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The mixed acid fermentation pathway in E. coli.[1][2] End products are highlighted in blue.

In biochemistry, mixed acid fermentation is the metabolic process by which a six-carbon sugar (e.g. glucose, C6H12O6) is converted into a complex and variable mixture of acids. It is a fermentation reaction that is common in bacteria. It is characteristic for members of the Enterobacteriaceae, a large family of Gram-negative bacteria that includes E. coli.[3]

The mixture of end products produced by mixed acid fermentation includes lactate, acetate, succinate, formate, ethanol and the gases H2 and CO2. The formation of these end products depends on the presence of certain key enzymes in the bacterium. The proportion in which they are formed varies between different bacterial species.[4] The mixed acid fermentation pathway differs from other fermentation pathways, which produce fewer end products in fixed amounts. The end products of mixed acid fermentation can have many useful applications in biotechnology and industry. For instance, ethanol is widely used as a biofuel.[5] Therefore, multiple bacterial strains have been metabolically engineered in the laboratory to increase the individual yields of certain end products.[2] This research has been carried out primarily in E. coli and is ongoing. Variations of mixed acid fermentation occur in a number of bacterial species, including bacterial pathogens such as Haemophilus influenzae where mostly acetate and succinate are produced and lactate can serve as a growth substrate.[6]

Mixed acid fermentation in E. coli

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E. coli use fermentation pathways as a final option for energy metabolism, as they produce very little energy in comparison to respiration.[7] Mixed acid fermentation in E. coli occurs in two stages. These stages are outlined by the biological database for E. coli, EcoCyc.[1]

The first of these two stages is a glycolysis reaction. Under anaerobic conditions, a glycolysis reaction takes place where glucose is converted into pyruvate:

glucose → 2 pyruvate

There is a net production of 2 ATP and 2 NADH molecules per molecule of glucose converted. ATP is generated by substrate-level phosphorylation. NADH is formed from the reduction of NAD.

In the second stage, pyruvate produced by glycolysis is converted to one or more end products via the following reactions. In each case, both of the NADH molecules generated by glycolysis are reoxidized to NAD+. Each alternative pathway requires a different key enzyme in E. coli. After the variable amounts of different end products are formed by these pathways, they are secreted from the cell.[1]

The conversion of pyruvate to lactate is catalysed by the enzyme lactate dehydrogenase.

Lactate formation

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Pyruvate produced by glycolysis is converted to lactate. This reaction is catalysed by the enzyme lactate dehydrogenase (LDHA).[1]

pyruvate + NADH + H+ → lactate + NAD+

Acetate formation

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Pyruvate is converted into acetyl-coenzyme A (acetyl-CoA) by the enzyme pyruvate dehydrogenase. This acetyl-CoA is then converted into acetate in E. coli, whilst producing ATP by substrate-level phosphorylation. Acetate formation requires two enzymes: phosphate acetyltransferase and acetate kinase.[1]

The mixed acid fermentation pathway is characteristic of the family Enterobacteriaceae, which includes E. coli
acetyl-CoA + phosphate → acetyl-phosphate + CoA
acetyl-phosphate + ADP → acetate + ATP

Ethanol formation

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Ethanol is formed in E. coli by the reduction of acetyl coenzyme A using NADH. This two-step reaction requires the enzyme alcohol dehydrogenase (ADHE).[1]

acetyl-CoA + NADH + H+ → acetaldehyde + NAD+ + CoA
acetaldehyde + NADH + H+ → ethanol + NAD+

Formate formation

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Formate is produced by the cleavage of pyruvate. This reaction is catalysed by the enzyme pyruvate-formate lyase (PFL), which plays an important role in regulating anaerobic fermentation in E. coli.[8]

pyruvate + CoA → acetyl-CoA + formate

Succinate formation

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Skeletal structure of succinate

Succinate is formed in E. coli in several steps.

Phosphoenolpyruvate (PEP), a glycolysis pathway intermediate, is carboxylated by the enzyme PEP carboxylase to form oxaloacetate.[9] This is followed by the conversion of oxaloacetate to malate by the enzyme malate dehydrogenase. Fumarate hydratase then catalyses the dehydration of malate to produce fumarate.[10]

phosphoenolpyruvate + HCO3 → oxaloacetate + phosphate
oxaloacetate + NADH + H+ → malate + NAD+
malate → fumarate + H2O

The final reaction in the formation of succinate is the reduction of fumarate. It is catalysed by the enzyme fumarate reductase.

fumarate + NADH + H+ → succinate + NAD+

This reduction is an anaerobic respiration reaction in E. coli, as it uses electrons associated with NADH dehydrogenase and the electron transport chain. ATP is generated by using an electrochemical gradient and ATP synthase. This is the only case in the mixed acid fermentation pathway where ATP is not produced via substrate-level phosphorylation.[1][2]

Vitamin K2, also known as menaquinone, is very important for electron transport to fumarate in E. coli.[11]

Hydrogen and carbon dioxide formation

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Formate can be converted to hydrogen gas and carbon dioxide in E. coli. This reaction requires the enzyme formate-hydrogen lyase. It can be used to prevent the conditions inside the cell becoming too acidic.[1]

formate → H2 and CO2

Methyl red test

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Methyl red test: The test tube on the left shows a positive result as acidic end products are formed by mixed acid fermentation in E. coli. The test tube on the right shows a negative result as no acidic products are formed by fermentation.

The methyl red (MR) test can detect whether the mixed acid fermentation pathway occurs in microbes when given glucose. A pH indicator is used that turns the test solution red if the pH drops below 4.4.[12] If the fermentation pathway has taken place, the mixture of acids it has produced will make the solution very acidic and cause a red colour change.

The methyl red test belongs to a group known as the IMViC tests.

