Control of synthetic microbial consortia in time, space, and composition

Synthetic microbial communities: A gateway to understanding resistance, resilience, and functionality in spontaneously fermented food microbiomes

This review delves into the intricate traits of microbial communities encountered in spontaneously fermented foods (SFF), contributing to resistance, resilience, and functionality drivers. Traits of SFF microbiomes comprise of fluctuations in community composition, genetic stability, and condition-specific phenotypes. Synthetic microbial communities (SMCs) serve as a portal for mechanistic insights and strategic re-programming of microbial communities. Current literature underscores the pivotal role of microbiomes in SFF in shaping quality attributes and preserving the cultural heritage of their origin. In contrast to starter driven fermentations that tend to be more controlled but lacking the capacity to maintain or reproduce the complex flavors and intricacies found in SFF. SMCs, therefore, become indispensable tools, providing a nuanced understanding and control over fermented food microbiomes. They empower the prediction and engineering of microbial interactions and metabolic pathways with the aim of optimizing outcomes in food processing. Summarizing the current application of SMCs in fermented foods, there is still space for improvement. Challenges in achieving stability and reproducibility in SMCs are identified, stemming from non-standardized approaches. The future direction should involve embracing standardized protocols, advanced monitoring tools, and synthetic biology applications. A holistic, multi-disciplinary approach is paramount to unleashing the full potential of SMCs and fostering sustainable and innovative applications in fermented food systems.

Horizon scanning of potential environmental applications of terrestrial animals, fish, algae and microorganisms produced by genetic modification, including the use of new genomic techniques

With scientific progress and the development of new genomic techniques (NGTs), the spectrum of organisms modified for various purposes is rapidly expanding and includes a wide range of taxonomic groups. An improved understanding of which newly developed products may be introduced into the market and released into the environment in the near and more distant future is of particular interest for policymakers, regulatory authorities, and risk assessors. To address this information need, we conducted a horizon scanning (HS) of potential environmental applications in four groups of organisms: terrestrial animals (excluding insects and applications with gene drives), fish, algae and microorganisms. We applied a formal scoping review methodology comprising a structured search of the scientific literature followed by eligibility screening, complemented by a survey of grey literature, and regulatory websites and databases. In all four groups of organisms we identified a broad range of potential applications in stages of basic as well as advanced research, and a limited number of applications which are on, or ready to be placed on, the market. Research on GM animals including fish is focused on farmed animals and primarily targets traits which increase performance, influence reproduction, or convey resistance against diseases. GM algae identified in the HS were all unicellular, with more than half of the articles concerning biofuel production. GM algae applications for use in the environment include biocontrol and bioremediation, which are also the main applications identified for GM microorganisms. From a risk assessor's perspective these potential applications entail a multitude of possible pathways to harm. The current limited level of experience and limited amount of available scientific information could constitute a significant challenge in the near future, for which risk assessors and competent authorities urgently need to prepare.

Identifying LasR Quorum Sensors with Improved Signal Specificity by Mapping the Sequence-Function Landscape

Programmable intercellular signaling using components of naturally occurring quorum sensing can allow for coordinated functions to be engineered in microbial consortia. LuxR-type transcriptional regulators are widely used for this purpose and are activated by homoserine lactone (HSL) signals. However, they often suffer from imperfect molecular discrimination of structurally similar HSLs, causing misregulation within engineered consortia containing multiple HSL signals. Here, we studied one such example, the regulator LasR from Pseudomonas aeruginosa. We elucidated its sequence-function relationship for ligand specificity using targeted protein engineering and multiplexed high-throughput biosensor screening. A pooled combinatorial saturation mutagenesis library (9,486 LasR DNA sequences) was created by mutating six residues in LasR's β5 sheet with single, double, or triple amino acid substitutions. Sort-seq assays were performed in parallel using cognate and noncognate HSLs to quantify each corresponding sensor's response to each HSL signal, which identified hundreds of highly specific variants. Sensor variants identified were individually assayed and exhibited up to 60.6-fold (p = 0.0013) improved relative activation by the cognate signal compared to the wildtype. Interestingly, we uncovered prevalent mutational epistasis and previously unidentified residues contributing to signal specificity. The resulting sensors with negligible signal crosstalk could be broadly applied to engineer bacteria consortia.

