Relationships between the use of Embden Meyerhof pathway (EMP) or Phosphoketolase pathway (PKP) and lactate production capabilities of diverse Lactobacillus reuteri strains

Estimating the contribution of the porcine fecal core microbiota to metabolite production via mathematical modeling and in vitro fermentation

The swine gut microbiota is a complex ecosystem found throughout the gastrointestinal tract, with multiple exchanges with the host and whose composition is linked to both external and internal factors, such as diet or breed. Diet, probiotic, or prebiotic interventions have been designed to boost beneficial host-microbiota interactions, such as the production of anti-inflammatory molecules, or the fermentation of otherwise undigested resources. In parallel, a smaller microbial population, shared among the same host species, independent of external or internal factors, has been described and defined as the "core microbiota." Therapies targeting the core microbiota could possibly lead to more precise and long-lasting effects. However, the metabolic role of the porcine core microbiota, especially in relation to the rest of the microbial community, is currently missing. We present here the first dynamic model of the porcine core microbiota, which we used to estimate the core-microbiota metabolite production and to forecast the effect of a synbiotic intervention targeting the core genera of the core microbiota. We developed a community model in which a total of 17 microbial groups were established based on culture-based information of representative species. First, the model parameters were estimated, and the resulting model simulations were compared favorably with in vitro experimentation. The model was then used to predict the microbial dynamics of the core and non-core members under different experimental conditions. Therefore, it was able to theorize the main-metabolite core microbiota contribution, hypothesizing that it could be mainly responsible for acetate and propionate, but not for butyrate production.IMPORTANCECurrently, little information is present in the literature to describe the generic metabolic role of the porcine core microbiota or to inform on the effect of interventions targeting the core genera. Moreover, both in vitro and in vivo experimentations aiming to explore the core microbiota dynamics are technically demanding, expensive, or restricted by ethical considerations. Modeling approaches can be used as an initial exploratory tool to develop hypotheses for targeted experimentation. Our mathematical model provides initial information on the microbial and metabolite dynamics of the core microbiota in relation to diet and therapeutic intervention.

Exploitation of microbial activities at low pH to enhance planetary health

Awareness is growing that human health cannot be considered in isolation but is inextricably woven with the health of the environment in which we live. It is, however, under-recognized that the sustainability of human activities strongly relies on preserving the equilibrium of the microbial communities living in/on/around us. Microbial metabolic activities are instrumental for production, functionalization, processing, and preservation of food. For circular economy, microbial metabolism would be exploited to produce building blocks for the chemical industry, to achieve effective crop protection, agri-food waste revalorization, or biofuel production, as well as in bioremediation and bioaugmentation of contaminated areas. Low pH is undoubtedly a key physical-chemical parameter that needs to be considered for exploiting the powerful microbial metabolic arsenal. Deviation from optimal pH conditions has profound effects on shaping the microbial communities responsible for carrying out essential processes. Furthermore, novel strategies to combat contaminations and infections by pathogens rely on microbial-derived acidic molecules that suppress/inhibit their growth. Herein, we present the state-of-the-art of the knowledge on the impact of acidic pH in many applied areas and how this knowledge can guide us to use the immense arsenal of microbial metabolic activities for their more impactful exploitation in a Planetary Health perspective.

In Silico Genomic and Metabolic Atlas of Limosilactobacillus reuteri DSM 20016: An Insight into Human Health

Probiotics are bacterial strains that are known to provide host health benefits. Limosilactobacillus reuteri is a well-documented lactic acid bacterium that has been cultured from numerous human sites. The strain investigated was L. reuteri DSM 20016, which has been found to produce useful metabolites. The strain was explored using genomic and proteomic tools, manual searches, and databases, including KEGG, STRING, BLAST Sequence Similarity Search, and UniProt. This study located over 200 key genes that were involved in human health benefit pathways. L. reuteri DSM 20016 has metabolic pathways to produce acetate, propionate, and lactate, and there is evidence of a pathway for butanoate production through a FASII mechanism. The bacterium produces histamine through the hdc operon, which may be able to suppress proinflammatory TNF, and the bacterium also has the ability to synthesize folate and riboflavin, although whether they are secreted is yet to be explored. The strain can bind to human Caco2 cells through srtA, mapA/cnb, msrB, and fbpA and can compete against enteric bacteria using reuterin, which is an antimicrobial that induces oxidative stress. The atlas could be used for designing metabolic engineering approaches to improve beneficial metabolite biosynthesis and better probiotic-based cures.

