The effects of fermentation acids on bacterial growth

Salt can antagonize the lethal effect of weak organic acids against Escherichia coli O157:H7 inoculated in laboratory culture media and acidic/acidified foods

From the last several decades, previous studies have found that salt can increase the resistance of Gram-negative human-pathogenic bacteria to acidic environments in the presence of weak organic acids (OAAs), significantly increasing or extending the survival of Escherichia coli O157:H7, Salmonella enterica serovar Typhimurium, Shigella sp., and Cronobacter sp., particularly in acidified foods. These pathogenic bacteria may be inclined to be less reduced after washing or dipping in weak OAAs combined with salt, thereby posing a potential food safety hazard. Particularly, it can be plausible that E. coli has varied and different mechanisms to cope with the detrimental effects imposed by weak OAAs with one carboxyl functional group by the addition of ionic or nonionic solutes, including salt, KCl, sucrose, glutamate, and fructose. Nevertheless, little is known about the intracellular physiological response of Gram-negative bacteria subjected to a simultaneous challenge with weak OAAs and salt, as well as the underlying principles of an antagonistic phenomenon (protection) affordable to E. coli by the combined treatments. Therefore, the objectives of this review are to introduce the current propensity of individual or combined treatments with weak OAAs and salt for inactivating food-borne pathogens, to compile a selected area of studies focusing on the antagonistic interaction between short-chained weak OAAs and salt for inhibiting or eliminating Gram-negative bacteria, and then to uncover the putative mechanisms mediating the improved resistance of E. coli O157:H7 to weak acids by the salt amendment.

Lysozyme Peptides as a Novel Nutra-Preservative to Control Some Food Poisoning and Food Spoilage Microorganisms

Foodborne illnesses and microbial food contamination are crucial concerns and still issues of great worldwide concern. Additionally, the serious health hazards associated with the use of chemical preservatives in food technology. Lysozyme (Lz) is an active protein against Gram-positive bacterial cell wall through its muramidase lytic activity; however, several authors could identify some antimicrobial peptides derived from Lz that have an exaggerated and broad-spectrum antibacterial activity. Therefore, a lysozyme peptides preparation (LzP) is developed to broaden the Lz spectrum. In this work, we investigated the potential efficacy of LzP as a novel Nutra-preservative (food origin) agent against some pathogenic and spoilage bacteria. Our results showed that LzP demonstrated only 11% of the lysozyme lytic activity. However, LzP exhibited strong antibacterial activity against Escherichia coli, Salmonella enteritidis, and Pseudomonas species, while Salmonella typhi and Aeromonas hydrophila exhibited slight resistance. Despite the lowest LzP concentration (0.1%) employed, it performs stronger antibacterial activity than weak organic acids (0.3%). Interestingly, the synergistic multi-component formulation (LzP, glycine, and citric acid) could inhibit 6 log10 cfu/ml of E. coli survival growth. The effect of heat treatment on LzP showed a decrease in its antibacterial activity at 5 and 67% by boiling at 100 °C/30 min, and autoclaving at 121 °C/15 min; respectively. On the other hand, LzP acquired stable antibacterial activity at different pH values (4-7). In conclusion, LzP would be an innovative, natural, and food origin preservative to control the growth of food poisoning and spoilage bacteria in food instead chemical one.

Optimising Nutrition for Sustainable Pig Production: Strategies to Quantify and Mitigate Environmental Impact

The intensifying global demand for food presents significant challenges for sustainable pig production, particularly in the context of escalating input costs, environmental degradation, and resource scarcity. Life cycle assessment provides a comprehensive framework for quantifying environmental impacts and identifying production hotspots within pig production systems. Feed production and manure management are consistently identified as major contributors, emphasising the need for targeted interventions. Although soybean meal remains a key protein source, its association with deforestation and biodiversity loss is driving an interest in more sustainable alternatives. In temperate climates, faba beans offer a promising, locally sourced option, though their wider adoption is limited by amino acid imbalances and anti-nutritional factors. Grain preservation is another critical consideration, as post-harvest losses and fungal contamination compromise feed quality and animal health. Organic acid preservation has emerged as an energy-efficient, cost-effective alternative to industrial drying, improving storage stability and reducing fossil fuel dependence. Additional nutritional strategies, including dietary crude protein reduction, carbohydrate source modification, feed additive inclusion, and maternal nutritional interventions, can enhance nutrient utilisation, intestinal health, and herd resilience while mitigating environmental impact. This review explores practical feed-based strategies to support sustainable, resilient, and resource-efficient pig production and contribute to global food security.

Value-added utilisation of industrial by-products from bioenergy processes for growth of the PHB synthesising bacterium Cupriavidus necator

The utilisation of low-value by-products derived from the production of bioenergy as nutrient media for microbial growth was investigated using the polyhydroxybutyrate (PHB) synthesising bacterium Cupriavidus necator as a case study. The potentially suitable by-products crude glycerol (derived from biodiesel production as carbon source) and digestate (resulting from biogas production as source for nitrogen and other nutrients) contain significant amounts of nutrients but also dissolved and solid impurities. In order to minimise negative effects such as clogging in bioreactor infrastructure and complications during product recovery in a future industrial production scale, the amount of solids was reduced by filtration and centrifugation. In addition, the treatment of the liquid anaerobic digestate (LAD) included dilution and pH stabilisation in order to reduce growth inhibition due to excessive concentrations of compounds in the digestate and an unsuitable pH. Experiments were carried out in a stirred tank bioreactor comparing growth on a medium consisting only of treated LAD and crude glycerol with growth on a reference media containing crude glycerol but mineral salts instead of LAD. Fermentation with crude glycerol and LAD showed slightly reduced specific growth rates (0.1 1/h) but a similar cell dry weight (8.8 gCDW/L) compared to the reference media with crude glycerol and mineral salts (0.14 1/h and 9.5 gCDW/L). As no specific conditions were set to promote PHB accumulation, only low levels of PHA of 5,45wPHB/wCDW-% ( ± 1,5) were observed for both medium variations at the end of growth.

Responses of Broiler Chickens to Diets of Different Nutritional Planes Supplemented With or Without Organic Acids

BACKGROUND

Scientific information on the diets of various nutritional planes supplemented with organic acids is scarce in tropical environments.

OBJECTIVES

This study was conducted to evaluate the response of broilers to diets of different nutritional planes supplemented with or without organic acids. A total of 240 one-day-old unsexed broiler chicks of the Cobb 500 strain were randomly assigned to 6 treatments, each with 4 replicates having 10 chicks.

METHODS

The treatments were chickens fed an optimal diet (optimal energy and protein) (Diet 1), a medium diet (medium energy and protein) (Diet 2) and a low diet (low energy and protein) (Diet 3), while diets 4, 5 and 6 were diets 1, 2 and 3 supplemented with 4, 6 and 8 g/kg organic acid (Fysal-MP), respectively. The study was laid out in a completely randomized design.

RESULTS

The birds fed diets with organic acid supplementation recorded similar (p > 0.05) final weights compared to those fed an optimal diet (T1); however, the weights were higher (p < 0.05) compared to the chickens on a low diet without organic acid (T3). The feed conversion ratio was better in birds fed diets containing organic acid, irrespective of the nutritional plane. Birds on medium diets with organic acids recorded a higher (p < 0.05) aspartate aminotransferase compared to those on low diets during the starter phase. Birds on a low diet without organic acid recorded a lower (p < 0.05) basal width compared to those on other diets. The microbial counts were reduced (p < 0.05) in broilers fed organic acids, with the lowest reduction in the group fed medium diets with 6 g/kg organic acids.

