In Vivo and In Vitro Detection of Luminescent and Fluorescent Lactobacillus reuteri and Application of Red Fluorescent mCherry for Assessing Plasmid Persistence

Targeted Bioimaging of Microencapsulated Recombinant LAB Vector Expressing Fluorescent Reporter Protein: A Non-invasive Approach for Microbial Tracking

Lactococcus lactis (L. lactis), the first genetically modified Generally Recognized As Safe (GRAS) category Lactic Acid producing Bacteria (LAB), is best known for its generalized health-promoting benefits and ability to express heterologous proteins. However, achieving the optimal probiotic effects requires a selective approach that would allow us to study in vivo microbial biodistribution, fate, and immunological consequences. Although the chemical conjugation of fluorophores and chromophores represent the standard procedure to tag microbial cells for various downstream applications, it requires a high-throughput synthesis scheme, which is often time-consuming and expensive. On the contrary, the genetic manipulation of LAB vector, either chromosomally or extra-chromosomally, to express bioluminescent or fluorescent reporter proteins has greatly enhanced our ability to monitor bacterial transit through a complex gut environment. However, with faster passage and quick washing out from the gut due to rhythmic contractions of the digestive tract, real-time tracking of LAB vectors, particularly non-commensal ones, remains problematic. To get a deeper insight into the biodistribution of non-commensal probiotic bacteria in vivo, we bioengineered L. lactis to express fluorescence reporter proteins, mCherry (bright red monomeric fluorescent protein) and mEGFP (monomeric enhanced green fluorescent protein), followed by microencapsulation with a mucoadhesive and biodegradable polymer, chitosan. We show that coating of recombinant Lactococcus lactis (rL. lactis) with chitosan polymer, cross-linked with tripolyphosphate (TPP), retains their ability to express the reporter proteins stably without altering the specificity and sensitivity of fluorescence detection in vitro and in vivo. Further, we provide evidence of enhanced intragastric stability by chitosan-TPP (CS) coating of rL. lactis cells, allowing us to study the spatiotemporal distribution for an extended time in the gut of two unrelated hosts, avian and murine. The present scheme involving genetic modification and chitosan encapsulation of non-commensal LAB vector demonstrates great promise as a non-invasive and intensive tool for active live tracking of gut microbes.

Oral administration of CXCL12-expressing Limosilactobacillus reuteri improves colitis by local immunomodulatory actions in preclinical models

Treatments of colitis, inflammation of the intestine, rely on induction of immune suppression associated with systemic adverse events, including recurrent infections. This treatment strategy is specifically problematic in the increasing population of patients with cancer with immune checkpoint inhibitor (ICI)-induced colitis, as immune suppression also interferes with the ICI-treatment response. Thus, there is a need for local-acting treatments that reduce inflammation and enhance intestinal healing. Here, we investigated the effect and safety of bacterial delivery of short-lived immunomodulating chemokines to the inflamed intestine in mice with colitis. Colitis was induced by dextran sulfate sodium (DSS) alone or in combination with ICI (anti-PD1 and anti-CTLA-4), and Limosilactobacillus reuteri R2LC (L. reuteri R2LC) genetically modified to express the chemokine CXCL12-1α (R2LC_CXCL12, emilimogene sigulactibac) was given perorally. In addition, the pharmacology and safety of the formulated drug candidate, ILP100-Oral, were evaluated in rabbits. Peroral CXCL12-producing L. reuteri R2LC significantly improved colitis symptoms already after 2 days in mice with overt DSS and ICI-induced colitis, which in benchmarking experiments was demonstrated to be superior to treatments with anti-TNF-α, anti-α4β7, and corticosteroids. The mechanism of action involved chemokine delivery to Peyer's patches (PPs), confirmed by local CXCR4 signaling, and increased numbers of colonic, regulatory immune cells expressing IL-10 and TGF-β1. No systemic exposure or engraftment could be detected in mice, and product feasibility, pharmacology, and safety were confirmed in rabbits. In conclusion, peroral CXCL12-producing L. reuteri R2LC efficiently ameliorates colitis, enhances mucosal healing, and has a favorable safety profile.NEW & NOTEWORTHY Colitis symptoms are efficiently reduced by peroral administration of probiotic bacteria genetically modified to deliver CXCL12 locally to the inflamed intestine in several mouse models.

Recent advances in genetic tools for engineering probiotic lactic acid bacteria

Synthetic biology has grown exponentially in the last few years, with a variety of biological applications. One of the emerging applications of synthetic biology is to exploit the link between microorganisms, biologics, and human health. To exploit this link, it is critical to select effective synthetic biology tools for use in appropriate microorganisms that would address unmet needs in human health through the development of new game-changing applications and by complementing existing technological capabilities. Lactic acid bacteria (LAB) are considered appropriate chassis organisms that can be genetically engineered for therapeutic and industrial applications. Here, we have reviewed comprehensively various synthetic biology techniques for engineering probiotic LAB strains, such as clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 mediated genome editing, homologous recombination, and recombineering. In addition, we also discussed heterologous protein expression systems used in engineering probiotic LAB. By combining computational biology with genetic engineering, there is a lot of potential to develop next-generation synthetic LAB with capabilities to address bottlenecks in industrial scale-up and complex biologics production. Recently, we started working on Lactochassis project where we aim to develop next generation synthetic LAB for biomedical application.

