Journal of Microbiology

Review

Metabolic engineering of Saccharomyces cerevisiae for efficient utilization of pectin-rich biomass: Dahye Lee, Fransheska Semidey, Luping Xu, Eun Joong Oh; J. Microbiol. 2025;63(7):e2503001. Published online July 31, 2025; DOI: https://doi.org/10.71150/jm.2503001

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Abstract PDF: Pectin-rich biomass, derived from fruit and citrus processing waste, presents a promising yet underutilized resource for sustainable biofuel and biochemical production. Its low lignin content and high concentrations of fermentable sugars, including D-galacturonic acid, L-arabinose, and D-xylose, make it an attractive feedstock. Unlike lignocellulosic biomass, pectin-rich hydrolysates require milder pretreatment, improving sugar recovery efficiency. However, industrial strains such as Saccharomyces cerevisiae exhibit strong glucose preference, limiting the efficient co-fermentation of mixed sugars. While prior reviews have broadly addressed lignocellulosic biomass utilization, this mini-review uniquely centers on the specific metabolic challenges and opportunities associated with pectin-rich feedstocks. In addition to incorporating established strategies for the co-utilization of cellobiose and xylose, we highlight recent advances that allow S. cerevisiae to metabolize carbon sources specifically from pectin-rich biomass, such as L-arabinose and D-galacturonic acid—monomers not prevalent in traditional lignocellulosic biomass. By integrating discussions on sugar transport engineering, redox balancing, and pathway optimization, this review offers a comprehensive framework to overcome glucose repression and support efficient co-fermentation of carbon sources from conventional and pectin-rich biomass. Drawing on these advances, we outline practical strategies to enhance fermentation performance and expand the valorization of food processing residues in biomanufacturing.

Full article

Glucose affects capsular polysaccharides synthesis via CcpA and HPr in Streptococcus pneumoniae: Rui Yang, Yapeng Zhang, Hong Wang, Hanyi Wang, Jiangming Xiao, Lian Li, Yuan Yuan, Yibing Yin, Xuemei Zhang; J. Microbiol. 2025;63(5):e2411024. Published online May 27, 2025; DOI: https://doi.org/10.71150/jm.2411024

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Streptococcus pneumoniae is a conditionally pathogenic bacteria that colonizes the nasopharynx of 27% to 65% of children and 10% of adults. Capsular polysaccharides are the most critical virulence factor of S. pneumoniae, and nonencapsulated strains are usually non-pathogenic. Previous studies have shown that glucose regulates capsule synthesis. To investigate the mechanism of carbon metabolism regulatory factors CcpA and HPr regulating capsule synthesis in the presence of glucose as the sole carbon source, we constructed deletion mutants (D39ΔccpA and ΔptsH) and complemented strains (D39ΔccpA::ccpA and ΔptsH::ptsH). In this study, we found that the promoting effect of capsule synthesis by glucose disappeared after the deletion of ccpA and ptsH, and demonstrated that the protein CcpA regulates capsule synthesis by binding to the cps promoter and altering the transcription level of the cps gene cluster. Increased glucose concentration up-regulated the level of HPr-Ser46~P, which enhanced the binding ability of CcpA to the DNA sequence of the cps promoter, thus promoting capsule synthesis. HPr also has a regulatory effect on capsule synthesis. These insights reveal a new synthesis mechanism of capsular polysaccharide and provide a new strategy of antibacterial drugs for S. pneumoniae.

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The metabolic, microbial and immunological demands of pneumococcal colonisation
Daniel R. Neill, Thomas B. Clarke, N.Luisa Hiller
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Journal Articles

Description of Nocardioides piscis sp. nov., Sphingomonas piscis sp. nov. and Sphingomonas sinipercae sp. nov., isolated from the intestine of fish species Odontobutis interrupta (Korean spotted sleeper) and Siniperca scherzeri (leopard mandarin fish): Dong-Wook Hyun , Yun-Seok Jeong , Jae-Yun Lee , Hojun Sung , So-Yeon Lee , Jee-Won Choi , Hyun Sik Kim , Pil Soo Kim , Jin-Woo Bae; J. Microbiol. 2021;59(6):552-562. Published online April 20, 2021; DOI: https://doi.org/10.1007/s12275-021-1036-5

