Article
Microbiology
Jiakang Yin, Ziliang Zhang, Yixiong Guo, Yue Chen, Yang Xu, Wenxuan Chen, Yanan Shao, Youfeng Yu, Lixia Zhu, Lingling Chen, Lifang Ruan
Summary: In this study, the differences in the microbiome between healthy and diseased soils used for tomato planting were surveyed in various climatic regions in China. The roles of species associated with disease symptoms were validated. Healthy soil exhibited more diverse bacterial communities and potential plant probiotics, while bacteria enriched in diseased soil promoted the progression of tomato bacterial wilt. The results highlight the importance of understanding the relationship between soil microbiota and disease occurrence for the precise control of soilborne diseases.
Article
Engineering, Environmental
Guofan Zhu, Huizhen Chao, Mingming Sun, Yuji Jiang, Mao Ye
Summary: Earthworm intestinal bacteria and indigenous soil bacteria collaborate in various biochemical processes and are important for maintaining soil stability. The response mechanism of these bacterial communities to external pesticide disturbance is unknown. This study used metagenomic sequencing to analyze the effects of nitro-chlorobenzene exposure on soil and earthworm gut contents. The results showed a significant decrease in microbial community composition and abundance under pesticide stress. The earthworm intestinal microbiome was found to assist in reducing pesticide toxicity in the soil microbiome. The toxicity sharing model provided quantitative information on the toxic effects of pesticides on the earthworm intestinal microbiome and highlighted the potential of earthworms for mitigating pesticide pollution and soil remediation.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Review
Biotechnology & Applied Microbiology
Xin Pan, Lei Xu, Yaru Li, Sihua Wu, Yong Wu, Wenping Wei
Summary: This paper systematically reviews the strategies adopted in the past 20 years to improve the biosynthesis of beta-lactam antibiotics through adjusting enzymatic properties and manipulating the reaction system. These strategies include enzyme mining, protein engineering, solvent engineering, in situ product removal, and one-pot reaction cascade. These advances provide important guidelines for future industrial production of beta-lactam antibiotics using enzymatic synthesis.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Toxicology
Ethan W. Morgan, Gary H. Perdew, Andrew D. Patterson
Summary: This review provides an overview of current methods used to characterize microbes in the context of toxicology and discusses commonly used techniques for conducting omic-based experiments, their strengths and deficiencies, and how forward-looking techniques may address present shortcomings. It also highlights common assumptions that impede microbiome studies from producing causal explanations of toxicologic mechanisms.
TOXICOLOGICAL SCIENCES
(2022)
Review
Agronomy
Isabel Cristina Velez-Bermudez, Wolfgang Schmidt
Summary: In concert with oxygen, soil alkalinity strongly restricts the availability of iron, an essential nutrient with a multitude of functions in living organisms. This versatile, reciprocal plant-microbiome interplay affects iron mobilization directly, but also collaterally by impacting growth, fitness, and health of the host.
Review
Green & Sustainable Science & Technology
Kishan Mahmud, Dinesh Panday, Anaas Mergoum, Ali Missaoui
Summary: Nitrogen plays a crucial role in agricultural ecosystems, but its loss can have significant impacts on crop production, soil sustainability, and environmental protection. Mitigation strategies are needed to reduce global nitrogen pollution and promote regenerative and sustainable agriculture.
Article
Chemistry, Multidisciplinary
Edurne Pena-Mendizabal, Bruce K. Hua, Ethel Ibanez-Echevarria, Dolores Hernandez-Fernandez de Rojas, Angel Maquieira, Stuart L. Schreiber, Sergi Morais
Summary: In this study, we synthesized beta-lactam-derived haptens using the principles of diversity-oriented synthesis and discovered compounds for drug allergy in vitro testing. The haptens exhibited excellent diagnostic sensitivity and specificity in detecting specific anti-beta-lactam immunoglobulins. This strategy could potentially assist in beta-lactam delabeling initiatives.
