Pub Date : 2025-09-29DOI: 10.1016/j.engmic.2025.100242
Coral Pardo-Esté , Juan Castro-Severyn , Jacqueline Aldridge , Diego Alvarez-Saravia , Lenka Kurte , Polette Aguilar-Muñoz , Pablo Paquis , Vilma Pérez , David Medina , Wade H Jeffrey , Verónica Molina , Martha B Hengst
Terrestrial hydrothermal systems provide a window for studying the biogeochemical interactions that occur in hot and gas-rich ecosystems resembling the conditions found in early life on Earth. The biogeochemical dynamics of the Andean hydrothermal systems in the Atacama Desert area are still understudied. Thus, we aimed to characterize the taxonomic composition and genomic potential of nitrogen transformations in a microbial community inhabiting a high-altitude hydrothermal system on the Altiplano Plateau of the Chilean Andes. Specifically, we sampled sediment and microbial mats in three ponds with water temperatures ranging from 42 to 64 °C. We found a high prevalence of photoheterotrophs, with differences in taxonomic composition and gene abundance between the microbial communities found in the sediment and microbial mats. Changes in physicochemical conditions, such as temperature and pH, and the concentrations of CO2, CH4 and Mn accounted for the variability in the microbial community structure. Our results indicated an enrichment of N-related genes associated with nitrate reduction, denitrification, and ammonia assimilation, suggesting a metabolically versatile community using nitrate, nitrite, and gaseous nitrogen species to assimilate ammonia into their biomass. This study contributes to our understanding of the taxonomy and functional microbial dynamics in a high-altitude thermal system, where ammonia assimilation is potentially critical for biomass formation, and particular environmental conditions favor adaptations to maintain biogeochemical cycles.
{"title":"Unraveling microbial life from a high-altitude hydrothermal system in the Andes plateau and their potential for nitrogen transformations","authors":"Coral Pardo-Esté , Juan Castro-Severyn , Jacqueline Aldridge , Diego Alvarez-Saravia , Lenka Kurte , Polette Aguilar-Muñoz , Pablo Paquis , Vilma Pérez , David Medina , Wade H Jeffrey , Verónica Molina , Martha B Hengst","doi":"10.1016/j.engmic.2025.100242","DOIUrl":"10.1016/j.engmic.2025.100242","url":null,"abstract":"<div><div>Terrestrial hydrothermal systems provide a window for studying the biogeochemical interactions that occur in hot and gas-rich ecosystems resembling the conditions found in early life on Earth. The biogeochemical dynamics of the Andean hydrothermal systems in the Atacama Desert area are still understudied. Thus, we aimed to characterize the taxonomic composition and genomic potential of nitrogen transformations in a microbial community inhabiting a high-altitude hydrothermal system on the Altiplano Plateau of the Chilean Andes. Specifically, we sampled sediment and microbial mats in three ponds with water temperatures ranging from 42 to 64 °C. We found a high prevalence of photoheterotrophs, with differences in taxonomic composition and gene abundance between the microbial communities found in the sediment and microbial mats. Changes in physicochemical conditions, such as temperature and pH, and the concentrations of CO<sub>2</sub>, CH<sub>4</sub> and Mn accounted for the variability in the microbial community structure. Our results indicated an enrichment of N-related genes associated with nitrate reduction, denitrification, and ammonia assimilation, suggesting a metabolically versatile community using nitrate, nitrite, and gaseous nitrogen species to assimilate ammonia into their biomass. This study contributes to our understanding of the taxonomy and functional microbial dynamics in a high-altitude thermal system, where ammonia assimilation is potentially critical for biomass formation, and particular environmental conditions favor adaptations to maintain biogeochemical cycles.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 4","pages":"Article 100242"},"PeriodicalIF":0.0,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145519646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-23DOI: 10.1016/j.engmic.2025.100241
Huan Du, Yang Liu
Fighting against antibiotic resistance has an unexpected ally, archaea. Despite the extensive exploration of antimicrobial peptides in bacteria and eukaryotes, the archaeal domain has been overlooked. A recent study employed deep learning to screen archaeasins. The synthesized versions showed a 93 % success rate against pathogens by depolarizing the cytoplasmic membrane, not the outer membrane. This highlights the promise and deep learning power of archaea for antibiotic discovery and the culture of uncultured archaea.
