Metabolome profiling reveals metabolic cooperation between Bacillus megaterium and Ketogulonicigenium vulgare during induced swarm motility

Recent Advances in 2-Keto-l-gulonic Acid Production Using Mixed-Culture Fermentation and Future Prospects

Vitamin C, also known as ascorbic acid, is an essential vitamin that cannot be synthesized by the human body and must be acquired through our diet. At present, the precursor of vitamin C, 2-keto-l-gulonic acid (2-KGA), is typically produced via a two-step fermentation process utilizing three bacterial strains. The second step of this traditional two-step fermentation method involves mixed-culture fermentation employing 2-KGA-producing bacteria (Ketogulonicigenium vulgare) along with associated bacteria. Because K. vulgare has defects in various metabolic pathways, associated bacteria are needed to provide key substances to promote K. vulgare growth and 2-KGA production. Unlike previous reviews where the main focus was the interaction between associated bacteria and K. vulgare, this Review presents the latest scientific research from the perspective of the metabolic pathways associated with 2-KGA production by K. vulgare and the mechanism underlying the interaction between K. vulgare and the associated bacteria. In addition, the dehydrogenases that are responsible for 2-KGA production, the 2-KGA synthesis pathway, strategies for simplifying 2-KGA production via a one-step fermentation route, and, finally, future prospects and research goals in vitamin C production are also presented.

Metabolite Cross-Feeding Promoting NADH Production and Electron Transfer during Efficient SMX Biodegradation by a Denitrifier and S. oneidensis MR-1 in the Presence of Nitrate

Antibiotics often coexist with other pollutants (e.g., nitrate) in an aquatic environment, and their simultaneous biological removal has attracted widespread interest. We have found that sulfamethoxazole (SMX) and nitrate can be efficiently removed by the coculture of a model denitrifier (Paracoccus denitrificans, Pd) and Shewanella oneidensis MR-1 (So), and SMX degradation is affected by NADH production and electron transfer. In this paper, the mechanism of a coculture promoting NADH production and electron transfer was investigated by proteomic analysis and intermediate experiments. The results showed that glutamine and lactate produced by Pd were captured by So to synthesize thiamine and heme, and the released thiamine was taken up by Pd as a cofactor of pyruvate and ketoglutarate dehydrogenase, which were related to NADH generation. Additionally, Pd acquired heme, which facilitated electron transfer as heme, was the important composition of complex III and cytochrome c and the iron source of iron sulfur clusters, the key component of complex I in the electron transfer chain. Further investigation revealed that lactate and glutamine generated by Pd prompted So chemotactic moving toward Pd, which helped the two bacteria effectively obtain their required substances. Obviously, metabolite cross-feeding promoted NADH production and electron transfer, resulting in efficient SMX biodegradation by Pd and So in the presence of nitrate. Its feasibility was finally verified by the coculture of an activated sludge denitrifier and So.

Enhancing plant growth in biofertilizer-amended soil through nitrogen-transforming microbial communities

Biofertilizers have immense potential for enhancing agricultural productivity. However, there is still a need for clarification regarding the specific mechanisms through which these biofertilizers improve soil properties and stimulate plant growth. In this research, a bacterial agent was utilized to enhance plant growth and investigate the microbial modulation mechanism of soil nutrient turnover using metagenomic technology. The results demonstrated a significant increase in soil fast-acting nitrogen (by 46.7%) and fast-acting phosphorus (by 88.6%) upon application of the bacterial agent. This finding suggests that stimulated soil microbes contribute to enhanced nutrient transformation, ultimately leading to improved plant growth. Furthermore, the application of the bacterial agent had a notable impact on the accumulation of key genes involved in nitrogen cycling. Notably, it enhanced nitrification genes (amo, hao, and nar), while denitrification genes (nir and nor) showed a slight decrease. This indicates that ammonium oxidation may be the primary pathway for increasing fast-acting nitrogen in soils. Additionally, the bacterial agent influenced the composition and functional structure of the soil microbial community. Moreover, the metagenome-assembled genomes (MAGs) obtained from the soil microbial communities exhibited complementary metabolic processes, suggesting mutual nutrient exchange. These MAGs contained widely distributed and highly abundant genes encoding plant growth promotion (PGP) traits. These findings emphasize how soil microbial communities can enhance vegetation growth by increasing nutrient availability and regulating plant hormone production. This effect can be further enhanced by introducing inoculated microbial agents. In conclusion, this study provides novel insights into the mechanisms underlying the beneficial effects of biofertilizers on soil properties and plant growth. The significant increase in nutrient availability, modulation of key genes involved in nitrogen cycling, and the presence of MAGs encoding PGP traits highlight the potential of biofertilizers to improve agricultural practices. These findings have important implications for enhancing agricultural sustainability and productivity, with positive societal and environmental impacts.

2-Keto-L-gulonic acid inhibits the growth of Bacillus pumilus and Ketogulonicigenium vulgare

The typical vitamin C mixed-fermentation process's second stage involves bioconversion of L-sorbose to 2-keto-L-gulonic acid (2-KLG), using a consortium comprising Ketogulonicigenium vulgare and Bacillus spp. (as helper strain). The concentration of the helper strain in the co-fermentation system was closely correlated with K. vulgare cell growth and 2-KLG accumulation. To understand the tolerance and response of the helper strain and K. vulgare to 2-KLG, 2-KLG was added to the single-strain system of Bacillus pumilus and K. vulgare and the basic physiological and biochemical properties were determined. In this study, the addition of 1 mg/mL 2-KLG reduced the number of viable and spore cells, lowered the levels of intracellular reactive oxygen species (ROS), enhanced the intra- and extracellular total antioxidant capacity (T-AOC), and significantly affected the B. pumilus sporulation-related genes expression levels. Furthermore, the addition of 1 mg/mL 2-KLG increased the intracellular ROS levels, decreased the intra- and extracellular T-AOC, and downregulated the antioxidant enzyme-related genes and 2-KLG production enzyme-related genes of K. vulgare. These results suggested that 2-KLG could induce acidic and oxidative stress in B. pumilus and K. vulgare, which could be a guide for a greater understanding of the interaction between the microorganisms.

