Metabolism of oligosaccharides and starch in lactobacilli: a review

Widely targeted metabolomics analysis reveals the effect of soybean hull polysaccharides on nonvolatile components of plant-based yogurt and its metabolic pattern

Soybean hull polysaccharides (SHPS) enhance the physicochemical properties of plant-based yogurt. However, their effects on the nutritional profile and biochemical mechanisms remain unclear. This study aimed to assess the impact of SHPS addition on the nonvolatile components of plant-based yogurt and its underlying mechanisms through widely targeted metabolomics analysis. The results demonstrated that the addition of SHPS (0.2 %-1.0 % w/v) enhanced the levels of free amino acids, sugars, and organic acids, with the addition of 0.6 % w/v being particularly effective in improving yogurt quality. Widely targeted metabolomics analysis revealed 278 differential metabolites between yogurt supplemented with 0.6 % SHPS (SPY) and the control sample. SHPS increased the content of various metabolites, including amino acids and derivatives, saccharides, organic acids, and flavonoids, among others. Key metabolic pathways affected by SHPS included pantothenate and CoA biosynthesis; valine, leucine, and isoleucine biosynthesis; and benzoate degradation. As the primary component of SHPS, galacturonic acid affected the metabolic products in yogurt by participating in the pentose and glucuronate interconversions and ascorbate and aldarate metabolism pathways. These findings elucidate the role of SHPS in modulating the nutritional composition of plant-based yogurt, offering valuable insights into its functional mechanisms in food processing.

Effect of Encapsulation of Lactobacillus casei in Alginate-Tapioca Flour Microspheres Coated with Different Biopolymers on the Viability of Probiotic Bacteria

To realize the health benefits of probiotic bacteria, they must withstand processing and storage conditions and remain viable after use. The encapsulation of these probiotics in the form of microspheres containing tapioca flour as a prebiotic and vehicle component in their structure or shell affords symbiotic effects that improve the survival of probiotics under unfavorable conditions. Microencapsulation is one such method that has proven to be effective in protecting probiotics from adverse conditions while maintaining their viability and functionality. The aim of the work was to obtain high-quality microspheres that can act as carriers of Lactobacillus casei bacteria and to assess the impact of encapsulation on the viability of probiotic microorganisms in alginate microspheres enriched with a prebiotic (tapioca flour) and additionally coated with hyaluronic acid, chitosan, or gelatin. The influence of the composition of microparticles on the physicochemical properties and the viability of probiotic bacteria during storage was examined. The optimal composition of microspheres was selected using the design of experiments using statistical methods. Subsequently, the size, morphology, and cross-section of the obtained microspheres, as well as the effectiveness of the microsphere coating with biopolymers, were analyzed. The chemical structure of the microspheres was identified by using Fourier-transform infrared spectrophotometry. Raman spectroscopy was used to confirm the success of coating the microspheres with the selected biopolymers. The obtained results showed that the addition of tapioca flour had a positive effect on the surface modification of the microspheres, causing the porous structure of the alginate microparticles to become smaller and more sealed. Moreover, the addition of prebiotic and biopolymer coatings of the microspheres, particularly using hyaluronic acid and chitosan, significantly improved the survival and viability of the probiotic strain during long-term storage. The highest survival rate of the probiotic strain was recorded for alginate-tapioca flour microspheres coated with hyaluronic acid, at 5.48 log CFU g-1. The survival rate of L. casei in that vehicle system was 89% after storage for 30 days of storage.

Characterization of the gastrointestinal microbiome of the Syrian hamster (Mesocricetus auratus) and comparison to data from mice

Syrian hamsters (Mesocricetus auratus) have been increasingly used as rodent models in recent years, especially for SARS-CoV-2 since the pandemic. However, the physiology of this animal model is not yet well-understood, even less when considering the digestive tract. Generally, the gastrointestinal microbiome influences the immune system, drug metabolism, and vaccination efficacy. However, a detailed understanding of the gastrointestinal microbiome of hamsters is missing. Therefore, we analyzed 10 healthy 11-week-old RjHan:AURA hamsters fed a pelleted standard diet. Their gastrointestinal content was sampled (i.e., forestomach, glandular stomach, ileum, cecum, and colon) and analyzed using 16S rRNA gene amplicon sequencing. Results displayed a distinct difference in the bacterial community before and after the cecum, possibly due to the available nutrients and digestive functions. Next, we compared hamsters with the literature data of young-adult C57BL/6J mice, another important animal model. We sampled the same gastrointestinal regions and analyzed the differences in the microbiome between both rodents. Surprisingly, we found strong differences in their specific gastrointestinal bacterial communities. For instance, Lactobacillaceae were more abundant in hamsters' forestomach and ileum, while Muribaculaceae dominated in the mouse forestomach and ileum. Similarly, in mouse cecum and colon, Muribaculaceae were dominant, while in hamsters, Lachnospiraceae and Erysipelotrichaceae dominated the bacterial community. Molecular strains of Muribaculaceae in both rodent species displayed some species specificity. This comparison allows a better understanding of the suitability of the Syrian hamster as an animal model, especially regarding its comparability to other rodent models. Thereby, this work contributes to the characterization of the hamster model and allows better experimental planning.

Prebiotic potential of spent brewery grain - In vitro study

Spent brewery grain (SBG) is a by-product of the brewery industry. The study aimed to investigate the prebiotic potential of SBG. The chemical composition and fermentation capacity of SBG were checked. The gut microbiota response to SBG was assessed in two in vitro models (batch fermentation and dynamic system). Substances with prebiotic properties, including arabinoxylans (16.7 g/100 g) and polyphenols (49.1 mg/100 g), were identified in SBG. Suitable growth and fermentation by probiotic bacteria were observed. The modulatory effect of gut microbiota depends on the in vitro system used. In batch fermentation, there was no stimulation of Bifidobacterium or lactic acid bacteria (LAB), but short-chain fatty acid (SCFA) and branched short-chain fatty acids (BCFA) synthesis increased. In dynamic, SBG exhibited a moderate bifidogenic effect, promoting Akkermansia and LAB growth while reducing Bacteroides and Escherichia-Shigella. SCFA stabilisation and reduction of BCFA content were noted. Moderate prebiotic effects were observed.

Metatranscriptomic analysis indicates prebiotic effect of isomalto/malto-polysaccharides on human colonic microbiota in-vitro

Isomalto/malto-polysaccharides (IMMPs) are a novel type of soluble dietary fibres with a prebiotic potential promoting growth of beneficial microbes in the gut. However, the mode of action of IMMPs remains unknown. Previous studies on IMMPs showed an increase in total bacteria, especially lactobacilli, and higher production of short chain fatty acids (SCFA) when IMMPs were fed to rats or used during in vitro fermentation. Here we used metatranscriptomics to investigate how IMMPs with different amounts of α - (1 → 6) glycosidic linkages affected microbial function during incubation with human fecal inoculum. We showed that active microbial community dynamics during fermentation varied depending on the type of IMMP used and that the observed changes were reflected in the community gene expression profiles. Based on metatranscriptome analysis, members of Bacteroides, Lactobacillus and Bifidobacterium were the predominant degraders of IMMPs, and the increased gene expression in these bacteria correlated with high amounts of α - (1 → 6) glycosidic linkages. We also noted an increase in relative abundance of these bacteria and an activation of pathways involved in SCFA synthesis. Our findings could provide a baseline for more targeted approaches in designing prebiotics for specific bacteria and to achieve more controlled modulation of microbial activity towards desired health outcomes.

Genomic Modifications of Lactic Acid Bacteria and Their Applications in Dairy Fermentation

Lactic Acid Bacteria (LAB) have a long history of safe use in milk fermentation and are generally recognized as health-promoting microorganisms when present in fermented foods. LAB are also important components of the human intestinal microbiota and are widely used as probiotics. Considering their safe and health-beneficial properties, LAB are considered appropriate vehicles that can be genetically modified for food, industrial and pharmaceutical applications. Here, this review describes (1) the potential opportunities for application of genetically modified LAB strains in dairy fermentation and (2) the various genomic modification tools for LAB strains, such as random mutagenesis, adaptive laboratory evolution, conjugation, homologous recombination, recombineering, and CRISPR (clustered regularly interspaced short palindromic repeat)- Cas (CRISPR-associated protein) based genome engineering. Lastly, this review also discusses the potential future developments of these genomic modification technologies and their applications in dairy fermentations.

