https://doi.org/10.5061/dryad.2rbnzs7xk

This study contains data from four different experiments (EXP1A & EXP1B (both part of testing the* Effect of environmental microbes and nutrients on oviposition*), EXP2 (Effect of antimicrobial preservatives alone on oviposition), EXP3 (Effect of commensal and pathogenic microbes on oviposition)). The data for each of the four experiments are presented across 9 .csv files. Data from each experiment are presented as DATA or CLUSTER.DATA. These data only differ in that CLUSTER.DATA contains information on each indivdual egg cluster in every vial, so is presented in a longer format to enable analysis and plotting. Some columns of data are presented in both the DATA and CLUSTER.DATA sheets - this is for ease of analysis so all relevant variables can always be found together regardless of the form of the datasheet. Repeated columns across data sheets within an experiment do not represent separately generated data.

The code used for analysis is available is presented in the R file MICROBE_MS_CODE_DRYAD.R

1) EXP1A.DATA.csv

• "VIAL.ID" Unique identifier for each vial in the experiment.
• "NUTRIENT" Two-level treatment variable referring to the amount of nutrients in the oviposition substrate: standard = standard SYA recipe; low = 25% of the sugar and yeast content of standard SYA).
• "PRESERVATIVES" Two-level treatment variable referring to the presence or absence of antimicrobial preservatives in the oviposition substrate media.
• "TOTAL.EGGS" Total number of eggs laid in a vial during the oviposition period. NA denotes unavailable data for that vial.
• "CLUSTERED.EGGS" Total number of eggs in a vial that were in any type of cluster (this is the sum of all cluster sizes in the vial). NA denotes unavailable data for that vial.
• "PROPORTION.CLUSTERED" The proportion of eggs in a vial that were clustered. Calculated as CLUSTERED.EGGS/TOTAL.EGGS. NA denotes unavailable data, or non-applicable cases where the number of eggs = 0.
• "HATCHED.EGGS" The number of eggs in a vial that had hatched after 48h. NA denotes unavailable data, or non-applicable cases where the number of eggs = 0.
• "EGG.HATCHABILITY" The proportion of eggs that had hatched after 48h, calculated as HATCHED.EGGS/TOTAL.EGGS. NA denotes unavailable data, or non-applicable cases where the number of eggs = 0.
• "PUPAE.COUNT" The number of pupae in a vial at 7 days after oviposition. NA denotes unavailable data, or non-applicable cases where the number of eggs = 0.
• "EGG.TO.PUPA.VIA" The proportion of eggs that had developed to pupae after 7 days, calculated as PUPAE.COUNT/TOTAL.EGGS. NA denotes unavailable data, or non-applicable cases where the number of eggs = 0.
• "OFFSPRING" The number of adult offspring that eclosed from a vial. NA denotes unavailable data.
• "HATCHED.EGG.TO ADULT.VIA" The proportion of hatched eggs that developed to the adult stage, calculated as OFFSPRING/HATCHED.EGGS. NA denotes unavailable data, or non-applicable cases where the number of hatched eggs = 0.
• "EGG.TO.ADULT.VIA" The proportion of eggs that developed to the adult stage, calculated as OFFSPRING/TOTAL.EGGS. NA denotes unavailable data, or non-applicable cases where the number of eggs = 0.

2) EXP1A.CLUSTER.DATA.csv

• "VIAL.ID" Unique identifier for each vial in the experiment.
• "NUTRIENT" Two-level treatment variable referring to the amount of nutrients in the oviposition substrate: standard = standard SYA recipe; low = 25% of the sugar and yeast content of standard SYA).
• "PRESERVATIVES" Two-level treatment variable referring to the presence or absence of antimicrobial preservatives in the oviposition substrate media.
• "TOTAL.EGGS" Total number of eggs laid in a vial during the oviposition period. NA denotes unavailable data for that vial.
• "CLUSTERED.EGGS" Total number of eggs in a vial that were in any type of cluster (this is the sum of all cluster sizes in the vial). NA denotes unavailable data for that vial.
• "N.CLUSTERS" Number of distinct egg clusters in a vial. NA denotes unavailable data for that vial. 
• "PROPORTION.CLUSTERED" The proportion of eggs in a vial that were clustered. Calculated as CLUSTERED.EGGS/TOTAL.EGGS. NA denotes unavailable data, or non-applicable cases where the number of eggs = 0.
• "CLUSTER.ID" Unique identifier for each distinct cluster within a vial.
• "CLUSTER.SIZE" Number of eggs within a cluster. NA denotes non-applicable cases for some cluster IDs when there were <10 clusters in the vial.

3) EXP1B.ICC.DATA.csv

• "FOCAL.EGG" Number of eggs in a vial that were scored as being laid by the focal female (i.e. the total number of non-dyed eggs in a vial).
• "FOCAL.OFFSPRING" Number of wild-type offspring eclosing from a vial.

