A functional analysis of the formyl-coenzyme A (frc) gene from Lactobacillus reuteri 100-23C

Isolation of derivatives from the food-grade probiotic Lactobacillus johnsonii CNCM I-4884 with enhanced anti-Giardia activity

Giardiasis, a widespread intestinal parasitosis affecting humans and animals, is a growing concern due to the emergence of drug-resistant strains of G. intestinalis. Probiotics offer a promising alternative for preventing and treating giardiasis. Recent studies have shown that the probiotic Lactobacillus johnsonii CNCM I-4884 inhibits G. intestinalis growth both in vitro and in vivo. This protective effect is largely mediated by bile salt hydrolase (BSH) enzymes, which convert conjugated bile acids (BAs) into free forms that are toxic to the parasite. The objective of this study was to use adaptive evolution to develop stress-resistant derivatives of L. johnsonii CNCM I-4884, with the aim of improving its anti-Giardia activity. Twelve derivatives with enhanced resistance to BAs and reduced autolysis were generated. Among them, derivative M11 exhibited the highest in vitro anti-Giardia effect with enhanced BSH activity. Genomic and proteomic analyses of M11 revealed two SNPs and the upregulation of the global stress response by SigB, which likely contributed to its increased BAs resistance and BSH overproduction. Finally, the anti-Giardia efficacy of M11 was validated in a murine model of giardiasis. In conclusion, our results demonstrate that adaptive evolution is an effective strategy to generate robust food-grade bacteria with improved health benefits.

Metabolic insights of lactic acid bacteria in reducing off-flavors and antinutrients in plant-based fermented dairy alternatives

Multiple sensorial, technological, and nutritional challenges must be overcome when developing plant-based fermented dairy alternatives (PBFDA) to mimic their dairy counterparts. The elimination of plant-derived off-flavors (green, earthy, bitter, astringent) and the degradation of antinutrients are crucial quality factors highlighted by the industry for their effect on consumer acceptance. The adaptation of plant-derived lactic acid bacteria (LAB) species into plant niches is relevant when developing starter cultures for PBFDA products due to their evolutionary acquired ability to degrade plant-based undesirable compounds (off-flavors and antinutrients). Some plant-isolated species, such as Lactiplantibacillus plantarum and Limosilactobacillus fermentum, have been associated with the degradation of phytates, phenolic compounds, oxalates, and raffinose-family oligosaccharides (RFOs), whereas some animal-isolated species, such as Lactobacillus acidophilus strains, can metabolize phytates, RFOs, saponins, phenolic compounds, and oxalates. Some proteolytic LAB strains, such as Lacticaseibacillus paracasei and Lacticaseibacillus rhamnosus, have been characterized to degrade phytates, protease inhibitors, and oxalates. Other species have also been described regarding their abilities to biotransform phytic acid, RFOs, saponins, phenolic compounds, protease inhibitors, oxalates, and volatile off-flavor compounds (hexanal, nonanal, pentanal, and benzaldehyde). In addition, we performed a blast analysis considering antinutrient metabolic genes (42 genes) to up to 5 strains of all qualified presumption of safety-listed LAB species (55 species, 240 strains), finding out potential genotypical capabilities of LAB species that have not conventionally been used as starter cultures such as Lactiplantibacillus pentosus, Lactiplantibacillus paraplantarum, and Lactobacillus diolivorans for plant-based fermentations. This review provides a detailed understanding of genes and enzymes from LAB that target specific compounds in plant-based materials for plant-based fermented food applications.

Engineered microorganisms: A new direction in kidney stone prevention and treatment

Numerous studies have shown that intestinal and urinary tract flora are closely related to the formation of kidney stones. The removal of probiotics represented by lactic acid bacteria and the colonization of pathogenic bacteria can directly or indirectly promote the occurrence of kidney stones. However, currently existing natural probiotics have limitations. Synthetic biology is an emerging discipline in which cells or living organisms are genetically designed and modified to have biological functions that meet human needs, or even create new biological systems, and has now become a research hotspot in various fields. Using synthetic biology approaches of microbial engineering and biological redesign to enable probiotic bacteria to acquire new phenotypes or heterologous protein expression capabilities is an important part of synthetic biology research. Synthetic biology modification of microorganisms in the gut and urinary tract can effectively inhibit the development of kidney stones by a range of means, including direct degradation of metabolites that promote stone production or indirect regulation of flora homeostasis. This article reviews the research status of engineered microorganisms in the prevention and treatment of kidney stones, to provide a new and effective idea for the prevention and treatment of kidney stones.

