Metabolomic Analysis of Cooperative Adaptation between Co-Cultured Bacillus cereus and Ketogulonicigenium vulgare

Ding, Ming-Zhu; Zou, Yang; Song, Hao; Yang, Yuan

doi:10.1371/journal.pone.0094889

Cited by 21 publications

(14 citation statements)

References 30 publications

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“…A metabolomics analysis has detected a number of metabolites exchange among K . vulgare and the Bacillus strain [ 8 ], where the transport system of the membranes plays an important role [ 65 ]. B .…”

Section: Resultsmentioning

confidence: 99%

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

Nan

Ding

et al. 2015

PLoS ONE

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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.

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Section: Resultsmentioning

confidence: 99%

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

Nan

Ding

et al. 2015

PLoS ONE

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“…Furthermore, K. vulgare harbores the complete valine, leucine and isoleucine biosynthesis pathways, but only contains several isolated reactions in the related degradation pathway. The lack of degradation ability may lead to the amino acid accumulation in K. vulgare , providing extracellular amino acids to companion strain in consortium 34 .…”

Section: Discussionmentioning

confidence: 99%

Insights into mutualism mechanism and versatile metabolism of Ketogulonicigenium vulgare Hbe602 based on comparative genomics and metabolomics studies

Nan

Ding

et al. 2016

Sci Rep

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Ketogulonicigenium vulgare has been widely used in vitamin C two steps fermentation and requires companion strain for optimal growth. However, the understanding of K. vulgare as well as its companion strain is still preliminary. Here, the complete genome of K. vulgare Hbe602 was deciphered to provide insight into the symbiosis mechanism and the versatile metabolism. K. vulgare contains the LuxR family proteins, chemokine proteins, flagellar structure proteins, peptides and transporters for symbiosis consortium. Besides, the growth state and metabolite variation of K. vulgare were observed when five carbohydrates (D-sorbitol, L-sorbose, D-glucose, D-fructose and D-mannitol) were used as carbon source. The growth increased by 40.72% and 62.97% respectively when K. vulgare was cultured on D-mannitol/D-sorbitol than on L-sorbose. The insufficient metabolism of carbohydrates, amino acids and vitamins is the main reason for the slow growth of K. vulgare. The combined analysis of genomics and metabolomics indicated that TCA cycle, amino acid and nucleotide metabolism were significantly up-regulated when K. vulgare was cultured on the D-mannitol/D-sorbitol, which facilitated the better growth. The present study would be helpful to further understand its metabolic structure and guide the engineering transformation.

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“…These results indicate the additional metabolic support K. vulgare receives from B. megaterium. It is interesting to note that this co-culture system has been widely studied for its applications in Vitamin C production; these studies also indicate that B. megaterium is a helper strain that enhances the growth and proliferation of K. vulgare (21)(22)(23).…”

Section: Metabolic Support Index Quantifies the Benefits Derived By Omentioning

confidence: 99%

Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments

Ravikrishnan

Blank

Srivastava

et al. 2019

Preprint

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Microbial co-cultures have been used in several biotechnological applications. Within these cocultures, the micro-organisms tend to interact with each other and perform complex actions visà-vis a single organism. Investigating metabolic interactions in microbial co-cultures is crucial in designing microbial consortia tailored for specific applications. In this study, we present a pipeline integrating modelling and experimental approaches to understand metabolic interactions between organisms in a community. We define a new index named Metabolic Support Index (MSI), which quantifies the benefits derived by each organism in the presence of the other when grown as a co-culture. We computed MSI for several experimentally demonstrated co-culture systems and showed that MSI, as a metric, accurately identifies the organism that derives the maximum benefit. We also computed MSI for a commonly used yeast co-culture consisting of Saccharomyces cerevisiae and Pichia stipitis and observed that the latter derives higher benefit from the interaction. Further, we designed two-stage experiments to study mutual interactions and showed that P. stipitis indeed derives the maximum benefit from the interaction, as shown from our computational predictions. Also, using our previously developed computational tool MetQuest, we identified all the metabolic exchanges happening between these organisms by analysing the pathways spanning the two organisms. By analysing the HPLC profiles and studying the isotope labelling, we show that P. stipitis consumes the ethanol produced by S. cerevisiae when grown on glucose-rich medium under aerobic conditions, as also indicated by our in silico pathway analyses. Our approach represents an important step in understanding metabolic interactions in microbial communities through an integrating framework of modelling and experiments.

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Metabolomic Analysis of Cooperative Adaptation between Co-Cultured Bacillus cereus and Ketogulonicigenium vulgare

Cited by 21 publications

References 30 publications

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

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

Insights into mutualism mechanism and versatile metabolism of Ketogulonicigenium vulgare Hbe602 based on comparative genomics and metabolomics studies

Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments

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