Introduction of Plasmid to the Murine Gut via Consumption of an Escherichia coli Carrier and Examining the Impact of Bacterial Dosing and Antibiotics on Persistence

Purpose

We examine the impacts of dosing strategies of plasmids on bacterial communities in the murine gut by measuring the quantity of plasmids in mouse feces.

Methods

We fed mice carrier bacteria, E. coli, that contain plasmids with both a reporter gene and an antibiotic resistant gene. We varied the quantity of the plasmid-carrying bacteria and the length of time the mice consumed the bacteria. We also pretreated the gut with broad-spectrum antibiotics and used continuous antibiotic treatment to investigate selection pressure. We collected bacteria from fecal pellets to quantify the number of plasmid-carrying bacteria via plate assay.

Results

Dosing regimens with plasmid-carrying bacteria resulted in a significantly increased duration of persistence of the plasmid within the gut when supplemented continuously with kanamycin during as well as after completion of bacterial dosing. The carrier bacteria concentration influenced the short-term abundance of carrier bacteria.

Conclusion

We evaluated the persistence of plasmid-carrying bacteria in the murine gut over time using varying dosage strategies. In future work, we will study how bacterial diversity in the gut impacts the degree of plasmid transfer and the prevalence of plasmid-carrying bacteria over time.

Lay Summary

Observing how plasmids persist within the gut can help us understand how newly introduced genes, including antibiotic resistance, are transmitted within the gut microbiome. In our experiments, mice were given bacteria containing a genetically engineered plasmid and were examined for the persistence of the plasmid in the gut. We found long-term persistence of the plasmid in the gut when administering antibiotics during and following dosing of the mice with bacteria carrying the plasmid. The use of higher concentrations of carrier bacteria influenced the short-term abundance of the plasmid-carrying bacteria in the gut.

Description of Future Works

Building on evidence from these initial studies that persistence of plasmids within the gut can be regulated by the dosage strategy, we will explore future studies and models of gene uptake in the context of spatial and taxonomic control and further determine if dosing strategies alter the compositional diversity of the gut microbiome.

Graphical abstract

Persistence and dynamics of fluorescent Lactobacillus plantarum in the healthy versus inflamed gut

The gastrointestinal tract is the main ecological niche in which Lactobacillus strains may provide health benefits in mammals. There is currently a need to characterize host-microbe interactions in space and time by tracking these bacteria in vivo. We combined noninvasive whole-body imaging with ex vivo fluorescence confocal microscopy imaging to monitor the impact of intestinal inflammation on the persistence of orally administered Lactobacillus plantarum NCIMB8826 in healthy and inflamed mouse colons. We developed fluorescent L. plantarum strains and demonstrated that mCherry is the best system for in vivo imaging and ex vivo fluorescence confocal microscopy of these bacteria. We also used whole-body imaging to show that this anti-inflammatory, orally administered strain persists for longer and at higher counts in the inflamed colon than in the healthy colon. We confirmed these results by the ex vivo confocal imaging of colons from mice with experimental colitis for 3 days after induction. Moreover, extended orthogonal view projections enabled us to localize individual L. plantarum in sites that differed for healthy versus inflamed guts. In healthy colons, orally administered bacteria were localized in the lumen (in close contact with commensal bacteria) and sometimes in the crypts (albeit very rarely in contact with intestinal cells). The bacteria were observed within and outside the mucus layer. In contrast, L. plantarum bacteria in the inflamed colon were mostly located in the lumen and (in less inflamed areas) within the mucus layer. In more intensely inflamed areas (i.e., where the colon had undergone structural damage), the L. plantarum were in direct contact with damaged epithelial cells. Taken as a whole, our results show that fluorescently labeled L. plantarum can be used to study the persistence of these bacteria in inflamed guts using both noninvasive whole-body imaging and ex vivo fluorescence confocal microscopy.

