Improvement of caproic acid production in a Clostridium kluyveri H068 and Methanogen 166 co-culture fermentation system

Converting methanogenesis into chain elongation for caproic acid production from food waste: Roles of pH and hydraulic retention time

Caproic acid production from food waste is a promising pathway for waste valorization, but how to restrict methanogenesis and enrich chain elongators during long-term continuous operation by adjusting operating parameters was not fully revealed. In this study, the impacts of pH and hydraulic retention time (HRT) on methane production and chain elongation were investigated. Results showed that pH 6 and 5.5 at long HRT would result in methanogenesis without caproic acid production. After a long-term acclimation at pH 5, methanogens could be effectively restricted, and chain elongation could be activated. When pH further increased to 5.5 at an HRT of 50 days, caproic acid content could be promoted to 52.94 mmol/L by enriching Caproiciproducens as the dominant chain elongators. However, short HRT (25 days) will cause the accumulation of lactic acid bacteria and finally reduce the caproic acid yield. This study proposed an effective pathway for establishing chain elongation from pit mud through operation adjustment, which provided useful information for caproic acid production from organic wastes.

Caproic acid production from short-chained carboxylic acids produced by arrested anaerobic digestion of green waste: Development and optimization of a mixed caproic acid producing culture

Caproic acid is an important compound for producing a variety of chemicals and a potential precursor for Sustainable Aviation Fuels (SAF). This study aimed at developing a stable mixed culture producing caproic acid using short-chain carboxylic acids (SCCAs) derived from arrested anaerobic digestion (AAD) of green waste and optimizing chain elongation (CE) conditions. The results showed that the mixed culture was dominated by Clostridium sensu stricto 12 (53.09 %), optimally producing caproic acid at 37 °C, pH 7.20, with a 15 % inoculum concentration. Under these conditions, 75.59 % of the consumed electrons contributed to caproic acid formation. Gradual ethanol feeding in bioreactor experiments resulted in caproic acid titer of 13.36 g/L, with carbon conversion efficiency (CCE) of 81.91 % and electron transfer efficiency (ETE) of 76.39 %, surpassing batch experiments without gradual ethanol addition. These findings demonstrate that the effectiveness of a mixed culture can be improved, resulting in increased caproic acid production.

A Review on the Interaction of Acetic Acid Bacteria and Microbes in Food Fermentation: A Microbial Ecology Perspective

In fermented foods, acetic acid bacteria (AAB), kinds of bacteria with a long history of utilization, contribute to safety, nutritional, and sensory properties primarily through acetic acid fermentation. AAB are commonly found in various fermented foods such as vinegar, sour beer, fermented cocoa and coffee beans, kefir beverages, kombucha, and sourdough. They interact and cooperate with a variety of microorganisms, resulting in the formation of diverse metabolites and the production of fermented foods with distinct flavors. Understanding the interactions between AAB and other microbes is crucial for effectively controlling and utilizing AAB in fermentation processes. However, these microbial interactions are influenced by factors such as strain type, nutritional conditions, ecological niches, and fermentation duration. In this review, we examine the relationships and research methodologies of microbial interactions and interaction studies between AAB and yeasts, lactic acid bacteria (LAB), and bacilli in different food fermentation processes involving these microorganisms. The objective of this review is to identify key interaction models involving AAB and other microorganisms. The insights gained will provide scientific guidance for the effective utilization of AAB as functional microorganisms in food fermentation processes.

Strategies to enhance production of metabolites in microbial co-culture systems

Increasing evidence shows that microbial synthesis plays an important role in producing high value-added products. However, microbial monoculture generally hampers metabolites production and limits scalability due to the increased metabolic burden on the host strain. In contrast, co-culture is a more flexible approach to improve the environmental adaptability and reduce the overall metabolic burden. The well-defined co-culturing microbial consortia can tap their metabolic potential to obtain yet-to-be discovered and pre-existing metabolites. This review focuses on the use of a co-culture strategy and its underlying mechanisms to enhance the production of products. Notably, the significance of comprehending the microbial interactions, diverse communication modes, genetic information, and modular co-culture involved in co-culture systems were highlighted. Furthermore, it addresses the current challenges and outlines potential future directions for microbial co-culture. This review provides better understanding the diversity and complexity of the interesting interaction and communication to advance the development of co-culture techniques.

