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Li B, Mao Z, Xue J, Xing P, Wu QL. Metabolic versatility of aerobic methane-oxidizing bacteria under anoxia in aquatic ecosystems. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e70002. [PMID: 39232853 PMCID: PMC11374530 DOI: 10.1111/1758-2229.70002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/26/2024] [Indexed: 09/06/2024]
Abstract
The potential positive feedback between global aquatic deoxygenation and methane (CH4) emission emphasizes the importance of understanding CH4 cycling under O2-limited conditions. Increasing observations for aerobic CH4-oxidizing bacteria (MOB) under anoxia have updated the prevailing paradigm that MOB are O2-dependent; thus, clarification on the metabolic mechanisms of MOB under anoxia is critical and timely. Here, we mapped the global distribution of MOB under anoxic aquatic zones and summarized four underlying metabolic strategies for MOB under anoxia: (a) forming a consortium with oxygenic microorganisms; (b) self-generation/storage of O2 by MOB; (c) forming a consortium with non-oxygenic heterotrophic bacteria that use other electron acceptors; and (d) utilizing alternative electron acceptors other than O2. Finally, we proposed directions for future research. This study calls for improved understanding of MOB under anoxia, and underscores the importance of this overlooked CH4 sink amidst global aquatic deoxygenation.
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Affiliation(s)
- Biao Li
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Zhendu Mao
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jingya Xue
- School of Geographical Sciences, Nanjing Normal University, Nanjing, China
| | - Peng Xing
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Qinglong L Wu
- Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, China
- The Fuxianhu Station of Plateau Deep Lake Research, Chinese Academy of Sciences, Yuxi, China
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2
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Boyanova L, Boyanova L, Hadzhiyski P, Gergova R, Markovska R. Oxygen tolerance in anaerobes as a virulence factor and a health-beneficial property. Anaerobe 2024; 89:102897. [PMID: 39154706 DOI: 10.1016/j.anaerobe.2024.102897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 07/28/2024] [Accepted: 08/06/2024] [Indexed: 08/20/2024]
Abstract
Oxygen tolerance of anaerobes is a virulence factor, but can also be a beneficial property. Many species have evolved to tolerate or take advantage of the presence of low, especially nanaerobic (≤0.14 %) oxygen concentrations. Oxygen tolerance is genus-, species- and strain-dependent according to their protective mechanisms. It was better expressed in some pathogenic species such as Bacteroides fragilis, Clostridioides difficile, and Clostridium perfringens, as well as in Akkermansia muciniphila than in other potential probiotics such as Alistipes, Blautia and Roseburia spp. Different degrees of oxygen sensitivity were found between the strains of Anaerostipes, Faecalibacterium, and Bifidobacterium spp. Importantly, clostridial spores and anaerobes in biofilms are protected from oxidation. Rubrerythrins and flavodiiron proteins and two regulators (sigma factor B and PerR) contribute to C. difficile protection from reactive oxygen species (ROS). The frequent pathogen, B. fragilis, has numerous protective factors such as enzymes (catalase, superoxide dismutase, alkyl hydroperoxidase, thioredoxin peroxidase, and aerobic-type NrdAB ribonucleotide reductase), and nanaerobic respiration. Seven proteins confer strain-specific oxygen adaptation of Faecalibacterium prausnitzii. Oxygen tolerance protects anaerobes from ROS, shields their DNA and modulates gene expression. Furthermore, oxygen can induce mutations leading to antibiotic resistance as shown in Prevotella melaninogenica. Some Faecalibacterium, Anaerostipes, Bifidobacterium, and Akkermansia strains from the intestinal microbiota exhibiting oxygen tolerance may become next-generation probiotic candidates. Further studies are needed to reveal oxygen effects on more anaerobic species and strains, and the influence of oxygen on antibiotic resistance. More studies on oxygen-tolerant probiotic strains can be useful to optimize biotechnological methods.
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Affiliation(s)
- Lyudmila Boyanova
- Department of Medical Microbiology, Medical University of Sofia, 2 Zdrave Str., 1431, Sofia, Bulgaria.
| | - Liliya Boyanova
- Department of Medical Microbiology, Medical University of Sofia, 2 Zdrave Str., 1431, Sofia, Bulgaria
| | - Petyo Hadzhiyski
- Specialized Hospital for Active Pediatric Treatment, Medical University of Sofia, "Acad. Ivan Evstatiev Geshov" Blvd, 1606, Sofia, Bulgaria
| | - Raina Gergova
- Department of Medical Microbiology, Medical University of Sofia, 2 Zdrave Str., 1431, Sofia, Bulgaria
| | - Rumyana Markovska
- Department of Medical Microbiology, Medical University of Sofia, 2 Zdrave Str., 1431, Sofia, Bulgaria
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3
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Nair PP, Annapure US. Fermentation dynamics of bile salt hydrolase production in Heyndrickxia coagulans ATCC 7050 and Lactiplantibacillus plantarum ATCC 10012: Addressing ninhydrin assay limitations with a novel HPTLC-MS method. J Microbiol Methods 2024; 226:107050. [PMID: 39353547 DOI: 10.1016/j.mimet.2024.107050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 09/27/2024] [Accepted: 09/27/2024] [Indexed: 10/04/2024]
Abstract
Bile salt hydrolase (BSH), a pivotal enzyme in cholesterol management, holds significant promise in both human and animal subjects. This study investigated the effect of fermentation dynamics in Heyndrickxia coagulans ATCC 7050 and Lactiplantibacillus plantarum ATCC 10012 to enhance BSH production. Cultivation of cultures in MRS and M17 media revealed that MRS medium enhanced BSH production by 235.98 % in H. coagulans ATCC 7050 and 147.37 % in L. plantarum ATCC 10012, compared to M 17 medium. Additionally, varying oxygen concentration levels indicated that H. coagulans ATCC 7050 exhibited its minimum doubling time of 79.8 ± 0.64 min in anaerobic conditions, whereas L. plantarum ATCC 10012 demonstrated its minimum doubling time of 85.5 ± 1.2 min under microaerophilic conditions. However, their highest BSH activity was observed during the stationary phase under anaerobic conditions, yielding 17.14 ± 0.78 U/mL by H. coagulans ATCC 7050 and 19.04 ± 0.81 U/mL by L. plantarum ATCC 10012. Furthermore, it was observed that both organisms did not retain BSH within their cells. BSH activity was assessed using ninhydrin assay that detected free taurine liberated from sodium taurocholate. However, ninhydrin can yield false-positive results owing to its interaction with other free amino acids. To subjugate this limitation, the study introduced a novel and sensitive HPTLC-MS method capable of accurately detecting taurine. By comprehending fermentation dynamics and selecting appropriate conditions, BSH production increased 2.1-fold in both organisms. These findings illuminate critical insights, offering a pathway for novel strategies to enhance the BSH-producing capabilities of these LAB strains.
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Affiliation(s)
- Pratisha P Nair
- Department of Food Engineering and Technology, Institute of Chemical Technology, Matunga, Mumbai, Maharashtra, India
| | - Uday S Annapure
- Department of Food Engineering and Technology, Institute of Chemical Technology, Matunga, Mumbai, Maharashtra, India.
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4
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Atasoy M, Bartkova S, Çetecioğlu-Gürol Z, P Mira N, O'Byrne C, Pérez-Rodríguez F, Possas A, Scheler O, Sedláková-Kaduková J, Sinčák M, Steiger M, Ziv C, Lund PA. Methods for studying microbial acid stress responses: from molecules to populations. FEMS Microbiol Rev 2024; 48:fuae015. [PMID: 38760882 PMCID: PMC11418653 DOI: 10.1093/femsre/fuae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 03/27/2024] [Accepted: 05/16/2024] [Indexed: 05/20/2024] Open
Abstract
The study of how micro-organisms detect and respond to different stresses has a long history of producing fundamental biological insights while being simultaneously of significance in many applied microbiological fields including infection, food and drink manufacture, and industrial and environmental biotechnology. This is well-illustrated by the large body of work on acid stress. Numerous different methods have been used to understand the impacts of low pH on growth and survival of micro-organisms, ranging from studies of single cells to large and heterogeneous populations, from the molecular or biophysical to the computational, and from well-understood model organisms to poorly defined and complex microbial consortia. Much is to be gained from an increased general awareness of these methods, and so the present review looks at examples of the different methods that have been used to study acid resistance, acid tolerance, and acid stress responses, and the insights they can lead to, as well as some of the problems involved in using them. We hope this will be of interest both within and well beyond the acid stress research community.
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Affiliation(s)
- Merve Atasoy
- UNLOCK, Wageningen University and Research, PO Box 9101, 6700 HB, the Netherlands
| | - Simona Bartkova
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
| | - Zeynep Çetecioğlu-Gürol
- Department of Industrial Biotechnology, KTH Royal Institute of Technology, Roslagstullsbacken 21 106 91 Stockholm, Stockholm, Sweden
| | - Nuno P Mira
- iBB, Institute for Bioengineering and Biosciences, Department of Bioengineering, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Conor O'Byrne
- Microbiology, School of Biological and Chemical Sciences, University of Galway, University Road, Galway, H91 TK33, Ireland
| | - Fernando Pérez-Rodríguez
- Department of Food Science and Tehcnology, UIC Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, 14014 Córdoba, Spain
| | - Aricia Possas
- Department of Food Science and Tehcnology, UIC Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, 14014 Córdoba, Spain
| | - Ott Scheler
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
| | - Jana Sedláková-Kaduková
- Institute of Chemistry and Environmental Sciences, University of Ss. Cyril and Methodius, 91701 Trnava, Republic of Slovakia
| | - Mirka Sinčák
- Institute of Chemistry and Environmental Sciences, University of Ss. Cyril and Methodius, 91701 Trnava, Republic of Slovakia
| | - Matthias Steiger
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Carmit Ziv
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, 7505101 Rishon LeZion, Israel
| | - Peter A Lund
- School of Biosciences and Institute of Microbiology of Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
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Wu R, Li C, Li J, Sjollema J, Geertsema-Doornbusch GI, de Haan-Visser HW, Dijkstra ESC, Ren Y, Zhang Z, Liu J, Flemming HC, Busscher HJ, van der Mei HC. Bacterial killing and the dimensions of bacterial death. NPJ Biofilms Microbiomes 2024; 10:87. [PMID: 39289404 PMCID: PMC11408613 DOI: 10.1038/s41522-024-00559-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 08/26/2024] [Indexed: 09/19/2024] Open
Abstract
Bacteria can be dead, alive, or exhibit slowed or suspended life forms, making bacterial death difficult to establish. Here, agar-plating, microscopic-counting, SYTO9/propidium-iodide staining, MTT-conversion, and bioluminescence-imaging were used to determine bacterial death upon exposure to different conditions. Rank correlations between pairs of assay outcomes were low, indicating different assays measure different aspects of bacterial death. Principal-component analysis yielded two principal components, named "reproductive-ability" (PC1) and "metabolic-activity" (PC2). Plotting of these principal components in two-dimensional space revealed a dead region, with borders defined by the PC1 and PC2 values. Sensu stricto implies an unpractical reality that all assays determining PC1 and PC2 must be carried out in order to establish bacterial death. Considering this unpracticality, it is suggested that at least one assay determining reproductive activity (PC1) and one assay determining metabolic activity (PC2) should be used to establish bacterial death. Minimally, researchers should specifically describe which dimension of bacterial death is assessed, when addressing bacterial death.
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Affiliation(s)
- Renfei Wu
- University of Groningen and University Medical Center Groningen, Department of Biomaterials & Biomedical Technology, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- Institute of Functional Nano and Soft Materials, Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren'ai Rd, Suzhou, 215123, Jiangsu, P. R. China
| | - Cong Li
- University of Groningen and University Medical Center Groningen, Department of Biomaterials & Biomedical Technology, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 199 Ren'ai Rd, Suzhou, 215123, Jiangsu, P. R. China
| | - Jiuyi Li
- School of Environment, Beijing Jiaotong University, Beijing, 100044, China
| | - Jelmer Sjollema
- University of Groningen and University Medical Center Groningen, Department of Biomaterials & Biomedical Technology, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Gésinda I Geertsema-Doornbusch
- University of Groningen and University Medical Center Groningen, Department of Biomaterials & Biomedical Technology, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - H Willy de Haan-Visser
- University of Groningen and University Medical Center Groningen, Department of Biomaterials & Biomedical Technology, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Emma S C Dijkstra
- University of Groningen and University Medical Center Groningen, Department of Biomaterials & Biomedical Technology, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Yijin Ren
- University of Groningen and University Medical Center of Groningen, Department of Orthodontics, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
| | - Zexin Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 199 Ren'ai Rd, Suzhou, 215123, Jiangsu, P. R. China
| | - Jian Liu
- Institute of Functional Nano and Soft Materials, Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren'ai Rd, Suzhou, 215123, Jiangsu, P. R. China
| | - Hans C Flemming
- University of Duisburg-Essen, Faculty of Chemistry, Biofilm Centre, Universitätsstrasse 5, 45141, Essen, Germany
- Institute of Oceanology, Chinese Academy of Sciences (IOCAS), 7 Nanhai Rd, Qingdao, 266071, China
| | - Henk J Busscher
- University of Groningen and University Medical Center Groningen, Department of Biomaterials & Biomedical Technology, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Henny C van der Mei
- University of Groningen and University Medical Center Groningen, Department of Biomaterials & Biomedical Technology, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
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6
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Flamholz AI, Goldford JE, Richter PA, Larsson EM, Jinich A, Fischer WW, Newman DK. Annotation-free prediction of microbial dioxygen utilization. mSystems 2024:e0076324. [PMID: 39230322 DOI: 10.1128/msystems.00763-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 09/05/2024] Open
Abstract
Aerobes require dioxygen (O2) to grow; anaerobes do not. However, nearly all microbes-aerobes, anaerobes, and facultative organisms alike-express enzymes whose substrates include O2, if only for detoxification. This presents a challenge when trying to assess which organisms are aerobic from genomic data alone. This challenge can be overcome by noting that O2 utilization has wide-ranging effects on microbes: aerobes typically have larger genomes encoding distinctive O2-utilizing enzymes, for example. These effects permit high-quality prediction of O2 utilization from annotated genome sequences, with several models displaying ≈80% accuracy on a ternary classification task for which blind guessing is only 33% accurate. Since genome annotation is compute-intensive and relies on many assumptions, we asked if annotation-free methods also perform well. We discovered that simple and efficient models based entirely on genomic sequence content-e.g., triplets of amino acids-perform as well as intensive annotation-based classifiers, enabling rapid processing of genomes. We further show that amino acid trimers are useful because they encode information about protein composition and phylogeny. To showcase the utility of rapid prediction, we estimated the prevalence of aerobes and anaerobes in diverse natural environments cataloged in the Earth Microbiome Project. Focusing on a well-studied O2 gradient in the Black Sea, we found quantitative correspondence between local chemistry (O2:sulfide concentration ratio) and the composition of microbial communities. We, therefore, suggest that statistical methods like ours might be used to estimate, or "sense," pivotal features of the chemical environment using DNA sequencing data.IMPORTANCEWe now have access to sequence data from a wide variety of natural environments. These data document a bewildering diversity of microbes, many known only from their genomes. Physiology-an organism's capacity to engage metabolically with its environment-may provide a more useful lens than taxonomy for understanding microbial communities. As an example of this broader principle, we developed algorithms that accurately predict microbial dioxygen utilization directly from genome sequences without annotating genes, e.g., by considering only the amino acids in protein sequences. Annotation-free algorithms enable rapid characterization of natural samples, highlighting quantitative correspondence between sequences and local O2 levels in a data set from the Black Sea. This example suggests that DNA sequencing might be repurposed as a multi-pronged chemical sensor, estimating concentrations of O2 and other key facets of complex natural settings.