4) EXP1B.FOCAL.DATA.csv

• "VIAL.ID" Unique identifier for each vial in the experiment.
• "PRESERVATIVE" Two-level treatment variable referring to the presence or absence of antimicrobial preservatives in the oviposition substrate media.
• "FOCAL.EGGS" Number of eggs in a vial that were scored as being laid by the focal female (i.e. the total number of non-dyed eggs in a vial).
• "UNCLUSTERED" Number of focal eggs in a vial that were unclustered. NA denotes non-applicable cases where focal eggs = 0.
• "MIXED" Number of focal eggs in a vial that were in clusters with at least one non-focal egg. NA denotes non-applicable cases where focal eggs = 0.
• "FOCAL ONLY" Number of focal eggs in a vial that were in focal-only clusters. NA denotes non-applicable cases where focal eggs = 0.
• "PROP.UNCLUSTERED" Proportion of focal eggs in a vial that were unclustered, calculated as UNCLUSTERED/FOCAL.EGGS. NA denotes non-applicable cases where focal eggs = 0.
• "PROP.MIXED" Proportion of focal eggs in a vial that were in mixed maternity clusters, calculated as MIXED/FOCAL.EGGS.
• NA denotes non-applicable cases where focal eggs = 0. "PROP.FOCAL.ONLY" Proportion of focal eggs in a vial that were in focal-only clusters, calculated as FOCAL.ONLY/FOCAL.EGGS.
• NA denotes non-applicable cases where focal eggs = 0. "NUMBER.FOCAL.ONLY.CLUSTERS" Number of clusters in a vial that consisted of focal eggs only. NA denotes non-applicable cases where focal eggs = 0, or clusters of any type where absent.
• "NUMBER.MIXED.CLUSTERS" Number of clusters in a vial that consisted of at least 1 focal and at least 1 non-focal egg.
• NA denotes non-applicable cases where focal eggs = 0, or clusters of any type where absent. "PROP.MIXED.CLUSTERS" Proportion of clusters in a vial that were mixed maternity, calculated as NUMBER.MIXED. CLUSTERS/(NUMBER.FOCAL.ONLY.CLUSTERS + NUMBER.MIXED.CLUSTERS). NA denotes non-applicable cases where focal eggs = 0, or clusters of any type where absent.

5) EXP1B.CLUSTER.DATA.csv

• "VIAL.ID" Unique identifier for each vial in the experiment.
• "PRESERVATIVES" Two-level treatment variable referring to the presence or absence of antimicrobial preservatives in the oviposition substrate media.
• "TOTAL.EGGS" Number of eggs in a vial of any maternity
• "FOCAL.EGGS" Number of eggs in a vial that were scored as being laid by the focal female (i.e. the total number of non-dyed eggs in a vial).
• "NUMBER.CLUSTERS" Number of distinct egg clusters in a vial.
• "CLUSTER.ID" Unique identifier for each distinct cluster within a vial. NA denotes non-applicable cases where number of clusters = 0.
• "CLUSTER.SIZE" Number of eggs within a cluster. NA denotes non-applicable cases where number of clusters = 0.
• "MIXED.MATERNITY" Binary factor stating whether a cluster was of mixed maternity (yes) or not (no). NA denotes non-applicable cases where number of clusters = 0.
• "FOCAL.EGG.IN.CLUSTER" Binary factor stating whether a cluster contained at least one focal egg (yes) or not (no). NA denotes non-applicable cases where number of clusters = 0.
• "CLUSTER.COMPOSITION" Description of the cluster composition consisting on three levels: focal-only, mixed or non-focal only. NA denotes non-applicable cases where number of clusters = 0.
• "TOTAL.OFFSPRING" Total number of offspring of any maternity eclosing from a vial. NA denotes non-applicable cases where number of eggs = 0.
• "FOCAL.OFFSPRING" Number of focal (wildtype) offspring eclosing from a vial. NA denotes non-applicable cases where number of focal eggs = 0.
• "FOCAL.VIABILITY" Egg to adult viability of the focal eggs, calculated as FOCAL.OFFSPRING/FOCAL.EGGS. NA denotes non-applicable cases where number of focal eggs = 0.

6) EXP2.DATA.csv

• "VIAL.ID" Unique identifier for each vial in the experiment.
• "TREATMENT" Five-level treatment variable, describing composition of oviposition substrate: NP = no antimicrobials in substrate; Std = all antimicrobial preservatives present, as standard; S-N = propionic acid present, but Nipagin+Ethanol absent; S-P = Nipagin+Ethanol present but propionic acid absent; EtOH = Ethanol present, but Nipagin and Propionic acid absent.
• "TOTAL.EGGS" Total number of eggs laid in a vial during the oviposition period.
• "CLUSTERED.EGGS" Total number of eggs in a vial that were in any type of cluster (this is the sum of all cluster sizes in the vial).
• "PROPORTION.CLUSTERED" The proportion of eggs in a vial that were clustered. Calculated as CLUSTERED.EGGS/TOTAL.EGGS.
• "OFFSPRING" The number of adult offspring that eclosed from a vial. NA denotes unavailable offspring data for that vial.
• "EGG.TO.ADULT.VIA" The proportion of eggs that developed to the adult stage, calculated as OFFSPRING/TOTAL.EGGS. NA denotes unavailable offspring data for that vial.