Thermodynamics of microbial consortia: Enthalpies and Gibbs energies of microorganism live matter and macromolecules of E. coli, G. oxydans, P. fluorescens, S. thermophilus and P. chrysogenum

Every microorganism represents a biothermodynamic system, characterized by an empirical formula and thermodynamic properties of biosynthesis. Gibbs energy of biosynthesis influences the multiplication rate of a microorganism. In case of a mixed culture (microbial consortia) biosynthesis processes of microbial species are competitive. This is why Gibbs energy of biosynthesis determines the growth in a mixed culture. This paper gives a mechanistic model that explains growth of microorganisms in mixed culture and ability to grow in microbial consortia. Detailed biosynthesis reactions were formulated for the first time for five microorganism species, which include metallic elements. Moreover, thermodynamic properties of live matter and biosynthesis were calculated for the first time for five microorganism species and macromolecules.

Optogenetic spatial patterning of cooperation in yeast populations

Microbial communities are shaped by complex metabolic interactions such as cooperation and competition for resources. Methods to control such interactions could lead to major advances in our ability to better engineer microbial consortia for synthetic biology applications. Here, we use optogenetics to control SUC2 invertase production in yeast, thereby shaping spatial assortment of cooperator and cheater cells. Yeast cells behave as cooperators (i.e., transform sucrose into hexose, a public good) upon blue light illumination or cheaters (i.e., consume hexose produced by cooperators to grow) in the dark. We show that cooperators benefit best from the hexoses they produce when their domain size is constrained between two cut-off length-scales. From an engineering point of view, the system behaves as a bandpass filter. The lower limit is the trace of cheaters' competition for hexoses, while the upper limit is defined by cooperators' competition for sucrose. Cooperation mostly occurs at the frontiers with cheater cells, which not only compete for hexoses but also cooperate passively by letting sucrose reach cooperators. We anticipate that this optogenetic method could be applied to shape metabolic interactions in a variety of microbial ecosystems.

A synthetic microbial consortium protects against obesity by regulating vitamin B6 metabolism

Constructing synthetic microbial consortia is a challenging task but holds enormous potential for various applications. Our previous droplet-based microfluidic approach allowed for the isolation of bacteria that could utilize metabolites from an engineered bacterium BsS-RS06551 with anti-obesity potential, facilitating the construction of synthetic microbial consortia. Here, we identified a strain of Bifidobacterium pseudocatenulatum JJ3 that interacted with BsS-RS06551, and in vitro coculture showed that BsS-RS06551 was likely to interact with JJ3 through five dipeptides. Pathway analysis revealed that the vitamin B6 metabolism pathway was enriched in the coculture of BsS-RS06551 and JJ3 compared with the individual culture of BsS-RS06551. Additionally, we confirmed that the administration of JJ3 significantly alleviated obesity and related disorders in mice fed a high-fat diet. Notably, continuous ingestion of the synthetic microbial consortium comprising BsS-RS06551 and JJ3 not only exhibited a more pronounced impact on alleviating obesity compared to the individual administration of BsS-RS06551 or JJ3 but also enriched the population of Bifidobacterium longum and perturbed the vitamin B6 metabolism pathway in the gut. Synthetic microbial consortia represent a promising frontier for synthetic biology, and our strategy provides guidance for constructing and applying such consortia.

Plant Growth-Promoting Bacteria of Soil: Designing of Consortia Beneficial for Crop Production

Plant growth-promoting bacteria are commonly used in agriculture, particularly for seed inoculation. Multispecies consortia are believed to be the most promising form of these bacteria. However, designing and modeling bacterial consortia to achieve desired phenotypic outcomes in plants is challenging. This review aims to address this challenge by exploring key antimicrobial interactions. Special attention is given to approaches for developing soil plant growth-promoting bacteria consortia. Additionally, advanced omics-based methods are analyzed that allow soil microbiomes to be characterized, providing an understanding of the molecular and functional aspects of these microbial communities. A comprehensive discussion explores the utilization of bacterial preparations in biofertilizers for agricultural applications, focusing on the intricate design of synthetic bacterial consortia with these preparations. Overall, the review provides valuable insights and strategies for intentionally designing bacterial consortia to enhance plant growth and development.

