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Du F, Li R, He R, Li K, Liu J, Xiang Y, Duan K, Li C. Exploring salivary metabolome alterations in people with HIV: towards early diagnostic markers. Front Public Health 2024; 12:1400332. [PMID: 38912274 PMCID: PMC11192068 DOI: 10.3389/fpubh.2024.1400332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024] Open
Abstract
Background The human immunodeficiency virus (HIV) remains a critical global health issue, with a pressing need for effective diagnostic and monitoring tools. Methodology This study explored distinctions in salivary metabolome among healthy individuals, individuals with HIV, and those receiving highly active antiretroviral therapy (HAART). Utilizing LC-MS/MS for exhaustive metabolomics profiling, we analyzed 90 oral saliva samples from individuals with HIV, categorized by CD4 count levels in the peripheral blood. Results Orthogonal partial least squares-discriminant analysis (OPLS-DA) and other analyses underscored significant metabolic alterations in individuals with HIV, especially in energy metabolism pathways. Notably, post-HAART metabolic profiles indicated a substantial presence of exogenous metabolites and changes in amino acid pathways like arginine, proline, and lysine degradation. Key metabolites such as citric acid, L-glutamic acid, and L-histidine were identified as potential indicators of disease progression or recovery. Differential metabolite selection and functional enrichment analysis, combined with receiver operating characteristic (ROC) and random forest analyses, pinpointed potential biomarkers for different stages of HIV infection. Additionally, our research examined the interplay between oral metabolites and microorganisms such as herpes simplex virus type 1 (HSV1), bacteria, and fungi in individuals with HIV, revealing crucial interactions. Conclusion This investigation seeks to contribute understanding into the metabolic shifts occurring in HIV infection and following the initiation of HAART, while tentatively proposing novel avenues for diagnostic and treatment monitoring through salivary metabolomics.
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Affiliation(s)
- Fei Du
- Department of Stomatology, Yan’an Hospital of Kunming City, Yan’an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, China
| | - Rong Li
- Department of Stomatology, The First Affiliated Hospital of Dali University, Dali, Yunnan, China
| | - Rui He
- Department of Stomatology, Kunming Maternal and Child Health Hospital, Kunming, Yunnan, China
| | - Kezeng Li
- Department of Stomatology, Yan’an Hospital of Kunming City, Yan’an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, China
| | - Jun Liu
- Department of Infectious Diseases, Kunming Third People’s Hospital, Kunming, Yunnan, China
| | - Yingying Xiang
- Department of Stomatology, Yan’an Hospital of Kunming City, Yan’an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, China
| | - Kaiwen Duan
- Department of Stomatology, Yan’an Hospital of Kunming City, Yan’an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, China
| | - Chengwen Li
- Department of Research Management, Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
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Serna-García R, Silvia Morlino M, Bucci L, Savio F, Favaro L, Morosinotto T, Seco A, Bouzas A, Campanaro S, Treu L. Biological carbon capture from biogas streams: Insights into Cupriavidus necator autotrophic growth and transcriptional profile. BIORESOURCE TECHNOLOGY 2024; 399:130556. [PMID: 38460564 DOI: 10.1016/j.biortech.2024.130556] [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: 01/17/2024] [Revised: 02/25/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Recycling carbon-rich wastes into high-value platform chemicals through biological processes provides a sustainable alternative to petrochemicals. Cupriavidus necator, known for converting carbon dioxide (CO2) into polyhydroxyalkanoates (PHA) was studied for the first time using biogas streams as the sole carbon source. The bacterium efficiently consumed biogenic CO2 from raw biogas with methane at high concentrations (50%) proving non-toxic. Continuous addition of H2 and O2 enabled growth trends comparable to glucose-based heterotrophic growth. Transcriptomic analysis revealed CO2-adaptated cultures exhibited upregulation of hydrogenases and Calvin cycle enzymes, as well as genes related to electron transport, nutrient uptake, and glyoxylate cycle. Non-adapted samples displayed activation of stress response mechanisms, suggesting potential lags in large-scale processes. These findings showcase the setting of growth parameters for a pioneering biological biogas upgrading strategy, emphasizing the importance of inoculum adaptation for autotrophic growth and providing potential targets for genetic engineering to push PHA yields in future applications.
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Affiliation(s)
- Rebecca Serna-García
- CALAGUA - Unidad Mixta UV-UPV, Department of Chemical Engineering, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, València, Spain.
