NDLI: Time-Resolved Metabolic Footprinting for Nonlinear Modeling of Bacterial Substrate Utilization▿

Content Provider	PubMed Central
Author	Behrends, Volker Ebbels, Tim M. D. Williams, Huw D. Bundy, Jacob G.
Abstract	Untargeted profiling of small-molecule metabolites from microbial culture supernatants (metabolic footprinting) has great potential as a phenotyping tool. We used time-resolved metabolic footprinting to compare one Escherichia coli and three Pseudomonas aeruginosa strains growing on complex media and show that considering metabolite changes over the whole course of growth provides much more information than analyses based on data from a single time point. Most strikingly, there was pronounced selectivity in metabolite uptake, even when the bacteria were growing apparently exponentially, with certain groups of metabolites not taken up until others had been entirely depleted from the medium. In addition, metabolite excretion showed some complex patterns. Fitting nonlinear equations (four-parameter sigmoids) to individual metabolite data allowed us to model these changes for metabolite uptake and visualize them by back-projecting the curve-fit parameters onto the original growth curves. These “uptake window” plots clearly demonstrated strain differences, with the uptake of some compounds being reversed in order between different strains. Comparison of an undefined rich medium with a defined complex medium designed to mimic cystic fibrosis sputum showed many differences, both qualitative and quantitative, with a greater proportion of excreted to utilized metabolites in the defined medium. Extending the strain comparison to a more closely related set of isolates showed that it was possible to discriminate two species of the Burkholderia cepacia complex based on uptake dynamics alone. We believe time-resolved metabolic footprinting could be a valuable tool for many questions in bacteriology, including isolate comparisons, phenotyping deletion mutants, and as a functional complement to taxonomic classifications.
Related Links	http://dx.doi.org/10.1128/aem.01742-08
Ending Page	2463
Page Count	11
Starting Page	2453
File Format	PDF
ISSN	00992240
e-ISSN	10985336
Journal	Applied and Environmental Microbiology
Issue Number	8
Volume Number	75
Language	English
Publisher	American Society for Microbiology (ASM)
Publisher Date	2009-04-15
Access Restriction	Open
Rights Holder	American Society for Microbiology (ASM)
Subject Keyword	Biotechnology Food Science Ecology Applied Microbiology and Biotechnology Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Ecology Food Science Applied Microbiology and Biotechnology Biotechnology

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Discrimination of Modes of Action of Antifungal Substances by Use of Metabolic Footprinting

Extension of the Substrate Utilization Range of Ralstonia eutropha Strain H16 by Metabolic Engineering To Include Mannose and Glucose ▿

Bacterial Cellulose as a Substrate for Microbial Cell Culture

Utilization of cyanide as nitrogenous substrate by Pseudomonas fluorescens NCIMB 11764: evidence for multiple pathways of metabolic conversion.

Cometabolism of a Nongrowth Substrate: l-Serine Utilization by Corynebacterium glutamicum

Characterization of Multiple-Substrate Utilization by Anthracene-Degrading Mycobacterium frederiksbergense LB501T

Influence of Substrate Mineralogy on Bacterial Mineralization of Calcium Carbonate: Implications for Stone Conservation

Carbohydrate Utilization Patterns for the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus Reveal Broad Growth Substrate Preferences ▿ †

Shared Metabolic Pathways in a Coevolved Insect-Bacterial Symbiosis

Time-Resolved Metabolic Footprinting for Nonlinear Modeling of Bacterial Substrate Utilization▿

Similar Documents

Discrimination of Modes of Action of Antifungal Substances by Use of Metabolic Footprinting

Extension of the Substrate Utilization Range of Ralstonia eutropha Strain H16 by Metabolic Engineering To Include Mannose and Glucose ▿

Bacterial Cellulose as a Substrate for Microbial Cell Culture

Utilization of cyanide as nitrogenous substrate by Pseudomonas fluorescens NCIMB 11764: evidence for multiple pathways of metabolic conversion.

Cometabolism of a Nongrowth Substrate: l-Serine Utilization by Corynebacterium glutamicum

Characterization of Multiple-Substrate Utilization by Anthracene-Degrading Mycobacterium frederiksbergense LB501T

Influence of Substrate Mineralogy on Bacterial Mineralization of Calcium Carbonate: Implications for Stone Conservation

Carbohydrate Utilization Patterns for the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus Reveal Broad Growth Substrate Preferences ▿ †

Shared Metabolic Pathways in a Coevolved Insect-Bacterial Symbiosis

Time-Resolved Metabolic Footprinting for Nonlinear Modeling of Bacterial Substrate Utilization▿