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A polyphasic taxonomic approach was used to characterize three novel bacterial strains, designated as HDW12AT, HDW- 15BT, and HDW15CT, isolated from the intestine of fish species Odontobutis interrupta or Siniperca scherzeri. All isolates were obligate aerobic, non-motile bacteria, and grew optimally at 30°C. Phylogenetic analysis based on 16S rRNA sequences revealed that strain HDW12AT was a member of the genus Nocardioides, and closely related to Nocardioides allogilvus CFH 30205T (98.9% sequence identities). Furthermore, strains HDW15BT and HDW15CT were members of the genus Sphingomonas, and closely related to Sphingomonas lutea JS5T and Sphingomonas sediminicola Dae 20T (97.1% and 97.9% sequence identities), respectively. Strain HDW12AT contained MK-8 (H4), and strains HDW15BT and HDW15CT contained Q-10 as the respiratory quinone. Major polar lipid components of strain HDW12AT were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylinositol, and those of strains HDW15BT and HDW15CT were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The G + C content of strains HDW12AT, HDW15BT, and HDW15CT were 69.7, 63.3, and 65.5%, respectively. The results of phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses suggest that strain HDW12AT represents a novel species within the genus Nocardioides, and strains HDW15BT and HDW15CT represent two novel species within the genus Sphingomonas. We propose the names Nocardioides piscis for strain HDW12AT (= KACC 21336T = KCTC 49321T = JCM 33670T), Sphingomonas piscis for strain HDW15BT (= KACC 21341T = KCTC 72588T = JCM 33738T), and Sphingomonas sinipercae for strain HDW15CT (= KACC 21342T = KCTC 72589T = JCM 33739T).

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Yousri Abdelhafiz, Jorge M. O. Fernandes, Claudio Donati, Massimo Pindo, Viswanath Kiron
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Aharon Oren, George M. Garrity
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Jae-Yun Lee, Woorim Kang, Na-Ri Shin, Dong-Wook Hyun, Pil Soo Kim, Hyun Sik Kim, June-Young Lee, Euon Jung Tak, Hojun Sung, Jin-Woo Bae
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The NADP+-dependent glutamate dehydrogenase Gdh1 is subjected to glucose starvation-induced reversible aggregation that affects stress resistance in yeast: Woo Hyun Lee , Ju Yeong Oh , Pil Jae Maeng; J. Microbiol. 2019;57(10):884-892. Published online August 3, 2019; DOI: https://doi.org/10.1007/s12275-019-9065-z

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The yeast Saccharomyces cerevisiae has two isoforms of NADP+-dependent glutamate dehydrogenase (Gdh1 and Gdh3) that catalyze the synthesis of glutamate from α-ketoglutarate and NH4 +. In the present study, we confirmed that Gdh3, but not Gdh1, mainly contributes to the oxidative stress resistance of stationary-phase cells and found evidence suggesting that the insignificance of Gdh1 to stress resistance is possibly resulted from conditional and reversible aggregation of Gdh1 into punctuate foci initiated in parallel with postdiauxic growth. Altered localization to the mitochondria or peroxisomes prevented Gdh1, which was originally localized in the cytoplasm, from stationary phase-specific aggregation, suggesting that some cytosolic factors are involved in the process of Gdh1 aggregation. Glucose starvation triggered the transition of the soluble form of Gdh1 into the insoluble aggregate form, which could be redissolved by replenishing glucose, without any requirement for protein synthesis. Mutational analysis showed that the N-terminal proximal region of Gdh1 (NTP1, aa 21-26, TLFEQH) is essential for glucose starvation-induced aggregation. We also found that the substitution of NTP1 with the corresponding region of Gdh3 (NTP3) significantly increased the contribution of the mutant Gdh1 to the stress resistance of stationary-phase cells. Thus, this suggests that NTP1 is responsible for the negligible role of Gdh1 in maintaining the oxidative stress resistance of stationary- phase cells and the stationary phase-specific stresssensitive phenotype of the mutants lacking Gdh3.

