Manipulating Bacterial Communities by in situ Microbiome Engineering

Sheth, Ravi U.; Cabral, Vitor; Chen, Sway P.; Wang, Harris H.

doi:10.1016/j.tig.2016.01.005

Cited by 233 publications

(194 citation statements)

References 73 publications

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“…The first tactic involves the introduction or elimination of selected microbial taxa from the host. 6−8 This approach was successfully tested in animal models of inflammatory bowel disease, 9−11 arthritis, 12 colon cancer, 13 cystic fibrosis, 14 and depression, 15 resulting in the restoration of disease-free phenotypes. This method was also effectively used in humans to restore resilience against Clostridium difficile colonization.…”

mentioning

confidence: 99%

Opportunistic Sampling of Roadkill as an Entry Point to Accessing Natural Products Assembled by Bacteria Associated with Non-anthropoidal Mammalian Microbiomes

Motley¹,

Stamps

Mitchell³

et al. 2016

J. Nat. Prod.

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Few secondary metabolites have been reported from mammalian microbiome bacteria despite the large numbers of diverse taxa that inhabit warm-blooded higher vertebrates. As a means to investigate natural products from these microorganisms, an opportunistic sampling protocol was developed, which focused on exploring bacteria isolated from roadkill mammals. This initiative was made possible through the establishment of a newly created discovery pipeline, which couples laser ablation electrospray ionization mass spectrometry (LAESIMS) with bioassay testing, to target biologically active metabolites from microbiome-associated bacteria. To illustrate this process, this report focuses on samples obtained from the ear of a roadkill opossum (Dideiphis virginiana) as the source of two bacterial isolates (Pseudomonas sp. and Serratia sp.) that produced several new and known cyclic lipodepsipeptides (viscosin and serrawettins, respectively). These natural products inhibited biofilm formation by the human pathogenic yeast Candida albicans at concentrations well below those required to inhibit yeast viability. Phylogenetic analysis of 16S rRNA gene sequence libraries revealed the presence of diverse microbial communities associated with different sites throughout the opossum carcass. A putative biosynthetic pathway responsible for the production of the new serrawettin analogues was identified by sequencing the genome of the Serratia sp. isolate. This study provides a functional roadmap to carrying out the systematic investigation of the genomic, microbiological, and chemical parameters related to the production of natural products made by bacteria associated with non-anthropoidal mammalian microbiomes. Discoveries emerging from these studies are anticipated to provide a working framework for efforts aimed at augmenting microbiomes to deliver beneficial natural products to a host.

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mentioning

confidence: 99%

Opportunistic Sampling of Roadkill as an Entry Point to Accessing Natural Products Assembled by Bacteria Associated with Non-anthropoidal Mammalian Microbiomes

Motley¹,

Stamps

Mitchell³

et al. 2016

J. Nat. Prod.

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“…With the recent revolution in genome engineering capabilities to manipulate microbes and higher-order organisms [2], the scale up of microbiome engineering to systems with more complex functions in dynamic environments is poised to become an exciting and fruitful endeavor for synthetic biology. New opportunities to engineer microbial communities in open and changing environments will require next-generation in situ approaches [61]. The bottom-up study of synthetic communities will likely yield a better understanding for natural microbial ecology by systematically evaluating individual parameters in a controlled environment in an iterative design-test-learn cycle.…”

Section: Conclusion and Future Outlookmentioning

confidence: 99%

Principles for designing synthetic microbial communities

Johns

Blazejewski

Gomes

et al. 2016

Current Opinion in Microbiology

236

158

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Advances in synthetic biology to build microbes with defined and controllable properties are enabling new approaches to design and program multispecies communities. This emerging field of synthetic ecology will be important for many areas of biotechnology, bioenergy and bioremediation. This endeavor draws upon knowledge from synthetic biology, systems biology, microbial ecology and evolution. Fully realizing the potential of this discipline requires the development of new strategies to control the intercellular interactions, spatiotemporal coordination, robustness, stability and biocontainment of synthetic microbial communities. Here, we review recent experimental, analytical and computational advances to study and build multispecies microbial communities with defined functions and behavior for various applications. We also highlight outstanding challenges and future directions to advance this field.

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“…It will also be necessary to fully understand the functional redundancy of the microbiome in invasive phytophagous insects to avoid functional compensation of the disrupted invasive traits. Finally, thoroughly testing the solutions in the field will be required as it has been previously shown that responses of hosts to "microbiome engineering" are not necessarily long-lasting (Sheth et al 2016), and unexpected variation in hosts/environmental conditions might occur.…”

Section: Outcomes and Important Considerationsmentioning

confidence: 99%

A response to Pennisi - “How do gut microbiomes help herbivores”, a hint into next-generation biocontrol solutions

Lefort¹,

Boyer²,

Glare³

2017

ReEco

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In a world where invasive invertebrate species can significantly compromise food security and where a dwindling range of synthetic pesticides remains our principal line of defence, testing a new invasion ecology hypothesis and understanding what makes a phytophagous insect invasive should be regarded as high priority research. Recent advances in microbiology strongly support the crucial and effective role of the gut microbiome in insect growth, development and, most importantly, environmental adaptation to their host plants. On the basis of recent literature, and following Elizabeth Pennisi's article published in the journal Science, we hypothesis that gut microbiome could be a critical determinant of invasion success in phytophagous insects, and that the uncovering of common traits in the gut microbiome of invasive insects, a "gut microbiome invasiveness signature", would open new avenues of research towards nextgeneration biocontrol solutions.

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Manipulating Bacterial Communities by in situ Microbiome Engineering

Cited by 233 publications

References 73 publications

Opportunistic Sampling of Roadkill as an Entry Point to Accessing Natural Products Assembled by Bacteria Associated with Non-anthropoidal Mammalian Microbiomes

Opportunistic Sampling of Roadkill as an Entry Point to Accessing Natural Products Assembled by Bacteria Associated with Non-anthropoidal Mammalian Microbiomes

Principles for designing synthetic microbial communities

A response to Pennisi - “How do gut microbiomes help herbivores”, a hint into next-generation biocontrol solutions

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