Comparative proteomics of the metabolic pathways involved in l-lactic acid production in Bacillus coagulans BCS13002 using different carbon sources

Bioelectrochemistry promotes microbial activity and accelerates wastewater methanogenesis in anaerobic digestion under combined exposure to antibiotics and microplastics

Antibiotics and microplastics (MPs), as pervasive environmental pollutants, coexist in wastewater and pose significant threats to public health. Bioelectrochemical systems (BES), which integrate microbial metabolism and electrochemical redox reactions, exhibit considerable potential for treating recalcitrant pollutants and recovering bioenergy from wastewater. This study represents the first comprehensive investigation into the application of BES for treating wastewater contaminated with multiple antibiotics and MPs, focusing on the synergistic effects of composite pollutants rather than isolated toxicological impacts. Compared to conventional anaerobic digestion, BES demonstrated enhanced wastewater treatment efficiency (14.39 %) and methane recovery (14.32 %). Under pollutant exposure and electrical stimulation, significant alterations in microbial cell viability and enzyme activities were observed. While pollutants reduced microbial species abundance, BES increased microbial diversity. The microbial community was predominantly composed of methanogens (Methanothrix), whereas fermentative bacteria (Proteiniphilum) dominated the cathode compartment. Although the addition of antibiotics did not significantly alter the overall abundance of antibiotic class and antibiotic resistance genes (ARGs), the cathode exhibited the potential to reduce their abundance. Functional gene abundance related to methane synthesis (EC:6.2.1.1) increased at the anode, while the cathode exacerbated inhibitory effects, primarily mediating acetate generation (EC:1.2.4.1, EC:2.3.1.12). These findings provide novel insights into the application of BES for treating co-contaminated wastewater, highlighting its capacity to mitigate emerging environmental challenges.

Expanded genome and proteome reallocation in a novel, robust Bacillus coagulans strain capable of utilizing pentose and hexose sugars

Bacillus coagulans, a Gram-positive thermophilic bacterium, is recognized for its probiotic properties and recent development as a microbial cell factory. Despite its importance for biotechnological applications, the current understanding of B. coagulans' robustness is limited, especially for undomesticated strains. To fill this knowledge gap, we characterized the metabolic capability and performed functional genomics and systems analysis of a novel, robust strain, B. coagulans B-768. Genome sequencing revealed that B-768 has the largest B. coagulans genome known to date (3.94 Mbp), about 0.63 Mbp larger than the average genome of sequenced B. coagulans strains, with expanded carbohydrate metabolism and mobilome. Functional genomics identified a well-equipped genetic portfolio for utilizing a wide range of C5 (xylose, arabinose), C6 (glucose, mannose, galactose), and C12 (cellobiose) sugars present in biomass hydrolysates, which was validated experimentally. For growth on individual xylose and glucose, the dominant sugars in biomass hydrolysates, B-768 exhibited distinct phenotypes and proteome profiles. Faster growth and glucose uptake rates resulted in lactate overflow metabolism, which makes B. coagulans a lactate overproducer; however, slower growth and xylose uptake diminished overflow metabolism due to the high energy demand for sugar assimilation. Carbohydrate Transport and Metabolism (COG-G), Translation (COG-J), and Energy Conversion and Production (COG-C) made up 60%-65% of the measured proteomes but were allocated differently when growing on xylose and glucose. The trade-off in proteome reallocation, with high investment in COG-C over COG-G, explains the xylose growth phenotype with significant upregulation of xylose metabolism, pyruvate metabolism, and tricarboxylic acid (TCA) cycle. Strain B-768 tolerates and effectively utilizes inhibitory biomass hydrolysates containing mixed sugars and exhibits hierarchical sugar utilization with glucose as the preferential substrate.IMPORTANCEThe robustness of B. coagulans makes it a valuable microorganism for biotechnology applications; yet, this phenotype is not well understood at the cellular level. Through phenotypic characterization and systems analysis, this study elucidates the functional genomics and robustness of a novel, undomesticated strain, B. coagulans B-768, capable of utilizing inhibitory switchgrass biomass hydrolysates. The genome of B-768, enriched with carbohydrate metabolism genes, demonstrates high regulatory capacity. The coordination of proteome reallocation in Carbohydrate Transport and Metabolism (COG-G), Translation (COG-J), and Energy Conversion and Production (COG-C) is critical for effective cell growth, sugar utilization, and lactate production via overflow metabolism. Overall, B-768 is a novel, robust, and promising B. coagulans strain that can be harnessed as a microbial biomanufacturing platform to produce chemicals and fuels from biomass hydrolysates.

