but stable, groups. When these groups grow in size and associate with other microorganisms, including parasites or viruses, they are called microbiomes. What was once known as the “intestinal flora” is now termed the intestinal microbiome. The intestinal microbiome is not the only type of microbiome; other parts of the body, and other organisms, feature their own. We now know that these microbiomes evolve and that they are unique to the individual they inhabit, based on their host’s specific eating habits, genetic heritage, underlying illnesses, and even personal behavior.
Even if bacteria seem to live independently in nature, many exist in symbiotic relationships not only with humans but also with all animals, including insects, and even plants. This cohabitation sometimes produces stunning effects on the host, such as sterility and even the eradication of males in insects. Bacteria present on plant roots can help them capture the soil nitrogen essential for the plant’s growth.
Bacteria have very elaborate social lives. In addition to their ability to live in groups, and in order to do so, they can communicate using a chemical language that allows them to recognize and distinguish one another by species or family. Bacteria use these chemical languages to cooperate against a common enemy. For example, some pathogenic bacteria will not deploy their attack mechanisms unless they are numerous enough to succeed. Some bacteria can also regulate the times when they become luminescent, lighting up only once their numbers reach a certain threshold.
In order to adapt to various situations and to decide when to use their special capabilities, bacteria employ very sophisticated regulatory mechanisms. Each bacterial component, from proteins to small molecules, including vitamins and metals, participates in multiple adaptation mechanisms that bacteria put into action at various points in their lives. The molecules that participate in the controlled expression of genomes, and on which researchers have made the most progress recently, are RNA molecules. François Jacob and Jacques Monod hypothesized that RNAs could regulate gene expression, but they never imagined that RNAs could regulate gene expression in so many different ways. Bacterial RNA, considered as recently as the end of the last century to be mostly a production intermediary between DNA and proteins (hence the term messenger RNA), plays various and sometimes surprising roles. One of the most important recent advances in biology is the discovery that bacteria have extremely effective RNA-dependent defense strategies in place, known as CRISPR (pronounced crisper) for clustered regularly interspaced palindromic repeats, which they use to prolect themselves from the bacteria-infecting viruses known as bacteriophages, or just phages. Specifically, bacteria remember their first encounter with a given phage and are able to put in place a kind of immunity, “vaccinating” themselves against this phage.
These bacterial systems work so well and are so adaptable that they are now the basis for a revolutionary technique, the CRISPR/Cas9 technology, that allows genome editing in all organisms that have been tested so far. This method makes genome modification quick and easy, and the mutations created allow for sophisticated studies of gene function or for the replacement of defective genes, paving the way for gene therapies. The CRISPR/Cas9 technology was recognized by a Breakthrough Prize in Life Sciences in 2015 in the United States and by numerous other prestigious international prizes that honor great scientific advances.
Bacteria defend themselves not only from viruses but also from their fellow bacteria, which are sometimes very aggressive. To do this, they produce many kinds of toxins and antibacterial poisons for which they themselves have one or more immunity proteins. In the bacterial world, the struggle for life is continually taking place on an infinitesimal scale. But could these antibacterial poisons also be used on a much larger scale, to fight and gain better control over pathogenic bacteria? They certainly constitute a foreseeable strategy for replacing antibiotics that have become ineffective.
In fact, antibiotics have been, for decades, the most used antibacterial agents. Unfortunately, bacteria have adapted accordingly, developing resistances that have dramatic medical consequences, as in the case of the bacterium responsible for tuberculosis (Mycobacterium tuberculosis, or the Koch bacillus). We are no longer able to treat certain serious illnesses, and, as a result, they are coming back with a vengeance. The alarm has been sounded. The public is aware that this is a worldwide concern. Nevertheless, there are now reasons for optimism, or at least hope. Based on our recent knowledge, we are discovering new, alternative ways of fighting pathogens, raising new hopes for more effective treatments. For example, we can use our knowledge of bacterial genomes to identify inhibitors of chemical reactions or metabolic pathways that exist only in bacteria, not in humans.
Nevertheless, the threat of returning to a “preantibiotic” era is real and must be taken into account. We must therefore maintain constant vigilance when putting in place new therapies or when halting formerly obligatory vaccinations. Would it be reasonable, for example, to continue the policy in France of restricting vaccination with BCG (bacille Calmette-Guérin) against tuberculosis? Such questions should be carefully considered, especially in our global society where travel to and from countries with lower vaccination rates can be easy.
The objective in this book is to illustrate that very important discoveries and new concepts have come to light in the last few decades. These developments clearly show that the field of microbiology has undergone a bona fide revolution and that the amazing renaissance that is taking place can have wide-ranging consequences. This new understanding is going to change our daily lives dramatically, from our eating habits and daily routines to our way of looking at the rest of the living organisms on Earth: bacteria, plants, animals, even insects. In addition, recent discoveries will help us implement new strategies for fighting pathogenic agents and battle not only infectious diseases, but also their vectors. An example already in place in Australia is a plan to eliminate certain disease-bearing mosquitoes by releasing into the wild male mosquitoes that have been rendered sterile by infection with Wolbachia bacteria.
This book is limited to the rebirth of bacteriology, in part because this is my own domain of expertise. That said, virology, parasitology, and mycology are also mentioned because these areas benefit from the same technological advances. Bacteriology, however, is the field that has been the most profoundly impacted by these advances and that consequently has benefited from the development of the greatest number of new concepts.
It was predicted that the 21st century would be the age of biology. This is indeed the case, and microbiology is at the forefront. In 2012, the French Academy of Sciences, with its sister institutions in England and Germany, the Royal Society and the Leopoldina, held a colloquium titled “The New Microbiology” that met with great success. I have used the same title for this book.
ACKNOWLEDGMENTS
I would like to sincerely thank my fellow collaborators Olivier Dussurget and Nathalie Rolhion for their meticulous critical reading of this manuscript, as well as Carla Saleh and Didier Mazel. Thanks to Juan J. Quereda for finalizing the drawings and the figures; Urs Jenal and Javier Lopez Garrido for the images of Caulobacter and Bacillus subtilis (cover photo); Caroline Dean, Jean-Pierre Caillaudeau, and Bruno Lemaitre for their suggestions; and Nicolas Witkowski for all his patience and advice.
I am grateful to Chloe A. M. Hagen for the primary transiation of the French text, and to Megan Angelini and Ellie Tupper for their skilled and careful editing to bring the spirit of the French edition to English speakers. I sincerely thank Christine Charlip for her careful and meticulous coordination of the English edition as well as Greg Payne for his enthusiasm for publishing the book.
Finally, thanks to Odile Jacob for her enthusiasm and the pleasure of our discussions on this new microbiology!
ABOUT THE AUTHOR
