Synthetic biology in probiotic lactic acid bacteria: At the frontier of living therapeutics

Genetically Engineered Microorganisms and Their Impact on Human Health

The emergence of antibiotic-resistant strains, the decreased effectiveness of conventional therapies, and the side effects have led researchers to seek a safer, more cost-effective, patient-friendly, and effective method that does not develop antibiotic resistance. With progress in synthetic biology and genetic engineering, genetically engineered microorganisms effective in treatment, prophylaxis, drug delivery, and diagnosis have been developed. The present study reviews the types of genetically engineered bacteria and phages, their impacts on diseases, cancer, and metabolic and inflammatory disorders, the biosynthesis of these modified strains, the route of administration, and their effects on the environment. We conclude that genetically engineered microorganisms can be considered promising candidates for adjunctive treatment of diseases and cancers.

Development of Zn2+-controlled expression system for lactic acid bacteria and its application in engineered probiotics

Lactococcus lactis and Streptococcus thermophilus are considered as ideal chassis of engineered probiotics, while food-grade genetic tools are limited in those strains. Here, a Zn2+-controlled gene expression (ZICE) system was identified in the genome of S. thermophilus CGMCC7.179, including a transcriptional regulator sczAst and a promoter region of cation transporter czcD (PczcDst). Specific binding of the SczAst to the palindromic sequences in PczcDst was demonstrated by EMSA analysis, suggesting the regulation role of SczAst on PczcDst. To evaluate their possibility to control gene expression in vivo, the sczAst-PczcDst was employed to drive the expression of green fluorescence protein (GFP) gene in L. lactis NZ9000 and S. thermophilus CGMCC7.179, respectively. Both of the transformants could express GFP under Zn2+ induction, while no fluorescence without Zn2+ addition. For optimal conditions, Zn2+ was used at a final concentration of 0.8 mM in L. lactis and 0.16 mM in S. thermophilus at OD600 close to 0.4, and omitting yeast extract powder in the medium unexpectedly improved GFP expression level by 2.2-fold. With the help of the ZICE system, engineered L. lactis and S. thermophilus strains were constructed to secret cytokine interleukin-10 (IL-10) with immunogenicity, and the IL-10 content in the supernatant of the engineered L. lactis was 59.37 % of that under the nisin controlled expression system. This study provided a tightly controlled expression system by the food-grade inducer Zn2+, having potential in development of engineered probiotics.

Expanding the genetic programmability of Lactiplantibacillus plantarum

Lactobacilli are ubiquitous in nature and symbiotically provide health benefits for countless organisms including humans, animals and plants. They are vital for the fermented food industry and are being extensively explored for healthcare applications. For all these reasons, there is considerable interest in enhancing and controlling their capabilities through the engineering of genetic modules and circuits. One of the most robust and reliable microbial chassis for these synthetic biology applications is the widely used Lactiplantibacillus plantarum species. However, the genetic toolkit needed to advance its applicability remains poorly equipped. This mini-review highlights the genetic parts that have been discovered to achieve food-grade recombinant protein production and speculates on lessons learned from these studies for L. plantarum engineering. Furthermore, strategies to identify, create and optimize genetic parts for real-time regulation of gene expression and enhancement of biosafety are also suggested.

Engineered probiotics introduced to improve intestinal microecology for the treatment of chronic diseases: present state and perspectives

Purpose

Correcting intestinal microecological imbalance has become one of the core strategies to treat chronic diseases. Some traditional microecology-based therapies targeting intestine, such as prebiotic therapy, probiotic therapy and fecal microbiota transplantation therapy, have been used in the prevention and treatment of clinical chronic diseases, which still facing low safety and poor controllability problems. The development of synthetic biology technology has promoted the development of intestinal microecology-based therapeutics for chronic diseases, which exhibiting higher robustness and controllability, and become an important part of the next generation of microecological therapy. The purpose of this review is to summarize the application of synthetic biology in intestinal microecology-based therapeutics for chronic diseases.

Methods

The available literatures were searched to find out experimental studies and relevant review articles on the application of synthetic biology in intestinal microecology-based therapeutics for chronic diseases from year 1990 to 2023.

Results

Evidence proposed that synthetic biology has been applied in the intestinal microecology-based therapeutics for chronic diseases, covering metabolic diseases (e.g. diabetes, obesity, nonalcoholic fatty liver disease and phenylketonuria), digestive diseases (e.g. inflammatory bowel disease and colorectal cancer), and neurodegenerative diseases (e.g. Alzheimer's disease and Parkinson's disease).

Conclusion

This review summarizes the application of synthetic biology in intestinal microecology-based therapeutics for major chronic diseases and discusses the opportunities and challenges in the above process, providing clinical possibilities of synthetic biology technology applied in microecological therapies.

An optimized electrotransformation protocol for Lactobacillus jensenii

Engineered bacteria are promising candidates for in situ detection and treatment of diseases. The female uro-genital tract presents several pathologies, such as sexually transmitted diseases or genital cancer, that could benefit from such technology. While bacteria from the gut microbiome are increasingly engineered, the use of chassis isolated from the female uro-genital resident flora has been limited. A major hurdle to implement the experimental throughput required for efficient engineering in these non-model bacteria is their low transformability. Here we report an optimized electrotransformation protocol for Lactobacillus jensenii, one the most widespread species across vaginal microflora. Starting from classical conditions, we optimized buffers, electric field parameters, cuvette type and DNA quantity to achieve an 80-fold improvement in transformation efficiency, with up to 3.5·103 CFUs/μg of DNA in L. jensenii ATCC 25258. We also identify several plasmids that are maintained and support reporter gene expression in L. jensenii. Finally, we demonstrate that our protocol provides increased transformability in three independent clinical isolates of L. jensenii. This work will facilitate the genetic engineering of L. jensenii and enable its use for addressing challenges in gynecological healthcare.