{"title":"Archaeasins as a promising resource for developing next-generation antibiotics uncovered via deep learning","authors":"Huan Du, Yang Liu","doi":"10.1016/j.engmic.2025.100241","DOIUrl":"10.1016/j.engmic.2025.100241","url":null,"abstract":"<div><div>Fighting against antibiotic resistance has an unexpected ally, archaea. Despite the extensive exploration of antimicrobial peptides in bacteria and eukaryotes, the archaeal domain has been overlooked. A recent study employed deep learning to screen archaeasins. The synthesized versions showed a 93 % success rate against pathogens by depolarizing the cytoplasmic membrane, not the outer membrane. This highlights the promise and deep learning power of archaea for antibiotic discovery and the culture of uncultured archaea.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 4","pages":"Article 100241"},"PeriodicalIF":0.0,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145319913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-23DOI: 10.1016/j.engmic.2025.100243
Zhiqi Hu , Mengyuan Su , Qibing Liu , Ying Li , Yunxiang Liang , Shuangquan Li , Yingjun Li
Glutathione (GSH), an essential tripeptide thiol critical for cellular redox regulation, has significant value in the pharmaceutical and nutraceutical industries. To overcome limitations of traditional GSH extraction methods, this study established a microbial cell factory platform in Saccharomyces cerevisiae through integrated metabolic engineering strategies: (1) host strain screening identified NJ-SQYY with superior GSH accumulation (74.14 mg·L⁻¹, 8.27 mg·g-1 dry cell weight [DCW]); (2) CRISPR/Cas9-mediated genomic integration of bacterial gshAB introduced with a bifunctional glutathione synthetase; (3) systematic optimization via promoter tuning and Gsh1-Gsh2 enzyme fusion, and CYS3 overexpression-resolved γ-glutamylcysteine bottlenecks. These interventions synergistically enhanced GSH synthesis to 339.3 mg·L⁻¹ in shake flasks (4.6-fold increase), representing the highest reported titer in chromosomally engineered S. cerevisiae. Scaling to dissolved oxygen-coupled fed-batch fermentation in a 5-L bioreactor produced 997.46 mg·L⁻¹ GSH at 33.85 mg·g⁻¹ DCW. This study demonstrated a holistic metabolic engineering-to-bioprocessing approach for industrial GSH biomanufacturing.
{"title":"Systems metabolic engineering of glutathione biosynthesis in Saccharomyces cerevisiae: Pathway balancing coupled with enzyme screening for high-titer production","authors":"Zhiqi Hu , Mengyuan Su , Qibing Liu , Ying Li , Yunxiang Liang , Shuangquan Li , Yingjun Li","doi":"10.1016/j.engmic.2025.100243","DOIUrl":"10.1016/j.engmic.2025.100243","url":null,"abstract":"<div><div>Glutathione (GSH), an essential tripeptide thiol critical for cellular redox regulation, has significant value in the pharmaceutical and nutraceutical industries. To overcome limitations of traditional GSH extraction methods, this study established a microbial cell factory platform in <em>Saccharomyces cerevisiae</em> through integrated metabolic engineering strategies: (1) host strain screening identified NJ-SQYY with superior GSH accumulation (74.14 mg·L⁻¹, 8.27 mg·g<sup>-1</sup> dry cell weight [DCW]); (2) CRISPR/Cas9-mediated genomic integration of bacterial <em>gshAB</em> introduced with a bifunctional glutathione synthetase; (3) systematic optimization via promoter tuning and Gsh1-Gsh2 enzyme fusion, and <em>CYS3</em> overexpression-resolved γ-glutamylcysteine bottlenecks. These interventions synergistically enhanced GSH synthesis to 339.3 mg·L⁻¹ in shake flasks (4.6-fold increase), representing the highest reported titer in chromosomally engineered <em>S. cerevisiae</em>. Scaling to dissolved oxygen-coupled fed-batch fermentation in a 5-L bioreactor produced 997.46 mg·L⁻¹ GSH at 33.85 mg·g⁻¹ DCW. This study demonstrated a holistic metabolic engineering-to-bioprocessing approach for industrial GSH biomanufacturing.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 4","pages":"Article 100243"},"PeriodicalIF":0.0,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145319912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-13DOI: 10.1016/j.engmic.2025.100240
Xiaodi Liu , Xiangyu Zhu , Wenxin Jiang , Huanmin Du