Detection of oxalyl-CoA decarboxylase (oxc) and formyl-CoA transferase (frc) genes in novel probiotic isolates capable of oxalate degradation in vitro

Oxalate degradation is one of lactic acid bacteria's desirable activities. It is achieved by two enzymes, formyl coenzyme A transferase (frc) and oxalyl coenzyme A decarboxylase (oxc). The current study aimed to screen 15 locally isolated lactic acid bacteria to select those with the highest oxalate degradation ability. It also aimed to amplify the genes involved in degradation. MRS broth supplemented with 20 mM sodium oxalate was used to culture the tested isolates for 72 h. This was followed by an enzymatic assay to detect remaining oxalate. All isolates showed oxalate degradation activity to variable degrees. Five isolates demonstrated high oxalate degradation, 78 to 88%. To investigate the oxalate-degradation potential of the selected isolates, they have been further tested for the presence of genes that encode for enzymes involved in oxalate catabolism, formyl coenzyme A transferase (frc) and oxalyl coenzyme A decarboxylase (oxc). Three strains showed bands with the specific OXC and FRC forward and reverse primers designated as (SA-5, 9 and 37). Species-level identification revealed Loigolactobacillus bifermentans, Lacticaseibacillus paracasei, and Lactiplantibacillus plantarum. Preliminary results revealed that the tested probiotic strains harbored both oxc and frc whose products are putatively involved in oxalate catabolism. The probiotic potential of the selected strains was evaluated, and they showed high survival rates to both simulated gastric and intestinal fluids and variable degrees of antagonism against the tested Gram-positive and negative pathogens and were sensitive to clarithromycin but resistant to both metronidazole and ceftazidime. Finally, these strains could be exploited as an innovative approach to establish oxalate homeostasis in humans and prevent kidney stone formation.

Exploring Bacterial Attributes That Underpin Symbiont Life in the Monogastric Gut

The large bowel of monogastric animals, such as that of humans, is home to a microbial community (microbiota) composed of a diversity of mostly bacterial species. Interrelationships between the microbiota as an entity and the host are complex and lifelong and are characteristic of a symbiosis. The relationships may be disrupted in association with disease, resulting in dysbiosis. Modifications to the microbiota to correct dysbiosis require knowledge of the fundamental mechanisms by which symbionts inhabit the gut. This review aims to summarize aspects of niche fitness of bacterial species that inhabit the monogastric gut, especially of humans, and to indicate the research path by which progress can be made in exploring bacterial attributes that underpin symbiont life in the gut.

Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease

Over-accumulation of oxalate in humans may lead to nephrolithiasis and nephrocalcinosis. Humans lack endogenous oxalate degradation pathways (ODP), but intestinal microbes can degrade oxalate using multiple ODPs and protect against its absorption. The exact oxalate-degrading taxa in the human microbiota and their ODP have not been described. We leverage multi-omics data (>3000 samples from >1000 subjects) to show that the human microbiota primarily uses the type II ODP, rather than type I. Furthermore, among the diverse ODP-encoding microbes, an oxalate autotroph, Oxalobacter formigenes, dominates this function transcriptionally. Patients with inflammatory bowel disease (IBD) frequently suffer from disrupted oxalate homeostasis and calcium oxalate nephrolithiasis. We show that the enteric oxalate level is elevated in IBD patients, with highest levels in Crohn's disease (CD) patients with both ileal and colonic involvement consistent with known nephrolithiasis risk. We show that the microbiota ODP expression is reduced in IBD patients, which may contribute to the disrupted oxalate homeostasis. The specific changes in ODP expression by several important taxa suggest that they play distinct roles in IBD-induced nephrolithiasis risk. Lastly, we colonize mice that are maintained in the gnotobiotic facility with O. formigenes, using either a laboratory isolate or an isolate we cultured from human stools, and observed a significant reduction in host fecal and urine oxalate levels, supporting our in silico prediction of the importance of the microbiome, particularly O. formigenes in host oxalate homeostasis.