Medium-chain carboxylates production from plant waste: kinetic study and effect of an enriched microbiome

BACKGROUND

The need for addition of external electron donors such as ethanol or lactate impairs the economic viability of chain elongation (CE) processes for the production of medium-chain carboxylates (MCC). However, using feedstocks with inherent electron donors such as silages of waste biomass can improve the economics. Moreover, the use of an appropriate inoculum is critical to the overall efficiency of the CE process, as the production of a desired MCC can significantly be influenced by the presence or absence of specific microorganisms and their metabolic interactions. Beyond, it is necessary to generate data that can be used for reactor design, simulation and optimization of a given CE process. Such data can be obtained using appropriate mathematical models to predict the dynamics of the CE process.

RESULTS

In batch experiments using silages of sugar beet leaves, cassava leaves, and Elodea/wheat straw as substrates, caproate was the only MCC produced with maximum yields of 1.97, 3.48, and 0.88 g/kgVS, respectively. The MCC concentrations were accurately predicted with the modified Gompertz model. In a semi-continuous fermentation with ensiled sugar beet leaves as substrate and digestate from a biogas reactor as the sole inoculum, a prolonged lag phase of 7 days was observed for the production of MCC (C6-C8). The lag phase was significantly shortened by at least 4 days when an enriched inoculum was added to the system. With the enriched inoculum, an MCC yield of 93.67 g/kgVS and a productivity of 2.05 gMCC/L/d were achieved. Without the enriched inoculum, MCC yield and productivity were 43.30 g/kgVS and 0.95 gMCC/L/d, respectively. The higher MCC production was accompanied by higher relative abundances of Lachnospiraceae and Eubacteriaceae.

CONCLUSIONS

Ensiled waste biomass is a suitable substrate for MCC production using CE. For an enhanced production of MCC from ensiled sugar beet leaves, the use of an enriched inoculum is recommended for a fast process start and high production performance.

Genome Analysis and Optimization of Caproic Acid Production of Clostridium butyricum GD1-1 Isolated from the Pit Mud of Nongxiangxing Baijiu

Caproic acid is a precursor substance for the synthesis of ethyl caproate, the main flavor substance of nongxiangxing baijiu liquor. In this study, Clostridium butyricum GD1-1, a strain with high caproic acid concentration (3.86 g/l), was isolated from the storage pit mud of nongxiangxing baijiu for sequencing and analysis. The strain's genome was 3,840,048 bp in length with 4,050 open reading frames. In addition, virulence factor annotation analysis showed C. butyricum GD1-1 to be safe at the genetic level. However, the annotation results using the Kyoto Encyclopedia of Genes and Genomes Automatic Annotation Server predicted a deficiency in the strain's synthesis of alanine, methionine, and biotin. These results were confirmed by essential nutrient factor validation experiments. Furthermore, the optimized medium conditions for caproic acid concentration by strain GD1-1 were (g/l): glucose 30, NaCl 5, yeast extract 10, peptone 10, beef paste 10, sodium acetate 11, L-cysteine 0.6, biotin 0.004, starch 2, and 2.0% ethanol. The optimized fermentation conditions for caproic acid production by C. butyricum GD1-1 on a single-factor basis were: 5% inoculum volume, 35°C, pH 7, and 90% loading volume. Under optimal conditions, the caproic acid concentration of strain GD1-1 reached 5.42 g/l, which was 1.40 times higher than the initial concentration. C. butyricum GD1-1 could be further used in caproic acid production, NXXB pit mud strengthening and maintenance, and artificial pit mud preparation.