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Affiliation(s)
- Avi I Flamholz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Joshua E Goldford
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Philippa A Richter
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Elin M Larsson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Adrian Jinich
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California, USA
- Department of Chemistry and Biochemistry, University of California at San Diego, San Diego, California, USA
| | - Woodward W Fischer
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, California, USA
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7
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Chang RR, Yao W, Pang JL, Dong KY, Lu YY, Huang BC, Jin RC. External redox couple enhanced anammox sludge activity at low temperature: Insight into intracellular resource synthesis. WATER RESEARCH 2024; 260:121904. [PMID: 38878317 DOI: 10.1016/j.watres.2024.121904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/28/2024] [Accepted: 06/06/2024] [Indexed: 07/27/2024]
Abstract
Anaerobic ammonium oxidation (anammox), an energy-efficient deamination biotechnology, faces operational challenges in low-temperature environments. Enhancing the metabolic activity of anammox bacteria (AnAOB) is pivotal for advancing its application in mainstream municipal wastewater treatment. Inspired by the metabolic adaptability of AnAOB and based on our previous findings, this work investigated the enhancement of intracellular ATP and NADH synthesis through the exogenous supply of reduced humic acid (HAred) and H2O2 redox couple, aiming to augment AnAOB activity under low-temperature conditions. Our experimental setup involved continuous dosing of 0.0067 μmol g-1 volatile suspended solid of H2O2 and 10 mg g-1 volatile suspended solid of HAred into a mainstream anammox reactor operated at 15 °C with an influent TN content of 60 mg/L. The results showed that HAred / H2O2 couple succeeded in maintaining the effluent TN at 10.72 ± 0.91 mg l-1. The specific anammox activity, ATP and NADH synthesis levels of sludge increased by 1.34, 2.33 and 6.50 folds, respectively, over the control setup devoid of the redox couple. High-throughput sequencing analysis revealed that the relative abundance of Candidatus Kuenenia after adding HAred / H2O2 couple reached 3.65 % at the end of operation, which was 5.14 folds higher than that of the control group. Further metabolomics analysis underscored an activation in the metabolism of amino acids, nucleotides, and phospholipids, which collectively enhanced the availability of ATP and NADH for the respiratory processes. These findings may provide guidance on strategy development for improving the electron transfer efficiency of AnAOB and underscore the potential of using redox couples to promote the mainstream application of anammox technology.
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Affiliation(s)
- Rong-Rong Chang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Wei Yao
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Jin-Luo Pang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Kai-Yue Dong
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yao-Yao Lu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Bao-Cheng Huang
- School of Engineering, Hangzhou Normal University, Hangzhou 311121, China.
| | - Ren-Cun Jin
- School of Engineering, Hangzhou Normal University, Hangzhou 311121, China
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8
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Urbauer E, Aguanno D, Mindermann N, Omer H, Metwaly A, Krammel T, Faro T, Remke M, Reitmeier S, Bärthel S, Kersting J, Huang Z, Xian F, Schmidt M, Saur D, Huber S, Stecher B, List M, Gómez-Varela D, Steiger K, Allez M, Rath E, Haller D. Mitochondrial perturbation in the intestine causes microbiota-dependent injury and gene signatures discriminative of inflammatory disease. Cell Host Microbe 2024; 32:1347-1364.e10. [PMID: 39013472 DOI: 10.1016/j.chom.2024.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 05/13/2024] [Accepted: 06/20/2024] [Indexed: 07/18/2024]
Abstract
Mitochondrial dysfunction is associated with inflammatory bowel diseases (IBDs). To understand how microbial-metabolic circuits contribute to intestinal injury, we disrupt mitochondrial function in the epithelium by deleting the mitochondrial chaperone, heat shock protein 60 (Hsp60Δ/ΔIEC). This metabolic perturbation causes self-resolving tissue injury. Regeneration is disrupted in the absence of the aryl hydrocarbon receptor (Hsp60Δ/ΔIEC;AhR-/-) involved in intestinal homeostasis or inflammatory regulator interleukin (IL)-10 (Hsp60Δ/ΔIEC;Il10-/-), causing IBD-like pathology. Injury is absent in the distal colon of germ-free (GF) Hsp60Δ/ΔIEC mice, highlighting bacterial control of metabolic injury. Colonizing GF Hsp60Δ/ΔIEC mice with the synthetic community OMM12 reveals expansion of metabolically flexible Bacteroides, and B. caecimuris mono-colonization recapitulates the injury. Transcriptional profiling of the metabolically impaired epithelium reveals gene signatures involved in oxidative stress (Ido1, Nos2, Duox2). These signatures are observed in samples from Crohn's disease patients, distinguishing active from inactive inflammation. Thus, mitochondrial perturbation of the epithelium causes microbiota-dependent injury with discriminative inflammatory gene profiles relevant for IBD.
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Affiliation(s)
- Elisabeth Urbauer
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
| | - Doriane Aguanno
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
| | - Nora Mindermann
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
| | - Hélène Omer
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
| | - Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
| | - Tina Krammel
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
| | - Tim Faro
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, 80337 Munich, Germany
| | - Marianne Remke
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany
| | - Sandra Reitmeier
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
| | - Stefanie Bärthel
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, 69120 Heidelberg, Germany; Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, 81675 Munich, Germany; Institute of Experimental Cancer Therapy, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Johannes Kersting
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 3, 85354 Freising, Germany
| | - Zihua Huang
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 3, 85354 Freising, Germany
| | - Feng Xian
- Systems Biology of Pain, Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| | - Manuela Schmidt
- Systems Biology of Pain, Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, 69120 Heidelberg, Germany; Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, 81675 Munich, Germany; Institute of Experimental Cancer Therapy, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Samuel Huber
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Bärbel Stecher
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilians University of Munich, 80336 Munich, Germany; German Center for Infection Research, Partner site LMU Munich, 80336 Munich, Germany
| | - Markus List
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 3, 85354 Freising, Germany; Munich Data Science Institute (MDSI), Technical University of Munich, 85748 Garching, Germany
| | - David Gómez-Varela
- Systems Biology of Pain, Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| | - Katja Steiger
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany
| | - Matthieu Allez
- Department of Gastroenterology, Hôpital Saint-Louis, APHP, INSERM UMRS 1160, Paris Diderot, Sorbonne Paris-Cité University, 75010 Paris, France
| | - Eva Rath
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
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9
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Coluccio A, Lopez Palomera F, Spero MA. Anaerobic bacteria in chronic wounds: Roles in disease, infection and treatment failure. Wound Repair Regen 2024. [PMID: 39129662 DOI: 10.1111/wrr.13208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/09/2024] [Accepted: 07/29/2024] [Indexed: 08/13/2024]
Abstract
Infection is among the most common factors that impede wound healing, yet standard treatments routinely fail to resolve chronic wound infections. The chronic wound environment is largely hypoxic/anoxic, and wounds are predominantly colonised by facultative and obligate anaerobic bacteria. Oxygen (O2) limitation is an underappreciated driver of microbiota composition and behaviour in chronic wounds. In this perspective article, we examine how anaerobic bacteria and their distinct physiologies support persistent, antibiotic-recalcitrant infections. We describe the anaerobic energy metabolisms bacteria rely on for long-term survival in the wound environment, and why many antibiotics become less effective under hypoxic conditions. We also discuss obligate anaerobes, which are among the most prevalent taxa to colonise chronic wounds, yet their potential roles in influencing the microbial community and wound healing have been overlooked. All of the most common obligate anaerobes found in chronic wounds are opportunistic pathogens. We consider how these organisms persist in the wound environment and interface with host physiology to hinder wound healing processes or promote chronic inflammation. Finally, we apply our understanding of anaerobic physiologies to evaluate current treatment practices and to propose new strategies for treating chronic wound infections.
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Affiliation(s)
- Alison Coluccio
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | | | - Melanie A Spero
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
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10
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Gough AM, Parker AC, O'Bryan PJ, Whitehead TR, Roy S, Garcia BL, Hoffman PS, Jeffrey Smith C, Rocha ER. New functions of pirin proteins and a 2-ketoglutarate: Ferredoxin oxidoreductase ortholog in Bacteroides fragilis metabolism and their impact on antimicrobial susceptibility to metronidazole and amixicile. Microbiologyopen 2024; 13:e1429. [PMID: 39109824 PMCID: PMC11304471 DOI: 10.1002/mbo3.1429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 07/05/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
The understanding of how central metabolism and fermentation pathways regulate antimicrobial susceptibility in the anaerobic pathogen Bacteroides fragilis is still incomplete. Our study reveals that B. fragilis encodes two iron-dependent, redox-sensitive regulatory pirin protein genes, pir1 and pir2. The mRNA expression of these genes increases when exposed to oxygen and during growth in iron-limiting conditions. These proteins, Pir1 and Pir2, influence the production of short-chain fatty acids and modify the susceptibility to metronidazole and amixicile, a new inhibitor of pyruvate: ferredoxin oxidoreductase in anaerobes. We have demonstrated that Pir1 and Pir2 interact directly with this oxidoreductase, as confirmed by two-hybrid system assays. Furthermore, structural analysis using AlphaFold2 predicts that Pir1 and Pir2 interact stably with several central metabolism enzymes, including the 2-ketoglutarate:ferredoxin oxidoreductases Kor1AB and Kor2CDAEBG. We used a series of metabolic mutants and electron transport chain inhibitors to demonstrate the extensive impact of bacterial metabolism on metronidazole and amixicile susceptibility. We also show that amixicile is an effective antimicrobial against B. fragilis in an experimental model of intra-abdominal infection. Our investigation led to the discovery that the kor2AEBG genes are essential for growth and have dual functions, including the formation of 2-ketoglutarate via the reverse TCA cycle. However, the metabolic activity that bypasses the function of Kor2AEBG following the addition of phospholipids or fatty acids remains undefined. Overall, our study provides new insights into the central metabolism of B. fragilis and its regulation by pirin proteins, which could be exploited for the development of new narrow-spectrum antimicrobials in the future.
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Affiliation(s)
- Andrea M. Gough
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Anita C. Parker
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | | | | | - Sourav Roy
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Brandon L. Garcia
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Paul S. Hoffman
- Department of Medicine, Division of Infectious Diseases and International HealthUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - C. Jeffrey Smith
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Edson R. Rocha
- Department of Microbiology and ImmunologyBrody School of Medicine at East Carolina UniversityGreenvilleNorth CarolinaUSA
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11
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Melki R, Litvak Y. From vacant to vivid: The nutritional landscape drives infant gut microbiota establishment. Mol Microbiol 2024. [PMID: 39044538 DOI: 10.1111/mmi.15296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 06/25/2024] [Accepted: 07/03/2024] [Indexed: 07/25/2024]
Abstract
From the moment of birth, the newborn gastrointestinal tract is infiltrated by various bacteria originating from both maternal and environmental sources. These colonizing bacteria form a complex microbiota community that undergoes continuous changes until adulthood and plays an important role in infant health. The maturation of the infant gut microbiota is driven by many factors and follows a distinct patterned trajectory, with specific bacterial taxa establish in the intestine in accordance with developmental milestones as the infant grows. In this review, we highlight how elements such as diet and host physiology select for specific microbial functions and shape the composition of the bacterial community in the large intestine.
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Affiliation(s)
- Reut Melki
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yael Litvak
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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12
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Khojasteh SC, Argikar UA, Chatzopoulou M, Cheruzel L, Cho S, Dhaware D, Johnson KM, Kalgutkar AS, Liu J, Ma B, Maw H, Rowley JA, Seneviratne HK, Wang S. Biotransformation research advances - 2023 year in review. Drug Metab Rev 2024:1-33. [PMID: 38989688 DOI: 10.1080/03602532.2024.2370330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/14/2024] [Indexed: 07/12/2024]
Abstract
This annual review marks the eighth in the series starting with Baillie et al. (2016) Our objective is to explore and share articles which we deem influential and significant in the field of biotransformation. Its format is to highlight important aspects captured in synopsis followed by a commentary with relevant figure and references.