Exporter protein systems play a crucial role in the efficient production of valuable chemicals. However, the lack of active exporters significantly limits the application of industrial bio-based production, making the identification and utilization of novel exporters highly important. In this study, we discovered a novel l-Homoserine exporter, Cg0701, in Corynebacterium glutamicum through homology analysis. First, tolerance assays revealed that the cg0701 overexpression strain (CgH-2) exhibited a 10.45% increase in cell growth compared to the control when cultivated with 30 g/L-Homoserine. Additionally, export assays demonstrated that the l-Homoserine export capacity of CgH-2 increased by approximately 30%. Furthermore, genomic overexpression of cg0701 in an l-Homoserine-producing chassis also enhanced both tolerance and export activity. As a result, the recombinant strain CgH-11 produced 10.79 g/L-Homoserine in shake flask cultures and 48.72 g/L in a 5 L fermenter, representing improvements of 19.89% and 24.44%, respectively. In summary, our results indicate that Cg0701 is a novel l-Homoserine exporter in C. glutamicum, enriching our understanding of amino acid export systems and providing a valuable target for the construction of l-Homoserine microbial cell factories.
{"title":"Identification and functional characterization of a potential l-Homoserine exporter in Corynebacterium glutamicum","authors":"Xiaodi Liu , Xiangyu Zhu , Wenxin Jiang , Huanmin Du","doi":"10.1016/j.engmic.2025.100240","DOIUrl":"10.1016/j.engmic.2025.100240","url":null,"abstract":"<div><div>Exporter protein systems play a crucial role in the efficient production of valuable chemicals. However, the lack of active exporters significantly limits the application of industrial bio-based production, making the identification and utilization of novel exporters highly important. In this study, we discovered a novel <span>l</span>-Homoserine exporter, Cg0701, in <em>Corynebacterium glutamicum</em> through homology analysis. First, tolerance assays revealed that the <em>cg0701</em> overexpression strain (CgH-2) exhibited a 10.45% increase in cell growth compared to the control when cultivated with 30 g/L-Homoserine. Additionally, export assays demonstrated that the <span>l</span>-Homoserine export capacity of CgH-2 increased by approximately 30%. Furthermore, genomic overexpression of <em>cg0701</em> in an <span>l</span>-Homoserine-producing chassis also enhanced both tolerance and export activity. As a result, the recombinant strain CgH-11 produced 10.79 g/L-Homoserine in shake flask cultures and 48.72 g/L in a 5 L fermenter, representing improvements of 19.89% and 24.44%, respectively. In summary, our results indicate that Cg0701 is a novel <span>l</span>-Homoserine exporter in <em>C. glutamicum</em>, enriching our understanding of amino acid export systems and providing a valuable target for the construction of <span>l</span>-Homoserine microbial cell factories.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 4","pages":"Article 100240"},"PeriodicalIF":0.0,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145121025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-19DOI: 10.1016/j.engmic.2025.100232
Yingbo Yuan , Tianyuan Su , Yi Zheng, Baoyue Liu, Yuanfei Han, Zhongcan Wang, Quanfeng Liang, Longyang Dian, Qingsheng Qi
Polystyrene (PS) is a polyolefin plastic that is used extensively in food packaging. The chemical structure of PS is extremely stable owing to its C-C backbone and styrene rings, making it highly resistant to biodegradation, which causes serious environmental pollution and health threats. Although certain microorganisms have been reported to degrade PS waste, most studies have focused on the changes in the molecular weight and surface structure of plastics. These slight degradation phenomena make it extremely difficult to detect the degradation products, thus challenging the definitive demonstration of PS degradation. This study investigated the co-cultivation of the polyolefin plastic-degrading bacterium Raoultella sp. DY2415 and the benzoic acid bioconversion strain Pseudomonas putida KT2440-ΔRBC. BA is a possible degradation product of PS and can be converted by P. putida KT2440-ΔRBC into the high value-added compound muconic acid (MA). After co-cultivation, MA was detected in the medium, indicating that Raoultella sp. DY2415 degraded PS and generated BA, which was subsequently utilized by P. putida KT2440-ΔRBC for MA synthesis. This study demonstrated the biodegradation of PS and the synthesis of MA through a fully biological process, thereby promoting the circular economy of plastics.