Biomarker-responsive engineered probiotic diagnoses, records, and ameliorates inflammatory bowel disease in mice

Rapid advances in synthetic biology have fueled interest in engineered microorganisms that can diagnose and treat disease. However, designing bacteria that detect dynamic disease-associated biomarkers that then drive treatment remains difficult. Here, we have developed an engineered probiotic that noninvasively monitors and records inflammatory bowel disease (IBD) occurrence and progression in real time and can release treatments via a self-tunable mechanism in response to these biomarkers. These intelligent responsive bacteria for diagnosis and therapy (i-ROBOT) consists of E. coli Nissle 1917 that responds to levels of the inflammatory marker thiosulfate by activating a base-editing system to generate a heritable genomic DNA sequence as well as producing a colorimetric signal. Fluctuations in thiosulfate also drive the tunable release of the immunomodulator AvCystatin. Orally administering i-ROBOT to mice with colitis generated molecular recording signals in processed fecal and colon samples and effectively ameliorated disease. i-ROBOT provides a promising paradigm for gastrointestinal and other metabolic disorders.

Microbes of traditional fermentation processes as synthetic biology chassis to tackle future food challenges

Microbial diversity is magnificent and essential to almost all life on Earth. Microbes are an essential part of every human, allowing us to utilize otherwise inaccessible resources. It is no surprise that humans started, initially unconsciously, domesticating microbes for food production: one may call this microbial domestication 1.0. Sourdough bread is just one of the miracles performed by microbial fermentation, allowing extraction of more nutrients from flour and at the same time creating a fluffy and delicious loaf. There are a broad range of products the production of which requires fermentation such as chocolate, cheese, coffee and vinegar. Eventually, with the rise of microscopy, humans became aware of microbial life. Today our knowledge and technological advances allow us to genetically engineer microbes - one may call this microbial domestication 2.0. Synthetic biology and microbial chassis adaptation allow us to tackle current and future food challenges. One of the most apparent challenges is the limited space on Earth available for agriculture and its major tolls on the environment through use of pesticides and the replacement of ecosystems with monocultures. Further challenges include transport and packaging, exacerbated by the 24/7 on-demand mentality of many customers. Synthetic biology already tackles multiple food challenges and will be able to tackle many future food challenges. In this perspective article, we highlight recent microbial synthetic biology research to address future food challenges. We further give a perspective on how synthetic biology tools may teach old microbes new tricks, and what standardized microbial domestication could look like.

Targeted Antimicrobial Agents as Potential Tools for Modulating the Gut Microbiome

The gut microbiome plays a pivotal role in maintaining the health of the hosts; however, there is accumulating evidence that certain bacteria in the host, termed pathobionts, play roles in the progression of diseases. Although antibiotics can be used to eradicate unwanted bacteria, the side effects of antibiotic treatment lead to a great need for more targeted antimicrobial agents as tools to modulate the microbiome more precisely. Herein, we reviewed narrow-spectrum antibiotics naturally made by plants and microorganisms, followed by more targeted antibiotic agents including synthetic peptides, phage, and targeted drug delivery systems, from the perspective of using them as potential tools for modulating the gut microbiome for favorable effects on the health of the host. Given the emerging discoveries on pathobionts and the increasing knowledge on targeted antimicrobial agents reviewed in this article, we anticipate targeted antimicrobial agents will emerge as a new generation of a drug to treat microbiome-involved diseases.

Engineered Probiotic Lactococcus lactis for Lycopene Production against ROS Stress in Intestinal Epithelial Cells

Lactococcus lactis is a food-grade chassis for delivery of bioactive molecules to the intestinal mucosa in situ, while its ability to produce lycopene for detoxification of reactive oxidative species (ROS) is not realized yet. Here, L. lactis NZ9000 was engineered to synthesize lycopene by heterologous expression of a gene cluster crtEBI in plasmids or chromosomes, yielding the recombinant strains NZ4 and NZ5 with 0.59 and 0.54 mg/L lycopene production, respectively. To reroute the pyruvate flux to lycopene, the main lactate dehydrogenase and α-acetolactate synthase pathways were sequentially disrupted. The resultant strains NZΔldh-1 and NZΔldhΔals-1 increased lycopene accumulation to 0.70 and 0.73 mg/L, respectively, while their biomasses were reduced by 12.42% and the intracellular NADH/NAD⁺ ratios increased by 3.05- and 2.10-fold. To increase the biomasses of these engineered strains, aerobic respiration was activated and tuned by the addition of exogenous heme and oxygen. As a result, the engineered L. lactis strains partly recovered the growth and redox balance, yielding the lycopene levels of 0.91-1.09 mg/L. The engineered L. lactis strain protected the intestinal epithelial cells NCM460 against H₂O₂ challenge, with a 30.09% increase of cell survival and a 29.2% decrease of the intracellular ROS level compared with strain NZ9000 treatment. In summary, this work established the use of the engineered probiotic L. lactis for lycopene production and prospected its potential in the prevention of intestinal oxidative damage.