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Affiliation(s)
- S Cyrus Khojasteh
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc, South San Francisco, CA, USA
| | - Upendra A Argikar
- Non-clinical Development, Bill and Melinda Gates Medical Research Institute, Cambridge, MA, USA
| | - Maria Chatzopoulou
- Early Clinical Development and Translational Science, UCB Biopharma UK, Slough, UK
| | - Lionel Cheruzel
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc, South San Francisco, CA, USA
| | - Sungjoon Cho
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc, South San Francisco, CA, USA
| | | | - Kevin M Johnson
- Drug Metabolism and Pharmacokinetics, Inotiv, MD Heights, MO, USA
| | - Amit S Kalgutkar
- Medicine Design, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| | - Joyce Liu
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc, South San Francisco, CA, USA
| | - Bin Ma
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc, South San Francisco, CA, USA
| | - Hlaing Maw
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc, Ridgefield, CT, USA
| | - Jessica A Rowley
- Early Clinical Development and Translational Science, UCB Biopharma UK, Slough, UK
| | - Herana Kamal Seneviratne
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - Shuai Wang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc, South San Francisco, CA, USA
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13
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Ye J, Zhuang M, Hong M, Zhang D, Ren G, Hu A, Yang C, He Z, Zhou S. Methanogenesis in the presence of oxygenic photosynthetic bacteria may contribute to global methane cycle. Nat Commun 2024; 15:5682. [PMID: 38971854 PMCID: PMC11227571 DOI: 10.1038/s41467-024-50108-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024] Open
Abstract
Accumulating evidences are challenging the paradigm that methane in surface water primarily stems from the anaerobic transformation of organic matters. Yet, the contribution of oxygenic photosynthetic bacteria, a dominant species in surface water, to methane production remains unclear. Here we show methanogenesis triggered by the interaction between oxygenic photosynthetic bacteria and anaerobic methanogenic archaea. By introducing cyanobacterium Synechocystis PCC6803 and methanogenic archaea Methanosarcina barkeri with the redox cycling of iron, CH4 production was induced in coculture biofilms through both syntrophic methanogenesis (under anoxic conditions in darkness) and abiotic methanogenesis (under oxic conditions in illumination) during the periodic dark-light cycles. We have further demonstrated CH4 production by other model oxygenic photosynthetic bacteria from various phyla, in conjunction with different anaerobic methanogenic archaea exhibiting diverse energy conservation modes, as well as various common Fe-species. These findings have revealed an unexpected link between oxygenic photosynthesis and methanogenesis and would advance our understanding of photosynthetic bacteria's ecological role in the global CH4 cycle. Such light-driven methanogenesis may be widely present in nature.
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Affiliation(s)
- Jie Ye
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Minghan Zhuang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mingqiu Hong
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dong Zhang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guoping Ren
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Andong Hu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chaohui Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhen He
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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14
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Wang D, Candry P, Hunt KA, Flinkstrom Z, Shi Z, Liu Y, Wofford NQ, McInerney MJ, Tanner RS, De Leόn KB, Zhou J, Winkler MKH, Stahl DA, Pan C. Metaproteomics-informed stoichiometric modeling reveals the responses of wetland microbial communities to oxygen and sulfate exposure. NPJ Biofilms Microbiomes 2024; 10:55. [PMID: 38961111 PMCID: PMC11222425 DOI: 10.1038/s41522-024-00525-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 06/07/2024] [Indexed: 07/05/2024] Open
Abstract
Climate changes significantly impact greenhouse gas emissions from wetland soil. Specifically, wetland soil may be exposed to oxygen (O2) during droughts, or to sulfate (SO42-) as a result of sea level rise. How these stressors - separately and together - impact microbial food webs driving carbon cycling in the wetlands is still not understood. To investigate this, we integrated geochemical analysis, proteogenomics, and stoichiometric modeling to characterize the impact of elevated SO42- and O2 levels on microbial methane (CH4) and carbon dioxide (CO2) emissions. The results uncovered the adaptive responses of this community to changes in SO42- and O2 availability and identified altered microbial guilds and metabolic processes driving CH4 and CO2 emissions. Elevated SO42- reduced CH4 emissions, with hydrogenotrophic methanogenesis more suppressed than acetoclastic. Elevated O2 shifted the greenhouse gas emissions from CH4 to CO2. The metabolic effects of combined SO42- and O2 exposures on CH4 and CO2 emissions were similar to those of O2 exposure alone. The reduction in CH4 emission by increased SO42- and O2 was much greater than the concomitant increase in CO2 emission. Thus, greater SO42- and O2 exposure in wetlands is expected to reduce the aggregate warming effect of CH4 and CO2. Metaproteomics and stoichiometric modeling revealed a unique subnetwork involving carbon metabolism that converts lactate and SO42- to produce acetate, H2S, and CO2 when SO42- is elevated under oxic conditions. This study provides greater quantitative resolution of key metabolic processes necessary for the prediction of CH4 and CO2 emissions from wetlands under future climate scenarios.
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Affiliation(s)
- Dongyu Wang
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Pieter Candry
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Zachary Flinkstrom
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Zheng Shi
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Yunlong Liu
- School of Computer Science, University of Oklahoma, Norman, OK, USA
| | - Neil Q Wofford
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | | | - Ralph S Tanner
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Kara B De Leόn
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Computer Science, University of Oklahoma, Norman, OK, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Chongle Pan
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA.
- School of Computer Science, University of Oklahoma, Norman, OK, USA.
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15
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Shi K, Liang B, Cheng HY, Wang HC, Liu WZ, Li ZL, Han JL, Gao SH, Wang AJ. Regulating microbial redox reactions towards enhanced removal of refractory organic nitrogen from wastewater. WATER RESEARCH 2024; 258:121778. [PMID: 38795549 DOI: 10.1016/j.watres.2024.121778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/10/2024] [Accepted: 05/12/2024] [Indexed: 05/28/2024]
Abstract
Biotechnology for wastewater treatment is mainstream and effective depending upon microbial redox reactions to eliminate diverse contaminants and ensure aquatic ecological health. However, refractory organic nitrogen compounds (RONCs, e.g., nitro-, azo-, amide-, and N-heterocyclic compounds) with complex structures and high toxicity inhibit microbial metabolic activity and limit the transformation of organic nitrogen to inorganic nitrogen. This will eventually result in non-compliance with nitrogen discharge standards. Numerous efforts suggested that applying exogenous electron donors or acceptors, such as solid electrodes (electrostimulation) and limited oxygen (micro-aeration), could potentially regulate microbial redox reactions and catabolic pathways, and facilitate the biotransformation of RONCs. This review provides comprehensive insights into the microbial regulation mechanisms and applications of electrostimulation and micro-aeration strategies to accelerate the biotransformation of RONCs to organic amine (amination) and inorganic ammonia (ammonification), respectively. Furthermore, a promising approach involving in-situ hybrid anaerobic biological units, coupled with electrostimulation and micro-aeration, is proposed towards engineering applications. Finally, employing cutting-edge methods including multi-omics analysis, data science driven machine learning, technology-economic analysis, and life-cycle assessment would contribute to optimizing the process design and engineering implementation. This review offers a fundamental understanding and inspiration for novel research in the enhanced biotechnology towards RONCs elimination.
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Affiliation(s)
- Ke Shi
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China.
| | - Hao-Yi Cheng
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Hong-Cheng Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Wen-Zong Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Zhi-Ling Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jing-Long Han
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Shu-Hong Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China.
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16
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Mrnjavac N, Nagies FSP, Wimmer JLE, Kapust N, Knopp MR, Trost K, Modjewski L, Bremer N, Mentel M, Esposti MD, Mizrahi I, Allen JF, Martin WF. The radical impact of oxygen on prokaryotic evolution-enzyme inhibition first, uninhibited essential biosyntheses second, aerobic respiration third. FEBS Lett 2024; 598:1692-1714. [PMID: 38750628 PMCID: PMC7616280 DOI: 10.1002/1873-3468.14906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 07/15/2024]
Abstract
Molecular oxygen is a stable diradical. All O2-dependent enzymes employ a radical mechanism. Generated by cyanobacteria, O2 started accumulating on Earth 2.4 billion years ago. Its evolutionary impact is traditionally sought in respiration and energy yield. We mapped 365 O2-dependent enzymatic reactions of prokaryotes to phylogenies for the corresponding 792 protein families. The main physiological adaptations imparted by O2-dependent enzymes were not energy conservation, but novel organic substrate oxidations and O2-dependent, hence O2-tolerant, alternative pathways for O2-inhibited reactions. Oxygen-dependent enzymes evolved in ancestrally anaerobic pathways for essential cofactor biosynthesis including NAD+, pyridoxal, thiamine, ubiquinone, cobalamin, heme, and chlorophyll. These innovations allowed prokaryotes to synthesize essential cofactors in O2-containing environments, a prerequisite for the later emergence of aerobic respiratory chains.
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Affiliation(s)
- Natalia Mrnjavac
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Falk S P Nagies
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Jessica L E Wimmer
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Nils Kapust
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Michael R Knopp
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Katharina Trost
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Luca Modjewski
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Nico Bremer
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | | | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and The National Institute for Biotechnology in the Negev, Be'er-Sheva, Israel
| | - John F Allen
- Research Department of Genetics, Evolution and Environment, University College London, UK
| | - William F Martin
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
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17
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Perez-Gil J, Behrendorff J, Douw A, Vickers CE. The methylerythritol phosphate pathway as an oxidative stress sense and response system. Nat Commun 2024; 15:5303. [PMID: 38906898 PMCID: PMC11192765 DOI: 10.1038/s41467-024-49483-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 06/05/2024] [Indexed: 06/23/2024] Open
Abstract
The methylerythritol phosphate (MEP) pathway is responsible for biosynthesis of the precursors of isoprenoid compounds in eubacteria and plastids. It is a metabolic alternative to the well-known mevalonate pathway for isoprenoid production found in archaea and eukaryotes. Recently, a role for the MEP pathway in oxidative stress detection, signalling, and response has been identified. This role is executed in part through the unusual cyclic intermediate, methylerythritol cyclodiphosphate (MEcDP). We postulate that this response is triggered through the oxygen sensitivity of the MEP pathway's terminal iron-sulfur (Fe-S) cluster enzymes. MEcDP is the substrate of IspG, the first Fe-S cluster enzyme in the pathway; it accumulates under oxidative stress conditions and acts as a signalling molecule. It may also act as an antioxidant. Furthermore, evidence is emerging for a broader and highly nuanced role of the MEP pathway in oxidative stress responses, implemented through a complex system of differential regulation and sensitivity at numerous nodes in the pathway. Here, we explore the evidence for such a role (including the contribution of the Fe-S cluster enzymes and different pathway metabolites, especially MEcDP), the evolutionary implications, and the many questions remaining about the behaviour of the MEP pathway in the presence of oxidative stress.
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Affiliation(s)
- Jordi Perez-Gil
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- School of Environmental and Biological Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia
| | - James Behrendorff
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- School of Environmental and Biological Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia
| | - Andrew Douw
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Claudia E Vickers
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
- School of Environmental and Biological Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia.
- BioBuilt Solutions, Corinda, QLD, 4075, Australia.
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18
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Li Y, Yu T, Feng X, Zhao B, Chen H, Yang H, Chen X, Zhang XH, Anderson HR, Burns NZ, Zeng F, Tao L, Zeng Z. Biosynthesis of GMGT lipids by a radical SAM enzyme associated with anaerobic archaea and oxygen-deficient environments. Nat Commun 2024; 15:5256. [PMID: 38898040 PMCID: PMC11186832 DOI: 10.1038/s41467-024-49650-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024] Open
Abstract
Archaea possess characteristic membrane-spanning lipids that are thought to contribute to the adaptation to extreme environments. However, the biosynthesis of these lipids is poorly understood. Here, we identify a radical S-adenosyl-L-methionine (SAM) enzyme that synthesizes glycerol monoalkyl glycerol tetraethers (GMGTs). The enzyme, which we name GMGT synthase (Gms), catalyzes the formation of a C(sp3)-C(sp3) linkage between the two isoprenoid chains of glycerol dialkyl glycerol tetraethers (GDGTs). This conclusion is supported by heterologous expression of gene gms from a GMGT-producing species in a methanogen, as well as demonstration of in vitro activity using purified Gms enzyme. Additionally, we show that genes encoding putative Gms homologs are present in obligate anaerobic archaea and in metagenomes obtained from oxygen-deficient environments, and appear to be absent in metagenomes from oxic settings.
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Affiliation(s)
- Yanan Li
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, China
| | - Ting Yu
- Department of Systems Biology and Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China
| | - Xi Feng
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Bo Zhao
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Huahui Chen
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Huan Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Xing Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | | | - Noah Z Burns
- Department of Chemistry, Stanford University, Stanford, USA
| | - Fuxing Zeng
- Department of Systems Biology and Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China.
| | - Lizhi Tao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, China.
| | - Zhirui Zeng
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.
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19
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Wang Y, He C, Xu C, Yang J, Feng J, Wang W. Influence of oxygen partial pressure on homoacetogenesis and promotion of acetic acid accumulation through low pH regulation under microaerobic conditions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:42766-42778. [PMID: 38878240 DOI: 10.1007/s11356-024-33952-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 06/05/2024] [Indexed: 07/04/2024]
Abstract
Homoacetogenesis is an important pathway for bio-utilization of CO2; however, oxygen is a key environmental influencing factor. This study explored the impact of different initial oxygen partial pressures (OPPs) on homoacetogenesis, while implementing low pH regulation enhanced acetic acid (HAc) accumulation under microaerobic conditions. Results indicated that cumulative HAc production increased by 18.2% in 5% OPP group, whereas decreases of 31.3% and 56.0% were observed in 10% and 20% OPP groups, respectively, compared to the control group. However, hydrogenotrophic methanogens adapted to microaerobic environment and competed with homoacetogens for CO2, thus limiting homoacetogenesis. Controlling influent pH 5.0 per cycle increased cumulative HAc production by 18.3% and 18.2% in 5% and 10% OPP groups, respectively, compared with the control group. Consequently, regulating low pH effectively inhibited methanogenic activity under microaerobic conditions, thus increasing HAc production. This study was expected to expand the practical application of homoacetogenesis in bio-utilization of CO2.