Metabolic engineering

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Multiple bacterial strains have been metabolically engineered to increase the individual yields of end products formed by mixed acid fermentation. For instance, strains for the increased production of ethanol, lactate, succinate and acetate have been developed due to the usefulness of these products in biotechnology.[2] The major limiting factor for this engineering is the need to maintain a redox balance in the mixture of acids produced by the fermentation pathway.[13]

For ethanol production

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Ethanol is the most commonly used biofuel and can be produced on large scale via fermentation. The maximum theoretical yield for the production of ethanol was achieved around 20 years.[14][15] A plasmid that carried the pyruvate decarboxylase and alcohol dehydrogenase genes from the bacteria Z. mobilis was used by scientists. This was inserted into E. coli and resulted in an increased yield of ethanol. The genome of this E. coli strain, KO11, has more recently been sequenced and mapped.[16]

The skeletal formula of polylactic acid
Teabags made from polylactic acid (PLA)

For acetate production

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The E. coli strain W3110 was genetically engineered to generate 2 moles of acetate for every 1 mole of glucose that undergoes fermentation. This is known as a homoacetate pathway.[17]

For lactate production

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Lactate can be used to produce a bioplastic called polylactic acid (PLA). The properties of PLA depend on the ratio of the two optical isomers of lactate (D-lactate and L-lactate). D-lactate is produced by mixed acid fermentation in E. coli.[18] Early experiments engineered the E. coli strain RR1 to produce either one of the two optical isomers of lactate.[19]

Later experiments modified the E. coli strain KO11, originally developed to enhance ethanol production. Scientists were able to increase the yield of D-lactate from fermentation by performing several deletions.[20]

For succinate production

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Increasing the yield of succinate from mixed acid fermentation was first done by overexpressing the enzyme PEP carboxylase.[21] This produced a succinate yield that was approximately 3 times greater than normal. Several experiments using a similar approach have followed.

Alternative approaches have altered the redox and ATP balance to optimize the succinate yield.[22]

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There are a number of other fermentation pathways that occur in microbes.[4] All these pathways begin by converting pyruvate, but their end products and the key enzymes they require are different. These pathways include:

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References

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Mixed acid fermentation

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Mixed acid fermentation is an anaerobic metabolic process primarily utilized by facultative anaerobic bacteria, such as those in the Enterobacteriaceae family, wherein glucose or other hexoses are converted through glycolysis into a diverse mixture of organic acids—including lactic acid, acetic acid, formic acid, and succinic acid—along with neutral products like ethanol, carbon dioxide (CO₂), and hydrogen gas (H₂), resulting in a characteristic acidification of the medium to a pH below 4.2.[1] This fermentation pathway enables bacteria to generate ATP under oxygen-limited conditions, yielding 2 moles of ATP per mole of glucose consumed, by employing multiple terminal electron acceptors and redox-balancing mechanisms beyond simple alcoholic or homolactic fermentation.[2] Key organisms involved include Escherichia coli, Salmonella spp., Shigella spp., Citrobacter spp., and certain species of Vibrio and Aeromonas, as well as select anaerobic fungi like Neocallimastix frontalis and some Clostridia; the process is oxygen-inhibited and relies on enzymes such as pyruvate formate-lyase (PFL) for formate production and lactate dehydrogenase (LDH) for lactate.[1] The end products typically exhibit a ratio of approximately 4:1 (acids to neutral compounds), with formate often further metabolized via the formate-hydrogen-lyase complex to yield additional CO₂ and H₂, allowing for redox balance and energy conservation in diverse environments ranging from the mammalian gut to industrial bioreactors.[2] In biotechnological contexts, mixed acid fermentation has been extensively engineered in E. coli to enhance yields of valuable chemicals like succinate and lactate for biofuel and pharmaceutical production, underscoring its metabolic flexibility and industrial relevance.[1]

Overview

Definition and Characteristics

Mixed acid fermentation is an anaerobic metabolic process in which facultative anaerobic bacteria, particularly members of the Enterobacteriaceae family such as Escherichia coli, catabolize glucose or other sugars to produce a mixture of organic acids—including lactic acid, acetic acid, formic acid, and succinic acid—along with neutral products such as ethanol, carbon dioxide (CO₂), and hydrogen gas (H₂). This pathway enables the regeneration of NAD⁺, which is essential for sustaining glycolysis in the absence of external electron acceptors like oxygen.[3] The process diverges from glycolysis at pyruvate or phosphoenolpyruvate, branching into multiple routes to balance redox and generate limited energy. Key characteristics of mixed acid fermentation include its strict dependence on anaerobic conditions, where oxygen represses the necessary enzymes, such as pyruvate formate-lyase, contrasting sharply with aerobic respiration that utilizes the electron transport chain for up to 38 ATP per glucose molecule. In this fermentation, energy production is confined to substrate-level phosphorylation during glycolysis, yielding approximately 2 ATP per glucose, with occasional additional ATP from acetate formation. The production of multiple acids results in a pronounced pH drop in the medium, often to below 4.2, which differentiates it from homolactic acid fermentation (producing primarily lactate without significant gas evolution) and provides a mixed acid profile detectable via methods like the methyl red test. Additionally, the ratio of acidic to neutral products is typically about 4:1, with CO₂ and H₂ produced in equimolar amounts when formate is cleaved by formate-hydrogen-lyase. In E. coli, the products from glucose under standard anaerobic conditions include acetate, ethanol, lactate, succinate, and formate, with a portion of the formate decomposed to yield equimolar H₂ and CO₂; these ratios can vary based on environmental factors like pH and substrate type, reflecting the pathway's flexibility in redox balancing.[3] The general reaction can be summarized as:
\text{C}_6\text{H}_{12}\text{O}_6 \rightarrow \text{[lactic acid](/page/Lactic_acid)} + \text{[acetic acid](/page/Acetate)} + \text{[formic acid](/page/Formic_acid)} + \text{[succinic acid](/page/Succinic_acid)} + \text{[ethanol](/page/Ethanol)} + \text{CO}_2 + \text{H}_2 + 2-4 \text{ ATP}
This unbalanced equation highlights the diversity of end products, which collectively account for the carbon and redox balance from one glucose molecule.

