|
11 Phages host range against 32 Phytopathogen Pseudomonas syringae pathovar phaseolicola and pathovar actinidiae
|
The experiment was realized by Gabriele Martino and Marina Ciuffo (gabriele.martino@ipsp.cnr.it, marina.ciuffo@ipsp.cnr.it).Bacteriophages were originally isolated using Pseudomonas syringae pv. actinidiae (Psa)
strain K7#8 and Pseudomonas syringae pv. phaseolicola (Pph)
strain Cuneo
#6_18, isolated from symptomatic plants. The host range of each selected phage was tested through an efficiency of plating
(EOP) analysis. Serially diluted phage lysates were applied (5 ul drops) to soft agar
containing one of the bacteria strains of our collection (4 mL of melted 0.6% LBLS soft-agar
and 250 ul of an overnight culture of Psa or Pph). For each bacteria phage combination
three different dilutions were spotted from the same phage crude lysate.
The plates were incubated at 26 °C for 24 h and then the plaques were counted to
obtain phage titration. For each phage, all the titration values were compared quantitatively
to the titration value of the same phage infecting the strain used for its isolation. |
MARTINO Gabriele |
2022‑01‑13 |
|
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 Host range data comes from past publications and unpublished results.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 |
|
Clostridium difficile phages
|
The experiments were realized by Ognjen Sekulovic, Julian R. Garneau, and Audrey Néron in Pr. Louis-Charles Fortier’s lab.
5 uL volumes of undiluted and 1/100 diluted phage lysates (10e7 to 10e9 PFU/mL) were deposited on top of soft agar overlays containing log-phase cultures of C. difficile test strains. The selected strain panel comprised major PCR ribotypes like 001, 014, 027, and 078, as well as other ribotypes from various origins (humans, animals, environment). The intensities of the clearing zones were recorded.
Results were published in :
Characterization of Temperate Phages Infecting Clostridium difficile Isolates of Human and Animal Origins, Ognjen Sekulovic, Julian R. Garneau, Audrey Néron, Louis-Charles Fortier, Applied and Environmental Microbiology, 2014. (PMID: 24532062) (DOI: 10.1128/AEM.00237-14) |
GARNEAU Julian |
2021‑03‑17 |
|
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 |
2021‑03‑17 |
|
Host range of phages isolated from a smear-ripened cheese
|
The spot assay experiment was realised by T. Paillet in the SayFood lab. 5μL of a phage solution were spotted on a lawn of bacteria. The results were assessed visually by the presence of plaques. The phages and hosts tested were isolated by T. Paillet from a smear-ripened cheese. Those results were published in Viruses, 2022. |
PAILLET Thomas |
2023‑03‑29 |
|
Hyperthermophilic archaeal viruses
|
The data is taken from several publications, including PMID: 22936928, 26884161, 10430569, 24433295, 22834906, 14592760. |
KRUPOVIC Mart |
2020‑04‑20 |
|
Klebsiella phage KLPN1
|
Experimental work was carried out by Lesley Hoyles. All methods and experiments associated with isolation and characterization of Klebsiella phage KLPN1 are reported in https://peerj.com/articles/1061/. It should be noted that phage KLPN1 infects only K. pneumoniae L4-FAA5 – it exhibits depolymerase activity on other K2 K. pneumoniae strains. |
HOYLES Lesley |
2021‑02‑17 |
|
S. epidermidis phages against human mastitis and healthy strains
|
Method: 5 µL of concentrated phage lysate (10^9 PFU/mL) was dropped onto a TSB plate overlaid with S. epidermidis (10^8 CFU/mL). The host range was confirmed by theplaque assay: 0.1 mL of stationary-phase host culture (10^8 CFU/mL) was mixed with several dilutions of individual phage suspensions in 3 ml of molten TSB top agar and the mixture was poured on TSA plates. Efficiency of plaque formation (EOP) of selected phages was determined by dividing the phage titer on the test strain by the phage titer on the reference strain S. epidermidis F12. This strain was selected because it is infected by all the isolated phages. Look at Table 1 of article for EOP values.
The strains are Staphylococcus epidermidis strains, which are either coming from human mastitis samples or healthy women (see Table 1 of article).
The bacteriophages were isolated by mytomycin C induction of S. epidermidis strains.
The intermediate value was used to represent "inhibition halo" phenotype. |
GARCÍA Pilar |
2021‑05‑25 |
|
Staphyloccocus phages phiIPLA-RODI and phiIPLA-C1C against staphylococcal isolates
|
Method: Bacteriophage host ranges were determined using phiIPLARODI (10^9 PFU/mL) and phiIPLA-C1C (10^9 PFU/mL) in the drop test, and titrations of the phages were further carried out with all sensitive strains to differentiate between infection and lysis due to bacteriocins. The efficiency of plaque formation (EOP) was determined by dividing the phage titer on the test strain by the phage titer on the reference strain (S. aureus IPLA1 for phage phiIPLA-RODI and S. epidermidis F12 for phage phiIPLA-C1C). See Table 1 of the article for EOP values.
The strains are diverse Staphyloccocal strains and one Macrococcus caseolyticus strain, see Table 1 of the article for more information.
Bacteriophages phiIPLA-RODI and phiIPLA-C1C were previously isolated (see dx.doi.org/10.1007/s00284-010-9659-5). |
GARCÍA Pilar |
2021‑05‑25 |
|
Streptomyces phages
|
This host-range assay was performed by Aël Hardy, a PhD student in the laboratory of Julia Frunzke (Forschungszentrum Jülich, j.frunzke@fz-juelich.de).
The method used was spotting assay, with serial dilutions of the phage solutions being spotted on a bacterial lawn propagated by mixing 200 µl of Streptomyces overnight culture with 4 ml top agar. Liquid cultures of Streptomyces was performed in Glucose Yeast Medium (GYM) medium - to which glass beads were added to favor dispersed growth - for all species except S. coelicolor which was grown in Yeast Extract Malt Extract (YEME) medium to ensure dispersion. For double agar overlays, GYM agar was used for all species, with 0.5% and 1.5% agar for the top and bottom layers, respectively. Temperature of cultivation was 30°C.
The viruses used in the study were all isolated from forest soil surrounding the Forschungszentrum Jülich. The outcome of the spot assays is reported as follows: plaque formation (2), clearance of the bacterial lawn without visible plaques (1), no plaque or lysis visible (0). |
HARDY Aël |
2023‑08‑01 |
|
Tests of AL505_P1, AL505_P2, AL505_P3 phages 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 |
2021‑01‑21 |
|
Tests of Citrobacter 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 |
2021‑01‑25 |
|
Tests of CLB_P1, CLB_P2, CLB_P3 E. coli phages 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 |
2023‑10‑10 |
|
Tests of E. coli Mt1B1 phages 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 |
2021‑05‑17 |
|
Tests of E. coli phages from D'Hérelle collection on 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 |
2021‑01‑21 |
|
Tests of LF82_P2, LF82_P6, LF82_P8 phages 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 |
2021‑01‑21 |
|
Tests of P. aeruginosa phages 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 |
2021‑01‑25 |
|
Tests of T4 subgroups of E. coli phages on 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 |
2021‑01‑21 |
|
Tests of the E. coli LF82_P10 phage 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 |
2021‑01‑25 |
|
vB_SauM-fRuSau02 against Staphyloccocus strains
|
The phage host range was analyzed by either a spot assay or by a liquid culture method. The full method is published in Leskinen et al., Viruses 2017, 9, 258; doi:10.3390/v9090258. |
KILJUNEN Saija |
2022‑01‑12 |