Engineered Escherichia coli Consortia Function in a Programmable Pattern for Multiple Enzymatic Biosynthesis

Coordinating microbial consortia to realize complex synthetic pathways is an area of great interest in the rapidly growing field of biomanufacturing. This work presents a programmable method for assembling living cells based on the surface display of affinity groups, enabling whole-cell catalysis with optimized catalytic efficiency through the rational arrangement of cell assemblies and enzymes. In the context of d-phenyllactic acid (d-PLA) synthesis, four enzymes were rationally arranged considering substrate channeling and protein expression levels. The production efficiencies of d-PLA catalyzed by engineered microbial consortia were 1.31- and 2.55-fold higher than those of biofilm and whole-cell catalysts, respectively. Notably, substrate channeling was identified between the coimmobilized rate-limiting enzymes, resulting in a 3.67-fold improvement in catalytic efficiency compared with hybrid catalysts (free enzymes coupled with whole-cell catalysts). The highest yield of d-PLA catalyzed by microbial consortia was 102.85 ± 3.39 mM with 140 mM benzaldehyde as the substrate. This study proposes a novel approach to cell enzyme assembly for coordinating microbial consortia in multiple enzymatic biosynthesis processes.

Synthesizing microbial biodiversity

The diversity of microbial ecosystems is linked to crucial ecological processes and functions. Despite its significance, the ecological mechanisms responsible for the initiation and maintenance of microbiome diversity are still not fully understood. The primary challenge lies in the difficulty of isolating, monitoring, and manipulating the complex and interrelated ecological processes that modulate the diversity of microbial communities in their natural habitats. Synthetic ecology experiments provide a suitable alternative for investigating the mechanisms behind microbial biodiversity in controlled laboratory settings, as the environment can be systematically and modularly manipulated by adding and removing components. This enables the testing of hypotheses and the advancement of predictive theories. In this review, we present an overview of recent progress toward achieving this goal.

Enhanced probiotic potential of Lactobacillus kefiranofaciens OSU-BDGOA1 through co-culture with Kluyveromyces marxianus bdgo-ym6

Introduction

Due to the increasing consumer demand for the development and improvement of functional foods containing probiotics, new probiotic candidates need to be explored as well as novel means to enhance their beneficial effects. Lactobacillus kefiranofaciens OSU-BDGOA1 is a strain isolated from kefir grains that has demonstrated probiotic traits. This species is the main inhabitant of kefir grains and is responsible for the production of an exopolysaccharide (EPS) whit vast technological applications and potential bioactivities. Research has shown that interkingdom interactions of yeast and lactic acid bacteria can enhance metabolic activities and promote resistance to environmental stressors.

Methods

Comparative genomic analyses were performed to distinguish OSU-BDGOA1 from other strains of the same species, and the genome was mined to provide molecular evidence for relevant probiotic properties. We further assessed the cumulative effect on the probiotic properties of OSU-BDGOA1 and Kluyveromyces marxianus bdgo-ym6 yeast co-culture compared to monocultures.

Results

Survival during simulated digestion assessed by the INFOGEST digestion model showed higher survival of OSU-BDGOA1 and bdgo-ym6 in co-culture. The adhesion to intestinal cells assessed with the Caco-2 intestinal cell model revealed enhanced adhesion of OSU-BDGOA1 in co-culture. The observed increase in survival during digestion could be associated with the increased production of EPS during the late exponential and early stationary phases of co-culture that, by enhancing co-aggregation between the yeast and the bacterium, protects the microorganisms from severe gastrointestinal conditions as observed by SEM images. Immune modulation and barrier function for recovery and prevention of flagellin-mediated inflammation by Salmonella Typhimurium heat-killed cells (HKSC) in Caco-2 cells were also measured. OSU-BDGOA1 in mono- and co-culture regulated inflammation through downregulation of pro-inflammatory cytokine expression and increased membrane barrier integrity assessed by TEER, FD4 permeability, and expression of tight junctions.

Discussion

The results of the study warrant further research into the application of co-cultures of yeast and LAB in functional probiotic products and the potential to increase EPS production by co-culture strategies.