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Affiliation(s)
- Yuwei Wang
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
- Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei, 230009, China
| | - Chunhua He
- Department of Municipal Engineering, School of Environment and Energy Engineering, Anhui JianZhu University, Hefei, 230009, China
| | - Changwen Xu
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
- Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei, 230009, China
| | - Jing Yang
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
- Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei, 230009, China
| | - Jingwei Feng
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
- Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei, 230009, China
| | - Wei Wang
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China.
- Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei, 230009, China.
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20
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Utzman PH, Mays VP, Miller BC, Fairbanks MC, Brazelton WJ, Horvath MP. Metagenome mining and functional analysis reveal oxidized guanine DNA repair at the Lost City Hydrothermal Field. PLoS One 2024; 19:e0284642. [PMID: 38718041 PMCID: PMC11078426 DOI: 10.1371/journal.pone.0284642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
The GO DNA repair system protects against GC → TA mutations by finding and removing oxidized guanine. The system is mechanistically well understood but its origins are unknown. We searched metagenomes and abundantly found the genes encoding GO DNA repair at the Lost City Hydrothermal Field (LCHF). We recombinantly expressed the final enzyme in the system to show MutY homologs function to suppress mutations. Microbes at the LCHF thrive without sunlight, fueled by the products of geochemical transformations of seafloor rocks, under conditions believed to resemble a young Earth. High levels of the reductant H2 and low levels of O2 in this environment raise the question, why are resident microbes equipped to repair damage caused by oxidative stress? MutY genes could be assigned to metagenome-assembled genomes (MAGs), and thereby associate GO DNA repair with metabolic pathways that generate reactive oxygen, nitrogen and sulfur species. Our results indicate that cell-based life was under evolutionary pressure to cope with oxidized guanine well before O2 levels rose following the great oxidation event.
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Affiliation(s)
- Payton H. Utzman
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Vincent P. Mays
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Briggs C. Miller
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary C. Fairbanks
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - William J. Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Martin P. Horvath
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
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21
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Lee J, Menon N, Lim CT. Dissecting Gut-Microbial Community Interactions using a Gut Microbiome-on-a-Chip. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2302113. [PMID: 38414327 PMCID: PMC11132043 DOI: 10.1002/advs.202302113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/21/2023] [Indexed: 02/29/2024]
Abstract
While the human gut microbiota has a significant impact on gut health and disease, understanding of the roles of gut microbes, interactions, and collective impact of gut microbes on various aspects of human gut health is limited by the lack of suitable in vitro model system that can accurately replicate gut-like environment and enable the close visualization on causal and mechanistic relationships between microbial constitutents and the gut. , In this study, we present a scalable Gut Microbiome-on-a-Chip (GMoC) with great imaging capability and scalability, providing a physiologically relevant dynamic gut-microbes interfaces. This chip features a reproducible 3D stratified gut epithelium derived from Caco-2 cells (µGut), mimicking key intestinal architecture, functions, and cellular complexity, providing a physiolocially relevant gut environment for microbes residing in the gut. Incorporating tumorigenic bacteria, enterotoxigenic Bacteroides fragilis (ETBF), into the GMoC enable the observation of pathogenic behaviors of ETBF, leading to µGut disruption and pro-tumorigenic signaling activations. Pre-treating the µGut with a beneficial gut microbe Lactobacillus spp., effectively prevent ETBF-mediated gut pathogenesis, preserving the healthy state of the µGut through competition-mediated colonization resistance. The GMoC holds potential as a valuable tool for exploring unknown roles of gut microbes in microbe-induced pathogenesis and microbe-based therapeutic development.
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Affiliation(s)
- Jeeyeon Lee
- Institute for Health Innovation and Technology (iHealthtech)National University of SingaporeSingapore117599Singapore
| | - Nishanth Menon
- Department of Biomedical EngineeringNational University of SingaporeSingapore117583Singapore
| | - Chwee Teck Lim
- Institute for Health Innovation and Technology (iHealthtech)National University of SingaporeSingapore117599Singapore
- Department of Biomedical EngineeringNational University of SingaporeSingapore117583Singapore
- Mechanobiology InstituteNational University of SingaporeSingapore117411Singapore
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22
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Li ZT, Song X, Yuan S, Zhao HP. Unveiling the inhibitory mechanisms of chromium exposure on microbial reductive dechlorination: Kinetics and microbial responses. WATER RESEARCH 2024; 253:121328. [PMID: 38382292 DOI: 10.1016/j.watres.2024.121328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024]
Abstract
Chromium and organochlorine solvents, particularly trichloroethene (TCE), are pervasive co-existing contaminants in subsurface aquifers due to their extensive industrial use and improper disposal practices. In this study, we investigated the microbial dechlorination kinetics under different TCE-Cr(Ⅲ/VI) composite pollution conditions and elucidated microbial response mechanisms based on community shift patterns and metagenomic analysis. Our results revealed that the reductive dechlorinating consortium had high resistance to Cr(III) but extreme sensitivity to Cr(VI) disturbance, resulting in a persistent inhibitory effect on subsequent dechlorination. Interestingly, the vinyl chloride-respiring organohalide-respiring bacteria (OHRB) was notably more susceptible to Cr(III/VI) exposure than the trichloroethene-respiring one, possibly due to inferior competition for growth substrates, such as electron donors. In terms of synergistic non-OHRB populations, Cr(III/VI) exposure had limited impacts on lactate fermentation but significantly interfered with H2-producing acetogenesis, leading to inhibited microbial dechlorination due to electron donor deficiencies. However, this inhibition can be effectively mitigated by the amendment of exogenous H2 supply. Furthermore, being the predominant OHRB, Dehalococcoides have inherent Cr(VI) resistance defects and collaborate with synergistic non-OHRB populations to achieve concurrent bio-detoxication of Cr(VI) and TCE. Our findings expand the understanding of the response patterns of different functional populations towards Cr(III/VI) stress, and provide valuable insights for the development of in situ bioremediation strategies for sites co-contaminated with chloroethene and chromium.
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Affiliation(s)
- Zheng-Tao Li
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310030, PR China
| | - Xin Song
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Songhu Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, PR China
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310030, PR China.
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23
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Martins MC, Alves CM, Teixeira M, Folgosa F. The flavodiiron protein from Syntrophomonas wolfei has five domains and acts both as an NADH:O 2 or an NADH:H 2 O 2 oxidoreductase. FEBS J 2024; 291:1275-1294. [PMID: 38129989 DOI: 10.1111/febs.17040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/10/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023]
Abstract
Flavodiiron proteins (FDPs) are a family of enzymes with a significant role in O2 /H2 O2 and/or NO detoxification through the reduction of these species to H2 O or N2 O, respectively. All FDPs contain a minimal catalytic unit of two identical subunits, each one having a metallo-β-lactamase-like domain harboring the catalytic diiron site, and a flavodoxin-like domain. However, more complex and diverse arrangements in terms of domains are found in this family, of which the class H enzymes are among the most complex. One of such FDPs is encoded in the genome of the anaerobic bacterium Syntrophomonas wolfei subsp. wolfei str. Goettingen G311. Besides the core domains, this protein is predicted to have three additional ones after the flavodoxin core domain: two short-chain rubredoxins and a NAD(P)H:rubredoxin oxidoreductase-like domain. This enzyme, FDP_H, was produced and characterized and the presence of the predicted cofactors was investigated by a set of biochemical and spectroscopic methodologies. Syntrophomonas wolfei FDP_H exhibited a remarkable O2 reduction activity with a kcat = 52.0 ± 1.2 s-1 and a negligible NO reduction activity (~ 100 times lower than with O2 ), with NADH as an electron donor, that is, it is an oxygen-selective FDP. In addition, this enzyme showed the highest turnover value for H2 O2 reduction (kcat = 19.1 ± 2.2 s-1 ) ever observed among FDPs. Kinetic studies of site-directed mutants of iron-binding cysteines at the two rubredoxin domains demonstrated the essential role of these centers since their absence leads to a significant decrease or even abolishment of O2 and H2 O2 reduction activities.
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Affiliation(s)
- Maria C Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Catarina M Alves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Filipe Folgosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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24
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Wei G, Liu W, Zhang Y, Zhou Z, Wang Y, Wang X, Zhu S, Li T, Wei H. Nanozyme-Enhanced Probiotic Spores Regulate the Intestinal Microenvironment for Targeted Acute Gastroenteritis Therapy. NANO LETTERS 2024; 24:2289-2298. [PMID: 38341876 DOI: 10.1021/acs.nanolett.3c04548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
Antibiotic therapeutics to combat intestinal pathogen infections often exacerbate microbiota dysbiosis and impair mucosal barrier functions. Probiotics are promising strategies, because they inhibit pathogen colonization and improve intestinal microbiota imbalance. Nevertheless, their limited targeting ability and susceptibility to oxidative stress have hindered their therapeutic potential. To tackle these challenges, Ces3 is synthesized by in situ growth of CeO2 nanozymes with positive charges on probiotic spores, facilitating electrostatic interactions with negatively charged pathogens and possessing a high reactive oxygen species (ROS) scavenging activity. Importantly, Ces3 can resist the harsh environment of the gastrointestinal tract. In mice with S. Typhimurium-infected acute gastroenteritis, Ces3 shows potent anti-S. Typhimurium activity, thereby alleviating the dissemination of S. Typhimurium into other organs. Additionally, owing to its O2 deprivation capacity, Ces3 promotes the proliferation of anaerobic probiotics, reshaping a healthy intestinal microbiota. This work demonstrates the promise of combining antibacterial, anti-inflammatory, and O2 content regulation properties for acute gastroenteritis therapy.
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Affiliation(s)
- Gen Wei
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Wanling Liu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yihong Zhang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Zijun Zhou
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yuting Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xiaoyu Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
- Department of Chemistry and Material Science, College of Science, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Shuaishuai Zhu
- School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing, Jiangsu 211167, China
| | - Tong Li
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hui Wei
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China
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25
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Morais BP, Magalhães CP, Martins G, Pereira MA, Cavaleiro AJ. Effect of micro-aeration on syntrophic and methanogenic activity in anaerobic sludge. Appl Microbiol Biotechnol 2024; 108:192. [PMID: 38305902 PMCID: PMC10837232 DOI: 10.1007/s00253-023-12969-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/14/2023] [Accepted: 11/28/2023] [Indexed: 02/03/2024]
Abstract
Micro-aeration was shown to improve anaerobic digestion (AD) processes, although oxygen is known to inhibit obligate anaerobes, such as syntrophic communities of bacteria and methanogens. The effect of micro-aeration on the activity and microbial interaction in syntrophic communities, as well as on the potential establishment of synergetic relationships with facultative anaerobic bacteria (FAB) or aerobic bacteria (AB), was investigated. Anaerobic sludge was incubated with ethanol and increasing oxygen concentrations (0-5% in the headspace). Assays with acetate or H2/CO2 (direct substrates for methanogens) were also performed. When compared with the controls (0% O2), oxygen significantly decreased substrate consumption and initial methane production rate (MPR) from acetate or H2/CO2. At 0.5% O2, MPR from these substrates was inhibited 30-40%, and close to 100% at 5% O2. With ethanol, significant inhibition (>36%) was only observed for oxygen concentrations higher than 2.5%. Oxygen was consumed in the assays, pointing to the stimulation of AB/FAB by ethanol, which helped to protect the syntrophic consortia under micro-aerobic conditions. This highlights the importance of AB/FAB in maintaining functional and resilient syntrophic communities, which is relevant for real AD systems (in which vestigial O2 amounts are frequently present), as well as for AD systems using micro-aeration as a process strategy. KEY POINTS: •Micro-aeration impacts syntrophic communities of bacteria and methanogens. •Oxygen stimulates AB/FAB, maintaining functional and resilient consortia. •Micro-aeration studies are critical for systems using micro-aeration as a process strategy.
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Affiliation(s)
- Bruno P Morais
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
- CICECO - Aveiro Institute of Materials, Universidade de Aveiro, Aveiro, Portugal
| | - Carla P Magalhães
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Gilberto Martins
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Maria Alcina Pereira
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Ana J Cavaleiro
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
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26
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Koppenol WH, Sies H. Was hydrogen peroxide present before the arrival of oxygenic photosynthesis? The important role of iron(II) in the Archean ocean. Redox Biol 2024; 69:103012. [PMID: 38183797 PMCID: PMC10808959 DOI: 10.1016/j.redox.2023.103012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/18/2023] [Accepted: 12/22/2023] [Indexed: 01/08/2024] Open
Abstract
We address the chemical/biological history of H2O2 back at the times of the Archean eon (2.5-3.9 billion years ago (Gya)). During the Archean eon the pO2 was million-fold lower than the present pO2, starting to increase gradually from 2.3 until 0.6 Gya, when it reached ca. 0.2 bar. The observation that some anaerobic organisms can defend themselves against O2 has led to the view that early organisms could do the same before oxygenic photosynthesis had developed at about 3 Gya. This would require the anaerobic generation of H2O2, and here we examine the various mechanisms which were suggested in the literature for this. Given the concentration of Fe2+ at 20-200 μM in the Archean ocean, the estimated half-life of H2O2 is ca. 0.7 s. The oceanic H2O2 concentration was practically zero. We conclude that early organisms were not exposed to H2O2 before the arrival of oxygenic photosynthesis.
