Data sources

Data source Description Owner/provider Last edition
AL505_P1, AL505_P2, AL505_P3 test on the ECOR collection Host range tests performed by Matthieu Galtier, PhD in Debarbieux lab. Technique: spotting phages on bacterial overlay (in exponential phase) on LB plates. AL505_ phages were isolated from sewage using Escherichia coli strain AL505 (clinical strain from an UTI collection described in Archambaud et al. (1988) Ann Inst Pasteur Microbiol 139: 557–573. The ECOR collection is a set of 72 strains representative of the genetic diversity of the Escherichia coli genus. This work was published in Environnemental Microbiology, 2016, Galtier. DEBARBIEUX Laurent     2020‑11‑11
Chloroviruses This data represents the host ranges for Chloroviruses in the collection of the James L. Van Etten lab at the University of Nebraska-Lincoln. The primary method of determining host range has been done by presence or absence of plaque formation via a plaque assay. Another method of determining host-virus interaction involves DNA staining to visualize infection initiation as described in Quispe et al, Virology, 2017. Furthermore, a liquid culture assay using high MOI (20) and low MOI (0.01) has been used to assess the cell-killing ability of the OSy-NE-5 virus on non-permissive host cells; the OSy-NE-5 virus initiates an unsuccessful infection on two Chlorella variabilis strains that kills the cells. The interactions are: 0 = no plaque formation, 1 = infection initiation/cell death, but no plaque formation, 2 = plaque formation. Chlorovirus isolates have been collected from fresh water sources globally. Many Chloroviruses have not had their host range tested. Host range data comes from past publications and unpublished results. Van Etten JL, Lane LC, Meints RH (1991). Viruses and viruslike particles of eukaryotic algae. Microbiol. Rev. 55: 586-620. Jeanniard A., Dunigan D.D., Gurnon J.R., et al. Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses. BMC Genomics 14, 158 (2013). Quispe CF, Esmael A, Sonderman O, McQuinn M, et al. Characterization of a new chlorovirus type with permissive and non-permissive features on phylogenetically related algal strains. Virology 2017, 500, 103–113. Quispe, Cristian F. "Expansion of the Chlorovirus Genus by Studies on Virus Natural History and Chlorella Host Metabolism" PhD diss., University of Nebraska-Lincoln, 2015 (http://digitalcommons.unl.edu/bioscidiss/78). Dunigan DD, Al-Sammak M, Al-Ameeli Z, Agarkova IV, DeLong JP, Van Etten JL. 2019. Chloroviruses lure hosts through long-distance chemical signaling. J Virol 93:e01688-18. Fitzgerald LA, Graves MV, Li X, Feldblyum T, Nierman WC, Van Etten JL. Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect Chlorella NC64A. Virology 2007, 358, 472-484. Fitzgerald LA, Graves MV, Li X, Feldblyum T, Hartigan J, Van Etten JL. Sequence and annotation of the 314-kb MT325 and the 321-kb FR483 viruses that infect Chlorella Pbi. Virology 2007, 358, 459-471. CARLSON Roger     2020‑07‑22
CLB_P1, CLB_P2, CLB_P3 test on the ECOR collection Host range tests performed by Damien Maura, PhD in Debarbieux lab. Technique: spotting phages on bacterial overlay (in exponential phase) on LB plates. CLB_ phages were isolated from sewage using Escherichia coli strain 55989 (serotype O104:H4) (NC_011748). The ECOR collection is a set of 73 strains representative of the genetic diversity of the Escherichia coli genus. This work was published in Environnemental Microbiology, 2012, Maura. DEBARBIEUX Laurent     2020‑04‑24
CrRp phages against E. coli and other strains Host range tests performed in Debarbieux lab. Technique: spotting phages on bacterial overlay (in exponential phase) on LB plates. CrRp_ phages were isolated from sewage (from Paris) using Citrobacter rodentium ICC180 (derived from DBS100, described in doi:10.1111/j.1462-5822.2004.00414.x). The newly isolated CrRp phages were tested against a panel of 27 E. coli strains and few other Gram negative bacteria belonging to Erwinia, Serratia and Rouxiella species. This work was published in Viruses, 2020, Mizuno. DEBARBIEUX Laurent     2020‑11‑14
E. coli phages from D'Hérelle collection against E. coli isolates from infant fecal samples Host range tests performed by Aurélie Mathieu, in Marie-Agnès Petit's lab. Technique : 1 mL of overnight culture was washed over the surface of a squared plate of dried LB supplemented with 5 mM CaCl2, 10 mM MgSO4 and 0.2% maltose. 5 μl of filtered supernatants containing coliphages or purified coliphage stocks were applied on plates inoculated with the strain of interest. Plates were incubated overnight at 37 °C. The interactions were classified as either positive (with clear or turbid lysis plaques or confluent lysis spots) or negative (no lysis spots and no lysis plaques). The coliphages are all coming from the D'Hérelle collection. The E. coli strains were isolated from infant fecal samples. Those results were published in Nature Communications, 2020, Mathieu. PETIT Marie-Agnès     2020‑03‑25