Assessment of Genomic and Metabolic Characteristics of Cholesterol-Reducing and GABA Producer Limosilactobacillus fermentum AGA52 Isolated from Lactic Acid Fermented Shalgam Based on "In Silico" and "In Vitro" Approaches

This study aimed to characterize the genomic and metabolic properties of a novel Lb. fermentum strain AGA52 which was isolated from a lactic acid fermented beverage called "shalgam." The genome size of AGA52 was 2,001,184 bp, which is predicted to carry 2024 genes, including 50 tRNAs, 3 rRNAs, 3 ncRNAs, 15 CRISPR repeats, 14 CRISPR spacers, and 1 CRISPR array. The genome has a GC content of 51.82% including 95 predicted pseudogenes, 56 complete or partial transposases, and 2 intact prophages. The similarity of the clusters of orthologous groups (COG) was analyzed by comparison with the other Lb. fermentum strains. The detected resistome on the genome of AGA52 was found to be intrinsic originated. Besides, it has been determined that AGA52 has an obligate heterofermentative carbohydrate metabolism due to the absence of the 1-phosphofructokinase (pfK) enzyme. Furthermore, the strain is found to have a better antioxidant capacity and to be tolerant to gastrointestinal simulated conditions. It was also observed that the AGA52 has antimicrobial activity against Yersinia enterocolitica ATCC9610, Bacillus cereus ATCC33019, Salmonella enterica sv. Typhimurium, Escherichia coli O157:h7 ATCC43897, Listeria monocytogenes ATCC7644, Klebsiella pneumoniae ATCC13883, and Proteus vulgaris ATCC8427. Additionally, AGA52 exhibited 42.74 ± 4.82% adherence to HT29 cells. Cholesterol assimilation (33.9 ± 0.005%) and GABA production capacities were also confirmed by "in silico" and "in vitro." Overall, the investigation of genomic and metabolic features of the AGA52 revealed that is a potential psychobiotic and probiotic dietary supplement candidate and can bring functional benefits to the host.

The effect of lactic acid bacteria fermentation on physicochemical properties of starch from fermented proso millet flour

A waxy and a non-waxy proso millet flour were each fermented by Lactobacillus amylovorus, Lactobacillus fermentum, and Lactobacillus plantarum. The samples were fermented for one to five days, and starch was isolated from the fermented flours. The pH of fermented proso millet flour ranged from 3.27 to 3.6. The starch morphology of fermented samples differed from that of raw starches, with surface indentations and small pores leading to granule channels observed on the granule. The gelatinization temperatures were significantly decreased, whereas the enthalpies were not affected by fermentation. Peak and final viscosities were decreased after fermentation. The hardness of Lb. fermentum and Lb. plantarum fermented waxy starch gels was decreased, but the non-waxy samples fermented by Lb. amylovorus had significantly increased hardness. The adhesiveness of the starch gels from fermented samples was significantly increased. Lactic acid fermentation had significant effects on the morphology and physicochemical properties of proso millet starch.

The effect of seed germination and Bacillus spp. on the ripening of plant cheese analogs

Consumer demand for plant cheeses is increasing, but challenges of improving both flavor and quality remain. This study investigated the microbiological and physicochemical impact of seed germination and fermentation with Bacillus velezensis and Bacillus amyloliquefaciens on the ripening of plant cheese analogs. Chlorine treatment or addition of Lactiplantibacillus plantarum and Lactococcus lactis controlled microbial growth during seed germination. Lp. plantarum and Lc. lactis also served as starter cultures for the acidification of soy and lupine milk and were subsequently present in the unripened plant cheese as dominant microbes. Acidification also inhibited the growth and metabolic activity of bacilli but Bacillus spores remained viable throughout ripening. During plant cheese ripening, Lc. lactis was inactivated before Lp. plantarum and the presence of bacilli during seed germination delayed Lc. lactis inactivation. Metagenomic sequencing of full-length 16S rRNA gene amplicons confirmed that the relative abundance of the inoculated strains in each ripened cheese sample exceeded 99%. Oligosaccharides including raffinose, stachyose, and verbascose were rapidly depleted in the initial stage of ripening. Both germination and the presence of bacilli during seed germination had impact on polysaccharide hydrolysis during ripening. Bacilli but not seed germination enhanced proteolysis of plant cheese during ripening. In conclusion, the use of germination with lactic acid bacteria in combination with Bacillus spp. exhibited the potential to improve the quality of ripened plant cheeses with a positive effect on the reduction of hygienic risks.

IMPORTANCE

The development of novel plant-based fermented food products for which no traditional templates exist requires the development of starter cultures. Although the principles of microbial flavor formation in plant-based analogs partially overlap with dairy fermentations, the composition of the raw materials and thus likely the selective pressure on the activity of starter cultures differs. Experiments that are described in this study explored the use of seed germination, the use of lactic acid bacteria, and the use of bacilli to reduce hygienic risks, to acidify plant milk, and to generate taste-active compounds through proteolysis and fermentative conversion of carbohydrates. The characterization of fermentation microbiota by culture-dependent and culture-independent methods also confirmed that the starter cultures used were able to control microbial communities throughout 90 d of ripening. Taken together, the results provide novel tools for the development of plant-based analogs of fermented dairy products.

Deciphering the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during soy juice fermentation using phenotypic and transcriptional analysis

In the context of sustainable diet, the development of soy-based yogurt fermented with lactic acid bacteria is an attractive alternative to dairy yogurts. To decipher the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during soy juice (SJ) fermentation, the whole genome of the strain CIRM-BIA865 (Ld865) was sequenced and annotated. Then Ld865 was used to ferment SJ. Samples were analyzed throughout fermentation for their cell number, carbohydrate, organic acid, free amino acid, and volatile compound contents. Despite acidification, the number of Ld865 cells did not rise, and microscopic observations revealed the elongation of cells from 3.6 µm (inoculation) to 36.9 µm (end of fermentation). This elongation was observed in SJ but not in laboratory-rich medium MRS. Using transcriptomic analysis, we showed that the biosynthesis genes of peptidoglycan and membrane lipids were stably expressed, in line with the cell elongation observed, whereas no genes implicated in cell division were upregulated. Among the main sugars available in SJ (sucrose, raffinose, and stachyose), Ld865 only used sucrose. The transcriptomic analysis showed that Ld865 implemented the two transport systems that it contains to import sucrose: a PTS system and an ABC transporter. To fulfill its nitrogen needs, Ld865 probably first consumed the free amino acids of the SJ and then implemented different oligopeptide transporters and proteolytic/peptidase enzymes. In conclusion, this study showed that Ld865 enables fast acidification of SJ, despite the absence of cell division, leads to a product rich in free amino acids, and also leads to the production of aromatic compounds of interest.

IMPORTANCE

To reduce the environmental and health concerns related to food, an alternative diet is recommended, containing 50% of plant-based proteins. Soy juice, which is protein rich, is a relevant alternative to animal milk, for the production of yogurt-like products. However, soy "beany" and "green" off-flavors limit the consumption of such products. The lactic acid bacteria (LAB) used for fermentation can help to improve the organoleptic properties of soy products. But metabolic data concerning LAB adapted to soy juice are lacking. The aim of this study was, thus, to decipher the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during fermentation of a soy juice, based on a multidisciplinary approach. This result will contribute to give tracks for a relevant selection of starter. Indeed, the improvement of the organoleptic properties of these types of products could help to promote plant-based proteins in our diet.

Conversion of Phytochemicals by Lactobacilli: (Phospho)-β-glucosidases Are Specific for Glucosylated Phytochemicals Rather than Disaccharides

Food-fermenting lactobacilli convert glycosylated phytochemicals to glycosyl hydrolases and thereby alter their biological activity. This study aimed to investigate the microbial transformation of β-glucosides of phytochemicals in comparison with utilization of cellobiose. Four homofermentative and four heterofermentative lactobacilli were selected to represent the metabolic diversity of Lactobacillaceae. The genomes of Lactobacillus crispatus, Companilactobacillus paralimentarius, Lacticaseibacillus paracasei, and Lactiplantibacillus plantarum encoded for 8 to 22 enzymes, predominantly phospho-β-glucosidases, with predicted activity on β-glucosides. Levilactobacillus hammesii and Furfurilactobacillus milii encoded for 3 β-glucosidases, Furfurilactobacillus rossiae for one, and Fructilactobacillus sanfranciscensis for none. The hydrolysis of amygdalin, esculin, salicin, glucosides of quercetin and genistein, and ginsenosides demonstrated that several strains hydrolyzed β-glucosides of phytochemicals but not cellobiose. Taken together, several of the carbohydrate-active enzymes of food-fermenting lactobacilli are specific for glycosides of phytochemicals.

Enzymatic production of cello-oligosaccharides with potential human prebiotic activity and release of polyphenols from grape marc

Grape marc, the main winemaking byproduct, is an excellent source of bioactive polyphenols, such as anthocyanins, resveratrol and quercetin. An enzyme-catalysed treatment of marc was developed using endo-1,4-β-d-glucanase to release polyphenol O-glucosides and simultaneously generate the optimal concentration of water-soluble cello-oligosaccharides (COS), including cellopentaose, cellotriose, and cellobiose from the marc matrix. The prebiotic properties of marc hydrolysate rich in COS was assessed using human probiotic monocultures of Lactobacillus spp. and Bifidobacterium spp. strains, and invitro human faecal fermentation. The COS-rich hydrolysate showed excellent prebiotic effect in both studies, successfully supporting the growth of beneficial probiotic strains, and was highly fermentable by faecal microbiota producing gas and short chain fatty acids. Acetate and propionate production were the highest when faecal bacteria fermented COS-rich solution compared with standard substrates. For the first time, COS was shown to be fermented by faecal microbiota, demonstrating the potential benefits of valorised grape marc.