Innovative omics strategies in fermented fruits and vegetables: Unveiling nutritional profiles, microbial diversity, and future prospects

Fermented fruits and vegetables (FFVs) are not only rich in essential nutrients but also contain distinctive flavors, prebiotics, and metabolites. Although omics techniques have gained widespread recognition as an analytical strategy for FFVs, its application still encounters several challenges due to the intricacies of biological systems. This review systematically summarizes the advances, obstacles and prospects of genomics, transcriptomics, proteomics, metabolomics, and multi-omics strategies in FFVs. It is evident that beyond traditional applications, such as the exploration of microbial diversity, protein expression, and metabolic pathways, omics techniques exhibit innovative potential in deciphering stress response mechanisms and uncovering spoilage microorganisms. The adoption of multi-omics strategies is paramount to acquire a multidimensional network fusion, thereby mitigating the limitations of single omics strategies. Although substantial progress has been made, this review underscores the necessity for a comprehensive repository of omics data and the establishment of universal databases to ensure precision in predictions. Furthermore, multidisciplinary integration with other physical or biochemical approaches is imperative, as it enriches our comprehension of this intricate process.

Applications of Proteomics in Probiotics Having Anticancer and Chemopreventive Properties

Proteomics has grown in importance in molecular sciences because it gives vital information on protein identification, expression levels, and alteration. Cancer is one of the world's major causes of death and is the major focus of much research. Cancer risk is determined by hereditary variables as well as the body's immunological condition. Probiotics have increasing medical importance due to their therapeutic influence on the human body in the prevention and treatment of numerous chronic illnesses, including cancer, with no adverse effects. Several anticancer, anti-inflammatory, and chemopreventive probiotics are studied using different proteomic approaches like two-dimensional gel electrophoresis, liquid chromatography-mass spectrometry, and matrix-assisted laser desorption/ionization mass spectrometry. To gain relevant information about probiotic characteristics, data from the proteomic analysis are evaluated and processed using bioinformatics pipelines. Proteomic studies showed the significance of different proteomic approaches in characterization, comparing strains, and determination of oxidative stress of different probiotics. Moreover, proteomic approaches identified different proteins that are involved in glucose metabolism and the formation of cell walls or cell membranes, and the differences in the expression of critical enzymes in the HIF-1 signaling pathway, starch, and sucrose metabolism, and other critical metabolic pathways.

Recent trends in lactic acid-producing microorganisms through microbial fermentation for the synthesis of polylactic acid

Polylactic acid (PLA) is a range of unique bioplastics that are bio-based and biodegradable. PLA is currently driving market expansion for lactic acid (LA) due to its high demand as a building block in production. One of the most practical and environmentally benign techniques for synthesising PLA is through enzymatic polymerisation of microbial LA monomers. However, microbial LA fermentation does have some limitations. Firstly, it requires the use of a nutritionally rich medium. Secondly, LA production can be disrupted by bacteriophage infection or other microorganisms. Lastly, the yield can be low due to the formation of by-products through heterofermentative pathway. Considering the potential use of PLA as a replacement for conventional petrochemical-based polymers in industrial applications, researchers are focused on exploring the diversity of LA-producing microorganisms from various niches. Their goal is to study the functional properties of these microorganisms and their ability to produce industrially valuable metabolites. This review highlights the advantages and disadvantages of lactic acid-producing microorganisms used in microbial fermentation for PLA synthesis.

