Bacteria and Its Concern and A Tool For Research

BACTERIA AND ITS CONCERN AND A
TOOL FOR RESEARCH
Overview
Bacteria and their phages are the oldest and most abundant life forms on the
planet. Bacteria have co-evolved with us and are beneficial for human health.
There are over 10 times more bacteria in our bodies than there are human
cells, and this natural microbiota is essential for proper development,
nutrition, and resistance to disease. However, we also live in an environment
replete with bacteria that can cause a wide variety of human diseases with
bacterial infections responsible for 25 percent of human deaths globally, a
number predicted to increase dramatically with the growing crisis of antibiotic
resistance. We understand very little about the interactions between bacteria
and the environment that influence the delicate ecological equilibrium
between humans and microbes and thereby determine the balance between
health and disease.
In addition to the bacteria that are in or on the human body, bacteria influence
humans in many other ways. Bacteria are the dominant occupant and architect
of our entire biosphere. Bacteria sustain the metabolic cycles that are essential
for all life on earth. Bacterial metabolism sculpts our physical environment as
well. Because they are ubiquitous and have such diverse metabolic capabilities,
bacteria influence essentially all disciplines of science, including fields such as
evolutionary biology, ecology, immunology, cell and developmental biology,
psychology, geology, chemistry, physics, climatology, computer science, and
engineering.
Bacteria are also instrumental for understanding fundamental life processes

that are required by all organisms, including central metabolism, replication,
transcription, translation, protein targeting, assembly and structure of
macromolecular complexes, protein folding, stress responses, error correction
mechanisms, signal transduction, and developmental programs. These
processes are more easily characterized in model bacteria and their phages
than in other organisms because microbes provide such tractable experimental
systems. The large repertoire of genetic and biochemical tools and data that
have been acquired from basic research on bacteria is crucial for dissecting the
complex metabolic and regulatory networks that control these processes. This
provides a launching point for understanding the enormous diversity in the
bacterial world and facilitates the understanding of these processes in
eukaryotes.
Evolving Priorities
Research on bacteria and their phages has led to many fundamental scientific
discoveries. Initial support for this research was justified in part because of the
role of bacteria in causing disease. With the advent of effective antibiotics it
seemed like the war on microbes had been won. Hence, for several decades
health-related research shifted to topics like cancer, heart disease, and genetic
diseases. Moreover, developments in molecular biology arising from research
on bacteria made it possible to study many basic biological processes in
mammalian cells, eliminating the argument that bacterial model systems were
the only doorway to eukaryotic molecular biology.
Impact of New Technologies

New approaches like genomics, transcriptomics, and proteomics allow the
identification of the entire genetic complement of bacteria and which of these
genes are turned on under particular conditions. Comparative genomics led to
the discovery that gene exchange between bacteria is rampant and has
dramatically influenced the acquisition of virulence, and had a major impact on
our understanding of the evolution of pathogenesis. However, interpretation
of data from these “omics” approaches relies on comparisons with databases
rather than direct functional assays. Thus, these new approaches have not
diminished the need for basic research because a detailed understanding of
microbial physiology and genetics is essential to interpret and test the resulting
predictions. In fact, the ability of “omics” approaches to generate a
tremendous number of predictions greatly increases the need for direct
experimental tests based upon genetics, biochemistry, and molecular biology.
Furthermore, the detailed characterization of the mechanisms of discrete
pathways and reactions, and molecular interactions that modulate these
interactions is required for understanding the integrated networks and for
developing new ways to modulate these processes for our purposes— a major
goal of systems biology.
Imaging is another technological advance that has provided useful insights into
bacterial physiology and pathogenesis. Sensitive new approaches allow the
visualization of molecules within bacteria and bacteria within an infected host.
The applications of these approaches in bacterial cell biology and ecology have
only begun to be tapped. Coupled with an understanding of bacterial
physiology and molecular biology, and the ability to genetically manipulate
these processes, will lead to new therapies that direct active agents to
particular sites in the host to combat disease or stimulate health. Because of
sophisticated instrumentation requirements and expense, efforts to develop
these new technological approaches are typically restricted to large groups of
scientists focused upon very specific problems. However, interpreting the vast
amount of data generated by these new technologies and asking critical
questions about what it means typically relies on individual scientists with
unique expertise on a particular aspect of bacterial genetics, physiology,
ecology, or molecular biology. To take optimal advantage of the intellectual
capital spread across academia and industry, individual scientists should have
access to the facilities needed to perform such experiments and the data
generated from these experiments.
Educational Needs
The fundamental concepts of bacterial physiology and genetics are essential
for both basic and translational research. For example, an in-depth knowledge
of bacterial physiology and genetics is essential for effective development of
new antibiotics, thwarting antibiotic resistance, construction of novel vaccines,
and treatment of diseases induced by asymptomatic infections. Bacteria are
also vital to fields like chemical biology, biophysics, geobiology, and chemical
engineering. However, newcomers from these other fields often lack core
knowledge of basic bacterial physiology and genetics needed to integrate the
disciplines.
Training in basic research on bacteria also provides the skills needed in

biotechnology, the pharmaceutical industry, and clinical microbiology.
Individualized research allows a student to learn from mistakes and develop
expertise in trouble-shooting scientific problems in close collaboration with a
scientific mentor. However, there is concern in the research community that
basic research in the microbial sciences has not flourished, resulting in fewer
scientists actively working in this area and fewer students trained to respond
to future microbial challenges.
There is a widespread perception among microbiologists that enough scientists

in bacterial physiology and genetics are not being trained, seriously
jeopardizing science, medicine, and industry. There are several potential
reasons for this neglect. First, other than the widespread publicity about the
impact of antibiotic resistance, the community has done a poor job of
explaining the importance of bacteria to the public. Because of this lack of
awareness, there is no forceful public lobby promoting research on bacteria. In
addition, this limits the exposure of young students to the exciting
opportunities in this field. Second, over the last several decades there have
been shifts in emphasis within academic institutions that have led to a decline
in department support, hiring, and curriculum emphasis on microbiology; in
some cases microbiological research has been subsumed within other
departments, e.g., cell biology. Thus, despite the critical importance of
microbiology research and education, many microbiology departments have
shrunk or disappeared.

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BACTERIA AND ITS CONCERN AND A

TOOL FOR RESEARCH

Bacteria are also instrumental for understanding fundamental life processes

Impact of New Technologies

Training in basic research on bacteria also provides the skills needed in

There is a widespread perception among microbiologists that enough scientists

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