Efficacy of Lactiplantibacillus plantarum PBS067, Bifidobacterium animalis subsp. lactis BL050, and Lacticaseibacillus rhamnosus LRH020 in the Amelioration of Vaginal Microbiota in Post-Menopausal Women: A Prospective Observational Clinical Trial

The menopausal transition marks a significant physiological shift in women. Menopause-related symptoms can significantly affect a woman's quality of life and probiotics have emerged as a promising avenue. This study aims to investigate the benefits of probiotics in improving vaginal well-being and microbiota composition in post-menopausal women. A prospective observational clinical trial was carried out enrolling 50 post-menopausal healthy women, aged between 45 and 65 years old, taking a supplement containing Lactiplantibacillus plantarum PBS067, Bifidobacterium animalis subsp. lactis BL050, and Lacticaseibacillus rhamnosus LRH020 (3B CFU/day) for 28 days. Vaginal swabs were collected to evaluate microbiota fluctuation and the inflammatory pattern was recorded. A Vaginal Health Index was provided to evaluate vaginal well-being throughout the trial. Clinical outcomes revealed a decrease in menopausal symptoms. Significant improvements were observed across various parameters: a 50% enhancement in the VHI score (p < 0.0001), alongside substantial reductions in inflammatory cytokine levels. An 87.8% decrease in IL-6, 57.6% in IL-1β, and 40.8% in TNF-α was observed (p < 0.05). Moreover, the probiotic intervention facilitated the restoration of vaginal microbiota, evidenced by an increase in lactobacilli abundance. In conclusion, the combination of these specific probiotic strains, previously clinically tested in childbearing-age women, showed to be effective also for post-menopausal women.

High-sugar diet leads to loss of beneficial probiotics in housefly larvae guts

The housefly (Musca domestica) is a common insect species with only a few recurrent bacterial taxa in its gut microbiota, because the numerous microbial acquisition routes in its septic habitats can favor transient microbes. Here, we investigated the role of the diet on the microbiota and the developmental success of a housefly strain reared on three substrates. We used a control wheat bran-based substrate, and added clotted cream and sucrose to make a high-fat, and a high-sugar substrate, respectively. The conducted survey revealed that, in contrast to the high-fat diet, the high-sugar diet caused lower developmental success and less diverse microbiota, in which several lactobacilli were replaced with Weissella bacterial phylotypes. Cultures with sucrose as the sole carbon source confirmed that a Weissella confusa strain, isolated from larvae, could utilize sucrose more efficiently than other tested lactic acid bacteria; a result also supported by gene function prediction analysis. Enhancing the rearing substrate with Limosilactobacillus fermentum and Lactiplantibacillus plantarum strains, which were isolated from control larvae, could not only revert the negative effect of the high-sucrose diet on development, but also increase the gut bacterial diversity. In our study, we show that the microbiota shifts in response to the high-sucrose diet did not benefit the host, that showed lower developmental success. In contrast, high-sucrose favored specific components of the microbiota, that continued to be enriched even after multiple generations, outcompeting beneficial bacteria. Also, microbiome manipulation showed the potential of probiotics to rescue host performance and restore the microbiome.

Impact of an oligosaccharide-based polymer on the metabolic profiles and microbial ecology of weanling pigs experimentally infected with a pathogenic E. coli

BACKGROUND

Our previous study has reported that supplementation of oligosaccharide-based polymer enhances gut health and disease resistance of pigs infected with enterotoxigenic E. coli (ETEC) F18 in a manner similar to carbadox. The objective of this study was to investigate the impacts of oligosaccharide-based polymer or antibiotic on the host metabolic profiles and colon microbiota of weaned pigs experimentally infected with ETEC F18.

RESULTS

Multivariate analysis highlighted the differences in the metabolic profiles of serum and colon digesta which were predominantly found between pigs supplemented with oligosaccharide-based polymer and antibiotic. The relative abundance of metabolic markers of immune responses and nutrient metabolisms, such as amino acids and carbohydrates, were significantly differentiated between the oligosaccharide-based polymer and antibiotic groups (q < 0.2 and fold change > 2.0). In addition, pigs in antibiotic had a reduced (P < 0.05) relative abundance of Lachnospiraceae and Lactobacillaceae, whereas had greater (P < 0.05) Clostridiaceae and Streptococcaceae in the colon digesta on d 11 post-inoculation (PI) compared with d 5 PI.

CONCLUSIONS

The impact of oligosaccharide-based polymer on the metabolic and microbial profiles of pigs is not fully understood, and further exploration is needed. However, current research suggest that various mechanisms are involved in the enhanced disease resistance and performance in ETEC-challenged pigs by supplementing this polymer.

Selective utilization of gluco-oligosaccharides by lactobacilli: A mechanism study revealing the impact of glycosidic linkages and degree of polymerization on their utilization

Gluco-oligosaccharides (GlcOS) are potential prebiotics that positively modulate beneficial gut commensals like lactobacilli. For the rational design of GlcOS as prebiotics or combined with lactobacilli as synbiotics, it is important to establish the structure requirements of GlcOS and specificity toward lactobacilli. Herein, the utilization of 10 GlcOS with varied degrees of polymerization (DP) and glycosidic linkages by 7 lactobacilli strains (Levilactobacillus brevis ATCC 8287, Limosilactobacillus reuteri ATCC PTA 6475, Lacticaseibacillus rhamnosus ATCC 53103, Lentilactobacillus buchneri ATCC 4005, Limosilactobacillus fermentum FUA 3589, Lactiplantibacillus plantarum WCFS1, and Lactobacillus gasseri ATCC 33323) was studied. L. brevis ATCC 8287 was the only strain that grew on α/β-(1→4/6) linked disaccharides, whereas other strains showed diverse patterns, dependent on the availability of genes encoding sugar transporters and catabolic enzymes. The effect of DP on GlcOS utilization was strain dependent. β-(1→4) Linked cello-oligosaccharides (COS) supported the growth of L. brevis ATCC 8287 and L. plantarum WCFS1, and shorter COS (DP 2-3) were preferentially utilized over longer COS (DP 4-7) (consumption ≥90% vs. 40%-60%). α-(1→4) Linked maltotriose and maltodextrin (DP 2-11) were effectively utilized by L. brevis ATCC 8287, L. reuteri ATCC 6475, and L. plantarum WCFS1, but not L. fermentum FUA 3589. Growth of L. brevis ATCC 8287 on branched isomalto-oligosaccharides (DP 2-6) suggested preferential consumption of DP 2-3, but no preference between α-(1→6) and α-(1→4) linkages. The knowledge of the structure-specific GlcOS utilization by different lactobacilli from this study helps the structural rationale of GlcOS for prebiotic development.

The rise of the sourdough: Genome-scale metabolic modeling-based approach to design sourdough starter communities with tailored-made properties

Sourdough starters harbor microbial consortia that benefit the final product's aroma and volume. The complex nature of these spontaneously developed communities raises challenges in predicting the fermentation phenotypes. Herein, we demonstrated for the first time in this field the potential of genome-scale metabolic modeling (GEMs) in the study of sourdough microbial communities. Broad in-silico modeling of microbial growth was applied on communities composed of yeast (Saccharomyces cerevisiae) and different Lactic Acid Bacteria (LAB) species, which mainly predominate in sourdough starters. Simulations of model-represented communities associated specific bacterial compositions with sourdough phenotypes. Based on ranking the phenotypic performances of different combinations, Pediococcus spp. - Lb. sakei group members were predicted to have an optimal effect considering the increase in S. cerevisiae growth abilities and overall CO2 secretion rates. Flux Balance Analysis (FBA) revealed mutual relationships between the Pediococcus spp. - Lb. sakei group members and S. cerevisiae through bidirectional nutrient dependencies, and further underlined that these bacteria compete with the yeast over nutrients to a lesser extent than the rest LAB species. Volatile compounds (VOCs) production was further modeled, identifying species-specific and community-related VOCs production profiles. The in-silico models' predictions were validated by experimentally building synthetic sourdough communities and assessing the fermentation phenotypes. The Pediococcus spp. - Lb. sakei group was indeed associated with increased yeast cell counts and fermentation rates, demonstrating a 25 % increase in the average leavening rates during the first 10 fermentation hours compared to communities with a lower representation of these group members. Overall, these results provide a possible novel strategy towards the de-novo design of sourdough starter communities with tailored-made characterizations, including a shortened leavening period.

Microbiology of fermented soy foods in Asia: Can we learn lessons for production of plant cheese analogues?