CONCLUSIONS

It was concluded that organic acid supplementation enhanced blood parameters, carcass traits, growth performance and microbial counts in broiler chickens.

Effects of Lactiplantibacillus plantarum HNU082 intervention on fungi and bacteriophages in different intestinal segments of mice

BACKGROUND

Gut fungi and bacteriophages, as members of the gut microbiota, can affect the interactions between gut bacteria and the host, participate in host metabolism, and are associated with various diseases. Probiotics substantially influence gut fungi and bacteriophages, modulating their composition through both direct and indirect mechanisms, thereby influencing host health. Current research primarily focuses on the effects of probiotics on the intestinal bacterial community. However, the alterations in the compositions of gut fungi and bacteriophages following probiotic intervention are not yet fully understood. Therefore, this study used Lactiplantibacillus plantarum HNU082 (Lp082) as the research subject and aimed to investigate the changes of the gut fungi and bacteriophages in the small intestine and the large intestine after the gavage of Lp082.

RESULTS

After probiotics entered the gut, the changes of the gut fungi and bacteriophages caused by the probiotics were more pronounced in the small intestine compared to the large intestine. The relative abundance of pathogenic fungi, such as Candida albicans, decreased in the small intestine. Furthermore, a strong positive correlation between the relative abundance of bacteriophages and their host bacteria in the gut was observed. The relative abundance of both Clostridia class bacteria and their bacteriophages increased.

CONCLUSIONS

In summary, the effects of probiotics on gut fungi and bacteriophages differed between the small intestine and the large intestine. This study contributed to a better understanding of the impact of probiotics on gut fungi and bacteriophages and provided data support for the association and dynamic changes between gut bacteria and their bacteriophages.

Long-Term Autotrophic Growth and Solar-to-Chemical Conversion in Shewanella Oneidensis MR-1 through Light-Driven Electron Transfer

Members of the genus Shewanella are known for their versatile electron accepting routes, which allow them to couple decomposition of organic matter to reduction of various terminal electron acceptors for heterotrophic growth in diverse environments. Here, we report autotrophic growth of Shewanella oneidensis MR-1 with photoelectrons provided by illuminated biogenic CdS nanoparticles. This hybrid system enables photosynthetic oscillatory acetate production from CO2 for over five months, far exceeding other inorganic-biological hybrid system that can only sustain for hours or days. Biochemical, electrochemical and transcriptomic analyses reveal that the efficient electron uptake of S. oneidensis MR-1 from illuminated CdS nanoparticles supplies sufficient energy to stimulate the previously overlooked reductive glycine pathway for CO2 fixation. The continuous solar-to-chemical conversion is achieved by photon induced electric recycling in sulfur species. Overall, our findings demonstrate that this mineral-assisted photosynthesis, as a widely existing and unique model of light energy conversion, could support the sustained photoautotrophic growth of non-photosynthetic microorganisms in nutrient-lean environments and mediate the reversal of coupled carbon and sulfur cycling, consequently resulting in previously unknown environmental effects. In addition, the hybrid system provides a sustainable and flexible platform to develop a variety of solar products for carbon neutrality.

Perspectives on Microbiome Therapeutics in Infectious Diseases: A Comprehensive Approach Beyond Immunology and Microbiology

Although global life expectancy has increased over the past 20 years due to advancements in managing infectious diseases, one-fifth of people still die from infections. In response to this ongoing threat, significant efforts are underway to develop vaccines and antimicrobial agents. However, pathogens evolve resistance mechanisms, complicating their control. The COVID-19 pandemic has underscored the limitations of focusing solely on the pathogen-killing strategies of immunology and microbiology to address complex, multisystemic infectious diseases. This highlights the urgent need for practical advancements, such as microbiome therapeutics, that address these limitations while complementing traditional approaches. Our review emphasizes key outcomes in the field, including evidence of probiotics reducing disease severity and insights into host-microbiome crosstalk that have informed novel therapeutic strategies. These findings underscore the potential of microbiome-based interventions to promote physiological function alongside existing strategies aimed at enhancing host immune responses and pathogen destruction. This narrative review explores microbiome therapeutics as next-generation treatments for infectious diseases, focusing on the application of probiotics and their role in host-microbiome interactions. While offering a novel perspective grounded in a cooperative defense system, this review also addresses the practical challenges and limitations in translating these advancements into clinical settings.

Adhesion Properties and Pathogen Inhibition of Vaginal-Derived Lactobacilli

In the present study, twenty-seven (27) lactobacilli strains, isolated from the vagina of healthy Italian women of reproductive age, were screened for probiotic properties. The strains were evaluated for antagonistic activity against pathogens, adhesion abilities, and potential to displace and/or inhibit the adhesion of previously adhered pathogens as a primary strain selection criterion. Overall, all the tested lactobacilli inhibited at least three pathogens, and the majority of them exhibited antimicrobial activity against Enterobacter cloacae DSM 30054, Pseudomonas aeruginosa DSM 3227, and Pseudomonas aeruginosa DSM 1117. The complete neutralization of antimicrobial activity after cell-free supernatant (CFS) neutralization suggested a pivotal role for lactic acid or other organic acids secreted by the lactobacilli. The strains showed variability in their adhesion levels, but all tested strains adhered to both human colonic epithelial cells (HT-29) and vaginal cells (VK2/E6E7) with adhesion percentages exceeding 1%. The ability to displace or inhibit pathogens was dependent on the pathogen and the lactobacilli strain; the pathogen displacement levels ranged from 9 to 82%, while pathogen exclusion levels varied from 1 to 99%. In conclusion, this study demonstrates the protective effect of vaginal lactobacilli against pathogens and confirms the suitability of the vaginal microbiota as a source of potential probiotic strains. The selected lactobacilli hold promise for the formulation of supplements to enhance genitourinary tract health.

Probiotics in piglet: from gut health to pathogen defense mechanisms

Various problems and obstacles are encountered during pig farming, especially the weaning phase when switching from liquid to solid feed. Infection by pathogenic bacteria causes damage to the intestinal barrier function of piglets, disrupts the balance of the intestinal microbiota, and destroys the chemical, mechanical, and immune barriers of the intestinal tract, which is one of the main causes of gut inflammation or gut diseases in piglets. The traditional method is to add antibiotics to piglet diets to prevent bacterial infections. However, long-term overuse of antibiotics leads to bacterial resistance and residues in animal products, threatening human health and causing gut microbiota dysbiosis. In this context, finding alternatives to antibiotics to maintain pre- and post-weaning gut health in piglets and prevent pathogenic bacterial infections becomes a real emergency. The utilization of probiotics in piglet nutrition has emerged as a pivotal strategy to promote gut health and defend against pathogenic infections, offering a sustainable alternative to traditional antibiotic usage. This review introduces recent findings that underscore the multifaceted roles of probiotics in enhancing piglet welfare, from fortifying the gut barrier to mitigating the impacts of common bacterial pathogens. Meanwhile, this study introduces the functions of probiotics from different perspectives: positive effects of probiotics on piglet gut health, protecting piglets against pathogen infection, and the mechanisms of probiotics in preventing pathogenic bacteria.