Mediation of Bacterial Interactions via a Novel Membrane-Based Segregator to Enhance Biological Nitrogen Removal

The regulation of microbial subpopulations in wastewater treatment plants (WWTPs) with desired functions can guarantee nutrient removal. In nature, "good fences make good neighbors," which can be applied to engineering microbial consortia. Herein, a membrane-based segregator (MBSR) was proposed, where porous membranes not only promote the diffusion of metabolic products but also isolate incompatible microbes. The MBSR was integrated with an anoxic/aerobic membrane bioreactor (i.e., an experimental MBR). The long-term operation showed that the experimental MBR exhibited higher nitrogen removal (10.45 ± 2.73 mg/L total nitrogen) than the control MBR (21.68 ± 4.23 mg/L) in the effluent. The MBSR resulted in much lower oxygen reduction potential in the anoxic tank of the experimental MBR (-82.00 mV) compared to that of the control MBR (83.25 mV). The lower oxygen reduction potential can inevitably aid in the occurrence of denitrification. The 16S rRNA sequencing showed that the MBSR significantly enriched acidogenic consortia, which yielded considerable volatile fatty acids by fermenting the added carbon sources and allowed efficient transfer of these small molecules to the denitrifying community. Moreover, the sludge communities of the experimental MBR harbored a higher abundance of denitrifying bacteria than those of the control MBR. Metagenomic analysis further corroborated these sequencing results. The spatially structured microbial communities in the experimental MBR system demonstrate the practicability of the MBSR, achieving nitrogen removal efficiency superior to that of mixed populations. Our study provides an engineering method for modulating the assembly and metabolic division of labor of subpopulations in WWTPs. IMPORTANCE This study provides an innovative and applicable method for regulating subpopulations (activated sludge and acidogenic consortia), which contributes to the precise control of the metabolic division of labor in biological wastewater treatment processes.

Yeast biofilms on abiotic surfaces: Adhesion factors and control methods

Biofilms are highly resistant to antimicrobials and are a common problem in many industries, including pharmaceutical, food and beverage. Yeast biofilms can be formed by various yeast species, including Candida albicans, Saccharomyces cerevisiae, and Cryptococcus neoformans. Yeast biofilm formation is a complex process that involves several stages, including reversible adhesion, followed by irreversible adhesion, colonization, exopolysaccharide matrix formation, maturation and dispersion. Intercellular communication in yeast biofilms (quorum-sensing mechanism), environmental factors (pH, temperature, composition of the culture medium), and physicochemical factors (hydrophobicity, Lifshitz-van der Waals and Lewis acid-base properties, and electrostatic interactions) are essential to the adhesion process. Studies on the adhesion of yeast to abiotic surfaces such as stainless steel, wood, plastic polymers, and glass are still scarce, representing a gap in the field. The biofilm control formation can be a challenging task for food industry. However, some strategies can help to reduce biofilm formation, such as good hygiene practices, including regular cleaning and disinfection of surfaces. The use of antimicrobials and alternative methods to remove the yeast biofilms may also be helpful to ensure food safety. Furthermore, physical control measures such as biosensors and advanced identification techniques are promising for yeast biofilms control. However, there is a gap in understanding why some yeast strains are more tolerant or resistant to sanitization methods. A better understanding of tolerance and resistance mechanisms can help researchers and industry professionals to develop more effective and targeted sanitization strategies to prevent bacterial contamination and ensure product quality. This review aimed to identify the most important information about yeast biofilms in the food industry, followed by the removal of these biofilms by antimicrobial agents. In addition, the review summarizes the alternative sanitizing methods and future perspectives for controlling yeast biofilm formation by biosensors.

Non-gene-editing microbiome engineering of spontaneous food fermentation microbiota-Limitation control, design control, and integration

Non-gene-editing microbiome engineering (NgeME) is the rational design and control of natural microbial consortia to perform desired functions. Traditional NgeME approaches use selected environmental variables to force natural microbial consortia to perform the desired functions. Spontaneous food fermentation, the oldest kind of traditional NgeME, transforms foods into various fermented products using natural microbial networks. In traditional NgeME, spontaneous food fermentation microbiotas (SFFMs) are typically formed and controlled manually by the establishment of limiting factors in small batches with little mechanization. However, limitation control generally leads to trade-offs between efficiency and the quality of fermentation. Modern NgeME approaches based on synthetic microbial ecology have been developed using designed microbial communities to explore assembly mechanisms and target functional enhancement of SFFMs. This has greatly improved our understanding of microbiota control, but such approaches still have shortcomings compared to traditional NgeME. Here, we comprehensively describe research on mechanisms and control strategies for SFFMs based on traditional and modern NgeME. We discuss the ecological and engineering principles of the two approaches to enhance the understanding of how best to control SFFM. We also review recent applied and theoretical research on modern NgeME and propose an integrated in vitro synthetic microbiota model to bridge gaps between limitation control and design control for SFFM.