Probabilistic Bayesian Deep Learning Approach for Online Forecasting of Fed-Batch Fermentation

The microbial fermentation process often involves various biological metabolic reactions and chemical processes. The mixed bacterial culture process of 2-keto-l-gulonic acid has strong nonlinear and time-varying characteristics. In this study, a probabilistic Bayesian deep learning approach is proposed to obtain a highly accurate and robust prediction of product formation. The Bayesian optimized deep neural network (BODNN) is utilized as basic model for prediction, the structural parameters of which are optimized. Then, the training datasets are classified into different categories according to the prior evaluation of prediction error. The final forecasting is a weighted combination of BODNN models based on the Bayesian hybrid method. The weights can be interpreted as Bayesian posterior probabilities and are computed recursively. The validation of 95 industrial batches is carried out, and the average root mean square errors are 1.51 and 2.01% for 4 and 8 h ahead prediction, respectively. The results illustrate that the proposed approach can capture the dynamics of fermentation batches and is suitable for online process monitoring.

Potential bacterial isolation by dosing metabolites in cross-feedings

Metabolic cross-feeding, in which species use metabolites of other members to promote their own growth, is vital for bacterial growth and survival. Thus, whether the unculturable bacteria can be isolated or purified from consortia by adding these essential metabolites remains elusive. In this study, mass spectrometry imaging vividly pictured symbionts supplied folate and gluconate to anammox bacteria to support their growth. After dosing folate and gluconate, the relative abundance and activity of anammox bacteria were substantially improved. Such enhancement is originated from the added folate and gluconate significantly eased metabolic burden of anammox bacteria as they no longer secreted the extracellular public goods to others for "resource exchange" during cross-feedings. On the other hand, the decreased supplement of extracellular "public goods" lead to the decay of symbionts with high demand for these metabolites in the consortia. This also deservedly increased the relative abundance of anammox bacteria. This study provides a new dimension to isolate specific functional bacteria based on metabolic cross-feedings.

Design and construction of microbial cell factories based on systems biology

Environmental sustainability is an increasingly important issue in industry. As an environmentally friendly and sustainable way, constructing microbial cell factories to produce all kinds of valuable products has attracted more and more attention. In the process of constructing microbial cell factories, systems biology plays a crucial role. This review summarizes the recent applications of systems biology in the design and construction of microbial cell factories from four perspectives, including functional genes/enzymes discovery, bottleneck pathways identification, strains tolerance improvement and design and construction of synthetic microbial consortia. Systems biology tools can be employed to identify functional genes/enzymes involved in the biosynthetic pathways of products. These discovered genes are introduced into appropriate chassis strains to build engineering microorganisms capable of producing products. Subsequently, systems biology tools are used to identify bottleneck pathways, improve strains tolerance and guide design and construction of synthetic microbial consortia, resulting in increasing the yield of engineered strains and constructing microbial cell factories successfully.

Metabolomic signatures of corals thriving across extreme reef habitats reveal strategies of heat stress tolerance

Anthropogenic stressors continue to escalate worldwide, driving unprecedented declines in reef environmental conditions and coral health. One approach to better understand how corals can function in the future is to examine coral populations that thrive within present day naturally extreme habitats. We applied untargeted metabolomics (gas chromatography-mass spectrometry (GC-MS)) to contrast metabolite profiles of Pocillopora acuta colonies from hot, acidic and deoxygenated mangrove environments versus those from adjacent reefs. Under ambient temperatures, P. acuta predominantly associated with endosymbionts of the genera Cladocopium (reef) or Durusdinium (mangrove), exhibiting elevated metabolism in mangrove through energy-generating and biosynthesis pathways compared to reef populations. Under transient heat stress, P. acuta endosymbiont associations were unchanged. Reef corals bleached and exhibited extensive shifts in symbiont metabolic profiles (whereas host metabolite profiles were unchanged). By contrast, mangrove populations did not bleach and solely the host metabolite profiles were altered, including cellular responses in inter-partner signalling, antioxidant capacity and energy storage. Thus mangrove P. acuta populations resist periodically high-temperature exposure via association with thermally tolerant endosymbionts coupled with host metabolic plasticity. Our findings highlight specific metabolites that may be biomarkers of heat tolerance, providing novel insight into adaptive coral resilience to elevated temperatures.

iTRAQ-based proteomics analysis of Bacillus pumilus responses to acid stress and quorum sensing in a vitamin C fermentation system

Microbial consortia play a key role in human health, bioenergy, and food manufacturing due to their strong stability, robustness and versatility. One of the microbial consortia consisting of Ketogulonicigenium vulgare and Bacillus megaterium for the production of the vitamin C precursor, 2-keto-L-gulonic acid (2-KLG), has been widely used for large-scale industrial production. To further investigate the cell-cell communication in microbial consortia, a microbial consortium consisting of Ketogulonicigenium vulgare and Bacillus pumilus was constructed and the differences in protein expression at different fermentation time points (18 h and 40 h) were analyzed by iTRAQ-based proteomics. The results indicated that B. pumilus was subjected to acid shocks in the coculture fermentation system and responded to it. In addition, the quorum sensing system existed in the coculture fermentation system, and B. pumilus could secrete quorum-quenching lactonase (YtnP) to inhibit the signaling pathway of K. vulgare. This study offers valuable guidance for further studies of synthetic microbial consortia.

Microbial Interactions in a Vitamin C Industrial Fermentation System: Novel Insights and Perspectives

In industrial production, the precursor of l-ascorbic acid (L-AA, also referred to as vitamin C), 2-keto-l-gulonic acid (2-KLG), is mainly produced using a classic two-step fermentation process performed by Gluconobacter oxydans, Bacillus megaterium, and Ketogulonicigenium vulgare. In the second step of the two-step fermentation process, the microbial consortium of K. vulgare and B. megaterium is used to achieve 2-KLG production. K. vulgare can transform l-sorbose to 2-KLG, but the yield of 2-KLG is much lower in the monoculture than in the coculture fermentation system. The relationship between the two strains is too diverse to analyze and has been a hot topic in the field of vitamin C fermentation. With the development of omics technology, the relationships between the two strains are well explained; nevertheless, the cell-cell communication is unclear. In this review, based on current omics results, the interactions between the two strains are summarized, and the potential cell-cell communications between the two strains are discussed, which will shed a light on the further understanding of synthetic consortia.

