Advances and Applications of Clostridium Co-culture Systems in Biotechnology

Environmentally responsive changes in mucus indicators and microbiota of Chinese sturgeon Acipensersinensis

The impact of environmental factors on the health of the endangered Chinese sturgeon (Acipenser sinensis) and the potential hazards associated with sample collection for health monitoring pose urgent need to its conservation. In this study, Chinese sturgeons were selected from indoor and outdoor environments to evaluate metabolic and tissue damage indicators, along with a non-specific immune enzyme in fish mucus. Additionally, the microbiota of both water bodies and fish mucus were determined using 16S rRNA high-throughput sequencing. The correlation between the indicators and the microbiota was investigated, along with the measurement of multiple environmental factors. The results revealed significantly higher levels of two metabolic indicators, total protein (TP) and cortisol (COR) in indoor fish mucus compared to outdoor fish mucus (p < 0.05). The activities of acid phosphatase (ACP), alkaline phosphatase (ALP), creatine kinase (CK), alanine aminotransferase (ALT), aspartate aminotransferase (AST), and lactate dehydrogenase (LDH) were significantly higher in indoor fish, serving as indicators of tissue damage (p < 0.05). The activity of lysozyme (LZM) was significantly lower in indoor fish (p < 0.01). Biomarker analysis at the phylum and genus levels in outdoor samples revealed that microorganisms were primarily related to the catabolism of organic nutrients. In indoor environments, microorganisms displayed a broader spectrum of functions, including ecological niche establishment, host colonization, potential pathogenicity, and antagonism of pathogens. KEGG functional enrichment corroborated these findings. Dissolved oxygen (DO), electrical conductivity (EC), ammonia nitrogen (NH3-N), turbidity (TU), and chemical oxygen demand (COD) exerted effects on outdoor microbiota. Temperature (TEMP), nitrate (NO3-), total phosphorus (TP), and total nitrogen (TN) influenced indoor microbiota. Changes in mucus indicators, microbial structure, and function in both environments were highly correlated with these factors. Our study provides novel insights into the health impacts of different environments on Chinese sturgeon using a non-invasive method.

Utilization of plant-derived wastes as the potential biohydrogen source: a sustainable strategy for waste management

The sustainable economy has shown a renewed interest in acquiring access to the resources required to promote innovative practices that favor recycling and the reuse of existing, unconsidered things over newly produced ones. The production of biohydrogen through dark anaerobic fermentation of organic wastes is one of the intriguing possibilities for replacing fossil-based fuels through the circular economy. At present, plant-derived waste from the agro-based industry is the main global concern. When these wastes are improperly disposed of in landfills, they become the habitat for several pathogens. Additionally, it contaminates surface water as a result of runoff, and the leachate that is created from the waste enters groundwater and degrades its quality. However, cellulose and hemicellulose-rich plant wastes from agriculture fields and agro-based industries have been employed as the most efficient feedstock since carbohydrates are the primary substrate for the synthesis of biohydrogen. To produce biohydrogen from plant-derived wastes on a large scale, it is necessary to explore comprehensive knowledge of lab-scale parameters and pretreatment strategies. This paper summarizes the problems associated with the improper management of plant-derived wastes and discusses the recent developments in dark fermentation and substrate pretreatment techniques with the goal of gaining significant insight into the biohydrogen production process. It also highlights the utilization of anaerobic digestate, which is left over after biohydrogen gas as feedstock for the development of value-added products such as volatile fatty acids (VFA), biochar, and biofertilizer.

Clostridium strain FAM25158, a unique endospore-forming bacterium related to Clostridium tyrobutyricum and isolated from Emmental cheese shows low tolerance to salt

The genus Clostridium is a large and diverse group of species that can cause food spoilage, including late blowing defect (LBD) in cheese. In this study, we investigated the taxonomic status of strain FAM25158 isolated from Emmental cheese with LBD using a polyphasic taxonomic and comparative genomic approach. A 16S rRNA gene sequence phylogeny suggested affiliation to the Clostridium sensu stricto cluster, with Clostridium tyrobutyricum DSM 2637T being the closest related type strain (99.16% sequence similarity). Average Nucleotide Identity (ANI) analysis revealed that strain FAM25158 is at the species threshold with C. tyrobutyricum, with ANI values ranging from 94.70 to 95.26%, while the digital DNA-DNA hybridization values were below the recommended threshold, suggesting that FAM25158 is significantly different from C. tyrobutyricum at the genomic level. Moreover, comparative genomic analysis between FAM25158 and its four closest C. tyrobutyricum relatives revealed a diversity of metabolic pathways, with FAM25158 differing from other C. tyrobutyricum strains by the presence of genes such as scrA, srcB, and scrK, responsible for sucrose utilization, and the absence of many important functional genes associated with cold and osmolality adaptation, which was further supported by phenotypic analyses. Surprisingly, strain FAM25158 exhibited unique physiologic traits, such as an optimal growth temperature of 30°C, in contrast to its closest relatives, C. tyrobutyricum species with an optimal growth temperature of 37°C. Additionally, the growth of FAM25158 was inhibited at NaCl concentrations higher than 0.5%, a remarkable observation considering its origin from cheese. While the results of this study provide novel information on the genetic content of strain FAM25158, the relationship between its genetic content and the observed phenotype remains a topic requiring further investigation.