Synthetic biology by controller design

Natural biological systems display complex regulation and synthetic biomolecular systems have been used to understand their natural counterparts and to parse sophisticated regulations into core design principles. At the same time, the engineering of biomolecular systems has unarguable potential to transform current and to enable new, yet-to-be-imagined, biotechnology applications. In this review, we discuss the progression of control systems design in synthetic biology, from the purpose of understanding the function of naturally occurring regulatory motifs to that of creating genetic circuits whose function is sufficiently robust for biotechnology applications.

Integrative biohydrogen- and biomethane-producing bioprocesses for comprehensive production of biohythane

The production of biohythane, a combination of energy-dense hydrogen and methane, from the anaerobic digestion of low-cost organic wastes has attracted attention as a potential candidate for the transition to a sustainable circular economy. Substantial research has been initiated to upscale the process engineering to establish a hythane-based economy by addressing major challenges associated with the process and product upgrading. This review provides an overview of the feasibility of biohythane production in various anaerobic digestion systems (single-stage, dual-stage) and possible technologies to upgrade biohythane to hydrogen-enriched renewable natural gas. The main goal of this review is to promote research in biohythane production technology by outlining critical needs, including meta-omics and metabolic engineering approaches for the advancements in biohythane production technology.

Controlling microbial co-culture based on substrate pulsing can lead to stability through differential fitness advantages

Microbial consortia are an exciting alternative for increasing the performances of bioprocesses for the production of complex metabolic products. However, the functional properties of microbial communities remain challenging to control, considering the complex interaction mechanisms occurring between co-cultured microbial species. Indeed, microbial communities are highly dynamic and can adapt to changing environmental conditions through complex mechanisms, such as phenotypic diversification. We focused on stabilizing a co-culture of Saccharomyces cerevisiae and Escherichia coli in continuous cultures. Our preliminary data pointed out that transient diauxic shifts could lead to stable co-culture by providing periodic fitness advantages to the yeast. Based on a computational toolbox called MONCKS (for MONod-type Co-culture Kinetic Simulation), we were able to predict the dynamics of diauxic shift for both species based on a cybernetic approach. This toolbox was further used to predict the frequency of diauxic shift to be applied to reach co-culture stability. These simulations were successfully reproduced experimentally in continuous bioreactors with glucose pulsing. Finally, based on a bet-hedging reporter, we observed that the yeast population exhibited an increased phenotypic diversification process in co-culture compared with mono-culture, suggesting that this mechanism could be the basis of the metabolic fitness of the yeast.

Being able to manipulate the dynamics of microbial co-cultures is a technical challenge that need to be addressed in order to get a deeper insight about how microbial communities are evolving in their ecological context, as well as for exploiting the potential offered by such communities in an applied context e.g., for setting up more robust bioprocesses relying on the use of several microbial species. In this study, we used continuous cultures of bacteria (E. coli) and yeast (S. cerevisiae) in order to demonstrate that a simple nutrient pulsing strategy can be used for adjusting the composition of the community with time. As expected, during growth on glucose, E. coli quickly outcompeted S. cerevisiae. However, when glucose is pulsed into the culture, increased metabolic fitness of the yeast was observed upon reconsumption of the main side metabolites i.e., acetate and ethanol, leading to a robust oscillating growth profile for both species. The optimal pulsing frequency was predicted based on a cybernetic version of a Monod growth model taking into account the main metabolic routes involved in the process. Considering the limited number of metabolic details needed, this cybernetic approach could be generalized to other communities.