{"title":"Bacterial co-cultivation for the degradation of polystyrene plastics","authors":"Yingbo Yuan , Tianyuan Su , Yi Zheng, Baoyue Liu, Yuanfei Han, Zhongcan Wang, Quanfeng Liang, Longyang Dian, Qingsheng Qi","doi":"10.1016/j.engmic.2025.100232","DOIUrl":"10.1016/j.engmic.2025.100232","url":null,"abstract":"<div><div>Polystyrene (PS) is a polyolefin plastic that is used extensively in food packaging. The chemical structure of PS is extremely stable owing to its C-C backbone and styrene rings, making it highly resistant to biodegradation, which causes serious environmental pollution and health threats. Although certain microorganisms have been reported to degrade PS waste, most studies have focused on the changes in the molecular weight and surface structure of plastics. These slight degradation phenomena make it extremely difficult to detect the degradation products, thus challenging the definitive demonstration of PS degradation. This study investigated the co-cultivation of the polyolefin plastic-degrading bacterium <em>Raoultella</em> sp. DY2415 and the benzoic acid bioconversion strain <em>Pseudomonas putida</em> KT2440-ΔRBC. BA is a possible degradation product of PS and can be converted by <em>P. putida</em> KT2440-ΔRBC into the high value-added compound muconic acid (MA). After co-cultivation, MA was detected in the medium, indicating that <em>Raoultella</em> sp. DY2415 degraded PS and generated BA, which was subsequently utilized by <em>P. putida</em> KT2440-ΔRBC for MA synthesis. This study demonstrated the biodegradation of PS and the synthesis of MA through a fully biological process, thereby promoting the circular economy of plastics.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 4","pages":"Article 100232"},"PeriodicalIF":0.0,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144893087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-14DOI: 10.1016/j.engmic.2025.100231
Ying Wang , Mengyan Xu , Hanne Ingmer
Staphylococcus aureus is a major public health threat, largely due to its remarkable capacity to develop antimicrobial resistance. Zhang et al. recently demonstrated a highly innovative approach to eradicate chronic methicillin-resistant S. aureus infections by inducing bacterial calcification with antibody-polysialic acid conjugates targeting wall teichoic acids, while simultaneously modulating host immune responses via enhanced calprotectin expression and macrophage activation. Despite limitations, this strategy represents a promising and unconventional therapy to combat resistant S. aureus infections.
{"title":"A novel therapeutic strategy of methicillin-resistant Staphylococcus aureus","authors":"Ying Wang , Mengyan Xu , Hanne Ingmer","doi":"10.1016/j.engmic.2025.100231","DOIUrl":"10.1016/j.engmic.2025.100231","url":null,"abstract":"<div><div><em>Staphylococcus aureus</em> is a major public health threat, largely due to its remarkable capacity to develop antimicrobial resistance. Zhang <em>et al.</em> recently demonstrated a highly innovative approach to eradicate chronic methicillin-resistant <em>S. aureus</em> infections by inducing bacterial calcification with antibody-polysialic acid conjugates targeting wall teichoic acids, while simultaneously modulating host immune responses via enhanced calprotectin expression and macrophage activation. Despite limitations, this strategy represents a promising and unconventional therapy to combat resistant <em>S. aureus</em> infections.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 3","pages":"Article 100231"},"PeriodicalIF":0.0,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144885416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-14DOI: 10.1016/j.engmic.2025.100230
Guangxin Yang , Xinchan Wang , Yunting Zhou , Xiuliang Ding , Jinxiu Huang , Shiyan Qiao , Aihua Deng , Haitao Yu