Two-Stage and One-Stage Anaerobic Co-digestion of Vinasse and Spent Brewer Yeast Cells for Biohydrogen and Methane Production

This study aimed to evaluate the two-stage and one-stage anaerobic co-digestion of vinasse and spent brewer yeast cells (SBY) for biohydrogen and methane production. Optimization of the vinasse-to-SBY ratio and fly ash concentration of the two-stage and one-stage production processes was investigated. In the two-stage process, the vinasse-to-SBY ratio and fly ash concentration were optimized, and the leftover effluent was used for methane production. The optimum conditions for biohydrogen production were a vinasse-to-SBY ratio of 7:3% v/w and fly ash concentration of 0.4% w/v, in which the maximum hydrogen yield was 43.7 ml-H2/g-VSadded. In contrast, a vinasse-to-SBY ratio of 10:0% v/w and fly ash concentration of 0.2% w/v were considered optimal for methane production, and resulted in a maximum methane yield of 214.6 ml-CH4/g-VSadded. For the one-stage process, a vinasse-to-SBY ratio of 10:0% v/w and fly ash concentration of 0.1% w/v were considered optimal, and resulted in a maximum methane yield of 243.6 ml-CH4/g-VSadded. In the two-stage process, the energy yield from hydrogen (0.05-0.47 kJ/g-VSadded) was 0.62%-11.78%, and the major fraction was approximately 88.22%-99.38% gain from methane (3.19-7.73 kJ/g-VSadded). For the one-stage process, the total energy yield distribution ranged from 4.20 to 8.77 kJ/g-VSadded.

Heterologous expression of NoxA confers aerotolerance in Clostridium sporogenes

Clostridium is a genus of gram-positive obligate anaerobic bacteria. Some species of Clostridium, including Clostridium sporogenes, may be of use in bacteria-mediated cancer therapy. Spores of Clostridium are inert in healthy normoxic tissue but germinate when in the hypoxic regions of solid tumors, causing tumor regression. However, such treatments fail to completely eradicate tumors partly because of higher oxygen levels at the tumor's outer rim. In this study, we demonstrate that a degree of aerotolerance can be introduced to C. sporogenes by transfer of the noxA gene from Clostridium aminovalericum. NoxA is a water-forming NADH oxidase enzyme, and so has no detrimental effect on cell viability. In addition to its potential in cancer treatment, the noxA-expressing strain described here could be used to alleviate challenges related to oxygen sensitivity of C. sporogenes in biomanufacturing.

Translational efficiency in gas-fermenting bacteria: Adding a new layer of regulation to gene expression in acetogens

Major advances in mastering metabolism of single carbon (C1) gaseous feedstocks in acetogenic microorganisms are primed to fuel the transition toward environmentally sustainable and cost-efficient production schemes of biofuels and value-added biochemicals. Since acetogens grow under autotrophic energy-limited conditions, protein synthesis is expected to be controlled. This survey integrated publicly available RNA sequencing and ribosome profiling studies of several acetogens, providing data on genome-scale transcriptional and translational responses of A. woodii, E. limosum, C. drakei, and C. ljungdahlii to autotrophic and heterotrophic growth conditions. The extent of translational efficiency turned out to vary across key functional modules in acetogens' metabolism. Translational control was confirmed to support stoichiometric protein production in multimeric complexes. Comparing the autotrophic to the heterotrophic growth condition revealed growth-dependent regulation of translational efficiency, pointing at translational buffering as a widespread phenomenon shared by acetogens.

Date seed waste derived nanocatalyst and its application in production of hydrolytic enzyme, fermentative sugars and biohydrogen

Biofuel production from cellulosic biomass is a promising approach; however, the cost-intensive utilization of cellulolytic enzymes is a major roadblock to economic production. This study reports the preparation of a nanocatalyst using date seed and evaluates the impact of nanocatalysts on cellulolytic enzyme production using solid-state fermentation of date pulp waste through bacterial co-cultivation. Under optimized conditions, 30 IU/gds filter paper activity is produced in the presence of 2 mg of nanocatalyst. Cellulase showed thermal stability at 50 °C and pH 7 up to 10 h in the presence of nanocatalyst, and it produced 32.31 g/L glucose through the hydrolysis of acidic-pretreated date seeds in 24 h. Subsequently, 1788 mL/L of cumulative H2 in 24 h through cocultured dark fermentation could be produced. The approach presented in this study can be effective for multiple value additions, including nanocatalyst preparation, cellulase enzyme, and biohydrogen production.

Design and validation of a multiplex PCR method for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans

Co-cultures of clostridia with distinct physiological properties have emerged as an alternative to increase the production of butanol and other added-value compounds from biomass. The optimal performance of mixed tandem cultures may depend on the stability and fitness of each species in the consortium, making the development of specific quantification methods to separate their members crucial. In this study, we developed and tested a multiplex qPCR method targeting the 16S rRNA gene for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans in co-cultures. Designed primer pairs and probes could specifically quantify the three Clostridium species with no cross-reactions thus allowing significant changes in their growth kinetics in the consortia to be detected and correlated with productivity. The method was used to test a suitable medium composition for simultaneous growth of the three species. We show that higher alcohol productions were obtained when combining C. carboxidivorans and C. acetobutylicum compared to individual cultures, and further improved (> 90%) in the triplet consortium. Altogether, the methodology could be applied to fermentation processes targeting butanol productions from lignocellulosic feedstocks with a higher substrate conversion efficiency.

