DOI: 10.5061/dryad.tmpg4f596
title: A phylogenetic host-range index reveals ecological constraints in phage specialisation and virulence

description: Phages are typically known for having a limited host range, targeting
 particular strains within a bacterial species, but accurately measuring
 their specificity remains challenging. Factors like the genetic diversity
 or epidemiology of host bacteria are often disregarded, despite their
 potential influence on phage specialisation and virulence. This study
 focuses on the Ralstonia solanacearum species complex (RSSC), which
 comprises genetically diverse bacteria responsible for a major plant
 disease. It uses a diversified collection of RSSC phages to develop new
 host-range analysis methods and to test ecological and evolutionary
 hypotheses on phage host range. We introduce a new "phylogenetic
 host-range index" that employs an ecological diversity index to
 account for the genetic diversity of bacterial hosts, allowing systematic
 classification of phages along a continuum between specialists and
 generalists. We propose and provide evidence that the CRISPR-Cas immune
 system of bacteria more frequently targets generalist phages than
 specialist phages. We explore the hypothesis that generalist phages might
 exhibit lower virulence than specialist ones due to potential evolutionary
 trade-offs between host-range breadth and virulence. Importantly,
 contrasted correlations between phage virulence and host range depend on
 the epidemiological context. A trade-off was confirmed in a context of low
 bacterial diversity, but not in a context of higher bacterial diversity,
 where no apparent costs were detected for phages adapted to a wide range
 of hosts. This study highlights the need for genetic analyses in phage
 host range and for investigating ecological trade-offs that could improve
 both fundamental phage knowledge and applications in biocontrol or
 therapy.
description: # A phylogenetic host-range index reveals ecological constraints in phage
 specialisation and virulence Dataset DOI:
 [10.5061/dryad.tmpg4f596](10.5061/dryad.tmpg4f596) ## Description of the
 data and file structure Here, we aim to assess phage host range by
 integrating available phylogenetic data with phenotypic data and applying
 quantitative network analyses of phage-bacteria interactions. In all the
 scripts included, this version of R was used: Posit Team (2024). RStudio:
 IDE for R (Version 2024.04 “Chocolate Cosmos”). Posit Software, PBC.
 [https://posit.co/](https://posit.co/) ### Files and variables #### File:
 TreeRalstoReu **Description:** The phylogenetic distance between bacterial
 hosts was calculated by using the phylogenetic tree of the RSSC
 endoglucanase (*egl*) gene, as previously established to study RSSC
 diversity (Fegan & Prior, 2005). #### File: TreeRalstoMauri
 **Description:** The phylogenetic distance between bacterial hosts was
 calculated by using the phylogenetic tree of the RSSC endoglucanase
 (*egl*) gene, as previously established to study RSSC diversity (Fegan
 & Prior, 2005). #### File: Stats\_tests\_all\_phage\_variables.md
 **Description:** R scripts with basic stats codes to associate phage
 variables #### File: Phylogenetic\_signal\_of\_bacterial\_hosts.md
 **Description:** R scripts with to calculate phylogenetic signal of phage
 bacterial hosts #### File: PHRI\_and\_phage\_load\_correlation\_test.md
 **Description:** R scripts with to calculate Phylogenetic host range index
 (PHRI) of phages and stats test to correlate it with phage load #### File:
 Nested\_Matrix\_Structure\_test.md **Description:** R scripts with to test
 the nested structure of a phage-bacteria interaction matrix #### File:
 Contingency\_table\_analysis\_moduls.md **Description:** R scripts with to
 analyse the matrix moduls #### File:
 Becket\_test\_for\_modular\_structure\_of\_matrices.md **Description:** R
 scripts with to test the modular structure of a phage-bacteria interaction
 matrix #### File: Modular\_Matrix\_Structure\_test.md **Description:** R
 scripts with to test the modular structure of a phage-bacteria interaction
