Is it a luxury to “think like a microbe” and to publish blogs such as “Adopt a Microbe“ and books like “The Other End of the Microscope: the Bacteria Tell Their Own Story“ (find it on Google Books)? Is it just about understanding or “getting to know” bacteria, or is it a necessity to be “microbe-oriented” for better understanding of pathogenesis and for developing the appropriate eradication and prevention strategies (I can’t think of better examples other than Reverse Vaccinology and H. pylori)?

When I first read this commentary “The Case for Biocentric Microbiology”* by Dr. Ramy Aziz, published by the journal “Gut Pathogens, I was shocked! The article was presenting a very different perspective, at least different from what I always dreamed of as a pharmacy student, to kill the bad bugs by designing an effective, highly selective chemotherapeutic! Plus it was my first time to read an opinion article, and I used to take the microbiology courses for granted; “this is a bad microorganism, causing this bad infectious disease with serious manifestations including these, diagnosed by the following and the antibiotic of choice is this.” And then Dr. Aziz came with this article with the cool, simple and exciting writing style that keeps one alerted the entire article, gathering all those thoughts and examples of our human-centered/self-centered view of microbiology.

Four parts I enjoyed the most in the commentary:

• The tabular form of “differences between the anthropocentric and biocentric views of microbes.”
• The final balancing paragraph –the conclusion.
• The “competing interests” part, which is funny.
• The questions part, which is an excellent idea to open up discussions, especially for those who are not-natural-born brain stormers like me!

Even though microbiology is a new science, it suffers from anthropocentric view that Galileo suffered from; starting with the field’s name itself, “microbiology” -liked what Dr. Elio Schaechter mentioned: “Small,” says who? Not the microbes… till the funding agencies that give priority to studying bad microbes (i.e., pathogens), and good microbes (i.e., fuel-producing and yogurt-making bacteria) nothing else!

We, in our human-centered view; automatically classify any newly-discovered bacterium to fall into one of three categories: the good, the bad and the ugly… no, not that one! They are: the useful guys, the harmful guys and the just-existing guys. Now, let’s take a look at the biocentric view of microbes: Humans and microbes share many ecosystems. To microbes, humans are just an ecosystem that is a “relatively safe” habitat with a source of nutrition.

As victims, we think about pathogenesis/infection as it’s shedding from the immune system, invasion and toxin production; but microbe-oriented microbiologists/bacteria whisperers know that, to bacteria, pathogenesis is  just defense, seeking nutrition, and excretion of metabolic byproducts. Being pathogenic or opportunistic is not their reason of existence, it’s just a form of adaptation to survive in this hostile environment (aka the human body).

You do not believe me!? OK, bacteria lived –happily- thousands of millennia before mammals and humans, so their reason of existence can’t be to harm humans, like what Dr. Aziz is mentioning: “Who attacks whom”, are the bacteria the “one” that start the fight, or is it the human immune system that starts the war against them?  A very interesting example to understand adaptation is Legionella pathogenesis, and how they adapted to human macrophages because they used to survive in amebas, which are similar to our macrophages.

Back to the basic question, is it a luxury or a necessity?

Studying “all” bacteria from their perspective will help us in understanding pathogenesis and subsequently developing strategies to combat infectious diseases (immunization and design highly selective chemotherapeutics), will give us a better idea of the tree of life and the metabolic map, and studying environmental microbiology will allow us to meet new “useful” microbes like what happened with the PCR Taq-polymerase, we knew how to make use of this bacterial polymerase that can work at those very high temperatures required for the PCR steps.

Here are two interviews about the commentary covering two segments of readers, the first one is with Dr. Betsey Dyer, Professor of Biology at Wheaton College, and the second one is made with Radwa Raed, a micro-writer and a final-year FOPCU student:

1- What is your opinion about (the commentary)? To what extent do you find it compatible with your bacteriocentric view of bacteriology? How strong are the arguments?

Dr. Betsey D. Dyer, Professor of Biology at Wheaton College.

“I thoroughly enjoyed Ramy Karam Aziz’s article “The Case for Biocentric Microbiology.” I think he is absolutely right that some old fashion thinking about the divisions of microbiology and anthropocentrism in general have hindered a more complete understanding of the microbial world. I also think Dr Aziz is quite bold and daring. I’m not sure I could have gotten such forceful statements accepted for publication! Good for “Gut Pathogens” to print it! I hope Dr Aziz gets lots of readers and citations.”

2- How did (the commentary) change your point of view? Are you with or against the biocentric view for microbiology? Do you think about it as a view against, or at least far from, your beliefs as a pharmacy student dreaming of fighting diseases? What are your opinions regarding studying environmental microbiology in pharmacy school?

Radwa Raed, Pharmacy student, Faculty of Pharmacy, Cairo University – Egypt.

“From my humble point of view, I would have to agree (with the biocentric view of microbiology). It goes without saying that studying more about certain bacteria “the ones some would consider to be of the least priority” will definitely expand our knowledge about the overall, and in many cases analogous or even similar, methods of survival, adaptation to existing conditions, etc.., which all pretty much ultimately serve medical microbiology. Plus, leaving a whole chunk, simply unexplored, can only raise several “what if” questions; one of which, that comes to mind, is what if the simplicity and less dramatic forms of life could help researchers better grasp the machinery behind these fascinating little creatures 🙂

As for studying environmental microbiology in pharmacy schools, I would have to oppose the idea, because the field of pharmaceutical science is taught so the future students can come to understand, and hopefully later suggest, treatment methods against pathogenic microorganisms, prophylaxis, and so forth..so studying the harmless ones would not point in this direction. It can only lead them to drift away from the pharmaceutical science branch of study into a more microbiology-oriented career.”