Microcin J25 (MccJ25) has received substantial attention as a potential solution to the global threat of infection caused by antibiotic-resistant bacteria. However, the industrial fermentation of MccJ25 faces production bottlenecks. It is imperative to further explore the production optimization strategies for MccJ25 to formulate comprehensive approaches for its industrial-scale production and other downstream applications. Here, Fe²⁺ in tap water was identified as a critical inhibitor of MccJ25 biosynthesis, selectively repressing mcjA transcription, which was reversible via 2,2′-bipyridine-mediated chelation. To decouple production from growth phase dependency and Fe²⁺ interference, we engineered Escherichia coli BL21 cells by performing two genetic modifications. First, we replaced the native mcjA promoter with a constitutive promoter (PQ) to allow its mid-log phase expression. Second, we replaced the native mcjBCD promoter with a medium-strength variant (P2223) that delayed production kinetics without affecting final yields. However, the genomic integration of mcjD alleviated plasmid-borne toxicity, increasing the expression timing and doubling the yield to 240 mg/L. Finally, we computationally optimized the mcjA ribosome-binding site (RBS) to enhance translation efficiency. RBS optimization revealed that a moderate translation initiation efficiency (550,584 arbitrary units [au]) maximized production, whereas excessive efficiency (2,019,712 au) impaired growth and output. These interventions synergistically increased the MccJ25 titer 10-fold, reaching 430 mg/L in batch culture. Our findings establish a robust platform for MccJ25 overproduction, highlighting promoter engineering and translational tuning as pivotal strategies for antimicrobial peptide biosynthesis. This study provides insights for overcoming metabolic constraints in microbial fermentation, advancing the development of peptide-based therapeutics against multidrug-resistant pathogens.
{"title":"Decoupling growth phase dependency and metal ion inhibition: A dual engineering strategy for the high-yield biosynthesis of microcin J25 in Escherichia coli","authors":"Guangxin Yang , Xinchan Wang , Yunting Zhou , Xiuliang Ding , Jinxiu Huang , Shiyan Qiao , Aihua Deng , Haitao Yu","doi":"10.1016/j.engmic.2025.100230","DOIUrl":"10.1016/j.engmic.2025.100230","url":null,"abstract":"<div><div>Microcin J25 (MccJ25) has received substantial attention as a potential solution to the global threat of infection caused by antibiotic-resistant bacteria. However, the industrial fermentation of MccJ25 faces production bottlenecks. It is imperative to further explore the production optimization strategies for MccJ25 to formulate comprehensive approaches for its industrial-scale production and other downstream applications. Here, Fe²⁺ in tap water was identified as a critical inhibitor of MccJ25 biosynthesis, selectively repressing <em>mcjA</em> transcription, which was reversible via 2,2′-bipyridine-mediated chelation. To decouple production from growth phase dependency and Fe²⁺ interference, we engineered <em>Escherichia coli</em> BL21 cells by performing two genetic modifications. First, we replaced the native <em>mcjA</em> promoter with a constitutive promoter (P<sub>Q</sub>) to allow its mid-log phase expression. Second, we replaced the native <em>mcjBCD</em> promoter with a medium-strength variant (P<sub>2223</sub>) that delayed production kinetics without affecting final yields. However, the genomic integration of <em>mcjD</em> alleviated plasmid-borne toxicity, increasing the expression timing and doubling the yield to 240 mg/L. Finally, we computationally optimized the <em>mcjA</em> ribosome-binding site (RBS) to enhance translation efficiency. RBS optimization revealed that a moderate translation initiation efficiency (550,584 arbitrary units [au]) maximized production, whereas excessive efficiency (2,019,712 au) impaired growth and output. These interventions synergistically increased the MccJ25 titer 10-fold, reaching 430 mg/L in batch culture. Our findings establish a robust platform for MccJ25 overproduction, highlighting promoter engineering and translational tuning as pivotal strategies for antimicrobial peptide biosynthesis. This study provides insights for overcoming metabolic constraints in microbial fermentation, advancing the development of peptide-based therapeutics against multidrug-resistant pathogens.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 4","pages":"Article 100230"},"PeriodicalIF":0.0,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145121026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-06DOI: 10.1016/j.engmic.2025.100229