Hardware, Software, and Wetware Codesign Environment for Synthetic Biology

Synthetic biology is the process of forward engineering living systems. These systems can be used to produce biobased materials, agriculture, medicine, and energy. One approach to designing these systems is to employ techniques from the design of embedded electronics. These techniques include abstraction, standards, modularity, automated design, and formal semantic models of computation. Together, these elements form the foundation of "biodesign automation," where software, robotics, and microfluidic devices combine to create exciting biological systems of the future. This paper describes a "hardware, software, wetware" codesign vision where software tools can be made to act as "genetic compilers" that transform high-level specifications into engineered "genetic circuits" (wetware). This is followed by a process where automation equipment, well-defined experimental workflows, and microfluidic devices are explicitly designed to house, execute, and test these circuits (hardware). These systems can be used as either massively parallel experimental platforms or distributed bioremediation and biosensing devices. Next, scheduling and control algorithms (software) manage these systems' actual execution and data analysis tasks. A distinguishing feature of this approach is how all three of these aspects (hardware, software, and wetware) may be derived from the same basic specification in parallel and generated to fulfill specific cost, performance, and structural requirements.

Engineering Escherichia coli asymmetry distribution-based synthetic consortium for shikimate production

Microbial consortia constitute a promising tool for achieving high-value chemical bio-production. However, customizing the consortium ratio remains challenging. Herein, an asymmetry distribution-based synthetic consortium (ADSC) was developed to switch cell phenotypes using shikimate synthesis for proof of concept. First, the cell pole-organizing protein PopZ was screened as a mediator of asymmetric protein distribution in Escherichia coli. The ADSC was then constructed to incorporate PopZ-mediated asymmetry distribution and a TetR-based transcription repression switch to achieve the dynamical control of microbial population ratio. Finally, the ADSC was used to decouple cell growth from shikimate synthesis by effectively coordinating the ratio of growing cells and production cells at the consortium level, thereby increasing shikimate titer to 30.1 g/L in the 7.5-L bioreactor with a minimal medium. This titer was further improved to 82.5 g/L when using rich medium fermentation. Our results illustrate a novel approach to control consortium structure through ADSC-mediated regulation, highlighting its potential as an efficient strategy for controlling metabolic state in microbes. This article is protected by copyright. All rights reserved.

Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback

Communities of microbes play important roles in natural environments and hold great potential for deploying division-of-labor strategies in synthetic biology and bioproduction. However, the difficulty of controlling the composition of microbial consortia over time hinders their optimal use in many applications. Here, we present a fully automated, high-throughput platform that combines real-time measurements and computer-controlled optogenetic modulation of bacterial growth to implement precise and robust compositional control of a two-strain E. coli community. In addition, we develop a general framework for dynamic modeling of synthetic genetic circuits in the physiological context of E. coli and use a host-aware model to determine the optimal control parameters of our closed-loop compositional control system. Our platform succeeds in stabilizing the strain ratio of multiple parallel co-cultures at arbitrary levels and in changing these targets over time, opening the door for the implementation of dynamic compositional programs in synthetic bacterial communities.

Engineering consortia by polymeric microbial swarmbots

Synthetic microbial consortia represent a new frontier for synthetic biology given that they can solve more complex problems than monocultures. However, most attempts to co-cultivate these artificial communities fail because of the winner-takes-all in nutrients competition. In soil, multiple species can coexist with a spatial organization. Inspired by nature, here we show that an engineered spatial segregation method can assemble stable consortia with both flexibility and precision. We create microbial swarmbot consortia (MSBC) by encapsulating subpopulations with polymeric microcapsules. The crosslinked structure of microcapsules fences microbes, but allows the transport of small molecules and proteins. MSBC method enables the assembly of various synthetic communities and the precise control over the subpopulations. These capabilities can readily modulate the division of labor and communication. Our work integrates the synthetic biology and material science to offer insights into consortia assembly and serve as foundation to diverse applications from biomanufacturing to engineered photosynthesis.

Sustainable production of algae-bacteria granular consortia based biological hydrogen: New insights

Microbes recycling nutrient and detoxifying ecosystems are capable to fulfil the future energy need by producing biohydrogen by due to the coupling of autotrophic and heterotrophic microbes. In granules microbes mutualy exchanging nutrients and electrons for hydrogen production. The consortial biohydrogen production depend upon constituent microbes, their interdependence, competition for resources, and other operating parameters while remediating a waste material in nature or bioreactor. The present review deals with development of granular algae-bacteria consortia, hydrogen yield in coculture, important enzymes and possible engineering for improved hydrogen production.