You can read the paper, share your comments and debate the arguments here, and you can also vote for it on BioWizard.

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*Full Citation:

Aziz, R. (2009). The case for biocentric microbiology Gut Pathogens, 1 (1) DOI: 10.1186/1757-4749-1-16

Tags: adopt a microbe, anthropocentric, bacteriocentric, Betsey D. Dyer, biocentric microbiology, commentary, competing interests, environmental microbiology, gut pathogens, H. pylori, metabolic map, microbe-oriented, microbiology, pathogenesis, pathogens, PCR, Ramy K. Aziz, reverse vaccinology, taq-polymerase, the case for biocentric microbiology, the other end of the microscope, tree of life

Dr. Betsey Dexter Dyer is a professor of Biology at Wheaton College, Massachusetts, USA. She received her Ph.D. from Boston University. Among her research interests are symbiosis, evolution of cells, field microbiology and genomics. She is also part of the Genomics Research Group, a student project that she launched in collaboration with Mark LeBlanc, professor of Computer Science. Dr. Dyer has written several books, including

The Modern Scholar: Unseen Diversity: The World of Bacteria (Audiobook), The Origin of Eukaryotic Cells (Benchmark Papers in Systematic and Evolutionary Biology, 9) (1986), Tracing the History of Eukaryotic Cells (1994 – with Robert A. Obar), Explore the World Using Protozoa (1997 – coauthor), A Field Guide to Bacteria (2003) and Perl for Exploring DNA (2007 – with Mark D. LeBlanc).

I recently read about her book “A Field Guide to Bacteria” and wanted to know more about her view on “Bacteriocentrism,” and how one becomes “bacteriocentric.” I was so lucky to be introduced to Dr. Dyer, who was kind enough to accept to be interviewed for Micro Writers, and immediately answered my questions about her book and her student project, Genomics Research Group, via email. So, here I am, sharing with you this very interesting interview.

1. Why did you decide to write the book “A Field Guide to Bacteria”? Field microbiology and symbiosis are among your research interests ; is this one of the reasons that made you dig deeper in bacterial populations and “think like a microbe”?

I first got the idea of a field guide when I was a graduate student and was very fortunate to be on a field microbiology expedition (in Baja California Mexico) with some world famous field microbiologists. I realized at once that a field guide should be written and one of them should write it and probably would! It did not occur to me that I would write it.   It took me years to get to the point of being secure enough with my career. First I had to get a PhD, then a job, and then tenure. I also got married and had two children. Finally, about 15 years after that original idea, I realized that I had been accumulating enough information that I should begin to write. And so I did. However, I am still a bit surprised that nobody else wrote it.
I am naturally drawn to tiny things. I got a microscope for a present when I was 11 years old and it transformed some of my views of biology. I found that I loved the microscopic world. But I also like miniatures in general such as tiny furniture and dishes and things in dolls houses. I have in my library at home, some shelves devoted to a doll house and two miniature rooms.

2. What is meant by “becoming bacteriocentric”? And how does this lead to better understanding of the biology of bacteria?

We humans are mostly visual and auditory, the primary senses by which we perceive and analyze the world. It is probably impossible for us to be otherwise. Furthermore, we are gigantic and multicellular and terrestrial in marked contrast to the vast majority of organsims on Earth. Nonetheless, I think it is an excellent exercise for any biologist at least to try bacteriocentricity. The bacterial or microbial world is primarily olfactory and tactile. They are single celled (intimate with their environments), tiny and aquatic. I cannot avoid being anthropocentric but I can at least be more aware of the limitations of my size, habitat, and senses. My goal is to have as much humility as I can manage when I observe the world of microbes.

3. “Many groups of bacteria can be easily identified in the field (or in the refrigerator) without a microscope” and “Bacteria can be seen and smelled”, as a pharmacy student, I want ask how could that be achieved?

Well, do you have the book yet?  There are many examples but the basis of all of them is that bacteria, when they are in an appropriate environment, are likely to do quite well: reproducing abundantly, taking in and transforming molecules, sending out wastes. In many cases (surprisingly many) the abundance is on a level perceptible by humans. The field marks just need to be revealed and interpreted. Otherwise, they may be easily overlooked or misunderstood. My first experience with this as a graduate student was being shown the distinctive pigmentations and odors of bacteria in sulfur cycles in Baja California.

4. You have a project with Dr. Mark LeBlanc, professor of Computer Science, called “Wheaton College Genomics Group.” Why did you do such a project for undergraduate students? How did it raise their potential?

One day about ten years ago, Mark asked me if I had any large datasets that his computer science students might analyze in their course on algorithms. It happens that I teach genetics and am fascinated with genomes. At that time, genome sequences were becoming more available at NCBI. I had not realized that it would be so easy to collaborate with a computer scientist. I had lots of questions about genomes and we just started right in with devising some answers. Right now, we are interested in characterizing horizontal transfer events of distantly related bacteria and archaea.  There are hundreds of complete microbial genomes at NCBI and most have not been completely analyzed. Therefore, there is plenty for us and our students to do.
We ended up writing a book on the topic because we wee in need of a text that could be used both by biologists and computer scientists.

Tags: A Field Guide to Bacteria, bacteriocentric, bacteriocentrism, Betsey D. Dyer, biologists, computer scientists, field microbiology, Mark LeBlanc, NCBI, Perl, Perl for Exploring DNA, sulfur cycles, symbiosis, Wheaton College Genomics Group