Use of the dynamic gastro-intestinal model TIM to explore the survival of the yogurt bacterium Streptococcus thermophilus and the metabolic activities induced in the simulated human gut

Transfer of the Integrative and Conjugative Element ICESt3 of Streptococcus thermophilus in Physiological Conditions Mimicking the Human Digestive Ecosystem

Metagenome analyses of the human microbiome suggest that horizontal gene transfer (HGT) is frequent in these rich and complex microbial communities. However, so far, only a few HGT studies have been conducted in vivo. In this work, three different systems mimicking the physiological conditions encountered in the human digestive tract were tested, including (i) the TNO gastro-Intestinal tract Model 1 (TIM-1) system (for the upper part of the intestine), (ii) the ARtificial COLon (ARCOL) system (to mimic the colon), and (iii) a mouse model. To increase the likelihood of transfer by conjugation of the integrative and conjugative element studied in the artificial digestive systems, bacteria were entrapped in alginate, agar, and chitosan beads before being placed in the different gut compartments. The number of transconjugants detected decreased, while the complexity of the ecosystem increased (many clones in TIM-1 but only one clone in ARCOL). No clone was obtained in a natural digestive environment (germfree mouse model). In the human gut, the richness and diversity of the bacterial community would offer more opportunities for HGT events to occur. In addition, several factors (SOS-inducing agents, microbiota-derived factors) that potentially increase in vivo HGT efficiency were not tested here. Even if HGT events are rare, expansion of the transconjugant clones can happen if ecological success is fostered by selecting conditions or by events that destabilize the microbial community. IMPORTANCE The human gut microbiota plays a key role in maintaining normal host physiology and health, but its homeostasis is fragile. During their transit in the gastrointestinal tract, bacteria conveyed by food can exchange genes with resident bacteria. New traits acquired by HGT (e.g., new catabolic properties, bacteriocins, antibiotic resistance) can impact the gut microbial composition and metabolic potential. We showed here that TIM-1, a system mimicking the upper digestive tract, is a useful tool to evaluate HGT events in conditions closer to the physiological ones. Another important fact pointed out in this work is that Enterococcus faecalis is a good candidate for foreign gene acquisition. Due to its high ability to colonize the gut and acquire mobile genetic elements, this commensal bacterium could serve as an intermediate for HGT in the human gut.

Functional Characterization of Fermented Beverages Based on Soy Milk and Sea Buckthorn Powder

Limitations of dairy products, such as lactose intolerance, problems related to a high cholesterol intake in diet, malabsorption, and the requirement for cold storage facilities, as well as an increasing demand for new foods and tastes, have initiated a trend in the development of non-dairy probiotic products. The possibility of producing beverages based on soy milk, sea buckthorn powder, and fermented by Bifidobacterium bifidus (Bb-12^®, Bb) strain at different temperatures (30 °C and 37 °C) was examined. Strain viability, pH, and titratable acidity were measured during the fermentation period while the viability, pH, titratable acidity, and water holding capacity were determined during the storage time at 4 °C ± 1 °C within 14 days. Additionally, the survival and stability of Bb-12^®, inoculated into a functional beverage when exposed to simulated gastrointestinal tract conditions, were assessed. The results obtained in this study revealed that the content of potent bioactive compounds in fermented soy milk and sea buckthorn powder depends on the processing conditions, the bacteria used in the fermentation step, and storage time.

The genomic basis of the Streptococcus thermophilus health-promoting properties

Background

Streptococcus thermophilus is a Gram-positive bacterium widely used as starter in the dairy industry as well as in many traditional fermented products. In addition to its technological importance, it has also gained interest in recent years as beneficial bacterium due to human health-promoting functionalities. The objective of this study was to inventory the main health-promoting properties of S. thermophilus and to study their intra-species diversity at the genomic and genetic level within a collection of representative strains.