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Affiliation(s)
- Willem H Koppenol
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, Zürich, Switzerland.
| | - Helmut Sies
- Institute for Biochemistry and Molecular Biology I, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany; Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
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27
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Chmelař D, Rozložník M, Hájek M, Pospíšilová N, Kuzma J. Effect of hyperbaric oxygen on the growth and susceptibility of facultatively anaerobic bacteria and bacteria with oxidative metabolism to selected antibiotics. Folia Microbiol (Praha) 2024; 69:101-108. [PMID: 38100018 PMCID: PMC10876729 DOI: 10.1007/s12223-023-01120-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 12/05/2023] [Indexed: 02/21/2024]
Abstract
Wild strains of Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis were tested in an experimental hyperbaric chamber to determine the possible effect of hyperbaric oxygen on the susceptibility of these strains to the antibiotics ampicillin, ampicillin + sulbactam, cefazolin, cefuroxime, cefoxitin, gentamicin, sulfamethoxazole + trimethoprim, colistin, oxolinic acid, ofloxacin, tetracycline, and aztreonam during their cultivation at 23 °C and 36.5 °C. Ninety-six-well inoculated microplates with tested antibiotics in Mueller-Hinton broth were cultured under standard incubator conditions (normobaric normoxia) for 24 h or in an experimental hyperbaric chamber (HAUX, Germany) for 24 h at 2.8 ATA of 100% oxygen (hyperbaric hyperoxia). The hyperbaric chamber was pressurised with pure oxygen (100%). Both cultures (normoxic and hyperoxic) were carried out at 23 °C and 36.5 °C to study the possible effect of the cultivation temperature. No significant differences were observed between 23 and 36.5 °C cultivation with or without the 2-h lag phase in Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis. Cultivation in a hyperbaric chamber at 23 °C and 36.5 °C with or without a 2-h lag phase did not produce significant changes in the minimum inhibitory concentration (MIC) of Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis. For the tested strains of Pseudomonas aeruginosa, the possible effect of hyperbaric oxygen on their antibiotic sensitivity could not be detected because the growth of these bacteria was completely inhibited by 100% hyperbaric oxygen at 2.8 ATA under all hyperbaric conditions tested at 23 °C and 36.5 °C. Subsequent tests with wild strains of pseudomonads, burkholderias, and stenotrophomonads not only confirmed the fact that these bacteria stop growing under hyperbaric conditions at a pressure of 2.8 ATA of 100% oxygen but also indicated that inhibition of growth of these bacteria under hyperbaric conditions is reversible.
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Affiliation(s)
- Dittmar Chmelař
- Institute of Laboratory Medicine, Institute of Microbiology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Centre for Hyperbaric Medicine of Faculty of Medicine and Ostrava City Hospital, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Miroslav Rozložník
- Institute of Laboratory Medicine, Institute of Microbiology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Centre for Hyperbaric Medicine of Faculty of Medicine and Ostrava City Hospital, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Michal Hájek
- Institute of Laboratory Medicine, Institute of Microbiology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic.
- Centre for Hyperbaric Medicine of Faculty of Medicine and Ostrava City Hospital, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic.
- Centre of Hyperbaric Medicine, Ostrava City Hospital, Nemocnicni 20, Ostrava, 728 80, Czech Republic.
| | - Nikol Pospíšilová
- Institute of Laboratory Medicine, Institute of Microbiology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Jozef Kuzma
- Institute of Laboratory Medicine, Institute of Microbiology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
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28
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McKinlay JB. Better off breathing: an explanation for the seemingly detrimental impact of aerobic respiration on Zymomonas mobilis. mBio 2024; 15:e0269023. [PMID: 38117086 PMCID: PMC10790775 DOI: 10.1128/mbio.02690-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023] Open
Abstract
The bacterium Zymomonas mobilis is best known for fermentatively producing more ethanol than yeast. However, Z. mobilis has also puzzled researchers for decades with the counterintuitive observation that disrupting aerobic respiration benefits aerobic growth, implying that fermentation remains favorable. Retention of detrimental respiration genes seemed to defy natural selection. New findings by Felczak et al. help clarify the importance of respiration for Z. mobilis and the factors that led to the confusing prior results (M. M. Felczak, M. P. Bernard, and M. A. TerAvest, 2023, mBio 14:e02043-23, https://doi.org/10.1128/mbio.02043-23). The team overcame redundancy from multiple genome copies to delete what turned out to be a key terminal oxidase. Unlike previous studies, wherein mutants exhibited low respiration rates and had improved aerobic growth, this mutant was incapable of respiration and had poor aerobic growth. Thus, respiration is important but surprisingly exceeds what is optimal under lab conditions. Respiration likely protects against toxic effects of oxygen, ensuring retention of respiration genes in the Z. mobilis genome.
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Affiliation(s)
- James B. McKinlay
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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29
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Xu X, Li C, Cao W, Yan L, Cao L, Han Q, Gao M, Chen Y, Shen Z, Jiang J, Chen C. Bacterial growth and environmental adaptation via thiamine biosynthesis and thiamine-mediated metabolic interactions. THE ISME JOURNAL 2024; 18:wrae157. [PMID: 39129674 PMCID: PMC11346370 DOI: 10.1093/ismejo/wrae157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 07/24/2024] [Accepted: 08/11/2024] [Indexed: 08/13/2024]
Abstract
Understanding the ancestral transition from anaerobic to aerobic lifestyles is essential for comprehending life's early evolution. However, the biological adaptations occurring during this crucial transition remain largely unexplored. Thiamine is an important cofactor involved in central carbon metabolism and aerobic respiration. Here, we explored the phylogenetic and global distribution of thiamine-auxotrophic and thiamine-prototrophic bacteria based on the thiamine biosynthetic pathway in 154 838 bacterial genomes. We observed strong coincidences of the origin of thiamine-synthetic bacteria with the "Great Oxygenation Event," indicating that thiamine biosynthesis in bacteria emerged as an adaptation to aerobic respiration. Furthermore, we demonstrated that thiamine-mediated metabolic interactions are fundamental factors influencing the assembly and diversity of bacterial communities by a global survey across 4245 soil samples. Through our newly established stable isotope probing-metabolic modeling method, we uncovered the active utilization of thiamine-mediated metabolic interactions by bacterial communities in response to changing environments, thus revealing an environmental adaptation strategy employed by bacteria at the community level. Our study demonstrates the widespread thiamine-mediated metabolic interactions in bacterial communities and their crucial roles in setting the stage for an evolutionary transition from anaerobic to aerobic lifestyles and subsequent environmental adaptation. These findings provide new insights into early bacterial evolution and their subsequent growth and adaptations to environments.
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Affiliation(s)
- Xihui Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Can Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Weimiao Cao
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lulu Yan
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lulu Cao
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qi Han
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Minling Gao
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiandong Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
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30
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Oliveira AR, Mota C, Vilela-Alves G, Manuel RR, Pedrosa N, Fourmond V, Klymanska K, Léger C, Guigliarelli B, Romão MJ, Cardoso Pereira IA. An allosteric redox switch involved in oxygen protection in a CO 2 reductase. Nat Chem Biol 2024; 20:111-119. [PMID: 37985883 DOI: 10.1038/s41589-023-01484-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/12/2023] [Indexed: 11/22/2023]
Abstract
Metal-dependent formate dehydrogenases reduce CO2 with high efficiency and selectivity, but are usually very oxygen sensitive. An exception is Desulfovibrio vulgaris W/Sec-FdhAB, which can be handled aerobically, but the basis for this oxygen tolerance was unknown. Here we show that FdhAB activity is controlled by a redox switch based on an allosteric disulfide bond. When this bond is closed, the enzyme is in an oxygen-tolerant resting state presenting almost no catalytic activity and very low formate affinity. Opening this bond triggers large conformational changes that propagate to the active site, resulting in high activity and high formate affinity, but also higher oxygen sensitivity. We present the structure of activated FdhAB and show that activity loss is associated with partial loss of the metal sulfido ligand. The redox switch mechanism is reversible in vivo and prevents enzyme reduction by physiological formate levels, conferring a fitness advantage during O2 exposure.
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Affiliation(s)
- Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cristiano Mota
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Guilherme Vilela-Alves
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Rita Rebelo Manuel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Neide Pedrosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Vincent Fourmond
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Kateryna Klymanska
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Christophe Léger
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Bruno Guigliarelli
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Maria João Romão
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal.
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal.
| | - Inês A Cardoso Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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31
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Keitel L, Braun K, Finger M, Kosfeld U, Yordanov S, Büchs J. Carbon dioxide and trace oxygen concentrations impact growth and product formation of the gut bacterium Phocaeicola vulgatus. BMC Microbiol 2023; 23:391. [PMID: 38062358 PMCID: PMC10701953 DOI: 10.1186/s12866-023-03127-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND The promising yet barely investigated anaerobic species Phocaeicola vulgatus (formerly Bacteroides vulgatus) plays a vital role for human gut health and effectively produces organic acids. Among them is succinate, a building block for high-value-added chemicals. Cultivating anaerobic bacteria is challenging, and a detailed understanding of P. vulgatus growth and metabolism is required to improve succinate production. One significant aspect is the influence of different gas concentrations. CO2 is required for the growth of P. vulgatus. However, it is a greenhouse gas that should not be wasted. Another highly interesting aspect is the sensitivity of P. vulgatus towards O2. In this work, the effects of varying concentrations of both gases were studied in the in-house developed Respiratory Activity MOnitoring System (RAMOS), which provides online monitoring of CO2, O2, and pressure under gassed conditions. The RAMOS was combined with a gas mixing system to test CO2 and O2 concentrations in a range of 0.25-15.0 vol% and 0.0-2.5 vol%, respectively. RESULTS Changing the CO2 concentration in the gas supply revealed a CO2 optimum of 3.0 vol% for total organic acid production and 15.0 vol% for succinate production. It was demonstrated that the organic acid composition changed depending on the CO2 concentration. Furthermore, unrestricted growth of P. vulgatus up to an O2 concentration of 0.7 vol% in the gas supply was proven. The viability decreased rapidly at concentrations larger than or equal to 1.3 vol% O2. CONCLUSIONS The study showed that P. vulgatus requires little CO2, has a distinct O2 tolerance and is therefore well suited for industrial applications.
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Affiliation(s)
- Laura Keitel
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Kristina Braun
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Maurice Finger
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Udo Kosfeld
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Stanislav Yordanov
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Jochen Büchs
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany.
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32
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Bosch B, Hartikainen A, Ronkainen A, Scheperjans F, Arkkila P, Satokari R. Development of a Protocol for Anaerobic Preparation and Banking of Fecal Microbiota Transplantation Material: Evaluation of Bacterial Richness in the Cultivated Fraction. Microorganisms 2023; 11:2901. [PMID: 38138045 PMCID: PMC10745795 DOI: 10.3390/microorganisms11122901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Fecal microbiota transplantation (FMT) has shown highly variable results in indications beyond recurrent Clostridioides difficile infection. Microbiota dysbiosis in many diseases is characterized by the depletion of strictly anaerobic bacteria, which may be crucial for FMT efficacy. We developed a protocol to ensure anaerobic conditions during the entire transplant preparation and banking process, from material collection to administration. The protocol necessitates an anaerobic cabinet, i.e., a non-standard laboratory equipment. We analyzed the population of viable anaerobes by combining cultivation and 16S rRNA gene profiling during the transplant preparation, and after 4, 8, and 12 months of anaerobic or aerobic storage at -80 °C, 78% of fecal species were captured via cultivation. Our findings suggest that strictly anaerobic transplant preparation and storage may preserve species richness better than oxic conditions, but the overall difference was not significant. However, specific anaerobes such as Neglecta and Anaerotruncus were affected by the oxygen exposure. A storage time of up to 12 months did not affect the presence of cultivated taxa. Noteworthy, our analysis focused on the richness of cultivated anaerobes rather than their abundance, which may have been affected. The benefits of the developed anaerobic protocol in FMT for specific indications remain to be demonstrated in clinical trials.
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Affiliation(s)
- Berta Bosch
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (A.H.); (A.R.)
| | - Anna Hartikainen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (A.H.); (A.R.)
| | - Aki Ronkainen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (A.H.); (A.R.)
| | - Filip Scheperjans
- Department of Neurology, Helsinki University Hospital, 00290 Helsinki, Finland;
- Clinicum, University of Helsinki, 00290 Helsinki, Finland;
| | - Perttu Arkkila
- Clinicum, University of Helsinki, 00290 Helsinki, Finland;
- Department of Gastroenterology, Helsinki University Hospital, 00290 Helsinki, Finland
| | - Reetta Satokari
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (A.H.); (A.R.)
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Aryee G, Luecke SM, Dahlen CR, Swanson KC, Amat S. Holistic View and Novel Perspective on Ruminal and Extra-Gastrointestinal Methanogens in Cattle. Microorganisms 2023; 11:2746. [PMID: 38004757 PMCID: PMC10673468 DOI: 10.3390/microorganisms11112746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Despite the extensive research conducted on ruminal methanogens and anti-methanogenic intervention strategies over the last 50 years, most of the currently researched enteric methane (CH4) abatement approaches have shown limited efficacy. This is largely because of the complex nature of animal production and the ruminal environment, host genetic variability of CH4 production, and an incomplete understanding of the role of the ruminal microbiome in enteric CH4 emissions. Recent sequencing-based studies suggest the presence of methanogenic archaea in extra-gastrointestinal tract tissues, including respiratory and reproductive tracts of cattle. While these sequencing data require further verification via culture-dependent methods, the consistent identification of methanogens with relatively greater frequency in the airway and urogenital tract of cattle, as well as increasing appreciation of the microbiome-gut-organ axis together highlight the potential interactions between ruminal and extra-gastrointestinal methanogenic communities. Thus, a traditional singular focus on ruminal methanogens may not be sufficient, and a holistic approach which takes into consideration of the transfer of methanogens between ruminal, extra-gastrointestinal, and environmental microbial communities is of necessity to develop more efficient and long-term ruminal CH4 mitigation strategies. In the present review, we provide a holistic survey of the methanogenic archaea present in different anatomical sites of cattle and discuss potential seeding sources of the ruminal methanogens.