The food industry is facing the challenge of creating innovative, nutritious, and flavored plant-based products, due to consumer's increasing demand for the health and environmental sustainability. Fermentation as a unique and effective tool plays an important role in the innovation of food products. Traditional fermented soy foods are popular in many Asian and African countries as nutritious, digestible and flavorful daily staples or condiments. They are produced by specific microorganisms with the unique fermentation process in which microorganisms convert the ingredients of whole soybean or soybean curd to flavorful and functional molecules. This review provides an overview on traditional fermented food produced from soy, including douchi, natto, tempeh, and sufu as well as stinky tofu, including the background of these products, the manufacturing process, and the microbial diversity involved in fermentation procedures as well as flavor volatiles that were identified in the final products. The contribution of microbes to the quality of these five fermented soy foods is discussed, with the comparison to the role of cheese ripening microorganisms in cheese flavor formation. This communication aims to summarize the microbiology of fermented soy foods in Asia, evoking innovative ideas for the development of new plant-based fermented foods especially plant-based cheese analogues.

Anti-Helicobacter pylori activity and gastroprotective effects of human stomach-derived Lactobacillus paragasseri strain LPG-9

The eradication of Helicobacter pylori is an urgent global issue. However, the traditional regimens have several limitations. Thus, we propose the idea of treating bacterial gastric disease with the objective of eliminating gastric pathogenic bacteria and enhancing gastroprotective effects using gastric probiotics. In this study, a total of 12 Lactobacillus strains were isolated from the gastric mucosa of healthy donors. After evaluation using a weight scoring system, Lactobacillus paragasseri strain LPG-9 was identified as the most promising probiotic for gastric disease, with the highest acid-resistance and the best adhesion characteristics. Gastric colonisation, H. pylori inhibition, anti-inflammatory, and gastric homeostasis effects of LPG-9 were confirmed in C57BL/6 mice. Finally, a safety evaluation and whole-genome sequencing were performed. Based on the results of this study, LPG-9 originates from the gastric microbiota and is a promising probiotic for gastric disease, particularly H. pylori-induced gastritis, providing a solution to this global issue.

Development of an improved colonization system for human-derived Bifidobacterium longum subsp. longum in conventional mice through the feeding of raffinose or 1-kestose

How bifidobacteria colonize and survive in the intestine is not fully understood. The administration of bifidobacteria to conventional mice can be used to evaluate their ability to colonize the intestine in the presence of endogenous gut microbiota. However, human-derived bifidobacteria do not readily colonize the intestines of conventional mice, and although colonization by Bifidobacterium breve UCC2003 has been achieved, the viability of such populations requires improvement. Therefore, we aimed to establish a colonization system with human-derived bifidobacteria of high viability in conventional mice using Bifidobacterium longum subsp. longum 105-A. Lactose, raffinose, and 1-kestose were identified as the preferred carbohydrate sources for the growth of this strain in culture. The administration of B. longum 105-A to conventional BALB/c mice fed these carbohydrates showed that diets containing 6% (w/w) raffinose or 1-kestose facilitated colonization with >108 colony-forming units/g feces for 2 weeks. The population of this strain was more stable in the raffinose-fed group than in the 1-kestose-fed group. The ingestion of these prebiotics had a greater impact on the composition of the microbiota than the administration of B. longum 105-A. The ingestion of these prebiotics also increased the fecal concentrations of organic acids, which was indicative of greater intestinal fermentation. Collectively, we established a colonization system for B. longum 105-A with high viability in conventional mice by feeding the mice raffinose or 1-kestose. This system should be useful for elucidation of the mechanisms of colonization and survival of bifidobacteria in the intestines in the presence of the endogenous gut microbiota.

Use of reconstituted kefir consortia to determine the impact of microbial composition on kefir metabolite profiles

Kefir is fermented traditionally with kefir grains, but commercial kefir production often relies on fermentation with planktonic cultures. Kefir has been associated with many health benefits, however, the utilization of kefir grains to facilitate large industrial production of kefir is challenging and makes to difficult to ensure consistent product quality and consistency. Notably, the microbial composition of kefir fermentations has been shown to impact kefir associated health benefits. This study aimed to compare volatile compounds, organic acids, and sugar composition of kefir produced through a traditional grain fermentation and through a reconstituted kefir consortium fermentation. Additionally, the impact of two key microbial communities on metabolite production in kefir was assessed using two modified versions of the consortium, with either yeasts or lactobacilli removed. We hypothesized that the complete kefir consortium would closely resemble traditional kefir, while the consortia without yeasts or lactobacilli would differ significantly from both traditional kefir and the complete consortium fermentation. Kefir fermentations were examined after 12 and 18 h using two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) to identify volatile compounds and high performance liquid chromatography (HPLC) to identify organic acid and sugar composition. The traditional kefir differed significantly from the kefir consortium fermentation with the traditional kefir having 15-20 log2(fold change) higher levels of esters and the consortium fermented kefir having between 1 and 3 log2(fold change) higher organic acids including lactate and acetate. The use of a version of kefir consortium that lacked lactobacilli resulted in between 2 and 20 log2(fold change) lower levels of organic acids, ethanol, and butanoic acid ethyl ester, while the absence of yeast from the consortium resulted in minimal change. In summary, the kefir consortium fermentation is significantly different from traditional grain fermented kefir with respect to the profile of metabolites present, and seems to be driven by lactobacilli, as evidenced by the significant decrease in multiple metabolites when the lactobacilli were removed from the fermentation and minimal differences observed upon the removal of yeast.

Leuconostoc performance in soy-based fermentations - Survival, acidification, sugar metabolism, and flavor comparisons

Leuconostoc spp. is often regarded as the flavor producer, responsible for the production of acetoin and diacetyl in dairy cheese. In this study, we investigate seven plant-derived Leuconostoc strains, covering four species, in their potential as a lyophilized starter culture for flavor production in fermented soy-based cheese alternatives. We show that the process of lyophilization of Leuconostoc can be feasible using a soy-based lyoprotectant, with survivability up to 63% during long term storage. Furthermore, the storage in this media improves the subsequent growth in a soy-based substrate in a strain specific manner. The utilization of individual raffinose family oligosaccharides was strain dependent, with Leuconostoc pseudomesenteroides NFICC99 being the best consumer. Furthermore, we show that all investigated strains were able to produce a range of volatile flavor compounds found in dairy cheese products, as well as remove certain dairy off-flavors from the soy-based substrate like hexanal and 2-pentylfuran. Also here, NFICC99 was strain producing most cheese-related volatile flavor compounds, followed by Leuconostoc mesenteroides NFICC319. These findings provide initial insights into the development of Leuconostoc as a potential starter culture for plant-based dairy alternatives, as well as a promising approach for generation of stable, lyophilized cultures.

Bifidobacteria define gut microbiome profiles of golden lion tamarin (Leontopithecus rosalia) and marmoset (Callithrix sp.) metagenomic shotgun pools

Gut microbiome disruptions may lead to adverse effects on wildlife fitness and viability, thus maintaining host microbiota biodiversity needs to become an integral part of wildlife conservation. The highly-endangered callitrichid golden lion tamarin (GLT-Leontopithecus rosalia) is a rare conservation success, but allochthonous callitrichid marmosets (Callithrix) serve as principle ecological GLT threats. However, incorporation of microbiome approaches to GLT conservation is impeded by limited gut microbiome studies of Brazilian primates. Here, we carried out analysis of gut metagenomic pools from 114 individuals of wild and captive GLTs and marmosets. More specifically, we analyzed the bacterial component of ultra filtered samples originally collected as part of a virome profiling study. The major findings of this study are consistent with previous studies in showing that Bifidobacterium, a bacterial species important for the metabolism of tree gums consumed by callitrichids, is an important component of the callitrichid gut microbiome - although GTLs and marmosets were enriched for different species of Bifidobacterium. Additionally, the composition of GLT and marmoset gut microbiota is sensitive to host environmental factors. Overall, our data expand baseline gut microbiome data for callitrichids to allow for the development of new tools to improve their management and conservation.

Development of a Novel D-Lactic Acid Production Platform Based on Lactobacillus saerimneri TBRC 5746

D-Lactic acid is a chiral, three-carbon organic acid, that bolsters the thermostability of polylactic acid. In this study, we developed a microbial production platform for the high-titer production of D-lactic acid. We screened 600 isolates of lactic acid bacteria (LAB) and identified twelve strains that exclusively produced D-lactic acid in high titers. Of these strains, Lactobacillus saerimneri TBRC 5746 was selected for further development because of its homofermentative metabolism. We investigated the effects of high temperature and the use of cheap, renewable carbon sources on lactic acid production and observed a titer of 99.4 g/L and a yield of 0.90 g/g glucose (90% of the theoretical yield). However, we also observed L-lactic acid production, which reduced the product's optical purity. We then used CRISPR/dCas9-assisted transcriptional repression to repress the two Lldh genes in the genome of L. saerimneri TBRC 5746, resulting in a 38% increase in D-lactic acid production and an improvement in optical purity. This is the first demonstration of CRISPR/dCas9-assisted transcriptional repression in this microbial host and represents progress toward efficient microbial production of D-lactic acid.