Engineering quorum sensing-based genetic circuits enhances growth and productivity robustness of industrial E. coli at low pH

BACKGROUND

Microbial organisms hold significant potential for converting renewable substrates into valuable chemicals. Low pH fermentation in industrial settings offers key advantages, including reduced neutralizer usage and decreased wastewater generation, particularly in the production of amino acids and organic acids. Engineering acid-tolerant strains represents a viable strategy to enhance productivity in acidic environments. Synthetic biology provides dynamic regulatory tools, such as gene circuits, facilitating precise expression of acid resistance (AR) modules in a just-in-time and just-enough manner.

RESULTS

In this study, we aimed to enhance the robustness and productivity of Escherichia coli, a workhorse for amino acid and organic acid production, in industrial fermentation under mild acidic conditions. We employed an Esa-type quorum sensing circuit to dynamically regulate the expression of an AR module (DsrA-Hfq) in a just-in-time and just-enough manner. Through careful engineering of the critical promoter PesaS and stepwise evaluation, we developed an optimal Esa-PBD(L) circuit that conferred upon an industrial E. coli strain SCEcL3 comparable lysine productivity and enhanced yield at pH 5.5 compared to the parent strain at pH 6.8.

CONCLUSIONS

This study exemplifies the practical application of gene circuits in industrial environments, which present challenges far beyond those of well-controlled laboratory conditions.

Staphylococcus aureus counters organic acid anion-mediated inhibition of peptidoglycan cross-linking through robust alanine racemase activity

Weak organic acids are commonly found in host niches colonized by bacteria, and they can inhibit bacterial growth as the environment becomes acidic. This inhibition is often attributed to the toxicity resulting from the accumulation of high concentrations of organic anions in the cytosol, which disrupts cellular homeostasis. However, the precise cellular targets that organic anions poison and the mechanisms used to counter organic anion intoxication in bacteria have not been elucidated. Here, we utilize acetic acid, a weak organic acid abundantly found in the gut to investigate its impact on the growth of Staphylococcus aureus. We demonstrate that acetate anions bind to and inhibit d-alanyl-d-alanine ligase (Ddl) activity in S. aureus. Ddl inhibition reduces intracellular d-alanyl-d-alanine (d-Ala-d-Ala) levels, compromising staphylococcal peptidoglycan cross-linking and cell wall integrity. To overcome the effects of acetate-mediated Ddl inhibition, S. aureus maintains a substantial intracellular d-Ala pool through alanine racemase (Alr1) activity and additionally limits the flux of d-Ala to d-glutamate by controlling d-alanine aminotransferase (Dat) activity. Surprisingly, the modus operandi of acetate intoxication in S. aureus is common to multiple biologically relevant weak organic acids indicating that Ddl is a conserved target of small organic anions. These findings suggest that S. aureus may have evolved to maintain high intracellular d-Ala concentrations, partly to counter organic anion intoxication.

Plasma activated water effects on behavior, performance, carcass quality, biochemical changes, and histopathological alterations in quail

BACKGROUND

Plasma-activated water (PAW) is an innovative promising technology which could be applied to improve poultry health. The current study investigated the effects of drinking water supply with PAW on quail behaviour, performance, biochemical parameters, carcass quality, intestinal microbial populations, and internal organs histopathology. A total of 54 twenty-one-day-old Japanese quail chicks were randomly allotted to three treatments provided with PAW at doses 0, 1 ml (PAW-1), and 2 ml (PAW-2) per one litter drinking water. Each treatment contained 6 replicates (3 birds/ cage; one male and two females).

RESULTS

The results clarified that there were no significant (P > 0.05) changes in behaviour, and performance. For the biochemical indicators, the PAW-1 group showed significantly higher serum H2O2, total protein and globulin levels compared with the other groups (P = 0.015, < 0.001, and 0.019; respectively). PAW groups had significantly lower serum creatinine and urea levels than the control (P = 0.003). For the carcass quality, the internal organs relative weight between different treatments was not changed. In contrast, there was a significant increase in the meat colour, taste, and overall acceptance scores in PAW groups compared with the control one (P = 0.013, 0.001, and < 0.001; respectively). For the intestinal microbial population, lactobacilli count was significantly higher in PAW-2 compared with the control group (P = 0.014), while there were no changes in the total bacterial count between different treatment groups. Moreover, mild histological changes were recorded in the intestine, liver, and spleen of PAW groups especially PAW-2 compared with the control one.

CONCLUSIONS

PAW offered benefits, such as reducing creatine and urea levels, improving meat characteristics, and increasing lactobacilli count, all of which are crucial for sustainable quail farming. Therefore, further research is needed.

Effectiveness of organic acids for inactivating pathogenic bacteria inoculated in laboratory media and foods: an updated minireview

Food processing industries commonly employ organic acids (OAAs) to determine bacterial contamination in acidified and fermented foods. OAAs are believed to possess potent antimicrobial properties by permeating cell membranes, altering proton and anion concentrations in the cytoplasm due to their lipophilic undissociated forms. The bacteriostatic or bactericidal effects of OAAs are influenced by various factors including microbial physiology, environmental pH, and acid dissociation ratios. Despite their utility, the precise mechanisms underlying OAA-mediated inhibition of pathogenic bacteria remain incompletely understood. Therefore, the objectives of this review are to compile a selected area of researches that focus on the current propensity of different OAAs for inactivating food-borne pathogens, and then to present a theoretical insight on the use of OAAs to prevent and control pathogenic bacteria present in acidic/acidified foods and their mode of mechanisms.

Achieving robust synthetic tolerance in industrial E. coli through negative auto-regulation of a DsrA-Hfq module

In industrial fermentation processes, microorganisms often encounter acid stress, which significantly impact their productivity. This study focused on the acid-resistant module composed of small RNA (sRNA) DsrA and the sRNA chaperone Hfq. Our previous study had shown that this module improved the cell growth of Escherichia coli MG1655 at low pH, but failed to obtain this desired phenotype in industrial strains. Here, we performed a quantitative analysis of DsrA-Hfq module to determine the optimal expression mode. We then assessed the potential of the CymR-based negative auto-regulation (NAR) circuit for industrial application, under different media, strains and pH levels. Growth assay at pH 4.5 revealed that NAR-05D04H circuit was the best acid-resistant circuit to improve the cell growth of E. coli MG1655. This circuit was robust and worked well in the industrial lysine-producing strain E. coli SCEcL3 at a starting pH of 6.8 and without pH control, resulting in a 250 % increase in lysine titer and comparable biomass in shaking flask fermentation compared to the parent strain. This study showed the practical application of NAR circuit in regulating DsrA-Hfq module, effectively and robustly improving the acid tolerance of industrial strains, which provides a new approach for breeding industrial strains with tolerance phenotype.