Metatranscriptome revealed how carbon brush addition affected the fermentation of food wastewater in the low-temperature environment

Improving the anaerobic digestion (AD) performance in low-temperature environments has become a key factor in the development of waste treatment and resource recovery in cold regions. The utilization of external carriers to form a biofilm is the simplest and most practical way to enhance the psychrophilic AD performance in cold regions. In this study, the effect of carrier addition on the fermentation performance of low-temperature (15 ± 2 °C) food wastewater was investigated by forming biofilms with carbon brushes. The results showed that although the biofilm formation enhanced methane yields (15.24%), it also caused more accumulation of propionic acid (306.99-626.89 mg/L), and the concentration of acetic acid (86.78-254.71 mg/L) was relatively low. The microbial community revealed the highest abundance of the fermentative bacterium Firmicutes and the carbon brush carrier significantly increased its relative abundance (23.74%). Metatranscriptomic sequencing revealed that the abundance level of Clostridium, Bacteroides, Sedimentibacter and Pelotomaculum was the highest, reaching 80% in all groups. In addition, the abundance level of electroactive microorganisms in biofilms was higher, while the fermentation bacteria and methanogens were lower. This showed that biofilm can enrich more electroactive microorganisms, and granular sludge needs to enrich more fermentation bacteria and methanogens to ensure metabolic activity. Further studies have found that carbon metabolism had the highest activity (27.86%-30.39%) and H+-transporting ATPase (atp) was the most dominant functional enzyme (85.50%-86.65%) involved in electron transport in low-temperature fermentation of food wastewater. Interestingly, these expression levels of active granular sludge were higher than the biofilm formed by carbon brushes. Meanwhile, analysis of the methanogenic pathway found that active granular sludge tends to be directly metabolized to realize acetate to acetyl-CoA by acetyl-CoA synthetase (ACSS), while biofilms were not significantly different in the two metabolic pathways of acetate. These results deepen the understanding of treating low-temperature food wastewater.

Bacillus sp. as a microbial cell factory: Advancements and future prospects

Bacillus sp. is one of the most distinctive gram-positive bacteria, able to grow efficiently using cheap carbon sources and secrete a variety of useful substances, which are widely used in food, pharmaceutical, agricultural and environmental industries. At the same time, Bacillus sp. is also recognized as a safe genus with a relatively clear genetic background, which is conducive to the industrial production of target metabolites. In this review, we discuss the reasons why Bacillus sp. has been so extensively studied and summarize its advances in systems and synthetic biology, engineering strategies to improve microbial cell properties, and industrial applications in several metabolic engineering applications. Finally, we present the current challenges and possible solutions to provide a reliable basis for Bacillus sp. as a microbial cell factory.

Integrated transcriptomic and metabolomic analyses identify key factors in the vitellogenesis of juvenile Sichuan bream (Sinibrama taeniatus)

Vitellogenesis is the most important stage of ovarian maturation in fish, involving the synthesis and transport of essential yolk substances and their complex mechanisms and coordination process. The liver is the main tissue involved in the vitellogenesis of oviparous animals, but studies of vitellogenesis in fish rarely include the liver and ovary as a whole. The aim of this study was to explore the molecular mechanism and associated regulatory factors behind vitellogenesis in Sichuan bream (Sinibrama taeniatus). The different stages of oogenesis were first identified by successive histological observations. Then, ovary and liver tissues that developed to 115 days (stage II, previtellogenesis stage), 165 days (stage III, vitellogenesis stage) and 185 days (stage IV, late-vitellogenesis stage) were collected for transcriptomic and metabolomic analyses, and serum testosterone (T), 17β-estradiol (E2), vitellogenin (Vtg), triiodothyronine (T3), and thyroxine (T4) levels were measured at the corresponding stages. We found that energy redistribution during vitellogenesis is mainly regulated through glycolysis, fatty acid biosynthesis and the citrate cycle pathway. In the liver, energy metabolism was promoted by activating glucolipid metabolic pathways to provide sufficient ATP, but at the same time, the ovary tends to retain nutrients rather than decompose them to produce energy. In addition, we have identified several key factors involved in the metabolism of neutral lipids, polar lipids, amino acids and vitamins, which are involved in the assembly and transport of important yolk nutrients. The initiation of vitellogenesis was found to be associated with a surge in serum E2 levels, but the sustained increase in Vtg levels in the late stage may be due more to upregulation of the estrogen receptor. These results provide valuable information about the regulation of ovarian development in cultured fish.