Treatment of fresh leachate by anaerobic membrane bioreactor: On-site investigation, long-term performance and response of microbial community

This study proposed fresh leachate treatment with anaerobic membrane bioreactor (AnMBR) based on the on-site investigation of the characteristics of fresh leachate. Temperature-related profiles of fresh leachate properties, like chemical oxygen demand (COD), were observed. In addition, AnMBR achieved a high COD removal of 98% with a maximum organic loading rate (OLR) of 19.27 kg-COD/m3/d at the shortest hydraulic retention time (HRT) of 1.5 d. The microbial analysis implied that the abundant protein and carbohydrate degraders (e.g., Thermovirga and Petrimonas) as well as syntrophic bacteria, such as Syntrophomonas, ensured the effective adaptation of AnMBR to the reduced HRTs. However, an excessive OLR at 36.55 kg-COD/m3/d at HRT of 1 d resulted in a sharp decrease in key microbes, such as archaea (from 37% to 15%), finally leading to the deterioration of AnMBR. This study provides scientific guidance for treating fresh leachate by AnMBR and its full-scale application for high-strength wastewater.

Does sourdough bread provide clinically relevant health benefits?

During the last decade, scientific interest in and consumer attention to sourdough fermentation in bread making has increased. On the one hand, this technology may favorably impact product quality, including flavor and shelf-life of bakery products; on the other hand, some cereal components, especially in wheat and rye, which are known to cause adverse reactions in a small subset of the population, can be partially modified or degraded. The latter potentially reduces their harmful effects, but depends strongly on the composition of sourdough microbiota, processing conditions and the resulting acidification. Tolerability, nutritional composition, potential health effects and consumer acceptance of sourdough bread are often suggested to be superior compared to yeast-leavened bread. However, the advantages of sourdough fermentation claimed in many publications rely mostly on data from chemical and in vitro analyzes, which raises questions about the actual impact on human nutrition. This review focuses on grain components, which may cause adverse effects in humans and the effect of sourdough microbiota on their structure, quantity and biological properties. Furthermore, presumed benefits of secondary metabolites and reduction of contaminants are discussed. The benefits claimed deriving from in vitro and in vivo experiments will be evaluated across a broader spectrum in terms of clinically relevant effects on human health. Accordingly, this critical review aims to contribute to a better understanding of the extent to which sourdough bread may result in measurable health benefits in humans.

Multiomics characterisation of the zoo-housed gorilla gut microbiome reveals bacterial community compositions shifts, fungal cellulose-degrading, and archaeal methanogenic activity

We carried out a comparative analysis between the bacterial microbiota composition of zoo-housed western lowland gorillas and their wild counterparts through 16S rRNA gene amplicon sequencing. In addition, we characterised the carbohydrate-active and methanogenic potential of the zoo-housed gorilla (ZHG) microbiome through shotgun metagenomics and RNA sequencing. The ZHG microbiota showed increased alpha diversity in terms of bacterial species richness and a distinct composition from that of the wild gorilla microbiota, including a loss of abundant fibre-degrading and hydrogenic Chloroflexi. Metagenomic analysis of the CAZyome indicated predominant oligosaccharide-degrading activity, while RNA sequencing revealed diverse cellulase and hemi-cellulase activities in the ZHG gut, contributing to a total of 268 identified carbohydrate-active enzymes. Metatranscriptome analysis revealed a substantial contribution of 38% of the transcripts from anaerobic fungi and archaea to the gorilla microbiome. This activity originates from cellulose-degrading and hydrogenic fungal species belonging to the class Neocallimastigomycetes, as well as from methylotrophic and hydrogenotrophic methanogenic archaea belonging to the classes Thermoplasmata and Methanobacteria, respectively. Our study shows the added value of RNA sequencing in a multiomics approach and highlights the contribution of eukaryotic and archaeal activities to the gut microbiome of gorillas.

Glycogen availability and pH variation in a medium simulating vaginal fluid influence the growth of vaginal Lactobacillus species and Gardnerella vaginalis

BACKGROUND

Glycogen metabolism by Lactobacillus spp. that dominate the healthy vaginal microbiome contributes to a low vaginal pH (3.5-4.5). During bacterial vaginosis (BV), strict and facultative anaerobes including Gardnerella vaginalis become predominant, leading to an increase in the vaginal pH (> 4.5). BV enhances the risk of obstetrical complications, acquisition of sexually transmitted infections, and cervical cancer. Factors critical for the maintenance of the healthy vaginal microbiome or the transition to the BV microbiome are not well defined. Vaginal pH may affect glycogen metabolism by the vaginal microflora, thus influencing the shift in the vaginal microbiome.

RESULTS

The medium simulating vaginal fluid (MSVF) supported growth of L. jensenii 62G, L. gasseri 63 AM, and L. crispatus JV-V01, and G. vaginalis JCP8151A at specific initial pH conditions for 30 d. L. jensenii at all three starting pH levels (pH 4.0, 4.5, and 5.0), G. vaginalis at pH 4.5 and 5.0, and L. gasseri at pH 5.0 exhibited the long-term stationary phase when grown in MSVF. L. gasseri at pH 4.5 and L. crispatus at pH 5.0 displayed an extended lag phase over 30 d suggesting inefficient glycogen metabolism. Glycogen was essential for the growth of L. jensenii, L. crispatus, and G. vaginalis; only L. gasseri was able to survive in MSVF without glycogen, and only at pH 5.0, where it used glucose. All four species were able to survive for 15 d in MSVF with half the glycogen content but only at specific starting pH levels - pH 4.5 and 5.0 for L. jensenii, L. gasseri, and G. vaginalis and pH 5.0 for L. crispatus.

CONCLUSIONS

These results suggest that variations in the vaginal pH critically influence the colonization of the vaginal tract by lactobacilli and G. vaginalis JCP8151A by affecting their ability to metabolize glycogen. Further, we found that L. jensenii 62G is capable of glycogen metabolism over a broader pH range (4.0-5.0) while L. crispatus JV-V01 glycogen utilization is pH sensitive (only functional at pH 5.0). Finally, our results showed that G. vaginalis JCP8151A can colonize the vaginal tract for an extended period as long as the pH remains at 4.5 or above.

Impact of Early Weaning on Development of the Swine Gut Microbiome

Considering that pigs are naturally weaned between 12 and 18 weeks of age, the common practice in the modern swine industry of weaning as early as between two and four weeks of age increases challenges during this transition period. Indeed, young pigs with an immature gut are suddenly separated from the sow, switched from milk to a diet consisting of only solid ingredients, and subjected to a new social hierarchy from mixing multiple litters. From the perspective of host gut development, weaning under these conditions causes a regression in histological structure as well as in digestive and barrier functions. While the gut is the main center of immunity in mature animals, the underdeveloped gut of early weaned pigs has yet to contribute to this function until seven weeks of age. The gut microbiota or microbiome, an essential contributor to the health and nutrition of their animal host, undergoes dramatic alterations during this transition, and this descriptive review aims to present a microbial ecology-based perspective on these events. Indeed, as gut microbial communities are dependent on cross-feeding relationships, the change in substrate availability triggers a cascade of succession events until a stable composition is reached. During this process, the gut microbiota is unstable and prone to dysbiosis, which can devolve into a diseased state. One potential strategy to accelerate maturation of the gut microbiome would be to identify microbial species that are critical to mature swine gut microbiomes, and develop strategies to facilitate their establishment in early post-weaning microbial communities.

Bioaugmentation of the green alga to enhance biogas production in an anaerobic hollow-fiber membrane bioreactor

Anaerobic membrane reactors (AnMBRs) offer an alternative wastewater treatment system, presenting both reclamation of value through biogas production, and efficient treatment of recalcitrant contaminants such as antibiotics from wastewater. The effects of bioaugmentation with the green alga Haematococcus pluvialis on anaerobic treatment of pharmaceutical wastewaters, alleviating membrane biofouling, biogas production and impact on the indigenous microbial communities were evaluated using AnMBRs. The outputs of the bioreactor experiments revealed that bioaugmentation strategies with the green alga increased removal of chemical oxygen demand by 12% and delayed membrane fouling by 25% and increased biogas production by 40%. Furthermore, bioaugmentation with the green alga led to a significant change in relative abundance of archaea and the main methanogenesis pathway shifted from Methanothermobacter to Methanosaeta, accompanied by their respective syntrophic bacteria.

Development and evaluation of a fish feed mixture containing the probiotic Lactiplantibacillus plantarum prepared using an innovative pellet coating method

Introduction

Due to the intensification of fish farming and the associated spread of antimicrobial resistance among animals and humans, it is necessary to discover new alternatives in the therapy and prophylaxis of diseases. Probiotics appear to be promising candidates because of their ability to stimulate immune responses and suppress the growth of pathogens.

