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PubMed1977

Computer-aided baker's yeast fermentations.

The economics of yeast production depend heavily upon the cellular yield coefficient on the carbon source and the volumetric productivity of the process. The application of an on-line computer to maximize these two terms during the fermentation requires a continuous method of measuring cell density and growth rate. Unfortunately, a direct sensor for biomass concentration suitable for use in industrial fermentations is not available. Material balancing, with the aid of on-line computer monitoring, offers an indirect method of measurement. Laboratory results from baker's yeast production in a 14-liter fermentor (with a PDP-11/10 computer for on-line analyses) show this indirect measurement technique to be a viable alternative. From the oxygen uptake and carbon dioxide production data, gas flow rate, and ammonia addition rate, the cell density during the fermentation has been estimated and found to compare well with actual fermentation data.

Ammonia↗

PubMed1979

Application of balancing methods in modeling the penicillin fermentation.

This paper shows the application of elementary balancing methods in combination with simple kinetic equations in the formulation of an unstructured model for the fed-batch process for the production of penicillin. The rate of substrate uptake is modeled with a Monod-type relationship. The specific penicillin production rate is assumed to be a function of growth rate. Hydrolysis of penicillin to penicilloic acid is assumed to be first order in penicillin. In simulations with the present model it is shown that the model, although assuming a strict relationship between specific growth rate and penicillin productivity, allows for the commonly observed lag phase in the penicillin concentration curve and the apparent separation between growth and production phase (idiophase-trophophase concept). Furthermore it is shown that the feed rate profile during fermentation is of vital importance in the realization of a high production rate throughout the duration of the fermentation. It is emphasized that the method of modeling presented may also prove rewarding for an analysis of fermentation processes other than the penicillin fermentation.

Chemical Phenomena↗

PubMed2026

Integrated ¹H-NMR Metabolomics and Growth Kinetics Uncover Three Distinct Metabolic Scenarios in Lactiplantibacillus pentosus P7 Fermentation of Plant-Derived Prebiotics.

Lactic acid bacteria (LAB) drive a broad range of food and biotechnological fermentations, the outcomes of which depend not only on the bacterial genotype but also on the chemical composition of the fermentation substrate. To resolve how a single strain reorganises chemically distinct plant matrices, we profiled fermentations of Lactiplantibacillus pentosus P7 (GenBank JBLMKZ000000000) on garlic, onion, and kiwifruit extracts prepared in water and 70% ethanol, using growth kinetics combined with solvent-suppressed 500-MHz proton nuclear magnetic resonance metabolomics over 48 h, and integrated the data with whole-genome pathway annotations. Three substrate-specific metabolic scenarios emerged. On garlic, P7 grew vigorously, with the water extract exceeding the de Man-Rogosa-Sharpe reference medium at every time point (peak ΔOD₆₀₀ of 9.38 versus 8.52 at 24 h) and accumulating sorbose, rhamnose, and the aromatic amino acids phenylalanine and tryptophan (3.04- to 3.70-fold increases), providing first metabolic evidence consistent with the strain's four-copy aroE shikimate-dehydrogenase expansion. On onion, the lowest cell density coincided with the highest lactate output of the dataset (5.21-fold rise at 48 h), transient 5-hydroxymethylfurfural reduction, and accumulation of acetoin and 1,3-propanediol, mapping onto a redundant set of pyridine-nucleotide-dependent oxidoreductases and a pdu-independent diol pathway. On kiwifruit, citrate accumulated 8.9-fold at 16 h and then declined, consistent with an intact citCDEFG citrate-lyase operon paired with absence of canonical oxidative tricarboxylic acid enzymes. The optimal extraction solvent was substrate-dependent, water for garlic and ethanol for onion and kiwifruit. Overall, these results show that substrate chemistry, rather than strain identity, dictates which genome-encoded pathways P7 engages, establishing P7 as a versatile, substrate-tunable platform for the functional fermentation and biorefining of furanic-rich substrate streams. Raw NMR data and ISA-Tab metadata are available via MetaboLights with identifier MTBLS14463.