Improving lactic acid yield of hemicellulose from garden garbage through pretreatment of a high solid loading coupled with semi-hydrolysis using low enzyme loading

Byproduct (acetate and ethanol) generation and carbon catabolite repression are two critical impediments to lactic acid production from the hemicellulose of lignocellulosic biomass. To reduce byproduct generations, acid pretreatment with high solid loading (solid-liquid ratio 1:7) of garden garbage was conducted. The byproduct yield was only 0.30 g/g during in the subsequent lactic acid fermentation from acid pretreatment liquid and 40.8% lower than that of low solid loading (0.48 g/g). Furthermore, semi-hydrolysis with low enzyme loading (10 FPU/g garden garbage cellulase) was conducted to regulate and reduce glucose concentration in the hydrolysate, thereby relieving carbon catabolite repression. During the lactic acid fermentation process, the xylose conversion rate was restored from 48.2% (glucose-oriented hydrolysis) to 85.7%, eventually achieving a 0.49 g/g lactic acid yield of hemicellulose. Additionally, RNA-seq revealed that semi-hydrolysis with low enzyme loading down-regulated the expression of ptsH and ccpA, thereby relieving carbon catabolite repression.

Essential characteristics improvement of metallic nanoparticles loaded carbohydrate polymeric films - A review

Petroleum-based films have contributed immensely to various environmental issues. Developing green-based films from carbohydrate polymers is crucial for addressing the harms encountered. However, some limitations exist on their property, processibility, and applicability that prohibit their processing for further developments. This review discusses the potential carbohydrate polymers and their sources, film preparation methods, such as solvent-casting, tape-casting, extrusion, and thermo-mechanical compressions for green-based films using various biological polymers with their merits and demerits. Research outcomes revealed that the essential characteristics improvement achieved by incorporating different metallic nanoparticles has significantly reformed the properties of biofilms, including crystallization, mechanical stability, thermal stability, barrier function, and antimicrobial activity. The property-enhanced bio-based films made with nanoparticles are potentially interested in replacing fossil-based films in various areas, including food-packaging applications. The review paves a new way for the commercial use of numerous carbohydrate polymers to help maintain a sustainable green environment.

Lactic acid production from co-fermentation of food waste and spent mushroom substance with Aspergillus niger cellulase

The feasibility of co-fermentation of food waste and spent mushroom substance for lactic acid with Aspergillus niger cellulase replacing commercial cellulase was explored. In this study, Enterococcus mundtii was used in this study because it could utilize hexose and pentose. When the ratio of food waste and spent mushroom substance was 1:2, lactic acid concentration was 39.22 g/L, 39.28% higher than the weighted average of experimental lactic acid concentrations, indicating that the co-fermentation had positive synergistic effects. Results showed 92.62% of sugars of pretreated spent mushroom substance was released by Aspergillus niger cellulase. Moreover, when Aspergillus niger cellulase was added into the lactic acid fermentation system at 24 h, lactic acid concentration reached 48.72 g/L, which was 22.97% higher than that of the control group with commercial cellulase, because of the disappearance of Veillonella and Saccharomycetales with the Aspergillus niger cellulase addition, thus making more substrates converted into lactic acid.