Fermented Foods and Their Role in Respiratory Health: A Mini-Review

Fermented foods (FFs) hold global attention because of their huge advantages. Their health benefits, palatability, preserved, tasteful, and aromatic properties impart potential importance in the comprehensive evaluation of FFs. The bioactive components, such as minerals, vitamins, fatty acids, amino acids, and other phytochemicals synthesized during fermentation, provide consumers with several health benefits. Fermentation of food is an ancient process that has met with many remarkable changes owing to the development of scientific technologies over the years. Initially, fermentation relied on back-slapping. Nowadays, starter cultures strains are specifically chosen for the type of fermentation process. Modern biotechnological methods are being implemented in the fermentation process to achieve the desired product in high quality. Respiratory and gastrointestinal tract infections are the most severe health issues affecting human beings of all age groups, especially children and older adults, during this COVID-19 pandemic period. Studies suggest that the consumption of probiotic Lactobacillus strains containing fermented foods protects the subjects from common infectious diseases (CIDs, which is classified as upper respiratory tract infections, lower respiratory tract infections and gastrointestinal infections) by improving the host’s immune system. Further studies are obligatory to develop probiotic-based functional FFs that are effective against CIDs. Presently, we are urged to find alternative, safe, and cost-effective prevention measures against CIDs. The current manuscript briefs the production of FFs, functional properties of FFs, and their beneficial effects against respiratory tract infections. It summarizes the outcomes of clinical trials using human subjects on the effects of supplementation of FFs.

Bioactive peptides produced by engineered probiotics and other food-grade bacteria: A review

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Synthetic biology improves probiotics therapeutic approaches.

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Engineering technologies contribute to design probiotics mechanisms of action.

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Edition of proteolytic systems induce the generation of specific bioactive peptides.

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Engineered probiotics should be evaluated as therapeutic agents in clinical trials.

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Therapeutical and technological uses of engineered probiotics are still controversial.

Synthetic biology is employed for the study and design of engineered microbes with new and improved therapeutic functions. The main advantage of synthetic biology is the selective genetic manipulation of living organisms with desirable beneficial effects such as probiotics. Engineering technologies have contributed to the edition of metabolic processes involved in the mechanisms of action of probiotics, such as the generation of bioactive peptides. Hence, current information related to bioactive peptides, produced by different engineering probiotics, with antimicrobial, antiviral, antidiabetic, and antihypertensive activities, as well as their potential use as functional ingredients, is discussed here. Besides, the effectiveness and safety aspects of these bioactive peptides were also described.

Lactic acid bacteria: isolation-characterization approaches and industrial applications

The current state-of-art research pertaining to lactic acid bacteria (LAB) calls for the screening and isolation of robust LAB strains to achieve holistic exploitation of LAB and their metabolites of marketable importance. Hence it is imperative to comprehend LAB sources, growth requisites, isolation and characterization strategies necessary for featured cataloging and appropriate culturing. This review comprehensively describes various growth media and biomasses used for supporting LAB sustenance, assay procedures needed for the isolation and characterization of LAB strains, and their application in diverse sectors. The various industrial patents and their summarized claims about novel LAB strains isolated and identified, methods and media (used for detection/screening, isolation, adaptation, culturing, preservation, growth improvement), the techniques and/or methodologies supporting LAB fermentation, and applications of produced industrial metabolites in various market scenarios are detailed.

Development of a novel expression system in lactic acid bacteria controlled by a broad-host-range promoter PsrfA

BACKGROUND

Latic acid bacteria (LAB) are exploited for development of gene expression system owing to its health promoting properties and a high degree of safety status. Most of the expression systems were constructed in Lactobacillus lactis with inducible promoters. It is necessary to exploit novel promoters to develop LAB host platforms which are indispensable in dairy and health application to satisfy the production demand of increased number of target-genes. Previously, promoter P_srfA had been displayed broad host range and used to construct auto-inducible expression system in B. subtilis and E. coli. In this work, the feasibility of P_srfA in LAB was estimated.

RESULTS

Plasmid with the green fluorescent protein (GFP) inserting downstream of P_srfA was transformed into L. casei 5257, L. plantarum 97, L. fermentum 087 and Weissella confusa 10, respectively. The recombinant strains grew well and displayed different fluorescence which could be detected by spectrophotometer and laser scanning confocal microscope. Moreover, the promoter activity was strain- specifically influenced by particular carbon and nitrogen sources. Heterologous laccase CotA could be expressed by P_srfA in L. casei 5257-05 and L. plantarum 97-06. By adjusting the pH value from 4.5 to 6.5 during incubation, the CotA activity detected from L. plantarum 97-05 and L. casei 5257-05 was increased by 137.7% and 61.5%, respectively. Finally, the fermentation pH was variably up-regulated along with the production of NADH oxidase which was controlled by the P_srfA and its derivative mutated with core regions.

CONCLUSIONS

These data suggested that P_srfA was valid for gene expression in different species of LAB. Moreover, P_srfA could be used as an attractive candidate for fine-tuning gene expression in a broad range of prokaryotic expression plants.

Human Microbiome and Its Medical Applications

The commensal microbiome is essential for human health and is involved in many processes in the human body, such as the metabolism process and immune system activation. Emerging evidence implies that specific changes in the microbiome participate in the development of various diseases, including diabetes, liver diseases, tumors, and pathogen infections. Thus, intervention on the microbiome is becoming a novel and effective method to treat such diseases. Synthetic biology empowers researchers to create strains with unique and complex functions, making the use of engineered microbes for clinical applications attainable. The aim of this review is to summarize recent advances about the roles of the microbiome in certain diseases and the underlying mechanisms, as well as the use of engineered microbes in the prevention, detection, and treatment of various diseases.