Biological and Industrial Importance

Mixed acid fermentation plays a crucial role in the physiology of facultative anaerobic bacteria, such as Escherichia coli, enabling survival in oxygen-limited environments like the mammalian gut and sediments. Under anaerobic conditions, this process generates energy through substrate-level phosphorylation while producing a mixture of organic acids and alcohols, which helps maintain cellular redox balance by regenerating NAD⁺ via pathways involving lactate dehydrogenase (LdhA) and alcohol/acetaldehyde dehydrogenase (AdhE).[4] Ecologically, mixed acid fermentation is prominent among enteric bacteria in the Enterobacteriaceae family, where it facilitates colonization and persistence in anaerobic niches. In the gut lumen, it allows pathogens like Salmonella Typhimurium to utilize hexoses for initial growth via acetate and ethanol branches, adapting to inflammation-induced shifts by increasing ethanol production for redox balancing.[5] This metabolic flexibility contributes to food spoilage by enteric bacteria in protein-rich environments, such as meats and dairy, where acid production leads to off-flavors and pH drops, and to pathogenesis during infections by lowering local pH and outcompeting commensal microbes.[6] Industrially, mixed acid fermentation serves as the foundation for producing biofuels and biochemicals using engineered E. coli strains. Ethanol yields reach up to 0.56 g/g glucose from lignocellulosic feedstocks, supporting biofuel applications, while lactate production at 0.9 g/g glucose enables synthesis of polylactic acid (PLA) bioplastics.[4] Acetate, a key product, is used in vinegar production and as a precursor for chemicals, and succinate achieves 1.1 g/g glucose for industrial solvents.[4] Furthermore, the process shows promise in bioremediation, as mixed-culture fermentation of dairy manure hydrolysates converts carbohydrate-rich wastes into medium-chain fatty acids (up to 0.17 mg COD/mg COD total), reducing greenhouse gas emissions from agricultural waste.[7]

Biochemical Pathway

Overall Mechanism and Entry from Glycolysis

Mixed acid fermentation begins with the metabolism of glucose through the Embden-Meyerhof-Parnas (EMP) pathway of glycolysis, which converts one molecule of glucose into two molecules of pyruvate while generating a net yield of 2 ATP and 2 NADH per glucose molecule.[4] This process occurs in the cytoplasm of facultative anaerobic bacteria such as those in the Enterobacteriaceae family and provides the foundational carbon flux for subsequent fermentative branches under oxygen-limited conditions. The EMP pathway is conserved across many microorganisms, ensuring efficient substrate-level phosphorylation without reliance on oxidative phosphorylation.[4] At the pyruvate branch point, under strictly anaerobic conditions, the primary fate of pyruvate is cleavage by the oxygen-sensitive enzyme pyruvate formate-lyase (PFL) into acetyl-CoA and formate, serving as a key diversion from aerobic respiration.[8] A minor pathway involves pyruvate dehydrogenase (PDH), but PFL predominates to avoid NADH production associated with oxidative decarboxylation, thereby preserving reducing equivalents for downstream fermentation.[4] This non-oxidative conversion maintains metabolic flux toward mixed acid end products and is essential for anaerobic energy conservation. The 2 NADH molecules generated during glycolysis must be reoxidized to NAD⁺ to sustain continuous glycolytic turnover in the absence of external electron acceptors, a balance achieved through the reduction of pyruvate-derived intermediates into mixed fermentation products such as lactate, ethanol, and succinate.[9] This internal redox homeostasis allows for net ATP production beyond glycolysis alone, as acetyl-CoA can be further metabolized to acetate via substrate-level phosphorylation.[9] Regulation of this entry into mixed acid fermentation is primarily triggered by oxygen absence, where the ArcA/B two-component system senses the redox state of the electron transport chain via reduced quinones, leading to phosphorylation and activation of ArcA as a transcriptional regulator.[10] Activated ArcA represses genes for aerobic pathways, including components of the tricarboxylic acid (TCA) cycle and respiratory dehydrogenases, thereby redirecting flux toward fermentative metabolism.[10] Additionally, environmental factors such as pH and the nature of the carbon source modulate pathway flux; for instance, acidic conditions and glucose availability enhance glycolytic commitment, while alternative sugars like fructose or ribose alter product ratios by influencing enzyme activities and proton gradients.[11][12] A simplified overall balanced equation for mixed acid fermentation in Escherichia coli, approximating the stoichiometric distribution under typical anaerobic conditions for the primary branches, is:
C6H12O6→1 [acetate](/page/Acetate)+1 [ethanol](/page/Ethanol)+2 [formate](/page/Formate)+3 ATP \text{C}_6\text{H}_{12}\text{O}_6 \rightarrow 1 \text{ [acetate](/page/Acetate)} + 1 \text{ [ethanol](/page/Ethanol)} + 2 \text{ [formate](/page/Formate)} + 3 \text{ ATP}
This equation focuses on the main acetyl-CoA pathway and excludes minor branches to lactate and succinate; actual stoichiometry varies with growth conditions, strain specifics, and environmental factors, often including approximately 0.2–0.3 mol lactate, 0.3 mol acetate, 0.2 mol ethanol, and 0.2–0.3 mol succinate per mol glucose, along with corresponding CO₂ and H₂ from formate cleavage.[1][13]