Carlos Cartin-Caballero , Christophe Collet , Daniel Gapes , Peter A. Gostomski , Matthew B. Stott , Carlo R. Carere
The verrucomicrobial methanotroph, Methylacidiphilum sp. RTK17.1, and the microalgae, Galdieria sp. RTK37.1 are both thermoacidophilic microorganisms isolated from geothermally heated soils at Rotokawa, Aotearoa-New Zealand. In this work, we used cocultures of Methylacidiphilum sp. RTK17.1 and Galdieria sp. RTK37.1 in batch and continuous systems (45 °C, pH 2.5) to assess their biomass productivity and performance; with the goal of removing methane and carbon dioxide from simulated waste gas streams and assessing the resultant biomass for its potential use as single cell protein. Coculture performance was compared to corresponding axenic cultures and the nutritional suitability of resultant biomass was assessed as a single cell protein feedstock. Stable coculture was achieved in both batch and chemostat systems. In batch experiments, Galdieria sp. RTK37.1 significantly enhanced growth (29 %) and methane oxidation (300 %) rates of Methylacidiphilum sp. RTK17.1, and complete methane removal was achieved without formation of an explosive gas mixture. In steady state chemostat coculture experiments, Galdieria sp. RTK37.1 decreased net volumetric oxygen consumption by 46 %, but its oxygenic activity was unable to supply Methylacidiphilum sp. RTK17.1 with the O2 required for complete CH4 removal. Nevertheless, Methylacidiphilum sp. RTK17.1 benefited from the presence of Galdieria sp. RTK37.1 in a low O2 environment; with O2 algae-methanotroph cross-feeding playing a fundamental role on their interactions. Methylacidiphilum sp. RTK17.1, Galdieria sp. RTK37.1, and their coculture each displayed similar nutritional profiles, with protein quality comparable to soybean meal and fishmeal feeds used for animals. The biomass needed to meet the daily indispensable amino acid requirements of a 62 kg adult human was 568 g for Methylacidiphilum sp. RTK17.1, 804 g Galdieria sp. RTK37.1, and 754 g for the coculture, with histidine being the limiting amino acid. These thermoacidophilic cocultures, which have not previously been investigated, offer great potential to convert low (or negative) value industrial gas streams into valuable products (e.g. supplementary biofeedstocks).
{"title":"Simultaneous co-cultivation of the thermoacidophilic methanotroph, Methylacidiphilum sp. RTK17.1, and the microalga, Galdieria sp. RTK37.1, for single cell protein production","authors":"Carlos Cartin-Caballero , Christophe Collet , Daniel Gapes , Peter A. Gostomski , Matthew B. Stott , Carlo R. Carere","doi":"10.1016/j.engmic.2025.100229","DOIUrl":"10.1016/j.engmic.2025.100229","url":null,"abstract":"<div><div>The verrucomicrobial methanotroph, <em>Methylacidiphilum</em> sp. RTK17.1, and the microalgae, <em>Galdieria</em> sp. RTK37.1 are both thermoacidophilic microorganisms isolated from geothermally heated soils at Rotokawa, Aotearoa-New Zealand. In this work, we used cocultures of <em>Methylacidiphilum</em> sp. RTK17.1 and <em>Galdieria</em> sp. RTK37.1 in batch and continuous systems (45 °C, pH 2.5) to assess their biomass productivity and performance; with the goal of removing methane and carbon dioxide from simulated waste gas streams and assessing the resultant biomass for its potential use as single cell protein. Coculture performance was compared to corresponding axenic cultures and the nutritional suitability of resultant biomass was assessed as a single cell protein feedstock. Stable coculture was achieved in both batch and chemostat systems. In batch experiments, <em>Galdieria</em> sp. RTK37.1 significantly enhanced growth (29 %) and methane oxidation (300 %) rates of <em>Methylacidiphilum</em> sp. RTK17.1, and complete methane removal was achieved without formation of an explosive gas mixture. In steady state chemostat coculture experiments, <em>Galdieria</em> sp. RTK37.1 decreased net volumetric oxygen consumption by 46 %, but its oxygenic activity was unable to supply <em>Methylacidiphilum</em> sp. RTK17.1 with the O<sub>2</sub> required for complete CH<sub>4</sub> removal. Nevertheless, <em>Methylacidiphilum</em> sp. RTK17.1 