Construction of synthetic microbial consortia for 2-keto-L-gulonic acid biosynthesis

Currently, the establishment of synthetic microbial consortia with rational strategies has gained extensive attention, becoming one of the important frontiers of synthetic biology. Systems biology can offer insights into the design and construction of synthetic microbial consortia. Taking the high-efficiency production of 2-keto-l-gulonic acid (2-KLG) as an example, we constructed a synthetic microbial consortium “Saccharomyces cerevisiae-Ketogulonigenium vulgare” based on systems biology analysis. In the consortium, K. vulgare was the 2-KLG producing strain, and S. cerevisiae acted as the helper strain. Comparative transcriptomic analysis was performed on an engineered S. cerevisiae (VTC2) and a wild-type S. cerevisiae BY4741. The results showed that the up-regulated genes in VTC2, compared with BY4741, were mainly involved in glycolysis, TCA cycle, purine metabolism, and biosynthesis of amino acids, B vitamins, and antioxidant proteases, all of which play important roles in promoting the growth of K. vulgare. Furthermore, Vitamin C produced by VTC2 could further relieve the oxidative stress in the environment to increase the production of 2-KLG. Therefore, VTC2 would be of great advantage in working with K. vulgare. Thus, the synthetic microbial consortium "VTC2-K. vulgare" was constructed based on transcriptomics analyses, and the accumulation of 2-KLG was increased by 1.49-fold compared with that of mono-cultured K. vulgare, reaching 13.2 ± 0.52 g/L. In addition, the increased production of 2-KLG was accompanied by the up-regulated activities of superoxide dismutase and catalase in the medium and the up-regulated oxidative stress-related genes (sod, cat and gpd) in K. vulgare. The results indicated that the oxidative stress in the synthetic microbial consortium was efficiently reduced. Thus, systems analysis confirmed a favorable symbiotic relationship between microorganisms, providing guidance for further engineering synthetic consortia.

Adaptation of metabolite leakiness leads to symbiotic chemical exchange and to a resilient microbial ecosystem

Microbial communities display remarkable diversity, facilitated by the secretion of chemicals that can create new niches. However, it is unclear why cells often secrete even essential metabolites after evolution. Based on theoretical results indicating that cells can enhance their own growth rate by leaking even essential metabolites, we show that such "leaker" cells can establish an asymmetric form of mutualism with "consumer" cells that consume the leaked chemicals: the consumer cells benefit from the uptake of the secreted metabolites, while the leaker cells also benefit from such consumption, as it reduces the metabolite accumulation in the environment and thereby enables further secretion, resulting in frequency-dependent coexistence of multiple microbial species. As supported by extensive simulations, such symbiotic relationships generally evolve when each species has a complex reaction network and adapts its leakiness to optimize its own growth rate under crowded conditions and nutrient limitations. Accordingly, symbiotic ecosystems with diverse cell species that leak and exchange many metabolites with each other are shaped by cell-level adaptation of leakiness of metabolites. Moreover, the resultant ecosystems with entangled metabolite exchange are resilient against structural and environmental perturbations. Thus, we present a theory for the origin of resilient ecosystems with diverse microbes mediated by secretion and exchange of essential chemicals.

Metabolic Profiling of Rhizobacteria Serratia plymuthica and Bacillus subtilis Revealed Intra- and Interspecific Differences and Elicitation of Plipastatins and Short Peptides Due to Co-cultivation

Rhizobacteria live in diverse and dynamic communities having a high impact on plant growth and development. Due to the complexity of the microbial communities and the difficult accessibility of the rhizosphere, investigations of interactive processes within this bacterial network are challenging. In order to better understand causal relationships between individual members of the microbial community of plants, we started to investigate the inter- and intraspecific interaction potential of three rhizobacteria, the S. plymuthica isolates 4Rx13 and AS9 and B. subtilis B2g, using high resolution mass spectrometry based metabolic profiling of structured, low-diversity model communities. We found that by metabolic profiling we are able to detect metabolite changes during cultivation of all three isolates. The metabolic profile of S. plymuthica 4Rx13 differs interspecifically to B. subtilis B2g and surprisingly intraspecifically to S. plymuthica AS9. Thereby, the release of different secondary metabolites represents one contributing factor of inter- and intraspecific variations in metabolite profiles. Interspecific co-cultivation of S. plymuthica 4Rx13 and B. subtilis B2g showed consistently distinct metabolic profiles compared to mono-cultivated species. Thereby, putative known and new variants of the plipastatin family are increased in the co-cultivation of S. plymuthica 4Rx13 and B. subtilis B2g. Interestingly, intraspecific co-cultivation of S. plymuthica 4Rx13 and S. plymuthica AS9 revealed a distinct interaction zone and showed distinct metabolic profiles compared to mono-cultures. Thereby, several putative short proline-containing peptides are increased in co-cultivation of S. plymuthica 4Rx13 with S. plymuthica AS9 compared to mono-cultivated strains. Our results demonstrate that the release of metabolites by rhizobacteria alters due to growth and induced by social interactions between single members of the microbial community. These results form a basis to elucidate the functional role of such interaction-triggered compounds in establishment and maintenance of microbial communities and can be applied under natural and more realistic conditions, since rhizobacteria also interact with the plant itself and many other members of plant and soil microbiota.

Application of Co-Culture Technology to Enhance Protease Production by Two Halophilic Bacteria, Marinirhabdus sp. and Marinobacter hydrocarbonoclasticus

Although axenic microbial cultures form the basis of many large successful industrial biotechnologies, the production of single commercial microbial strains for use in large environmental biotechnologies such as wastewater treatment has proved less successful. This study aimed to evaluate the potential of the co-culture of two halophilic bacteria, Marinirhabdus sp. and Marinobacter hydrocarbonoclasticus for enhanced protease activity. The co-culture was significantly more productive than monoculture (1.6–2.0 times more growth), with Marinobacter hydrocarbonoclasticus being predominant (64%). In terms of protease activity, enhanced total activity (1.8–2.4 times) was observed in the co-culture. Importantly, protease activity in the co-culture was found to remain active over a much broader range of environmental conditions (temperature 25 °C to 60 °C, pH 4–12, and 10–30% salinity, respectively). This study confirms that the co-culturing of halophilic bacteria represents an economical approach as it resulted in both increased biomass and protease production, the latter which showed activity over arange of environmental conditions.

One-Step Biosynthesis of Vitamin C in Saccharomyces cerevisiae

Vitamin C (VC) is comprehensively applied in foods, cosmetics, pharmaceuticals, and especially clinical medicine. Nowadays, the industrial production of VC mainly relies on the classic two-step fermentation route, and researchers have explored the way for one-step fermentation of VC in recent years. In this study, a VC biosynthesis pathway that directly produced VC from glucose was reconstructed in Saccharomyces cerevisiae, and the protein engineering and metabolic engineering strategies were adopted to improve it. First, five exogenous modules from Arabidopsis were introduced into the chassis cells by synthetic biology approaches to obtain the strain YLAA harboring VC biosynthesis. In addition, L-galactose dehydrogenase (L-GalDH) and L-galactono-1,4-lactone dehydrogenase (L-GLDH) were fused and expressed in S. cerevisiae cells for the first time, which increased the intracellular VC accumulation by 2.78-fold, reaching 9.97 ± 0.09 mg/L. Through copy number engineering, it was further confirmed that the last step catalyzed by L-GLDH is the rate-limiting step. GDP-L-galactose phosphorylase (GPP) encoded by vtc2 is another rate-limiting enzyme confirmed by GAL1p overexpression results. Finally, by balancing gene expression and cell growth, the highest production strain with overexpressing vtc2 by multicopy plasmids was constructed. The VC accumulation reached 24.94 ± 1.16 mg/L, which was currently the highest production from glucose in S. cerevisiae. The production of the recombinant strain reached nearly 44 mg/L with the exogenous addition of L-galactose or glutathione. The results further emphasized the importance of the step catalyzed by GPP. The investigation provided experience for the efficient biosynthesis of VC and the determination of rate-limiting steps.

