A low-cost, open-source evolutionary bioreactor and its educational use

  1. Vishhvaan Gopalakrishnan
  2. Dena Crozier
  3. Kyle J Card
  4. Lacy D Chick
  5. Nikhil P Krishnan
  6. Erin McClure
  7. Julia Pelesko
  8. Drew FK Williamson
  9. Daniel Nichol
  10. Soumyajit Mandal
  11. Robert A. Bonomo
  12. Jacob G Scott  Is a corresponding author
  1. Cleveland Clinic, United States
  2. Hawken School, United States
  3. Case Western Reserve University, United States
  4. Massachusetts General Hospital, United States
  5. Institute of Cancer Research, United Kingdom
  6. Louis Stokes Cleveland VA Medical Center, United States

Abstract

A morbidostat is a bioreactor that uses antibiotics to control the growth of bacteria, making it well-suited for studying the evolution of antibiotic resistance. However, morbidostats are often too expensive to be used in educational settings. Here we present a low-cost morbidostat called the EVolutionary biorEactor (EVE) that can be built by students with minimal engineering and programming experience. We describe how we validated EVE in a real classroom setting by evolving replicate Escherichia coli populations under chloramphenicol challenge, thereby enabling students to learn about bacterial growth and antibiotic resistance.

Data availability

We provide the materials to build an EVE on our Github: https://github.com/vishhvaan/eve-pi. We have also included the data to generate figure 2 on the Github.

Article and author information

Author details

  1. Vishhvaan Gopalakrishnan

    Lerner College of Medicine, Cleveland Clinic, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0532-7710
  2. Dena Crozier

    Lerner College of Medicine, Cleveland Clinic, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1841-0011
  3. Kyle J Card

    Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0462-2777
  4. Lacy D Chick

    Hawken School, Gates Mills, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3059-4300
  5. Nikhil P Krishnan

    Case Western Reserve University, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Erin McClure

    Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6604-1273
  7. Julia Pelesko

    Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Drew FK Williamson

    Department of Pathology, Massachusetts General Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1745-8846
  9. Daniel Nichol

    Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2662-1836
  10. Soumyajit Mandal

    Case Western Reserve University, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Robert A. Bonomo

    Department of Medicine, Louis Stokes Cleveland VA Medical Center, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Jacob G Scott

    Louis Stokes Cleveland Department of Veteran Affairs Medical Center, Cleveland Clinic, Cleveland, United States
    For correspondence
    scottj10@ccf.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2971-7673

Funding

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Peter Rodgers, eLife, United Kingdom

Publication history

  1. Preprint posted: August 9, 2019 (view preprint)
  2. Received: August 30, 2022
  3. Accepted: October 20, 2022
  4. Accepted Manuscript published: November 1, 2022 (version 1)
  5. Version of Record published: November 23, 2022 (version 2)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

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  1. Vishhvaan Gopalakrishnan
  2. Dena Crozier
  3. Kyle J Card
  4. Lacy D Chick
  5. Nikhil P Krishnan
  6. Erin McClure
  7. Julia Pelesko
  8. Drew FK Williamson
  9. Daniel Nichol
  10. Soumyajit Mandal
  11. Robert A. Bonomo
  12. Jacob G Scott
(2022)
A low-cost, open-source evolutionary bioreactor and its educational use
eLife 11:e83067.
https://doi.org/10.7554/eLife.83067
  1. Further reading

Further reading

    1. Ecology
    2. Evolutionary Biology
    Hannah J Williams, Vivek H Sridhar ... Amanda D Melin
    Review Article

    Groups of animals inhabit vastly different sensory worlds, or umwelten, which shape fundamental aspects of their behaviour. Yet the sensory ecology of species is rarely incorporated into the emerging field of collective behaviour, which studies the movements, population-level behaviours, and emergent properties of animal groups. Here, we review the contributions of sensory ecology and collective behaviour to understanding how animals move and interact within the context of their social and physical environments. Our goal is to advance and bridge these two areas of inquiry and highlight the potential for their creative integration. To achieve this goal, we organise our review around the following themes: (1) identifying the promise of integrating collective behaviour and sensory ecology; (2) defining and exploring the concept of a ‘sensory collective’; (3) considering the potential for sensory collectives to shape the evolution of sensory systems; (4) exploring examples from diverse taxa to illustrate neural circuits involved in sensing and collective behaviour; and (5) suggesting the need for creative conceptual and methodological advances to quantify ‘sensescapes’. In the final section, (6) applications to biological conservation, we argue that these topics are timely, given the ongoing anthropogenic changes to sensory stimuli (e.g. via light, sound, and chemical pollution) which are anticipated to impact animal collectives and group-level behaviour and, in turn, ecosystem composition and function. Our synthesis seeks to provide a forward-looking perspective on how sensory ecologists and collective behaviourists can both learn from and inspire one another to advance our understanding of animal behaviour, ecology, adaptation, and evolution.

    1. Evolutionary Biology
    John S Favate, Kyle S Skalenko ... Premal Shah
    Research Article

    Changes in an organism’s environment, genome, or gene expression patterns can lead to changes in its metabolism. The metabolic phenotype can be under selection and contributes to adaptation. However, the networked and convoluted nature of an organism’s metabolism makes relating mutations, metabolic changes, and effects on fitness challenging. To overcome this challenge, we use the long-term evolution experiment (LTEE) with E. coli as a model to understand how mutations can eventually affect metabolism and perhaps fitness. We used mass spectrometry to broadly survey the metabolomes of the ancestral strains and all 12 evolved lines. We combined this metabolic data with mutation and expression data to suggest how mutations that alter specific reaction pathways, such as the biosynthesis of nicotinamide adenine dinucleotide, might increase fitness in the system. Our work provides a better understanding of how mutations might affect fitness through the metabolic changes in the LTEE and thus provides a major step in developing a complete genotype–phenotype map for this experimental system.