benefited from the presence of <em>Galdieria</em> sp. RTK37.1 in a low O<sub>2</sub> environment; with O<sub>2</sub> algae-methanotroph cross-feeding playing a fundamental role on their interactions. <em>Methylacidiphilum</em> sp. RTK17.1, <em>Galdieria</em> sp. RTK37.1, and their coculture each displayed similar nutritional profiles, with protein quality comparable to soybean meal and fishmeal feeds used for animals. The biomass needed to meet the daily indispensable amino acid requirements of a 62 kg adult human was 568 g for <em>Methylacidiphilum</em> sp. RTK17.1, 804 g <em>Galdieria</em> sp. RTK37.1, and 754 g for the coculture, with histidine being the limiting amino acid. These thermoacidophilic cocultures, which have not previously been investigated, offer great potential to convert low (or negative) value industrial gas streams into valuable products (e.g. supplementary biofeedstocks).</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 4","pages":"Article 100229"},"PeriodicalIF":0.0,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144893086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A unicellular-colonial cyanobacterium, designated “BRSZ,” was isolated from a neutral-alkaline hot spring in Thailand. Morphological characterization revealed distinctive features consistent with those of the genus Gloeocapsa. Physiological assessments demonstrated that BRSZ is a moderately thermophilic and halotolerant cyanobacterium with the potential for chemoheterotrophic growth in dark conditions. Molecular phylogenetic analysis based on 16S ribosomal RNA (rRNA) gene sequences placed BRSZ within a well-defined Gloeocapsa clade, a finding corroborated by 16S–23S internal transcribed spacer (ITS) rRNA secondary structure analyses. Genome comparisons, including average nucleotide identity (ANI), genome-to-genome distance (GGD), and digital DNA-DNA hybridization (dDDH), between strain BRSZ and closely related taxa showed an ANI value of 95.45 %, near the lower boundary of the species delineation threshold (95–96 %). A GGD of 0.0374 (>0.0258) and dDDH of 69 % (<70 %) further supported genomic differentiation. Genome-based analysis revealed a mycosporine-like amino acid biosynthetic gene cluster likely involved in sunscreen compound production. Cultivation-based production of a UV-absorbing compound confirmed the functional relevance of this gene cluster. These findings expand the described diversity within the Gloeocapsa complex and enhance our understanding of the taxonomy of this group. In addition, they underscored the importance of hot spring environments as sources of novel extremophiles.
{"title":"Genotypic and molecular characterization of a moderately thermophilic cyanobacterium, Gloeocapsa sp. strain BRSZ","authors":"Sasiprapa Samsri , Tanwalee Deprom , Chananwat Kortheerakul , Sophon Sirisattha , Stephen B. Pointing , Hakuto Kageyama , Rungaroon Waditee-Sirisattha","doi":"10.1016/j.engmic.2025.100226","DOIUrl":"10.1016/j.engmic.2025.100226","url":null,"abstract":"<div><div>A unicellular-colonial cyanobacterium, designated “BRSZ,” was isolated from a neutral-alkaline hot spring in Thailand. Morphological characterization revealed distinctive features consistent with those of the genus <em>Gloeocapsa</em>. Physiological assessments demonstrated that BRSZ is a moderately thermophilic and halotolerant cyanobacterium with the potential for chemoheterotrophic growth in dark conditions. Molecular phylogenetic analysis based on 16S ribosomal RNA (rRNA) gene sequences placed BRSZ within a well-defined <em>Gloeocapsa</em> clade, a finding corroborated by 16S–23S internal transcribed spacer (ITS) rRNA secondary structure analyses. Genome comparisons, including average nucleotide identity (ANI), genome-to-genome distance (GGD), and digital DNA-DNA hybridization (dDDH), between strain BRSZ and closely related taxa showed an ANI value of 95.45 %, near the lower boundary of the species delineation threshold (95–96 %). A GGD of 0.0374 (>0.0258) and dDDH of 69 % (<70 %) further supported genomic differentiation. Genome-based analysis revealed a mycosporine-like amino acid biosynthetic gene cluster likely involved in sunscreen compound production. Cultivation-based production of a UV-absorbing compound confirmed the functional relevance of this gene cluster. These findings expand the described diversity within the <em>Gloeocapsa</em> complex and enhance our understanding of the taxonomy of this group. In addition, they underscored the importance of hot spring environments as sources of novel extremophiles.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 3","pages":"Article 100226"},"PeriodicalIF":0.0,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144866338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-07-30DOI: 10.1016/j.engmic.2025.100228