Results

In this study various health-related functions were analyzed at the genome level from 79 genome sequences of strains isolated over a long time period from diverse products and different geographic locations. While some functions are widely conserved among isolates (e.g., degradation of lactose, folate production) suggesting their central physiological and ecological role for the species, others including the tagatose-6-phosphate pathway involved in the catabolism of galactose, and the production of bioactive peptides and gamma-aminobutyric acid are strain-specific. Most of these strain-specific health-promoting properties seems to have been acquired via horizontal gene transfer events. The genetic basis for the phenotypic diversity between strains for some health related traits have also been investigated. For instance, substitutions in the galK promoter region correlate with the ability of some strains to catabolize galactose via the Leloir pathway. Finally, the low occurrence in S. thermophilus genomes of genes coding for biogenic amine production and antibiotic resistance is also a contributing factor to its safety status.

Conclusions

The natural intra-species diversity of S. thermophilus, therefore, represents an interesting source for innovation in the field of fermented products enriched for healthy components that can be exploited to improve human health. A better knowledge of the health-promoting properties and their genomic and genetic diversity within the species may facilitate the selection and application of strains for specific biotechnological and human health-promoting purpose. Moreover, by pointing out that a substantial part of its functional potential still defies us, our work opens the way to uncover additional health-related functions through the intra-species diversity exploration of S. thermophilus by comparative genomics approaches.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08459-y.

Impact of oral galenic formulations of Lactobacillus salivarius on probiotic survival and interactions with microbiota in human in vitro gut models

Health benefits of probiotics in humans essentially depend on their ability to survive during gastrointestinal (GI) transit and to modulate gut microbiota. To date, there is few data on the impact of galenic formulations of probiotics on these parameters. Even if clinical studies remain the gold standard to evaluate the efficacy of galenic forms, they stay hampered by technical, ethical and cost reasons. As an alternative approach, we used two complementary in vitro models of the human gut, the TNO gastrointestinal (TIM-1) model and the Artificial Colon (ARCOL), to study the effect of three oral formulations of a Lactobacillus salivarius strain (powder, capsule and sustained-release tablet) on its viability and interactions with gut microbiota. In the TIM-1 stomach, no or low numbers of bacteria were respectively released from the capsule and tablet, confirming their gastro-resistance. The capsule was disintegrated in the jejunum on average 76 min after administration while the core of sustained-release tablet was still intact at the end of digestion. Viability in TIM-1 was significantly influenced by the galenic form with survival percentages of 0.003±0.004%, 2.8±0.6% and 17.0±1.8% (n=3) for powder, capsule and tablet, respectively. In the ARCOL, the survival of the strain tended to be higher in the post-treatment phase with the tablet compared to capsule, but gut microbiota composition and activity were not differently modulated by the two formulations. In conclusion, the sustained-release tablet emerged as the formulation that most effectively preserved viability of the tested strain during GI passage. This study highlights the usefulness of in vitro gut models for the pre-screening of probiotic pharmaceutical forms. Their use could also easily be extended to the evaluation of the effects of food matrices and age on probiotic survival and activity during GI transit.

Identification of Streptococcus thermophilus Genes Specifically Expressed under Simulated Human Digestive Conditions Using R-IVET Technology

Despite promising health effects, the probiotic status of Streptococcus thermophilus, a lactic acid bacterium widely used in dairy industry, requires further documentation of its physiological status during human gastrointestinal passage. This study aimed to apply recombinant-based in vivo technology (R-IVET) to identify genes triggered in a S. thermophilus LMD-9 reference strain under simulated digestive conditions. First, the R-IVET chromosomal cassette and plasmid genomic library were designed to positively select activated genes. Second, recombinant clones were introduced into complementary models mimicking the human gut, the Netherlands Organization for Applied Scientific Research (TNO) gastrointestinal model imitating the human stomach and small intestine, the Caco-2 TC7 cell line as a model of intestinal epithelium, and anaerobic batch cultures of human feces as a colon model. All inserts of activated clones displayed a promoter activity that differed from one digestive condition to another. Our results also showed that S. thermophilus adapted its metabolism to stressful conditions found in the gastric and colonic competitive environment and modified its surface proteins during adhesion to Caco-2 TC7 cells. Activated genes were investigated in a collection of S. thermophilus strains showing various resistance levels to gastrointestinal stresses, a first stage in the identification of gut resistance markers and a key step in probiotic selection.