Biotechnological production of omega-3 fatty acids: current status and future perspectives

Omega-3 fatty acids, including alpha-linolenic acids (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), have shown major health benefits, but the human body's inability to synthesize them has led to the necessity of dietary intake of the products. The omega-3 fatty acid market has grown significantly, with a global market from an estimated USD 2.10 billion in 2020 to a predicted nearly USD 3.61 billion in 2028. However, obtaining a sufficient supply of high-quality and stable omega-3 fatty acids can be challenging. Currently, fish oil serves as the primary source of omega-3 fatty acids in the market, but it has several drawbacks, including high cost, inconsistent product quality, and major uncertainties in its sustainability and ecological impact. Other significant sources of omega-3 fatty acids include plants and microalgae fermentation, but they face similar challenges in reducing manufacturing costs and improving product quality and sustainability. With the advances in synthetic biology, biotechnological production of omega-3 fatty acids via engineered microbial cell factories still offers the best solution to provide a more stable, sustainable, and affordable source of omega-3 fatty acids by overcoming the major issues associated with conventional sources. This review summarizes the current status, key challenges, and future perspectives for the biotechnological production of major omega-3 fatty acids.

Sulfate reduction behavior in response to changing of pressure coupling with temperature inside landfill

The behavior of sulfate reduction, which was the source of hydrogen sulfide (H2S) odor, was investigated under changing pressure and temperature conditions inside landfills. The results showed that the release of H2S and methyl mercaptan (MM) was significantly inhibited at 25 °C and 50 °C under pressure, and the highest H2S and MM concentrations released were only 0.82 %-1.30 % and 1.87 %-4.32 % of atmospheric pressure, respectively. Analysis of the microbial community structure and identification of sulfate-reducing bacteria (SRB) revealed that temperature significantly altered the microbial community in the landfill environment, while pressure inhibited some bacteria and induced the growth and reproduction of specific bacteria. Key SRB (Desulfosporosinus-ASV212, Desulfitibacter-ASV1744) mediated differentiated sulfate reduction behavior in the pressure-bearing environment at 25 °C, while key SRB (Dethiobacter-ASV177, Desulfitibacter-ASV2355 and ASV316) were involved at 50 °C. This study provides a theoretical basis for the formulation of landfill gas management and control strategies.

Inorganic Carbon Assimilation and Electrosynthesis of Platform Chemicals in Bioelectrochemical Systems (BESs) Inoculated with Clostridium saccharoperbutylacetonicum N1-H4

The need for greener processes to satisfy the demand of platform chemicals together with the possibility of reusing CO2 from human activities has recently encouraged research on the set-up, optimization, and development of bioelectrochemical systems (BESs) for the electrosynthesis of organic compounds from inorganic carbon (CO2, HCO3−). In the present study, we tested the ability of Clostridium saccharoperbutylacetonicum N1-4 (DSMZ 14923) to produce acetate and D-3-hydroxybutyrate from inorganic carbon present in a CO2:N2 gas mix. At the same time, we tested the ability of a Shewanella oneidensis MR1 and Pseudomonas aeruginosa PA1430/CO1 consortium to provide reducing power to sustain carbon assimilation at the cathode. We tested the performance of three different systems with the same layouts, inocula, and media, but with the application of 1.5 V external voltage, of a 1000 Ω external load, and without any connection between the electrodes or external devices (open circuit voltage, OCV). We compared both CO2 assimilation rate and production of metabolites (formate, acetate 3-D-hydroxybutyrate) in our BESs with the values obtained in non-electrogenic control cultures and estimated the energy used by our BESs to assimilate 1 mol of CO2. Our results showed that C. saccharoperbutylacetonicum NT-1 achieved the maximum CO2 assimilation (95.5%) when the microbial fuel cells (MFCs) were connected to the 1000 Ω external resistor, with the Shewanella/Pseudomonas consortium as the only source of electrons. Furthermore, we detected a shift in the metabolism of C. saccharoperbutylacetonicum NT-1 because of its prolonged activity in BESs. Our results open new perspectives for the utilization of BESs in carbon capture and electrosynthesis of platform chemicals.

Biotic stress-induced changes in root exudation confer plant stress tolerance by altering rhizospheric microbial community

Every organism on the earth maintains some kind of interaction with its neighbours. As plants are sessile, they sense the varied above-ground and below-ground environmental stimuli and decipher these dialogues to the below-ground microbes and neighbouring plants via root exudates as chemical signals resulting in the modulation of the rhizospheric microbial community. The composition of root exudates depends upon the host genotype, environmental cues, and interaction of plants with other biotic factors. Crosstalk of plants with biotic agents such as herbivores, microbes, and neighbouring plants can change host plant root exudate composition, which may permit either positive or negative interactions to generate a battlefield in the rhizosphere. Compatible microbes utilize the plant carbon sources as their organic nutrients and show robust co-evolutionary changes in changing circumstances. In this review, we have mainly focused on the different biotic factors responsible for the synthesis of alternative root exudate composition leading to the modulation of rhizosphere microbiota. Understanding the stress-induced root exudate composition and resulting change in microbial community can help us to devise strategies in engineering plant microbiomes to enhance plant adaptive capabilities in a stressful environment.