CHEMICAL COMMUNICATIONS
(2022)
Review
Agriculture, Multidisciplinary
Chi In Vong, Thirumurugan Rathinasabapathy, Marvin Moncada, Slavko Komarnytsky
Summary: The dietary intake of plant polyphenols is significant, but the complexity of phenolic metabolites and the lack of appropriate tools and methods have made it difficult to study their health effects. Recent findings have described novel and complex downstream metabolite profiles, including microbial dihydrophenolic acids, methylated phenolic metabolites, and small phenolic metabolites derived from different classes of phenolic compounds. Precise identification of the individual phenolic metabolite signatures is crucial for future nutritional interventions and dietary guidelines.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Review
Plant Sciences
Elizabeth French, Ian Kaplan, Anjali Lyer-Pascuzzi, Cindy H. Nakatsu, Laramy Enders
Summary: Efforts to characterize soil, plant, and insect-associated microbial communities have revealed the complexity of crop-associated microbiomes. Plant-associated microorganisms have potential in improving agricultural sustainability, but research faces challenges in harnessing the beneficial properties of agricultural microbiomes for crop performance. Enhancing microbiome manipulation is a key strategy in achieving precision microbiome management for diverse agricultural systems.
Review
Environmental Sciences
Annapurna Bhattacharjee, Shubham Dubey, Shilpi Sharma
Summary: The article discusses the challenges and methods of storing soil microbiome, including how to assess its integrity, successful cases, as well as the limitations and unanswered questions in the field.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Nelson Frazao, Isabel Gordo
Summary: Social networks can shape the species composition of the gut microbiome by influencing the ecology of gut bacteria. In an experimental evolution study in mice, it was found that there is a transmission rate of 7% (& PLUSMN;3% 2SE) of E. coli cells per day between hosts living in the same household. The results also showed that hosts with similar diets and habits are expected to have similar microbiome species compositions and evolutionary dynamics.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Fredrika Rajer, Lisa Allander, Philip A. Karlsson, Linus Sandegren
Summary: β-lactam antibiotics are the first choice for the treatment of bacterial infections, but the prevalence of β-lactamases limits their effectiveness. Combining β-lactam antibiotics with β-lactamase inhibitors can restore treatment efficacy. However, clinical isolates often carry multiple β-lactamases and other resistance genes, which impact the development of resistance.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Agriculture, Dairy & Animal Science
Hye-Ri Jung, Yu Jin Lee, Serim Hong, Sunghyun Yoon, Suk-Kyung Lim, Young Ju Lee
Summary: Beta-lactam antibiotics are widely used in human and veterinary medicine, but their excessive use has led to the spread of deadly antibiotic-resistant bacteria. This study found that beta-lactam antibiotics were commonly prescribed in integrated broiler operations, and their use was associated with an increase in beta-lactam-resistant E. coli isolates. These findings highlight the importance of strengthening farm management practices and reducing antibiotic use.
Review
Immunology
Chunhui Gao, Bowen Ma, Wei Liu, Liqin Zhu
Summary: Beta-lactam antibiotics are frequently used drugs in pediatrics but also common causes of allergic reactions. Skin testing, such as penicillin and cephalosporin tests, are used to predict allergic reactions in children. However, false-positive results are more common in pediatric skin tests, leading to unnecessary use of alternative antibiotics and increasing antibiotic resistance. There is controversy over whether beta-lactam antibiotic skin tests should be conducted in children. This study analyzes the mechanism of anaphylaxis, the significance of skin tests, and the problems with current practices to establish a unified standard for skin tests in pediatrics.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Zongzhuan Shen, Linda S. Thomashow, Yannan Ou, Chengyuan Tao, Jiabao Wang, Wu Xiong, Hongjun Liu, Rong Li, Qirong Shen, George A. Kowalchuk
Summary: By analyzing the composition and functional potentials of soil microbiomes, this study identified specific microbial communities and genes associated with the suppression of banana Panama disease caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc4). Pseudomonas was identified as a potential key taxon linked to pathogen suppression, and the microbiomes in suppressive soils displayed a greater incidence of genes related to quorum sensing, biofilm formation, and synthesis of antimicrobial compounds. These findings suggest the importance of specific microbial communities and functional capacities in disease suppression.
