Small World Initiative: Research Protocols and Research Guide to Microbial and Chemical Diversity Package

(Fourth Edition, two-book set)

Research Protocols CoverAuthor: Small World Initiative, Inc.

Two-book set/package contains:

  • Research Protocols print (Paperback: 66 pages) with digital e-Book access
  • Research Guide print (Paperback: 116 pages) with digital e-Book access

Package ISBN: 978-1-50669-699-7

Research Guide CoverPrice: $28.57 suggested retail

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About the Book

This guide is part of the official materials used in the Small World Initiative™ (SWI). Formulated at Yale University in 2012 by the author, Dr. Jo Handelsman, SWI is an innovative program that inspires and retains students in the sciences while addressing a worldwide health threat—the diminishing supply of effective antibiotics. SWI centers around a discovery-based introductory biology course in which students from around the world perform hands-on field and laboratory research on soil samples in the hunt for new antibiotics. This is particularly relevant since over two thirds of antibiotics originate from soil bacteria or fungi.

Differentiating itself from traditional courses, SWI’s biology course provides original research opportunities rather than relying on cookbook experiments with predetermined results. Through a series of student-driven experiments, students collect soil samples, isolate diverse bacteria, test their bacteria against clinically relevant microorganisms, and characterize those showing inhibitory activity. SWI’s approach also provides a platform to crowdsource antibiotic discovery by tapping into the intellectual power of many student researchers concurrently addressing a global challenge and advances promising candidates into the drug development pipeline. This unique class approach harnesses the power of active learning to achieve both educational and scientific goals.


About the Authors

Over the past four years, SWI has grown rapidly to include 167 participating schools across 35 U.S. states, Puerto Rico, and 12 countries. The program seeks to inspire the next generation of Partner Instructors and collaborators who will pledge to further SWI’s mission to transform science education and promote antibiotic discovery through the curiosity and creativity of young scientists around the world. SWI’s Partner Instructors are committed to making meaningful and measurable improvements in the education landscape and expanding opportunities for their students while addressing real-world health challenges.

If you are interested in learning more about the Small World Initiative, please visit


Table of Contents

Research Protocols


Lab Safety and Best Practices

Agarose Gel Electrophoresis

Aligning and Combining 16S rRNA Gene Sequences

Analyzing Organic Extracts for Antibiotic Production

Analyzing Sequences with BLAST Search

Antibiotic Resistance Test

Catalase Test

Colony Morphology

Colony PCR


Gram Stain

MacConkey Agar Test

Making Glycerol Stocks

Methanol Extraction

Obtaining Soil Sample

Picking and Patching Colonies

Plating Soil Sample

Screen for Isolate Antibiotic Production #1—Patch/Patch

Screen for Isolate Antibiotic Production #2—Spread/Patch

Screen for Isolate Antibiotic Production #3—Top Agar

Serial Dilutions

Silica Column Chromatography Protocol

Spread Plate

Streak Plate

Sulfide and Indole Production and Motility

Thin Layer Chromatography (TLC)

Typical Media Menu


Research Guide


Small World Initiative™ Overview

Introduction: The Antibiotic Crisis

Section 1: Living on a Bacterial Planet: Experiment 1: Devise a method to transfer microbes from a soil sample to a medium in the lab

Section 2: More Than Just “Dirt:” Experiment 2: Find a local soil environment you wish to sample

Section 3: Redefining “Growth” and “Culture:” Experiment 3: Find a method to isolate single colonies of bacteria from your soil sample

Section 4: Bacteria Are What They Eat, Too: Experiment 4: Choose your own media and culture conditions

Section 5: Solid Versus Liquid Cultures: Experiment 5: Isolate unique colonies to test for antibiotic production

Section 6: Meet the ESKAPE Pathogens: Experiment 6: Understand the significance of the ESKAPE pathogens and using safe relatives in the lab

Section 7: Antibiotic Discovery, Structure, & Targets: Experiment 7: Design a method to screen for antibiotic producers

Section 8: Getting to Know Your Isolates: Experiment 8: Conduct initial identification of your antibiotic-producing isolate

Section 9: It All Comes Down to Chemistry: Experiment 9: Test an organic extract of your isolate for antibiotic activity

Section 10: Resisting Antibiotics: Experiment 10: Test your isolate’s resistance to common antibiotics

Section 11: “Classic” versus “Modern:” Experiment 11: Conduct biochemical characterization of your isolates

Section 12: Bacteria in Context: Experiment 12: Assess your isolate’s activity against eukaryotes, potential use as biological control, and ecological relationships with other organisms

Future Directions

Concluding Remarks