Butyriproducens baijiuensis BJN0003: a potential new member of the family Oscillospiraceae isolated from Chinese Baijiu

Acid-producing bacteria are one kind of crucial species for Baijiu fermentation. The strain BJN0003 with the ability of producing butyric acid was isolated from the cellar mud of Baijiu, and the 16S rRNA gene sequence similarity was 94.2% to its most closely related type species Caproicibacterium lactiferaments JNU-WLY1368T, less than the threshold value of 94.5% for distinguishing genera. Furthermore, the genome of BJN0003 showed a length of 2,458,513 bp and a DNA G + C content of 43.3% through high throughput sequence. BJN0003 exhibited whole-genome average nucleotide identity value of 68.9% to the most closely related species, while the whole-genome digital DNA-DNA hybridization value was only 23.1%, which were both below the delineation thresholds of species. These results indicated BJN0003 could represent a potential novel species of a new genus of the family Oscillospiraceae, and was proposed the name as Butyriproducens baijiuensis. In addition, gene annotation and metabolic analysis showed that BJN0003 harbored the metabolic pathway of converting glucose to butyric acid. The discovery of the new species provided bacterial resource for Baijiu production and the revealing of genetic characteristics would promote the investigation of acid synthesis during Baijiu manufacturing process.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03624-w.

Adding glucose delays the conversion of ethanol and acetic acid to caproic acid in Lacrimispora celerecrescens JSJ-1

Caproic acid is an important fatty acid with diverse applications. In this study, the biomass growth and metabolites of Lacrimispora celerecrescens JSJ-1 were investigated under different carbon sources (ethanol, starch, sucrose, and glucose), with a focus on the effect of the coexistence of glucose and ethanol on the synthesis of caproic acid. The results showed that starch, glucose, and sucrose all contributed to the biomass of L. celerecrescens JSJ-1. Under the three carbon sources, L. celerecrescens JSJ-1 produced acetic acid, butyric acid, lactic acid, ethanol, and butanol, but caproic acid was not produced. Ethanol was the optimal substrate for the production of caproic acid. When glucose and ethanol coexisted, the generation time of caproic acid was delayed compared with that in ethanol sodium acetate medium (ES medium). This was because glucose was preferentially consumed over ethanol. Lactic acid was generated as a result of glucose consumption, which led to a significant decrease in pH from 6.45 to 4.68. The low pH (< 5) inhibited the synthesis of caproic acid. Then, the strain's usage of lactic acid and the reaction between CaCO₃ and lactic acid caused the pH to increase. L. celerecrescens JSJ-1 did not start producing caproic acid using ethanol and acetic acid until the pH increased to 5.8. This research enriches the knowledge regarding the metabolism of L. celerecrescens JSJ-1 and provides guidelines for the industrial production of caproic acid by using L. celerecrescences JSJ-1. KEY POINTS: • Ethanol is the optimal substrate for the synthesis of caproic acid by Lacrimispora celerecrescens JSJ-1. • Lacrimispora celerecrescens JSJ-1 produced lactic acid rapidly when it used glucose, causing a sharp drop in pH. • pH is a crucial factor affecting the synthesis of caproic acid from ethanol by Lacrimispora celerecrescens JSJ-1.

Production of caproic acid by Rummeliibacillus suwonensis 3B-1 isolated from the pit mud of strong-flavor baijiu

Caproic acid is the precursor of ethyl caproate, the main representative flavor substance of strong-flavor baijiu (SFB). Caproic acid-producing bacteria are considered to be the most important type of acid-producing microorganisms in the pit mud of the SFB ecosystem. In this study, the Rummeliibacillus suwonensis 3B-1 with a high yield of caproic acid (4.064g/L) was screened from SFB pit mud. The genome of the R. suwonensis 3B-1 was sequenced, the total size was found to be 4,117,671bp and a calculated GC content of 35.86%. The caproic acid biosynthesis pathway was identified and analyzed, and it showed that 3B-1 could not only use ethanol, but it could also use glucose and other carbon sources as substrates to produce caproic acid. According to the genome analysis and with an optimized medium, the optimal conditions for caproic acid production were yeast powder at 3g/L, sodium acetate at 15g/L, and 1% biotin at 8mL/100mL. The yield of caproic acid reached 4.627g/L, an increase of 13.9%, which was higher than that of general caproic acid bacteria. This is the first report of the synthesis of caproic acid by R. suwonensis. This strain could be used to produce caproic acid, an artificial pit mud preparation, and/or an enhanced inoculum in the production of SFB.