Acids produced by lactobacilli inhibit the growth of commensal Lachnospiraceae and S24-7 bacteria

The Lactobacillaceae are an intensively studied family of bacteria widely used in fermented food and probiotics, and many are native to the gut and vaginal microbiota of humans and other animals. Various studies have shown that specific Lactobacillaceae species produce metabolites that can inhibit the colonization of fungal and bacterial pathogens, but less is known about how Lactobacillaceae affect individual bacterial species in the endogenous animal microbiota. Here, we show that numerous Lactobacillaceae species inhibit the growth of the Lachnospiraceae family and the S24-7 group, two dominant clades of bacteria within the gut. We demonstrate that inhibitory activity is a property common to homofermentative Lactobacillaceae species, but not to species that use heterofermentative metabolism. We observe that homofermentative Lactobacillaceae species robustly acidify their environment, and that acidification alone is sufficient to inhibit growth of Lachnospiraceae and S24-7 growth, but not related species from the Clostridiales or Bacteroidales orders. This study represents one of the first in-depth explorations of the dynamic between Lactobacillaceae species and commensal intestinal bacteria, and contributes valuable insight toward deconvoluting their interactions within the gut microbial ecosystem.

Mannitol Production by Heterofermentative Lactic Acid Bacteria: a Review

Obesity, diabetes, and other cardiovascular diseases are directly related to the high consumption of processed sugars with high caloric content. The current food industry has novel trends related to replacing highly caloric sugars with non-caloric or low-calorie sweeteners. Mannitol, a polyol, represents a suitable substitute because it has a low caloric content and does not induce a glycemic response, which is crucial for diabetic people. Consequently, this polyol has multiple applications in the food, pharmaceutical, and medicine industries. Mannitol can be produced by plant extraction, chemical or enzymatic synthesis, or microbial fermentation. Different in vitro processes have been developed regarding enzymatic synthesis to obtain mannitol from fructose, glucose, or starch-derived substrates. Various microorganisms such as yeast, fungi, and bacteria are applied for microbial fermentation. Among them, heterofermentative lactic acid bacteria (LAB) represent a reliable and feasible alternative due to their metabolic characteristics. In this regard, the yield and productivity of mannitol depend on the culture system, the growing conditions, and the culture medium composition. In situ mannitol production represents a novel approach to decrease the sugar content in food and beverages. Also, genetic engineering offers an interesting option to obtain mannitol-producing strains. This review presents and discusses the most significant advances that have been made in the mannitol production through fermentation by heterofermentative LAB, including the pertinent and critical analysis of culture conditions considering broth composition, reaction systems, and their effects on productivities and yields.

High-resolution structure of phosphoketolase from Bifidobacterium longum determined by cryo-EM single-particle analysis

In bifidobacteria, phosphoketolase (PKT) plays a key role in the central hexose fermentation pathway called "bifid shunt." The three-dimensional structure of PKT from Bifidobacterium longum with co-enzyme thiamine diphosphate (ThDpp) was determined at 2.1 Å resolution by cryo-EM single-particle analysis using 196,147 particles to build up the structural model of a PKT octamer related by D4 symmetry. Although the cryo-EM structure of PKT was almost identical to the X-ray crystal structure previously determined at 2.2 Å resolution, several interesting structural features were observed in the cryo-EM structure. Because this structure was solved at relatively high resolution, it was observed that several amino acid residues adopt multiple conformations. Among them, Q546-D547-H548-N549 (the QN-loop) demonstrate the largest structural change, which seems to be related to the enzymatic function of PKT. The QN-loop is at the entrance to the substrate binding pocket. The minor conformer of the QN-loop is similar to the conformation of the QN-loop in the crystal structure. The major conformer is located further from ThDpp than the minor conformer. Interestingly, the major conformer in the cryo-EM structure of PKT resembles the corresponding loop structure of substrate-bound Escherichia coli transketolase. That is, the minor and major conformers may correspond to "closed" and "open" states for substrate access, respectively. Moreover, because of the high-resolution analysis, many water molecules were observed in the cryo-EM structure of PKT. Structural features of the water molecules in the cryo-EM structure are discussed and compared with water molecules observed in the crystal structure.