Dietary Intervention of Benzoic Acid for Intestinal Health and Growth of Nursery Pigs

The objectives of this review are to investigate how benzoic acid can mitigate the negative effects of weaning stress, improve the intestinal microbiota, intestinal health, and growth of nursery pigs, determine the optimal dose level of benzoic acid for the growth rate in nursery pigs, and compare the efficacy of benzoic acid and other acids in pig feeds. After weaning, pigs are exposed to less lactose and solid feed with high acid-binding capacity at infrequent intervals, causing an increase in digesta pH, reducing protein digestion, and increasing ammonia-producing bacteria in the stomach. Benzoic acid supplementation has improved the intestinal health and growth of nursery pigs through its antimicrobial properties and pH reduction in the digesta. The positive modulation of luminal microbiota in the small intestine of pigs by benzoic acid improves intestinal morphology and enhances nutrient utilization, especially nitrogen, of nursery pigs. Benzoic acid supplementation of up to 1% in feeds also increases hippuric acid contents in the urine of nursery pigs, decreasing urinary pH, which is related to ammonia emission and barn conditions in intensive pig production. Supported by the beneficial impacts of benzoic acid, the growth performance of nursery pigs was also improved. However, excessive benzoic acid (over 2.5% up to 5%) in feeds reduces the growth performance of nursery pigs. Thus, this review conducted a meta-analysis of the results from 16 papers to determine the optimal dose level of benzoic acid for body weight gain of nursery pigs, which was found to be 0.60%. The efficacy of benzoic acid was similar to that of other organic acids, including citric acid, fumaric acid, formic acid, and formate salts. Collectively, benzoic acid supplementation can positively modulate the luminal and mucosal microbiota in the small intestine, increase nutrient utilization and intestinal health, decrease urinary pH, and improve the growth performance of nursery pigs.

Glutamine enhances pneumococcal growth under methionine semi-starvation by elevating intracellular pH

Introduction

Bacteria frequently encounter nutrient limitation in nature. The ability of living in this nutrient shortage environment is vital for bacteria to preserve their population and important for some pathogenic bacteria to cause infectious diseases. Usually, we study how bacteria survive after nutrient depletion, a total starvation condition when bacteria almost cease growth and try to survive. However, nutrient limitation may not always lead to total starvation.

Methods

Bacterial adaptation to nutrient shortage was studied by determining bacterial growth curves, intracellular pH, intracellular amino acid contents, gene transcription, protein expression, enzyme activity, and translation and replication activities.

Results

No exogenous supply of methionine results in growth attenuation of Streptococcus pneumoniae, a human pathogen. In this paper, we refer to this inhibited growth state between ceased growth under total starvation and full-speed growth with full nutrients as semi-starvation. Similar to total starvation, methionine semi-starvation also leads to intracellular acidification. Surprisingly, it is intracellular acidification but not insufficient methionine synthesis that causes growth attenuation under methionine semi-starvation. With excessive glutamine supply in the medium, intracellular methionine level was not changed, while bacterial intracellular pH was elevated to ~ 7.6 (the optimal intracellular pH for pneumococcal growth) by glutamine deamination, and bacterial growth under semi-starvation was restored fully. Our data suggest that intracellular acidification decreases translation level and glutamine supply increases intracellular pH to restore translation level, thus restoring bacterial growth.

Discussion

This growth with intracellular pH adjustment by glutamine is a novel strategy we found for bacterial adaptation to nutrient shortage, which may provide new drug targets to inhibit growth of pathogenic bacteria under semi-starvation.

Itaconic acid production by co-feeding of Ustilago maydis: A combined approach of experimental data, design of experiments, and metabolic modeling

Itaconic acid is a platform chemical with a range of applications in polymer synthesis and is also discussed for biofuel production. While produced in industry from glucose or sucrose, co-feeding of glucose and acetate was recently discussed to increase itaconic acid production by the smut fungus Ustilago maydis. In this study, we investigate the optimal co-feeding conditions by interlocking experimental and computational methods. Flux balance analysis indicates that acetate improves the itaconic acid yield up to a share of 40% acetate on a carbon molar basis. A design of experiment results in the maximum yield of 0.14 itaconic acid per carbon source from 100 g L - 1 $\,\text{g L}{}^{-1}$ glucose and 12 g L - 1 $\,\text{g L}{}^{-1}$ acetate. The yield is improved by around 22% when compared to feeding of glucose as sole carbon source. To further improve the yield, gene deletion targets are discussed that were identified using the metabolic optimization tool OptKnock. The study contributes ideas to reduce land use for biotechnology by incorporating acetate as co-substrate, a C2-carbon source that is potentially derived from carbon dioxide.

Active pH regulation facilitates Bacillus subtilis biofilm development in a minimally buffered environment

Biofilms provide individual bacteria with many advantages, yet dense cellular proliferation can also create intrinsic metabolic challenges including excessive acidification. Because such pH stress can be masked in buffered laboratory media-such as MSgg commonly used to study Bacillus subtilis biofilms-it is not always clear how such biofilms cope with minimally buffered natural environments. Here, we report how B. subtilis biofilms overcome this intrinsic metabolic challenge through an active pH regulation mechanism. Specifically, we find that these biofilms can modulate their extracellular pH to the preferred neutrophile range, even when starting from acidic and alkaline initial conditions, while planktonic cells cannot. We associate this behavior with dynamic interplay between acetate and acetoin biosynthesis and show that this mechanism is required to buffer against biofilm acidification. Furthermore, we find that buffering-deficient biofilms exhibit dysregulated biofilm development when grown in minimally buffered conditions. Our findings reveal an active pH regulation mechanism in B. subtilis biofilms that could lead to new targets to control unwanted biofilm growth.IMPORTANCEpH is known to influence microbial growth and community dynamics in multiple bacterial species and environmental contexts. Furthermore, in many bacterial species, rapid cellular proliferation demands the use of overflow metabolism, which can often result in excessive acidification. However, in the case of bacterial communities known as biofilms, these acidification challenges can be masked when buffered laboratory media are employed to stabilize the pH environment for optimal growth. Our study reveals that B. subtilis biofilms use an active pH regulation mechanism to mitigate both growth-associated acidification and external pH challenges. This discovery provides new opportunities for understanding microbial communities and could lead to new methods for controlling biofilm growth outside of buffered laboratory conditions.

The role of gut microbiota in human metabolism and inflammatory diseases: a focus on elderly individuals

Background

The gut microbiota plays a crucial role in regulating the host’s immune responses during aging, which was characterized by a different abundance of bacteria in several age groups.

Main body

Gut microbiota dysbiosis is associated with aging, antibiotic exposure, underlying diseases, infections, hormonal variations, circadian rhythm, and malnutrition, either singularly or in combination. The appropriate use of prebiotics and probiotics may be able to prevent or reduce this disruption.

Conclusion

The current review focuses on the gut microbiota composition across the life cycle, factors affecting gut microbiota changes with aging, and interventions to modulate gut microbiota.

Altered rumen microbiome and correlations of the metabolome in heat-stressed dairy cows at different growth stages

IMPORTANCE

Heat stress is one of the main causes of economic losses in the dairy industry worldwide; however, the mechanisms associated with the metabolic and microbial changes in heat stress remain unclear. Here, we characterized both the changes in metabolites, rumen microbial communities, and their functional potential indices derived from rumen fluid and serum samples from cows at different growth stages and under different climates. This study highlights that the rumen microbe may be involved in the regulation of lipid metabolism by modulating the fatty acyl metabolites. Under heat stress, the changes in the metabolic status of growing heifers, heifers, and lactating cows were closely related to arachidonic acid metabolism, fatty acid biosynthesis, and energy metabolism. Moreover, this study provides new markers for further research to understand the effects of heat stress on the physiological metabolism of Holstein cows and the time-dependent changes associated with growth stages.

Is there a role for microbiome-based approach in common variable immunodeficiency?