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Affiliation(s)
- Godson Aryee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Sarah M. Luecke
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Carl R. Dahlen
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Kendall C. Swanson
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
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Gong X, Geng H, Yang Y, Zhang S, He Z, Fan Y, Yin F, Zhang Z, Chen GQ. Metabolic engineering of commensal bacteria for gut butyrate delivery and dissection of host-microbe interaction. Metab Eng 2023; 80:94-106. [PMID: 37717646 DOI: 10.1016/j.ymben.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/19/2023]
Abstract
An overwhelming number of studies have reported the correlation of decreased abundance of butyrate-producing commensals with a wide range of diseases. However, the molecular-level mechanisms whereby gut butyrate causally affects the host mucosal immunity and pathogenesis were poorly understood, hindered by the lack of efficient tools to control intestinal butyrate. Here we engineered a facultative anaerobic commensal bacterium to delivery butyrate at the intestinal mucosal surface, and implemented it to dissect the causal role of gut butyrate in regulating host intestinal homeostasis in a model of murine chronic colitis. Mechanistically, we show that gut butyrate protected against colitis and preserved intestinal mucosal homeostasis through its inhibiting effect on the key pyroptosis executioner gasdermin D (GSDMD) of colonic epithelium, via functioning as an HDAC3 inhibitor. Overall, our work presents a new avenue to build synthetic living delivery bacteria to decode causal molecules at the host-microbe interface with molecular-level insights.
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Affiliation(s)
- Xu Gong
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Engineering Medicine, Beihang University, Beijing, 100191, PR China; Key Laboratory of Big Data-Based Precision Medicine, Ministry of Industry and Information Technology, Beihang University, Beijing, 100191, PR China
| | - Hongwei Geng
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Engineering Medicine, Beihang University, Beijing, 100191, PR China; Key Laboratory of Big Data-Based Precision Medicine, Ministry of Industry and Information Technology, Beihang University, Beijing, 100191, PR China
| | - Yun Yang
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Engineering Medicine, Beihang University, Beijing, 100191, PR China; Key Laboratory of Big Data-Based Precision Medicine, Ministry of Industry and Information Technology, Beihang University, Beijing, 100191, PR China.
| | - Shuyi Zhang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, PR China; Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, PR China
| | - Zilong He
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Engineering Medicine, Beihang University, Beijing, 100191, PR China
| | - Yubo Fan
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Engineering Medicine, Beihang University, Beijing, 100191, PR China
| | - Fengyi Yin
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Engineering Medicine, Beihang University, Beijing, 100191, PR China
| | - Zhifa Zhang
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Engineering Medicine, Beihang University, Beijing, 100191, PR China
| | - Guo-Qiang Chen
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, PR China; MOE Key Lab of Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, PR China; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, PR China.
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Liang J, Chen Z, Yin P, Hu H, Cheng W, Shang J, Yang Y, Yuan Z, Pan J, Yin Y, Li W, Chen X, Gao X, Qiu B, Wang B. Efficient Semi-Artificial Photosynthesis of Ethylene by a Self-Assembled InP-Cyanobacterial Biohybrid System. CHEMSUSCHEM 2023; 16:e202300773. [PMID: 37381086 DOI: 10.1002/cssc.202300773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 06/30/2023]
Abstract
Biomanufacturing of ethylene is particularly important for modern society. Cyanobacterial cells are able to photosynthesize various valuable chemicals. A promising platform for next-generation biomanufacturing, the semiconductor-cyanobacterial hybrid systems are capable of enhancing the solar-to-chemical conversion efficiency. Herein, the native ethylene-producing capability of a filamentous cyanobacterium Nostoc sphaeroides is confirmed experimentally. The self-assembly characteristic of N. sphaeroides is exploited to facilitate its interaction with InP nanomaterial, and the resulting biohybrid system gave rise to further elevated photosynthetic ethylene production. Based on chlorophyll fluorescence measurement and metabolic analysis, the InP nanomaterial-augmented photosystem I activity and enhanced ethylene production metabolism of biohybrid cells are confirmed, the mechanism underlying the material-cell energy transduction as well as nanomaterial-modulated photosynthetic light and dark reactions are established. This work not only demonstrates the potential application of semiconductor-N. sphaeroides biohybrid system as a good platform for sustainable ethylene production but also provides an important reference for future studies to construct and optimize nano-cell biohybrid systems for efficient solar-driven valuable chemical production.
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Affiliation(s)
- Jun Liang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Zhen Chen
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Panqing Yin
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Haitao Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Wenbo Cheng
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, P. R. China
| | - Jinlong Shang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, P. R. China
| | - Yiwen Yang
- College of Pharmacy and Life Sciences, Jiujiang University, Jiujiang, Jiangxi, 332000, P.R. China
| | - Zuwen Yuan
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Jinlong Pan
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Yongqi Yin
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Weizhi Li
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Xiongwen Chen
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Xiang Gao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Baosheng Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, P. R. China
| | - Bo Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
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Abstract
Metabolic switches are a crucial hallmark of cellular development and regeneration. In response to changes in their environment or physiological state, cells undergo coordinated metabolic switching that is necessary to execute biosynthetic demands of growth and repair. In this Review, we discuss how metabolic switches represent an evolutionarily conserved mechanism that orchestrates tissue development and regeneration, allowing cells to adapt rapidly to changing conditions during development and postnatally. We further explore the dynamic interplay between metabolism and how it is not only an output, but also a driver of cellular functions, such as cell proliferation and maturation. Finally, we underscore the epigenetic and cellular mechanisms by which metabolic switches mediate biosynthetic needs during development and regeneration, and how understanding these mechanisms is important for advancing our knowledge of tissue development and devising new strategies to promote tissue regeneration.
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Affiliation(s)
- Ahmed I. Mahmoud
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
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37
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Lin S, Wu F, Zhang Y, Chen H, Guo H, Chen Y, Liu J. Surface-modified bacteria: synthesis, functionalization and biomedical applications. Chem Soc Rev 2023; 52:6617-6643. [PMID: 37724854 DOI: 10.1039/d3cs00369h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
The past decade has witnessed a great leap forward in bacteria-based living agents, including imageable probes, diagnostic reagents, and therapeutics, by virtue of their unique characteristics, such as genetic manipulation, rapid proliferation, colonization capability, and disease site targeting specificity. However, successful translation of bacterial bioagents to clinical applications remains challenging, due largely to their inherent susceptibility to environmental insults, unavoidable toxic side effects, and limited accumulation at the sites of interest. Cell surface components, which play critical roles in shaping bacterial behaviors, provide an opportunity to chemically modify bacteria and introduce different exogenous functions that are naturally unachievable. With the help of surface modification, a wide range of functionalized bacteria have been prepared over the past years and exhibit great potential in various biomedical applications. In this article, we mainly review the synthesis, functionalization, and biomedical applications of surface-modified bacteria. We first introduce the approaches of chemical modification based on the bacterial surface structure and then highlight several advanced functions achieved by modifying specific components on the surface. We also summarize the advantages as well as limitations of surface chemically modified bacteria in the applications of bioimaging, diagnosis, and therapy and further discuss the current challenges and possible solutions in the future. This work will inspire innovative design thinking for the development of chemical strategies for preparing next-generation biomedical bacterial agents.
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Affiliation(s)
- Sisi Lin
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Feng Wu
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Yifan Zhang
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Huan Chen
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Haiyan Guo
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Yanmei Chen
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Jinyao Liu
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
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38
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Jin XEF, Low DY, Ang L, Lu L, Yin X, Tan YQ, Lee AKY, Seow WJ. Exposure to cooking fumes is associated with perturbations in nasal microbiota composition: A pilot study. ENVIRONMENTAL RESEARCH 2023; 234:116392. [PMID: 37302739 DOI: 10.1016/j.envres.2023.116392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/02/2023] [Accepted: 06/09/2023] [Indexed: 06/13/2023]
Abstract
Air pollution is one of the leading causes of overall mortality globally. Cooking emissions are a major source of fine particulate matter (PM2.5). However, studies on their potential perturbations on the nasal microbiota as well as their association with respiratory health are lacking. This pilot study aims to assess the environmental air quality among occupational cooks and its associations with nasal microbiota and respiratory symptoms. A total of 20 cooks (exposed) and 20 unexposed controls (mainly office workers), were recruited in Singapore from 2019 to 2021. Information on sociodemographic factors, cooking methods, and self-reported respiratory symptoms were collected using a questionnaire. Personal PM2.5 concentrations and reactive oxygen species (ROS) levels were measured using portable sensors and filter samplers. DNA was extracted from nasal swabs and sequenced using 16s sequencing. Alpha-diversity and beta-diversity were calculated, and between-group variation analysis of species was performed. Multivariable logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for associations between exposure groups and self-reported respiratory symptoms. Higher daily mean PM2.5 (P = 2 × 10-7) and environmental ROS exposure (P = 3.25 × 10-7) were observed in the exposed group. Alpha diversity of the nasal microbiota between the two groups was not significantly different. However, beta diversity was significantly different (unweighted UniFrac P = 1.11 × 10-5, weighted UniFrac P = 5.42 × 10-6) between the two exposure groups. In addition, certain taxa of bacteria were slightly more abundant in the exposed group compared to unexposed controls. There were no significant associations between the exposure groups and self-reported respiratory symptoms. In summary, the exposed group had higher PM2.5 and ROS exposure levels and altered nasal microbiotas as compared to unexposed controls, though further studies are required to replicate these findings in a larger population.
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Affiliation(s)
- Xin Er Frances Jin
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore.
| | - Dorrain Yanwen Low
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Lina Ang
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Lu Lu
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Xin Yin
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Yue Qian Tan
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Alex King Yin Lee
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore; Air Quality Processes Research Section, Environment and Climate Change Canada, Toronto, ON, Canada
| | - Wei Jie Seow
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore.
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Lara B, Sassot M, Calo G, Paparini D, Gliosca L, Chaufan G, Loureiro I, Vota D, Ramhorst R, Pérez Leirós C, Hauk V. Extracellular Vesicles of Porphyromonas gingivalis Disrupt Trophoblast Cell Interaction with Vascular and Immune Cells in an In Vitro Model of Early Placentation. Life (Basel) 2023; 13:1971. [PMID: 37895353 PMCID: PMC10608595 DOI: 10.3390/life13101971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Extracellular vesicles released by the primary pathogen of periodontal disease Porphyromonas gingivalis (Pg), referred to as outer membrane vesicles (OMVs), have been associated with the pathogenesis of systemic diseases like cardiovascular disease, rheumatoid arthritis, and Alzheimer's disease. A pathogenic role for Pg by disrupting placental homeostasis was proposed in the association between periodontal disease and adverse pregnancy outcomes. On the basis that trophoblast-derived factors modulate endothelial and immune cell profiles in normal pregnancy and the scarce presence of Pg in placenta, we hypothesized that OMVs from Pg affect trophoblast cell phenotype, impairing trophoblast-endothelium and trophoblast-neutrophil interactions. By means of in vitro designs with first-trimester human trophoblast cells, endothelial cells, and freshly isolated neutrophils, we showed that Pg OMVs are internalized by trophoblast cells and modulate the activity and expression of functional markers. Trophoblast cells primed with Pg OMVs enhanced neutrophil chemoattraction and lost their anti-inflammatory effect. In addition, reduced migration with enhanced adhesion of monocytes was found in endothelial cells upon incubation with the media from trophoblast cells pretreated with Pg OMVs. Taken together, the results support a pathogenic role of Pg OMVs at early stages of pregnancy and placentation through disruption of trophoblast contribution to vascular transformation and immune homeostasis maintenance.
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Affiliation(s)
- Brenda Lara
- Universidad de Buenos Aires—CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires C1428EGA, Argentina; (B.L.); (M.S.); (G.C.); (D.P.); (L.G.); (G.C.); (I.L.); (D.V.); (R.R.)
| | - Matías Sassot
- Universidad de Buenos Aires—CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires C1428EGA, Argentina; (B.L.); (M.S.); (G.C.); (D.P.); (L.G.); (G.C.); (I.L.); (D.V.); (R.R.)
| | - Guillermina Calo
- Universidad de Buenos Aires—CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires C1428EGA, Argentina; (B.L.); (M.S.); (G.C.); (D.P.); (L.G.); (G.C.); (I.L.); (D.V.); (R.R.)
| | - Daniel Paparini
- Universidad de Buenos Aires—CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires C1428EGA, Argentina; (B.L.); (M.S.); (G.C.); (D.P.); (L.G.); (G.C.); (I.L.); (D.V.); (R.R.)
| | - Laura Gliosca
- Universidad de Buenos Aires—CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires C1428EGA, Argentina; (B.L.); (M.S.); (G.C.); (D.P.); (L.G.); (G.C.); (I.L.); (D.V.); (R.R.)
- Universidad de Buenos Aires, Facultad de Odontología, Cátedra de Microbiología, Buenos Aires C1122AAH, Argentina
| | - Gabriela Chaufan
- Universidad de Buenos Aires—CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires C1428EGA, Argentina; (B.L.); (M.S.); (G.C.); (D.P.); (L.G.); (G.C.); (I.L.); (D.V.); (R.R.)
| | - Iñaki Loureiro
- Universidad de Buenos Aires—CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires C1428EGA, Argentina; (B.L.); (M.S.); (G.C.); (D.P.); (L.G.); (G.C.); (I.L.); (D.V.); (R.R.)
| | - Daiana Vota
- Universidad de Buenos Aires—CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires C1428EGA, Argentina; (B.L.); (M.S.); (G.C.); (D.P.); (L.G.); (G.C.); (I.L.); (D.V.); (R.R.)
| | - Rosanna Ramhorst
- Universidad de Buenos Aires—CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires C1428EGA, Argentina; (B.L.); (M.S.); (G.C.); (D.P.); (L.G.); (G.C.); (I.L.); (D.V.); (R.R.)
| | - Claudia Pérez Leirós
- Universidad de Buenos Aires—CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires C1428EGA, Argentina; (B.L.); (M.S.); (G.C.); (D.P.); (L.G.); (G.C.); (I.L.); (D.V.); (R.R.)
| | - Vanesa Hauk
- Universidad de Buenos Aires—CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires C1428EGA, Argentina; (B.L.); (M.S.); (G.C.); (D.P.); (L.G.); (G.C.); (I.L.); (D.V.); (R.R.)