Genome-based analysis to understanding rapid resuscitation of cryopreserved anammox consortia via sequential supernatant addition

Simple cryopreservation of anaerobic ammonium-oxidation (anammox) consortia has become a promising preservation technology for the fast start-up of the anammox process. Here, we use genome-resolved metagenomics and metatranscriptomics to understand of the microbial interaction in a simple and effective resuscitation process for long-term cryopreserved anammox consortia by sequential addition of anammox SBR supernatant. Performance results showed that sequential addition of anammox supernatant significantly reduced the resuscitation time of the granule-based anammox process from 40 to 20 days. Genome-centric metagenomics were used to recover 19 high-quality draft genomes of anammox and heterotrophic bacteria. Comparative metatranscriptomic analysis was conducted to examine the gene expression of Candidatus Kuenenia stuttgartiensis, the dominant anammox bacterium, and heterotrophic bacteria to better understand their potential interactions. Proteobacteria-affiliated bacteria found in the supernatant were highly active in producing the secondary metabolites molybdopterin cofactor and folate which are needed for growth of the auxotrophic anammox bacteria. In addition, the significantly higher expression levels of hzsA and CO₂-fixtion genes in the Candidatus Kuenenia genome indicated the anammox bacteria were likely more active and growing faster after sequential anammox supernatant addition during the resuscitation process. The resuscitation treatment pulse assays confirmed that sequential addition of supernatant was an effective way for the rapid resuscitation of anammox consortia. Our findings offer the first evidence of cross-feeding during the rapid resuscitation of cryopreserved anammox consortia.

High-Throughput Screening of a 2-Keto-L-Gulonic Acid-Producing Gluconobacter oxydans Strain Based on Related Dehydrogenases

High-throughput screening is a powerful tool for discovering strains in the natural environment that may be suitable for target production. Herein, a novel enzyme-based high-throughput screening method was developed for rapid screening of strains overproducing 2-keto-L-gulonic acid (2-KLG). The screening method detects changes in the fluorescence of reduced nicotinamide adenine dinucleotide (NADH) at 340 nm using a microplate reader when 2-KLG is degraded by 2-KLG reductase. In this research, three different 2-KLG reductases were expressed, purified, and studied. The 2-KLG reductase from Aspergillus niger were selected as the best appropriate reductase to establishment the method for its high activity below pH 7. Using the established method, and coupled with fluorescence-activated cell sorting, we achieved a high 2-KLG-producing strain of Gluconobacter oxydans WSH-004 from soil. When cultured with D-sorbitol as the substrate, the 2-KLG yield was 2.5 g/L from 50 g/L D-sorbitol without any side products. Compared with other reported screening methods, our enzyme-based method is more efficient and accurate for obtaining high-producing 2-KLG strains, and it is also convenient and cost-effective. The method is broadly applicable for screening keto acids and other products that can be oxidized via nicotinamide adenine dinucleotide (NAD⁺) or nicotinamide adenine dinucleotide phosphate (NADP⁺).

Simulations reveal challenges to artificial community selection and possible strategies for success

Multispecies microbial communities often display "community functions" arising from interactions of member species. Interactions are often difficult to decipher, making it challenging to design communities with desired functions. Alternatively, similar to artificial selection for individuals in agriculture and industry, one could repeatedly choose communities with the highest community functions to reproduce by randomly partitioning each into multiple "Newborn" communities for the next cycle. However, previous efforts in selecting complex communities have generated mixed outcomes that are difficult to interpret. To understand how to effectively enact community selection, we simulated community selection to improve a community function that requires 2 species and imposes a fitness cost on one or both species. Our simulations predict that improvement could be easily stalled unless various aspects of selection are carefully considered. These aspects include promoting species coexistence, suppressing noncontributors, choosing additional communities besides the highest functioning ones to reproduce, and reducing stochastic fluctuations in the biomass of each member species in Newborn communities. These considerations can be addressed experimentally. When executed effectively, community selection is predicted to improve costly community function, and may even force species to evolve slow growth to achieve species coexistence. Our conclusions hold under various alternative model assumptions and are therefore applicable to a variety of communities.

Biochemical engineering in China

Chinese biochemical engineering is committed to supporting the chemical and food industries, to advance science and technology frontiers, and to meet major demands of Chinese society and national economic development. This paper reviews the development of biochemical engineering, strategic deployment of these technologies by the government, industrial demand, research progress, and breakthroughs in key technologies in China. Furthermore, the outlook for future developments in biochemical engineering in China is also discussed.

Integrated proteomic and metabolomic analysis of a reconstructed three-species microbial consortium for one-step fermentation of 2-keto-l-gulonic acid, the precursor of vitamin C

Microbial consortia, with the merits of strong stability, robustness, and multi-function, played critical roles in human health, bioenergy, and food manufacture, etc. On the basis of ‘build a consortium to understand it’, a novel microbial consortium consisted of Gluconobacter oxydans, Ketogulonicigenium vulgare and Bacillus endophyticus was reconstructed to produce 2-keto-l-gulonic acid (2-KGA), the precursor of vitamin C. With this synthetic consortium, 73.7 g/L 2-KGA was obtained within 30 h, which is comparable to the conventional industrial method. A combined time-series proteomic and metabolomic analysis of the fermentation process was conducted to further investigate the cell–cell interaction. The results suggested that the existence of B. endophyticus and G. oxydans together promoted the growth of K. vulgare by supplying additional nutrients, and promoted the 2-KGA production by supplying more substrate. Meanwhile, the growth of B. endophyticus and G. oxydans was compromised from the competition of the nutrients by K. vulgare, enabling the efficient production of 2-KGA. This study provides valuable guidance for further study of synthetic microbial consortia.

