title: One step forwards for the routine use of high-throughput DNA sequencing in environmental monitoring. An efficient and standardizable method to maximize the detection of environmental bacteria.
abstract: We propose an innovative, repeatable, and reliable experimental workflow to concentrate and detect environmental bacteria in drinking water using molecular techniques. We first concentrated bacteria in water samples using tangential flow filtration and then we evaluated two methods of environmental DNA extraction. We performed tests on both artificially contaminated water samples and real drinking water samples. The efficiency of the experimental workflow was measured through qPCR. The successful applicability of the high-throughput DNA sequencing (HTS) approach was demonstrated on drinking water samples. Our results demonstrate the feasibility of our approach in high-throughput-based studies, and we suggest incorporating it in monitoring strategies to have a better representation of the microbial community. In the recent years, HTS techniques have become key tools in the study of microbial communities. To make the leap from academic laboratories to the routine monitoring (e.g., water treatment plants laboratories), we here propose an experimental workflow suitable for the introduction of HTS as a standard method for detecting environmental bacteria.
authors: ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy.
authors: Antonia
authors: A
authors: Bruno
authors: ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy.
authors: Anna
authors: A
authors: Sandionigi
authors: ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy.
authors: Andrea
authors: A
authors: Galimberti
authors: ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy.
authors: Eleonora
authors: E
authors: Siani
authors: ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy.
authors: Massimo
authors: M
authors: Labra
authors: Medicine and Surgery Department, University of Milano-Bicocca, Monza, Italy.
authors: Clementina
authors: C
authors: Cocuzza
authors: FEM2-Ambiente, University of Milano-Bicocca, Milan, Italy.
authors: Emanuele
authors: E
authors: Ferri
authors: ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy.
authors: Maurizio
authors: M
authors: Casiraghi
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics; D060766:Drinking Water / Q000382:microbiology*; D004784:Environmental Monitoring / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D057188:Workflow
chemical_list: D004269:DNA, Bacterial; D060766:Drinking Water
keywords: 
  qPCR
  ; DNA extraction; complex matrix; environmental bacteria; high-throughput sequencing; next-generation sequencing; tangential flow concentration; water