Anthocyanin-Colored Microencapsulation Effects on Survival Rate of Lactobacillus rhamnosus GG, Color Stability, and Sensory Parameters in Strawberry Nectar Model

Probiotic microencapsulation is a promising way to produce functional food, while their stability and sensory acceptability still a challenge. This study aims to enhance the functional properties of strawberry (Fragaria × ananassa, cultivar Camarosa) nectar and sensory acceptance using novel anthocyanin-colored microencapsulation of Lactobacillus rhamnosus. Four formulations (F1–F4) of coated materials (alginate, whey protein, and pullulan) integrated with anthocyanin pigment were used for encapsulation. The physical properties of microencapsulated probiotics (size, color, efficiency, stability, and survival rate) and quality parameters of nectar (pH, anthocyanin, and sensory acceptability) during 4 weeks of storage at 4 and 25 °C were evaluated. All formulations exhibited high encapsulation efficiency (> 89%), medium bead size (406–504 μm), and proper color (red color). The microencapsulated cells were stable in simulated gastrointestinal and processing conditions (up 7 log10 CFU mL−1) compared to free cells. F4 (alginate 2% + anthocyanin 0.1% + whey protein 2% + pullulan 2% + cocoa butter 1% + L. rhamnosus GG) showed the greatest viability in nectar during storage (6.72 log10 CFU mL−1/4 °C/4 weeks), while a significant decrease in pH (< 2) and anthocyanin (< 60 mg 100 g−1) was observed in nectar-containing free cells. The sensory scores with a difference-preference test as exploratory and preliminary responses revealed that colored probiotic microcapsules enhanced the sensory characters (up to 4 weeks) and commercially accepted (> 80% agreed) of strawberry nectar. Results demonstrated that anthocyanin-colored alginate-whey protein-pullulan matrix had the potential to enhance probiotic viability in functional nectar without negative impact.

Conjugative DNA Transfer From E. coli to Transformation-Resistant Lactobacilli

Lactic acid bacteria (LAB) belonging to the genus classically known as Lactobacillus, recently split into 25 different genera, include many relevant species for the food industry. The well-known properties of lactobacilli as probiotics make them an attractive model also for vaccines and therapeutic proteins delivery in humans. However, scarce tools are available to accomplish genetic modification of these organisms, and most are only suitable for laboratory strains. Here, we test bacterial conjugation as a new tool to introduce genetic modifications into many biotechnologically relevant laboratory and wild type lactobacilli. Using mobilizable shuttle plasmids from a donor Escherichia coli carrying either RP4 or R388 conjugative systems, we were able to get transconjugants to all tested Lactocaseibacillus casei strains, including many natural isolates, and to several other genera, including Lentilactobacillus parabuchneri, for which no transformation protocol has been reported. Transconjugants were confirmed by the presence of the oriT and 16S rRNA gene sequencing. Serendipitously, we also found transconjugants into researcher-contaminant Staphylococcus epidermidis. Conjugative DNA transfer from E. coli to S. aureus was previously described, but at very low frequencies. We have purified this recipient strain and used it in standard conjugation assays, confirming that both R388 and RP4 conjugative systems mediate mobilization of plasmids into S. epidermidis. This protocol could be assayed to introduce DNA into other Gram-positive microorganisms which are resistant to transformation.

A quantitative model for metabolic intervention using gut microbes

As medicine shifts toward precision-based and personalized therapeutics, utilizing more complex biomolecules to treat increasingly difficult and rare conditions, microorganisms provide an avenue for realizing the production and processing necessary for novel drug pipelines. More so, probiotic microbes can be co-opted to deliver therapeutics by oral administration as living drugs, able to survive and safely transit the digestive tract. As living therapeutics are in their nascency, traditional pharmacokinetic-pharmacodynamic (PK-PD) models for evaluating drug candidates are not appropriate for this novel platform. Using a living therapeutic in late-stage clinical development for phenylketonuria (PKU) as a case study, we adapt traditional oral drug delivery models to properly evaluate and inform the engineering of living therapeutics. We develop the adapted for living therapeutics compartmental absorption and transit (ALT-CAT) model to provide metrics for drug efficacy across nine age groups of PKU patients and evaluate model parameters that are influenced by patient physiology, microbe selection and therapeutic production, and dosing formulations. In particular, the ALT-CAT model describes the mathematical framework to model the behavior of orally delivered engineered bacteria that act as living therapeutics by adapting similar methods that have been developed and widely-used for small molecular drug delivery and absorption.

The Role of Mucosal Immunity and Recombinant Probiotics in SARS-CoV2 Vaccine Development

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), causing the 2019 novel coronavirus disease (COVID-19), was introduced by WHO (World Health Organization) as "pandemic" in March 2020. According to WHO, thus far (23 November 2020) 58,425,681 infected cases including 1,385,218 deaths have been reported worldwide. In order to reduce transmission and spread of this lethal virus, attempts are globally being made to develop an appropriate vaccine. Intending to neutralize pathogens at their initial entrance site, protective mucosal immunity is inevitably required. In SARS-CoV2 infection and transmission, respiratory mucosa plays a key role; hence, apparently mucosal vaccination could be a superior approach to elicit mucosal and systemic immune responses simultaneously. In this review, the advantages of mucosal vaccination to control COVID-19 infection, limitations, and outcomes of mucosal vaccines have been highlighted. Considering the gut microbiota dysregulation in COVID-19, we further provide evidences on utilization of recombinant probiotics, particularly lactic acid bacteria (LAB) as vaccine carrier. Their intrinsic immunomodulatory features, natural adjuvanticity, and feasible expression of relevant antigen in the mucosal surface make them more appealing as live cell factory. Among all available platforms, bioengineered probiotics are considered as the most affordable, most practical, and safest vaccination approach to halt this emerging virus.