Article
Microbiology
Sailesh Malla, Eric van der Helm, Behrooz Darbani, Stefan Wieschalka, Jochen Foerster, Irina Borodina, Morten Otto Alexander Sommer
Summary: The lack of an active export system limits the accumulation and purification of intracellular products in industrial bio-based production processes. In this study, a novel L-lysine exporter belonging to the uncharacterized EamA superfamily was identified using metagenomic functional selection. This exporter significantly improved L-lysine tolerance and enhanced the yield and production of L-lysine in an industrial strain. This approach allows for the discovery of novel exporters and can be used to increase the productivity of bioprocesses with toxicity limitations.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Pharmacology & Pharmacy
Hitesh P. Gelli, Ruben Vazquez-Uribe, Morten Otto Alexander Sommer
Summary: Using cell-penetrating peptides (CPPs) is an effective strategy to improve drug absorption. Among the 9 most promising CPPs studied, 4 of them significantly increased the paracellular permeability of the intestinal barrier without compromising cellular health. Furthermore, these 4 CPPs also affected the growth of the majority of tested commensal strains.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemical Research Methods
Max van't Hof, Omkar S. Mohite, Jonathan M. Monk, Tilmann Weber, Bernhard O. Palsson, Morten O. A. Sommer
Summary: The study developed an updated metabolic model, iHM1533, of Escherichia coli Nissle 1917 (EcN) with extended representation of secondary metabolites. The model was validated and improved, and it successfully predicted targets for optimizing secondary metabolite production. This model provides a better understanding of the metabolic capabilities of EcN and aids future metabolic engineering efforts.
BMC BIOINFORMATICS
(2022)
Article
Dermatology
Jonathan I. I. Silverberg, Lars E. E. French, Richard B. B. Warren, Bruce Strober, Kim Kjoller, Morten O. A. Sommer, Philippe Andres, Jakob Felding, Anne Weiss, Deniz Tutkunkardas, Tine Skak-Nielsen, Emma Guttman
Summary: This study examined the PDE4 enzymatic activity and anti-inflammatory effects of orismilast in vitro, ex vivo, and in vivo. The results showed that orismilast selectively and potently inhibited PDE4 and demonstrated broad-spectrum anti-inflammatory activity. These findings support the clinical development of oral orismilast as a novel treatment option for chronic inflammatory skin diseases.
JOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY AND VENEREOLOGY
(2023)
Article
Dermatology
Richard B. B. Warren, Bruce Strober, Jonathan I. I. Silverberg, Emma Guttman, Philippe Andres, Jakob Felding, Deniz Tutkunkardas, Kim Kjoller, Morten O. A. Sommer, Lars E. E. French
Summary: This study aimed to examine the efficacy and safety of orismilast for psoriasis treatment. The phase 2a trial found that orismilast significantly improved the condition of patients with psoriasis. The phase 1 trial tested new formulations to minimize gastrointestinal adverse reactions.
JOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY AND VENEREOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Rebecca M. Lennen, Hyun Gyu Lim, Kristian Jensen, Elsayed T. Mohammed, Patrick V. Phaneuf, Myung Hyun Noh, Sailesh Malla, Rosa A. Borner, Ksenia Chekina, Emre Ozdemir, Ida Bonde, Anna Koza, Jerome Maury, Lasse E. Pedersen, Lars Y. Schoning, Nikolaus Sonnenschein, Bernhard O. Palsson, Alex T. Nielsen, Morten O. A. Sommer, Markus J. Herrgard, Adam M. Feist
Summary: This study used an automated platform to evolve Escherichia coli to grow optimally in the presence of 11 industrial chemicals and uncovered the tolerance mechanisms. The results showed that cells are tolerized through frequent mutation of membrane transporters, cell wall-associated proteins, transcription and translation machineries, and stress signaling proteins. Osmotic stress plays a significant role in tolerance, and pre-tolerized starting isolates can greatly enhance the subsequent production of chemicals.
METABOLIC ENGINEERING
(2023)
Article
Multidisciplinary Sciences
Philip Wismer, Sarah Aparecida Soares, Kasper Alnor Einarson, Morten Otto Alexander Sommer
Summary: This study demonstrates the use of virtual reality (VR) behaviometrics for assessing compliance and physical laboratory skills. By employing machine learning and classical statistics, significant behavioral predictors were identified from a logistic regression model, accurately classifying students and biopharma company employees as experts or novices in pH meter handling tasks with 77% accuracy. Specifically, the game score and number of interactions in VR tasks requiring practical skills were found to be performance predictors. The study offers biopharma companies and academic institutions the potential to assess performance using an automatic, reliable, and simple alternative to traditional in-person assessment methods. Integrating this assessment into training tools eliminates the need for tedious post-training evaluations.
Article
Immunology
Anne Weiss, Rodinde Hendrickx, Eva Stensgaard, Mads Jellingso, Morten O. A. Sommer
Summary: Immunocompromised patients, including dialysis and kidney transplant patients, have faced an increased risk of mortality due to COVID-19 despite available countermeasures. Additional protection measures are necessary for this vulnerable population.