Common variable immunodeficiency (CVID) is a primary immunodeficiency characterized by low levels of serum immunoglobulins and increased susceptibility to infections, autoimmune disorders and cancer. CVID embraces a plethora of heterogeneous manifestations linked to complex immune dysregulation. While CVID is thought to be due to genetic defects, the exact cause of this immune disorder is unknown in the large majority of cases. Compelling evidences support a linkage between the gut microbiome and the CVID pathogenesis, therefore a potential for microbiome-based treatments to be a therapeutic pathway for this disorder. Here we discuss the potential of treating CVID patients by developing a gut microbiome-based personalized approach, including diet, prebiotics, probiotics, postbiotics and fecal microbiota transplantation. We also highlight the need for a better understanding of microbiota-host interactions in CVID patients to prime the development of improved preventive strategies and specific therapeutic targets.

The pH-dependent lactose metabolism of Lactobacillus delbrueckii subsp. bulgaricus: An integrative view through a mechanistic computational model

The fermentation process of milk to yoghurt using Lactobacillus delbrueckii subsp. bulgaricus in co-culture with Streptococcus thermophilus is hallmarked by the breakdown of lactose to organic acids such as lactate. This leads to a substantial decrease in pH - both in the medium, as well as cytosolic. The latter impairs metabolic activities due to the pH-dependence of enzymes, which compromises microbial growth. To quantitatively elucidate the impact of the acidification on metabolism of L. bulgaricus in an integrated way, we have developed a proton-dependent computational model of lactose metabolism and casein degradation based on experimental data. The model accounts for the influence of pH on enzyme activities as well as cellular growth and proliferation of the bacterial population. We used a machine learning approach to quantify the cell volume throughout fermentation. Simulation results show a decrease in metabolic flux with acidification of the cytosol. Additionally, the validated model predicts a similar metabolic behaviour within a wide range of non-limiting substrate concentrations. This computational model provides a deeper understanding of the intricate relationships between metabolic activity and acidification and paves the way for further optimization of yoghurt production under industrial settings.

In vitro evaluation of microencapsulated organic acids and pure botanicals as a supplement in lactating dairy cows diet on in vitro ruminal fermentation

The utilization of microencapsulated organic acids and pure botanicals (mOAPB) is widely used in the monogastric livestock industry as an alternative to antibiotics; in addition, it can have gut immunomodulatory functions. More recently, an interest in applying those compounds in the ruminant industry has increased; thus, we evaluated the effects of mOAPB on ruminal fermentation kinetics and metabolite production in an in vitro dual-flow continuous-culture system. For this study, two ruminal cannulated lactating dairy Holstein cows were used as ruminal content donors, and the inoculum was incubated in eight fermenters arranged in a 4 × 4 Latin square design. The basal diet was formulated to meet the nutritional requirements of a 680-kg Holstein dairy cow producing 45 kg/d of milk and supplemented with increasing levels of mOAPB (0; 0.12; 0.24; or 0.36% of dry matter [DM]), which contained 55.6% hydrogenated and refined palm oil, 25% citric acid, 16.7% sorbic acid, 1.7% thymol, and 1% vanillin. Diet had 16.1 CP, 30.9 neutral detergent fiber (NDF), and 32.0 starch, % of DM basis, and fermenters were fed 106 g/d split into two feedings. After a 7 d adaptation, samples were collected for 3 d in each period. Samples of the ruminal content from the fermenters were collected at 0, 1, 2, 4, 6, and 8 h postmorning feeding for evaluation of the ruminal fermentation kinetics. For the evaluation of the daily production of total metabolites and for the evaluation of nutrient degradability, samples from the effluent containers were collected daily at days 8 to 10. The statistical analysis was conducted using MIXED procedure of SAS and treatment, time, and its interactions were considered as fixed effects and day, Latin square, and fermenter as random effects. To depict the treatment effects, orthogonal contrasts were used (linear and quadratic). The supplementation of mOAPB had no major effects on the ruminal fermentation, metabolite production, and degradability of nutrients. The lack of statistical differences between control and supplemented fermenters indicates effective ruminal protection and minor ruminal effects of the active compounds. This could be attributed to the range of daily variation of pH, which ranged from 5.98 to 6.45. The pH can play a major role in the solubilization of lipid coat. It can be concluded that mOAPB did not affect the ruminal fermentation, metabolite production, and degradability of dietary nutrients using an in vitro rumen simulator.

The Impacts of Acidophilic Lactic Acid Bacteria on Food and Human Health: A Review of the Current Knowledge

The need to improve the safety/quality of food and the health of the hosts has resulted in increasing worldwide interest in acidophilic lactic acid bacteria (LAB) for the food, livestock as well as health industries. In addition to the use of acidophilic LAB with probiotic potential for food fermentation and preservation, their application in the natural disposal of acidic wastes polluting the environment is also being investigated. Considering this new benefit that has been assigned to probiotic microorganisms in recent years, the acceleration in efforts to identify new, efficient, promising probiotic acidophilic LAB is not surprising. One of these effots is to determine both the beneficial and harmful compounds synthesized by acidophilic LAB. Moreover, microorganisms are of concern due to their possible hemolytic, DNase, gelatinase and mucinolytic activities, and the presence of virulence/antibiotic genes. Hence, it is argued that acidophilic LAB should be evaluated for these parameters before their use in the health/food/livestock industry. However, this issue has not yet been fully discussed in the literature. Thus, this review pays attention to the less-known aspects of acidophilic LAB and the compounds they release, clarifying critical unanswered questions, and discussing their health benefits and safety.

Amino Acid Starvation-Induced Glutamine Accumulation Enhances Pneumococcal Survival

Bacteria are known to cope with amino acid starvation by the stringent response signaling system, which is mediated by the accumulation of the (p)ppGpp alarmones when uncharged tRNAs stall at the ribosomal A site. While a number of metabolic processes have been shown to be regulatory targets of the stringent response in many bacteria, the global impact of amino acid starvation on bacterial metabolism remains obscure. This work reports the metabolomic profiling of the human pathogen Streptococcus pneumoniae under methionine starvation. Methionine limitation led to the massive overhaul of the pneumococcal metabolome. In particular, methionine-starved pneumococci showed a massive accumulation of many metabolites such as glutamine, glutamic acid, lactate, and cyclic AMP (cAMP). In the meantime, methionine-starved pneumococci showed a lower intracellular pH and prolonged survival. Isotope tracing revealed that pneumococci depend predominantly on amino acid uptake to replenish intracellular glutamine but cannot convert glutamine to methionine. Further genetic and biochemical analyses strongly suggested that glutamine is involved in the formation of a "prosurvival" metabolic state by maintaining an appropriate intracellular pH, which is accomplished by the enzymatic release of ammonia from glutamine. Methionine starvation-induced intracellular pH reduction and glutamine accumulation also occurred to various extents under the limitation of other amino acids. These findings have uncovered a new metabolic mechanism of bacterial adaptation to amino acid limitation and perhaps other stresses, which may be used as a potential therapeutic target for infection control. IMPORTANCE Bacteria are known to cope with amino acid starvation by halting growth and prolonging survival via the stringent response signaling system. Previous investigations have allowed us to understand how the stringent response regulates many aspects of macromolecule synthesis and catabolism, but how amino acid starvation promotes bacterial survival at the metabolic level remains largely unclear. This paper reports our systematic profiling of the methionine starvation-induced metabolome in S. pneumoniae. To the best of our knowledge, this represents the first reported bacterial metabolome under amino acid starvation. These data have revealed that the significant accumulation of glutamine and lactate enables S. pneumoniae to form a "prosurvival" metabolic state with a lower intracellular pH, which inhibits bacterial growth for prolonged survival. Our findings have provided insightful information on the metabolic mechanisms of pneumococcal adaptation to nutrient limitation during the colonization of the human upper airway.