Tweak to Treat: Reprograming Bacteria for Cancer Treatment

Recent advancements in cancer biology, microbiology, and bioengineering have spurred the development of engineered live biotherapeutics for targeted cancer therapy. In particular, natural tumor-targeting and probiotic bacteria have been engineered for controlled and sustained delivery of anticancer agents into the tumor microenvironment (TME). Here, we review the latest advancements in the development of engineered bacteria for cancer therapy and additional engineering strategies to potentiate the delivery of therapeutic payloads. We also explore the use of combination therapies comprising both engineered bacteria and conventional anticancer therapies for addressing intratumor heterogeneity. Finally, we discuss prospects for the development and clinical translation of engineered bacteria for cancer prevention and treatment.

Artificial intelligence and synthetic biology approaches for human gut microbiome

The gut microbiome comprises a variety of microorganisms whose genes encode proteins to carry out crucial metabolic functions that are responsible for the majority of health-related issues in human beings. The advent of the technological revolution in artificial intelligence (AI) assisted synthetic biology (SB) approaches will play a vital role in the modulating the therapeutic and nutritive potential of probiotics. This can turn human gut as a reservoir of beneficial bacterial colonies having an immense role in immunity, digestion, brain function, and other health benefits. Hence, in the present review, we have discussed the role of several gene editing tools and approaches in synthetic biology that have equipped us with novel tools like Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR-Cas) systems to precisely engineer probiotics for diagnostic, therapeutic and nutritive value. A brief discussion over the AI techniques to understand the metagenomic data from the healthy and diseased gut microbiome is also presented. Further, the role of AI in potentially impacting the pace of developments in SB and its current challenges is also discussed. The review also describes the health benefits conferred by engineered microbes through the production of biochemicals, nutraceuticals, drugs or biotherapeutics molecules etc. Finally, the review concludes with the challenges and regulatory concerns in adopting synthetic biology engineered microbes for clinical applications. Thus, the review presents a synergistic approach of AI and SB toward human gut microbiome for better health which will provide interesting clues to researchers working in the area of rapidly evolving food and nutrition science.

Fermented food products in the era of globalization: tradition meets biotechnology innovations

Omics tools offer the opportunity to characterize and trace traditional and industrial fermented foods. Bioinformatics, through machine learning, and other advanced statistical approaches, are able to disentangle fermentation processes and to predict the evolution and metabolic outcomes of a food microbial ecosystem. By assembling microbial artificial consortia, the biotechnological advances will also be able to enhance the nutritional value and organoleptics characteristics of fermented food, preserving, at the same time, the potential of autochthonous microbial consortia and metabolic pathways, which are difficult to reproduce. Preserving the traditional methods contributes to protecting the hidden value of local biodiversity, and exploits its potential in industrial processes with the final aim of guaranteeing food security and safety, even in developing countries.

Engineered lactobacilli display anti-biofilm and growth suppressing activities against Pseudomonas aeruginosa

Biofilms are an emerging target for new therapeutics in the effort to address the continued increase in resistance and tolerance to traditional antimicrobials. In particular, the distinct nature of the biofilm growth state often means that traditional antimcirobials, developed to combat planktonic cells, are ineffective. Biofilm treatments are designed to both reduce pathogen load at an infection site and decrease the development of resistance by rendering the embedded organisms more susceptible to treatment at lower antimicrobial concentrations. In this work, we developed a new antimicrobial treatment modality using engineered lactic acid bacteria (LAB). We first characterized the natural capacity of two lactobacilli, L. plantarum and L. rhamnosus, to inhibit P. aeruginosa growth, biofilm formation, and biofilm viability, which we found to be dependent upon the low pH generated during culture of the LAB. We further engineered these LAB to secrete enzymes known to degrade P. aeruginosa biofilms and show that our best performing engineered LAB, secreting a pathogen-derived enzyme (PelAh), degrades up to 85% of P. aeruginosa biofilm.

Angiotensin (1-7) delivered orally via probiotic, but not subcutaneously, benefits the gut-brain axis in older rats

To (1) investigate the efficacy of multiple doses of an orally delivered probiotic bacteria Lactobacillus paracasei (LP) modified to express angiotensin (1-7) (LP-A) in altering physiologic parameters relevant to the gut-brain axis in older rats and to (2) compare this strategy with subcutaneous delivery of synthetic Ang(1-7) peptide on circulating Ang(1-7) concentrations and these gut-brain axis parameters. Male 24-month-old F344BN rats received oral gavage of LP-A, or subcutaneous injection of Ang(1-7) for 0×, 1×, 3×, or 7×/week over 4 weeks. Circulating RAS analytes, inflammatory cytokines, and tryptophan and its downstream metabolites were measured by ELISA, electrochemiluminescence, and LC-MS respectively. Microbiome taxonomic analysis of fecal samples was performed via 16S-based PCR. Inflammatory and tryptophan-related mRNA expression was measured in colon and pre-frontal cortex. All dosing regimens of LP-A induced beneficial changes in fecal microbiome including overall microbiota community structure and α-diversity, while the 3×/week also significantly increased expression of the anti-inflammatory species Akkermansia muciniphila. The 3×/week also increased serum serotonin and the neuroprotective analyte 2-picolinic acid. In the colon, LP-A increased quinolinate phosphoribosyltransferase expression (1×/week) and increased kynurenine aminotransferase II (1× and 3×/week) mRNA expression. LP-A also significantly reduced neuro-inflammatory gene expression in the pre-frontal cortex (3×/week: COX2, IL-1β, and TNFα; 7×/week: COX2 and IL-1β). Subcutaneous delivery of Ang(1-7) increased circulating Ang(1-7) and reduced angiotensin II, but most gut-brain parameters were unchanged in response. Oral-but not subcutaneous-Ang(1-7) altered physiologic parameters related to gut-brain axis, with the most effects observed in 3×/week oral dosing regimen in older rats.

