Table of Contents


Welcome to Biofilms: The Hypertextbook!  We are glad you have found us, and we hope you enjoy learning about biofilms from this hypertextbook.

We need to let you know a few things before you proceed.  First, you should know that Biofilms: The Hypertextbook is a work in progress.  There is already a lot of good stuff in the book, but more is coming. The table of contents presented below is intended to reflect the current  view of the content of the hypertextbook. Not all chapters contain content at this point, although most are either near completion or in progress. 

Also be aware that as new revisions are released, chapters may have been moved around, new content added, old content revised, and other enhancements made to the hypertextbook as it evolves.  One of the really cool features of a hypertextbook is that it can evolve dynamically.  Indeed, content that is useful even in draft form can be included and used immediately.  We will utilize this dynamic aspect of the hypertextbook to bring you updates in real time.

Please note that the chapters below are not linked to the content.  To access a chapter, hover your mouse over the Chapters dropdown menu in the top bar of this page and click on the desired chapter.

Chapter 1. Introduction to Biofilms (various contributing authors)

This chapter provides an introduction to the concept and study of biofilms along with historical recognition of the importance of biofilms to an understanding of microbiology.  What are biofilms?  Where are they found?  Are they harmful?  Are they beneficial?  Why are they important?  These questions, and more, are found in this chapter.  More content will be added to this chapter over time, but it is now ready for use.  It appears on both the green (novice) and blue (intermediate) tracks (this chapter is finished, although enhancements are planned).

Chapter 2. Biofilm Growth and Developement (John Lennox)

In this chapter we explore the biofilm phenomenon: biofilms as  natural phenomena; formation, growth, colonization, and defense mechanisms of biofilms. (More content is planned for this chapter, and there are still a few images and video clips to identify and include, but it is quite usable now as it stands.  It appears only at the blue (intermediate) level at this time. Green and Black levels to come.)

Chapter 3. Beneficial and Naturally Occurring Biofilms (Al Cunningham)

Not all biofilms are bad. Biofilms are a natural phenomenon in our everyday environments and even thrive in extremely hot and cold environment. Biofilms can also be engineered for beneficial purposes.  For example, since certain biofilms can subsist on petroleum oil (and hence clog oil pipelines) these same types of biofilms can be engineered to aid in the cleanup of an oil spill.  This chapter presents a view of naturally occurring and engineered biofilms that are either benign or beneficial.  (This chapter is underway, but does not yet appear in the hypertextbook.)

Chapter 4. Biofilms in Health and Diseases (Garth James and John Lennox)

This chapter explores the negative impact of biofilms on health. Some diseases and adverse medical conditions are now recognized to be the result of a biofilm infection.  For example, when a medical implant becomes infected, it is usually a biofilm infection that is much more difficult to treat than other non-biofilm infections resulting from the same microbes not in a biofilm.  Medical and dental practices can be enhanced through an understanding of biofilms and their treatment as a biofilm.  (This chapter is ready to use.  It will be expanded from its focus at this point on wounds to other medical and dental conditions).

Chapter 5.  Biofilms in Industrial Environments (Al Cunningham)

Many industries encounter pesky biofilms that can plague their manufacturing processes and/or foul their products. It is estimated that biofilms cause industry literally billions of dollars a year in lost production and treatment.  As is true with biofilms in any environment, it is important to recognize when problems are the result of a biofilm, as their treatment will differ accordingly.  This chapter discusses these issues (in first draft form). It will eventually also include a section on biofilms in drinking water by Anne Camper.

Chapter 6. Characterizing and Understanding Biofilms (Al Cunningham and Phil Stewart)

In this chapter biofilm processes are explored. How do they form?  How are they structured? How do they evolve? The answers to these (and other similar questions) are important to the understanding and treatment of harmful biofilms and for engineering beneficial biofilms for various tasks.  For example, standard practice for many years has been to test the effect of anti-bacterial remedies on bacteria in isolation. Such treatments are often ineffective for treating bacteria as they exist in a biofilm, because a biofilm colony has defense mechanisms and a structure that hinders the treatment agent from penetrating (diffusing into) the biofilm and from having the same effect on targeted microbes as it would on those same microbes in a planktonic environment. 

Intended topics include

(This chapter is in usable form at the blue level.  It will be enhanced and also reformulated for the green and black levels.)

Chapter 7.  Controlling Biofilms (Phil Stewart)

Harmful biofilms must be recognized and treated. This chapter provides an overview of methodologies for controlling biofilms.  This is, of course, the crux of the matter for industry, health, and medicine.  If biofilms are so hard to treat, what methods are available or being discovered for their control (in first draft form).

Chapter 8.  Methods for Studying Biofilms (Phil Stewart, John Lennox, et. al.)

In order to treat detrimental biofilms and harness the power of beneficial biofilms, engineers and scientists must continuously enhance their knowledge and understanding biofilms.  This chapter explores various methods employed for studying biofilms in the laboratory and through microscopy. (This chapter is at this moment in the formative stage.  No draft of it appears in the hypertextbook at this juncture.)

Chapter 9. Mathematical Models of Biofilms (Robin Gerlach)

One way to study any physical phenomenon is to try to capture its properties as a mathematical system. The result is a computer-based computational model that can be used to study the behavior of that physical phenomenon. The state of modeling biofilms is presented in this chapter. (This chapter is in the formative stage and does not yet appear in the hypertextbook.)

Chapter 10. Diffusion in Biofilms (Phil Stewart)

Say you get up in the morning. You shower, comb your hair, brush your teeth. You even decide to be extra attentive and use a swish of mouthwash to beat back those bad-breath causing oral bacteria. How long will you need to swish to make a difference? The answer lies in figuring out the phenomenon of diffusion.

How long it takes for an antimicrobial agent to penetrate a biofilm has profound impact on the the formulation of antimicrobial chemicals and their application.

Chapter 11. Lab Exercises (Instructor and student versions)

Twenty-three peer reviewed biofilm laboratory exercises are currently included in this chapter. They are formulated for an instructor who wants to assign biofilm laboratory exercises. There are corresponding exercises formulated for the student rather than the instructor.  (More laboratory exercises and experiments are in the review process, and yet more are in the formative stage.  These will be incorporated into the hypertextbook as they become available.)

Other Chapters Still in the Formative Stage


Appendix 1.  Aids for Instructors

It is intended that the instructor aids be included as an appendix in the hypertextbook 

Appendix 2.  References

As citations are made to literature, the corresponding references are kept in this appendix.  Links to this appendix accompany the citations.