Response mechanisms to acid stress of acid-resistant bacteria and biotechnological applications in the food industry

Acid-resistant bacteria are more and more widely used in industrial production due to their unique acid-resistant properties. In order to survive in various acidic environments, acid-resistant bacteria have developed diverse protective mechanisms such as sensing acid stress and signal transduction, maintaining intracellular pH homeostasis by controlling the flow of H⁺, protecting and repairing biological macromolecules, metabolic modification, and cross-protection. Acid-resistant bacteria have broad biotechnological application prospects in the food field. The production of fermented foods with high acidity and acidophilic enzymes are the main applications of this kind of bacteria in the food industry. Their acid resistance modules can also be used to construct acid-resistant recombinant engineering strains for special purposes. However, they can also cause negative effects on foods, such as spoilage and toxicity. Herein, the aim of this paper is to summarize the research progress of molecular mechanisms against acid stress of acid-resistant bacteria. Moreover, their effects on the food industry were also discussed. It is useful to lay a foundation for broadening our understanding of the physiological metabolism of acid-resistant bacteria and better serving the food industry.

Microbial Electrosynthesis of Acetate Powered by Intermittent Electricity

Microbial electrosynthesis (MES) of acetate is a process using electrical energy to reduce CO₂ to acetic acid in an integrated bioelectrochemical system. MES powered by excess renewable electricity produces carbon-neutral acetate while benefitting from inexpensive but intermittent energy sources. Interruptions in electricity supply also cause energy limitation and starvation of the microbial cells performing MES. Here, we studied the effect of intermittent electricity supply on the performance of hydrogen-mediated MES of acetate. Thermoanaerobacter kivui produced acetic acid for more than 4 months from intermittent electricity supplied in 12 h on-off cycles in a semicontinuously-fed MES system. After current interruptions, hydrogen utilization and acetate synthesis rates were severely diminished. They did not recover to the steady-state rates of continuous MES within the 12 h current-on period under most conditions. Accumulating high product (acetate) concentration exacerbated this effect and prolonged recovery. However, supply of a low background current of 1-5% of the maximum current during "off-times" reduced the impact of current interruptions on subsequent MES performance. This study presents sustained MES at a rate of up to 2 mM h^-1 acetate at an average concentration of 60-90 mM by a pure thermophilic microbial culture powered by intermittent electricity. We identified product inhibition of accumulating acetic acid as a key challenge to improving the efficiency of intermittently powered MES.

Lactic acid bacteria: prominent player in the fight against human pathogens

INTRODUCTION

The human microbiome is a unique repository of diverse bacteria. Over 1000 microbial species reside in the human gut, which predominantly influences the host's internal environment and plays a significant role in host health. Lactic acid bacteria have long been employed for multiple purposes, ranging from food to medicines. Lactobacilli, which are often used in commercial food fermentation, have improved to the point that they might be helpful in medical applications.

AREAS COVERED

This review summarises various clinical and experimental evidence on efficacy of lactobacilli in treating a wide range of infections. Both laboratory based and clinical studies have been discussed.

EXPERT OPINION

Lactobacilli are widely accepted as safe biological treatments and host immune modulators (GRAS- Generally regarded as safe) by the US Food and Drug Administration and Qualified Presumption of Safety. Understanding the molecular mechanisms of lactobacilli in the treatment and pathogenicity of bacterial infections can help with the prediction and development of innovative therapeutics aimed at pathogens which have gained resistance to antimicrobials. To formulate effective lactobacilli based therapy significant research on the effectiveness of different lactobacilli strains and its association with demographic distribution is required. Also, the side effects of such therapy needs to be evaluated.

Differential Amino Acid Uptake and Depletion in Mono-Cultures and Co-Cultures of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus in a Novel Semi-Synthetic Medium

The mechanistic understanding of the physiology and interactions of microorganisms in starter cultures is critical for the targeted improvement of fermented milk products, such as yogurt, which is produced by Streptococcus thermophilus in co-culture with Lactobacillus delbrueckii subsp. bulgaricus. However, the use of complex growth media or milk is a major challenge for quantifying metabolite production, consumption, and exchange in co-cultures. This study developed a synthetic medium that enables the establishment of defined culturing conditions and the application of flow cytometry for measuring species-specific biomass values. Time courses of amino acid concentrations in mono-cultures and co-cultures of L. bulgaricus ATCC BAA-365 with the proteinase-deficient S. thermophilus LMG 18311 and with a proteinase-positive S. thermophilus strain were determined. The analysis revealed that amino acid release rates in co-culture were not equivalent to the sum of amino acid release rates in mono-cultures. Data-driven and pH-dependent amino acid release models were developed and applied for comparison. Histidine displayed higher concentrations in co-cultures, whereas isoleucine and arginine were depleted. Amino acid measurements in co-cultures also confirmed that some amino acids, such as lysine, are produced and then consumed, thus being suitable candidates to investigate the inter-species interactions in the co-culture and contribute to the required knowledge for targeted shaping of yogurt qualities.

Review of glucose oxidase as a feed additive: production, engineering, applications, growth-promoting mechanisms, and outlook

The regulation and prohibition of antibiotics used as growth promoters (AGP) in the feed field are increasing because they cause antimicrobial resistance and drug residue issues and threaten community health. Recently, glucose oxidase (GOx) has attracted increasing interest in the feed industry as an alternative to antibiotics. GOx specifically catalyzes the production of gluconic acid (GA) and hydrogen peroxide (H₂O₂) by consuming molecular oxygen, and plays an important role in relieving oxidative stress, preserving health, and promoting animal growth. To expand the application of GOx in the feed field, considerable efforts have been made to mine new genetic resources. Efforts have also been made to heterologously overexpress relevant genes to reduce production costs and to engineer proteins by modifying enzyme properties, both of which are bottleneck problems that limit industrial feed applications. Herein, the: different sources, diverse biochemical properties, distinct structural features, and various strategies of GOx engineering and heterologous overexpression are summarized. The mechanism through which GOx promotes growth in animal production, including the improvement of antioxidant capacity, maintenance of intestinal microbiota homeostasis, and enhancement of gut function, are also systematically addressed. Finally, a new perspective is provided for the future development of GOx applications in the feed field.

Microbial fuel cell compared to a chemostat

Microbial Fuel Cells (MFCs) represent a green and sustainable energy conversion system that integrate bacterial biofilms within an electrochemical two-electrode set-up to produce electricity from organic waste. In this review, we focus on a novel exploratory model, regarding "thin" biofilms forming on highly perfusable (non-diffusible) anodes in small-scale, continuous flow MFCs due to the unique properties of the electroactive biofilm. We discuss how this type of MFC can behave as a chemostat in fulfilling common properties including steady state growth and multiple steady states within the limit of biological physicochemical conditions imposed by the external environment. With continuous steady state growth, there is also continuous metabolic rate and continuous electrical power production, which like the chemostat can be controlled. The model suggests that in addition to controlling growth rate and power output by changing the external resistive load, it will be possible instead to change the flow rate/dilution rate.