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Research Support, Non-U.S. Gov'ts

Relationships between the use of Embden Meyerhof pathway (EMP) or Phosphoketolase pathway (PKP) and lactate production capabilities of diverse Lactobacillus reuteri strains: Grégoire Burgé , Claire Saulou-Bérion , Marwen Moussa , Florent Allais , Violaine Athes , Henry-Eric Spinnler; J. Microbiol. 2015;53(10):702-710. Published online October 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5056-x

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Abstract

The aims of this study is to compare the growth and glucose metabolism of three Lactobacillus reuteri strains (i.e. DSM 20016, DSM 17938, and ATCC 53608) which are lactic acid bacteria of interest used for diverse applications such as probiotics implying the production of biomass, or for the production of valuable chemicals (3-hydroxypropionaldehyde, 3-hydroxypropionic acid, 1,3-propanediol). However, the physiological diversity inside the species, even for basic metabolisms, like its capacity of acidification or glucose metabolism, has not been studied yet. In the present work, the growth and metabolism of three strains representative of the species diversity have been studied in batch mode. The strains were compared through characterization of growth kinetics and evaluation of acidification kinetics, substrate consumption and product formation. The results showed significant differences between the three strains which may be explained, at least in part, by variations in the distribution of carbon source between two glycolytic pathways during the bacterial growth: the phosphoketolase or heterolactic pathway (PKP) and the Embden-Meyerhof pathway (EMP). It was also shown that, in the context of obtaining a large amount of biomass, DSM 20016 and DSM 17938 strains were the most effective in terms of growth kinetics. The DSM 17938 strain, which shows the more significant metabolic shift from EMP to PKP when the pH decreases, is more effective for lactate production.

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Cyclic AMP-Receptor Protein Activates Aerobactin Receptor IutA Expression in Vibrio vulnificus: Choon-Mee Kim , Seong-Jung Kim , Sung-Heui Shin; J. Microbiol. 2012;50(2):320-325. Published online April 27, 2012; DOI: https://doi.org/10.1007/s12275-012-2056-y

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Abstract PDF: The ferrophilic bacterium Vibrio vulnificus can utilize the siderophore aerobactin of Escherichia coli for iron acquisition via its specific receptor IutA. This siderophore piracy by V. vulnificus may contribute to its survival and proliferation, especially in mixed bacterial environments. In this study, we examined the effects of glucose, cyclic AMP (cAMP), and cAMP-receptor protein (Crp) on iutA expression in V. vulnificus. Glucose dose-dependently repressed iutA expression. A mutation in cya encoding adenylate cyclase required for cAMP synthesis severely repressed iutA expression, and this change was recovered by in trans complementing cya or the addition of exogenous cAMP. Furthermore, a mutation in crp encoding Crp severely repressed iutA expression, and this change was recovered by complementing crp. Accordingly, glucose deprivation under iron-limited conditions is an environmental signal for iutA expression, and Crp functions as an activator that regulates iutA expression in response to glucose availability.

Purification and Biochemical Properties of a Glucose-Stimulated β-D-Glucosidase Produced by Humicola grisea var. thermoidea Grown on Sugarcane Bagasse: Cesar Vanderlei Nascimento , Flávio Henrique Moreira Souza , Douglas Chodi Masui , Francisco Assis Leone , Rosane Marina Peralta , João Atílio Jorge , Rosa Prazeres Melo Furriel; J. Microbiol. 2010;48(1):53-62. Published online March 11, 2010; DOI: https://doi.org/10.1007/s12275-009-0159-x