Effect of microbial interaction on flavor quality in Chinese baijiu fermentation

Chinese baijiu brewing is an open, complex, and synergetic functional microbiota fermentation process. Microbial interaction is pivotal for the regulation of microbial structure and function in the brewing microecosystem, consequently affecting the flavor and quality of baijiu. This article mainly summarizes the effect of microbial interactions among functional microbiota on the growth performance, flavor formation, and safe quality of baijiu fermentation process. In addition, the review specifically emphasizes on the microbial interactions for the regulation of “Ethyl Caproate-Increasing and Ethyl Lactate-Decreasing” in Chinese strong-flavor baijiu. Furthermore, the construction of synthetic microbiota by metabolic characteristics of the functional microbes and their interactions for regulating and controlling flavor quality of Chinese baijiu is also reviewed and prospected.

The potential of caproate (hexanoate) production using Clostridium kluyveri syntrophic cocultures with Clostridium acetobutylicum or Clostridium saccharolyticum

Caproate (hexanoate) and other medium-chain fatty acids are valuable platform chemicals produced by processes utilizing petroleum or plant oil. Clostridium kluyveri, growing on short chain alcohols (notably ethanol) and carboxylic acids (such as acetate) is noted for its ability to perform chain elongation to produce 4- to 8-carbon carboxylates. C. kluyveri has been studied in monoculture and coculture conditions, which lead to relatively modest carboxylate titers after long fermentation times. To assess the biosynthetic potential of C. kluyveri for caproate production from sugars through coculture fermentations, in the absence of monoculture data in the literature suitable for our coculture experiments, we first explored C. kluyveri monocultures. Some monocultures achieved caproate titers of 150 to over 200 mM in 40–50 h with a production rate of 7.9 mM/h. Based on that data, we then explored two novel, syntrophic coculture partners for producing caproate from sugars: Clostridium acetobutylicum and Clostridium saccharolyticum. Neither species has been cocultured with C. kluyveri before, and both demonstrate promising results. Our experiments of C. kluyveri monocultures and C. kluyveri—C. saccharolyticum cocultures demonstrate exceptionally high caproate titers (145–200 mM), fast production rates (3.25–8.1 mM/h), and short fermentation times (18–45 h). These results represent the most caproate produced by a C. kluyveri coculture in the shortest known fermentation time. We also explored the possibility of heterologous cell fusion between the coculture pairs similar to the results seen previously in our group with C. acetobutylicum and Clostridium ljungdahlii. Fusion events were observed only in the C. acetobutylicum—C. kluyveri coculture pair, and we offer an explanation for the lack of fusion between C. saccharolyticum and C. kluyveri. This work supports the promise of coculture biotechnology for sustainable production of caproate and other platform chemicals.

Metabolite-Based Mutualistic Interaction between Two Novel Clostridial Species from Pit Mud Enhances Butyrate and Caproate Production

Pit mud microbial consortia play crucial roles in the formation of Chinese strong-flavor baijiu's key flavor-active compounds, especially butyric and caproic acids. Clostridia, one of the abundant bacterial groups in pit mud, were recognized as important butyric and caproic acid producers. Research on the interactions of the pit mud microbial community mainly depends on correlation analysis at present. Interaction between Clostridium and other microorganisms and its involvement in short/medium-chain fatty acid (S/MCFA) metabolism are still unclear. We previously found coculture of two clostridial strains isolated from pit mud, Clostridium fermenticellae JN500901 (C.901) and Novisyntrophococcus fermenticellae JN500902 (N.902), could enhance S/MCFA accumulation. Here, we investigated their underlying interaction mechanism through the combined analysis of phenotype, genome, and transcriptome. Compared to monocultures, coculture of C.901 and N.902 obviously promoted their growth, including shortening the growth lag phase and increasing biomass, and the accumulation of butyric acid and caproic acid. The slight effects of inoculation ratio and continuous passage on the growth and metabolism of coculture indicated the relative stability of their interaction. Transwell coculture and transcriptome analysis showed the interaction between C.901 and N.902 was accomplished by metabolite exchange, i.e., formic acid produced by C.901 activated the Wood-Ljungdahl pathway of N.902, thereby enhancing its production of acetic acid, which was further converted to butyric acid and caproic acid by C.901 through reverse β-oxidation. This work demonstrates the potential roles of mutually beneficial interspecies interactions in the accumulation of key flavor compounds in pit mud. IMPORTANCE Microbial interactions played crucial roles in influencing the assembly, stability, and function of the microbial community. The metabolites of pit mud microbiota are the key to flavor formation of Chinese strong-flavor baijiu. So far, researches on the interactions of the pit mud microbial community have been mainly based on the correlation analysis of sequencing data, and more work needs to be performed to unveil the complicated interaction patterns. Here, we identified a material exchange-based mutualistic interaction system involving two fatty acid-producing clostridial strains (Clostridium fermenticellae JN500901 and Novisyntrophococcus fermenticellae JN500902) isolated from pit mud and systematically elucidated their interaction mechanism for promoting the production of butyric acid and caproic acid, the key flavor-active compounds of baijiu. Our findings provide a new perspective for understanding the complicated interactions of pit mud microorganisms.

