Tools for the Microbiome: Nano and Beyond

Biteen, Julie S.; Blainey, Paul C.; Cardon, Zoë G.; Chun, Miyoung; Church, George M.; Dorrestein, Pieter C.; Fraser, Scott E.; Gilbert, Jack A.; Jansson, Janet; Knight, Rob; Miller, Jeff F.; Ozcan, Aydogan; Prather, Kimberly A.; Quake, Stephen R.; Ruby, Edward G.; Silver, Pamela A.; Taha, Sharif; Engh, Ger van den; Weiss, Paul S.; Wong, Gerard C. L.; Wright, Aaron; Young, Thomas D.

doi:10.1021/acsnano.5b07826

Cited by 138 publications

(145 citation statements)

References 331 publications

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“…1,2 While most of the GI microbes live in harmony with the host, some are hostile and cause a variety of diseases. These bacteria colonize in different segments of the GI tract, dependent on local factors.…”

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confidence: 99%

Enteric Micromotor Can Selectively Position and Spontaneously Propel in the Gastrointestinal Tract

et al. 2016

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The gastrointestinal (GI) tract, which hosts hundreds of bacteria species, becomes the most exciting organ for the emerging microbiome research. Some of these GI microbes are hostile and cause a variety of diseases. These bacteria colonize in different segments of the GI tract dependent on the local physicochemical and biological factors. Therefore, selectively locating therapeutic or imaging agents to specific GI segments is of significant importance for studying gut microbiome and treating various GI-related diseases. Herein, we demonstrate an enteric micromotor system capable of precise positioning and controllable retention in desired segments of the GI tract. These motors, consisting of magnesium-based tubular micromotors coated with an enteric polymer layer, act as a robust nanobiotechnology tool for site-specific GI delivery. The micromotors can deliver payload to particular location via dissolution of their enteric coating to activate their propulsion at the target site towards localized tissue penetration and retention.

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confidence: 99%

Enteric Micromotor Can Selectively Position and Spontaneously Propel in the Gastrointestinal Tract

et al. 2016

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“…Mass-production of the starter microbiome inoculum can be thought of with improvements in the additive printing technology (3D printing technology) of microscopic bacterial communities (Connell et al, 2013). Though the plant microbiome research is in its growing stage, with increased understanding of the mechanisms by which community coalescence takes place vis-a-vis the microbial assemblage (Rillig et al, 2016) and several new methods available for studying the rhizosphere environment (Oburger and Schmidt, 2016) including nano-scale tools (Biteen et al, 2016), the challenge can be surmounted with improvement in the knowledge of the microbe-to-microbe and microbe-to-plant interactions by the end of the decade (Mitter et al, 2016) to be able to provide solutions for 21st century crises (Blaser et al, 2016). …”

Section: Co-propagating the Co-evolvedmentioning

confidence: 99%

Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies

2016

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“No plant is an island too…”Plants, though sessile, have developed a unique strategy to counter biotic and abiotic stresses by symbiotically co-evolving with microorganisms and tapping into their genome for this purpose. Soil is the bank of microbial diversity from which a plant selectively sources its microbiome to suit its needs. Besides soil, seeds, which carry the genetic blueprint of plants during trans-generational propagation, are home to diverse microbiota that acts as the principal source of microbial inoculum in crop cultivation. Overall, a plant is ensconced both on the outside and inside with a diverse assemblage of microbiota. Together, the plant genome and the genes of the microbiota that the plant harbors in different plant tissues, i.e., the ‘plant microbiome,’ form the holobiome which is now considered as unit of selection: ‘the holobiont.’ The ‘plant microbiome’ not only helps plants to remain fit but also offers critical genetic variability, hitherto, not employed in the breeding strategy by plant breeders, who traditionally have exploited the genetic variability of the host for developing high yielding or disease tolerant or drought resistant varieties. This fresh knowledge of the microbiome, particularly of the rhizosphere, offering genetic variability to plants, opens up new horizons for breeding that could usher in cultivation of next-generation crops depending less on inorganic inputs, resistant to insect pest and diseases and resilient to climatic perturbations. We surmise, from ever increasing evidences, that plants and their microbial symbionts need to be co-propagated as life-long partners in future strategies for plant breeding. In this perspective, we propose bottom–up approach to co-propagate the co-evolved, the plant along with the target microbiome, through – (i) reciprocal soil transplantation method, or (ii) artificial ecosystem selection method of synthetic microbiome inocula, or (iii) by exploration of microRNA transfer method – for realizing this next-generation plant breeding approach. Our aim, thus, is to bring closer the information accrued through the advanced nucleotide sequencing and bioinformatics in conjunction with conventional culture-dependent isolation method for practical application in plant breeding and overall agriculture.

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“…In an affirmation of the significance of these multispecies ecosystems, our nation’s newest national research initiative—the National Microbiome Initiative—seeks to develop a better understanding of complex microbial communities and their relationship to food, energy, and health. 4,5 …”

Section: Introductionmentioning

confidence: 99%

Mass Spectrometry Imaging of Complex Microbial Communities

et al. 2016

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ConspectusIn the two decades since mass spectrometry imaging (MSI) was first applied to visualize the distribution of peptides across biological tissues and cells, the technique has become increasingly effective and reliable. MSI excels at providing complementary information to existing methods for molecular analysis—such as genomics, transcriptomics, and metabolomics—and stands apart from other chemical imaging modalities through its capability to generate information that is simultaneously multiplexed and chemically specific. Today a diverse family of MSI approaches are applied throughout the scientific community to study the distribution of proteins, peptides, and small-molecule metabolites across many biological models.The inherent strengths of MSI make the technique valuable for studying microbial systems. Many microbes reside in surface-attached multicellular and multispecies communities, such as biofilms and motile colonies, where they work together to harness surrounding nutrients, fend off hostile organisms, and shield one another from adverse environmental conditions. These processes, as well as many others essential for microbial survival, are mediated through the production and utilization of a diverse assortment of chemicals. Although bacterial cells are generally only a few microns in diameter, the ecologies they influence can encompass entire ecosystems, and the chemical changes that they bring about can occur over time scales ranging from milliseconds to decades. Because of their incredible complexity, our understanding of and influence over microbial systems requires detailed scientific evaluations that yield both chemical and spatial information. MSI is well-positioned to fulfill these requirements. With small adaptations to existing methods, the technique can be applied to study a wide variety of chemical interactions, including those that occur inside single-species microbial communities, between cohabitating microbes, and between microbes and their hosts.In recognition of this potential for scientific advancement, researchers have adapted MSI methodologies for the specific needs of the microbiology research community. As a result, workflows exist for imaging microbial systems with many of the common MSI ionization methods. Despite this progress, there is substantial room for improvements in instrumentation, sample preparation, and data interpretation. This Account provides a brief overview of the state of technology in microbial MSI, illuminates selected applications that demonstrate the potential of the technique, and highlights a series of development challenges that are needed to move the field forward. In the coming years, as microbial MSI becomes easier to use and more universally applicable, the technique will evolve into a fundamental tool widely applied throughout many divisions of science, medicine, and industry.

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Tools for the Microbiome: Nano and Beyond

Cited by 138 publications

References 331 publications

Enteric Micromotor Can Selectively Position and Spontaneously Propel in the Gastrointestinal Tract

Enteric Micromotor Can Selectively Position and Spontaneously Propel in the Gastrointestinal Tract

Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies

Mass Spectrometry Imaging of Complex Microbial Communities

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