Synthetic biology for the engineering of complex wine yeast communities

Wine fermentation is a representation of complex higher-order microbial interactions. Despite the beneficial properties that these communities bring to wine, their complexity poses challenges in predicting the nature and outcome of fermentation. Technological developments in synthetic biology enable the potential to engineer synthetic microbial communities for new purposes. Here we present the challenges and applications of engineered yeast communities in the context of a wine fermentation vessel, how this represents a model system to enable novel solutions for winemaking and introduce the concept of a 'synthetic' terroir. Furthermore, we introduce our vision for the application of control engineering.

Microbial associations for bioremediation. What does "microbial consortia" mean?

Microbial associations arise as useful tools in several biotechnological processes. Among them, bioremediation of contaminated environments usually takes advantage of these microbial associations. Despite being frequently used, these associations are indicated using a variety of expressions, showing a lack of consensus by specialists in the field. The main idea of this work is to analyze the variety of microbial associations referred to as "microbial consortia" (MC) in the context of pollutants biodegradation and bioremediation. To do that, we summarize the origin of the term pointing out the features that an MC is expected to meet, according to the opinion of several authors. An analysis of related bibliography was done seeking criteria to rationalize and classify MC in the context of bioremediation. We identify that the microbe's origin and the level of human intervention are usually considered as a category to classify them as natural microbial consortia (NMC), artificial microbial consortia (AMC), and synthetic microbial consortia (SMC). In this sense, NMC are those associations composed by microorganisms obtained from a single source while AMC members come from different sources. SMC are a class of AMC in which microbial composition is defined to accomplish a certain specific task. We propose that the effective or potential existence of the interaction among MC members in the source material should be considered as a category in the classification as well, in combination with the origin of the source and level of intervention. Cross-kingdom MC and new developments were also considered. Finally, the existence of grey zones in the limits between each proposed microbial consortia category is addressed. KEY POINTS: • Microbial consortia for bioremediation can be obtained through different methods. • The use of the term "microbial consortia" is unclear in the specialized literature. • We propose a simplified classification for microbial consortia for bioremediation.

Design, mutate, screen: Multiplexed creation and arrayed screening of synchronized genetic clocks

A major goal in synthetic biology is coordinating cellular behavior using cell-cell interactions; however, designing and testing complex genetic circuits that function only in large populations remains challenging. Although directed evolution has commonly supplemented rational design methods for synthetic gene circuits, this method relies on the efficient screening of mutant libraries for desired phenotypes. Recently, multiple techniques have been developed for identifying dynamic phenotypes from large, pooled libraries. These technologies have advanced library screening for single-cell, time-varying phenotypes but are currently incompatible with population-level phenotypes dependent on cell-cell communication. Here, we utilize directed mutagenesis and multiplexed microfluidics to develop an arrayed-screening workflow for dynamic, population-level genetic circuits. Specifically, we create a mutant library of an existing oscillator, the synchronized lysis circuit, and discover variants with different period-amplitude characteristics. Lastly, we utilize our screening workflow to construct a transcriptionally regulated synchronized oscillator that functions over long timescales. A record of this paper's transparent peer review process is included in the supplemental information.

Construction of Synthetic Microbial Ecosystems and the Regulation of Population Proportion

With the development of synthetic biology, the design and application of microbial consortia have received increasing attention. However, the construction of synthetic ecosystems is still hampered by our limited ability to rapidly develop microbial consortia with the required dynamics and functions. By using modular design, we constructed synthetic competitive and symbiotic ecosystems with Escherichia coli. Two ecological relationships were realized by reconfiguring the layout between the communication and effect modules. Furthermore, we designed inducible synthetic ecosystems to regulate subpopulation ratios. With the addition of different inducers, a wide range of strain ratios between subpopulations was achieved. These inducible synthetic ecosystems enabled a larger volume of population regulation and simplified culture conditions. The synthetic ecosystems we constructed combined both basic and applied functionalities and expanded the toolkit of synthetic biology research.

Synthesis of (-)-deoxypodophyllotoxin and (-)-epipodophyllotoxin via a multi-enzyme cascade in E. coli

Background

The aryltetralin lignan (−)−podophyllotoxin is a potent antiviral and anti-neoplastic compound that is mainly found in Podophyllum plant species. Over the years, the commercial demand for this compound rose notably because of the high clinical importance of its semi-synthetic chemotherapeutic derivatives etoposide and teniposide. To satisfy this demand, (−)−podophyllotoxin is conventionally isolated from the roots and rhizomes of Sinopodophyllum hexandrum, which can only grow in few regions and is now endangered by overexploitation and environmental damage. For these reasons, targeting the biosynthesis of (−)−podophyllotoxin precursors or analogues is fundamental for the development of novel, more sustainable supply routes.