Branching Pathways to Acid Products

In mixed acid fermentation, pyruvate serves as a central metabolic hub, diverging into multiple branches to produce a variety of acid and neutral products while balancing redox equivalents under anaerobic conditions. From glycolysis, phosphoenolpyruvate (PEP) is converted to pyruvate by pyruvate kinase, after which pyruvate formate-lyase (PFL) cleaves pyruvate into acetyl-CoA and formate, or pyruvate is directly reduced to lactate. These branches allow for the regeneration of NAD⁺ and ATP, with pyruvate as the key node connecting to lactate production, the acetyl-CoA pathway, and the succinate route via PEP carboxylation.[14] The acetyl-CoA branch leads to acetate and ethanol formation. Acetyl-CoA is converted to acetyl-phosphate by phosphotransacetylase (Pta), then to acetate by acetate kinase (AckA), yielding ATP in the process. Alternatively, acetyl-CoA is reduced to acetaldehyde and then ethanol by the bifunctional alcohol/acetaldehyde dehydrogenase (AdhE), consuming two molecules of NADH to maintain redox balance. Formate, produced alongside acetyl-CoA by PFL, is either exported into the medium or cleaved by the formate hydrogen-lyase (FHL) complex into hydrogen gas (H₂) and carbon dioxide (CO₂), providing an additional redox-neutral outlet.[14][14][15] Succinate production occurs through a reductive branch of the tricarboxylic acid (TCA) cycle, starting from PEP carboxylation to oxaloacetate by phosphoenolpyruvate carboxylase (Ppc). Oxaloacetate is then reduced to malate by malate dehydrogenase (Mdh), converted to fumarate by fumarase (Fum), and finally reduced to succinate by fumarate reductase (Frd), consuming NADH equivalents. In parallel, lactate is formed directly from pyruvate by lactate dehydrogenase (LdhA), oxidizing one NADH molecule and serving as a simple redox sink. These pathways collectively direct carbon flux toward mixed acid products in wild-type cells.[14][15][14] Flux distribution among these branches is regulated by the NADH/NAD⁺ ratio and enzyme affinities, ensuring stoichiometric balance of reducing equivalents from glycolysis. For instance, high NADH levels favor NADH-consuming routes like ethanol, lactate, and succinate production, while lower ratios promote acetate formation for ATP yield. Conceptually, pathway diagrams highlight pyruvate as the hub, with direct arrows to lactate, to acetyl-CoA (via PFL) for acetate/ethanol, and to PEP-derived succinate, illustrating the interconnected nature of these divergences.[15][14]

Product Formation in Escherichia coli

Lactate and Succinate Production

In Escherichia coli, lactate production during mixed acid fermentation occurs through the reduction of pyruvate to D-lactate, catalyzed by the NAD-dependent D-lactate dehydrogenase encoded by the ldhA gene. This reaction serves as a direct mechanism to regenerate NAD⁺ from NADH generated in upstream glycolysis, helping maintain redox balance under anaerobic conditions. The enzymatic conversion is represented by the equation:
CH3COCOO−+NADH+H+→CH3CH(OH)COO−+NAD+ \text{CH}_3\text{COCOO}^- + \text{NADH} + \text{H}^+ \rightarrow \text{CH}_3\text{CH(OH)COO}^- + \text{NAD}^+
In wild-type strains, lactate typically accounts for approximately 25% of the carbon flux from glucose, though its formation is highly sensitive to environmental pH, with increased production at lower pH values due to enhanced ldhA activity.[16][2] Succinate production in E. coli proceeds primarily via a dual-route pathway that branches from the phosphoenolpyruvate (PEP) pool, involving carboxylation to oxaloacetate followed by reduction through the TCA cycle's reductive arm. The initial step is catalyzed by phosphoenolpyruvate carboxylase (encoded by ppc), which fixes CO₂ to form oxaloacetate; this is then reduced to malate by malate dehydrogenase (mdh), dehydrated to fumarate by fumarase, and finally reduced to succinate by fumarate reductase (frd). A minor alternative route involves the glyoxylate shunt, but it contributes negligibly under anaerobic conditions. The overall stoichiometry for the primary route is:
PEP+CO2+2NADH→succinate+2NAD++Pi \text{PEP} + \text{CO}_2 + 2\text{NADH} \rightarrow \text{succinate} + 2\text{NAD}^+ + \text{P}_\text{i}
Succinate typically represents about 15% of fermentation products and functions as an electron sink, oxidizing two equivalents of NADH per molecule produced while indirectly influencing CO₂ levels through carboxylation.[17][16] Lactate and succinate pathways share the central PEP/pyruvate pool derived from glycolysis, allowing flexible partitioning of carbon flux based on redox demands. The ldhA gene is repressed during aerobic growth and exponential phase but induced under anaerobic conditions, particularly at low pH, through transcriptional and translational mechanisms involving global regulators like FNR. In E. coli, lactate formation directly balances one NADH per pyruvate reduced, whereas succinate oxidation consumes two NADH equivalents, contributing disproportionately to NADH reoxidation in the mixed acid profile.[18][19]