Chinese Baijiu: The Perfect Works of Microorganisms

Chinese Baijiu is one of the famous distilled liquor series with unique flavors in the world. Under the open environment, Chinese Baijiu was produced by two solid-state fermentation processes: jiuqu making and baijiu making. Chinese Baijiu can be divided into different types according to the production area, production process, starter type, and product flavor. Chinese Baijiu contains rich flavor components, such as esters and organic acids. The formation of these flavor substances is inseparable from the metabolism and interaction of different microorganisms, and thus, microorganisms play a leading role in the fermentation process of Chinese Baijiu. Bacteria, yeasts, and molds are the microorganisms involved in the brewing process of Chinese Baijiu, and they originate from various sources, such as the production environment, production workers, and jiuqu. This article reviews the typical flavor substances of different types of Chinese Baijiu, the types of microorganisms involved in the brewing process, and their functions. Methods that use microbial technology to enhance the flavor of baijiu, and for detecting flavor substances in baijiu were also introduced. This review systematically summarizes the role and application of Chinese Baijiu flavor components and microorganisms in baijiu brewing and provides data support for understanding Chinese Baijiu and further improving its quality.

Caproic Acid-Producing Bacteria in Chinese Baijiu Brewing

Caproic acid can be used as spices, preservatives, animal feed additives, and biofuels. At the same time, caproic acid plays an important role in Chinese Baijiu. It is the precursor substance for the synthesis of ethyl caproate, which directly affects the quality of Chinese Baijiu. Caproic acid-producing bacteria are the main microorganisms that synthesize caproic acid in Chinese Baijiu, and the most common strain is Clostridium kluyveri. Caproic acid-producing bacteria synthesize n-caproic acid through reverse β-oxidation to extend the carboxylic acid chain. This method mainly uses ethanol and lactic acid as substrates. Ethanol and lactic acid are converted into acetyl-CoA, and acetyl-CoA undergoes a series of condensation, dehydrogenation, dehydration, and reduction to extend the carboxylic acid chain. This review addresses the important issues of caproic acid-producing bacteria in the brewing process of Baijiu: the common caproic acid-producing bacteria that have been reported metabolic pathways, factors affecting acid production, biological competition pathways, and the effect of mixed bacteria fermentation on acid production. It is hoped that this will provide new ideas for the study of caproic acid-producing bacteria in Chinese Baijiu.

Gene Mining and Flavour Metabolism Analyses of Wickerhamomyces anomalus Y-1 Isolated From a Chinese Liquor Fermentation Starter