Methods

The aim of this study was to prepare fish feed mixtures with various compositions and, based on their physical characteristics (sphericity, flow rate, density, hardness, friability, and loss on drying), choose the most suitable one for coating with the selected probiotic strain Lactobacillus plantarum R2 Biocenol™ CCM 8674 (new nom. Lactiplantibacillus plantarum). The probiotic strain was examined through sequence analysis for the presence of plantaricin- related genes. An invented coating technology based on a dry coating with colloidal silica followed by starch hydrogel containing L. plantarum was applied to pellets and tested for the viability of probiotics during an 11-month period at different temperatures (4°C and 22°C). The release kinetics of probiotics in artificial gastric juice and in water (pH = 2 and pH = 7) were also determined. Chemical and nutritional analyses were conducted for comparison of the quality of the control and coated pellets.

Results and discussion

The results showed a gradual and sufficient release of probiotics for a 24-hour period, from 10⁴ CFU at 10 mi up to 10⁶ at the end of measurement in both environments. The number of living probiotic bacteria was stable during the whole storage period at 4°C (10⁸), and no significant decrease in living probiotic bacteria was observed. Sanger sequencing revealed the presence of plantaricin A and plantaricin EF. Chemical analysis revealed an increase in multiple nutrients compared to the uncoated cores. These findings disclose that the invented coating method with a selected probiotic strain improved nutrient composition and did not worsen any of the physical characteristics of pellets. Applied probiotics are also gradually released into the environment and have a high survival rate when stored at 4°C for a long period of time. The outputs of this study confirm the potential of prepared and tested probiotic fish mixtures for future use in in vivo experiments and in fish farms for the prevention of infectious diseases.

Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization

The liquid residue resulting from various agroindustrial processes is both rich in organic material and an attractive source to produce a variety of chemicals. Using microbial communities to produce chemicals from these liquid residues is an active area of research, but it is unclear how to deploy microbial communities to produce specific products from the different agroindustrial residues. To address this, we fed anaerobic bioreactors one of several agroindustrial residues (carbohydrate-rich lignocellulosic fermentation conversion residue, xylose, dairy manure hydrolysate, ultra-filtered milk permeate, and thin stillage from a starch bioethanol plant) and inoculated them with a microbial community from an acid-phase digester operated at the wastewater treatment plant in Madison, WI, United States. The bioreactors were monitored over a period of months and sampled to assess microbial community composition and extracellular fermentation products. We obtained metagenome assembled genomes (MAGs) from the microbial communities in each bioreactor and performed comparative genomic analyses to identify common microorganisms, as well as any community members that were unique to each reactor. Collectively, we obtained a dataset of 217 non-redundant MAGs from these bioreactors. This metagenome assembled genome dataset was used to evaluate whether a specific microbial ecology model in which medium chain fatty acids (MCFAs) are simultaneously produced from intermediate products (e.g., lactic acid) and carbohydrates could be applicable to all fermentation systems, regardless of the feedstock. MAGs were classified using a multiclass classification machine learning algorithm into three groups, organisms fermenting the carbohydrates to intermediate products, organisms utilizing the intermediate products to produce MCFAs, and organisms producing MCFAs directly from carbohydrates. This analysis revealed common biological functions among the microbial communities in different bioreactors, and although different microorganisms were enriched depending on the agroindustrial residue tested, the results supported the conclusion that the microbial ecology model tested was appropriate to explain the MCFA production potential from all agricultural residues.

Alteration of Community Metabolism by Prebiotics and Medicinal Herbs

Several studies have examined the impact of prebiotics on gut microbiota and associated changes in host physiology. Here, we used the in vitro cultivation of human fecal samples stimulated with a series of chemically related prebiotics and medicinal herbs commonly used in Ayurvedic medicine, followed by 16S rRNA sequencing. We applied a genome-wide metabolic reconstruction of enumerated communities to compare and contrast the structural and functional impact of prebiotics and medicinal herbs. In doings so, we examined the relationships between discrete variations in sugar composition and sugar linkages associated with each prebiotic to drive changes in microbiota composition. The restructuring of microbial communities with glycan substrates alters community metabolism and its potential impact on host physiology. We analyzed sugar fermentation pathways and products predicted to be formed and prebiotic-induced changes in vitamin and amino acid biosynthesis and degradation. These results highlight the utility of combining a genome-wide metabolic reconstruction methodology with 16S rRNA sequence-based community profiles to provide insights pertaining to community metabolism. This process also provides a rational means for prioritizing in vivo analysis of prebiotics and medicinal herbs in vivo to test hypotheses related to therapeutic potential in specific diseases of interest.

Anti-Inflammation and Anti-Melanogenic Effects of Maca Root Extracts Fermented Using Lactobacillus Strains

Maca is a well-known biennial herb with various physiological properties, such as antioxidant activity and immune response regulation. In this study, the antioxidant, anti-inflammatory, and anti-melanogenic effects of fermented maca root extracts were investigated. The fermentation was carried out using Lactobacillus strains, such as Lactiplantibacillus plantarum subsp. plantarum, Lacticaseibacillus rhamnosus, Lacticaseibacillus casei, and Lactobacillus gasseri. In RAW 264.7 cells, the non-fermented maca root extracts increased the secretion of nitric oxide (NO), an inflammatory mediator, in a dose-dependent manner. In contrast, the fermented extracts showed considerably lower NO secretion than the non-fermented extracts at concentrations of 5% and 10%. This indicates the effective anti-inflammatory effects of fermented maca. The fermented maca root extracts also inhibited tyrosinase activity, melanin synthesis, and melanogenesis by suppressing MITF-related mechanisms. These results show that fermented maca root extracts exhibit higher anti-inflammatory and anti-melanogenesis effects than non-fermented maca root extracts. Thus, maca root extracts fermented using Lactobacillus strains have the potential to be used as an effective cosmeceutical raw material.

Dietary yeast cell wall enhanced intestinal health of broiler chickens by modulating intestinal integrity, immune responses, and microbiota

This study was conducted to determine the effects of dietary yeast cell wall (YCW) on growth performance, intestinal health, and immune responses of broiler chickens. In a randomized completely block design (block: initial body weight), a total of 800 broilers (Ross 308; 45.18 ± 3.13 g of initial body weight) were assigned to 2 dietary treatments (40 birds/pen; 10 replicates/treatment) and fed for 5 wk: 1) a basal broiler diet based on corn-soybean meal (CON) and 2) CON + 0.05% dietary YCW. Growth performance was measured at intervals in 3 phase feed program. On the final day of the study, one bird per pen was randomly selected and euthanized for sample collection. Broilers fed YCW had decreased (P < 0.05) feed conversion ratio during the grower phase compared with those fed CON. The YCW increased (P < 0.05) villus height to crypt depth ratio in the duodenum, jejunum, and ileum compared with the CON. In addition, the YCW tended to higher (P < 0.10) number of goblet cells in the duodenum than in the CON. Broilers fed YCW had increased (P < 0.05) serum TGF- β1, ileal gene expression of the claudin family, and relative abundance of Lactobacillus, Prevotella, and Enterococcus compared with the CON, but decreased serum TNF-α (P < 0.05), IL-1β (P < 0.05), and IL-6 (P < 0.10), ileal gene expression of IL-6 (P < 0.05), and relative abundance of Clostridium (P < 0.05). The present study demonstrated that the addition of dietary YCW in broiler diets enhanced the intestinal health of broiler chickens and may be associated with modulated intestinal morphology and integrity by upregulating tight junction-related protein gene expression and modifying the ileal microbiota. In addition, dietary YCW modulated immune responses and inflammatory cytokine gene expression in the ileum.

Genome analysis revealed a repertoire of oligosaccharide utilizing CAZymes in Weissella confusa CCK931 and Weissella cibaria YRK005

Weissella bacteria are gram-positive, anaerobic, fermentative, and have probiotic potential. This study aimed to compare the genomes of W. cibaria YRK005 and W. confusa CCK931 isolated from young radish and kimchi, respectively. The genomic size of W. cibaria YRK005 and W. confusa CCK931 with GC content is 2.36 Mb (45%) and 2.28 Mb (44.67%), respectively. The genome study identified 92 and 83 CAZymes genes, respectively, for W. cibaria YRK005 and W. confusa CCK931, that are responsible for 26 and 27 glycoside hydrolases (GH) and 21 and 27 glycosyl transferases. Both species have one gene for carbohydrate esterases and three genes for carbohydrate-binding modules. The primary CAZymes found in both species that are involved in oligosaccharide utilization are GH1, GH2, GH30, GH13_30, GH13_31, GH42, GH43, and GH65. The study also details the production pathways for glycogen and folate. Both strains include a unique repertoire of genes, including hypothetical proteins, showing adaptability to diverse ecological niches and evolution over time.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-022-01232-7.

