Microbiome engineering: Current applications and its future

Foo, Jee Loon; Ling, Hua; Lee, Yung Seng

doi:10.1002/biot.201600099

Cited by 148 publications

(83 citation statements)

References 64 publications

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“…In host associated communities, the metabolic activity of the microbiota can also profoundly affect the host's health, and has been found to modulate life history traits such as flowering timing in plants [3,4] or the lifespan and reproductive behavior of animals [5,6] . In more applied settings, microbial consortia are being designed for the processing of undesirable materials into valuable products [7][8][9][10][11] , to protect valuable crops from pathogens [12,13] or other stressors [14,15] , or even to increase crop yields [16] . All of these effects that microbial communities have on the environment and their hosts are often referred to as "functions" of these communities.…”

Section: Introductionmentioning

confidence: 99%

High-order interactions dominate the functional landscape of microbial consortia

Sánchez-Gorostiaga

Bajić

Osborne

et al. 2018

Preprint

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Understanding the link between community composition and function is a major challenge in microbial ecology, with implications for the management of natural microbiomes and the design of synthetic consortia. For this purpose, it is critical to understand the extent to which community functions and properties can be predicted from species traits and what role is played by complex interactions. Inspired by the study of complex genetic interactions and fitness landscapes, here we have examined how the amylolytic function of combinatorial assemblages of seven starch-degrading soil bacteria depends on the functional contributions from each species and their interactions. Filtering our experimental results through the theory of enzyme kinetics, we show that high-order functional interactions dominate the amylolytic rate of our consortia, even though this function is biochemically simple, redundantly distributed in the community, and additive in the absence of inter-species interactions. As the community grows in size, the contribution of high-order functional interactions grows too, making the community function increasingly unpredictable. We can explain the prevalence of high order effects and their sign from the redundancy of ecological interactions in the network, in particular from redundant facilitation towards a high-performing community member. Our results suggest that even simple functions can be dominated by complex interactions, posing challenges for the predictability and bottom-up engineering of ecosystem function in complex multi-species communities.

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Section: Introductionmentioning

confidence: 99%

High-order interactions dominate the functional landscape of microbial consortia

Sánchez-Gorostiaga

Bajić

Osborne

et al. 2018

Preprint

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“…funduliforme 1_1_36S (11), F. nucleatum subsp. animalis 11_3_2 (12), Lachnospiraceae bacterium 8_1_57FAA (13), L. bacterium 3_1_46FAA (14), Streptococcus bovis 1212 (15), S. bovis 1459 (16), S. bovis 1417 (17), S. bovis 207 (18), Pediococcus acidilactici 7_4 (19), Pseudomonas sp. 2_1_26 (20), D. sp.…”

Section: Reproducibility Of Growth Rate Alterations By Bacterial Cellmentioning

confidence: 99%

“…The newly acquired bacteria may in turn affect tumor development, by potential inhibiting, enhancing, or neutral effects on tumor cell growth (6). These CRC-specific changes offer the opportunity to use the bacterial community for diagnostic, prognostic, preventive, and treatment measures (11)(12)(13)(14)(15)(16)(17)(18)(19)(20).…”