Salinity enhances high optically active L-lactate production from co-fermentation of food waste and waste activated sludge: Unveiling the response of microbial community shift and functional profiling

Lactic acid (LA), a versatile platform molecule, can be fermented from organic wastes, such as food waste and waste activated sludge. In this study, an efficient approach using salt, a component of food waste as an additive, was proposed to increase LA production. The LA productivity was increased at 10 g NaCl/L and optical pure L-lactate was obtained at 30 g NaCl/L. The enhancement of LA was in accordance with the increased solubilization and the critical hydrolase activities under saline conditions. Moreover, high salinity (30-50 g NaCl/L) changed the common conversion of LA to volatile fatty acids. In addition, the key LA bacteria genera (Bacillus, Enterococcus, Lactobacillus) were selectively enriched under saline conditions. Strong correlations between salinity and functional genes for L-LA production were also observed. This study provides a practical way for the enrichment of L-LA with high optical activity from organic wastes.

Oriented Fermentation of Food Waste towards High-Value Products: A Review

Food waste has a great potential for resource recovery due to its huge yield and high organic content. Oriented fermentation is a promising method with strong application prospects due to high efficiency, strong robustness, and high-value products. Different fermentation types lead to different products, which can be shifted by adjusting fermentation conditions such as inoculum, pH, oxidation-reduction potential (ORP), organic loading rate (OLR), and nutrients. Compared with other types, lactic acid fermentation has the lowest reliance on artificial intervention. Lactic acid and volatile fatty acids are the common products, and high yield and high purity are the main targets of food waste fermentation. In addition to operational parameters, reactors and processes should be paid more attention to for industrial application. Currently, continuously stirred tank reactors and one-stage processes are used principally for scale-up continuous fermentation of food waste. Electro-fermentation and iron-based or carbon-based additives can improve food waste fermentation, but their mechanisms and application need further investigation. After fermentation, the recovery of target products is a key problem due to the lack of green and economic methods. Precipitation, distillation, extraction, adsorption, and membrane separation can be considered, but the recovery step is still the most expensive in the entire treatment chain. It is expected to develop more efficient fermentation processes and recovery strategies based on food waste composition and market demand.

Pre-fermentation of malt whisky wort using Lactobacillus plantarum and its influence on new-make spirit character

Distillery fermentations are non-sterile, which allow bacterial communities to flourish, typically towards the end of fermentation. The effect of beginning the bacterial fermentation at the start of fermentation was investigated. Wort was treated for 48 h using a commercial strain of Lactobacillus plantarum followed by fermentation using a distilling strain of Saccharomyces cerevisiae. The treated wash showed a substantial increase in lactic, acetic and succinic acids Sensory analysis determined that the spirit produced with bacterial treatment were significantly different (p < 0.05) and chemical analysis demonstrated an increase in the production of ethyl acetate. These results show that pre-treatment using species of Lactobacillus could be utilised to alter the quality of new-make spirit in a distillery. By using bacterial cultures present in the surroundings or raw materials, distillers could allow naturally occurring or commercially available microflora to be added thus enhancing flavour development during fermentation and producing different spirit characters.

A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory

Background

Lactobacillus reuteri is a heterofermentative Lactic Acid Bacterium (LAB) that is commonly used for food fermentations and probiotic purposes. Due to its robust properties, it is also increasingly considered for use as a cell factory. It produces several industrially important compounds such as 1,3-propanediol and reuterin natively, but for cell factory purposes, developing improved strategies for engineering and fermentation optimization is crucial. Genome-scale metabolic models can be highly beneficial in guiding rational metabolic engineering. Reconstructing a reliable and a quantitatively accurate metabolic model requires extensive manual curation and incorporation of experimental data.