Model-driven approach for the production of butyrate from CO2/H2 by a novel co-culture of C. autoethanogenum and C. beijerinckii

One-carbon (C1) compounds are promising feedstocks for the sustainable production of commodity chemicals. CO₂ is a particularly advantageous C1-feedstock since it is an unwanted industrial off-gas that can be converted into valuable products while reducing its atmospheric levels. Acetogens are microorganisms that can grow on CO₂/H₂ gas mixtures and syngas converting these substrates into ethanol and acetate. Co-cultivation of acetogens with other microbial species that can further process such products, can expand the variety of products to, for example, medium chain fatty acids (MCFA) and longer chain alcohols. Solventogens are microorganisms known to produce MCFA and alcohols via the acetone-butanol-ethanol (ABE) fermentation in which acetate is a key metabolite. Thus, co-cultivation of an acetogen and a solventogen in a consortium provides a potential platform to produce valuable chemicals from CO₂. In this study, metabolic modeling was implemented to design a new co-culture of an acetogen and a solventogen to produce butyrate from CO₂/H₂ mixtures. The model-driven approach suggested the ability of the studied solventogenic species to grow on lactate/glycerol with acetate as co-substrate. This ability was confirmed experimentally by cultivation of Clostridium beijerinckii on these substrates in batch serum bottles and subsequently in pH-controlled bioreactors. Community modeling also suggested that a novel microbial consortium consisting of the acetogen Clostridium autoethanogenum, and the solventogen C. beijerinckii would be feasible and stable. On the basis of this prediction, a co-culture was experimentally established. C. autoethanogenum grew on CO₂/H₂ producing acetate and traces of ethanol. Acetate was in turn, consumed by C. beijerinckii together with lactate, producing butyrate. These results show that community modeling of metabolism is a valuable tool to guide the design of microbial consortia for the tailored production of chemicals from renewable resources.

Enzymatic Characterization of Unused Biomass Degradation Using the Clostridium cellulovorans Cellulosome

The cellulolytic system of Clostridium cellulovorans mainly consisting of a cellulosome that synergistically collaborates with non-complexed enzymes was investigated using cellulosic biomass. The cellulosomes were isolated from the culture supernatants with shredded paper, rice straw and sugarcane bagasse using crystalline cellulose. Enzyme solutions, including the cellulosome fractions, were analyzed by SDS-PAGE and Western blot using an anti-CbpA antibody. As a result, C. cellulovorans was able to completely degrade shredded paper for 9 days and to be continuously cultivated by the addition of new culture medium containing shredded paper, indicating, through TLC analysis, that its degradative products were glucose and cellobiose. Regarding the rice straw and sugarcane bagasse, while the degradative activity of rice straw was most active using the cellulosome in the culture supernatant of rice straw medium, that of sugarcane bagasse was most active using the cellulosome from the supernatant of cellobiose medium. Based on these results, no alcohols were found when C. acetobutylicum was cultivated in the absence of C. cellulovorans as it cannot degrade the cellulose. While 1.5 mM of ethanol was produced with C. cellulovorans cultivation, both n-butanol (1.67 mM) and ethanol (1.89 mM) were detected with the cocultivation of C. cellulovorans and C. acetobutylicum. Regarding the enzymatic activity evaluation against rice straw and sugarcane bagasse, the rice straw cellulosome fraction was the most active when compared against rice straw. Furthermore, since we attempted to choose reaction conditions more efficiently for the degradation of sugarcane bagasse, a wet jet milling device together with L-cysteine as a reducing agent was used. As a result, we found that the degradation activity was almost twice as high with 10 mM L-cysteine compared with without it. These results will provide new insights for biomass utilization.

Leveraging substrate flexibility and product selectivity of acetogens in two-stage systems for chemical production

Carbon dioxide (CO₂ ) stands out as sustainable feedstock for developing a circular carbon economy whose energy supply could be obtained by boosting the production of clean hydrogen from renewable electricity. H₂ -dependent CO₂ gas fermentation using acetogenic microorganisms offers a viable solution of increasingly demonstrated value. While gas fermentation advances to achieve commercial process scalability, which is currently limited to a few products such as acetate and ethanol, it is worth taking the best of the current state-of-the-art technology by its integration within innovative bioconversion schemes. This review presents multiple scenarios where gas fermentation by acetogens integrate into double-stage biotechnological production processes that use CO₂ as sole carbon feedstock and H₂ as energy carrier for products' synthesis. In the integration schemes here reviewed, the first stage can be biotic or abiotic while the second stage is biotic. When the first stage is biotic, acetogens act as a biological platform to generate chemical intermediates such as acetate, formate and ethanol that become substrates for a second fermentation stage. This approach holds the potential to enhance process titre/rate/yield metrics and products' spectrum. Alternatively, when the first stage is abiotic, the integrated two-stage scheme foresees, in the first stage, the catalytic transformation of CO₂ into C₁ products that, in the second stage, can be metabolized by acetogens. This latter scheme leverages the metabolic flexibility of acetogens in efficient utilization of the products of CO₂ abiotic hydrogenation, namely formate and methanol, to synthesize multicarbon compounds but also to act as flexible catalysts for hydrogen storage or production.