Luzhou-flavoured liquor is one of Chinese most popular distilled liquors. Hundreds of flavoured components have been detected from this liquor, with esters as its primary flavouring substance. Among these esters, ethyl hexanoate was the main component. As an essential functional microbe that produces ethyl hexanoate, yeast is an important functional microorganism that produces ethyl hexanoate. The synthesis of ethyl hexanoate in yeast mainly involves the lipase/esterase synthesis pathway, alcohol transferase pathway and alcohol dehydrogenase pathway. In this study, whole-genome sequencing of W. anomalus Y-1 isolated from a Chinese liquor fermentation starter, a fermented wheat starter containing brewing microorganisms, was carried out using the Illumina HiSeq X Ten platform. The sequence had a length of 15,127,803 bp with 34.56% GC content, encoding 7,024 CDS sequences, 69 tRNAs and 1 rRNA. Then, genome annotation was performed using three high-quality databases, namely, COG, KEGG and GO databases. The annotation results showed that the ko7019 pathway of gene 6,340 contained the Eht1p enzyme, which was considered a putative acyltransferase similar to Eeb1p and had 51.57% homology with two known medium-chain fatty acid ethyl ester synthases, namely, Eht1 and Eeb1. Ethyl hexanoate in W. anomalus was found to be synthesised through the alcohol acyltransferase pathway, while acyl-coenzyme A and alcohol were synthesised under the catalytic action of Eht1p. The results of this study are beneficial to the exploration of key genes of ester synthesis and provide reference for the improvement of liquor flavoured.

Mining the Factors Driving the Evolution of the Pit Mud Microbiome under the Impact of Long-Term Production of Strong-Flavor Baijiu

The mud cellar creates a unique microenvironment for the fermentation of strong-flavor baijiu (SFB). Recent research and long-term practice have highlighted the key roles of microbes inhabiting pit mud in the formation of SFB’s characteristic flavor. A positive correlation between the quality of SFB and cellar age was extracted from practice; however, the evolutionary patterns of pit mud microbiome and driving factors remain unclear. Here, based on the variation regularity analysis of microbial community structure and metabolites of samples from cellars of different ages (∼30/100/300 years), we further investigated the effects of lactate and acetate (main microbial metabolites in fermented grains) on modulating the pit mud microbiome. Esters (50.3% to 64.5%) dominated the volatile compounds identified in pit mud, and contents of the four typical acids (lactate, hexanoate, acetate, and butyrate) increased with cellar age. Bacteria (9.5 to 10.4 log₁₀ [lg] copies/g) and archaea (8.3 to 9.1 lg copies/g) mainly constituted pit mud microbiota, respectively dominated by Clostridia (39.7% to 81.2%) and Methanomicrobia (32.8% to 92.9%). An upward trend with cellar age characterized the relative and absolute abundance of the most predominant bacterial and archaeal genera, Caproiciproducens and Methanosarcina. Correlation analysis revealed significantly (P < 0.05) positive relationships between the two genera and major metabolites. Anaerobic fermentation with acetate and lactate as carbon sources enhanced the enrichment of Clostridia, and furthermore, the relative abundance of Caproiciproducens (40.9%) significantly increased after 15-day fed-batch fermentation with lactate compared with the initial pit mud (0.22%). This work presents a directional evolutionary pattern of pit mud microbial consortia and provides an alternative way to accelerate the enrichment of functional microbes.

IMPORTANCE The solid-state anaerobic fermentation in a mud cellar is the most typical feature of strong-flavor baijiu (SFB). Metabolites produced by microbes inhabiting pit mud are crucial to create the unique flavor of SFB. Accordingly, craftspeople have always highlighted the importance of the pit mud microbiome and concluded by centuries of practice that the production rate of high-quality baijiu increases with cellar age. To deepen the understanding of the pit mud microbiome, we determined the microbial community and metabolites of different-aged pit mud, inferred the main functional groups, and explored the forces driving the microbial community evolution through metagenomic, metabolomic, and multivariate statistical analyses. The results showed that the microbial consortia of pit mud presented a regular and directional evolutionary pattern under the impact of continuous batch-to-batch brewing activities. This work provides insight into the key roles of the pit mud microbiome in SFB production and supports the production optimization of high-quality pit mud.

Synthetic co-cultures: novel avenues for bio-based processes

In nature, microorganisms live in multi-species communities allowing microbial interactions. These interactions are lost upon establishing a pure culture, increasing the metabolic burden and limiting the metabolic potential of the isolated microbe. In the past years, synthetic microbial co-cultivation, using well-defined consortia of two or more microbes, was increasingly explored for innovative applications in biotechnology. As such, interspecies interactions take place without the complexity of an open mixed culture, minimizing undesired side reactions. Ultimately, synthetic co-cultivation allows to take well-characterized microbes 'off-the-shelf' to create ecosystems with improved process capabilities. This review highlights some of the recent developments on co-cultivation, focusing on waste-to-chemicals conversions. It also addresses fundamental knowledge on microbial interactions deriving from these studies, which is important to further develop our ability to engineer functional co-cultures for bioproduction.