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Bénard MV, Arretxe I, Wortelboer K, Harmsen HJM, Davids M, de Bruijn CMA, Benninga MA, Hugenholtz F, Herrema H, Ponsioen CY. Anaerobic Feces Processing for Fecal Microbiota Transplantation Improves Viability of Obligate Anaerobes. Microorganisms 2023; 11:2238. [PMID: 37764082 PMCID: PMC10535047 DOI: 10.3390/microorganisms11092238] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Fecal microbiota transplantation (FMT) is under investigation for several indications, including ulcerative colitis (UC). The clinical success of FMT depends partly on the engraftment of viable bacteria. Because the vast majority of human gut microbiota consists of anaerobes, the currently used aerobic processing protocols of donor stool may diminish the bacterial viability of transplanted material. This study assessed the effect of four processing techniques for donor stool (i.e., anaerobic and aerobic, both direct processing and after temporary cool storage) on bacterial viability. By combining anaerobic culturing on customized media for anaerobes with 16S rRNA sequencing, we could successfully culture and identify the majority of the bacteria present in raw fecal suspensions. We show that direct anaerobic processing of donor stool is superior to aerobic processing conditions for preserving the bacterial viability of obligate anaerobes and butyrate-producing bacteria related to the clinical response to FMT in ulcerative colitis patients, including Faecalibacterium, Eubacterium hallii, and Blautia. The effect of oxygen exposure during stool processing decreased when the samples were stored long-term. Our results confirm the importance of sample conditioning to preserve the bacterial viability of oxygen-sensitive gut bacteria. Anaerobic processing of donor stool may lead to increased clinical success of FMT, which should further be investigated in clinical trials.
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Affiliation(s)
- Mèlanie V. Bénard
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.V.B.); (I.A.); (C.M.A.d.B.); (M.A.B.)
- Department of Endocrinology and Metabolism, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Iñaki Arretxe
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.V.B.); (I.A.); (C.M.A.d.B.); (M.A.B.)
| | - Koen Wortelboer
- Department of Experimental Vascular Medicine, Amsterdam Cardiovascular Sciences (ACS), Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (K.W.); (M.D.); (H.H.)
| | - Hermie J. M. Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands;
| | - Mark Davids
- Department of Experimental Vascular Medicine, Amsterdam Cardiovascular Sciences (ACS), Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (K.W.); (M.D.); (H.H.)
| | - Clara M. A. de Bruijn
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.V.B.); (I.A.); (C.M.A.d.B.); (M.A.B.)
- Pediatric Gastroenterology, Hepatology and Nutrition, Emma Children’s Hospital, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Emma Children’s Hospital, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Marc A. Benninga
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.V.B.); (I.A.); (C.M.A.d.B.); (M.A.B.)
- Pediatric Gastroenterology, Hepatology and Nutrition, Emma Children’s Hospital, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Emma Children’s Hospital, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Floor Hugenholtz
- Center for Experimental and Molecular Medicine, Amsterdam Medical Center, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Hilde Herrema
- Department of Experimental Vascular Medicine, Amsterdam Cardiovascular Sciences (ACS), Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (K.W.); (M.D.); (H.H.)
| | - Cyriel Y. Ponsioen
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.V.B.); (I.A.); (C.M.A.d.B.); (M.A.B.)
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Wang C, Hou Y, Fu S, Zhang E, Zhang Z, Bai B. Titanium alloys with varying surface micro-area potential differences have antibacterial abilities and a favorable cellular response. Clin Oral Investig 2023; 27:4957-4971. [PMID: 37329465 DOI: 10.1007/s00784-023-05115-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 06/07/2023] [Indexed: 06/19/2023]
Abstract
OBJECTIVES Surface micro-area potential difference (MAPD) can achieve bacteriostatic performance independent of metal ion dissolution. To study the influence of MAPD on antibacterial properties and the cellular response, Ti-Ag alloys with different surface potentials were designed and prepared by changing the preparation and heat treatment processes. MATERIALS AND METHODS Ti-Ag alloys (T4, T6, and S) were prepared by vacuum arc smelting, water quenching, and sintering. Cp-Ti was set as a control group in this work. The microstructures and surface potential distributions of the Ti-Ag alloys were analyzed by SEM and energy dispersive spectrometry. Plate counting and live/dead staining methods were used to evaluate the antibacterial properties of the alloys, and the mitochondrial function, ATP levels, and apoptosis were assessed in MC3T3-E1 cells to analyze the cellular response. RESULTS Due to the formation of the Ti-Ag intermetallic phase in the Ti-Ag alloys, Ti-Ag (T4) without the Ti-Ag phase had the lowest MAPD, Ti-Ag (T6) with a fine Ti2Ag phase had a moderate MAPD, and Ti-Ag (S) with a Ti-Ag intermetallic phase had the highest MAPD. The primary results demonstrated that the Ti-Ag samples with different MAPDs exhibited different bacteriostatic effects, ROS expression levels, and apoptosis-related protein expression levels in cells. The alloy with a high MAPD exhibited a strong antibacterial effect. A moderate MAPD stimulated cellular antioxidant regulation (GSH/GSSG) and downregulated the expression of intracellular ROS. MAPD could also promote the transformation of the inactive mitochondria to biologically active mitochondria by increasing the ΔΨm and reducing apoptosis. CONCLUSION The results here indicated that moderate MAPD not only had bacteriostatic effects but also promoted mitochondrial function and inhibited cell apoptosis, which provides a new strategy to improve the surface bioactivity of titanium alloys and a new idea for titanium alloy design. CLINICAL RELEVANCE There are some limitations of the mechanism of MAPD. However, researchers will become increasingly aware of the advantages and disadvantages of MAPD and MAPD might provide an affordable solution of peri-implantitis.
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Affiliation(s)
- Chunxia Wang
- Department of Ophthalmology, Eye Hospital of China Medical University, Key Lens Research Laboratory of Liaoning Province, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110005, China
| | - Yueru Hou
- Department of Prosthodontics, School and Hospital of Stomatology, Liaoning Provincial Key Laboratory of Oral Diseases, China Medical University, Shenyang, 110001, China
| | - Shan Fu
- Key Lab for Anisotropy and Texture of Materials, Education Ministry of China, School of Materials Science and Engineering, Northeastern University, Shenyang, 110819, China
| | - Erlin Zhang
- Key Lab for Anisotropy and Texture of Materials, Education Ministry of China, School of Materials Science and Engineering, Northeastern University, Shenyang, 110819, China
| | - Zhongti Zhang
- Department of VIP, School and Hospital of Stomatology, Liaoning Provincial Key Laboratory of Oral Diseases, China Medical University, Shenyang, 110001, China
| | - Bing Bai
- Department of Prosthodontics, School and Hospital of Stomatology, Liaoning Provincial Key Laboratory of Oral Diseases, China Medical University, Shenyang, 110001, China.
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Camargo FP, Sakamoto IK, Delforno TP, Midoux C, Duarte ICS, Silva EL, Bize A, Varesche MBA. Microbial and functional characterization of granulated sludge from full-scale UASB thermophilic reactor applied to sugarcane vinasse treatment. ENVIRONMENTAL TECHNOLOGY 2023; 44:3141-3160. [PMID: 35298346 DOI: 10.1080/09593330.2022.2052361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Considering the scarcity of data in the literature regarding phylogenetic and metabolic composition of different inocula, especially those from thermophilic conditions, this research aimed at characterizing the microbial community and preferable metabolic pathways of an UASB reactor sludge applied to the thermophilic treatment (55°C) of sugarcane vinasse, by means of shotgun metagenomics. After its metabolic potential was depicted, it was possible to observe several genes encoding enzymes that are of great importance to anaerobic digestion processes with different wastes as substrate, especially regarding the biodegradation of carbohydrates and ligninolytic compounds, glycerolypids, volatile fatty acids and alcohols metabolism and biogas (H2 and CH4) production. The genera identified in higher relative abundances for Bacteria domain were Sulfirimonas (37.52 ± 1.8%), possibly related to the sludge endogenic activity due to its strong relation with a peptidoglycan lyase enzymes family, followed by Fluviicola (5.01 ± 1.0%), Defluviitoga (4.36 ± 0.2%), Coprothermobacter (4.32 ± 0.5%), Fervidobacterium (2.93 ± 0.3%), Marinospirillum (2.75 ± 0.2%), Pseudomonas (2.14 ± 0.2%) and Flavobacterium (1.78 ± 0.1%), mostly related with carbohydrates fermentations and/or H2 production. For Archaea domain, Methanosarcina (0.61 ± 0.1%), Methanothermobacter (0.38 ± 0.0%), Methanoculleus (0.30 ± 0.1%), Thermococcus (0.03 ± 0.0%), Methanolobus (0.02 ± 1.8%), Methanobacterium (0.013 ± 0.0%), Aciduliprofundum and Pyrococcus (0.01 ± 0.0%) were the most dominant ones, being Methanosarcina the most related with methanogenesis. It was concluded that the robust inoculum description performed in this study may subside future biotechnological researches by using similar inocula (UASB sludges), focusing on the obtainment of value-added by-products by means of anaerobic digestion, such as volatile fatty acids, alcohols and biogas (H2 and CH4), by using several types of waste as substrate.
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Affiliation(s)
- Franciele Pereira Camargo
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo (USP), São Carlos, Brazil
| | - Isabel Kimiko Sakamoto
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo (USP), São Carlos, Brazil
| | | | - Cédric Midoux
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement (PROSE), Antony, France
| | | | - Edson Luiz Silva
- Department of Chemical Engineering, Federal University of São Carlos (UFSCar) São Carlos, Brazil
| | - Ariane Bize
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement (PROSE), Antony, France
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Huang C, Zeng Y, Hu K, Jiang Y, Zhang Y, Lu Q, Liu YE, Gao S, Wang S, Luo X, Mai B. Anaerobic biotransformation of two novel brominated flame retardants: Kinetics, isotope fractionation and reaction mechanisms. WATER RESEARCH 2023; 243:120360. [PMID: 37481998 DOI: 10.1016/j.watres.2023.120360] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023]
Abstract
1,2,5,6-tetrabromocyclooctane (TBCO) and 2,3-dibromopropyl-2,4,6-tribromophenyl ether (DPTE), as safer alternatives to traditional brominated flame retardants, have been extensively detected in various environmental media and pose emerging risks. However, much less is known about their fate in the environment. Anaerobic microbial transformation is a key pathway for the natural attenuation of contaminants. This study investigated, for the first time, the microbial transformation behaviors of β-TBCO and DPTE by Dehalococcoides mccartyi strain CG1. The results indicated that both β-TBCO and DPTE could be easily transformed by D. mccartyi CG1 with kobs values of 0.0218 ± 0.0015 h-1 and 0.0089 ± 0.0003 h-1, respectively. In particular, β-TBCO seemed to undergo dibromo-elimination and then epoxidation to form 4,5-dibromo-9-oxabicyclo[6.1.0]nonane, while DPTE experienced debromination at the benzene ring (ortho-bromine being removed prior to para-bromine) rather than at the carbon chain. Additionally, pronounced carbon and bromine isotope fractionations were observed during biotransformation of β-TBCO and DPTE, suggesting that C-Br bond breaking is the rate-limiting step of their biotransformation. Finally, coupled with identified products and isotope fractionation patterns, β-elimination (E2) and Sn2-nucleophilic substitution were considered the most likely microbial transformation mechanisms for β-TBCO and DPTE, respectively. This work provides important information for assessing the potential of natural attenuation and environmental risks of β-TBCO and DPTE.
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Affiliation(s)
- Chenchen Huang
- School of Environmental Science & Spatial Informatics, China University of Mining & Technology, Xuzhou, Jiangsu 221116, China; State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Hangzhou 310015, China
| | - Yanhong Zeng
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong-Hong Kong-MaCao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China.
| | - Keqi Hu
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong-Hong Kong-MaCao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yiye Jiang
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong-Hong Kong-MaCao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yanting Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong-Hong Kong-MaCao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Qihong Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, China
| | - Yin-E Liu
- School of Environmental Science & Spatial Informatics, China University of Mining & Technology, Xuzhou, Jiangsu 221116, China; State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Shutao Gao
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong-Hong Kong-MaCao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Shanquan Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, China
| | - Xiaojun Luo
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong-Hong Kong-MaCao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Bixian Mai
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong-Hong Kong-MaCao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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Botin T, Ramirez-Chamorro L, Vidic J, Langella P, Martin-Verstraete I, Chatel JM, Auger S. The Tolerance of Gut Commensal Faecalibacterium to Oxidative Stress Is Strain Dependent and Relies on Detoxifying Enzymes. Appl Environ Microbiol 2023; 89:e0060623. [PMID: 37382539 PMCID: PMC10370306 DOI: 10.1128/aem.00606-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023] Open
Abstract
Obligate anaerobic bacteria in genus Faecalibacterium are among the most dominant taxa in the colon of healthy individuals and contribute to intestinal homeostasis. A decline in the abundance of this genus is associated with the occurrence of various gastrointestinal disorders, including inflammatory bowel diseases. In the colon, these diseases are accompanied by an imbalance between the generation and elimination of reactive oxygen species (ROS), and oxidative stress is closely linked to disruptions in anaerobiosis. In this work, we explored the impact of oxidative stress on several strains of faecalibacteria. An in silico analysis of complete genomes of faecalibacteria revealed the presence of genes encoding O2- and/or ROS-detoxifying enzymes, including flavodiiron proteins, rubrerythrins, reverse rubrerythrins, superoxide reductases, and alkyl peroxidase. However, the presence and the number of these detoxification systems varied greatly among faecalibacteria. These results were confirmed by O2 stress survival tests, in which we found that strains differed widely in their sensitivity. We showed the protective role of cysteine, which limited the production of extracellular O2•- and improved the survival of Faecalibacterium longum L2-6 under high O2 tension. In the strain F. longum L2-6, we observed that the expression of genes encoding detoxifying enzymes was upregulated in the response to O2 or H2O2 stress but with different patterns of regulation. Based on these results, we propose a first model of the gene regulatory network involved in the response to oxidative stress in F. longum L2-6. IMPORTANCE Commensal bacteria in the genus Faecalibacterium have been proposed for use as next-generation probiotics, but efforts to cultivate and exploit the potential of these strains have been limited by their sensitivity to O2. More broadly, little is known about how commensal and health-associated bacterial species in the human microbiome respond to the oxidative stress that occurs as a result of inflammation in the colon. In this work, we provide insights regarding the genes that encode potential mechanisms of protection against O2 or ROS stress in faecalibacteria, which may facilitate future advances in work with these important bacteria.
