METHODS TO WATCH | SPECIAL FEATURE ❯❯Capturing microbial slate that can be colo- interactions nized by different gut bacteria and exposed New approaches will expose microbial to various diets for dependencies and environmental comparative studies. For interactions. human environments, Microbial communities define and are defined organ-on-chip technologies that mimic epi- by their environment. Marina Corral Spence/Springer Nature The science of metagenomics has helped thelia and accommodate bacterial culture researchers characterize microbes as com- can also help assess microbial interactions. munities, but we are only beginning to Combinatorial testing of experimental ­understand microbial dependencies and understand the complexities of interac- conditions, such as finding which bacteria coevolution. tions within these communities and with need to be cocultured in order to grow, can Other in situ methods can also help to the environment. The rhizosphere of a also help to untangle relationships between capture microbial interactions. Techniques single plant root includes commensal and individual components. for quantitative imaging of labeled bacteria pathogenic bacteria that interact with each Sequencing and other omic technologies and their surroundings (Cell Host Microbe other as well as with the plant, soil and are effective ways to track microbial com- 18, 478–488, 2015), including fluorescence fungi. Tumorigenesis has been linked to position and metabolic activity, and they in situ hybridization labeling of bacteria and microbiome-induced inflammation in the allow correlations to be made in the con- noninvasive imaging of extracellular milieu gut. Complex interactions such as these text of well-controlled studies. Sequencing components, add a critical spatial dimen- clearly have important consequences for RNA from both prokaryotic and eukary- sion to microbial studies. Metabolic labeling agriculture as well as disease and health, otic cells simultaneously—in the case of and other methods that can track microbial and methods are needed for deeper intracellular parasites, for example (Nature activity will likewise provide benefits. ­exploration. 529, 496–501, 2016)—can reveal how host New approaches to understanding A key to understanding microbial ecol- and microbe interact at the level of gene microbial interactions should help to solve ogy and host–microbe interactions will be expression. Computational modeling and longstanding and emerging questions, such to develop controlled experimental plat- analysis tools need to be developed to tease as how microbiomes can protect against forms. Gnotobiotic mice provide a blank out environmental correlations and to pathogenic bacteria. Tal Nawy ❯❯Organoid culture ­fragments that contain the major cell the outcomes, correct for it, and ideally Ex vivo organoid culture could types of a particular organ and approxi- control it. We already know from work mate its in vivo organization. They are with differentiating pluripotent stem cells revolutionize biology, but variability typically generated by culturing multipo- in 2D that factors inherent to a cell line must be understood. tent or pluripotent stem cells in a three- can contribute to variability. This is like- dimensional (3D) matrix (most often ly to only be compounded when grow- Imagine if biologists did not depend Matrigel) under conditions that permit ing more complex 3D self-organizing upon two-dimensional (2D) culture of or promote self-organization of the cells. structures, for which even quantitative transformed cell lines on glass or plastic These conditions are determined experi- measures of correct structure and func- and could instead study cellular processes mentally but are often informed by prior tion are still being defined. Work geared in a more realistic ex vivo context. The knowledge of the signals that drive devel- toward improved control of the process, day when this is widely a reality may not opment or regeneration. such as with defined matrices, will be be too far off, given the explosive interest Organoids have been reported for a important, as are attempts to understand in the culture of organoids. range of tissues—retina, kidney, intes- organoid formation using the arsenal of The term ‘organoid’ is used nowa- tine, stomach, lung, brain, and liver, to research techniques—gene editing, imag- days to describe ex vivo multicellular name just a few. As interest in the tech- ing—now available to biologists. nology grows, research efforts are geared The very origins of cell culture lie in toward improved maturation, even to the ‘tissue culture’, in attempts to grow out point of attempting to integrate immune cells from tissue explants. With a return cells and blood vessels into the struc- to methods for growing self-organizing tures. Increasingly, researchers are also organoids, tissue culture has come full growing organoids from primary tumors, circle. But close attention to variability either as models for tumor biology or as and the development and use of quantita- a more realistic system for in vitro drug tive methods to characterize these struc- screens. tures will be necessary if organoids are to Marina Corral Spence/Springer Nature These developments are important. fulfill their potential as ex vivo systems for There are now many methods to form different But the technology will stand or fall with the study of cellular and developmental types of organoids. the ability to understand variability in processes. Natalie de Souza NATURE METHODS | VOL.14 NO.1 | JANUARY 2017 | 35.