Lactiplantibacillus pentosus↗

PubMed2026

Adaptive laboratory evolution enables carbon-negative mixotrophic fermentation and enhanced chain elongation in Clostridium sp. JS66.

Improving carbon recovery during sugar fermentation remains a major challenge because a substantial fraction of substrate carbon is lost as CO2 during central metabolism. To overcome this limitation, Clostridium sp. JS66 (JS66), an acetogen producing hexanoic acid from glucose, was subjected to adaptive laboratory evolution under autotrophic CO2/H2 conditions to enhance H2-assisted CO2 reassimilation during glucose fermentation. The evolved strain, ALECO2, exhibited CO2 consumption without a lag phase under autotrophic conditions and reached a 9.5-fold higher CO2 uptake rate than JS66. Under fed-batch mixotrophic conditions, glucose-only fermentation yielded a carbon molar yield (Cmetabolite/Csugar, CM/CS) of 0.60, whereas H2 supplementation increased CM/CS to 0.91 and redirected carbon flux toward C6 products (hexanoic acid and hexanol), which accounted for 49% of total C_output. With additional CO2 supplementation, ALECO2 further assimilated externally supplied CO2, increasing the CM/CS to 1.10 and demonstrating carbon-negative fermentation. Assimilation of externally supplied CO2 further redirected carbon flux toward chain elongation, producing 7.14 g/L hexanoic acid and increasing the C6 carbon fraction to 57% of total C_output. Constraint-based flux analysis supported increased acetyl-CoA formation through the Wood-Ljungdahl pathway and enhanced flux toward reverse β-oxidation under H2- and CO2/H2-supplemented conditions. Genome analysis identified mutations including genes encoding a putative HytB homolog and a LysR-type transcriptional regulator. These results establish ALECO2 as a promising evolved anaerobic non-photosynthetic (ANP) mixotrophy platform that links CO2 reassimilation and external CO2 assimilation with chain elongation, enabling carbon-neutral and carbon-negative production of value-added C6 products from glucose.

Anaerobic non-photosyntheticmixotrophy (ANP)↗

PubMed2026

Integrated GC-HRAM-MS and UHPLC-QTOF-MS metabolomics reveal mineral-induced metabolic adaptation of Lactiplantibacillus pentosus 9D3 during milk fermentation.

Milk fermentation by plant-associated probiotic strains is constrained by poor adaptation to dairy matrices. This study evaluated genome-guided micronutrient supplementation to improve the performance and metabolomic profile of Lactiplantibacillus pentosus 9D3 in milk. Individual supplementation with Mn2+ or Mg2+ significantly enhanced bacterial growth and acidification, whereas Fe2+, Zn2+, and B-group vitamins showed limited effects. Optimal supplementation with 50 mg/L Mn2+ and 100 mg/L Mg2+ increased viable counts from 7.54 to 8.89 log CFU/mL. A cell population increase of ∼1.9 log CFU/mL was achieved despite reducing the inoculum level from 10% to 6%. Integrated metabolomic profiling using GC-HRAM-MS and UHPLC-QTOF-MS identified 299 metabolites across supplemented fermented milk, non-supplemented fermented milk, and unfermented milk, with group separation. Pathway analysis revealed significant enrichment of seven metabolic pathways, including purine, pyrimidine, galactose, propanoate, butanoate, amino sugar and nucleotide sugar, and α-linolenic acid metabolism. These findings support cost-efficient precision fermentation of functional dairy products.

Dairy products↗

PubMed2026

Multi-omics insights into aroma formation in congou black tea during fermentation.