Acetate and Ethanol Production

In Escherichia coli, acetate production occurs via the acetyl-CoA-derived pathway involving phosphotransacetylase (Pta) and acetate kinase (AckA). The overall reaction is acetyl-CoA + ADP + P_i → acetate + ATP + CoA, which generates one molecule of ATP through substrate-level phosphorylation per acetate formed.[20] This pathway enables high-yield acetate excretion, typically accounting for approximately 30% of the carbon flux in mixed acid fermentation, thereby enhancing the net energy yield beyond the two ATP from glycolysis.[4] Ethanol is produced from acetyl-CoA by the bifunctional enzyme alcohol/aldehyde dehydrogenase (AdhE), which sequentially reduces acetyl-CoA to acetaldehyde and then to ethanol while consuming NADH. The reactions are: CH_3COSCoA + NADH + H^+ \rightleftharpoons CH_3CHO + CoA + NAD^+ (aldehyde dehydrogenase activity) and CH_3CHO + NADH + H^+ \rightleftharpoons CH_3CH_2OH + NAD^+ (alcohol dehydrogenase activity), with the net process being CH_3COSCoA + 2 NADH + 2 H^+ → CH_3CH_2OH + 2 NAD^+ + CoA.[21] AdhE combines both dehydrogenase activities in a single polypeptide and is allosterically activated by NADH, making it a key regulator of this pathway.[22] Ethanol formation typically represents about 20% of the end products, serving primarily as a redox sink to regenerate NAD^+ for sustained glycolysis without net ATP production.[4] The interplay between acetate and ethanol pathways from acetyl-CoA (derived from pyruvate via pyruvate formate-lyase) allows E. coli to maintain metabolic balance during anaerobiosis. Acetate production prioritizes ATP generation to support growth, while ethanol production addresses excess reducing equivalents from glycolysis. The acetate-to-ethanol ratio dynamically shifts with growth phase, favoring acetate accumulation in stationary phase to optimize energy conservation under nutrient limitation.[23]

Formate, Hydrogen, and Carbon Dioxide Production

In Escherichia coli, formate is produced during mixed acid fermentation through the action of pyruvate formate-lyase (PFL), encoded by the pflB gene, which catalyzes the non-oxidative cleavage of pyruvate to acetyl-CoA and formate under anaerobic conditions.[24] The reaction proceeds as follows:
pyruvate+CoA→acetyl-CoA+formate \text{pyruvate} + \text{CoA} \rightarrow \text{acetyl-CoA} + \text{formate}
This pathway diverts approximately 30% of pyruvate flux toward formate initially, serving as a key branch point in anaerobic glucose metabolism.[25] Accumulated formate can exert toxicity on E. coli cells by disrupting intracellular pH and metabolic homeostasis, particularly in large-scale cultures where export is limited.[26] Formate is subsequently metabolized by the formate hydrogen-lyase (FHL) complex to generate hydrogen gas (H₂) and carbon dioxide (CO₂), alleviating toxicity and supporting redox balance. The FHL complex, comprising a periplasmically oriented molybdenum-selenium-dependent formate dehydrogenase (FDH-H, encoded by fdhF) and a cytoplasmic [NiFe]-hydrogenase (Hyd-3, from the hyc operon), facilitates this conversion.[27] The core reaction is:
HCOOH→CO2+H2 \text{HCOOH} \rightarrow \text{CO}_2 + \text{H}_2
This process occurs across the inner membrane, with formate oxidation in the periplasm and proton reduction in the cytoplasm, and is thermodynamically energy-neutral under standard conditions.[28] Expression of the FHL complex is tightly regulated under anaerobic conditions by the global regulator FNR, which activates transcription of anaerobic genes including pflB, and the formate-specific transcriptional activator FhlA, which responds to elevated extracellular formate levels to induce the hyc and fdhF operons.[29] This induction is further modulated by low pH, ensuring FHL activity during acid stress in fermentation. H₂ evolution via FHL relieves cellular redox pressure by enabling continued formate production without net NADH accumulation, as PFL bypasses NADH-dependent steps in pyruvate decarboxylation.[30] In wild-type E. coli, mixed acid fermentation of glucose typically yields approximately 1 mol of H₂ and 1 mol of CO₂ per mol of glucose, corresponding to the net conversion of about half the initially produced formate (roughly 2 mol per glucose via two PFL reactions), with the remainder excreted or diverted to other pathways.[2] These gaseous products contribute to the identification of anaerobic Enterobacteriaceae in microbiological assays through observable gas formation.[31]

Occurrence in Microorganisms

In Enterobacteriaceae

Mixed acid fermentation is prevalent among facultative anaerobic members of the Enterobacteriaceae family, particularly in genera such as Escherichia, Salmonella, Shigella, and to a partial extent Klebsiella, where it serves as a primary mode of anaerobic glucose catabolism via the Embden-Meyerhof-Parnas (EMP) pathway coupled with pyruvate formate-lyase (PFL) activation.[32][1] These organisms generate a mixture of organic acids (lactate, acetate, formate, succinate) and neutral products (ethanol, CO₂, H₂) in a typical ratio of approximately 4:1 acids to neutrals, enabling redox balance and ATP production under oxygen-limited conditions.[1] In contrast, some Klebsiella and related species like Enterobacter and Serratia may shift toward 2,3-butanediol fermentation, reducing acid output.[33] Product profiles vary across species and strains, reflecting adaptations to specific ecological niches. For instance, Escherichia coli typically yields higher levels of formate and ethanol alongside lactate and acetate, while Salmonella species, such as S. Typhimurium, produce elevated succinate and lactate, particularly during gut colonization phases where inflammation triggers shifts in fermentation to optimize energy conservation.[34][35] Strain-specific differences are notable; laboratory strains like E. coli K-12 emphasize formate/ethanol pathways, whereas pathogenic variants of E. coli or Shigella may enhance acid production for virulence.[33] These variations arise from differential enzyme expression and substrate availability, with ratios adjusting based on pH and redox potential.[1] In the intestinal environment, mixed acid fermentation aids Enterobacteriaceae in gut colonization by conferring acid tolerance through mechanisms like formate hydrogen lyase activity, which deacidifies the medium during stationary phase and enhances survival at low pH.[33] The resulting acid mixture lowers local pH below 4.2, inhibiting competitor growth and facilitating niche establishment in the gastroenteric tract.[1][34] Genomically, this pathway is supported by conserved core genes such as pflB (encoding PFL) and ldhA (encoding lactate dehydrogenase), present across the Enterobacteriaceae pan-genome for essential mixed acid metabolism, with some regulatory elements potentially acquired via horizontal gene transfer within the family to fine-tune adaptations.[36][37][38]