Engineering of Vaginal Lactobacilli to Express Fluorescent Proteins Enables the Analysis of Their Mixture in Nanofibers

Lactobacilli are a promising natural tool against vaginal dysbiosis and infections. However, new local delivery systems and additional knowledge about their distribution and mechanism of action would contribute to the development of effective medicine. This will be facilitated by the introduction of the techniques for effective, inexpensive, and real-time tracking of these probiotics following their release. Here, we engineered three model vaginal lactobacilli (Lactobacillus crispatus ATCC 33820, Lactobacillus gasseri ATCC 33323, and Lactobacillus jensenii ATCC 25258) and a control Lactobacillus plantarum ATCC 8014 to express fluorescent proteins with different spectral properties, including infrared fluorescent protein (IRFP), green fluorescent protein (GFP), red fluorescent protein (mCherry), and blue fluorescent protein (mTagBFP2). The expression of these fluorescent proteins differed between the Lactobacillus species and enabled quantification and discrimination between lactobacilli, with the longer wavelength fluorescent proteins showing superior resolving power. Each Lactobacillus strain was labeled with an individual fluorescent protein and incorporated into poly (ethylene oxide) nanofibers using electrospinning, as confirmed by fluorescence and scanning electron microscopy. The lactobacilli retained their fluorescence in nanofibers, as well as after nanofiber dissolution. To summarize, vaginal lactobacilli were incorporated into electrospun nanofibers to provide a potential solid vaginal delivery system, and the fluorescent proteins were introduced to distinguish between them and allow their tracking in the future probiotic-delivery studies.

Indole-3-glycerolphosphate synthase, a branchpoint for the biosynthesis of tryptophan, indole, and benzoxazinoids in maize

The maize (Zea mays) genome encodes three indole-3-glycerolphosphate synthase enzymes (IGPS1, 2, and 3) catalyzing the conversion of 1-(2-carboxyphenylamino)-l-deoxyribulose-5-phosphate to indole-3-glycerolphosphate. Three further maize enzymes (BX1, benzoxazinoneless 1; TSA, tryptophan synthase alpha subunit; and IGL, indole glycerolphosphate lyase) convert indole-3-glycerolphosphate to indole, which is released as a volatile defense signaling compound and also serves as a precursor for the biosynthesis of tryptophan and defense-related benzoxazinoids. Phylogenetic analyses showed that IGPS2 is similar to enzymes found in both monocots and dicots, whereas maize IGPS1 and IGPS3 are in monocot-specific clades. Fusions of yellow fluorescent protein with maize IGPS enzymes and indole-3-glycerolphosphate lyases were all localized in chloroplasts. In bimolecular fluorescence complementation assays, IGPS1 interacted strongly with BX1 and IGL, IGPS2 interacted primarily with TSA, and IGPS3 interacted equally with all three indole-3-glycerolphosphate lyases. Whereas IGPS1 and IGPS3 expression was induced by insect feeding, IGPS2 expression was not. Transposon insertions in IGPS1 and IGPS3 reduced the abundance of both benzoxazinoids and free indole. Spodoptera exigua (beet armyworm) larvae show improved growth on igps1 mutant maize plants. Together, these results suggest that IGPS1 and IGPS3 function mainly in the biosynthesis of defensive metabolites, whereas IGPS2 may be involved in the biosynthesis of tryptophan. This metabolic channeling is similar to, though less exclusive than, that proposed for the three maize indole-3-glycerolphosphate lyases.

Reduction of intestinal trimethylamine by probiotics ameliorated lipid metabolic disorders associated with atherosclerosis

OBJECTIVES

The purpose of this study was to explore the effect of trimethylamine (TMA)-degrading probiotic agents on trimethylamine oxide (TMAO) and the related lipid metabolism in mice.

METHODS

Ten lipid-lowering strains were detected with TMA-degradation capacity in vitro. After probiotic intervention for the mice on a high-choline diet, TMA content in cecum and TMA and TMAO in serum was explored, as well as the expression of key gene flavin-containing monooxygenase 3 (FMO3) of the TMA-TMAO metabolism. The expression of genes related to the lipid metabolism was also investigated by real-time polymerase chain reaction and Western blot. Finally, the colonization of functional strains in the intestine were examined.

RESULTS

Five of 10 lipid-lowering strains effectively degraded TMA in vitro, and the TMA level in the cecum of mice were reduced after probiotic intervention. TMA level and TMAO in serum were also significantly reduced by the strains (P < 0.05), but not due to the regulation of FMO3. Probiotic agents could improve the lipid metabolism by acting on the Farnesoid X receptor and cholesterol 7-alpha hydroxy-lase. Among the strains, Bifidobacterium animalis subsp. lactis F1-3-2 showed the most prominent performance and colonized in the cecum of mice.

CONCLUSIONS

Bif. animalis subsp. lactis F1-3-2 could be colonized in the cecum, and might directly degrade TMA or change the structure of intestinal flora. The strain had an effect on TMA and TMAO levels in vivo by decreasing cecum TMA. The strain was demonstrated to participate in the TMA-TMAO regulation, improve the lipid metabolism, and alleviate atherosclerosis caused by TMAO. However, FMO3 had not changed in this process, and needs further study.