Article
Biochemical Research Methods
Troels Holger Vaaben, Ruben Vazquez-Uribe, Morten Otto Alexander Sommer
Summary: Advanced microbial therapeutics, which engineer microbial cells to produce and deliver therapeutics in the human body, offer precise and self-regulating treatment options. This study characterized sensors in probiotic Escherichia coli that respond to physiological conditions and molecules found in the human body, demonstrating their functionality in vivo and their potential for advanced microbiome therapeutics.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Karl Alex Hedin, Vibeke Kruse, Ruben Vazquez-Uribe, Morten Otto Alexander Sommer
Summary: The human gastrointestinal tract plays a crucial role in human health and microorganisms engineered for therapeutic purposes have emerged as a novel approach to managing diseases. To prevent the spread of these microorganisms outside the treated individual, safe and robust biocontainment strategies are necessary.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Akanksha Rajput, Siddharth M. Chauhan, Omkar S. Mohite, Jason C. Hyun, Omid Ardalani, Leonie J. Jahn, Morten O. A. Sommer, Bernhard O. Palsson
Summary: Lactobacillaceae is an important microbial family in the food industry. Through a comprehensive pangenome analysis, we found the characteristics of core, accessory, and rare genomes, as well as a richness of biosynthetic gene clusters.
Article
Multidisciplinary Sciences
Justin E. Silpe, Olivia P. Duddy, Grace E. Johnson, Grace A. Beggs, Fatima A. Hussain, Kevin J. Forsberg, Bonnie L. Bassler
Summary: Most bacteria in the biosphere are polylysogens that contain multiple prophages. Prophage induction is universally triggered by DNA-damaging agents, but this study discovered regulatory modules that control induction independently of this cue. These modules share a regulatory logic and involve a small protein that inactivates the master repressor of lysis, resulting in phage production. The stimulus used to induce lysis determines phage productivity in polylysogens, highlighting the importance of additional phage-encoded sensory pathways.
Article
Multidisciplinary Sciences
Sarunas Tumas, Trine Sundebo Meldgaard, Troels Holger Vaaben, Sara Suarez Hernandez, Annemette Tengstedt Rasmussen, Ruben Vazquez-Uribe, Sine Reker Hadrup, Morten O. A. Sommer
Summary: In this study, we optimized the delivery of biologically active IL-2 using engineered E. coli Nissle 1917. The engineered strain showed high biological activity of microbially produced IL-2 (mi-IL2) in vitro and demonstrated strong immune cell activation in a 3D tumor spheroid model. Furthermore, the engineered strain selectively colonized tumors in a murine CT26 tumor model and resulted in a modest reduction in tumor growth rate and increased levels of IL-2 in the tumor. This study provides a workflow for researchers interested in utilizing E. coli Nissle for microbial therapy against cancer.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Chrysoula Dimopoulou, Mareike Bongers, Mikael Pedersen, Martin Bahl, Morten O. A. Sommer, Martin F. Laursen, Tine R. Licht
Summary: We successfully transferred the ability to produce the health-beneficial microbial metabolite indole lactic acid (ILA) into Escherichia coli, and demonstrated its expression in vitro and in vivo. The expanding knowledge of gut microbiota's metabolic activities and their impact on health has led to growing interest in engineered probiotics. Tryptophan metabolites, especially ILA, are potential therapeutic agents with multiple beneficial effects. Our study engineered an E. coli strain that produces ILA and showed its robust production in a mouse model, offering efficient options for therapeutic interventions against gastrointestinal inflammation.
FEMS MICROBIOLOGY LETTERS
(2023)
Article
Endocrinology & Metabolism
Valeria Iannone, Ambrin Farizah Babu, Johnson Lok, Carlos Gomez-Gallego, Giuseppe D'Auria, Ruben Vazquez-Uribe, Troels Holger Vaaben, Mareike Bongers, Santtu Mikkonen, Maija Vaittinen, Ida Tikkanen, Mikko Kettunen, Anton Klavus, Ratika Sehgal, Dorota Kaminska, Jussi Pihlajamaki, Kati Hanhineva, Hani El-Nezami, Morten Otto Alexander Sommer, Marjukka Kolehmainen
Summary: This study found that Escherichia coli Nissle 1917 expressing aldafermin, combined with dietary changes, can alleviate symptoms of MASLD, including reducing body weight, liver steatosis, plasma aspartate aminotransferase, and plasma cholesterol levels. RNA sequencing and metabolomics analysis revealed the downregulation of amino acid metabolism and related receptor signaling pathways, which may be implicated in the reduction of hepatic steatosis and insulin resistance.
MOLECULAR METABOLISM
(2023)