Gut Microbiota Metabolism and Interaction with Food Components

The human gut contains trillions of microbes that play a central role in host biology, including the provision of key nutrients from the diet. Food is a major source of precursors for metabolite production; in fact, diet modulates the gut microbiota (GM) as the nutrients, derived from dietary intake, reach the GM, affecting both the ecosystem and microbial metabolic profile. GM metabolic ability has an impact on human nutritional status from childhood. However, there is a wide variability of dietary patterns that exist among individuals. The study of interactions with the host via GM metabolic pathways is an interesting field of research in medicine, as microbiota members produce myriads of molecules with many bioactive properties. Indeed, much evidence has demonstrated the importance of metabolites produced by the bacterial metabolism from foods at the gut level that dynamically participate in various biochemical mechanisms of a cell as a reaction to environmental stimuli. Hence, the GM modulate homeostasis at the gut level, and the alteration in their composition can concur in disease onset or progression, including immunological, inflammatory, and metabolic disorders, as well as cancer. Understanding the gut microbe–nutrient interactions will increase our knowledge of how diet affects host health and disease, thus enabling personalized therapeutics and nutrition.

Sparse estimation of mutual information landscapes quantifies information transmission through cellular biochemical reaction networks

Measuring information transmission from stimulus to response is useful for evaluating the signaling fidelity of biochemical reaction networks (BRNs) in cells. Quantification of information transmission can reveal the optimal input stimuli environment for a BRN and the rate at which the signaling fidelity decreases for non-optimal input probability distributions. Here we present sparse estimation of mutual information landscapes (SEMIL), a method to quantify information transmission through cellular BRNs using commonly available data for single-cell gene expression output, across a design space of possible input distributions. We validate SEMIL and use it to analyze several engineered cellular sensing systems to demonstrate the impact of reaction pathways and rate constants on mutual information landscapes.

Sarkar et al. present a method called sparse estimation of mutual information landscapes (SEMIL) that quantifies information transmission landscapes through cellular biochemical reaction networks across a space of input distributions using single-cell gene expression data. This study suggests that mutual information landscapes can be used as a performance metric for biochemical reaction networks.

Quorum sensing for population-level control of bacteria and potential therapeutic applications

Quorum sensing (QS), a microbial cell-to-cell communication process, dynamically regulates a variety of metabolism and physiological activities. In this review, we provide an update on QS applications based on autoinducer molecules including acyl-homoserine lactones (AHLs), auto-inducing peptides (AIPs), autoinducer 2 (AI-2) and indole in population-level control of bacteria, and highlight the potential in developing novel clinical therapies. We summarize the development in the combination of various genetic circuits such as genetic oscillators, toggle switches and logic gates with AHL-based QS devices in Gram-negative bacteria. An overview is then offered to the state-of-the-art of much less researched applications of AIP-based QS devices with Gram-positive bacteria, followed by a review of the applications of AI-2 and indole based QS for interspecies communication among microbial communities. Building on these general-purpose QS applications, we highlight the disruptions and manipulations of QS devices as potential clinical therapies for diseases caused by biofilm formation, antibiotic resistance and the phage invasion. The last part of reviewed literature is dedicated to mathematical modelling for QS applications. Finally, the key challenges and future perspectives of QS applications in monoclonal synthetic biology and synthetic ecology are discussed.

New perspectives on the treatment of mycobacterial infections using antibiotics

More than 100 years have passed since the discovery of Mycobacterium tuberculosis, in 1882, as the pathogen that causes tuberculosis (TB). However, globally, TB is still one of the leading causes of death by infectious diseases. In 2018, approximately 10.0 million people were diagnosed with TB owing to the development of advanced strategies by M. tuberculosis to resist antibiotics, including the development of a dormant state. The World Health Organization (WHO) and the Sustainable Development Goals (SDGs) are dedicated to ending TB by 2030. However, the development of strategies to discover new TB drugs and new therapies is crucial for the achievement of this goal. Unfortunately, the rapid occurrence of multidrug-resistant strains of M. tuberculosis has worsened the current situation, thereby warranting prioritized discovery of new anti-TB drugs and the development of new treatment regimens in academia and the pharmaceutical industry. In this mini review, we provide a brief overview of the current research and development pipeline for new anti-TB drugs and present our perspective of TB drug innovation. The data presented herein may enable the introduction of more effective medicines and therapeutic regimens into the market.Key Points• The Updated Global New TB Drug Pipelines are briefly summarized.• Novel strategies for the discovery of new TB drugs, including novel sources, bioinformatics, and synthetic biology strategies, are discussed.• New therapeutic options, including living therapeutics and phage therapy, are proposed.

Quantifying and Engineering Mucus Adhesion of Probiotics

Mucus in the gastrointestinal (GI) tract is the primary point-of-interaction between humans and their gut microbiota. This intimates that mucus not only ensures protection against endogenous and exogenous opportunists but also provisions for the human microbiota to reside and flourish. With the emergence of living therapeutics, engineered microbes can deliver and produce increasingly complex medicine, and controlling the mucoadhesive properties of different microbial chassis can dictate dose-response in a patient. Here we present a redesigned, in vitro, plate-based assay to measure the mucus adhesion of various probiotics. Cell-mucus interactions were isolated by immobilizing mucus to the plate surface. Binding parameters were derived for each probiotic strain by measuring cell adhesion over a wide range of cell concentrations, providing dose-dependent adhesion metrics. Surface proteins and cell components known to influence mucoadhesion were then heterologously expressed or altered in Lactococcus lactis MG1363 and Escherichia coli Nissle 1917 to control mucus-binding capacity, avidity, and cooperativity.