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The effect of several carbon sources on the production of mycelial-bound β-glucosidase by Humicola grisea var. thermoidea in submerged fermentation was investigated. Maximum production occurred when cellulose was present in the culture medium, but higher specific activities were achieved with cellobiose or sugarcane bagasse. Xylose or glucose (1%) in the reaction medium stimulated β-glucosidase activity by about 2-fold in crude extracts from mycelia grown in sugarcane bagasse. The enzyme was purified by ammonium sulfate precipitation, followed by Sephadex G-200 and DEAE-cellulose chromatography, showing a single band in PAGE and SDS-PAGE. The β-glucosidase had a carbohydrate content of 43% and showed apparent molecular masses of 57 and 60 kDa, as estimated by SDS-PAGE and gel filtration, respectively. The optimal pH and temperature were 6.0 and 50°C, respectively. The purified enzyme was thermostable up to 60 min in water at 55°C and showed half-lives of 7 and 14 min when incubated in the absence or presence of 50 mM glucose, respectively, at 60°C. The enzyme hydrolyzed p-nitrophenyl-β-D-glucopyranoside, p-nitrophenyl-β-galactopyranoside, p-nitrophenyl-β-D-fucopyranoside, p-nitrophenyl-β-D-xylopyranoside, o-nitrophenyl-β-Dgalactopyranoside, lactose, and cellobiose. The best synthetic and natural substrates were p-nitrophenyl-β-Dfucopyranoside and cellobiose, respectively. Purified enzyme activity was stimulated up to 2-fold by glucose or xylose at concentrations from 25 to 200 mM. The addition of purified or crude β-glucosidase to a reaction medium containing Trichoderma reesei cellulases increased the saccharification of sugarcane bagasse by about 50%. These findings suggest that H. grisea var. thermoidea β-glucosidase has a potential for biotechnological applications in the bioconversion of lignocellulosic materials.

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Molecular Cloning and Expression of a Thermostable Xylose (Glucose) Isomerase Gene, xylA, from Streptomyces chibaensis J-59: Gil-Jae Joo , Jae-Ho Shin , Gun-Young Heo , Young-Mog Kim , In-Koo Rhee; J. Microbiol. 2005;43(1):34-37.; DOI: https://doi.org/2141 [pii]

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Abstract PDF: In the present study, the xylA gene encoding a thermostable xylose (glucose) isomerase was cloned from Streptomyces chibaensis J-59. The open reading frame of xylA (1167 bp) encoded a protein of 388 amino acids with a calculated molecular mass of about 43 kDa. The XylA showed high sequence homology (92% identity) with that of S. olivochromogenes. The xylose (glucose) isomerase was expressed in Escherichia coli and purified. The purified recombinant XylA had an apparent molecular mass of 45 kDa, which corresponds to the molecular mass calculated from the deduced amino acid and that of the purified wild-type enzyme. The N-terminal sequences (14 amino acid residues) of the purified protein revealed that the sequences were identical to that deduced from the DNA sequence of the xylA gene. The optimum temperature of the purified enzyme was 85oC and the enzyme exhibited a high level of heat stability.

Bacterial Aggregates Formation After Addition of Glucose in Lake Baikal Water: Lev P. Spiglazov , Valentin V. Drucker , Tae Seok Ahn; J. Microbiol. 2004;42(4):357-360.; DOI: https://doi.org/2098 [pii]

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Abstract PDF: For determining the process of bacterial aggregation, glucose was added into water from Lake Baikal which had been stored for seven months. In the presence of a higher concentration of glucose, the abundance of single bacteria and aggregates were higher, but the biovolumes of both bacteria were similar. Theses results mean that both free-living and aggregated bacteria have similar maximum sizes and that aggregates are forming with available organic materials. With available organic materials, the biovolume of aggregates becomes larger.

Optimal Fermentation Conditions for Enhanced Glutathione Production by Saccharomyces cerevisiae FF-8: Jae-Young Cha , Jin-Chul Park , Beong-Sam Jeon , Young-Choon Lee , Young-Su Cho; J. Microbiol. 2004;42(1):51-55.; DOI: https://doi.org/2000 [pii]

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Abstract PDF: The influence of feedstock amino acids, salt, carbon and nitrogen sources on glutathione production by Saccharomyces cerevisiae FF-8 was investigated. Glucose, yeast extract, KH_2PO_4, and L-cysteine were found to be suitable feedstock. Highest glutathione production was obtained after cultivation with shaking for 72 h in a medium containing glucose 3.0% (w/v), yeast extract 3.0%, KH_2PO_4 0.06% and L-cysteine 0.06%. The glutathione concentration achieved using this medium increased 2.27-fold to 204 mg/l compared to YM basal medium.