Biosynthesis of value-added bioproducts from hemicellulose of biomass through microbial metabolic engineering

Hemicellulose is the second most abundant carbohydrate in lignocellulosic biomass and has extensive applications. In conventional biomass refinery, hemicellulose is easily converted to unwanted by-products in pretreatment and therefore can't be fully utilized. The present study aims to summarize the most recent development of lignocellulosic polysaccharide degradation and fully convert it to value-added bioproducts through microbial and enzymatic catalysis. Firstly, bioprocess and microbial metabolic engineering for enhanced utilization of lignocellulosic carbohydrates were discussed. The bioprocess for degradation and conversion of natural lignocellulose to monosaccharides and organic acids using anaerobic thermophilic bacteria and thermostable glycoside hydrolases were summarized. Xylose transmembrane transporting systems in natural microorganisms and the latest strategies for promoting the transporting capacity by metabolic engineering were summarized. The carbon catabolite repression effect restricting xylose utilization in microorganisms, and metabolic engineering strategies developed for co-utilization of glucose and xylose were discussed. Secondly, the metabolic pathways of xylose catabolism in microorganisms were comparatively analyzed. Microbial metabolic engineering for converting xylose to value-added bioproducts based on redox pathways, non-redox pathways, pentose phosphate pathway, and improving inhibitors resistance were summarized. Thirdly, strategies for degrading lignocellulosic polysaccharides and fully converting hemicellulose to value-added bioproducts through microbial metabolic engineering were proposed.

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Hemicellulose is the main carbohydrate of biomass and has valuable applications.

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Hemicellulose is underutilized in conventional biomass refinery and pretreatment.

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Microbial and enzymatic catalysis were applied for hemicellulose utilization.

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Xylose is converted to value-added bioproducts by metabolic engineering.

The effects of pH on the production of volatile fatty acids and microbial dynamics in long-term reactor operation

Volatile fatty acids, intermediate products of anaerobic digestion, are one of the most promising biobased products. In this study, the effects of acidic (pH 5), neutral (without pH adjustment) and alkali (pH 10) pH on production efficiency and composition of volatile fatty acids (VFAs) and bacterial community profile were analyzed. The anaerobic sequencing batch reactors were fed cheese production wastewater as substrate and inoculated by anaerobic granular seed sludge. The results showed that acidic pH improved VFA production yield (0.92 at pH 5; 0.42 at pH 10 and 0.21 gCOD/gVS at neutral pH). Furthermore, propionic acid was dominant under both pH 10 (64 ± 20%) and neutral pH (72 ± 8%), whereas, acetic acid (23 ± 20%4), propionic acid (22 ± 3%), butyric acid (21 ± 4%) and valeric acid (15 ± 8%) were almost equally distributed under pH 5. Adaptation of bacterial community to different pH conditions might steer the acid profile: Bacteroidetes (50.07 ± 2%) under pH 10, Proteobacteria (40.74 ± 7%) under neutral pH and Firmicutes (47.64 ± 9%) under pH 5 were the most dominant phylum, respectively. Results indicated pH plays a significant role in VFA production, acid composition, and bacterial community structure. However, in order to gain a concrete understanding effects of pH, characterization of intracellular and extracellular metabolites with dynamics of the microbial community is required.

Probiotic Potential of Clostridium spp.-Advantages and Doubts

Clostridium spp. is a large genus of obligate anaerobes and is an extremely heterogeneous group of bacteria that can be classified into 19 clusters. Genetic analyses based on the next-generation sequencing of 16S rRNA genes and metagenome analyses conducted on human feces, mucosal biopsies, and luminal content have shown that the three main groups of strict extremophile anaerobes present in the intestines are Clostridium cluster IV (also known as the Clostridium leptum group), Clostridium cluster XIVa (also known as the Clostridium coccoides group) and Bacteroides. In addition to the mentioned clusters, some C. butyricum strains are also considered beneficial for human health. Moreover, this bacterium has been widely used as a probiotic in Asia (particularly in Japan, Korea, and China). The mentioned commensal Clostridia are involved in the regulation and maintenance of all intestinal functions. In the literature, the development processes of new therapies are described based on commensal Clostridia activity. In addition, some Clostridia are associated with pathogenic processes. Some C. butyricum strains detected in stool samples are involved in botulism cases and have also been implicated in severe diseases such as infant botulism and necrotizing enterocolitis in preterm neonates. The aim of this study is to review reports on the possibility of using Clostridium strains as probiotics, consider their positive impact on human health, and identify the risks associated with the expression of their pathogenic properties.

Hydrogen Production from Enzymatic Hydrolysates of Alkali Pre-Treated Giant Reed (Arundo donax L.)