This study used multi-omics technologies to analyze aroma formation during Congou black tea fermentation. Volatile compounds were analyzed by headspace solid phase microextraction coupled with gas chromatography mass spectrometry using two columns of different polarity. Fermentation increased total volatile normalized peak area fivefold, with alcohols, aldehydes, and acids increasing over sevenfold. 29 differential metabolites were screened, including amino acid derived phenylacetaldehyde, phenylethanol, and 2-methylbutanal; fatty acid derived (E,E)-2,4-heptadienal, hexanal, and 1-hexanol; and isoprenoid derived linalool, geraniol, and beta ionone. Transcriptomic, proteomic, and enzyme analyses revealed that biosynthesis contributed to early accumulation of amino acid and isoprenoid derived aromas, whereas ortho quinone mediated Strecker degradation and free radical induced fatty acid auto oxidation dominated generation of amino and fatty acid derived aromas during middle and late fermentation. In conclusion, aroma formation during fermentation results from biosynthesis and non-enzymatic oxidation, with the latter possibly dominating amino and fatty acid derived aromas.

Fermentation↗

PubMed1978

Injury to Staphylococcus aureus during sausage fermentation.

Staphylococcus aureus 196E added to a beef sausage containing starter culture and 0.5 to 2.0% glucose and incubated at 35 degrees C was unable to grow when plated on tryptic soy agar (TSA) containing 7.5% NaCl. The injury, presumed to be due to the lactic acid produced during fermentation, was more pronounced at the lower concentrations of glucose (and lower acid levels). In the absence of glucose and/or starter culture, no injury was observed. When sausages containing S. aureus injured by fermentation at 35 degrees C were incubated at 5 degrees C, the counts on TSA (measures both injured and uninjured cells) and TSA containing 7.5% NaCl (measures uninjured cells only) remained constant; however, upon reincubation of the cold-stored sausage at 35 degrees C, the staphylococcus counts on TSA and TSA containing 7.5% NaCl and were similar to the counts of S. aureus present in fermenting sausages that had never been subjected to 5 degrees C. The demonstration of acid injury indicated that the injury phenomenon must be considered when determining numbers of viable S. aureus in fermented sausages.

Animals↗

PubMed1979

Xylose, arabinose, and rhamnose fermentation by Bacteroides ruminicola.

Metabolism and growth yields of Bacteroides ruminicola grown on d-xylose, l-arabinose, and l-rhamnose were studied. Growth yields were 62, 68, and 35.5 g (dry weight) per mol of carbohydrate fermented after correction for storage polysaccharide. Experiments with [1-(14)C]arabinose indicated that pentose was fermented by a pentose phosphate cycle plus glycolysis, with some indication of a minor phosphoketolase-type pathway. The product ratios from pentose were similar to those previously described for hexose. Rhamnose was fermented mainly to 1,2-propanediol, succinate, and acetate, although the latter was quantitatively less than expected. Estimates of adenosine 5'-triphosphate (ATP) molar growth yields could not be calculated with any certainty, as ATP generation by electron transport-linked phosphorylation cannot yet be assessed. If ATP were generated by substrate-level phosphorylation reactions alone, ATP molar growth yields for xylose, arabinose, and rhamnose would be 30, 28, and 35 g/mol. If calculations are based on an assumption that two ATP are generated by electron transport-linked phosphorylation per succinate, ATP molar growth yields become 15, 14, and 22 g/mol; if the assumption is also made that the pathway of lactaldehyde reduction is coupled to production of one ATP per 1,2-propanediol by electron transport-linked phosphorylation, the ATP molar growth yield for rhamnose fermentation becomes 14 g/mol. No preference can be expressed between these alternatives at present.

Adenosine Triphosphate↗

PubMed2026

Biocontrol effect of a solid-state fermentation-derived extract mixture of Trichoderma asperellum on sunflower Sclerotinia rot and associated host defense responses.