Synthetic acid stress-tolerance modules improve growth robustness and lysine productivity of industrial Escherichia coli in fermentation at low pH

Background

During fermentation, industrial microorganisms encounter multiple stresses that inhibit cell growth and decrease fermentation yields, in particular acid stress, which is due to the accumulation of acidic metabolites in the fermentation medium. Although the addition of a base to the medium can counteract the effect of acid accumulation, the engineering of acid-tolerant strains is considered a more intelligent and cost-effective solution. While synthetic biology theoretically provides a novel approach for devising such tolerance modules, in practice it is difficult to assemble stress-tolerance modules from hundreds of stress-related genes.

Results

In this study, we designed a set of synthetic acid-tolerance modules for fine-tuning the expression of multi-component gene blocks comprising a member of the proton-consuming acid resistance system (gadE), a periplasmic chaperone (hdeB), and reactive oxygen species (ROS) scavengers (sodB and katE). Directed evolution was used to construct an acid-responsive asr promoter library, from which four variants were selected and used in the synthetic modules. The module variants were screened in a stepwise manner under mild acidic conditions (pH 5–6), first by cell growth using the laboratory Escherichia coli strain MG1655 cultured in microplates, and then by lysine production performance using the industrial lysine-producing E. coli strain MG1655 SCEcL3 cultured first in multiple 10-mL micro-bioreactors, and then in 1.3-L parallel bioreactors. The procedure resulted in the identification of a best strain with lysine titer and yield at pH 6.0 comparable to the parent strain at pH 6.8.

Conclusion

Our results demonstrate a promising synthetic-biology strategy to enhance the growth robustness and productivity of E. coli upon the mildly acidic conditions, in both a general lab strain MG1655 and an industrial lysine-producing strain SCEcL3, by using the stress-responsive synthetic acid-tolerance modules comprising a limited number of genes. This study provides a reliable and efficient method for achieving synthetic modules of interest, particularly in improving the robustness and productivity of industrial strains.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01795-4.

Alternatives to antibiotics for organic poultry production: types, modes of action and impacts on bird's health and production

The poultry industry contributes significantly to bridging the nutritional gap in many countries because of its meat and eggs products rich in protein and valuable nutrients at a cost less than other animal meat sources. The natural antibiotics alternatives including probiotics, prebiotics, symbiotics, organic acids, essential oils, enzymes, immunostimulants, and phytogenic (phytobiotic) including herbs, botanicals, essential oils, and oleoresins are the most common feed additives that acquire popularity in poultry industry following the ban of antibiotic growth promoters (AGPs). They are commonly used worldwide because of their unique properties and positive impact on poultry production. They can be easily mixed with other feed ingredients, have no tissue residues, improve feed intake, feed gain, feed conversion rate, improve bird immunity, improve digestion, increase nutrients availability as well as absorbability, have antimicrobial effects, do not affect carcass characters, decrease the usage of antibiotics, acts as antioxidants, anti-inflammatory, compete for stress factors and provide healthy organic products for human consumption. Therefore, the current review focuses on a comprehensive description of different natural antibiotic growth promoters' alternatives, the mode of their action, and their impacts on poultry production.

The effect of low-pH concrete on microbial community development in bentonite suspensions as a model for microbial activity prediction in future nuclear waste repository

Concrete as an important component of an engineered barrier system in deep geological repositories (DGR) for radioactive waste may come into contact with bentonite, or other clays, rich in indigenous microorganisms, with potentially harmful impacts on barrier integrity. Our study aimed to assess the effect of a concrete environment on indigenous bentonite and groundwater microbial communities as these particular conditions will select for the potentially harmful microorganisms to the concrete in the future DGR. The two-month experiment under anoxic conditions consisted of crushed, aged, low-pH concrete, Czech Ca-Mg bentonite, and anoxic groundwater, with control samples without concrete or with sterile groundwater. The microbial diversity and proliferation were estimated by qPCR and 16S rRNA gene amplicon sequencing. The presence of concrete had a strong effect on microbial diversity and reduced the increase in total microbial biomass, though low-pH concrete harbored indigenous bacteria. The growth of sulfate reducers was also limited in concrete samples. Several genera, such as Massilia, Citrifermentans, and Lacunisphaera, dominant in bentonite controls, were suppressed in concrete-containing samples. In contrast, genera such as Bacillus, Dethiobacter and Anaerosolibacter specifically proliferated in the presence of concrete. Genera such as Thermincola or Pseudomonas exhibited high versatility and proliferated well under both conditions. Because several of the detected bacterial genera are known to affect concrete integrity, further long-term studies are needed to estimate the effect of bentonite and groundwater microorganisms on concrete stability in future DGR.

Dual Antimicrobial Effect of Medium-Chain Fatty Acids against an Italian Multidrug Resistant Brachyspira hyodysenteriae Strain

The fastidious nature of Brachyspira hyodysenteriae limits an accurate in vitro pre-screening of conventionally used antibiotics and other candidate alternative antimicrobials. This results in a non-judicious use of antibiotics, leading to an exponential increase of the antibiotic resistance issue and a slowdown in the research for new molecules that might stop this serious phenomenon. In this study we tested four antibiotics (tylosin, lincomycin, doxycycline, and tiamulin) and medium-chain fatty acids (MCFA; hexanoic, octanoic, decanoic, and dodecanoic acid) against an Italian field strain of B. hyodysenteriae and the ATCC 27164 strain as reference. We determined the minimal inhibitory concentrations of these substances, underlining the multidrug resistance pattern of the field strain and, on the contrary, a consistent and stable inhibitory effect of the tested MCFA against both strains. Then, sub-inhibitory concentrations of antibiotics and MCFA were examined in modulating a panel of B. hyodysenteriae virulence genes (tlyA, tlyB, bhlp16, bhlp29.7, and bhmp39f). Results of gene expression analysis were variable, with up- and downregulations not properly correlated with particular substances or target genes. Decanoic and dodecanoic acid with their direct and indirect antimicrobial property were the most effective among MCFA, suggesting them as good candidates for subsequent in vivo trials.

Necrotic enteritis in chickens: a review of pathogenesis, immune responses and prevention, focusing on probiotics and vaccination

Necrotic enteritis (NE), caused by Clostridium perfringens (CP), is one of the most common of poultry diseases, causing huge economic losses to the poultry industry. This review provides an overview of the pathogenesis of NE in chickens and of the interaction of CP with the host immune system. The roles of management, nutrition, probiotics, and vaccination in reducing the incidence and severity of NE in poultry flocks are also discussed.

Biovalorization of Market Surplus Bread for Development of Probiotic-Fermented Potential Functional Beverages

Bread wastage is a growing concern in many developed countries. This research aimed to explore the biovalorization of market surplus bread for the development of probiotic-fermented beverages in a zero-waste approach. Bread slurries with different initial total solid contents were inoculated with probiotics Lacticaseibacillus rhamnosus GG (LGG) and Saccharomyces cerevisiae CNCM I-3856, alone and in combination. Our results showed that, of all percentages tested, 5% (w/w, dry weight) initial total solid content resulted in better growth of the probiotics and higher cell counts, while the texture of bread slurries with concentrations higher than 5.0% was too thick and viscous for bread beverage developments. In addition, the development of probiotic-fermented bread beverages was feasible on various types of bread. Furthermore, food additives (sweetener and stabilizer) did not affect the growth of LGG and S. cerevisiae CNCM I-3856 in both mono- and co-culture fermentation. During shelf life measurement, co-inoculation of LGG with S. cerevisiae CNCM I-3856 significantly improved the survival of LGG compared to the mono-culture at 5 and 30 °C, demonstrating the protective effects provided by the yeast. Our study suggests the potential of using market surplus bread as raw materials to deliver live probiotics with sufficient cell counts.