Bacterial Biofilm Bioinspired Persistent Luminescence Nanoparticles with Gut-Oriented Drug Delivery for Colorectal Cancer Imaging and Chemotherapy

Colorectal cancer (CRC) is now one of the leading causes of cancer incidence and mortality. Although nanomaterial-based drug delivery has been used for the treatment of colorectal cancer, inferior targeting ability of existing nanocarriers leads to inefficient treatment and side effects. Moreover, the majority of intravenously administered nanomaterials aggregate into the reticuloendothelial system, leaving a certain hidden risk to human health. All those problems gave great demands for further construction of well-performed and biocompatible nanomaterials for in vivo theranostics. In the present work, from a biomimetic point of view, Lactobacillus reuteri biofilm (LRM) was coated on the surface of trackable zinc gallogermanate (ZGGO) near-infrared persistent luminescence mesoporous silica to create the bacteria bioinspired nanoparticles (ZGGO@SiO₂@LRM), which hold the inherent capability of withstanding the digestion of gastric acid and targeted release 5-FU to colorectum. Through the background-free persistent luminescence bioimaging of ZGGO, the coating of LRM facilitated the localization of ZGGO@SiO₂@LRM to the tumor area of colorectum for more than 24 h after intragastric administration. Furthermore, ZGGO@SiO₂@LRM hardly entered the blood, which avoided possible damage to immune organs such as the liver and spleen. In vivo chemotherapy experiment demonstrated the number of tumors per mouse in ZGGO@SiO₂@LRM group decreased by one-half compared with the 5-FU group (P < 0.001). To sum up, this LRM bioinspired nanoparticles could tolerate the digestion of gastric acid, avoid aggregation by the immune system, favor gut-oriented drug delivery, and targeted release oral 5-FU into colorectum for more than 24 h, which may give new application prospects for targeted delivery of oral drugs into the colorectum.

Combining Modules for Versatile and Optimal Labeling of Lactic Acid Bacteria: Two pMV158-Family Promiscuous Replicons, a Pneumococcal System for Constitutive or Inducible Gene Expression, and Two Fluorescent Proteins

Labeling of bacterial cells with fluorescent proteins allows tracking the bacteria in competition and interactomic in vivo and in vitro studies. During the last years, a few plasmid vectors have been developed aimed at the fluorescent labeling of specific members of the lactic acid bacteria (LAB), a heterogeneous group that includes microorganisms used in the food industry, as probiotics, or as live vectors for mucosal vaccines. Successful and versatile labeling of a broad range of LAB not only requires a vector containing a promiscuous replicon and a widely recognized expression system for the constitutive or regulated expression of the fluorescence determinant, but also the knowledge of the main features of the entire plasmid/host/fluorescent protein ensemble. By using the LAB model species Lactococcus lactis, we have compared the utility properties of a set of labeling vectors constructed by combining a promiscuous replicon (pMV158 or pSH71) of the pMV158 plasmid family with the gene encoding either the EGFP or the mCherry fluorescent protein placed under control of promoter P_X or P_M from the pneumococcal mal gene cluster for maltosaccharide uptake and utilization, respectively. Some vectors carrying P_M also harbor the malR gene, whose product represses transcription from this promoter, thus enabling maltose-inducible synthesis of the fluorescent proteins. We have determined the plasmid copy number (PCN) and segregational stability of the different constructs, as well as the effect of these features on the fitness and fluorescence intensity of the lactococcal host. Constructs based on the pSH71 replicon had a high copy number (∼115) and were segregationally stable. The copy number of vectors based on the pMV158 replicon was lower (∼8–45) and varied substantially depending on the genetic context of the plasmid and on the bacterial growth conditions; as a consequence, inheritance of these vectors was less stable. Synthesis of the fluorescent proteins encoded by these plasmids did not significantly decrease the host fitness. By employing inducible expression vectors, the fluorescent proteins were shown to be very stable in this bacterium. Importantly, conditions for accurate quantification of the emitted fluorescence were established based on the maturation times of the fluorescent proteins.

In-Taken Labeling and in Vivo Tracing Foodborne Probiotics via DNA-Encapsulated Persistent Luminescence Nanoprobe Assisted Autofluorescence-Free Bioimaging

An in vivo probing strategy that can real-time and in situ trace target probiotics inside the living body is herein proposed by employing plasmid-like DNA as in-taken assistance, persistent luminescence nanophosphors (PLNPs) as optical labeling, and background-free fluorescence bioimaging as signal readout. PLNPs with superlong afterglow and excellent biocompatibility and stability were surface-modified by DNA molecules with a specific sequence, which greatly promoted the nanoparticle penetration into the bacteria and facilitated the in vivo bioimaging with high sensitivity and signal-to-noise ratio. Compared with the previous surface-labeling strategy by antibody recognition, the in-taken optical labeling demonstrated improved stability, and reached ideal results of real-time and in situ monitoring the in vivo behaviors of target probiotics, supporting the further development of in vivo investigation methodology for foodborne probiotics. Moreover, such a strategy offers a promising platform that leverage nanoscience to food nutrition as well as food-safety research, aiming to collect more accurate and fresh information from the living body.