Sclerotinia disease is a destructive fungal disease of sunflowers, soybeans, and other economically important crops, causing substantial yield loss and quality deterioration. Long-term reliance on dose-dependent broad-spectrum fungicides is constrained by resistance risks and potential environmental burdens, creating tension with the sustainability goal of "reducing pesticide use while improving efficacy." Here, we explore a Trichoderma spp.-based microbial disease management strategy. Whole-genome sequencing of Trichoderma asperellum TCS007 isolated from Antarctic marine sediments, coupled with genome mining, predicted diverse biosynthetic gene clusters putatively associated with siderophores, polyketides, nonribosomal peptides, and terpenoids; the corresponding metabolites are not chemically confirmed and require further validation. Using a solid-state fermentation workflow, we prepared a fermentation-derived extract mixture (TCS007-SSF-Ex). In vitro assays showed dose-dependent inhibition of Sclerotinia sclerotiorum by TCS007-SSF-Ex (EC50 = 1.252 mg/L), and microscopy revealed cellular damage-consistent changes, including organelle disruption and plasmolysis. Pathogen transcriptomic and metabolism-related analyses indicated broad perturbations in organelle biogenesis and metabolic processes, with significant alterations in pathways associated with succinate, D-glucose, and phenylacetate; these results are consistent with growth inhibition and reduced pathogenicity, but specific molecular targets and causal links remain to be validated. In vivo, under certain application conditions, triple applications increased APX activity (+492.5%) and β-1,3-glucanase activity (+419.6%). Collectively, this work supports a "pathogen suppression-host defense induction" framework and facilitates subsequent identification of active components and mechanistic validation.IMPORTANCESclerotinia diseases cause recurrent and economically important losses in oilseed crops, while long-term fungicide use is constrained by resistance risks and environmental burdens. Trichoderma-based biocontrol is a promising complementary strategy, yet evidence supporting metabolite-containing Trichoderma-derived preparations as immune elicitors remains less consolidated than that for living inoculants, and scalable production routes are still needed. Here, we examine an Antarctic marine sediment-derived strain, Trichoderma asperellum TCS007, and a solid-state fermentation (SSF)-derived extract mixture (TCS007-SSF-Ex) produced via solid-state fermentation. We combine in vitro antifungal assays, pathogen ultrastructural observations, and correlative omics analyses with in vivo measurements of sunflower defense enzymes (APX and β-1,3-glucanase) to evaluate a "pathogen suppression-host defense induction" framework. Our findings support the potential of SSF-derived Trichoderma metabolite mixtures for greener management of Sclerotinia disease and provide a foundation for future chemical identification of active components and mechanistic validation.

Ascomycota↗

PubMed1976

The fermentative production of acetone-butanol by Clostridium acetobutylicum.

Fourteen different media were used in the fermentative production of acetone-butanol. The highest total yields were achieved in medium I. Potato starch and soluble starch were suitable as carbon sources. The best concentrations of potato starch and soluble starch were 500.0 and 10.0 g/l, respectively. Peptone was the most favourable nitrogen source. The best concentration of peptone was 4.0 g/l. Calcium carbonate in 3.6 g/l acted as buffering agent in the fermentation process. The best initial pH value of the fermentation medium was 6.0. The optimum temperature was 32--33degreesC. The fermentation process required 120 h to obtain maximum yields of acetone-butanol.

Acetone↗

PubMedDate not supplied

[The various functions of steroids on the yeast metabolism in grape must during fermentation: the notion of survival factor (author's transl)].

The physiological effects of steroids supplied to the yeasts in grape must is complicated. These substances may function as inhibitors, as growth factors or survival factors. The steroids have a "survival factor" action when they act on aerobically cultivated yeasts, fermenting under anaerobic conditions, in grape must of high sugar concentration. In this case, the substances have no effect on the cellular multiplication but they maintain viability and fermentation activity in the resting cells. Consequently, a greater quantity of sugar is consumed and the content of secondary products is modified by the end of the fermentation. Certain growth conditions during fermentation affect the survival factor action of steroids: high temperature, low pH, vitamin deficiency, low amount of inoculum, insufficient aeration, excessive sugar concentration.

Aerobiosis↗

PubMedDate not supplied

[Effect of prolonged, continuous fermentation on the morphology and physiology of fixed yeasts].

As a result of long continuous fermentation of brewing wort by fixed yeast cells, the number of cells in the fermenter increased as well as their wet weight. The average dimensions of cells (length, width, volume) also increased. The length-to-width ratio of cells decreased. The fermenting activity decreased if calculated per wet weight but remained at the same level if calculated per cell. The overall productiveness of the fermenter with a carrier increased in proportion to the number of cells but not to their weight. The morphological and physiological properties of yeast cells changed as compared to the original ones.