Hierarchical Effects of Lactic Fermentation and Grain Germination on the Microbial and Metabolomic Profile of Rye Doughs

A multi-omics approach was adopted to investigate the impact of lactic acid fermentation and seed germination on the composition and physicochemical properties of rye doughs. Doughs were prepared with either native or germinated rye flour and fermented with Saccharomyces cerevisiae, combined or not with a sourdough starter including Limosilactobacillus fermentum, Weissella confusa and Weissella cibaria. LAB fermentation significantly increased total titrable acidity and dough rise regardless of the flour used. Targeted metagenomics revealed a strong impact of germination on the bacterial community profile of sprouted rye flour. Doughs made with germinated rye displayed higher levels of Latilactobacillus curvatus, while native rye doughs were associated with higher proportions of Lactoplantibacillus plantarum. The oligosaccharide profile of rye doughs indicated a lower carbohydrate content in native doughs as compared to the sprouted counterparts. Mixed fermentation promoted a consistent decrease in both monosaccharides and low-polymerization degree (PD)-oligosaccharides, but not in high-PD carbohydrates. Untargeted metabolomic analysis showed that native and germinated rye doughs differed in the relative abundance of phenolic compounds, terpenoids, and phospholipids. Sourdough fermentation promoted the accumulation of terpenoids, phenolic compounds and proteinogenic and non-proteinogenic amino acids. Present findings offer an integrated perspective on rye dough as a multi-constituent system and on cereal-sourced bioactive compounds potentially affecting the functional properties of derived food products.

Complexity of acclimatization substrate affects anaerobic digester microbial community response to organic load shocks

This study elucidated the changes in the short-term response to organic load shocks of the anaerobic digestion (AD) microbiome acclimatized to a simple substrate and a complex substrate. Batch vial reactors were inoculated with AD sludge acclimatized to either a simple (starch and hipolypeptone) or a complex (dog food and starch) substrate, both with carbon-to-nitrogen ratio of 25. Organic loads in the form of an easily degradable substrate mix (starch and hipolypeptone) with concentrations varying from 0 to 5 g VS/L were applied to the reactors. Runs utilizing the inoculum acclimatized to a complex substrate sustained its methane productivity despite the high organic load shocks which the inoculum acclimatized to a simple substrate was unable to handle efficiently. The alpha-diversity of the microbiome decreased with increase in organic load for inoculum acclimatized with a simple substrate but was unaffected for the case of the inoculum acclimatized with a complex substrate. LactobacillalesandCloacimonadales were inferred to be major players in starch degradation pathways for the inoculum acclimatized using a simple substrate as predicted by the bioinformatics package PICRUSt2. However, acclimatizing using a complex substrate did not support their growth and were replaced by Coriobacteriales which provided higher flexibility in terms of the predicted regulated metabolic functions. The predicted functional regulation of Synergistales and Syntrophales increased with acclimatization using a complex substrate which also showed increase in the flexibility of the microbiome towards handling organic load shocks. Acetoclastic pathway was upregulated with increase in organic load regardless of the acclimatization substrate while the hydrogenotrophic pathway was downregulated. Overall, acclimatization using a complex substrate increased the robustness and flexibility of the microbiome towards organic load shocks.

Systematic evaluation of genome-wide metabolic landscapes in lactic acid bacteria reveals diet- and strain-specific probiotic idiosyncrasies

Lactic acid bacteria (LAB) are well known to elicit health benefits in humans, but their functional metabolic landscapes remain unexplored. Here, we analyze differences in growth, intestinal persistence, and postbiotic biosynthesis of six representative LAB and their interactions with 15 gut bacteria under 11 dietary regimes by combining multi-omics and in silico modeling. We confirmed predictions on short-term persistence of LAB and their interactions with commensals using cecal microbiome abundance and spent-medium experiments. Our analyses indicate that probiotic attributes are both diet and species specific and cannot be solely explained using genomics. For example, although both Lacticaseibacillus casei and Lactiplantibacillus plantarum encode similarly sized genomes with diverse capabilities, L. casei exhibits a more desirable phenotype. In addition, "high-fat/low-carb" diets more likely lead to detrimental outcomes for most LAB. Collectively, our results highlight that probiotics are not "one size fits all" health supplements and lay the foundation for personalized probiotic design.

An in vitro study: prebiotic effects of edible palm hearts in batch human fecal fermentation system

BACKGROUND

Edible palm hearts (EPH), known as palmito, chonta or swamp cabbage in America or umbut in Malaysia, is a type of vegetable harvested from palm tree species. EPH is firm and smooth and described as having a flavor resembling artichoke. It has underlying prebiotic potential that selectively stimulates the growth and activity of beneficial colonic microbiota, thus enhancing the host's health. This study is the first to present results of EPH from local species such as oil palm (Elaeis guineensis), sago palm (Metroxylon sagu) and coconut (Cocos nucifera) using in vitro colonic fermentation with human fecal slurry. Samples obtained at 0, 6, 12 and 24 h were evaluated by bacterial enumeration using fluorescent in situ hybridization (FISH), and short-chain fatty acids (SCFA) were analyzed by high-performance liquid chromatography (HPLC).

RESULTS

All EPH samples revealed induction effects towards Bifidobacterium spp., Lactobacillus-Enterococcus and Bacteroidaceae/Prevotellaceae populations similar to those in inulin fermentation. A significant decrease (P ≤ 0.05) in pathogenic Clostridium histolyticum group was observed in the response of raw sago palm hearts. In general, all samples stimulate the production of SCFA. Particularly in the colonic fermentation of sago palm heart, acetate and propionate revealed the highest concentrations of 286.18 and 284.83 mmol L^-1 in raw and cooked form, respectively.

CONCLUSION

This study concluded that edible palm hearts can be a potential prebiotic ingredient that promotes human gastrointestinal health, as well as discovering a new direction towards an alternative source of functional foods. © 2022 Society of Chemical Industry.

In Vitro Production of Galactooligosaccharides by a Novel β-Galactosidase of Lactobacillus bulgaricus

β-galactosidase is an enzyme with dual activity and important industrial application. As a hydrolase, the enzyme eliminates lactose in milk, while as a trans-galactosidase it produces prebiotic galactooligosaccharides (GOS) with various degrees of polymerization (DP). The aim of the present study is the molecular characterization of β-galactosidase from a Bulgarian isolate, Lactobacillus delbrueckii subsp. bulgaricus 43. The sequencing of the β-gal gene showed that it encodes a new enzyme with 21 amino acid replacements compared to all other β-galactosidases of this species. The molecular model revealed that the new β-galactosidase acts as a tetramer. The amino acids D207, H386, N464, E465, Y510, E532, H535, W562, N593, and W980 form the catalytic center and interact with Mg²⁺ ions and substrate. The β-gal gene was cloned into a vector allowing heterologous expression of E. coli BL21(DE3) with high efficiency, as the crude enzyme reached 3015 U/mL of the culture or 2011 U/mg of protein. The enzyme's temperature optimum at 55 °C, a pH optimum of 6.5, and a positive influence of Mg²⁺, Mn²⁺, and Ca²⁺ on its activity were observed. From lactose, β-Gal produced a large amount of GOS with DP3 containing β-(1→3) and β-(1→4) linkages, as the latter bond is particularly atypical for the L. bulgaricus enzymes. DP3-GOS formation was positively affected by high lactose concentrations. The process of lactose conversion was rapid, with a 34% yield of DP3-GOS in 6 h, and complete degradation of 200 g/L of lactose for 12 h. On the other hand, the enzyme was quite stable at 55 °C and retained about 20% of its activity after 24 h of incubation at this temperature. These properties expand our horizons as regards the use of β-galactosidases in industrial processes for the production of lactose-free milk and GOS-enriched foods.

Biochemical and Microbiological Changes Associated with Fermentation of Durum Wheat for Lemzeïet Processing, a Traditional Algerian Fermented Food

In Algeria, “Lemzeïet” is prepared by the natural fermentation of wheat. This study aimed to follow the evolution of microbiological and biochemical properties of Lemzeïet with and without vinegar addition for 3, 6, 9 and 12 months. Lactic acid bacteria (LAB) were identified and the microbial count, as well as pH, acidity, protein, fat, ash and starch contents were determined. Results showed that Lemzeïet samples represented a safe product after the gradual absence of fungi. It also contained a significant load of LAB that were cocci or rods, white or yellow, grouped in chain, pair and tetrad. LAB isolates were mannitol positive, grew between 10 and 45 °C, showed resistance at 63.5 °C and the majority were homo-fermentative. Results showed a significant decrease in pH during fermentation regardless of the vinegar addition. Protein content increased up to 14.90% and 15.50% at the end of fermentation. The fat and starch contents decreased after 12 months of fermentation, regardless of the vinegar addition. Ash content remained high (1.41% and 1.45%) after six months of fermentation with and without vinegar, respectively. The microbiological and the biochemical characteristics of Lemzeïet make it a very interesting raw material in the manufacturing of healthy foods.