In Other Bacteria

Mixed acid fermentation occurs in various non-Enterobacteriaceae bacteria, where it often deviates from the canonical pathways observed in enteric species, resulting in distinct product profiles and metabolic adaptations. In Clostridium species, such as C. butyricum, the process is partially mixed, combining acid production with butyrate formation as a major end product, alongside acetate and lower levels of lactate and ethanol.[39] These bacteria typically employ pyruvate:ferredoxin oxidoreductase (PFOR) rather than pyruvate formate-lyase (PFL) for pyruvate decarboxylation, generating reduced ferredoxin that supports hydrogenase activity but yields lower hydrogen gas compared to enteric fermenters, while favoring solvent production like butanol under certain conditions.[40] Acid yields in these fermentations generally range from 10-20% of substrate carbon, emphasizing butyrate over the broader acid spectrum.[41] Certain Vibrio species, such as V. cholerae and V. natriegens, perform mixed acid fermentation under anaerobic conditions, producing lactate, acetate, formate, succinate, ethanol, CO₂, and H₂ to support growth in hypoxic environments like aquatic sediments or the host gut.[42][43] Similarly, Aeromonas species, including A. hydrophila and A. caviae, engage in mixed acid fermentation, yielding acids like lactate, acetate, and succinate, often coupled with formate hydrogen lyase for deacidification in stationary phase, which aids survival in diverse habitats from freshwater to infected tissues.[33][44] Anaerobic fungi, such as Neocallimastix frontalis in the rumen, utilize mixed acid fermentation to metabolize carbohydrates like cellulose, producing formate, acetate, lactate, ethanol, CO₂, and H₂ via hydrogenosomes, which supports their role in lignocellulosic biomass degradation and energy generation in oxygen-free environments.[45][46] Lactobacillus species, primarily known for homolactic fermentation, can exhibit facultative mixed acid patterns under specific conditions, such as nutrient limitation or citrate availability, producing lactate as the dominant product with low acetate levels (typically <5% of total acids) and trace succinate.[47] In the gut microbiome, certain Bacteroides species, like B. fragilis and B. thetaiotaomicron, perform mixed acid fermentation of carbohydrates, yielding acetate, succinate, and propionate as key short-chain fatty acids, which contribute to pH regulation and cross-feeding with other microbes.[48][49] These variations highlight adaptations to oxygen-limited environments, with Bacteroides prioritizing succinate via fumarate reduction pathways.[50] Ecologically, mixed acid fermentation by these bacteria plays roles in anaerobic digesters, where Clostridium and Bacteroides contribute to volatile fatty acid pools that drive biogas production and waste stabilization.[51] In silage fermentation, Lactobacillus strains facilitate initial acidification through mixed acid outputs, preserving forage by lowering pH and inhibiting spoilage organisms, though this process is less studied than in Enterobacteriaceae due to the dominance of lactic acid pathways.[52] Recent post-2020 research links mixed acid-derived short-chain fatty acids from Bacteroides and Clostridium in the human gut to microbiome dysbiosis, where imbalances elevate acetate and succinate levels, potentially exacerbating inflammation in conditions like inflammatory bowel disease and metabolic disorders by altering epithelial barrier function and immune responses.[53][54]

Detection Methods

Methyl Red Test Procedure

The Methyl Red (MR) test is a biochemical assay used to detect the ability of bacteria to perform mixed acid fermentation by assessing the stability of acidic end products from glucose metabolism, resulting in a sustained low pH.[55] The test is conducted using MR-VP broth, a medium containing peptone, glucose, and a phosphate buffer adjusted to pH 6.9, which supports fermentation without initially altering the pH indicator.[56] To perform the test, begin by preparing the MR-VP broth and equilibrating it to room temperature. Inoculate 5 ml of the broth with a light inoculum from an 18- to 24-hour pure culture of the test organism using a sterile loop, ensuring even distribution without heavy turbidity. Incubate the culture aerobically at 35–37°C for a minimum of 48 hours to allow sufficient time for acid production; shorter incubations may lead to false negatives due to unstable acids.[55] After incubation, transfer 1–2.5 ml of the culture to a clean test tube. Add 2–5 drops of the methyl red indicator solution, prepared by dissolving 0.1 g of methyl red in 300 ml of 95% ethanol and diluting to 500 ml with distilled water (yielding a 0.02% solution), to the aliquot.[56] Observe the color change immediately, as the indicator turns red at pH 4.4 or below, orange between pH 4.4 and 6.0, and yellow above pH 6.0.[55] The biochemical basis of the test relies on the production of stable mixed acids, such as lactic, acetic, formic, and succinic acids, during glucose fermentation, which lowers and maintains the pH below 4.4 without reversion to neutral due to the absence of neutralizing products like acetoin.[57] This contrasts with fermentations producing neutral or less acidic end products, which do not sustain the low pH. For quality control, use Escherichia coli ATCC 25922 as a positive control, which typically yields a red color indicating mixed acid fermentation, and Enterobacter aerogenes or Klebsiella pneumoniae as negative controls, which remain yellow due to lower acid stability.[56] Incubation time is critical, as extending beyond 48 hours can enhance sensitivity for weak acid producers, but the test should not exceed 5 days to avoid overgrowth effects.[55] The Methyl Red test was developed in 1915 by William Mansfield Clark and Herbert A. Lubs as part of the MR-VP broth system for differentiating coliform bacteria within the Enterobacteriaceae family, and it later became a key component of the IMViC test series for enteric pathogen identification.[58]