The perennial rhizomatous grass giant reed (Arundo donax L.) can be exploited to produce hydrogen by dark fermentation. This implies a high availability of simple sugars, like glucose and xylose, and, thus, a pre-treatment is necessary to remove lignin and expose the holocellulose to enzymatic attack. This study aimed at evaluating the hydrogen production from giant reed hydrolysates. Giant reed dry meal was pre-treated with diluted NaOH (1.2% weight/weight), then the solid fraction was separated from the alkaline black liquor by filtration, enzymatically hydrolyzed with a cellulase blend (Cellic CTec2), and fermented in mesophilic batch conditions with a microbial consortium derived from pig slurry. The impact on hydrogen yield of initial pH was evaluated by comparing the hydrogen production from hydrolysates with not adjusted (5.3) or adjusted initial pH (8.7) using NaOH or alkaline black liquor. The highest hydrogen yield, 2.0 mol/mol of hexoses, was obtained with alkaline initial pH 8.7, regardless of how the pH adjustment was managed. The yield was 39% higher than that obtained in reactors with initial pH 5.3. In conclusion, thermo-alkaline pre-treatment followed by enzymatic saccharification and initial pH adjustment at 8.7 with the black liquor remaining after pre-treatment is a promising strategy to produce hydrogen from giant reeds in dark fermentation.

Novel strategies towards efficient molecular biohydrogen production by dark fermentative mechanism: present progress and future perspective

In the scenario of alarming increase in greenhouse and toxic gas emissions from the burning of conventional fuels, it is high time that the population drifts towards alternative fuel usage to obviate pollution. Hydrogen is an environment-friendly biofuel with high energy content. Several production methods exist to produce hydrogen, but the least energy intensive processes are the fermentative biohydrogen techniques. Dark fermentative biohydrogen production (DFBHP) is a value-added, less energy-consuming process to generate biohydrogen. In this process, biohydrogen can be produced from sugars as well as complex substrates that are generally considered as organic waste. Yet, the process is constrained by many factors such as low hydrogen yield, incomplete conversion of substrates, accumulation of volatile fatty acids which lead to the drop of the system pH resulting in hindered growth and hydrogen production by the bacteria. To circumvent these drawbacks, researchers have come up with several strategies that improve the yield of DFBHP process. These strategies can be classified as preliminary methodologies concerned with the process optimization and the latter that deals with pretreatment of substrate and seed sludge, bioaugmentation, co-culture of bacteria, supplementation of additives, bioreactor design considerations, metabolic engineering, nanotechnology, immobilization of bacteria, etc. This review sums up some of the improvement techniques that profoundly enhance the biohydrogen productivity in a DFBHP process.

An artificial coculture fermentation system for industrial propanol production

Converting plant biomass into biofuels and biochemicals via microbial fermentation has received considerable attention in the quest for finding renewable energies and materials. Most approaches have so far relied on cultivating a single microbial strain, tailored for a specific purpose. However, this contrasts to how nature works, where microbial communities rather than single species perform all tasks. In artificial coculture systems, metabolic synergies are rationally designed by carefully selecting and simultaneously growing different microbes, taking advantage of the broader metabolic space offered by the use of multiple organisms.

1-propanol and 2-propanol, as biofuels and precursors for propylene, are interesting target molecules to valorize plant biomass. Some solventogenic Clostridia can naturally produce 2-propanol in the so-called Isopropanol-Butanol-Ethanol (IBE) fermentation, by coupling 2-propanol synthesis to acetate and butyrate reduction into ethanol and 1-butanol.

In this work, we hypothesized propanoate would be converted into 1-propanol by the IBE metabolism, while driving at the same time 2-propanol synthesis. We first verified this hypothesis and chose two propionic acid bacteria (PAB) strains as propanoate producers. While consecutive PAB and IBE fermentations only resulted in low propanol titers, coculturing Propionibacterium freudenreichii and Clostridium beijerinckii at various inoculation ratios yielded much higher solvent concentrations, with as much as 21 g/L of solvents (58% increase compared to C. beijerinckii monoculture) and 12 g/L of propanol (98% increase). Taken together, our results underline how artificial cocultures can be used to foster metabolic synergies, increasing fermentative performances and orienting the carbon flow towards a desired product.

Microbial Utilization of Next-Generation Feedstocks for the Biomanufacturing of Value-Added Chemicals and Food Ingredients

Global shift to sustainability has driven the exploration of alternative feedstocks beyond sugars for biomanufacturing. Recently, C1 (CO₂, CO, methane, formate and methanol) and C2 (acetate and ethanol) substrates are drawing great attention due to their natural abundance and low production cost. The advances in metabolic engineering, synthetic biology and industrial process design have greatly enhanced the efficiency that microbes use these next-generation feedstocks. The metabolic pathways to use C1 and C2 feedstocks have been introduced or enhanced into industrial workhorses, such as Escherichia coli and yeasts, by genetic rewiring and laboratory evolution strategies. Furthermore, microbes are engineered to convert these low-cost feedstocks to various high-value products, ranging from food ingredients to chemicals. This review highlights the recent development in metabolic engineering, the challenges in strain engineering and bioprocess design, and the perspectives of microbial utilization of C1 and C2 feedstocks for the biomanufacturing of value-added products.