Safety Aspects of Genetically Modified Lactic Acid Bacteria

Lactic acid bacteria (LAB) have a long history of use in the food industry. Some species are part of the normal human microbiota and have beneficial properties for human health. Their long-standing use and considerable biotechnological potential have led to the development of various systems for their engineering. Together with novel approaches such as CRISPR-Cas, the established systems for engineering now allow significant improvements to LAB strains. Nevertheless, genetically modified LAB (GM-LAB) still encounter disapproval and are under extensive regulatory requirements. This review presents data on the prospects for LAB to obtain 'generally recognized as safe' (GRAS) status. Genetic modification of LAB is discussed, together with problems that can arise from their engineering, including their dissemination into the environment and the spread of antibiotic resistance markers. Possible solutions that would allow the use of GM-LAB are described, such as biocontainment, alternative selection markers, and use of homologous DNA. The use of GM-LAB as cell factories in closed systems that prevent their environmental release is the least problematic aspect, and this is also discussed.

Multi-Product Lactic Acid Bacteria Fermentations: A Review

Industrial biotechnology is a continuously expanding field focused on the application of microorganisms to produce chemicals using renewable sources as substrates. Currently, an increasing interest in new versatile processes, able to utilize a variety of substrates to obtain diverse products, can be observed. A robust microbial strain is critical in the creation of such processes. Lactic acid bacteria (LAB) are used to produce a wide variety of chemicals with high commercial interest. Lactic acid (LA) is the most predominant industrial product obtained from LAB fermentations, and its production is forecasted to rise as the result of the increasing demand of polylactic acid. Hence, the creation of new ways to revalorize LA production processes is of high interest and could further enhance its economic value. Therefore, this review explores some co-products of LA fermentations, derived from LAB, with special focus on bacteriocins, lipoteichoic acid, and probiotics. Finally, a multi-product process involving LA and the other compounds of interest is proposed.

Galactose to tagatose isomerization at moderate temperatures with high conversion and productivity

There are many industrially-relevant enzymes that while active, are severely limited by thermodynamic, kinetic, or stability issues (isomerases, lyases, transglycosidases). In this work, we study Lactobacillus sakeil-arabinose isomerase (LsLAI) for d-galactose to d-tagatose isomerization—that is limited by all three reaction parameters. The enzyme demonstrates low catalytic efficiency, low thermostability at temperatures > 40 °C, and equilibrium conversion < 50%. After exploring several strategies to overcome these limitations, we show that encapsulating LsLAI in gram-positive Lactobacillus plantarum that is chemically permeabilized enables reactions at high rates, high conversions, and elevated temperatures. In a batch process, this system enables ~ 50% conversion in 4 h starting with 300 mM galactose (an average productivity of 37 mM h⁻¹), and 85% conversion in 48 h. We suggest that such an approach may be invaluable for other enzymatic processes that are similarly kinetically-, thermodynamically-, and/or stability-limited.

Production of tagatose, a sugar substitute, by isomerization of galactose suffers from unfavorable enzymatic kinetics, low enzyme stability, and low equilibrium constant. Here, the authors simultaneously overcome these limitations by encapsulating l-arabinose isomerase in permeabilized Lactobacillus plantarum.

Efficient engineered probiotics using synthetic biology approaches: A review

The uses of probiotics-based food supplements are getting emphasis due to their power to ensure better health conditions. Probiotics have diverse and significant applications in the health sector, so probiotic strains require an understanding of the genome level organizations. Probiotics elucidate various functional parameters that control their metabolic functions. In this review, we have compiled aspects of synthetic biology, which are used for the optimization of metabolic processes in probiotics for their use as a supplement in allopathic medicines. Synthetic biology approaches provide information about diverse biosynthetic pathways and also facilitate the novel metabolic engineering approaches for probiotics strain improvement. We have discussed the synthetic biology approaches for producing engineered probiotics via genetic circuits, expression systems, and genome editing tools like CRISPR-Cas and PEVLAB. This review also enlightens future challenges in the development of engineered probiotics.

Genome editing of lactic acid bacteria: opportunities for food, feed, pharma and biotech

This mini-review provides a perspective of traditional, emerging and future applications of lactic acid bacteria (LAB) and how genome editing tools can be used to overcome current challenges in all these applications. It also describes available tools and how these can be further developed, and takes current legislation into account. Genome editing tools are necessary for the construction of strains for new applications and products, but can also play a crucial role in traditional ones, such as food and probiotics, as a research tool for gaining mechanistic insights and discovering new properties. Traditionally, recombinant DNA techniques for LAB have strongly focused on being food-grade, but they lack speed and the number of genetically tractable strains is still rather limited. Further tool development will enable rapid construction of multiple mutants or mutant libraries on a genomic level in a wide variety of LAB strains. We also propose an iterative Design–Build–Test–Learn workflow cycle for LAB cell factory development based on systems biology, with ‘cell factory’ expanding beyond its traditional meaning of production strains and making use of genome editing tools to advance LAB understanding, applications and strain development.