Beer↗

PubMed1976

Pyruvate fermentation in Rhodospirillum rubrum and after transfer from aerobic to anaerobic conditions in the dark.

The fermentative metabolism of Rhodospirillum rubrum (strain Ha, F1, S1) was studied after transfering the cells from aerobic to anaerobic dark culture conditions. Pyruvate was metabolized mainly to acetate and formate, and to a lesser extent to CO2 and priopionate, by all strains. Therefore, pyruvate formate lyase would appear to be the characteristic key enzyme of the dark anaerobic fermentation metabolism in R. rubrum. Strain F1 and S1 metabolized the formate further to H2 and CO2. It is concluded that this cleavage was catalysed by a formate hydrogen lyase system. Strain Ha was unable to metabolize formate. The cleavage of formate and the synthesis of poly-beta-hydroxy-butyric acid were increased by a low pH value (approximately 6.5). Fermentation equations and schemes of the pyruvate metabolism are discussed.

Acetates↗

PubMed1977

Effect of the petite mutation on maltose and alpha-methylgucoside fermentation inSaccharomyces cerevisiae.

Several hundred petite mutants were isolated from yeast strains of different genotype to examine the effect of the petite mutation on maltose and alpha-methylglucoside fermentation. In most cases petite mutants isolated retain the ability to ferment maltose and alpha-methylglucoside, although at a slower rate. In one strain (1403-7A), however, the ability to ferment alpha-methylglucoside is completely lost in all petite mutants isolated from this strain. It is suggested that mitochondrial factors may be involved in the utilization of alpha-methylglucoside in strain 1403-7A.

Erythromycin↗

PubMed2026

Liquid fermentation and an adapted cetyltrimethylammonium bromide (CTAB) method enable sequencing-grade DNA extraction from Phanerodontia australis.

High-quality genomic DNA extraction from basidiomycete fungi remains challenging due to polysaccharide co-purification and nuclease-mediated DNA degradation. We systematically compared 22 experimental conditions combining five DNA extraction methods (one Dellaporta-based method, three CTAB-based variants, and one commercial kit) with five mycelium preparation techniques (scalpel scraping, fungal suspension, silica bead homogenization, liquid fermentation, and liquid nitrogen treatment) for Phanerodontia australis (BRM62389). DNA quality was assessed by 1% agarose gel electrophoresis, NanoDrop spectrophotometry, and Qubit fluorimetry. The optimal protocol combined liquid-fermentation mycelium with an adapted CTAB method, yielding Qubit-quantified concentrations of 34.2 and 62.6 ng/µL (samples S21 and S22), 260/280 ratios of 2.06 and 2.05, 260/230 ratios of 1.88 and 1.85, and no detectable DNA degradation by agarose gel electrophoresis. This protocol enabled whole-genome sequencing, yielding a 37.62 Mb assembly with 98.5% completeness as assessed by BUSCO v5 (basidiomycota_odb10 lineage dataset, n = 1,764). Liquid fermentation is associated with the production of younger, actively growing hyphae with reduced cell wall thickness, and the adapted CTAB method effectively removed residual polysaccharides. This protocol provides a reliable, cost-effective approach for obtaining sequencing-grade DNA from P. australis.

Basidiomycota↗

PubMed2026

A black soybean yoghurt fermented with a reusable probiotic cellulose gel: beneficial effects and metabolic characteristics.