In vivo bioluminescence imaging of the spatial and temporal colonization of lactobacillus plantarum 423 and enterococcus mundtii ST4SA in the intestinal tract of mice

Background

Lactic acid bacteria (LAB) are major inhabitants and part of the normal microflora of the gastrointestinal tract (GIT) of humans and animals. Despite substantial evidence supporting the beneficial properties of LAB, only a few studies have addressed the migration and colonization of probiotic bacteria in the GIT. The reason for this is mostly due to the limitations, or lack of, efficient reporter systems. Here we describe the development and application of a non-invasive in vivo bioluminescence reporter system to study, in real-time, the spatial and temporal persistence of Lactobacillus plantarum 423 and Enterococcus mundtii ST4SA in the intestinal tract of mice.

Results

This study reports on the application of the firefly luciferase gene (ffluc) from Photinus pyralis to develop luciferase-expressing L. plantarum 423 and E. mundtii ST4SA, using a Lactococcus lactis NICE system on a high copy number plasmid (pNZ8048) and strong constitutive lactate dehydrogenase gene promoters (Pldh and STldh). The reporter system was used for in vivo and ex vivo monitoring of both probiotic LAB strains in the GIT of mice after single and multiple oral administrations. Enterococcus mundtii ST4SA reached the large intestine 45 min after gavage, while L. plantarum 423 reached the cecum/colon after 90 min. Both strains predominantly colonized the cecum and colon after five consecutive daily administrations. Enterococcus mundtii ST4SA persisted in faeces at higher numbers and for more days compared to L. plantarum 423.

Conclusions

Our findings demonstrate the efficiency of a high-copy number vector, constitutive promoters and bioluminescence imaging to study the colonization and persistence of L. plantarum 423 and E. mundtii ST4SA in the murine GIT. The system allowed us to differentiate between intestinal transit times of the two strains in the digestive tract. This is the first report of bioluminescence imaging of a luciferase-expressing E. mundtii strain to study colonization dynamics in the murine model. The bioluminescence system developed in this study may be used to study the in vivo colonization dynamics of other probiotic LAB.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1315-4) contains supplementary material, which is available to authorized users.

Construction of a Bioluminescent Labelling Plasmid Vector for Bifidobacteria

Bifidobacterium is recognized as one of the most beneficial microorganisms in our gut. Many researches on bifidobacteria have been done to understand their roles in the gut. The objective of the present study was to develop a bioluminescent labelling plasmid vector for bifidobacteria to facilitate their visualization in vitro, in situ, and in vivo. A plasmid replicon (2.0 kb) of plasmid pFI2576 previously identified from B. longum FI10564 was amplified by PCR and cloned into pUC19 plasmid vector (2.68 kb). The cloned replicon was subcloned into pTG262 (luc⁺) recombinant plasmid vector (7.4 kb) where a luciferase gene (luc⁺) from pLuc2 (8.5 kb), an Escherichia coli and lactobacilli shuttle vector, was inserted into pTG262 plasmid vector. The final recombinant DNA, pTG262::pFI2576 rep (luc⁺), was transferred into a B. catenulatum strain. This recombinant strain showed 3,024 relative luminescence units at OD₆₀₀ value of 0.352. Thus, this recombinant plasmid construct can be broadly used for labelling bifidobacteria.

Can an in vivo imaging system be used to determine localization and biodistribution of AAV5-mediated gene expression following subretinal and intravitreal delivery in mice?

Recombinant adeno associated viruses (AAV) are the most commonly used vectors in animal model studies of gene therapy for retinal diseases. The ability of a vector to localize and remain in the target tissue, and in this manner to avoid off-target effects beyond the site of delivery, is critical to the efficacy and safety of the treatment. The in vivo imaging system (IVIS) is a non-invasive imaging tool used for detection and quantification of bioluminescence activity in rodents. Our aim was to investigate whether IVIS can detect localization and biodistribution of AAV5 vector in mice following subretinal (SR) and intravitreal (IVT) injections. AAV5 carrying firefly luciferase DNA under control of the ubiquitous cytomegalovirus (CMV) promoter was injected unilaterally IVT or SR (in the central or peripheral retina) of forty-one mice. Luciferase activity was tracked for up to 60 weeks in the longest surviving animals, using repeated (up to 12 times) IVIS bioluminescence imaging. Luciferase presence was also confirmed immunohistochemically (IHC) and by PCR in representative animals. In the SR group, IVIS readings demonstrated luciferase activity in all (32/32) eyes, and luciferase presence was confirmed by IHC (4/4 eyes) and PCR (12/12 eyes). In the IVT group, IVIS readings demonstrated luciferase activity in 7/9 eyes, and luciferase presence was confirmed by PCR in 5/5 eyes and by IHC (2/2 eyes). In two SR-injected animals (one each from the central and peripheral injection sites), PCR detected luciferase presence in the ipsilateral optic nerves, a finding that was not detected by IVIS or IHC. Our results show that when evaluating SR delivery, IVIS has a sensitivity and specificity of 100% compared with the gold standard PCR. When evaluating IVT delivery, IVIS has a sensitivity of 78% and specificity of 100%. These finding confirm the ability of IVIS to detect in-vivo localized expression of AAV following SR delivery in the retina up to 60 weeks post-treatment, using repeated imaging for longitudinal evaluation, without fading of the biological signal, thereby replacing the need for post mortem processing in order to confirm vector expression. However, IVIS is probably not sensitive enough, compared with genome detection, to demonstrate biodistribution to the optic nerve, as it could not detect luciferase activity in ipsilateral optic nerves following SR delivery in mice.