Interpretation and Limitations

A positive result in the Methyl Red test is indicated by the development of a red color upon addition of the indicator, signifying a pH below 4.4 due to the production of stable acids from mixed acid fermentation of glucose.[57] This outcome is characteristic of bacteria in the Enterobacteriaceae family, such as Escherichia coli, which lower the medium's pH through the accumulation of organic acids like acetate, lactate, and formate. In contrast, a negative result appears as a yellow or orange color, reflecting a neutral pH around 6.0 or higher, often seen in organisms performing 2,3-butanediol fermentation that do not produce sufficient acid to maintain low pH.[56] False negatives can occur if the test is read before 48 hours of incubation, as some mixed acid fermenters may not yet generate enough acid for detection.[57] The Methyl Red test has several limitations that affect its reliability for precise identification of mixed acid fermentation. It lacks specificity, as homofermentative lactic acid bacteria, such as certain Lactobacillus species, can also produce enough acid to yield a positive red color, without engaging in mixed acid pathways.[59] Results can be influenced by variations in incubation temperature, medium composition, or glucose concentration, potentially leading to inconsistent pH drops.[57] For more accurate quantification of fermentation products, modern alternatives like high-performance liquid chromatography (HPLC) are preferred, as they directly measure individual acids such as lactate and acetate with higher precision and without relying on pH indicators.[60] To enhance differentiation, the Methyl Red test is often combined with the Voges-Proskauer (VP) test as part of the IMViC battery, where a positive MR and negative VP confirms mixed acid fermentation in enterics, while the reverse indicates butanediol producers. This paired approach improves overall accuracy in bacterial identification within the Enterobacteriaceae.[56]

Metabolic Engineering

Enhancing Ethanol and Acetate Yields

Genetic engineering strategies have been developed to redirect metabolic flux in Escherichia coli towards higher ethanol production during mixed acid fermentation by blocking competing pathways. Specifically, knockout of the ldhA gene, which encodes lactate dehydrogenase, and the pflB gene, encoding pyruvate formate-lyase, prevents the formation of lactate and formate, thereby channeling pyruvate-derived acetyl-CoA towards ethanol synthesis via alcohol dehydrogenase.[3] Overexpression of the native adhE gene, which encodes bifunctional alcohol/acetaldehyde dehydrogenase, further enhances this flux by improving the conversion of acetyl-CoA to ethanol while regenerating NAD⁺.[3] These modifications, often implemented through plasmid-based expression systems, have achieved ethanol yields approaching theoretical maxima. For instance, the engineered strain SZ420, with ldhA and pflB deletions, produced ethanol at 90% of the theoretical yield from glucose under anaerobic conditions.[3] To address redox imbalances, co-factor engineering strategies focus on increasing NADH availability, which is essential for AdhE-catalyzed ethanol production. Techniques such as integrating heterologous genes like pdc and adhB from Zymomonas mobilis into the chromosome, combined with evolutionary adaptation, have pushed yields higher; strain LY160 reached 95% theoretical yield from xylose.[3] More recently, CRISPR-Cas9 systems enable precise, multiplex genome editing for simultaneous knockouts and insertions, facilitating rapid strain optimization for ethanol pathways in E. coli. A notable case is the KO11 strain, developed in the 1990s, which achieved 89% ethanol yield from xylose and demonstrated tolerance to lignocellulosic inhibitors, though ethanol toxicity limited titers to around 50-60 g/L.[3][61] For acetate enhancement, amplification of the ackA and pta genes, encoding acetate kinase and phosphotransacetylase, respectively, boosts the conversion of acetyl-CoA to acetate via substrate-level phosphorylation. This is typically paired with knockouts of ldhA, pflB, and adhE to eliminate competing products, redirecting flux solely to acetate.[3] Process engineering, such as maintaining neutral pH (around 7.0) to optimize enzyme activity and acetate export, supports accumulation without severe inhibition.[62] The strain TC36, engineered with these modifications plus disruptions in the TCA cycle (sucA) and fumarate reductase (frdBC), attained an acetate titer of approximately 50 g/L (878 mM) from glucose, corresponding to 86% of the theoretical yield (0.50 g acetate per g glucose).[62] Challenges include acetate toxicity, which inhibits growth above 300-400 mM, and by-product accumulation like pyruvate due to metabolic bottlenecks, necessitating further redox and tolerance engineering.[62] These approaches highlight the potential of mixed acid fermentation platforms for biofuel and biochemical production, though scaling remains hindered by toxicity issues.[3]

Optimizing Lactate and Succinate Production

Metabolic engineering strategies for enhancing lactate production in Escherichia coli during mixed acid fermentation primarily involve the overexpression of the lactate dehydrogenase gene (ldhA) to direct pyruvate flux toward lactate, coupled with the deletion of competing pathways such as the acetate kinase-phosphotransacetylase (pta-ackA) system to minimize carbon diversion to acetate.[63] These modifications enable near-homofermentative production, achieving optical purities exceeding 99% for D-lactate in engineered strains.[64] For instance, optimized E. coli strains have demonstrated titers of approximately 100 g/L D-lactate under fed-batch conditions, supporting industrial scalability.[64] Succinate optimization leverages upregulation of phosphoenolpyruvate carboxylase (ppc) and fumarate reductase (frd) to boost the reductive branch of the tricarboxylic acid cycle, often integrated with hybrid aerobic-anaerobic fermentation regimes that balance NAD+ regeneration and carbon fixation.[17] This shifts the stoichiometry toward efficient succinate formation, approximated by the equation:
Glucose+2 CO2→succinate+acetate+2 CO2+2 H2 \text{Glucose} + 2 \text{ CO}_2 \to \text{succinate} + \text{acetate} + 2 \text{ CO}_2 + 2 \text{ H}_2
(simplified for net production via reductive TCA with CO₂ incorporation and further formate/H₂ metabolism, achieving a theoretical yield of 1 mol succinate per mol glucose).[17] Engineered E. coli strains, such as those derived from AFP111 mutants, have attained titers of 80–100 g/L succinate in fed-batch processes, positioning it as a key precursor for bio-based polymers like polybutylene succinate.[65][66] Key optimization strategies include metabolic flux analysis (MFA) to identify bottlenecks in carbon partitioning and adaptive laboratory evolution to enhance tolerance to product inhibition and substrate utilization.[67] Nutrient adjustments, such as CO₂ sparging, further promote succinate yields by supplying substrate for ppc-mediated carboxylation, increasing flux through the C4 pathway by up to 20–30% in anaerobic cultures.[68] Recent advances in the 2020s utilize synthetic biology for consolidated bioprocessing, where E. coli chassis integrate lignocellulosic hydrolysis and fermentation modules to directly convert pretreated biomass to lactate or succinate, reducing process costs. As of 2025, further advances include evolution-assisted E. coli strains achieving >100 g/L succinate and optimized CBP for lactate from biomass, improving yields and tolerance.[69][70] These developments enhance economic viability, particularly for polylactic acid (PLA) plastics derived from lactate, by reducing process costs through integrated bioprocessing.[71]

