About

PMkbase is a web based bacterial phenotypic database based on the BiOLOG Phenotype MicroArray. The database reports phenotypes for various strain types and modifications based on a 4 step workflow of 1) Curation, 2) Quality Check, 3) Parameter extraction and 4) Growth calls. These phenotypes can be leveraged to:

Curate, gapfill and validate genome scale metabolic models
Look for interesting nutritional sources for generation of unique media conditions
Gain phenotypic insights into the pangenome of a species

PMkbase is free for non-commerical use and is hosted and maintained at the Systems Biology Research Group at the University of California San Diego.

Data Submission

To submit any data you have, contact kkrishnan@ucsd.edu

Curation and Quality Check

High quality data should include samples with well annotated strain names/IDs, the species they belong to, any genomic modifications done to it and the media conditions used (usually minimal media for metabolic plates). At least 2 replicates for a strain and plate combination are required to make a conclusive growth call.

How do we make the Growth Calls?

We use our in-house pipeline available here, to make growth/no growth calls. First, we denoise the fluorescence signals using a Savgol filter and generate the following kinetic parameters for every well in a plate + strain sample:

Maximum Respiration observed
Maximum Rate of Respiration
Time taken to get to maximum respiration
Area under the curve

A z-test is run on the Max Respiration observed in each well against all control wells to assign growth/no growth. A substrate/inhibitor is assigned as a trait to a strain if majority replicates display growth.

Media formulations

M9 Minimal media (without glucose) [For 2L solution]:
Milli-Q water - 1.6L
1 M CaCl2 - 200uL
1 M MgSO4 - 4ml
Trace elements solution [Detailed below] - 500uL
10X M9 Salt solution [Detailed below] - 200mL

10X M9 Salt solution
Anhydrous Na2HPO4 - 136g
KH2PO4 - 60g
NaCl - 10g
NH4Cl - 20g

Trace elements solution
FeCl3.6H20 - 2.7g
Anhydrous ZnCl2 - 0.13g
CoCl2.6H2O - 0.2g
Na2MoO4.2H2O - 0.2g
Anhydrous CaCl2 - 0.075g
CuCl2.2H2O - 0.091g
H3BO3 - 0.05g
concentrated HCL - 10mL

Mueller Hinton Broth
Ordered from Sigma-Aldrich

Roswell Park Memorial Institute medium
Ordered from ThermoFisher

IF0 medium
Ordered from Biolog