Development of a semi-dynamic in vitro model and its testing using probiotic Bacillus coagulans GBI-30, 6086 in orange juice and yogurt

A dynamic system mimicking the gastrointestinal tract (GIT) conditions (fluids, pH, temperature, and residence time) was used to evaluate the behavior of Bacillus coagulans GBI-30, 6086 (BC) incorporated in yogurt and orange juice. BC counts were monitored in samples collected before the in vitro digestion, after initial contact with gastric fluids (30 min), static (1 h 15 min) and dynamic (2 h) stages in the gastric compartment, static (3 h) and dynamic (4 h) stages in the duodenal compartment, static (5 h) and dynamic (6 h) stages in the jejunal compartment, and after digestion. BC presented high survival in juice and yogurt over the digestion stages. The number of decimal reductions (γ) of BC caused by exposure to simulated GIT conditions was ≥0.89 in orange juice and ≥1.17 in yogurt. No differences (p ≥ 0.05) were observed on the survival of BC among the samples collected over the digestion in juice or yogurt, or between these matrices. After the in vitro digestion, BC counts were ≥7 log CFU/mL or g. Results show the great survival of BC under GIT conditions and suggest both, juice and yogurt as appropriate carries for delivering this probiotic to the diet. The semi-dynamic in vitro system was easily built and to operate, comprising an intermediate approach to assess the resistance of probiotic or potentially probiotic strains under simulated gut conditions.

Soymilk fermentation: effect of cooling protocol on cell viability during storage and in vitro gastrointestinal stress

This work covers soymilk fermentation by starter and probiotic cultures and explores the influence of cooling protocol on cell viability, organic acid production, sugar consumption, fatty acid profile, and cell survival to in vitro gastrointestinal stress. After fermentation at 37 °C by mono- or co-cultures of Streptococcus thermophilus (St), Lactobacillus bulgaricus (Lb), and Lactobacillus paracasei (Lp), fermented soymilk was cooled directly at 4 °C for 28 days or cooled in two phases (TPC), i.e., by preceding that step by another at 25 °C for 8 h. Soybean milk fermentation by Lb alone lasted longer (15 h) than by StLb or StLbLp (9 h). In ternary culture, TPC increased Lp viability, linoleic, and lactic acid concentrations by 3.8, 22.6, and 96.2%, respectively, whereas the cooling protocol did not influence Lp and St counts after in vitro gastrointestinal stress. Graphical abstract.

In Vitro and In Vivo Models for Evaluating the Oral Toxicity of Nanomedicines

Toxicity studies for conventional oral drug formulations are standardized and well documented, as required by the guidelines of administrative agencies such as the US Food & Drug Administration (FDA), the European Medicines Agency (EMA) or European Medicines Evaluation Agency (EMEA), and the Japanese Pharmaceuticals and Medical Devices Agency (PMDA). Researchers tend to extrapolate these standardized protocols to evaluate nanoformulations (NFs) because standard nanotoxicity protocols are still lacking in nonclinical studies for testing orally delivered NFs. However, such strategies have generated many inconsistent results because they do not account for the specific physicochemical properties of nanomedicines. Due to their tiny size, accumulated surface charge and tension, sizeable surface-area-to-volume ratio, and high chemical/structural complexity, orally delivered NFs may generate severe topical toxicities to the gastrointestinal tract and metabolic organs, including the liver and kidney. Such toxicities involve immune responses that reflect different mechanisms than those triggered by conventional formulations. Herein, we briefly analyze the potential oral toxicity mechanisms of NFs and describe recently reported in vitro and in vivo models that attempt to address the specific oral toxicity of nanomedicines. We also discuss approaches that may be used to develop nontoxic NFs for oral drug delivery.

Application of Recombinase-Based In Vivo Expression Technology to Bifidobacterium longum subsp. longum for Identification of Genes Induced in the Gastrointestinal Tract of Mice

Bifidobacteria are one of the major components in human gut microbiota and well-known as beneficial microbes. However, clarification of commensal mechanisms of bifidobacteria in the intestines is still ongoing, especially in the presence of the gut microbiota. Here, we applied recombinase-based in vivo expression technology (R-IVET) using the bacteriophage P1 Cre/loxP system to Bifidobacterium longum subsp. longum 105-A (B. longum 105-A) to identify genes that are specifically expressed in the gastrointestinal tract of conventionally raised mice. Oral administration of the genomic DNA library of B. longum 105-A to conventionally raised mice resulted in the identification of 73 in vivo-induced genes. Four out of seven tested genes were verified in vivo-specific induction at least in the cecum by quantitative reverse transcription PCR. Although there is still room for improvement of the system, our findings can contribute to expanding our understanding of the commensal behavior of B. longum in the gut ecosystem.