Bioproduction of l- and d-lactic acids: advances and trends in microbial strain application and engineering

Lactic acid is an important platform chemical used in the food, agriculture, cosmetic, pharmaceutical, and chemical industries. It serves as a building block for the production of polylactic acid (PLA), a biodegradable polymer, which can replace traditional petroleum-based plastics and help to reduce environmental pollution. Cost-effective production of optically pure l- and d-lactic acids is necessary to achieve a quality and thermostable PLA product. This paper evaluates research advances in the bioproduction of l- and d-lactic acids using microbial fermentation. Special emphasis is given to the development of metabolically engineered microbial strains and processes tailored to alternative and flexible feedstock concepts such as: lignocellulose, glycerol, C1-gases, and agricultural-food industry byproducts. Alternative fermentation concepts that can improve lactic acid production are discussed. The potential use of inducible gene expression systems for the development of biosensors to facilitate the screening and engineering of lactic acid-producing microorganisms is discussed.

Regulatory Mechanisms of L-Lactic Acid and Taste Substances in Chinese Acid Rice Soup (Rice-Acid) Fermented With a Lacticaseibacillus paracasei and Kluyveromyces marxianus

Rice-acid has abundant taste substances and health protection function due to the various bioactive compounds it contains, including organic acids. L-lactic acid is the most abundant organic acid in rice-acid, but the regulatory mechanisms of L-lactic acid accumulation in rice-acid are obscure. In this study, we analyzed the dynamic changes in organic acids and taste substances in rice-acid in various fermentation phases and different inoculation methods. We identified the key genes involved in taste substance biosynthesis by RNA-Seq analysis and compared the data of four experimental groups. We found that the interaction of the differences in key functional genes (L-lactate dehydrogenase and D-lactate dehydrogenase) and key metabolism pathways (glycolysis, pyruvate metabolism, TCA cycle, amino acid biosynthesis, and metabolism) might interpret the accumulation of L-lactic acid, other organic acids, and taste substances in rice-acid fermented with Lacticaseibacillus paracasei. The experimental data provided the basis for exploring regulatory mechanisms of taste substance accumulation in rice-acid.

Explore the difference between the single-chamber and dual-chamber microbial electrosynthesis for biogas production performance

Microbial electrosynthesis (MES) is an advanced technology for efficient treatment of organic wastewater and recovery of new energy, with the advantages and disadvantages of single-chamber and dual-chamber MES reactors being less understood. Therefore, we explored the effects of single-chamber and dual-chamber structures on the methane production performance and microbial community structure of MES. Results indicated that methane concentration and current density of single-chamber MES were higher than those of dual-chamber MES, and the system stability was better, while chemical oxygen demand (COD) removal rate and cumulative methane production were not significantly different. Analysis of microbial community structure showed the abundance of acidogens and H₂-producing bacteria was higher in single-chamber MES, while fermentation bacteria and methanogens was lower. The abundance of methanogens of dual-chamber MES (21.74-24.70%) was superior to the single-chamber MES (8.23-10.10%). Moreover, in dual-chamber MES, methane was produced primarily through acetoclastic methanogenic pathway, while in single-chamber MES cathode, methane production was mainly by hydrogenotrophic methanogenic pathway. Information provided will be useful to select suitable reactors and optimize reaction design.

Lactic acid production - producing microorganisms and substrates sources-state of art

Lactic acid is an organic compound produced via fermentation by different microorganisms that are able to use different carbohydrate sources. Lactic acid bacteria are the main bacteria used to produce lactic acid and among these, Lactobacillus spp. have been showing interesting fermentation capacities. The use of Bacillus spp. revealed good possibilities to reduce the fermentative costs. Interestingly, lactic acid high productivity was achieved by Corynebacterium glutamicum and E. coli, mainly after engineering genetic modification. Fungi, like Rhizopus spp. can metabolize different renewable carbon resources, with advantageously amylolytic properties to produce lactic acid. Additionally, yeasts can tolerate environmental restrictions (for example acidic conditions), being the wild-type low lactic acid producers that have been improved by genetic manipulation. Microalgae and cyanobacteria, as photosynthetic microorganisms can be an alternative lactic acid producer without carbohydrate feed costs. For lactic acid production, it is necessary to have substrates in the fermentation medium. Different carbohydrate sources can be used, from plant waste as molasses, starchy, lignocellulosic materials as agricultural and forestry residues. Dairy waste also can be used by the addition of supplementary components with a nitrogen source.