In Vitro Transcriptome Response to a Mixture of Lactobacilli Strains in Intestinal Porcine Epithelial Cell Line

Background: Food and feed supplements containing microorganisms with probiotic potential are of increasing interest due to their healthy promoting effect on human and animals. Their mechanism of action is still unknown. Using a microarray approach, the aim of this study was to investigate the differences in genome-wide gene expression induced by a mixture of three Lactobacillus strains (L. rhamnosus, L. plantarum, and L. paracasei) in intestinal porcine epithelial cells (IPEC-1) and to identify the genes and pathways involved in intestinal barrier functions. Methods: Undifferentiated IPEC-1 cells seeded at a density of 2.0 × 10⁵/mL in 24-wells culture plates were cultivated at 37 °C and 5% CO₂ until they reached confluence (2–3 days). Confluent cells monolayer were then cultivated with 1 mL of fresh lactobacilli (LB) mixture suspension prepared for a concentration of approximately 3.3 × 10⁷ CFU/mL for each strain (1 × 10⁸ CFU/mL in total) for 3 h and analyzed by microarray using Gene Spring GX v.11.5. Results: The functional analysis showed that 1811 of the genes modulated by LB treatment are involved in signaling (95% up-regulation, 121 genes with a fold change higher than 10). The most enhanced expression was registered for AXIN2 (axis inhibition protein 2-AXIN2) gene (13.93 Fc, p = 0.043), a negative regulator of β-catenin with a key role in human cancer. LB affected the cellular proliferation by increasing 10 times (Fc) the NF1 gene encoding for the neurofibromin protein, a tumor suppressor that prevent cells from uncontrolled proliferation. The induction of genes like serpin peptidase inhibitor, clade A member 3 (SERPINA 3), interleukin-20 (IL-20), oncostatin M(OSM), granulocyte-macrophage colony-stimulating factor (GM-CSF), and the suppression of chemokine (C-X-C motif) ligand 2/macrophage inflammatory protein 2-alpha (CXCL-2/MIP-2), regulator of G-protein signaling 2 (RGS2), and of pro-inflammatory interleukin-18 (IL-18) genes highlights the protective role of lactobacilli in epithelial barrier function against inflammation and in the activation of immune response. Conclusion: Gene overexpression was the predominant effect produced by lactobacilli treatment in IPEC-1 cells, genes related to signaling pathways being the most affected. The protective role of lactobacilli in epithelial barrier function against inflammation and in the activation of immune response was also noticed.

Tracking of Engineered Bacteria In Vivo Using Nonstandard Amino Acid Incorporation

The rapidly growing field of microbiome research presents a need for better methods of monitoring gut microbes in vivo with high spatial and temporal resolution. We report a method of tracking microbes in vivo within the gastrointestinal tract by programming them to incorporate nonstandard amino acids (NSAA) and labeling them via click chemistry. Using established machinery constituting an orthogonal translation system (OTS), we engineered Escherichia coli to incorporate p-azido-l-phenylalanine (pAzF) in place of the UAG (amber) stop codon. We also introduced a mutant gene encoding for a cell surface protein (CsgA) that was altered to contain an in-frame UAG codon. After pAzF incorporation and extracellular display, the engineered strains could be covalently labeled via copper-free click reaction with a Cy5 dye conjugated to the dibenzocyclooctyl (DBCO) group. We confirmed the functionality of the labeling strategy in vivo using a murine model. Labeling of the engineered strain could be observed using oral administration of the dye to mice several days after colonization of the gastrointestinal tract. This work sets the foundation for the development of in vivo tracking microbial strategies that may be compatible with noninvasive imaging modalities and are capable of longitudinal spatiotemporal monitoring of specific microbial populations.

Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications

An increasing number of studies have strongly correlated the composition of the human microbiota with many human health conditions and, in several cases, have shown that manipulating the microbiota directly affects health. These insights have generated significant interest in engineering indigenous microbiota community members and nonresident probiotic bacteria as biotic diagnostics and therapeutics that can probe and improve human health. In this review, we discuss recent advances in synthetic biology to engineer commensal and probiotic lactic acid bacteria, bifidobacteria, and Bacteroides for these purposes, and we provide our perspective on the future potential of these technologies.

