Journal ArticleDOI
In situ cultivation of previously uncultivable microorganisms using the ichip.
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This work moved cultivation into the microbes' natural habitat by placing cells taken from varying environmental samples into diffusion chambers, which are then returned to nature for incubation, and called this cultivation platform the 'isolation chip', or 'ichip'.Abstract:
Most microbial species remain uncultivated, and modifying artificial nutrient media brings only an incremental increase in cultivability We reasoned that an alternative way to cultivate species with unknown requirements is to use naturally occurring combinations of growth factors To achieve this, we moved cultivation into the microbes' natural habitat by placing cells taken from varying environmental samples into diffusion chambers, which are then returned to nature for incubation By miniaturizing the chambers and placing only one to several cells into each chamber, we can grow and isolate microorganisms in axenic culture in one step We call this cultivation platform the 'isolation chip', or 'ichip' This platform has been shown to increase microbial recovery from 5- to 300-fold, depending on the study Furthermore, it provides access to a unique set of microbes that are inaccessible by standard cultivation Here we provide a simple protocol for building and applying ichips for environmental cultivation of soil bacteria as an example; the protocol consists of (i) preparing the ichip; (ii) collecting an environmental sample; (iii) serially diluting cells and loading them into the ichip; (iv) returning the ichip to the environment for incubation; (v) retrieving the ichip and harvesting grown material; and (vi) domestication of the ichip-derived colonies for growth in the laboratory The ichip's full assembly and deployment is a relatively simple procedure that, with experience, takes ∼2-3 h After in situ incubation, retrieval of the ichip and processing of its contents will take ∼1-4 h, depending on which specific procedures are usedread more
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Journal ArticleDOI
Human Gut Microbiome: Function Matters
Anna Heintz-Buschart,Paul Wilmes +1 more
TL;DR: It is argued that the closing of existing gaps in functional knowledge should be addressed by a most-wanted gene list, the development and application of molecular and cellular high-throughput measurements, theDevelopment and sensible use of experimental models, as well as the direct study of observable molecular effects in the human host.
Journal ArticleDOI
High proportions of bacteria and archaea across most biomes remain uncultured.
Andrew D. Steen,Alexander Crits-Christoph,Paul Carini,Kristen M. DeAngelis,Kristen M. DeAngelis,Noah Fierer,Noah Fierer,Karen G. Lloyd,J. Cameron Thrash +8 more
TL;DR: The evidence supports the conclusion that most bacterial and archaeal taxa remain uncultured, as sequence similarity cannot be used to infer “culturability" because one cannot infer physiology from 16S rRNA gene sequences.
Journal ArticleDOI
Targeted isolation and cultivation of uncultivated bacteria by reverse genomics.
Karissa L. Cross,Karissa L. Cross,James H. Campbell,James H. Campbell,Manasi Balachandran,Alisha G. Campbell,Alisha G. Campbell,Alisha G. Campbell,Sarah J. Cooper,Sarah J. Cooper,Ann L. Griffen,Matthew Heaton,Snehal S. Joshi,Dawn M. Klingeman,Eugene J. Leys,Zamin Yang,Jerry M. Parks,Jerry M. Parks,Mircea Podar,Mircea Podar +19 more
TL;DR: Reverse-genomics-enabled cultivation of microorganisms can be applied to any species from any environment and has the potential to unlock the isolation, cultivation and characterization of species from as-yet-uncultured branches of the microbial tree of life.
Journal ArticleDOI
The Inherent Conflicts in Developing Soil Microbial Inoculants.
TL;DR: A holistic temporal model of the shifting constraints on inoculants at five stages of product development and application is proposed, and potential conflicts between stages are highlighted.
Journal ArticleDOI
Thinking Outside the Box-Novel Antibacterials To Tackle the Resistance Crisis.
TL;DR: This Review encompasses several aspects of the antibiotic development pipeline from very early strategies to mature drugs, and aims to connect innovative antimicrobial approaches to stimulate interdisciplinary partnerships between chemists from academia and industry.
References
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Journal ArticleDOI
The use of DAPI for identifying and counting aquatic microflora1
Karen G. Porter,Yvette S. Feig +1 more
TL;DR: Use of DAPI improved visualization and counting of <1-µm bacteria and blue-green algae in seston-rich samples and extended sample storage to at least 24 weeks.
Journal ArticleDOI
A new antibiotic kills pathogens without detectable resistance
Losee Lucy Ling,Tanja Schneider,Aaron J. Peoples,Amy Spoering,Ina Engels,Brian P. Conlon,A. Mueller,Till F. Schäberle,Dallas Hughes,Slava S. Epstein,M. Jones,Linos Lazarides,Victoria Alexandra Steadman,Cohen Dr,Cintia R. Felix,Fetterman Ka,William Millett,Anthony Nitti,Ashley Zullo,Chao Chen,Kim Lewis +20 more
TL;DR: The properties of this compound suggest a path towards developing antibiotics that are likely to avoid development of resistance, as well as several methods to grow uncultured organisms by cultivation in situ or by using specific growth factors.
Journal ArticleDOI
The Uncultured Microbial Majority
TL;DR: Genome sequence information that would allow ribosomal RNA gene trees to be related to broader patterns in microbial genome evolution is scant, and therefore microbial diversity remains largely unexplored territory.
Journal ArticleDOI
Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats.
James T. Staley,Allan E. Konopka +1 more
TL;DR: Comparisons between Methods and Applications are compared and problems in Interpreting the Measurement are addressed.
Journal ArticleDOI
Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment.
TL;DR: A diffusion chamber was designed that allowed the growth of previously uncultivated microorganisms in a simulated natural environment and isolated representative marine organisms, which formed colonies in the presence of other microorganisms.
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