Results

We recently established a four-step multi-enzyme cascade to convert (+)−pinoresinol into (−)−matairesinol in E. coli. Herein, a five-step multi-enzyme biotransformation of (−)−matairesinol to (−)−deoxypodophyllotoxin was proven effective with 98 % yield at a concentration of 78 mg/L. Furthermore, the extension of this cascade to a sixth step leading to (−)−epipodophyllotoxin was evaluated. To this end, seven enzymes were combined in the reconstituted pathway involving inter alia three plant cytochrome P450 monooxygenases, with two of them being functionally expressed in E. coli for the first time.

Conclusions

Both, (−)−deoxypodophyllotoxin and (−)−epipodophyllotoxin, are direct precursors to etoposide and teniposide. Thus, the reconstitution of biosynthetic reactions of Sinopodophyllum hexandrum as an effective multi-enzyme cascade in E. coli represents a solid step forward towards a more sustainable production of these essential pharmaceuticals.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01673-5.

A bioprocess perspective on the production of secondary metabolites by Streptomyces in submerged co-cultures

Filamentous microorganisms are potent sources of bioactive secondary metabolites, the molecules formed in response to complex environmental signals. The chemical diversity encoded in microbial genomes is only partially revealed by following the standard microbiological approaches. Mimicking the natural stimuli through laboratory co-cultivation is one of the most effective methods of awakening the formation of high-value metabolic products. Whereas the biosynthetic outcomes of co-cultures are reviewed extensively, the bioprocess aspects of such efforts are often overlooked. The aim of the present review is to discuss the submerged co-cultivation strategies used for triggering and enhancing secondary metabolites production in Streptomyces, a heavily investigated bacterial genus exhibiting an impressive repertoire of secondary metabolites, including a vast array of antibiotics. The previously published studies on influencing the biosynthetic capabilities of Streptomyces through co-cultivation are comparatively analyzed in the bioprocess perspective, mainly with the focus on the approaches of co-culture initiation, the experimental setup, the design of experimental controls and the ways of influencing the outcomes of co-cultivation processes. These topics are discussed in the general context of secondary metabolites production in submerged microbial co-cultures by referring to the Streptomyces-related studies as illustrative examples.

Engineering Tropism of Pseudomonas putida toward Target Surfaces through Ectopic Display of Recombinant Nanobodies

Gram-negative bacteria are endowed with complex outer membrane (OM) structures that allow them to both interact with other organisms and attach to different physical structures. However, the design of reliable bacterial coatings of solid surfaces is still a considerable challenge. In this work, we report that ectopic expression of a fibrinogen-specific nanobody on the envelope of Pseudomonas putida cells enables controllable formation of a bacterial monolayer strongly bound to an antigen-coated support. To this end, either the wild type or a surface-naked derivative of P. putida was engineered to express a hybrid between the β-barrel of an intimin-type autotransporter inserted in the outer membrane and a nanobody (VHH) moiety that targets fibrinogen as its cognate interaction partner. The functionality of the thereby presented VHH and the strength of the resulting cell attachment to a solid surface covered with the cognate antigen were tested and parametrized with Quartz Crystal Microbalance technology. The results not only demonstrated the value of using bacteria with reduced OM complexity for efficient display of artificial adhesins, but also the potential of this approach to engineer specific bacterial coverings of predetermined target surfaces.

Design and engineering of artificial microbial consortia for biohydrogen production

In natural microbial ecosystems the metabolic diversity of the organisms enables interaction among the community members and allows them to engage in syntrophic interactions. With regard to biotechnology, artificial microbial consortium engineering is used to improve productivities and yields of bioprocesses. However, to achieve supreme productivity or efficiency at industrial scale, defined ecosystems must be physiologically well-selected to meet eco-biotechnological demands. Here, we present an artificial microbial consortia design and engineering pipeline for developing dark fermentative biohydrogen production processes. The proposed pipeline might be considered as a blue-print for enhancing other bioprocesses that fundamentally face metabolic restrictions or kinetic limitations.