Synergy between oligosaccharides and probiotics: From metabolic properties to beneficial effects

Synbiotic is defined as the dietary mixture that comprises both probiotic microorganisms and prebiotic substrates. The concept has been steadily gaining attention owing to the rising recognition of probiotic, prebiotics, and gut health. Among prebiotic substances, oligosaccharides demonstrated considerable health beneficial effects in varieties of food products and their combination with probiotics have been subjected to full range of evaluations. This review delineated the landscape of studies using microbial cultures, cell lines, animal model, and human subjects to explore the functional properties and host impacts of these combinations. Overall, the results suggested that these combinations possess respective metabolic properties that could facilitate beneficial activities therefore could be employed as dietary interventions for human health improvement and therapeutic purposes. However, uncertainties, such as applicational practicalities, underutilized analytical tools, contradictory results in studies, unclear mechanisms, and legislation hurdles, still challenges the broad utilization of these combinations. Future studies to address these issues may not only advance current knowledge on probiotic-prebiotic-host interrelationship but also promote respective applications in food and nutrition.

Microbiota independent effects of oligosaccharides on Caco-2 cells -A semi-targeted metabolomics approach using DI-FT-ICR-MS coupled with pathway enrichment analysis

Milk oligosaccharides (MOS) and galactooligosaccharides (GOS) are associated with many benefits, including anti-microbial effects and immune-modulating properties. However, the cellular mechanisms of these are largely unknown. In this study, the effects of enriched GOS and MOS mixtures from caprine and bovine milk consisting mainly 6'-galactosyllactose, 3'-sialyllactose, and 6'-sialyllactose on Caco-2 cells were investigated, and the treatment-specific metabolomes were described. In the control, the cells were treated with a sugar mix consisting of one-third each of glucose, galactose and lactose. A local metabolomics workflow with pathway enrichment was established, which specifically addresses DI-FT-ICR-MS analyses and includes adaptations in terms of measurement technology and sample matrices. By including quality parameters, especially the isotope pattern, we increased the precision of annotation. The independence from online tools, the fast adaptability to changes in databases, and the specific adjustment to the measurement technology and biomaterial used, proved to be a great advantage. For the first time it was possible to find 71 active pathways in a Caco-2 cell experiment. These pathways were assigned to 12 main categories, with amino acid metabolism and carbohydrate metabolism being the most dominant categories in terms of the number of metabolites and metabolic pathways. Treatment of Caco-2 cells with high GOS and glucose contents resulted in significant effects on several metabolic pathways, whereas the MOS containing treatments resulted only for individual metabolites in significant changes. An effect based on bovine or caprine origin alone could not be observed. Thus, it was shown that MOS and GOS containing treatments can exert microbiome-independent effects on the metabolome of Caco-2 cells.

The plasmid-encoded lactose operon plays a vital role in the acid production rate of Lacticaseibacillus casei during milk beverage fermentation

Lacticaseibacillus casei is used extensively in the fermented milk-beverage industry as a starter culture. Acid production capacity during fermentation is the main criterion for evaluating starters although it is strain-dependent. In this study, the acid production rates of 114 L. casei strains were determined and then classified into high acid (HC), medium acid (MC), and low acid (LC) groups. Comparative genomics analysis found that the lac operon genes encoding the phosphoenolpyruvate-lactose phosphotransferase system (PTSLac) were located on plasmids in the HC strains; however, it is notable that the corresponding operons were located on the chromosome in LC strains. Real-time PCR analysis showed that the copy numbers of lac operon genes in HC strains were between 3.1 and 9.3. To investigate the relationship between copy number and acid production rate, the lac operon cluster of the HC group was constitutively expressed in LC strains. The resulting copy numbers of lac operon genes were between 15.8 and 18.1; phospho-β-galactosidase activity increased by 1.68-1.99-fold; and the acid production rates increased by 1.24-1.40-fold, which enhanced the utilization rate of lactose from 17.5 to 42.6% in the recombinant strains. The markedly increased expression of lac operon genes increased lactose catabolism and thereby increased the acid production rate of L. casei.

The plasmid-encoded lactose operon plays a vital role in the acid production rate of Lacticaseibacillus casei during milk beverage fermentation

Lacticaseibacillus casei is used extensively in the fermented milk-beverage industry as a starter culture. Acid production capacity during fermentation is the main criterion for evaluating starters although it is strain-dependent. In this study, the acid production rates of 114 L. casei strains were determined and then classified into high acid (HC), medium acid (MC), and low acid (LC) groups. Comparative genomics analysis found that the lac operon genes encoding the phosphoenolpyruvate-lactose phosphotransferase system (PTS^Lac) were located on plasmids in the HC strains; however, it is notable that the corresponding operons were located on the chromosome in LC strains. Real-time PCR analysis showed that the copy numbers of lac operon genes in HC strains were between 3.1 and 9.3. To investigate the relationship between copy number and acid production rate, the lac operon cluster of the HC group was constitutively expressed in LC strains. The resulting copy numbers of lac operon genes were between 15.8 and 18.1; phospho-β-galactosidase activity increased by 1.68–1.99-fold; and the acid production rates increased by 1.24–1.40-fold, which enhanced the utilization rate of lactose from 17.5 to 42.6% in the recombinant strains. The markedly increased expression of lac operon genes increased lactose catabolism and thereby increased the acid production rate of L. casei.

Advances in isolation, characterization, modification, and application of Chenopodium starch: A comprehensive review

The Chenopodium genus includes >250 species, among which only quinoa, pigweed, djulis, and kaniwa have been explored for starches. Chenopodium is a non-conventional and rich source of starch, which has been found effective in producing different classes of food. Chenopodium starches are characterized by their smaller granule size (0.4-3.5 μm), higher swelling index, shorter/lower gelatinization regions/temperature, good emulsifying properties, and high digestibility, making them suitable for food applications. However, most of the investigations into Chenopodium starches are in the primary stages (isolation, modification, and characterization), except for quinoa. This review comprehensively explores the major developments in Chenopodium starch research, emphasizing isolation, structural composition, functionality, hydrolysis, modification, and application. A critical analysis of the trends, limitations, and scope of these starches for novel food applications has also been provided to promote further scientific advancement in the field.

Unraveling the mechanism of raffinose utilization in Ligilactobacillus salivarius Ren by transcriptomic analysis

In the gastrointestinal tract, some dietary carbohydrates, such as xylose, raffinose and arabinose, are able to stimulate the growth of Lactobacillus and Bifidobacterium. In this study, the growth rate of Ligilactobacillus salivarius Ren in raffinose was 0.91 ± 0.03 h-1, which was higher than that in glucose (0.83 ± 0.01 h-1). However, limited information is available on specific transporters and glycoside hydrolases responsible for raffinose uptake and catabolism in L. salivarius. Transcriptomic analysis revealed the differential expression of 236 genes (∣log2FoldChange∣ > 0.8) in response to raffinose, which were mainly associated with raffinose transport, raffinose hydrolysis, galactose metabolism and pyruvate metabolism. Notably, gene rafP encoding lactose/raffinose permease was 101.86-fold up-regulated. Two α-galactosidase gene galA1 and galA2 were 117.82-fold and 2.66-fold up-regulated, respectively. To further investigate the role of these genes in raffinose utilization, insertional inactivation was performed using the pORI28-pTRK669 system. The growth assay of these mutants in modified MRS containing 2% (w/v) raffinose indicated that RafP played an important role in raffinose transport and GalA1 was the primary enzyme involved in raffinose hydrolysis. To our knowledge, this is the first report on the molecular mechanism of raffinose utilization in L. salivarius.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03280-6.

Comparative study of sugar extraction procedures for HPLC analysis and proposal of an ethanolic extraction method for plant-based high-protein ingredients

BACKGROUND

The increasing importance of plant-based proteins in the food sector makes a reliable compositional analysis of plant-based high-protein ingredients a necessity. Specifically, the quantification of short-chain carbohydrates is relevant for multiple areas, including food product development, food labelling and fundamental food chemistry and food technology research. Commonly used extraction procedures for subsequent high-performance liquid chromatographic separation and quantification of short-chain carbohydrates have been discussed controversially regarding a range of complications that can potentially lead to inaccurate sugar determination. The present study compares the sugar levels in wheat flour and wholemeal wheat flour determined with different aqueous and ethanolic extraction procedures. These procedures included measures to prevent enzyme activity and microbial growth, which represent two of the most relevant challenges in sugar extraction from food samples.

RESULTS

Differences in sugar levels (sum of sucrose/maltose, glucose and fructose) as high as 1.8% dry matter (wheat flour) were observed between the employed extraction procedures. Ethanolic extraction (80% ethanol in ultrapure water) with the use of the antimicrobial agent sodium azide but without Carrez clarification was identified as most promising for sugar determination in plant-based high-protein ingredients.

CONCLUSION

A screening of high-protein ingredients derived from cereals (wheat gluten), pseudocereals (quinoa, amaranth, buckwheat) and legumes (soy, pea, lupin, lentil, carob, chickpea, faba bean) concerning their levels of sucrose, maltose, glucose and fructose confirmed the applicability of the chosen extraction procedure. © 2021 Society of Chemical Industry.