Using Co-Culture to Functionalize Clostridium Fermentation

Clostridium fermentations have been developed for producing butanol and other value-added chemicals, but their development is constrained by some limitations, such as relatively high substrate cost and the need to maintain an anaerobic condition. Recently, co-culture is emerging as a popular way to address these limitations by introducing a partner strain with Clostridium. Generally speaking, the co-culture strategy enables the use of a cheaper substrate, maintains the growth of Clostridium without any anaerobic treatment, improves product yields, and/or widens the product spectrum. Herein, we review recent developments of co-culture strategies involving Clostridium species according to their partner stains' functions with representative examples. We also discuss research challenges that need to be addressed for the future development of Clostridium co-cultures.

Microbial Upgrading of Acetate into Value-Added Products-Examining Microbial Diversity, Bioenergetic Constraints and Metabolic Engineering Approaches

Ecological concerns have recently led to the increasing trend to upgrade carbon contained in waste streams into valuable chemicals. One of these components is acetate. Its microbial upgrading is possible in various species, with Escherichia coli being the best-studied. Several chemicals derived from acetate have already been successfully produced in E. coli on a laboratory scale, including acetone, itaconic acid, mevalonate, and tyrosine. As acetate is a carbon source with a low energy content compared to glucose or glycerol, energy- and redox-balancing plays an important role in acetate-based growth and production. In addition to the energetic challenges, acetate has an inhibitory effect on microorganisms, reducing growth rates, and limiting product concentrations. Moreover, extensive metabolic engineering is necessary to obtain a broad range of acetate-based products. In this review, we illustrate some of the necessary energetic considerations to establish robust production processes by presenting calculations of maximum theoretical product and carbon yields. Moreover, different strategies to deal with energetic and metabolic challenges are presented. Finally, we summarize ways to alleviate acetate toxicity and give an overview of process engineering measures that enable sustainable acetate-based production of value-added chemicals.

Advances and Applications of Clostridium Co-culture Systems in Biotechnology

Clostridium spp. are important microorganisms that can degrade complex biomasses such as lignocellulose, which is a widespread and renewable natural resource. Co-culturing Clostridium spp. and other microorganisms is considered to be a promising strategy for utilizing renewable feed stocks and has been widely used in biotechnology to produce bio-fuels and bio-solvents. In this review, we summarize recent progress on the Clostridium co-culture system, including system unique advantages, composition, products, and interaction mechanisms. In addition, biochemical regulation and genetic modifications used to improve the Clostridium co-culture system are also summarized. Finally, future prospects for Clostridium co-culture systems are discussed in light of recent progress, challenges, and trends.

Profiling prokaryotic community in pit mud of Chinese strong-aroma type liquor by using oligotrophic culturing

Pit mud microbiota plays a key role in flavour production for Chinese strong-aroma type liquor. However, the pit mud microbiota cannot be cultured in laboratory. In this study, an oligotrophic medium with acetate as carbon source was used to enrich pit mud microbiota. The 16S rRNA gene amplicon sequencing was applied to examine the microbial dynamics of the enrichment consortia. Both methanogens and bacteria were simultaneously enriched. Euryarchaeota, Bacteroidetes and Firmicutes were the top 3 enriched phyla, and 31 genera were successfully enriched. More specifically, 11 genera (65%) out of the 17 dominant genera in pit mud were successfully enriched, including Petrimonas, Proteiniphilum, Anaerocella, Hydrogenispora, Methanosarcina, Fermentimonas, LNR_A2-18, Sedimentibacter, Lutispora, Syntrophomonas and Aminobacterium. Furthermore, 20 rare genera in the analyzed pit mud samples were also enriched. Aceticlastic Methanosaeta and Methanosarcina were found to be dominant methanogens in the enrichment consortia. Metagenomic sequencing was then applied to the enriched microbial consortia to explore the metabolic potentials of pit mud microbes. Aceticlastic methanogenesis pathway of Methanosaeta was reconstructed. Furthermore, 26 high-quality metagenome-assembled genomes (MAGs) were obtained based on the metagenomic binning analysis. Moreover, nutrients in pit mud were found to be crucial to sustain the methanogenesis of the enriched microbial consortia. These results suggested that the enrichment approach by using oligotrophic culturing can effectively cultivate the pit mud microbiota. Combined with metagenomics, the oligotrophic culturing will be greatly helpful to decipher the community composition and metabolic potentials of pit mud microbiota.

