Date of this Version


Document Type



We extend Flint, a Spark-based metagenomic profiling tool, to efficiently measure bacterial growth rates for large data sets. The tool bPTR for bacterial growth rate measurement from metagenomic samples [Brown et al., Nat Biotech, 2016] was adapted and integrated into Flint’s MapReduce framework in order to take advantage of Flint's efficient read alignments and mapping, thus enabling the creation of bacterial abundance profiles that are enhanced with growth-rate information.
To show the viability of our method we analyzed whole metagenome sequence data from a longitudinal study of sampled preterm infants [Gibson et al., Nat Micro, 2016], computing the abundance profile enhanced with growth rate information. The conclusions shed light on the new perspective obtained on antibiotics treatments and antibiotic resistance by looking at replication rates.


Presented at:

27th Conference on Intelligent Systems for Molecular Biology and the 18th European Conference on Computational Biology (ISMB ECCB, 2019), Basel, Switzerland, July 21-25th



Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.



Rights Statement

Rights Statement

In Copyright. URI:
This Item is protected by copyright and/or related rights. You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s).