 matrix #### File: All\_phage\_variables.csv **Description:** Data on phage
 phenotypic and genotypic traits NA stands for "not applicable"
 data ##### Variables * island: island * ph_name: taxonomic name of clone *
 phsp: phage species * phgenera: phage genus * phmorph: morphology *
 phgensize: genome size * phGC: GC content * phprot: encoded protein number
 * phlifecyc: temperate or virulent * haplotype: bacterial host * inh:
 phage inhibitory capacity of bacterial growth * maxinh: phage maximum
 inhibitory capacity of bacterial growth * PHRI: Phylogenetic host range
 index * MODULE_July2024: module * mean_logpfu: average phage load *
 phylosignal: phylogenetic signal value of the bacterial hosts targeted by
 the phage * fitness: #### File: Phage\_virulence raw data Reunion.csv
 **Description:** Data on bacterial growth with and without phages for
 Reunion ##### Variables * plate: day block of the experiment * phname:
 phage name * phage: yes (presence); no (absence) * replicate (a, b or c) *
 haplotype (of bacteria) * od (OD 600 nm) ### File: Phage\_virulence raw
 data Mauritius.csv **Description:** Data on bacterial growth with and
 without phages for Mauritius ##### Variables * plate: day block of the
 experiment * phname: phage name * phage: yes (presence); no (absence) *
 replicate (a, b or c) * haplotype (of bacteria) * od (OD 600 nm) ####
 File: Phage\_virulence.csv **Description:** Data on phage inhibitory
 capacity of bacterial growth ##### Variables * phname: see above *
 phsp: see above * phgenera: see above * phfamily: see above * phgensize:
 see above * phGC: see above * phprot: see above * phlifecyc: see above *
 phage: see above * replicate: experimental replicate * sequevar: bacterial
 sequevar * average_od: cumulated OD values over 24h * positive_noph:
 bacterial strain with no phage average OD values * inhibition_value: phage
 inhibitory capacity of bacterial growth * island: see above #### File:
 OTUReu.csv **Description:** Data on average Reunion phage load per strain
 ##### Variables * : bacterial strain names * Simangalove: average phage
 LOG10 pfu/mL on each bacterial strain * Adzire: average phage LOG10 pfu/mL
 on each bacterial strain * Sarlave: average phage LOG10 pfu/mL on each
 bacterial strain * Elie: average phage LOG10 pfu/mL on each bacterial
 strain * Anchaing: average phage LOG10 pfu/mL on each bacterial strain *
 Albius: average phage LOG10 pfu/mL on each bacterial strain * Raharianne:
 average phage LOG10 pfu/mL on each bacterial strain * Cimandef: average
 phage LOG10 pfu/mL on each bacterial strain * Dimitile: average phage
 LOG10 pfu/mL on each bacterial strain * Heva: average phage LOG10 pfu/mL
 on each bacterial strain #### File: OTUMauri.csv **Description:** Data on
 average Mauritian phage load per strain ##### Variables * : bacterial
 strain names * Jenny: average phage LOG10 pfu/mL on each bacterial strain
 * Bakoly: average phage LOG10 pfu/mL on each bacterial strain * Dina:
 average phage LOG10 pfu/mL on each bacterial strain * Hennie: average
 phage LOG10 pfu/mL on each bacterial strain * Firinga: average phage LOG10
 pfu/mL on each bacterial strain * Hyacinthe: average phage LOG10 pfu/mL on
 each bacterial strain * Alix: average phage LOG10 pfu/mL on each bacterial
 strain * Claudette: average phage LOG10 pfu/mL on each bacterial strain *
 Darius: average phage LOG10 pfu/mL on each bacterial strain * Gervaise:
 average phage LOG10 pfu/mL on each bacterial strain * Eline: average phage
 LOG10 pfu/mL on each bacterial strain * Gamede: average phage LOG10 pfu/mL
 on each bacterial strain * Gerry: average phage LOG10 pfu/mL on each
 bacterial strain #### Files: Table\_S1\_Reunion.csv and
 Table\_S1\_Mauritius.csv **Description:** List of Ralstonia solanacearum
 strains used for assessing the host range of phages from Reunion islands.
 It includes phylogenetic assignment, year and location of isolation, along
 with the corresponding egl sequence used for sequevar classification. NA
 stands for "not applicable", ND stands for "not
 determined" ##### Variables * Species * Phylotype-sequevar * Code
 (strain name) * Haplotype * Origin (country) * Sequence EGL