Surface display of PbrR on Escherichia coli and evaluation of the bioavailability of lead associated with engineered cells in mice

Human exposure to lead mainly occurs by ingestion of contaminated food, water and soil. Blocking lead uptake in the gastrointestinal tract is a novel prevention strategy. Whole-cell biosorbent for lead was constructed with PbrR genetically engineered on the cell surface of Escherichia coli (E. coli), a predominant strain among intestinal microflora, using lipoprotein (Lpp)-OmpA as the anchoring protein. In vitro, the PbrR displayed cells had an enhanced ability for immobilizing toxic lead(II) ions from the external media at both acidic and neutral pH, and exhibited a higher specific adsorption for lead compared to other physiological two valence metal ions. In vivo, the persistence of recombinant E. coli in the murine intestinal tract and the integrity of surface displayed PbrR were confirmed. In addition, oral administration of surface-engineered E. coli was safe in mice, in which the concentrations of physiological metal ions in blood were not affected. More importantly, lead associated with PbrR-displayed E. coli was demonstrated to be less bioavailable in the experimental mouse model with exposure to oral lead. This is reflected by significantly lower blood and femur lead concentrations in PbrR-displayed E. coli groups compared to the control. These results open up the possibility for the removal of toxic metal ions in vivo using engineered microorganisms as adsorbents.

Evaluation of Streptococcus thermophilus IFFI 6038 Microcapsules Prepared Using an Ultra-fine Particle Processing System

Microencapsulation technology has the potential to protect probiotics and to deliver them to the gut, and extrusion is one of the most commonly used methods. However, the rather large diameters of 1~5 mm produced tend to cause oral grittiness and result in low compliance. In this article, Streptococcus thermophilus IFFI 6038 (IFFI 6038) microcapsules were prepared using an ultra-fine particle processing system (UPPS) previously developed by this research group. IFFI 6038 suspension was pumped by a peristaltic pump to the feeding inlet nozzle and then dispersed into micro-droplets by a rotating disk, followed by solidification. Trehalose (16%) was used as a cryoprotectant to protect IFFI 6038 from damage by lyophilization used in the process. Alginate (3%) resulted in IFFI 6038 microcapsules with a median particle diameter (d ₅₀) of 29.32 ± 0.12 μm and a span value of 1.00 ± 0.02, indicating uniform particle size distribution. To evaluate the potential of microencapsulation in protecting IFFI 6038 from the gastric conditions, the viable counts of IFFI 6038 following incubation of IFFI 6038 microcapsules in simulated gastric juices for 120 min were determined and compared with those of free IFFI 6038. The stability of microencapsulated IFFI 6038 upon storage for 3 months at 4°C and 25°C, respectively, was also determined. The results showed that microcapsules prepared by UPPS protected IFFI 6038 from gastric conditions. The results from a rat diarrhea model showed that microcapsules prepared by the UPPS method were able to effectively improve the diarrhea conditions in rats.