Expression of fluorescent proteins in Lactobacillus rhamnosus to study host-microbe and microbe-microbe interactions

Probiotic Lactobacillus strains are widely used to benefit human and animal health, although the exact mechanisms behind their interactions with the host and the microbiota are largely unknown. Fluorescent tagging of live probiotic cells is an important tool to unravel their modes of action. In this study, the implementation of different heterologously expressed fluorescent proteins for the labelling of the model probiotic strains Lactobacillus rhamnosusGG (gastrointestinal) and Lactobacillus rhamnosusGR-1 (vaginal) was explored. Heterologous expression of mTagBFP2 and mCherry resulted in long-lasting fluorescence of L. rhamnosusGG and GR-1 cells, using the nisin-controlled expression (NICE) system. These novel fluorescent strains were then used to study in vitro aspects of their microbe-microbe and microbe-host interactions. Lactobacillus rhamnosusGG and L. rhamnosusGR-1 expressing mTagBFP2 and mCherry could be visualized in mixed-species biofilms, where they inhibited biofilm formation by Salmonella Typhimurium-gfpmut3 expressing the green fluorescent protein. Likewise, fluorescent L. rhamnosusGG and L. rhamnosusGR-1 were implemented for the visualization of their adhesion patterns to intestinal epithelial cell cultures. The fluorescent L. rhamnosus strains developed in this study can therefore serve as novel tools for the study of probiotic interactions with their environment.

Development of a Click Beetle Luciferase Reporter System for Enhanced Bioluminescence Imaging of Listeria monocytogenes: Analysis in Cell Culture and Murine Infection Models

Listeria monocytogenes is a Gram-positive facultative intracellular pathogen that is widely used as a model organism for the analysis of infection biology. In this context, there is a current need to develop improved reporters for enhanced bioluminescence imaging (BLI) of the pathogen in infection models. We have developed a click beetle red luciferase (CBR-luc) based vector (pPL2CBR^opt) expressing codon optimized CBR-luc under the control of a highly expressed Listerial promoter (P_HELP) for L. monocytogenes and have compared this to a lux-based system expressing bacterial luciferase for BLI of the pathogen using in vitro growth experiments and in vivo models. The CBR-luc plasmid stably integrates into the L. monocytogenes chromosome and can be used to label field isolates and laboratory strains of the pathogen. Growth experiments revealed that CBR-luc labeled L. monocytogenes emits a bright signal in exponential phase that is maintained during stationary phase. In contrast, lux-labeled bacteria produced a light signal that peaked during exponential phase and was significantly reduced during stationary phase. Light from CBR-luc labeled bacteria was more efficient than the signal from lux-labeled bacteria in penetrating an artificial tissue depth assay system. A cell invasion assay using C2Bbe1 cells and a systemic murine infection model revealed that CBR-luc is suited to BLI approaches and demonstrated enhanced sensitivity relative to lux in the context of Listeria infection models. Overall, we demonstrate that this novel CBR reporter system provides efficient, red-shifted light production relative to lux and may have significant applications in the analysis of L. monocytogenes pathogenesis.

Persistent Luminescence Nanophosphor Involved Near-Infrared Optical Bioimaging for Investigation of Foodborne Probiotics Biodistribution in Vivo: A Proof-of-Concept Study

Probiotics has attracted great attention in food nutrition and safety research field, but thus far there are limited analytical techniques for visualized and real-time monitoring of the probiotics when they are ingested in vivo. Herein, the optical bioimaging technique has been introduced for investigation of foodborne probiotics biodistribution in vivo, employing the near-infrared (NIR) emitting persistent luminescence nanophosphors (PLNPs) of Cr³⁺-doped zinc gallogermanate (ZGGO) as the contrast nanoprobes. The ultrabrightness, super long afterglow, polydispersed size, low toxicity, and excellent photostability and biocompatibility of PLNPs were demonstrated to be qualified as a tracer for labeling probiotics via antibody (anti-Gram positive bacteria LTA antibody) recognition as well as contrast agent for long-term bioimaging the probiotics. In vivo optical bioimaging assay showed that the LTA antibody functionalized ZGGO nanoprobes that could be efficiently tagged to the probiobics were successfully applied for real-time monitoring and nondamaged probing of the biodistribution of probiotics inside the living body after oral administration. This work presents a proof-of-concept that exploited the bioimaging methodology for real-time and nondamaged researching the foodborne probiotics behaviors in vivo, which would open up a novel way of food safety detection and nutrition investigation.

Genetic Tools for the Enhancement of Probiotic Properties

The Lactobacillus genus is a diverse group of microorganisms, many of which are of industrial and medical relevance. Several Lactobacillus species have been used as probiotics, organisms that when present in sufficient quantities confer a health benefit to the host. A significant limitation to the mechanistic understanding of how these microbes provide health benefits to their hosts and how they can be used as therapeutic delivery systems has been the lack of genetic strategies to efficiently manipulate their genomes. This article will review the development and employment of traditional genetic tools in lactobacilli and highlight the latest methodologies that are allowing for precision genome engineering of these probiotic organisms. The application of these tools will be key in providing mechanistic insights into probiotics as well as maximizing the value of lactobacilli as either a traditional probiotic or as a platform for the delivery of therapeutic proteins. Finally, we will discuss concepts that we consider relevant for the delivery of engineered therapeutics to the human gut.