Recent Advances in Bioutilization of Marine Macroalgae Carbohydrates: Degradation, Metabolism, and Fermentation

Marine macroalgae are considered renewable natural resources due to their high carbohydrate content, which gives better utilization value in biorefineries and higher value conversion than first- and second-generation biomass. However, due to the diverse composition, complex structure, and rare metabolic pathways of macroalgae polysaccharides, their bioavailability needs to be improved. In recent years, enzymes and pathways related to the degradation and metabolism of macroalgae polysaccharides have been continuously developed, and new microbial fermentation platforms have emerged. Aiming at the bioutilization and transformation of macroalgae resources, this review describes the latest research results from the direction of green degradation, biorefining, and metabolic pathway design, including summarizing the the latest biorefining technology and the fermentation platform design of agarose, alginate, and other polysaccharides. This information will provide new research directions and solutions for the biotransformation and utilization of marine macroalgae.

ACETONE-BUTYL FERMENTATION PECULIARITIES OF THE BUTANOL STRAINS -PRODUCER

The aim of this review was to generalize and analyze the features of acetone-butyl fermentation as a type of butyric acid fermentation in the process of obtaining butanol as an alternative biofuel. Methods. The methods of analysis and generalization of analytical information and literature sources were used in the review. The results were obtained using the following methods such as microbiological (morphological properties of strains), chromatographic (determination of solvent concentration), spectrophotometric (determination of bacterial concentration), and molecular genetic (phylogenetic analysis of strains). Results. The process of acetone-butyl fermentation was analyzed, the main producer strains were considered, the features of the relationship between alcohol formation and sporulation were described, the possibility of butanol obtaining from synthesis gas was shown, and the features of the industrial production of butanol were considered. Conclusions. The features of the mechanism of acetone-butyl fermentation (the relationships between alcohol formation and sporulation, the duration of the acid-forming and alcohol-forming stages during batch fermentation depending on the change in the concentration of H2, CO, partial pressure, organic acids and mineral additives) and obtaining an enrichment culture during the production of butanol as an alternative fuel were shown. The possibility of using synthesis gas as a substrate for reducing atmospheric emissions during the fermentation process was shown. The direction of increasing the productivity of butanol-producing strains to create a competitive industrial biofuel technology was proposed.

Hexavalent Chromium Removal and Prokaryotic Community Analysis in Glass Column Reactor Packed with Aspen Wood as Solid Organic Substrate

Microbial hexavalent chromium (Cr(VI)) reduction is a promising method for Cr(VI)-laden wastewater treatment. However, the soluble organic substrate required for heterotrophic microbial Cr(VI) reduction necessitates constant supervision, and an excessive supply of soluble organic substrate can result in deterioration of the quality of the effluent. In this study, we evaluated aspen wood, a low-cost lignocellulose biomass, as a solid organic substrate for heterotrophic Cr(VI) reduction. A laboratory-scale aspen wood-packed glass column reactor inoculated with activated sludge was operated for 148 days for evaluation. Following reactor operation, an effective average dissolved Cr(VI) removal rate of 0.75 mg L^-1 h^-1 was confirmed under an average dissolved Cr(VI) loading rate of 0.90 mg L^-1 h^-1. Subsequently, 16S ribosomal ribonucleic acid gene amplicon sequencing analysis revealed that the dominant prokaryotic operational taxonomic units detected in the reactor were associated with prokaryotic lineages with the capacity for lignocellulose biodegradation, Cr compound resistance, and Cr(VI) reduction. Proteobacteria and Chloroflexi were two major prokaryotic phyla in the reactor. Our data indicate that aspen wood is an effective solid organic substrate for the development of simplified, effective, and low-cost microbial Cr(VI)-removing reactors.

Monitoring co-cultures of Clostridium carboxidivorans and Clostridium kluyveri by fluorescence in situ hybridization with specific 23S rRNA oligonucleotide probes

The development of co-cultures of clostridial strains which combine different physiological traits represents a promising strategy to achieve the environmentally friendly production of biofuels and chemicals. For the optimization of such co-cultures it is essential to monitor their composition and stability throughout fermentation. FISH is a quick and sensitive method for the specific labeling and quantification of cells within microbial communities. This technique is neither limited by the anaerobic fermenter environment nor by the need of prior genetic modification of strains. In this study, two specific 23S rRNA oligonucleotide probes, ClosKluy and ClosCarb, were designed for the monitoring of C. kluyveri and C. carboxidivorans, respectively. After the optimization of hybridization conditions for both probes, which was achieved at 30% (v/v) formamide, a high specificity was observed with epifluorescence microscopy using cells from different pure reference strains. The discriminating properties of the ClosKluy and ClosCarb probes was verified with samples from heterotrophic co-cultures in anaerobic flasks as well as autotrophic stirred-tank bioreactor co-cultures of C. kluyveri and C. carboxidivorans. Besides being suited to monitor defined co-cultures of these two species, the new specific FISH oligonucleotide probes for C. kluyveri and C. carboxidivorans additionally have potential to be applied in environmental studies.