The demand for plant-based yoghurts is continuously increasing. However, achieving stable physicochemical properties and acceptable flavor of the plant-based yoghurts remains challenging. In our previous work, we encapsulated Lactiplantibacillus plantarum (L. plantarum) LCC-605 biofilm into bacterial cellulose (BC), obtaining a LP605@BC gel. LP605@BC gel exhibited excellent harsh-environment resistance abilities and storage stability, and is very suitable as a starter culture. In this work, we used LP605@BC as a starter culture to prepare the fermented plant-based yoghurt (e.g., black soybean yoghurt, BSY-LP605@BC). After fermentation, the inverted nonflowing yoghurt was formed due to the strong interaction between protein and exopolysaccharide (EPS) produced by LCC-605 during fermentation. In addition, the water holding capacity (67.2%) of BSY-LP605@BC was also greatly improved. The viable bacterial counts in BSY-LP605@BC reached 11.2 log CFU/mL after 21 days of storage. BSY-LP605@BC showed increased antioxidant, cholesterol-lowering abilities, and hypoglycemic potential compared with the unfermented black soybean milk. Interestingly, LP605@BC could be reused at least 5 times, demonstrating excellent sustainability. Significant metabolomic differences between BSY-LP605@BC and the black soybean milk were observed via untargeted metabolomic analysis, further proving the beneficial effects of BSY-LP605@BC. Overall, our work developed an effective reusable starter culture for preparing the plant-based yoghurt in a sustainable manner, providing a new design direction and form of starter culture.

Yogurt↗

PubMed2026

Insights into the mechanism of enhanced tetramethylpyrazine production in dehulled adlay fermented by Bacillus subtilis BJ3-2.

Tetramethylpyrazine (TTMP) is a vital bioactive alkaloid and characteristic flavor compound in fermented foods. Our previous study found that fermentation of adlay by Bacillus subtilis BJ3-2 efficiently accumulates TTMP, whereas the underlying high-yield mechanism remains unclear. This study investigated the fermentation characteristics, gene transcription and protein expression of B. subtilis BJ3-2 in dehulled adlay (BDA) and soybean (BSB), respectively, and elucidated the mechanism responsible for high-yield TTMP production. The results showed that glutamate, leucine and phenylalanine were major free amino acids in BDA. The TTMP yield in BDA at 48 h (6.11 mg/g dry weight) was 360-fold higher than that in BSB. Transcriptomic and proteomic analysis demonstrated that compared with the soybean substrate, dehulled adlay substrate significantly up-regulated the expression of alsSD and ilvBH genes and their encoding proteins in B. subtilis BJ3-2, which were involved in C5-branched dibasic acid metabolism, 2-oxocarboxylic acid metabolism, and valine, leucine and isoleucine biosynthesis. Meanwhile, acetoin degradation was inhibited by down-regulating acetoin dehydrogenase complex (acoABCL) in citrate cycle, glycolysis/gluconeogenesis and carbon metabolism. Additionally, nitrogen metabolism pathway was transcriptionally enhanced to guarantee sufficient ammonium supply. Notably, protein-protein interaction and molecular docking analyses revealed that acetohydroxyacid synthase (ilvBH) interacted tightly with α-acetolactate decarboxylase (alsD), potentially forming a metabolic channel for acetoin synthesis. In conclusion, the efficient synthesis of TTMP in BDA was primarily attributed to the high synthesis and low degradation of acetoin, and the moderate synthesis of ammonium/ammonia. This study provided a theoretical basis for the targeted and efficient biosynthesis of TTMP.

Bacillus subtilis↗

PubMed1977

Fermentation of cellulose by Ruminococcus flavefaciens in the presence and absence of Methanobacterium ruminantium.

The anaerobic cellulolytic rumen bacterium Ruminococcus flavefaciens normally produces succinic acid as a major fermentation product together with acetic and formic acids, H2, and CO2. When grown on cellulose and in the presence of the methanogenic rumen bacterium Methanobacterium ruminantium, acetate was the major fermentation product; succinate was formed in small amounts; little formate was detected; H2 did not accumulate; and large amounts of CH4 were formed. M. ruminantium depends for growth on the reduction of CO2 to CH4 by H2, which it can obtain directly or by producing H2 and CO2 from formate. In mixed culture, the methanobacterium utilized the H2 and possibly the formate produced by the ruminococcus and in so doing stimulated the flow of electrons generated during glycolysis by the ruminococcus toward H2 formation and away from formation of succinate. This type of interaction may be of significance in determining the flow of cellulose carbon to the normal rumen fermentation products.

Acetates↗