Results

A genome-scale metabolic model of L. reuteri JCM 1112^T was reconstructed and the resulting model, Lreuteri_530, was validated and tested with experimental data. Several knowledge gaps in the metabolism were identified and resolved during this process, including presence/absence of glycolytic genes. Flux distribution between the two glycolytic pathways, the phosphoketolase and Embden–Meyerhof–Parnas pathways, varies considerably between LAB species and strains. As these pathways result in different energy yields, it is important to include strain-specific utilization of these pathways in the model. We determined experimentally that the Embden–Meyerhof–Parnas pathway carried at most 7% of the total glycolytic flux. Predicted growth rates from Lreuteri_530 were in good agreement with experimentally determined values. To further validate the prediction accuracy of Lreuteri_530, the predicted effects of glycerol addition and adhE gene knock-out, which results in impaired ethanol production, were compared to in vivo data. Examination of both growth rates and uptake- and secretion rates of the main metabolites in central metabolism demonstrated that the model was able to accurately predict the experimentally observed effects. Lastly, the potential of L. reuteri as a cell factory was investigated, resulting in a number of general metabolic engineering strategies.

Conclusion

We have constructed a manually curated genome-scale metabolic model of L. reuteri JCM 1112^T that has been experimentally parameterized and validated and can accurately predict metabolic behavior of this important platform cell factory.

Impact of the fermentation parameters pH and temperature on stress resilience of Lactobacillus reuteri DSM 17938

This study was undertaken to investigate the impact of culture pH (4.5-6.5) and temperature (32-37 °C) on the stress resilience of Lactobacillus reuteri DSM 17938 during freeze-drying and post freeze-drying exposure to low pH (pH 2) and bile salts. Response-surface methodology analysis revealed that freeze-drying survival rates [Formula: see text] were linearly related to pH with the highest survival rate of 80% when cells were cultured at pH 6.5 and the lowest was 40% when cells were cultured at pH 4.5. The analysis further revealed that within the chosen temperature range the culture temperature did not significantly affect the freeze-drying survival rate. However, fermentation at pH 4.5 led to better survival rates when rehydrated cells were exposed to low pH shock or bile salts. Thus, the effect of pH on freeze-drying survival was in contrast to effects on low pH and bile salts stress tolerance. The rationale behind this irreconcilability is based on the responses being dissimilar and are not tuned to each other. Culturing strain DSM 17938 at pH values higher than 5.5 could be a useful option to improve the survivability and increase viable cell numbers in the final freeze-dried product. However, the dissimilar responses for the process- and application parameters tested here suggest that an optimal compromise has to be found in order to obtain the most functional probiotic product possible.

Conversion of Glycerol to 3-Hydroxypropanoic Acid by Genetically Engineered Bacillus subtilis

3-Hydroxypropanoic acid (3-HP) is an important biomass-derivable platform chemical that can be converted into a number of industrially relevant compounds. There have been several attempts to produce 3-HP from renewable sources in cell factories, focusing mainly on Escherichia coli, Klebsiella pneumoniae, and Saccharomyces cerevisiae. Despite the significant progress made in this field, commercially exploitable large-scale production of 3-HP in microbial strains has still not been achieved. In this study, we investigated the potential of Bacillus subtilis as a microbial platform for bioconversion of glycerol into 3-HP. Our recombinant B. subtilis strains overexpress the two-step heterologous pathway containing glycerol dehydratase and aldehyde dehydrogenase from K. pneumoniae. Genetic engineering, driven by in silico optimization, and optimization of cultivation conditions resulted in a 3-HP titer of 10 g/L, in a standard batch cultivation. Our findings provide the first report of successful introduction of the biosynthetic pathway for conversion of glycerol into 3-HP in B. subtilis. With this relatively high titer in batch, and the robustness of B. subtilis in high density fermentation conditions, we expect that our production strains may constitute a solid basis for commercial production of 3-HP.

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.