Waste-to-nutrition: a review of current and emerging conversion pathways

Residual biomass is acknowledged as a key sustainable feedstock for the transition towards circular and low fossil carbon economies to supply whether energy, chemical, material and food products or services. The latter is receiving increasing attention, in particular in the perspective of decoupling nutrition from arable land demand. In order to provide a comprehensive overview of the technical possibilities to convert residual biomasses into edible ingredients, we reviewed over 950 scientific and industrial records documenting existing and emerging waste-to-nutrition pathways, involving over 150 different feedstocks here grouped under 10 umbrella categories: (i) wood-related residual biomass, (ii) primary crop residues, (iii) manure, (iv) food waste, (v) sludge and wastewater, (vi) green residual biomass, (vii) slaughterhouse by-products, (viii) agrifood co-products, (ix) C₁ gases and (x) others. The review includes a detailed description of these pathways, as well as the processes they involve. As a result, we proposed four generic building blocks to systematize waste-to-nutrition conversion sequence patterns, namely enhancement, cracking, extraction and bioconversion. We further introduce a multidimensional representation of the biomasses suitability as potential as nutritional sources according to (i) their content in anti-nutritional compounds, (ii) their degree of structural complexity and (iii) their concentration of macro- and micronutrients. Finally, we suggest that the different pathways can be grouped into eight large families of approaches: (i) insect biorefinery, (ii) green biorefinery, (iii) lignocellulosic biorefinery, (iv) non-soluble protein recovery, (v) gas-intermediate biorefinery, (vi) liquid substrate alternative, (vii) solid-substrate fermentation and (viii) more-out-of-slaughterhouse by-products. The proposed framework aims to support future research in waste recovery and valorization within food systems, along with stimulating reflections on the improvement of resources' cascading use.

Comparative genome analysis of Clostridium beijerinckii strains isolated from pit mud of Chinese strong flavor baijiu ecosystem

Clostridium beijerinckii is a well-known anaerobic solventogenic bacterium which inhabits a wide range of different niches. Previously, we isolated five butyrate-producing C. beijerinckii strains from pit mud (PM) of strong-flavor baijiu (SFB) ecosystems. Genome annotation of the five strains showed that they could assimilate various carbon sources as well as ammonium to produce acetate, butyrate, lactate, hydrogen, and esters but did not produce the undesirable flavors isopropanol and acetone, making them useful for further exploration in SFB production. Our analysis of the genomes of an additional 233 C. beijerinckii strains revealed an open pangenome based on current sampling and will likely change with additional genomes. The core genome, accessory genome, and strain-specific genes comprised 1567, 8851, and 2154 genes, respectively. A total of 298 genes were found only in the five C. beijerinckii strains from PM, among which only 77 genes were assigned to Clusters of Orthologous Genes categories. In addition, 15 transposase and 12 phage integrase families were found in all five C. beijerinckii strains from PM. Between 18 and 21 genome islands were predicted for the five C. beijerinckii genomes. The existence of a large number of mobile genetic elements indicated that the genomes of the five C. beijerinckii strains evolved with the loss or insertion of DNA fragments in the PM of SFB ecosystems. This study presents a genomic framework of C. beijerinckii strains from PM that could be used for genetic diversification studies and further exploration of these strains.

Biorefinery Gets Hot: Thermophilic Enzymes and Microorganisms for Second-Generation Bioethanol Production

To mitigate the current global energy and the environmental crisis, biofuels such as bioethanol have progressively gained attention from both scientific and industrial perspectives. However, at present, commercialized bioethanol is mainly derived from edible crops, thus raising serious concerns given its competition with feed production. For this reason, lignocellulosic biomasses (LCBs) have been recognized as important alternatives for bioethanol production. Because LCBs supply is sustainable, abundant, widespread, and cheap, LCBs-derived bioethanol currently represents one of the most viable solutions to meet the global demand for liquid fuel. However, the cost-effective conversion of LCBs into ethanol remains a challenge and its implementation has been hampered by several bottlenecks that must still be tackled. Among other factors related to the challenging and variable nature of LCBs, we highlight: (i) energy-demanding pretreatments, (ii) expensive hydrolytic enzyme blends, and (iii) the need for microorganisms that can ferment mixed sugars. In this regard, thermophiles represent valuable tools to overcome some of these limitations. Thus, the aim of this review is to provide an overview of the state-of-the-art technologies involved, such as the use of thermophilic enzymes and microorganisms in industrial-relevant conditions, and to propose possible means to implement thermophiles into second-generation ethanol biorefineries that are already in operation.

Control of n-Butanol Induced Lipidome Adaptations in E. coli

The versatile compound n-butanol is one of the most promising biofuels for use in existing internal combustion engines, contributing to a smooth transition towards a clean energy society. Furthermore, n-butanol is a valuable resource to produce more complex molecules such as bioplastics. Microbial production of n-butanol from waste materials is hampered by the biotoxicity of n-butanol as it interferes with the proper functioning of lipid membranes. In this study we perform a large-scale investigation of the complete lipid-related enzyme machinery and its response to exposure to a sublethal concentration of n-butanol. We profiled, in triplicate, the growth characteristics and phospholipidomes of 116 different genetic constructs of E. coli, both in the presence and absence of 0.5% n-butanol (v/v). This led to the identification of 230 lipid species and subsequently to the reconstruction of the network of metabolites, enzymes and lipid properties driving the homeostasis of the E. coli lipidome. We were able to identify key lipids and biochemical pathways leading to altered n-butanol tolerance. The data led to new conceptual insights into the bacterial lipid metabolism which are discussed.