7) EXP2.CLUSTER.DATA.csv

• "VIAL.ID" Unique identifier for each vial in the experiment.
• "TREATMENT" Five-level treatment variable, describing composition of oviposition substrate: NP = no antimicrobials in substrate; Std = all antimicrobial preservatives present, as standard; S-N = propionic acid present, but Nipagin+Ethanol absent; S-P = Nipagin+Ethanol present but propionic acid absent; EtOH = Ethanol present, but Nipagin and Propionic acid absent.
• "TOTAL.EGGS" Total number of eggs laid in a vial during the oviposition period.
• "CLUSTERED.EGGS" Total number of eggs in a vial that were in any type of cluster (this is the sum of all cluster sizes in the vial).
• "PROPORTION.CLUSTERED" The proportion of eggs in a vial that were clustered. Calculated as CLUSTERED.EGGS/TOTAL.EGGS.
• "OFFSPRING" The number of adult offspring that eclosed from a vial. NA denotes unavailable offspring data for that vial.
• "EGG.TO.ADULT.VIA" The proportion of eggs that developed to the adult stage, calculated as OFFSPRING/TOTAL.EGGS. NA denotes unavailable offspring data for that vial.
• "CLUSTER.ID" Unique identifier for each distinct cluster within a vial.
• "CLUSTER.SIZE" Number of eggs within a cluster. NA denotes non-applicable cases for some cluster IDs when there were <10 clusters in the vial.

8) EXP3.DATA.csv

• "VIAL.ID" Unique identifier for each vial in the experiment.
• "TREATMENT" Four-level treatment variable, describing microbial washes applied to the oviposition substrate: none = buffer only; commensal = wash containing fly-associated microbes; filtered = commensal wash passed through a filter to remove microbes; A. faecalis = a culture of the bacterium Alcaligenes faecalis.
• "TOTAL.EGGS" Total number of eggs laid in a vial during the oviposition period.
• "CLUSTERED.EGGS" Total number of eggs in a vial that were in any type of cluster (this is the sum of all cluster sizes in the vial).
• "PROPORTION.CLUSTERED" The proportion of eggs in a vial that were clustered. Calculated as CLUSTERED.EGGS/TOTAL.EGGS. NA denotes non-applicable cases where total eggs = 0.
• "OFFSPRING" The number of adult offspring that eclosed from a vial.
• "EGG.TO.ADULT.VIA" The proportion of eggs that developed to the adult stage, calculated as OFFSPRING/TOTAL.EGGS. NA denotes non-applicable cases where total eggs = 0.

9) EXP3.CLUSTER.DATA.csv

• "VIAL.ID" Unique identifier for each vial in the experiment.
• "TREATMENT" Four-level treatment variable, describing microbial washes applied to the oviposition substrate: none = buffer only; commensal = wash containing fly-associated microbes; filtered = commensal wash passed through a filter to remove microbes; A. faecalis = a culture of the bacterium Alcaligenes faecalis.
• "TOTAL.EGGS" Total number of eggs laid in a vial during the oviposition period.
• "CLUSTERED.EGGS" Total number of eggs in a vial that were in any type of cluster (this is the sum of all cluster sizes in the vial).
• "PROPORTION.CLUSTERED" The proportion of eggs in a vial that were clustered. Calculated as CLUSTERED.EGGS/TOTAL.EGGS. NA denotes non-applicable cases where total eggs = 0 or 1.
• "EGG.TO.ADULT.VIA" The proportion of eggs that developed to the adult stage, calculated as OFFSPRING/TOTAL.EGGS. NA denotes non-applicable cases where total eggs  = 0. "OFFSPRING" The number of adult offspring that eclosed from a vial.
• "CLUSTER.ID" Unique identifier for each distinct cluster within a vial.
• "CLUSTER.SIZE" Number of eggs within a cluster. NA denotes non-applicable case for some cluster IDs when there were <10 clusters in the vial.

10) original_antimicrobial_assay_photos.zip

Each image shows an individual well in a radial diffusion antimicrobial assay. Images were captured using a GXCAM HiChrome-S camera (GT Vision Ltd.) mounted on a Leica MZ75 dissecting microscope. Files names are initials of the microbial species used in the assay, followed by the identity of the sample being tested, as follows:

Af = Alcaligenes faecalis

Ec = Eschericia coli

Ml = Micrococcus luteus

Sc = Saccharomyces cerevisiae

Dmel = soluble egg wash from Drosophila melanogaster eggs.

Ccap = soluble egg wash from Ceratitis capitata eggs.

purp = negative background control for D. melanogaster egg wash

PBS = negative background control for C. capitata egg wash