Related Fermentation Pathways

Butanediol Fermentation

Butanediol fermentation is an anaerobic metabolic pathway in which glucose is converted to the neutral product 2,3-butanediol (2,3-BDO) and the intermediate acetoin, primarily through the sequential action of three key enzymes: α-acetolactate synthase (ALS, EC 4.1.3.18), α-acetolactate decarboxylase (ALDC, EC 4.1.1.5), and butanediol dehydrogenase (BDH, EC 1.1.1.4 or 1.1.1.202).[72] This process generates fewer acidic end products than alternative fermentative routes, leading to a less pronounced drop in pH and a more neutral extracellular environment.[73] The pathway is prevalent among facultative anaerobic bacteria in the Enterobacteriaceae family, notably species of Enterobacter (e.g., Enterobacter aerogenes) and Klebsiella (e.g., Klebsiella pneumoniae and Klebsiella oxytoca).[74][75] It begins from pyruvate, a common intermediate in glycolysis, and proceeds as follows:
2 pyruvate→ALSα-acetolactate→ALDCacetoin+CO2→BDH, NADH2,3-BDO 2 \text{ pyruvate} \xrightarrow{\text{ALS}} \alpha\text{-acetolactate} \xrightarrow{\text{ALDC}} \text{acetoin} + \text{CO}_2 \xrightarrow{\text{BDH, NADH}} 2,3\text{-BDO}
This reaction reoxidizes NADH, balancing the redox state during anaerobic growth, with the overall simplified stoichiometry yielding 2,3-BDO and CO₂ without significant formate or hydrogen gas production.[72][73] The primary product is 2,3-BDO, which can constitute up to 92% of the theoretical maximum yield from glucose (e.g., 0.461 g/g glucose in engineered K. pneumoniae strains under optimized conditions), alongside acetoin as a key intermediate and minor byproducts such as lactate, acetate, succinate, and ethanol.[75][76] These neutral diols and reduced acid output distinguish the pathway from more acidic fermentations. Industrially, 2,3-BDO serves as a versatile platform chemical for manufacturing solvents, plasticizers, polyesters, pharmaceuticals, cosmetics, and fuel additives, with microbial fermentation offering a sustainable alternative to petrochemical synthesis.[77][78] A hallmark of butanediol fermentation is its biochemical detectability: it yields a positive Voges-Proskauer (VP) test due to acetoin accumulation, which reacts to form a red complex, while producing a negative Methyl Red (MR) test because of the limited acid formation and higher final pH.[79][80] In contrast to mixed acid fermentation, which generates substantial organic acids and lowers pH, this pathway emphasizes neutral products like 2,3-BDO without formate or H₂ evolution.[79]

Homofermentative Lactic Acid Fermentation

Homofermentative lactic acid fermentation is an anaerobic metabolic process in which certain bacteria convert glucose primarily into lactic acid as the sole end product. This pathway is characteristic of facultative anaerobes such as species of Lactobacillus, including L. plantarum and L. delbrueckii, which utilize the enzyme lactate dehydrogenase (LDH) to reduce pyruvate directly to lactate.[81][82] The mechanism begins with the Embden-Meyerhof-Parnas (EMP) pathway of glycolysis, where one molecule of glucose is phosphorylated and cleaved into two molecules of pyruvate, generating a net gain of two ATP molecules through substrate-level phosphorylation. Pyruvate is then reduced to lactate by LDH, using NADH as the electron donor, regenerating NAD⁺ to sustain glycolysis under anaerobic conditions. The overall balanced equation for this process is:
C6H12O6→2 CH3CH(OH)COOH+2 ATP \mathrm{C_6H_{12}O_6 \rightarrow 2\ CH_3CH(OH)COOH + 2\ ATP}
This results in 100% of the carbon from glucose being directed to lactic acid, with no production of gases, ethanol, or other organic acids.[81][82] Key characteristics of homofermentative lactic acid fermentation include a rapid and significant decrease in pH due to the accumulation of lactic acid, often reaching levels as low as 3.5, which creates an acidic environment that inhibits the growth of competing spoilage microorganisms. Unlike pathways with branched metabolisms, this process is streamlined, producing no gaseous byproducts or neutral compounds such as ethanol, which enhances its efficiency in acid production but yields only two ATP per glucose molecule.[82][81] This fermentation is widely applied in food preservation and production, such as in the manufacture of yogurt through the action of Lactobacillus bulgaricus and Streptococcus thermophilus, where it imparts the characteristic tangy flavor and extends shelf life. It is also essential for silage production in agriculture, where Lactobacillus species ferment plant sugars to preserve fodder for animal feed by lowering pH and preventing aerobic deterioration.[82][81]

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