Published Erratum

[Erratum] A split face study on the effect of an anti-acne product containing fermentation products of Enterococcus faecalis CBT SL-5 on skin microbiome modification and acne improvement: Hye Sung Han , Sun Hye Shin , Bo-Yun Choi , Nayeon Koo , Sanghyun Lim , Dooheon Son , Myung Jun Chung , Kui Young Park , Woo Jun Sul; J. Microbiol. 2022;60(7):766-766.; DOI: https://doi.org/10.1007/s12275-022-1682-2

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Skin Microbiome and Acne: Microbial Imbalances and Impact – Interview with Three Key Opinion Leaders
Brigitte Scott
EMJ Dermatology.2024; : 83. CrossRef

Physiological importance of trypsin-like protease during morphological differentiation of streptomycetes: Kim, In Seop , Kang, Sung Gyun , Lee, Kye Joon; J. Microbiol. 1995;33(4):315-321.

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Abstract PDF: The relationship between morphological differentiation and production of trypsin-like protease (TLP_ in streptomycetes was studied. All the Streptomyces spp. In this study produced TLP just before the onset of aerial mycelium formation. Addition of TLP inhibitor, TLCK, to the top surface of colonies inhibited aerial mycelium formation as well as TLP inhibitor, TLCK, to the top surface of colonies inhibited aerial mycelium formation as well as TLP activity. Addition of 2% glucose to the Bennett agar medium repressed both the aerial mycelium formation and TLP production in S. abuvaviensis, S. coelicolor A3(2), S exfoliatus, S. microflavus, S. roseus, s. lavendulae, and S. rochei. However the addition of glucose did not affect S. limosus, S. felleus, S. griseus, S. phaechromogenes, and S. rimosus. The glucose repression on aerial mycelium formation and production of TLP was relieved by the addition of glucose anti-metabolite (methyl α-glucopyranoside). Therefore, it was concluded that TLP production is coordinately regulated with morphological differentiation and TLP activity is essential for morphological differentiation in streptomycetes. The proposed role of TLP is that TLP participates in the degradation of substrate mycelium protein for providing nutrient for aerial mycelial growth.

Isolation of Glucose Utilizing Mutant of Alcaligenes eutrophus, its Substrate Selectivity, and Accumulation of Poly-β-hydroxybutyrate: Kim, Hye Yeon , Park, Jin Seo , Shin, Hyun Dong , Lee, yong Hyun; J. Microbiol. 1995;33(1):51-58.

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Abstract PDF: A glucose utilizing mutant was selected from parent strain Alcaligenes eutrophus H16, and named as Glu-9. The mechanisms of glucose utilization of the mutant Glu-9 was investigated by measuring the D-[1-¹⁴C] glucose transport activity and the activities of key enzymes related to glucose and fructose uptake via facilitated diffusion. The uptaken glucose seems to activate key enzymes related to glucose matabolism. The selectivity between glucose and fructose of mutant Glu-9 was also analyzed by measuring glucose transport activity and enzyme activities under the various cultivation conditions using different carbon sources. Mutant Alcaligenes eutrophus Glu-9 preferentially consumed fructose from mixed substrates of glucose and fructose due to the inhibition of fructose to glucose transport activity. The characteristics of cell growth and PHB accumulation of Alcaligenes eutrophus Glu-9 were examined under various cultural conditions. Mutant strain Glu-9 showed tolerance in high concentration of glucose and increased yield of PHB production.

Incorpotation and production of glucose in Lake Soyang: kwag, No Tae , Choi, Seung Ik , Ahn, Tae Young , Ahn, Tae Seok; J. Microbiol. 1995;33(1):74-79.

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Abstract PDF: Kinetics of heterotrophic activity (glucose uptake) and extracellular enzyme activity(β-glucosidase, cellobiohydrolase) and cell numbers were measured in Lake Soyang during phytoplankton bloom development and after its breakdown. V_max for glucose was lower during Diatom bloom and that was higher after its breakdown. But the increase ion β-glucosidase activity was detected in late of Diatom bloom. Glucose uptake did not associated with β-glucosidase activity. The tight relationship between β-glucosidase and the incorporation of glucose by bacteria was not shown and the significance of depolymerization on the incorporation of glucose in lake water are discussed.

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