Model Microbial Consortia as Tools for Understanding Complex Microbial Communities

A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions. In this review, we surveyed several approaches that have effectively used tractable model consortia to elucidate the complex behavior of microbial communities. We go further to provide some perspectives on the limitations and new opportunities with these approaches and highlight where these efforts are likely to lead as advances are made in molecular ecology and systems biology.

Genome-Centered Metagenomics Analysis Reveals the Symbiotic Organisms Possessing Ability to Cross-Feed with Anammox Bacteria in Anammox Consortia

Although using anammox communities for efficient wastewater treatment has attracted much attention, the pure anammox bacteria are difficult to obtain, and the potential roles of symbiotic bacteria in anammox performance are still elusive. Here, we combined long-term reactor operation, genome-centered metagenomics, community functional structure, and metabolic pathway reconstruction to reveal multiple potential cross-feedings during anammox reactor start-up according to the 37 recovered metagenome-assembled genomes (MAGs). We found Armatimonadetes and Proteobacteria could contribute the secondary metabolites molybdopterin cofactor and folate for anammox bacteria to benefit their activity and growth. Chloroflexi-affiliated bacteria encoded the function of biosynthesizing exopolysaccharides for anammox consortium aggregation, based on the partial nucleotide sugars produced by anammox bacteria. Chlorobi-affiliated bacteria had the ability to degrade extracellular proteins produced by anammox bacteria to amino acids to affect consortium aggregation. Additionally, the Chloroflexi-affiliated bacteria harbored genes for a nitrite loop and could have a dual role in anammox performance during reactor start-up. Cross-feeding in anammox community adds a different dimension for understanding microbial interactions and emphasizes the importance of symbiotic bacteria in the anammox process for wastewater treatment.

Antioxidant effect of glutathione on promoting 2-keto-l-gulonic acid production in vitamin C fermentation system

AIMS

Oxidative stress limited the growth of cells and 2-keto-l-gulonic acid (2-KGA) production in vitamin C (Vc) fermentation system. The study aims to investigate the antioxidant effect of glutathione on promoting 2-KGA in Vc fermentation system using Ketogulonicigenium vulgare 25B-1 and Bacillus endophyticus ST-1 as the co-culturing microbes.

METHODS AND RESULTS

The activities of antioxidant-related enzymes and qPCR were used to study the antioxidant effect of glutathione addition in Vc fermentation system. The addition of GSH and GSH/GSSG increased 2-KGA production and decreased fermentation time, and the highest 2-KGA production increased by 40·63% and the lowest fermentation time shortened to 60 h when the addition of optimal concentration ratio of GSH/GSSG was 50 : 1. Moreover, the increased production of 2-KGA was accompanied by up-regulated the activities of total antioxidant capacity (T-AOC), total superoxide dismutase (T-SOD), catalase (CAT) and over-expressed oxidative stress-related genes sod, gst, gr, zwf, gp, which resulted in scavenging reactive oxygen species to reduce oxidative stress in Vc fermentation system.

CONCLUSIONS

Glutathione showed a significant effect on increasing 2-KGA production and decreasing fermentation time in Vc fermentation system. GSH/GSSG could maintain a dynamic balance with two forms of glutathione and the optimal concentration ratio of GSH/GSSG was 50 : 1.

SIGNIFICANCE AND IMPACT OF THE STUDY

Glutathione is proved to be effective to relieve oxidative stress. The promotion effects of GSSG and GSH on 2-KGA production could help to further explore the optimization of co-culture fermentation process for Vc industrial production.

Ecology and evolution of metabolic cross-feeding interactions in bacteria

Literature covered: early 2000s to late 2017Bacteria frequently exchange metabolites with other micro- and macro-organisms. In these often obligate cross-feeding interactions, primary metabolites such as vitamins, amino acids, nucleotides, or growth factors are exchanged. The widespread distribution of this type of metabolic interactions, however, is at odds with evolutionary theory: why should an organism invest costly resources to benefit other individuals rather than using these metabolites to maximize its own fitness? Recent empirical work has shown that bacterial genotypes can significantly benefit from trading metabolites with other bacteria relative to cells not engaging in such interactions. Here, we will provide a comprehensive overview over the ecological factors and evolutionary mechanisms that have been identified to explain the evolution and maintenance of metabolic mutualisms among microorganisms. Furthermore, we will highlight general principles that underlie the adaptive evolution of interconnected microbial metabolic networks as well as the evolutionary consequences that result for cells living in such communities.

Novel Method Reveals a Narrow Phylogenetic Distribution of Bacterial Dispersers in Environmental Communities Exposed to Low-Hydration Conditions

In this study, we developed a method that provides profiles of community-level surface dispersal from environmental samples under controlled hydration conditions and enables us to isolate and uncover the diversity of the fastest bacterial dispersers. The method expands on the porous surface model (PSM), previously used to monitor the dispersal of individual bacterial strains in liquid films at the surface of a porous ceramic disc. The novel procedure targets complex communities and captures the dispersed bacteria on a solid medium for growth and detection. The method was first validated by distinguishing motile Pseudomonas putida and Flavobacterium johnsoniae strains from their nonmotile mutants. Applying the method to soil and lake water bacterial communities showed that community-scale dispersal declined as conditions became drier. However, for both communities, dispersal was detected even under low-hydration conditions (matric potential, -3.1 kPa) previously proven too dry for P. putida strain KT2440 motility. We were then able to specifically recover and characterize the fastest dispersers from the inoculated communities. For both soil and lake samples, 16S rRNA gene amplicon sequencing revealed that the fastest dispersers were substantially less diverse than the total communities. The dispersing fraction of the soil microbial community was dominated by Pseudomonas species cells, which increased in abundance under low-hydration conditions, while the dispersing fraction of the lake community was dominated by Aeromonas species cells and, under wet conditions (-0.5 kPa), also by Exiguobacterium species cells. The results gained in this study bring us a step closer to assessing the dispersal ability within complex communities under environmentally relevant conditions.IMPORTANCE Dispersal is a key process of bacterial community assembly, and yet, very few attempts have been made to assess bacterial dispersal at the community level, as the focus has previously been on pure-culture studies. A crucial factor for dispersal in habitats where hydration conditions vary, such as soils, is the thickness of the liquid films surrounding solid surfaces, but little is known about how the ability to disperse in such films varies within bacterial communities. Therefore, we developed a method to profile community dispersal and identify fast dispersers on a rough surface resembling soil surfaces. Our results suggest that within the motile fraction of a bacterial community, only a minority of the bacterial types are able to disperse in the thinnest liquid films. During dry periods, these efficient dispersers can gain a significant fitness advantage through their ability to colonize new habitats ahead of the rest of the community.

