We have a community problem

Abstract

W ith the explosion of studies on microbial communities, from the human micro biome to characterizing microbes in the ocean, in soil, and on plants, it is clear that assemblages of microbes are an area of active research interest across the microbial sciences.This focus on communities, on one hand, seems quite natural as most microbes, perhaps outside of implant infections and a few extreme environments, live in a world where they co-exist with myriad other microbes.In contrast, since the development of Koch's postulates in 1890 (a nice summary of Koch's postulates and their history was published recently [1]), focusing on infectious diseases, as well as efforts by Beijerinck and Winogradsky to develop enrichment and isolation techniques, we have often viewed the microbial world through the lens of single species.The microbial species that have received the lion's share of attention are often referred to as "model systems, " maybe better called "model microbes." The best studied model microbe is Escherichia coli, as highlighted in a recent article in the Journal of Bacteriology (2).Other model organisms that have received a great deal of attention include Bacillus subtilis, Pseudomonas aeruginosa, Staphylococcus aureus, Mycobacterium tuberculosis, Streptococcus pneumoniae, Caulobacter crescentus, Candida albicans, Saccharomyces cerevisiae, and Schizosaccharomyces pombe.More recently, steady progress in the development of molecular genetic techniques has enabled our ability to work with "non-traditional" model organisms such as various archaea, sulfate-reducing bacteria, as well as photosynthetic, electrogenic, intestinal, marine microbes, pathogenic fungi, parasites, and others.Thus, the foundation of the microbial knowledge base on which we can build is becoming both broader and deeper.This singular focus on model microbes has helped us make stunning advances in understanding host-microbe interactions, fostered the discovery of antimicrobial agents, been the backbone of clinical microbiology, and allowed us to probe the depths of microbial biology.Indeed, a recently launched and ongoing collection of articles at JB titled "History of Microbial Model Systems" celebrates how a variety of microbial model organisms, typically studied in pure culture in the lab, have been key to enhancing our understanding of the microbial world.A theme running through these articles is that the models are studied via a variety of approaches to answer a spectrum of questions.A more holistic appreciation of microbial systems can be gained by tackling questions from different perspectives.Investigators from different disciplines-genetics, molecular biology, structural, biophysics, mathematics, ecology, evolution, etc.-will bring to their research very different viewpoints and tools.I would argue this is a good thing-when all this information is brought together, we cannot help but have a broad and deep appreciation and understanding of a microbe and its biology.Within the pure-culture research framework of the past ~140 years, our picture can be quite comprehensive for a given microbe, but we are left with an important knowledge gap: how does the microbe relate to the others in its world?Here is where thinking about microbial communities is the critical next step.However, before I talk more about microbial communities, there is an important aside.I contend that before

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