Enteric hyperoxaluria: role of microbiota and antibiotics

PURPOSE OF REVIEW

Enteric hyperoxaluria is commonly observed in malabsorptive conditions including Roux en Y gastric bypass (RYGB) and inflammatory bowel diseases (IBD). Its incidence is increasing secondary to an increased prevalence of both disorders. In this review, we summarize the evidence linking the gut microbiota to the risk of enteric hyperoxaluria.

RECENT FINDINGS

In enteric hyperoxaluria, fat malabsorption leads to increased binding of calcium to free fatty acids resulting in more soluble oxalate in the intestinal lumen. Bile acids and free fatty acids in the lumen also cause increased gut permeability allowing more passive absorption of oxalate. In recent years, there is more interest in the role of the gut microbiota in modulating urinary oxalate excretion in enteric hyperoxaluria, stemming from our knowledge that microbiota in the intestines can degrade oxalate. Oxalobacter formigenes reduced urinary oxalate in animal models of RYGB. The contribution of other oxalate-degrading organisms and the microbiota community to the pathophysiology of enteric hyperoxaluria are also currently under investigation.

SUMMARY

Gut microbiota might play a role in modulating the risk of enteric hyperoxaluria through oxalate degradation and bile acid metabolism. O. formigenes is a promising therapeutic target in this population; however, further studies in humans are needed to test its effectiveness.

Complex Responses to Hydrogen Peroxide and Hypochlorous Acid by the Probiotic Bacterium Lactobacillus reuteri

Inflammatory diseases of the gut are associated with increased intestinal oxygen concentrations and high levels of inflammatory oxidants, including hydrogen peroxide (H₂O₂) and hypochlorous acid (HOCl), which are antimicrobial compounds produced by the innate immune system. This contributes to dysbiotic changes in the gut microbiome, including increased populations of proinflammatory enterobacteria (Escherichia coli and related species) and decreased levels of health-associated anaerobic Firmicutes and Bacteroidetes The pathways for H₂O₂ and HOCl resistance in E. coli have been well studied, but little is known about how commensal and probiotic bacteria respond to inflammatory oxidants. In this work, we have characterized the transcriptomic response of the anti-inflammatory, gut-colonizing Gram-positive probiotic Lactobacillus reuteri to both H₂O₂ and HOCl. L. reuteri mounts distinct but overlapping responses to each of these stressors, and both gene expression and survival were strongly affected by the presence or absence of oxygen. Oxidative stress response in L. reuteri required several factors not found in enterobacteria, including the small heat shock protein Lo18, polyphosphate kinase 2, and RsiR, an L. reuteri-specific regulator of anti-inflammatory mechanisms.IMPORTANCE Reactive oxidants, including hydrogen peroxide and hypochlorous acid, are antimicrobial compounds produced by the immune system during inflammation. Little is known, however, about how many important types of bacteria present in the human microbiome respond to these oxidants, especially commensal and other health-associated species. We have now mapped the stress response to both H₂O₂ and HOCl in the intestinal lactic acid bacterium Lactobacillus reuteri.

Manipulation of oxalate metabolism in plants for improving food quality and productivity

Oxalic acid is a naturally occurring metabolite in plants and a common constituent of all plant-derived human diets. Oxalic acid has diverse unrelated roles in plant metabolism, including pH regulation in association with nitrogen metabolism, metal ion homeostasis and calcium storage. In plants, oxalic acid is also a pathogenesis factor and is secreted by various fungi during host infection. Unlike those of plants, fungi and bacteria, the human genome does not contain any oxalate-degrading genes, and therefore, the consumption of large amounts of plant-derived oxalate is considered detrimental to human health. In this review, we discuss recent biotechnological approaches that have been used to reduce the oxalate content of plant tissues.