Lactobacilli and pediococci as versatile cell factories - Evaluation of strain properties and genetic tools

This review discusses opportunities and bottlenecks for cell factory development of Lactic Acid Bacteria (LAB), with an emphasis on lactobacilli and pediococci, their metabolism and genetic tools. In order to enable economically feasible bio-based production of chemicals and fuels in a biorefinery, the choice of product, substrate and production organism is important. Currently, the most frequently used production hosts include Escherichia coli and Saccharomyces cerevisiae, but promising examples are available of alternative hosts such as LAB. Particularly lactobacilli and pediococci can offer benefits such as thermotolerance, an extended substrate range and increased tolerance to stresses such as low pH or high alcohol concentrations. This review will evaluate the properties and metabolism of these organisms, and provide an overview of their current biotechnological applications and metabolic engineering. We substantiate the review by including experimental results from screening various lactobacilli and pediococci for transformability, growth temperature range and ability to grow under biotechnologically relevant stress conditions. Since availability of efficient genetic engineering tools is a crucial prerequisite for industrial strain development, genetic tool development is extensively discussed. A range of genetic tools exist for Lactococcus lactis, but for other species of LAB like lactobacilli and pediococci such tools are less well developed. Whereas lactobacilli and pediococci have a long history of use in food and beverage fermentation, their use as platform organisms for production purposes is rather new. By harnessing their properties such as thermotolerance and stress resistance, and by using emerging high-throughput genetic tools, these organisms are very promising as versatile cell factories for biorefinery applications.

Monitoring of Bioluminescent Lactobacillus plantarum in a Complex Food Matrix

A bioluminescent Lactobacillus plantarum (pLuc2) strain was constructed. The luminescent signal started to increase during the early exponential phase and reached its maximum in the mid-exponential phase in a batch culture of the strain. The signal detection sensitivity of the strain was the highest in PBS (phosphate buffered saline), followed by milk and MRS broth, indicating that the sensitivity was influenced by the matrix effect. The strain was used in millet seed fermentation which has a complex matrix and native lactic acid bacteria (LAB). The luminescent signal was gradually increased until 9 h during fermentation and abolished at 24 h, indicating that the strain could be specifically tracked in the complex matrix and microflora. Therefore, the bioluminescent labeling system can be used for monitoring LAB in food and dairy sciences and industries.

In-capillary probing of quantum dots and fluorescent protein self-assembly and displacement using Förster resonance energy transfer

Herein, a Förster resonance energy transfer system was designed, which consisted of CdSe/ZnS quantum dots donor and mCherry fluorescent protein acceptor. The quantum dots and the mCherry proteins were conjugated to permit Förster resonance energy transfer. Capillary electrophoresis with fluorescence detection was used for the analyses for the described system. The quantum dots and mCherry were sequentially injected into the capillary, while the real-time fluorescence signal of donor and acceptor was simultaneously monitored by two channels with fixed wavelength detectors. An effective separation of complexes from free donor and acceptor was achieved. Results showed quantum dots and hexahistidine tagged mCherry had high affinity and the assembly was affected by His6 -mCherry/quantum dot molar ratio. The kinetics of the self-assembly was calculated using the Hill equation. The microscopic dissociation constant values for out of- and in-capillary assays were 10.49 and 23.39 μM, respectively. The capillary electrophoresis with fluorescence detection that monitored ligands competition assay further delineated the different binding capacities of histidine containing peptide ligands for binding sites on quantum dots. This work demonstrated a novel approach for the improvement of Förster resonance energy transfer for higher efficiency, increased sensitivity, intuitionistic observation, and low sample requirements of the in-capillary probing system.

Fluorescent reporter systems for tracking probiotic lactic acid bacteria and bifidobacteria

In the last two decades, there has been increasing evidence supporting the role of the intestinal microbiota in health and disease, as well as the use of probiotics to modulate its activity and composition. Probiotic bacteria selected for commercial use in foods, mostly lactic acid bacteria and bifidobacteria, must survive in sufficient numbers during the manufacturing process, storage, and passage through the gastro-intestinal tract. They have several modes of action and it is crucial to unravel the mechanisms underlying their postulated beneficial effects. To track their survival and persistence, and to analyse their interaction with the gastro-intestinal epithelia it is essential to discriminate probiotic strains from endogenous microbiota. Fluorescent reporter proteins are relevant tools that can be exploited as a non-invasive marker system for in vivo real-time imaging in complex ecosystems as well as in vitro fluorescence labelling. Oxygen is required for many of these reporter proteins to fluoresce, which is a major drawback in anoxic environments. However, some new fluorescent proteins are able to overcome the potential problems caused by oxygen limitations. The current available approaches and the benefits/disadvantages of using reporter vectors containing fluorescent proteins for labelling of bacterial probiotic species commonly used in food are addressed.