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Affiliation(s)
- Tatiana Botin
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Luis Ramirez-Chamorro
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Jasmina Vidic
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Philippe Langella
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Isabelle Martin-Verstraete
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Laboratoire Pathogénèse des Bactéries Anaérobies, Paris, France
- Institut Universitaire de France, Paris, France
| | - Jean-Marc Chatel
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Sandrine Auger
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
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Cheong KL, Zhang Y, Li Z, Li T, Ou Y, Shen J, Zhong S, Tan K. Role of Polysaccharides from Marine Seaweed as Feed Additives for Methane Mitigation in Ruminants: A Critical Review. Polymers (Basel) 2023; 15:3153. [PMID: 37571046 PMCID: PMC10420924 DOI: 10.3390/polym15153153] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Given the increasing concerns regarding greenhouse gas emissions associated with livestock production, the need to discover effective strategies to mitigate methane production in ruminants is clear. Marine algal polysaccharides have emerged as a promising research avenue because of their abundance and sustainability. Polysaccharides, such as alginate, laminaran, and fucoidan, which are extracted from marine seaweeds, have demonstrated the potential to reduce methane emissions by influencing the microbial populations in the rumen. This comprehensive review extensively examines the available literature and considers the effectiveness, challenges, and prospects of using marine seaweed polysaccharides as feed additives. The findings emphasise that marine algal polysaccharides can modulate rumen fermentation, promote the growth of beneficial microorganisms, and inhibit methanogenic archaea, ultimately leading to decreases in methane emissions. However, we must understand the long-term effects and address the obstacles to practical implementation. Further research is warranted to optimise dosage levels, evaluate potential effects on animal health, and assess economic feasibility. This critical review provides insights for researchers, policymakers, and industry stakeholders dedicated to advancing sustainable livestock production and methane mitigation.
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Affiliation(s)
- Kit-Leong Cheong
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China; (K.-L.C.)
| | - Yiyu Zhang
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China; (K.-L.C.)
| | - Zhuoting Li
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China; (K.-L.C.)
| | - Tongtong Li
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China; (K.-L.C.)
| | - Yiqing Ou
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China; (K.-L.C.)
| | - Jiayi Shen
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China; (K.-L.C.)
| | - Saiyi Zhong
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China; (K.-L.C.)
| | - Karsoon Tan
- Guangxi Key Laboratory of Beibu Gulf Biodiversity Conservation, Beibu Gulf University, Qinzhou 535000, China
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Müller-Heupt LK, Eckelt A, Eckelt J, Groß J, Opatz T, Kommerein N. An In Vitro Study of Local Oxygen Therapy as Adjunctive Antimicrobial Therapeutic Option for Patients with Periodontitis. Antibiotics (Basel) 2023; 12:990. [PMID: 37370309 DOI: 10.3390/antibiotics12060990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Periodontitis is a common global disease caused by bacterial dysbiosis leading to tissue destruction, and it is strongly associated with anaerobic bacterial colonization. Therapeutic strategies such as oxygen therapy have been developed to positively influence the dysbiotic microbiota, and the use of oxygen-releasing substances may offer an added benefit of avoiding systemic effects commonly associated with antibiotics taken orally or hyperbaric oxygen therapy. Therefore, the oxygen release of calcium peroxide (CaO2) was measured using a dissolved oxygen meter, and CaO2 solutions were prepared by dissolving autoclaved CaO2 in sterile filtered and deionized water. The effects of CaO2 on planktonic bacterial growth and metabolic activity, as well as on biofilms of Streptococcus oralis and Porphyromonas gingivalis, were investigated through experiments conducted under anaerobic conditions. The objective of this study was to investigate the potential of CaO2 as an antimicrobial agent for the treatment of periodontitis. Results showed that CaO2 selectively inhibited the growth and viability of P. gingivalis (p < 0.001) but had little effect on S. oralis (p < 0.01), indicating that CaO2 has the potential to selectively affect both planktonic bacteria and mono-species biofilms of P. gingivalis. The results of this study suggest that CaO2 could be a promising antimicrobial agent with selective activity for the treatment of periodontitis.
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Affiliation(s)
- Lena Katharina Müller-Heupt
- Department of Oral and Maxillofacial Surgery, University Medical Center Mainz, Augustusplatz 2, 55131 Mainz, Germany
| | - Anja Eckelt
- WEE-Solve GmbH, Auf der Burg 6, 55130 Mainz, Germany
| | - John Eckelt
- WEE-Solve GmbH, Auf der Burg 6, 55130 Mainz, Germany
| | - Jonathan Groß
- Department of Chemistry, Johannes Gutenberg University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Till Opatz
- Department of Chemistry, Johannes Gutenberg University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Nadine Kommerein
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
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47
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Okabe S, Ye S, Lan X, Nukada K, Zhang H, Kobayashi K, Oshiki M. Oxygen tolerance and detoxification mechanisms of highly enriched planktonic anaerobic ammonium-oxidizing (anammox) bacteria. ISME COMMUNICATIONS 2023; 3:45. [PMID: 37137967 PMCID: PMC10156729 DOI: 10.1038/s43705-023-00251-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/05/2023]
Abstract
Oxygen is a key regulatory factor of anaerobic ammonium oxidation (anammox). Although the inhibitory effect of oxygen is evident, a wide range of oxygen sensitivities of anammox bacteria have been reported so far, which makes it difficult to model the marine nitrogen loss and design anammox-based technologies. Here, oxygen tolerance and detoxification mechanisms of four genera of anammox bacteria; one marine species ("Ca. Scalindua sp.") and four freshwater anammox species ("Ca. Brocadia sinica", "Ca. Brocadia sapporoensis", "Ca. Jettenia caeni", and "Ca. Kuenenia stuttgartiensis") were determined and then related to the activities of anti-oxidative enzymes. Highly enriched planktonic anammox cells were exposed to various levels of oxygen, and oxygen inhibition kinetics (50% inhibitory concentration (IC50) and upper O2 limits (DOmax) of anammox activity) were quantitatively determined. A marine anammox species, "Ca. Scalindua sp.", exhibited much higher oxygen tolerance capability (IC50 = 18.0 µM and DOmax = 51.6 µM) than freshwater species (IC50 = 2.7-4.2 µM and DOmax = 10.9-26.6 µM). The upper DO limit of "Ca. Scalindua sp." was much higher than the values reported so far (~20 µM). Furthermore, the oxygen inhibition was reversible even after exposed to ambient air for 12-24 h. The comparative genome analysis confirmed that all anammox species commonly possess the genes considered to function for reduction of O2, superoxide anion (O2•-), and H2O2. However, the superoxide reductase (Sor)-peroxidase dependent detoxification system alone may not be sufficient for cell survival under microaerobic conditions. Despite the fact that anaerobes normally possess no or little superoxide dismutase (Sod) or catalase (Cat), only Scalindua exhibited high Sod activity of 22.6 ± 1.9 U/mg-protein with moderate Cat activity of 1.6 ± 0.7 U/mg-protein, which was consistent with the genome sequence analysis. This Sod-Cat dependent detoxification system could be responsible for the higher O2 tolerance of Scalindua than other freshwater anammox species lacking the Sod activity.
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Affiliation(s)
- Satoshi Okabe
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan.
| | - Shaoyu Ye
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Xi Lan
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Keishi Nukada
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Haozhe Zhang
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Kanae Kobayashi
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Mamoru Oshiki
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
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48
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MacLean A, Legendre F, Appanna VD. The tricarboxylic acid (TCA) cycle: a malleable metabolic network to counter cellular stress. Crit Rev Biochem Mol Biol 2023; 58:81-97. [PMID: 37125817 DOI: 10.1080/10409238.2023.2201945] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The tricarboxylic acid (TCA) cycle is a primordial metabolic pathway that is conserved from bacteria to humans. Although this network is often viewed primarily as an energy producing engine fueling ATP synthesis via oxidative phosphorylation, mounting evidence reveals that this metabolic hub orchestrates a wide variety of pivotal biological processes. It plays an important part in combatting cellular stress by modulating NADH/NADPH homeostasis, scavenging ROS (reactive oxygen species), producing ATP by substrate-level phosphorylation, signaling and supplying metabolites to quell a range of cellular disruptions. This review elaborates on how the reprogramming of this network prompted by such abiotic stress as metal toxicity, oxidative tension, nutrient challenge and antibiotic insult is critical for countering these conditions in mostly microbial systems. The cross-talk between the stressors and the participants of TCA cycle that results in changes in metabolite and nucleotide concentrations aimed at combatting the abiotic challenge is presented. The fine-tuning of metabolites mediated by disparate enzymes associated with this metabolic hub is discussed. The modulation of enzymatic activities aimed at generating metabolic moieties dedicated to respond to the cellular perturbation is explained. This ancient metabolic network has to be recognized for its ability to execute a plethora of physiological functions beyond its well-established traditional roles.
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Affiliation(s)
- Alex MacLean
- School of Natural Sciences, Laurentian University, Sudbury, Canada
| | - Felix Legendre
- School of Natural Sciences, Laurentian University, Sudbury, Canada
| | - Vasu D Appanna
- School of Natural Sciences, Laurentian University, Sudbury, Canada
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49
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Partipilo M, Claassens NJ, Slotboom DJ. A Hitchhiker's Guide to Supplying Enzymatic Reducing Power into Synthetic Cells. ACS Synth Biol 2023; 12:947-962. [PMID: 37052416 PMCID: PMC10127272 DOI: 10.1021/acssynbio.3c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Indexed: 04/14/2023]
Abstract
The construction from scratch of synthetic cells by assembling molecular building blocks is unquestionably an ambitious goal from a scientific and technological point of view. To realize functional life-like systems, minimal enzymatic modules are required to sustain the processes underlying the out-of-equilibrium thermodynamic status hallmarking life, including the essential supply of energy in the form of electrons. The nicotinamide cofactors NAD(H) and NADP(H) are the main electron carriers fueling reductive redox reactions of the metabolic network of living cells. One way to ensure the continuous availability of reduced nicotinamide cofactors in a synthetic cell is to build a minimal enzymatic module that can oxidize an external electron donor and reduce NAD(P)+. In the diverse world of metabolism there is a plethora of potential electron donors and enzymes known from living organisms to provide reducing power to NAD(P)+ coenzymes. This perspective proposes guidelines to enable the reduction of nicotinamide cofactors enclosed in phospholipid vesicles, while avoiding high burdens of or cross-talk with other encapsulated metabolic modules. By determining key requirements, such as the feasibility of the reaction and transport of the electron donor into the cell-like compartment, we select a shortlist of potentially suitable electron donors. We review the most convenient proteins for the use of these reducing agents, highlighting their main biochemical and structural features. Noting that specificity toward either NAD(H) or NADP(H) imposes a limitation common to most of the analyzed enzymes, we discuss the need for specific enzymes─transhydrogenases─to overcome this potential bottleneck.
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Affiliation(s)
- Michele Partipilo
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Nico J. Claassens
- Laboratory
of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Jan Slotboom
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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50
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Ďúranová H, Šimora V, Ďurišová Ľ, Olexiková L, Kovár M, Požgajová M. Modifications in Ultrastructural Characteristics and Redox Status of Plants under Environmental Stress: A Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:1666. [PMID: 37111889 PMCID: PMC10144148 DOI: 10.3390/plants12081666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/30/2023] [Accepted: 04/05/2023] [Indexed: 06/19/2023]
Abstract
The rate of global environmental change is unprecedented, with climate change causing an increase in the oscillation and intensification of various abiotic stress factors that have negative impacts on crop production. This issue has become an alarming global concern, especially for countries already facing the threat of food insecurity. Abiotic stressors, such as drought, salinity, extreme temperatures, and metal (nanoparticle) toxicities, are recognized as major constraints in agriculture, and are closely associated with the crop yield penalty and losses in food supply. In order to combat abiotic stress, it is important to understand how plant organs adapt to changing conditions, as this can help produce more stress-resistant or stress-tolerant plants. The investigation of plant tissue ultrastructure and subcellular components can provide valuable insights into plant responses to abiotic stress-related stimuli. In particular, the columella cells (statocytes) of the root cap exhibit a unique architecture that is easily recognizable under a transmission electron microscope, making them a useful experimental model for ultrastructural observations. In combination with the assessment of plant oxidative/antioxidative status, both approaches can shed more light on the cellular and molecular mechanisms involved in plant adaptation to environmental cues. This review summarizes life-threatening factors of the changing environment that lead to stress-related damage to plants, with an emphasis on their subcellular components. Additionally, selected plant responses to such conditions in the context of their ability to adapt and survive in a challenging environment are also described.
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Affiliation(s)
- Hana Ďúranová
- AgroBioTech Research Centre, Slovak University of Agriculture, Trieda Andreja Hlinku 2, 949 76 Nitra, Slovakia;
| | - Veronika Šimora
- AgroBioTech Research Centre, Slovak University of Agriculture, Trieda Andreja Hlinku 2, 949 76 Nitra, Slovakia;
| | - Ľuba Ďurišová
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Trieda Andreja Hlinku 2, 949 76 Nitra, Slovakia; (Ľ.Ď.); (M.K.)
| | - Lucia Olexiková
- Agricultural and Food Centre (NPPC), Research Institute for Animal Production Nitra, Hlohovecká 2, 951 41 Lužianky, Slovakia;
| | - Marek Kovár
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Trieda Andreja Hlinku 2, 949 76 Nitra, Slovakia; (Ľ.Ď.); (M.K.)
| | - Miroslava Požgajová
- AgroBioTech Research Centre, Slovak University of Agriculture, Trieda Andreja Hlinku 2, 949 76 Nitra, Slovakia;
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