Novel molecular, structural and evolutionary characteristics of the phosphoketolases from bifidobacteria and Coriobacteriales

Members from the order Bifidobacteriales, which include many species exhibiting health promoting effects, differ from all other organisms in using a unique pathway for carbohydrate metabolism, known as the “bifid shunt”, which utilizes the enzyme phosphoketolase (PK) to carry out the phosphorolysis of both fructose-6-phosphate (F6P) and xylulose-5-phosphate (X5P). In contrast to bifidobacteria, the PKs found in other organisms (referred to XPK) are able to metabolize primarily X5P and show very little activity towards F6P. Presently, very little is known about the molecular or biochemical basis of the differences in the two forms of PKs. Comparative analyses of PK sequences from different organisms reported here have identified multiple high-specific sequence features in the forms of conserved signature inserts and deletions (CSIs) in the PK sequences that clearly distinguish the X5P/F6P phosphoketolases (XFPK) of bifidobacteria from the XPK homologs found in most other organisms. Interestingly, most of the molecular signatures that are specific for the XFPK from bifidobacteria are also shared by the PK homologs from the Coriobacteriales order of Actinobacteria. Similarly to the Bifidobacteriales, the order Coriobacteriales is also made up of commensal organisms, that are saccharolytic and able to metabolize wide variety of carbohydrates, producing lactate and other metabolites. Phylogenetic studies provide evidence that the XFPK from bifidobacteria are specifically related to those found in the Coriobacteriales and suggest that the gene for PK (XFPK) was horizontally transferred between these two groups. A number of the identified CSIs in the XFPK sequence, which serve to distinguish the XFPK homologs from XPK homologs, are located at the subunit interface in the structure of the XFPK dimer protein. The results of protein modelling and subunit docking studies indicate that these CSIs are involved in the formation/stabilization of the protein dimer. The significance of these observations regarding the differences in the activities of the XFPK and XPK homologs are discussed. Additionally, this work also discusses the significance of the XFPK-like homologs, similar to those found in bifidobacteria, in the order Coriobacteriales.

Redox Balance in Lactobacillus reuteri DSM20016: Roles of Iron-Dependent Alcohol Dehydrogenases in Glucose/ Glycerol Metabolism

Lactobacillus reuteri, a heterofermentative bacterium, metabolizes glycerol via a Pdu (propanediol-utilization) pathway involving dehydration to 3-hydroxypropionaldehyde (3-HPA) followed by reduction to 1,3-propandiol (1,3-PDO) with concomitant generation of an oxidized cofactor, NAD+ that is utilized to maintain cofactor balance required for glucose metabolism and even for oxidation of 3-HPA by a Pdu oxidative branch to 3-hydroxypropionic acid (3-HP). The Pdu pathway is operative inside Pdu microcompartment that encapsulates different enzymes and cofactors involved in metabolizing glycerol or 1,2-propanediol, and protects the cells from the toxic effect of the aldehyde intermediate. Since L. reuteri excretes high amounts of 3-HPA outside the microcompartment, the organism is likely to have alternative alcohol dehydrogenase(s) in the cytoplasm for transformation of the aldehyde. In this study, diversity of alcohol dehydrogenases in Lactobacillus species was investigated with a focus on L. reuteri. Nine ADH enzymes were found in L. reuteri DSM20016, out of which 3 (PduQ, ADH6 and ADH7) belong to the group of iron-dependent enzymes that are known to transform aldehydes/ketones to alcohols. L. reuteri mutants were generated in which the three ADHs were deleted individually. The lagging growth phenotype of these deletion mutants revealed that limited NAD+/NADH recycling could be restricting their growth in the absence of ADHs. Notably, it was demonstrated that PduQ is more active in generating NAD+ during glycerol metabolism within the microcompartment by resting cells, while ADH7 functions to balance NAD+/NADH by converting 3-HPA to 1,3-PDO outside the microcompartment in the growing cells. Moreover, evaluation of ADH6 deletion mutant showed strong decrease in ethanol level, supporting the role of this bifuctional alcohol/aldehyde dehydrogenase in ethanol production. To the best of our knowledge, this is the first report revealing both internal and external recycling for cofactor homeostasis during 3-HPA conversion in L. reuteri.