Section: Introductionmentioning

confidence: 99%

Growth rate alterations of human colorectal cancer cells by 157 gut bacteria

Taddese

Garza²,

Ruiter

et al. 2019

Preprint

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Several bacteria in the human gut microbiome have been associated with colorectal cancer (CRC) by high-throughput screens. In some cases, molecular mechanisms have been elucidated that drive tumorigenesis, including bacterial membrane proteins or secreted molecules that interact with the human cancer cells. For most gut bacteria, however, it remains unknown if they enhance or inhibit cancer cell growth. Here, we screened bacteria-free supernatants (secretomes) and inactivated cells of over 150 cultured bacterial strains for their effect on CRC cell growth. We observed family-level and strain-level effects that often differed between bacterial cells and secretomes, suggesting that different molecular mechanisms are at play.Secretomes of Bacteroidaceae , Enterobacteriaceae, and Erysipelotrichaceae bacteria enhanced CRC cell growth, while most Fusobacteriaceae cells and secretomes inhibited growth, contrasting prior findings. In some bacteria, the presence of specific functional genes was associated with CRC cell growth rates, including the virulence genes TcdA in Clostridiales and FadA in Fusobacteriaceae , which both inhibited growth. Bacteroidaceae cells that enhanced growth were enriched for genes of the cobalamin synthesis pathway, while Fusobacteriaceae cells that inhibit growth were enriched for genes of the ethanolamine utilization pathway.Together, our results reveal how different gut bacteria have wide-ranging effects on cancer cells, contribute a better understanding of the effects of the gut microbiome on the human host, and provide a valuable resource for identifying candidate target genes for potential microbiome-based diagnostics and treatment strategies. 2 5 difficile (47, 48) , Bacteroides sp. (27), and the two potentially beneficial bacteria Lactobacillus casei Shirota (49-51) and Akkermansia muciniphila ATCC BAA-835 TM

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“…Microbial signaling within and across cell communities enables them to perform more complex tasks than single organisms, utilize resources more efficiently, and coordinate their activities . Modeling the relationships within microbiomes and the interactions between microbiome and host in a well‐controlled and spatially analogous manner is of great interest in microbiome engineering and developing new biological technologies …”

Section: Introductionmentioning

confidence: 99%

Constructing Synthetic Ecosystems with Biopolymer Fluitrodes

et al. 2018

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the relationships within microbiomes and the interactions between microbiome and host in a well-controlled and spatially analogous manner is of great interest in microbiome engineering and developing new biological technologies. [4] Microfluidic platforms have been of great interest for cellular studies in the last two decades. Recent transition from two dimensional (2D) to three dimensional (3D) cell culture in microfluidics provides the ability to control and monitor in vitro interactions between cells and extracellular matrix, establish stable chemical gradients and stimuli, deliver oxygen and nutrients, and to remove metabolites and reduce shear stress by laminar flows. [5] For example, natural and synthetic calcium alginate hydrogels were assembled into 3D geometries with high aspect ratio and curvature by combination of laser ablation and sacrificial molding technique. [4b,c] Calcium alginate with target cells was electrodeposited on electrodes or flow-assembled in microfluidics to model biofilms or construct synthetic ecosystems with spatiotemporal programmability. [6] Great advances have been made in organ-on-a-chip systems and synthetic systems that enable spatially controlled cocultures of cells and model various biological events including cancer metastasis and vascular functions. [7] The vast majority of microbial models or the microbehost systems, however, are limited to mixed or binary cultures that either are challenging if not impossible to track changes occurring in individual populations, or lack the compatibility to deliver different nutrients for different species. Challenges remain in culturing cells with a spatial resolution that can be used to study complex interactions between multiple species within microbial communities.This study presents, for the first time, the concept of fluitrodes to conveniently embed multiple cell populations in 3D hydrogels in microfluidics with a spatial resolution of biological relevance. The fluitrodes are freestanding biopolymer membranes that, like electrodes in transmitting electrons, transmit ions and small molecules with spatiotemporal programmability. Since biology information is mainly transmitted via ions and small molecules rather than electrons, the fluitrodes provide a novel platform to communicate with cell populations through ions and molecules in aqueous condition complementary to the communication in solids through an electrode. The spatially patterned cell populations were assembled either side by side or layer by layer in Modeling the complex interactions among organisms found within microbiomes is of great interest for the development of new biological technologies. Challenges remain in culturing cells of multiple species with spatial resolutions similar to microbial communities. Here, a fluitrode concept in microfluidics using biofabrication of functional biopolymers is demonstrated to efficiently assemble multiple cell populations in 3D hydrogels of spatial and biological relevance. The fluitrodes are freestanding biopolymer membranes...

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Microbiome engineering: Current applications and its future

Cited by 148 publications

References 64 publications

High-order interactions dominate the functional landscape of microbial consortia

High-order interactions dominate the functional landscape of microbial consortia

Growth rate alterations of human colorectal cancer cells by 157 gut bacteria

Constructing Synthetic Ecosystems with Biopolymer Fluitrodes

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