E. coli phages T4 subgroups against EPEC and ETEC strains This experiment was realized by checking for lysis in test tubes. The phages are T4 phages representing four of the five known subgroups of T4 coliphages whose genomes were all sequenced. The strains are Escherichia coli strains, for which some are Enteropathogenic Escherichia coli (EPEC) and others Enterotoxigenic Escherichia coli (ETEC). E. coli K12 was used as a reference. These strains were collected at the Division of Enteric Pathogens of the Central Public Health Laboratory, Enteric division, Colindale, London/UK during the 1970s (kindly provided by B. Rowe) associated with infant diarrhea. This work was published in Virology, 2009, Denou. LAMY-BESNIER Quentin     2020‑09‑17
E. coli strain Mt1B1 phages test on the ECOR collection and other strains Host range tests performed by Marta Lourenço, PhD in Debarbieux lab. Technique: spotting phages on bacterial overlay (in exponential phase) on LB plates. Mt1B1_ phages were isolated from sewage using Escherichia coli strain Mt1B1. 17 phages were tested on 90 strains including the ECOR collection. The ECOR collection is a set of 72 strains representative of the genetic diversity of the Escherichia coli genus. This work is available on BioRxiv (bioRxiv 810705; doi: https://doi.org/10.1101/810705). DEBARBIEUX Laurent     2020‑11‑11
Félix D'Hérelle collection of bacterial viruses This data corresponds to the entire Félix d'Hérelle Reference Center for bacterial viruses of the Université Laval (https://www.phage.ulaval.ca/en/home/). Each virus/host pair of the collection has been entered in this data source with a "Infection" response. For viruses, their "HER" identifier is added and a direct link to the corresponding page on the d'Hérelle collection website is available by clicking on this identifier. LAMY-BESNIER Quentin     2020‑09‑15
Host range of 3 phapecoctavirus on avian pathogenic Escherichia coli strains (APEC) of various serogroup The experiment was realized by Catherine Schouler in the team "pathogenesis of avian colibacillosis" of UMR1282 Infectiology and Public Health (catherine.schouler@inrae.fr). It was a spotting method, on which 10 µL of undiluted lysate was spotted on a lawn of bacteria grown to mid-exponantial phase (LB medium Miller formula). The results were assessed visually by the presence of a lysis zone. If this one was clear, result was scored 2, absence of lysis zone was scored 0, a more or less clear zone was scored 1. Phages vB_EcoM_ ESCO37 and vB_EcoM_ ESCO5 were isolated by us from chicken ceacal content on Escherichia coli strains. Phage vB_EcoM_ ESCO37-5 resulted from a recombination between genome of phages vB_EcoM_ ESCO37 and vB_EcoM_ ESCO5. Those three phages were tested on a collection of avian pathogenic E. coli strains of various serogroup. SCHOULER Catherine     2020‑03‑12
Hyperthermophilic archaeal viruses The data is taken from several publications, including PMID: 22936928, 26884161, 10430569, 24433295, 22834906, 14592760. KRUPOVIC Mart     2020‑04‑20
LF82_P10 test on AIEC strains and Enterobacteria Host range tests performed by Luisa De Sordi, Post-doc in Debarbieux lab. Technique: spotting phages on bacterial overlay (in exponential phase) on LB plates. Phage LF82_P10 was isolated from sewage using Escherichia coli strain LF82 (clinical strain associated to Crohn's disease). The bacterial strains tested include E. coli strains from both AIEC and lab collections as well as Citrobacter rodentium, Erwinia carotovora, Rouxiella chamberiensis and Serratia marcescens. This work was published in Cell Host & Microbe, 2017, De Sordi. DEBARBIEUX Laurent     2020‑11‑11
LF82_P2, LF82_P6, LF82_P8 test on the ECOR collection Host range tests performed by Matthieu Galtier, PhD in Debarbieux lab. Technique: spotting phages on bacterial overlay (in exponential phase) on LB plates. LF82_P phages were isolated from sewage using Escherichia coli strain LF82 (clinical strain associated to Crohn's disease). The ECOR collection is a set of 72 strains representative of the genetic diversity of the Escherichia coli genus. This work was published in Journal of Crohn's and Colitis, 2017, Galtier. DEBARBIEUX Laurent     2020‑04‑24
P. aeruginosa phages test on cystic fibrosis isolates and lab strains Host range tests performed by Emilie Saussereau, PhD in Debarbieux lab. Technique: double-spot on LB plates (see publication). 10 Pseudomonas aeruginosa phages were tested on a collection of P. aeruginosa isolates from the sputum of cystic fibrosis patients (20 isolates per patients) This work was published in Clinical Microbiology and Infection, 2014, Saussereau DEBARBIEUX Laurent     2020‑04‑24
Data source Description Owner/provider Last edition