The FastGroup program simplifies the dereplication of 16S rDNA sequence libraries and prepares the raw sequences for subsequent analyses.

Pictures of live/dead Legionella pneumophila under confocal microscope before and after treatment. This dataset is associated with the following publication: Oh, Y., R. Noga, V. Shanov, H. Ryu, H. Chandra, B. Yadav, J. Yadav, and S. Chae. Simultaneous Separation and Inactivation of Legionella pneumophila using Electrically Heatable Carbon Nanotube Sheet Composite Membranes. Chemical Engineering Journal. Elsevier BV, AMSTERDAM, NETHERLANDS, 366: 21-26, (2019).

The fasta file (BM_OTU.fasta) contain the sequences of the bacterial 16S rRNA-encoding V4 region gene (≈250 nt) for each Operational Taxonomic Unit (OTU). This dataset is associated with the following publication: Gomez-Alvarez, V., and R. Revetta. Monitoring of Nitrification in Chloraminated Drinking Water Distribution Systems With Microbiome Bioindicators Using Supervised Machine Learning. Frontiers in Microbiology. Frontiers, Lausanne, SWITZERLAND, 11: 2254-2267, (2020).