Antimicrobial Activity of a Vaginal Gel Formulation: Considerations Related to Vaginal Infection and Dysbiosis

Many non-prescription preparations intended to treat or alleviate symptoms of vaginal infection are available in American and European markets, but many have scant preclinical or clinical research underpinning. Respecta^®Balance Gel (RBG) is marketed as an adjunct to probiotic treatment and its relevant antimicrobial properties were studied. Key findings with the manufacturer-supplied gel showed reduced turbidity in broth-dilution tests by 50% against Candida albicans and Candida glabrata at RBG concentrations 0.2-0.4% of neat product, respectively. A 50% reduction in turbidity of Escherichia coli, Streptococcus agalactiae, Enterococcus faecalis ranged from 1.6-2.2% and Gardnerella vaginalis was shown by flow cytometry counts to undergo a 50% reduction at 0.3% RBG. Propidium iodide staining indicated a rapid reduction of cell integrity of G. vaginalis almost immediately while after 4 h 45% of E. coli cells were stained. The lactic acid in BHI inhibited bacteria and yeast at concentrations ranging from 0.2-1.8% but inhibition was not solely due to pH since a 1:4 dilution of RBG resulted in a pH near neutral (6.75). Other findings showed biofilm accumulation assessed after 10-days exposure of Candida spp. to RBG and was reduced by an average of one-third (community strains) to one-half (drug-resistant strains). One excipient of the RBG, disodium EDTA, inhibited the growth of bacteria and yeast at concentrations below those present in RBG and may accentuate the activity of the host defense factor, lactoferrin. We conclude that RBG is a potent inhibitor of vaginal microorganisms relevant to vaginitis or intrapartum infections and contains excipients that may contribute to its antimicrobial activity.

Advances in research on solid-state fermented feed and its utilization: The pioneer of private customization for intestinal microorganisms

With sustainable development of biotechnology, increasing attention has been placed on utilization of solid-state fermented feed (SFF). Solid-state fermented feed has been a candidate strategy to alleviate the contradiction between supply and demand of feed resources, ensure food hygiene safety, promoting energy conservation, and emission reduction. In production of SFF, a variety of organic acids, enzymes, vitamins, peptides, and other unknown growth factors are produced, which could affect performance of animals. Solid-state fermented feed produced by different fermentation techniques has great instability on different physiological stages of different animals, which hinders the application and standardized production of SFF. Herein, we summarize the current advances in the role of the characteristics of SFF prepared by different manufacturing technique and its research progress in animal experiments on growth performance, gastrointestinal ecology, and immune system, so as to provide references for further acquiring a relatively perfect set of SFF production and evaluation systems.

Predictive Monitoring of Shake Flask Cultures with Online Estimated Growth Models

Simplicity renders shake flasks ideal for strain selection and substrate optimization in biotechnology. Uncertainty during initial experiments may, however, cause adverse growth conditions and mislead conclusions. Using growth models for online predictions of future biomass (BM) and the arrival of critical events like low dissolved oxygen (DO) levels or when to harvest is hence important to optimize protocols. Established knowledge that unfavorable metabolites of growing microorganisms interfere with the substrate suggests that growth dynamics and, as a consequence, the growth model parameters may vary in the course of an experiment. Predictive monitoring of shake flask cultures will therefore benefit from estimating growth model parameters in an online and adaptive manner. This paper evaluates a newly developed particle filter (PF) which is specifically tailored to the requirements of biotechnological shake flask experiments. By combining stationary accuracy with fast adaptation to change the proposed PF estimates time-varying growth model parameters from iteratively measured BM and DO sensor signals in an optimal manner. Such proposition of inferring time varying parameters of Gompertz and Logistic growth models is to our best knowledge novel and here for the first time assessed for predictive monitoring of Escherichia coli (E. coli) shake flask experiments. Assessments that mimic real-time predictions of BM and DO levels under previously untested growth conditions demonstrate the efficacy of the approach. After allowing for an initialization phase where the PF learns appropriate model parameters, we obtain accurate predictions of future BM and DO levels and important temporal characteristics like when to harvest. Statically parameterized growth models that represent the dynamics of a specific setting will in general provide poor characterizations of the dynamics when we change strain or substrate. The proposed approach is thus an important innovation for scientists working on strain characterization and substrate optimization as providing accurate forecasts will improve reproducibility and efficiency in early-stage bioprocess development.

Analysis of six tonB gene homologs in Bacteroides fragilis revealed that tonB3 is essential for survival in experimental intestinal colonization and intra-abdominal infection

The opportunistic, anaerobic pathogen and commensal of the human large intestinal tract, Bacteroides fragilis strain 638R, contains six predicted TonB proteins, termed TonB1-6, four ExbBs orthologs, ExbB1-4, and five ExbDs orthologs, ExbD1-5. The inner membrane TonB/ExbB/ExbD complex harvests energy from the proton motive force (Δp) and the TonB C-terminal domain interacts with and transduces energy to outer membrane TonB-dependent transporters (TBDTs). However, TonB's role in activating nearly one hundred TBDTs for nutrient acquisition in B. fragilis during intestinal colonization and extraintestinal infection has not been established. In this study, we show that growth was abolished in the ΔtonB3 mutant when heme, vitamin B12, Fe(III)-ferrichrome, starch, mucin-glycans, or N-linked glycans were used as a substrate for growth in vitro. Genetic complementation of the ΔtonB3 mutant with the tonB3 gene restored growth on these substrates. The ΔtonB1, ΔtonB2, ΔtonB4, ΔtonB5, and ΔtonB6 single mutants did not show a growth defect. This indicates that there was no functional compensation for the lack of TonB3, and it demonstrates that TonB3, alone, drives the TBDTs involved in the transport of essential nutrients. The ΔtonB3 mutant had a severe growth defect in a mouse model of intestinal colonization compared to the parent strain. This intestinal growth defect was enhanced in the ΔtonB3 ΔtonB6 double mutant strain which completely lost its ability to colonize the mouse intestinal tract compared to the parent strain. The ΔtonB1, ΔtonB2, ΔtonB4, and ΔtonB5 mutants did not significantly affect intestinal colonization. Moreover, the survival of the ΔtonB3 mutant strain was completely eradicated in a rat model of intra-abdominal infection. Taken together, these findings show that TonB3 was essential for survival in vivo. The genetic organization of tonB1, tonB2, tonB4, tonB5, and tonB6 gene orthologs indicates that they may interact with periplasmic and nonreceptor outer membrane proteins, but the physiological relevance of this has not been defined. Because anaerobic fermentation metabolism yields a lower Δp than aerobic respiration and B. fragilis has a reduced redox state in its periplasmic space - in contrast to an oxidative environment in aerobes - it remains to be determined if the diverse system of TonB/ExbB/ExbD orthologs encoded by B. fragilis have an increased sensitivity to PMF (relative to aerobic bacteria) to allow for the harvesting of energy under anaerobic conditions.