Effect of tungsten and selenium on C1 gas bioconversion by an enriched anaerobic sludge and microbial community analysis

The effect of trace metals, namely tungsten and selenium, on the production of acids and alcohols through gas fermentation by a CO-enriched anaerobic sludge in a continuous gas-fed bioreactor was investigated. The CO-enriched sludge was first supplied with a tungsten-deficient medium (containing selenium) and in a next assay, a selenium-deficient medium (containing tungsten) was fed to the bioreactor, at a CO gas flow rate of 10 mL/min. In the absence of tungsten (tungstate), an initial pH of 6.2 followed by a pH decrease to 4.9 yielded 7.34 g/L acetic acid as the major acid during the high pH period. Subsequently, bioconversion of the acids at a lower pH of 4.9 yielded only 1.85 g/L ethanol and 1.2 g/L butanol in the absence of tungsten (tungstate). A similar follow up assay in the same bioreactor with two consecutive periods at different pH values (i.e., 6.2 and 4.9) with a selenium deficient medium yielded 6.6 g/L acetic acid at pH 6.2 and 4 g/L ethanol as well as 1.88 g/L butanol at pH 4.9. The results from the microbial community analysis showed that the only known CO fixing microorganism able to produce alcohols detected in the bioreactor was Clostridium autoethanogenum, both in the tungsten and the selenium deprived media, although that species has so far not been reported to be able to produce butanol. No other solventogenic acetogen was detected.

Effect of pH, yeast extract and inorganic carbon on chain elongation for hexanoic acid production

Several anaerobic bioconversion technologies produce short chain volatile fatty acids and sometimes ethanol, which can together be elongated to hexanoic acid (C6 acid) by Clostridium kluyveri in a secondary fermentation process. Initiatives are needed to further optimize the process. Therefore, five strategies were tested aiming at elucidating their influence on hexanoic acid production from mixtures of acetic acid, butyric acid and ethanol. pH-regulated bioreactors, maintained at pH 7.5, 6.8 or 6.4 led to maximum C6 acid concentrations of, respectively, 19.4, 18.3 and 13.3 g L^-1. At pH 6.8, yeast extract omission resulted in a decrease of the hexanoic acid concentration to 12.0 g L^-1 while the addition of an inorganic carbon source, such as bicarbonate, for pH control, increased the C6 acid concentration up to 21.4 g L^-1. This research provides guidelines for efficient improved production of hexanoic acid by pure cultures of C. kluyveri, contributing to the state of art.

Road to full bioconversion of biowaste to biochemicals centering on chain elongation: A mini review

Production of biochemicals from waste streams has been attracting increasing worldwide interest to achieve climate protection goals. Chain elongation (CE) for production of medium-chain carboxylic acids (MCCAs, especially caproate, enanthate and caprylate) from diverse biowaste has emerged as a potential economic and environmental technology for a sustainable society. The present mini review summarizes the research utilizing various synthetic or real waste-derived substrates available for MCCA production. Additionally, the microbial characteristics of the CE process are surveyed and discussed. Considering that a large proportion of recalcitrantly biodegradable biowaste and residues cannot be further utilized by CE systems and remain to be treated and disposed, we propose here a loop concept of bioconversion of biowaste to MCCAs making full use of the biowaste with zero emission. This could make possible an alternative technology for synthesis of value-added products from a wide range of biowaste, or even non-biodegradable waste (such as, plastics and rubbers). Meanwhile, the remaining scientific questions, unsolved problems, application potential and possible developments for this technology are discussed.