Comparative genomics and metabolomics analyses of the adaptation mechanism in Ketogulonicigenium vulgare-Bacillus thuringiensis consortium

Adaptive evolution by serial subcultivation of co-cultured Bacillus thuringiensis and Ketogulonicigenium vulgare significantly enhanced the productivity of 2-keto-L-gulonic acid in two-step vitamin C production. The adaptation mechanism in K. vulgare-B. thuringiensis consortium was investigated in this study based on comparative genomics and metabolomics studies. It was found that the growth, anti-oxidation, transcription and regulation were significantly enhanced in the adapted consortium. The mutation of the genes, which encode amidohydrolase in adapted K. vulgare (K150) and amino acid permease in adapted B. thuringiensis (B150), resulted in the increase of some amino acids levels in each species, and further enhanced the metabolic exchange and growth ability of the two species. Besides, the mutation of the gene encoding spore germination protein enhanced the metabolic levels of tricarboxylic acid cycle, and decreased the sporulation in B150, which induced its growth. The mutation of the genes, which encode NADPH nitroreductase in K150 and NADPH-dependent FMN reductase in B150, may enhance the ability of anti-oxidation. Overall, the long-term adaptation of K. vulgare and B. thuringiensis influenced the global regulation and made them more inseparable in metabolite exchange. Our work will provide ideas for the molecular design and optimization in microbial consortium.

A plate method for rapid screening of Ketogulonicigenium vulgare mutants for enhanced 2-keto-l-gulonic acid production

A new plate method was developed for rapid screening of Ketogulonicigenium vulgare mutants overproducing 2-keto-l-gulonic acid (2-KLG). The screening methodology took the advantage of the acidity caused by 2-KLG, which changes the color of bromothymol blue (pH indicator) from blue to yellow. Using the proposed method, a mutant, K. vulgare 65, was selected from 20,000 colonies produced by a strain subjected to spaceflight mutagenesis. When co-cultured with Bacillus megaterium 2980 in 20-L fermenters, K. vulgare 65 showed a high conversion rate (94.45%) of l-sorbose to 2-KLG. In contrast to the traditional screening method, this one significantly improved the frequency of obtaining positive mutants. The proposed plate screening method is cost-effective and easy to run and is thus useful for the isolation and screening of K. vulgare mutants overproducing 2-KLG.

Design and construction of synthetic microbial consortia in China

The rapid development of synthetic biology enables the design, construction and optimization of synthetic microbial consortia to achieve specific functions. In China, the "973" project-"Design and Construction of Microbial Consortia" was funded by the National Basic Research Program of China in January 2014. It was proposed to address the fundamental challenges in engineering natural microbial consortia and reconstructing microbial consortia to meet industrial demands. In this review, we will introduce this "973" project, including the significance of microbial consortia, the fundamental scientific issues, the recent research progresses, and some case studies about synthetic microbial consortia in the past two and a half years.

Comparative genomics analysis of the companion mechanisms of Bacillus thuringiensis Bc601 and Bacillus endophyticus Hbe603 in bacterial consortium

Bacillus thuringiensis and Bacillus endophyticus both act as the companion bacteria, which cooperate with Ketogulonigenium vulgare in vitamin C two-step fermentation. Two Bacillus species have different morphologies, swarming motility and 2-keto-L-gulonic acid productivities when they co-culture with K. vulgare. Here, we report the complete genome sequencing of B. thuringiensis Bc601 and eight plasmids of B. endophyticus Hbe603, and carry out the comparative genomics analysis. Consequently, B. thuringiensis Bc601, with greater ability of response to the external environment, has been found more two-component system, sporulation coat and peptidoglycan biosynthesis related proteins than B. endophyticus Hbe603, and B. endophyticus Hbe603, with greater ability of nutrients biosynthesis, has been found more alpha-galactosidase, propanoate, glutathione and inositol phosphate metabolism, and amino acid degradation related proteins than B. thuringiensis Bc601. Different ability of swarming motility, response to the external environment and nutrients biosynthesis may reflect different companion mechanisms of two Bacillus species. Comparative genomic analysis of B. endophyticus and B. thuringiensis enables us to further understand the cooperative mechanism with K. vulgare, and facilitate the optimization of bacterial consortium.

The composition analysis and preliminary cultivation optimization of a PHA-producing microbial consortium with xylose as a sole carbon source

This work aimed at using xylose as sole substrate, and combining feast-famine process with Nile blue staining as well as denaturing gradient gel electrophoresis (DGGE) analysis to screen polyhydroxyalkanoate (PHA)-producing bacteria from waste activated sludge (WAS). Composition changes of the microbial consortium during domestication were analyzed by DGGE, and the results indicated that there were mainly four classes of bacteria in the final stable system, which were γ-Proteobacteria, Cellvibrio sp., an uncultured bacterium and Pseudomonas sp., respectively. After preliminary optimization, the optimal conditions for the microbial consortium to produce PHA were also obtained as follows: temperature 33°C, pH 8, xylose concentration 2.4g/L, C/N ratio 160 and C/P ratio 125. The final PHA accumulation was up to 31% of dry cell weight (DCW), compared to 23.8% of the original consortia. Though our process is at the very beginning and the PHA yield is relatively low, producing PHA from xylose by using microbial consortia is a promising way to save the PHA production cost.

Design, analysis and application of synthetic microbial consortia

The rapid development of synthetic biology has conferred almost perfect modification on single cells, and provided methodological support for synthesizing microbial consortia, which have a much wider application potential than synthetic single cells. Co-cultivating multiple cell populations with rational strategies based on interacting relationships within natural microbial consortia provides theoretical as well as experimental support for the successful obtaining of synthetic microbial consortia, promoting it into extensive research on both industrial applications in plenty of areas and also better understanding of natural microbial consortia. According to their composition complexity, synthetic microbial consortia are summarized in three aspects in this review and are discussed in principles of design and construction, insights and methods for analysis, and applications in energy, healthcare, etc.

Bacterial-Plant-Interactions: Approaches to Unravel the Biological Function of Bacterial Volatiles in the Rhizosphere

Rhizobacteria produce an enormous amount of volatile compounds, however, the function of these metabolites is scarcely understood. Investigations evaluating influences on plants performed in various laboratories using individually developed experimental setups revealed different and often contradictory results, e.g., ranging from a significant plant growth promotion to a dramatic suppression of plant development. In addition to these discrepancies, these test systems neglected properties and complexity of the rhizosphere. Therefore, to pursue further investigations of the role of bacterial volatiles in this underground habitat, the applied methods have to simulate its natural characteristics as much as possible. In this review, we will describe and discuss pros and cons of currently used bioassays, give insights into rhizosphere characteristics, and suggest improvements for test systems that would consider in natura conditions and would allow gaining further knowledge of the potential function and significance of rhizobacterial volatiles in plant life.