Inducible Plasmid Self-Destruction (IPSD) Assisted Genome Engineering in Lactobacilli and Bifidobacteria

Genome engineering is essential for application of synthetic biology in probiotics including lactobacilli and bifidobacteria. Several homologous recombination system-based mutagenesis tools have been developed for these bacteria, but still have many limitations in different species or strains. Here we developed a genome engineering method based on an inducible self-destruction plasmid delivering homologous DNA into bacteria. Excision of the replicon by induced recombinase facilitates selection of homologous recombination events. This new genome editing tool called inducible plasmid self-destruction (IPSD) was successfully used to perform gene knockout and knock-in in lactobacilli and bifidobacteria. Due to its simplicity and universality, the IPSD strategy may provide a general approach for genetic engineering of various bacterial species.

An Expanded Synthetic Biology Toolkit for Gene Expression Control in Acetobacteraceae

The availability of different host chassis will greatly expand the range of applications in synthetic biology. Members of the Acetobacteraceae family of Gram-negative bacteria form an attractive class of nonmodel microorganisms that can be exploited to produce industrial chemicals, food and beverage, and biomaterials. One such biomaterial is bacterial cellulose, which is a strong and ultrapure natural polymer used in tissue engineering scaffolds, wound dressings, electronics, food additives, and other products. However, despite the potential of Acetobacteraceae in biotechnology, there has been considerably little effort to fundamentally reprogram the bacteria for enhanced performance. One limiting factor is the lack of a well-characterized, comprehensive toolkit to control expression of genes in biosynthetic pathways and regulatory networks to optimize production and cell viability. Here, we address this shortcoming by building an expanded genetic toolkit for synthetic biology applications in Acetobacteraceae. We characterized the performance of multiple natural and synthetic promoters, ribosome binding sites, terminators, and degradation tags in three different strains, namely, Gluconacetobacter xylinus ATCC 700178, Gluconacetobacter hansenii ATCC 53582, and Komagataeibacter rhaeticus iGEM. Our quantitative data revealed strain-specific and common design rules for the precise control of gene expression in these industrially relevant bacterial species. We further applied our tools to synthesize a biodegradable cellulose-chitin copolymer, adjust the structure of the cellulose film produced, and implement CRISPR interference for ready down-regulation of gene expression. Collectively, our genetic parts will enable the efficient engineering of Acetobacteraceae bacteria for the biomanufacturing of cellulose-based materials and other commercially valuable products.

Biotechnology of health-promoting bacteria

Over the last decade, there has been an increasing scientific and public interest in bacteria that may positively contribute to human gut health and well-being. This interest is reflected by the ever-increasing number of developed functional food products containing health-promoting bacteria and reaching the market place as well as by the growing revenue and profits of notably bacterial supplements worldwide. Traditionally, the origin of probiotic-marketed bacteria was limited to a rather small number of bacterial species that mostly belong to lactic acid bacteria and bifidobacteria. Intensifying research efforts on the human gut microbiome offered novel insights into the role of human gut microbiota in health and disease, while also providing a deep and increasingly comprehensive understanding of the bacterial communities present in this complex ecosystem and their interactions with the gut-liver-brain axis. This resulted in rational and systematic approaches to select novel health-promoting bacteria or to engineer existing bacteria with enhanced probiotic properties. In parallel, the field of gut microbiomics developed into a fertile framework for the identification, isolation and characterization of a phylogenetically diverse array of health-promoting bacterial species, also called next-generation therapeutic bacteria. The present review will address these developments with specific attention for the selection and improvement of a selected number of health-promoting bacterial species and strains that are extensively studied or hold promise for future food or pharma product development.

Application of A Novel Potential Probiotic Lactobacillus paracasei Strain Isolated from Kefir Grains in the Production of Feta-Type Cheese

In the present study 38 lactic acid bacteria strains were isolated from kefir grains and were monitored regarding probiotic properties in a series of established in vitro tests, including resistance to low pH, resistance to pepsin and pancreatin, and tolerance to bile salts, as well as susceptibility against common antibiotics. Among them, the strain SP3 displayed potential probiotic properties. Multiplex PCR analysis indicated that the novel strain belongs to the paracasei species. Likewise, the novel strain (Lactobacillus paracasei SP3) was applied as a starter culture for Feta-type cheese production. Feta-type cheese production resulted in significantly higher acidity; lower pH; reduced counts of coliforms, yeasts and fungi; and improved quality characteristics compared with cheese samples produced with no starter culture. Finally, it is highlighted that the application of the novel strain led to Feta-type cheese production with improved overall quality and sensory characteristics.

Delivery of IL-35 by Lactococcus lactis Ameliorates Collagen-Induced Arthritis in Mice

IL-35, a relatively newly discovered cytokine belonging to the larger IL-12 family, shows unique anti-inflammatory properties, believed to be associated with dedicated receptors and signaling pathways. IL-35 plays a pivotal role in the development and the function of both regulatory B (Bregs) and T cells (Tregs). In order to further its therapeutic potential, a dairy Lactococcus lactis strain was engineered to express murine IL-35 (LL-IL35), and this recombinant strain was applied to suppress collagen-induced arthritis (CIA). Oral administration of LL-IL35 effectively reduced the incidence and disease severity of CIA. When administered therapeutically, LL-IL35 abruptly halted CIA progression with no increase in disease severity by reducing neutrophil influx into the joints. LL-IL35 treatment reduced IFN-γ and IL-17 3.7- and 8.5-fold, respectively, and increased IL-10 production compared to diseased mice. Foxp3+ and Foxp3- CD39+ CD4+ T cells were previously shown to be the Tregs responsible for conferring protection against CIA. Inquiry into their induction revealed that both CCR6+ and CCR6- Foxp3+or- CD39+ CD4+ T cells act as the source of the IL-10 induced by LL-IL35. Thus, this study demonstrates the feasibility and benefits of engineered probiotics for treating autoimmune diseases.