Formulation, stabilisation and encapsulation of bacteriophage for phage therapy

Against a backdrop of global antibiotic resistance and increasing awareness of the importance of the human microbiota, there has been resurgent interest in the potential use of bacteriophages for therapeutic purposes, known as phage therapy. A number of phage therapy phase I and II clinical trials have concluded, and shown phages don't present significant adverse safety concerns. These clinical trials used simple phage suspensions without any formulation and phage stability was of secondary concern. Phages have a limited stability in solution, and undergo a significant drop in phage titre during processing and storage which is unacceptable if phages are to become regulated pharmaceuticals, where stable dosage and well defined pharmacokinetics and pharmacodynamics are de rigueur. Animal studies have shown that the efficacy of phage therapy outcomes depend on the phage concentration (i.e. the dose) delivered at the site of infection, and their ability to target and kill bacteria, arresting bacterial growth and clearing the infection. In addition, in vitro and animal studies have shown the importance of using phage cocktails rather than single phage preparations to achieve better therapy outcomes. The in vivo reduction of phage concentration due to interactions with host antibodies or other clearance mechanisms may necessitate repeated dosing of phages, or sustained release approaches. Modelling of phage-bacterium population dynamics reinforces these points. Surprisingly little attention has been devoted to the effect of formulation on phage therapy outcomes, given the need for phage cocktails, where each phage within a cocktail may require significantly different formulation to retain a high enough infective dose. This review firstly looks at the clinical needs and challenges (informed through a review of key animal studies evaluating phage therapy) associated with treatment of acute and chronic infections and the drivers for phage encapsulation. An important driver for formulation and encapsulation is shelf life and storage of phage to ensure reproducible dosages. Other drivers include formulation of phage for encapsulation in micro- and nanoparticles for effective delivery, encapsulation in stimuli responsive systems for triggered controlled or sustained release at the targeted site of infection. Encapsulation of phage (e.g. in liposomes) may also be used to increase the circulation time of phage for treating systemic infections, for prophylactic treatment or to treat intracellular infections. We then proceed to document approaches used in the published literature on the formulation and stabilisation of phage for storage and encapsulation of bacteriophage in micro- and nanostructured materials using freeze drying (lyophilization), spray drying, in emulsions e.g. ointments, polymeric microparticles, nanoparticles and liposomes. As phage therapy moves forward towards Phase III clinical trials, the review concludes by looking at promising new approaches for micro- and nanoencapsulation of phages and how these may address gaps in the field.

Preparation of Acid-Resistant Microcapsules with Shell-Matrix Structure to Enhance Stability of Streptococcus Thermophilus IFFI 6038

Microencapsulation is an effective technology used to protect probiotics against harsh conditions. Extrusion is a commonly used microencapsulation method utilized to prepare probiotics microcapsules that is regarded as economical and simple to operate. This research aims to prepare acid-resistant probiotic microcapsules with high viability after freeze-drying and optimized storage stability. Streptococcus thermophilus IFFI 6038 (IFFI 6038) cells were mixed with trehalose and alginate to fabricate microcapsules using extrusion. These capsules were subsequently coated with chitosan to obtain chitosan-trehalose-alginate microcapsules with shell-matrix structure. Chitosan-alginate microcapsules (without trehalose) were also prepared using the same method. The characteristics of the microcapsules were observed by measuring the freeze-dried viability, acid resistance, and long-term storage stability of the cells. The viable count of IFFI 6038 in the chitosan-trehalose-alginate microcapsules was 8.34 ± 0.30 log CFU g^-1 after freeze-drying (lyophilization), which was nearly 1 log units g^-1 greater than the chitosan-alginate microcapsules. The viability of IFFI 6038 in the chitosan-trehalose-alginate microcapsules was 6.45 ± 0.09 log CFU g^-1 after 120 min of treatment in simulated gastric juices, while the chitosan-alginate microcapsules only measured 4.82 ± 0.22 log CFU g^-1 . The results of the long-term storage stability assay indicated that the viability of IFFI 6038 in chitosan-trehalose-alginate microcapsules was higher than in chitosan-alginate microcapsules after storage at 25 °C. Trehalose played an important role in the stability of IFFI 6038 during storage. The novel shell-matrix chitosan-trehalose-alginate microcapsules showed optimal stability and acid resistance, demonstrating their potential as a delivery vehicle to transport probiotics.

Impact of multi-functional fermented goat milk beverage on gut microbiota in a dynamic colon model

The aim of this research was to evaluate the effect of grape probiotic fermented beverages made of goat milk, with or without added grape pomace on gut microbiota in a Simulator of Human Intestinal Microbial Ecosystem (SHIME®). SHIME® model was used to investigate to assess changes in microbial composition and fermentation metabolites (short- and branched-chain fatty acids and ammonium), as well as under the antioxidant capacity. The results demonstrated that the beverages formulated, with or without grape pomace extract, exhibited high dietary fiber, oleic acid, phenolic compounds content and antioxidant activity. Both beverages also kept L. rhamnosus and S. thermophilus viable during their passage through the intestinal tract and had a positive effect on gut microbiota metabolism, increasing the antioxidant capacity and the production of short-chain fatty acids, and decreasing the ammonium concentration. Therefore, the multifunctional beverages formulated in this study can offer a new perspective for the production of foods with positive potential effects on human health.