Cooperative Mn(II) oxidation between two bacterial strains in an aquatic environment

In natural or engineered environments, diverse interspecific interactions among two or more microbial taxa may profoundly affect the transformation of organic compounds in the media. Little is known, however, about how these organisms and interactions affect the transformation of heavy metals. Recently, we found an interaction between two non-Mn(II)-oxidizing (when in monoculture) strains, Arthrobacter sp. QXT-31 and Sphingopyxis sp. QXT-31, which, when cultured in combination, resulted in Mn(II)-oxidizing activity in synthetic media. In order to study the occurrence likelihood of cooperative Mn(II) oxidation in natural water and discharged effluent, we initially identified an optimal ratio of the two strains in a combined culture, as well as the impacts of external factors on the cooperative oxidation. Once preferred initial conditions were established, we assessed the degree and rate of Mn(II) oxidation mediated by the combined QXT-31 strains (henceforth referred to as simply 'QXT-31') in three different water types: groundwater, domestic sewage and coking wastewater. Results showed that Mn(II) oxidation only occurred when the two strains were within a specific ratios range. When introduced to the test waters at the preferred ratio, QXT-31 demonstrated high Mn(II)-oxidizing activities, even when relative abundance of QXT-31 was very low (roughly 1.6%, calculated by 454 pyrosequencing events on 16S rcDNA). Interestingly, even under low relative abundance of QXT-31, removal of total organic carbon and total nitrogen in the test waters was significantly higher than the control treatments that were not inoculated with QXT-31. Data from our study indicate that cooperative Mn(II) oxidation is most likely to occur in natural aquatic ecosystems, and also suggests an alternative method to treat wastewater containing high concentrations of Mn(II).

Acknowledging selection at sub-organismal levels resolves controversy on pro-cooperation mechanisms

Cooperators who pay a cost to produce publically-available benefits can be exploited by cheaters who do not contribute fairly. How might cooperation persist against cheaters? Two classes of mechanisms are known to promote cooperation: 'partner choice', where a cooperator preferentially interacts with cooperative over cheating partners; and 'partner fidelity feedback', where repeated interactions between individuals ensure that cheaters suffer as their cooperative partners languish (see, for example, Momeni et al., 2013). However when both mechanisms can act, differentiating them has generated controversy. Here, I resolve this controversy by noting that selection can operate on organismal and sub-organismal 'entities' such that partner fidelity feedback at sub-organismal level can appear as partner choice at organismal level. I also show that cooperation between multicellular eukaryotes and mitochondria is promoted by partner fidelity feedback and partner choice between sub-organismal entities, in addition to being promoted by partner fidelity feedback between hosts and symbionts, as was previously known.

Genome Sequence of Bacillus endophyticus and Analysis of Its Companion Mechanism in the Ketogulonigenium vulgare-Bacillus Strain Consortium

Bacillus strains have been widely used as the companion strain of Ketogulonigenium vulgare in the process of vitamin C fermentation. Different Bacillus strains generate different effects on the growth of K. vulgare and ultimately influence the productivity. First, we identified that Bacillus endophyticus Hbe603 was an appropriate strain to cooperate with K. vulgare and the product conversion rate exceeded 90% in industrial vitamin C fermentation. Here, we report the genome sequencing of the B. endophyticus Hbe603 industrial companion strain and speculate its possible advantage in the consortium. The circular chromosome of B. endophyticus Hbe603 has a size of 4.87 Mb with GC content of 36.64% and has the highest similarity with that of Bacillus megaterium among all the bacteria with complete genomes. By comparing the distribution of COGs with that of Bacillus thuringiensis, Bacillus cereus and B. megaterium, B. endophyticus has less genes related to cell envelope biogenesis and signal transduction mechanisms, and more genes related to carbohydrate transport and metabolism, energy production and conversion, as well as lipid transport and metabolism. Genome-based functional studies revealed the specific capability of B. endophyticus in sporulation, transcription regulation, environmental resistance, membrane transportation, extracellular proteins and nutrients synthesis, which would be beneficial for K. vulgare. In particular, B. endophyticus lacks the Rap-Phr signal cascade system and, in part, spore coat related proteins. In addition, it has specific pathways for vitamin B12 synthesis and sorbitol metabolism. The genome analysis of the industrial B. endophyticus will help us understand its cooperative mechanism in the K. vulgare-Bacillus strain consortium to improve the fermentation of vitamin C.

l-sorbose is not only a substrate for 2-keto-l-gulonic acid production in the artificial microbial ecosystem of two strains mixed fermentation

The co-culture system of the fermentation process of vitamin C can be regarded as an artificial microbial ecosystem (AME). To extend our understanding of this AME, an investigation of the relationship between strains, substrate and product was carried out in this study. The results showed that both Ketogulonicigenium vulgare and 2-keto-l-gulonic acid (2-KLG, the precursor of vitamin C) can inhibit the growth of the helper strain, while the helper strain promoted the growth of K. vulgare and 2-KLG production. Moreover, l-sorbose is not only a substrate for 2-KLG production in the AME, but also a promoter of K. vulgare and an inhibitor of the helper strain. In the earlier stage of fermentation, the inhibition of l-sorbose on the helper strain’s growth is a key factor for ensuring an efficient fermentation. In the condition of adding the extra helper strain (OD: 0.57, ratio of inoculation: 2 %), the yields of 2-KLG is increased by 9 % in the 14 % l-sorbose medium. To the best of our knowledge, this is the first report about the inhibition of substrate in the AME of 2-KLG production.

Bacterial swarms recruit cargo bacteria to pave the way in toxic environments

Swarming bacteria are challenged by the need to invade hostile environments. Swarms of the flagellated bacterium Paenibacillus vortex can collectively transport other microorganisms. Here we show that P. vortex can invade toxic environments by carrying antibiotic-degrading bacteria; this transport is mediated by a specialized, phenotypic subpopulation utilizing a process not dependent on cargo motility. Swarms of beta-lactam antibiotic (BLA)-sensitive P. vortex used beta-lactamase-producing, resistant, cargo bacteria to detoxify BLAs in their path. In the presence of BLAs, both transporter and cargo bacteria gained from this temporary cooperation; there was a positive correlation between BLA resistance and dispersal. P. vortex transported only the most beneficial antibiotic-resistant cargo (including environmental and clinical isolates) in a sustained way. P. vortex displayed a bet-hedging strategy that promoted the colonization of nontoxic niches by P. vortex alone; when detoxifying cargo bacteria were not needed, they were lost. This work has relevance for the dispersal of antibiotic-resistant microorganisms and for strategies for asymmetric cooperation with agricultural and medical implications.