Yao-Kun Zhang , Liang Zhang , Xue Ni , Shu-Wen Zhang , Min-Zhi Jiang , Si-Lu Zhang , Guo-Xun Xiao , He Jiang , Ming-Xia Bi , Yu-Lin Wang , Chang Liu , Shuang-Jiang Liu
Bifidobacterium animalis subsp. lactis is a well-known probiotic with potential benefits for alleviating sub-health symptoms, including immune dysfunction and anxiety. Given the strain-specific nature of its probiotic effects, identifying effective strains for sub-health alleviation is crucial. In this study, we characterized 16 B animalis subsp. lactis isolates from fecal samples and probiotic sources. We assessed the genotype-phenotype correlations related to growth, carbon source utilization, and stress tolerance in vitro. Subsequently, we profiled 107 metabolites (including 28 alcohols and 17 esters) and quantified the levels of short-chain fatty acids and three other organic acids. Three B. animalis strains, GOLDGUT-BB21, WLBA7, and WLBA6, were selected and evaluated in a sleep-deprived mouse model. In vivo, WLBA3 reduced inflammation and oxidative stress by inhibiting the NLRP3 inflammasome pathway and modulating gut microbiota (e.g., Lactobacillus and Alistipes), which in turn significantly improved weight gain and fatigue resistance, attenuated cognitive function, and anxiety-like behavior. These findings provide insights into the diversity of B. animalis subsp. lactis strain resources and highlight the potential of WLBA3 as a candidate for alleviating sub-health symptoms.
{"title":"Bifidobacterium animalis subsp. lactis genome resources and metabolite profiling at the strain level and their ability to alleviate anxiety-like behavior in a sleep-deprived mouse model","authors":"Yao-Kun Zhang , Liang Zhang , Xue Ni , Shu-Wen Zhang , Min-Zhi Jiang , Si-Lu Zhang , Guo-Xun Xiao , He Jiang , Ming-Xia Bi , Yu-Lin Wang , Chang Liu , Shuang-Jiang Liu","doi":"10.1016/j.engmic.2025.100228","DOIUrl":"10.1016/j.engmic.2025.100228","url":null,"abstract":"<div><div><em>Bifidobacterium animalis</em> subsp. <em>lactis</em> is a well-known probiotic with potential benefits for alleviating sub-health symptoms, including immune dysfunction and anxiety. Given the strain-specific nature of its probiotic effects, identifying effective strains for sub-health alleviation is crucial. In this study, we characterized 16 <em>B animalis</em> subsp. <em>lactis</em> isolates from fecal samples and probiotic sources. We assessed the genotype-phenotype correlations related to growth, carbon source utilization, and stress tolerance <em>in vitro</em>. Subsequently, we profiled 107 metabolites (including 28 alcohols and 17 esters) and quantified the levels of short-chain fatty acids and three other organic acids. Three <em>B. animalis</em> strains, GOLDGUT-BB21, WLBA7, and WLBA6, were selected and evaluated in a sleep-deprived mouse model. <em>In vivo</em>, WLBA3 reduced inflammation and oxidative stress by inhibiting the NLRP3 inflammasome pathway and modulating gut microbiota (e.g., <em>Lactobacillus</em> and <em>Alistipes</em>), which in turn significantly improved weight gain and fatigue resistance, attenuated cognitive function, and anxiety-like behavior. These findings provide insights into the diversity of <em>B. animalis</em> subsp. <em>lactis</em> strain resources and highlight the potential of WLBA3 as a candidate for alleviating sub-health symptoms.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 4","pages":"Article 100228"},"PeriodicalIF":0.0,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144866543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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