Antibiotic resistance is a major health threat. We show a novel mechanism for the local spread of antibiotic resistance. This involves interactions between different bacteria: one species provides an enzyme that detoxifies the antibiotic (a sessile cargo bacterium carrying a resistance gene), while the other (Paenibacillus vortex) moves itself and transports the cargo. P. vortex used a bet-hedging strategy, colonizing new environments alone when the cargo added no benefit, but cooperating when the cargo was needed. This work is of interest in an evolutionary context and sheds light on fundamental questions, such as how environmental antibiotic resistance may lead to clinical resistance and also microbial social organization, as well as the costs, benefits, and risks of dispersal in the environment.

Synthetic microbial consortia: from systematic analysis to construction and applications

Synthetic biology is an emerging research field that focuses on using rational engineering strategies to program biological systems, conferring on them new functions and behaviours. By developing genetic parts and devices based on transcriptional, translational, post-translational modules, many genetic circuits and metabolic pathways had been programmed in single cells. Extending engineering capabilities from single-cell behaviours to multicellular microbial consortia represents a new frontier of synthetic biology. Herein, we first reviewed binary interaction modes of microorganisms in microbial consortia and their underlying molecular mechanisms, which lay the foundation of programming cell-cell interactions in synthetic microbial consortia. Systems biology studies on cellular systems enable systematic understanding of diverse physiological processes of cells and their interactions, which in turn offer insights into the optimal design of synthetic consortia. Based on such fundamental understanding, a comprehensive array of synthetic microbial consortia constructed in the last decade were reviewed, including isogenic microbial communities programmed by quorum sensing-based cell-cell communications, sender-receiver microbial communities with one-way communications, and microbial ecosystems wired by two-way (bi-directional) communications. Furthermore, many applications including using synthetic microbial consortia for distributed bio-computations, chemicals and bioenergy production, medicine and human health, and environments were reviewed. Synergistic development of systems and synthetic biology will provide both a thorough understanding of naturally occurring microbial consortia and rational engineering of these complicated consortia for novel applications.

Metabolic model reconstruction and analysis of an artificial microbial ecosystem for vitamin C production

An artificial microbial ecosystem (AME) consisting of Ketogulonicigenium vulgare and Bacillus megaterium is currently used in a two-step fermentation process for vitamin C production. In order to obtain a comprehensive understanding of the metabolic interactions between the two bacteria, a two-species stoichiometric metabolic model (iWZ-KV-663-BM-1055) consisting of 1718 genes, 1573 metabolites, and 1891 reactions (excluding exchange reactions) was constructed based on separate genome-scale metabolic models (GSMMs) of K. vulgare and B. megaterium. These two compartments (k and b) of iWZ-KV-663-BM-1055 shared 453 reactions and 548 metabolites. Compartment b was richer in subsystems than compartment k. In minimal media with glucose (MG), metabolite exchange between compartments was assessed by constraint-based analysis. Compartment b secreted essential amino acids, nucleic acids, vitamins and cofactors important for K. vulgare growth and biosynthesis of 2-keto-l-gulonic acid (2-KLG). Further research showed that when co-cultured with B. megaterium in l-sorbose-CSLP medium, the growth rate of K. vulgare and 2-KLG production were increased by 111.9% and 29.42%, respectively, under the constraints employed. Our study demonstrated that GSMMs and constraint-based methods can be used to decode the physiological features and inter-species interactions of AMEs used in industrial biotechnology, which will be of benefit for improving regulation and refinement in future industrial processes.

Metabolomic analysis of cooperative adaptation between co-cultured Bacillus cereus and Ketogulonicigenium vulgare

The cooperative adaptation of subcultivated Bacillus cereus and Ketogulonicigenium vulgare significantly increased the productivity of 2-keto-L-gulonic acid, the precursor of vitamin C. The mechanism of cooperative adaptation of the serial subcultivated B. cereus and K. vulgare was investigated in this study by culturing the two strains orthogonally on agar plates. It was found that the swarming distance of B. cereus along the trace of K. vulgare on the plate decreased after 150 days' subcultivation. Metabolomic analysis on these co-cultured B. cereus and K. vulgare strains showed that their cooperative adaptation was accomplished by three key events: (i) the ability of nutrients (e.g., amino acids and purines) searching and intaking, and proteins biosynthesis is increased in the evolved B. cereus; (ii) the capability of protein degradation and amino acids transportation is enhanced in evolved K. vulgare; (iii) the evolved B. cereus was found to provide more nutrients (mostly amino acids and purines) to K. vulgare, thus strengthening the oxidation and energy generation of K. vulgare. Our results provided novel insights into the systems-level understanding of the cooperative adaptation between strains in synergistic consortium.

Metabolite induction via microorganism co-culture: a potential way to enhance chemical diversity for drug discovery

Microorganisms have a long track record as important sources of novel bioactive natural products, particularly in the field of drug discovery. While microbes have been shown to biosynthesize a wide array of molecules, recent advances in genome sequencing have revealed that such organisms have the potential to yield even more structurally diverse secondary metabolites. Thus, many microbial gene clusters may be silent under standard laboratory growth conditions. In the last ten years, several methods have been developed to aid in the activation of these cryptic biosynthetic pathways. In addition to the techniques that demand prior knowledge of the genome sequences of the studied microorganisms, several genome sequence-independent tools have been developed. One of these approaches is microorganism co-culture, involving the cultivation of two or more microorganisms in the same confined environment. Microorganism co-culture is inspired by the natural microbe communities that are omnipresent in nature. Within these communities, microbes interact through signaling or defense molecules. Such compounds, produced dynamically, are of potential interest as new leads for drug discovery. Microorganism co-culture can be achieved in either solid or liquid media and has recently been used increasingly extensively to study natural interactions and discover new bioactive metabolites. Because of the complexity of microbial extracts, advanced analytical methods (e.g., mass spectrometry methods and metabolomics) are key for the successful detection and identification of co-culture-induced metabolites. This review focuses on co-culture studies that aim to increase the diversity of metabolites obtained from microbes. The various strategies are summarized with a special emphasis on the multiple methods of performing co-culture experiments. The analytical approaches for studying these interaction phenomena are discussed, and the chemical diversity and biological activity observed among the induced metabolites are described.