| | - Maria Silvia Morlino
- Department of Biology, Università di Padova, Via U. Bassi 58/b, 35121, Padova, Italy
| | - Luca Bucci
- Department of Biology, Università di Padova, Via U. Bassi 58/b, 35121, Padova, Italy
| | - Filippo Savio
- Department of Biology, Università di Padova, Via U. Bassi 58/b, 35121, Padova, Italy
| | - Lorenzo Favaro
- Department of Agronomy, Food, Natural resources, Animals and Environment, Università di Padova, Viale dell'università 16, 35020, Legnaro, Italy; Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Tomas Morosinotto
- Department of Biology, Università di Padova, Via U. Bassi 58/b, 35121, Padova, Italy
| | - Aurora Seco
- CALAGUA - Unidad Mixta UV-UPV, Department of Chemical Engineering, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, València, Spain
| | - Alberto Bouzas
- CALAGUA - Unidad Mixta UV-UPV, Department of Chemical Engineering, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, València, Spain
| | - Stefano Campanaro
- Department of Biology, Università di Padova, Via U. Bassi 58/b, 35121, Padova, Italy
| | - Laura Treu
- Department of Biology, Università di Padova, Via U. Bassi 58/b, 35121, Padova, Italy
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Wang S, Meng D, Feng M, Li C, Wang Y. Efficient Plant Triterpenoids Synthesis in Saccharomyces cerevisiae: from Mechanisms to Engineering Strategies. ACS Synth Biol 2024; 13:1059-1076. [PMID: 38546129 DOI: 10.1021/acssynbio.4c00061] [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] [Indexed: 04/20/2024]
Abstract
Triterpenoids possess a range of biological activities and are extensively utilized in the pharmaceutical, food, cosmetic, and chemical industries. Traditionally, they are acquired through chemical synthesis and plant extraction. However, these methods have drawbacks, including high energy consumption, environmental pollution, and being time-consuming. Recently, the de novo synthesis of triterpenoids in microbial cell factories has been achieved. This represents a promising and environmentally friendly alternative to traditional supply methods. Saccharomyces cerevisiae, known for its robustness, safety, and ample precursor supply, stands out as an ideal candidate for triterpenoid biosynthesis. However, challenges persist in industrial production and economic feasibility of triterpenoid biosynthesis. Consequently, metabolic engineering approaches have been applied to improve the triterpenoid yield, leading to substantial progress. This review explores triterpenoids biosynthesis mechanisms in S. cerevisiae and strategies for efficient production. Finally, the review also discusses current challenges and proposes potential solutions, offering insights for future engineering.
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Affiliation(s)
- Shuai Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Dong Meng
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Meilin Feng
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Chun Li
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ying Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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Shan S, Manyakhin AY, Wang C, Ge B, Han J, Zhang X, Zhou C, Yan X, Ruan R, Cheng P. Mixotrophy, a more promising culture mode: Multi-faceted elaboration of carbon and energy metabolism mechanisms to optimize microalgae culture. BIORESOURCE TECHNOLOGY 2023; 386:129512. [PMID: 37481043 DOI: 10.1016/j.biortech.2023.129512] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/15/2023] [Accepted: 07/16/2023] [Indexed: 07/24/2023]
Abstract
Some mixotrophic microalgae appear to exceed the sum of photoautotrophy and heterotrophy in terms of biomass production. This paper mainly reviews the carbon and energy metabolism of microalgae to reveal the synergistic mechanisms of the mixotrophic mode from multiple aspects. It explains the shortcomings of photoautotrophic and heterotrophic growth, highlighting that the mixotrophic mode is not simply the sum of photoautotrophy and heterotrophy. Specifically, microalgae in mixotrophic mode can be divided into separate parts of photoautotrophic and heterotrophic cultures, and the synergistic parts of photoautotrophic culture enhance aerobic respiration and heterotrophic culture enhance the Calvin cycle. Additionally, this review argues that current deficiencies in mixotrophic culture can be improved by uncovering the synergistic mechanism of the mixotrophic mode, aiming to increase biomass growth and improve quality. This approach will enable the full utilization of advantagesin various fields, and provide research directions for future microalgal culture.
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Affiliation(s)
- Shengzhou Shan
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Artem Yurevich Manyakhin
- Far Eastern Branch, Russian Academy of Sciences, Federal Scientific Center of East Asian Terrestrial Biodiversity, 100-letiya Vladivostoka Prospect, 159, Vladivostok 690022, Russia
| | - Chun Wang
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Jichang Han
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Xuezhi Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Chengxu Zhou
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Xiaojun Yan
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Roger Ruan
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota-Twin Cities, Saint Paul, MN 55108, USA
| | - Pengfei Cheng
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China; Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota-Twin Cities, Saint Paul, MN 55108, USA.
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Gu J, Xiao Y, Wu M, Wang A, Cui X, Xin Y, Paithoonrangsarid K, Lu Y. Artificial switches induce the bespoke production of functional compounds in marine microalgae Chlorella by neutralizing CO 2. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:143. [PMID: 37759320 PMCID: PMC10537470 DOI: 10.1186/s13068-023-02381-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/11/2023] [Indexed: 09/29/2023]
Abstract
To improve the CO2 tolerance of a marine microalga Chlorella sp. of which the production capacity has been demonstrated industrially, a mutant library was created and a strain hct53 was screened. Compared to the parental strain, hct53 shows a high CO2 capture capacity, while starch biosynthesis is compromised, with increases in health beneficial metabolites and antioxidant capacity. Global gene expression and genome-wide mutation distribution revealed that transcript choreography was concomitant with more active CO2 sequestration, an increase in the lipid synthesis, and a decrease in the starch and protein synthesis. These results suggest that artificial trait improvement via mutagenesis, couple with multiomics analysis, helps discover genetic switches that induce the bespoke conversion of carbon flow from "redundant metabolites" to valuable ones for functional food.
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Affiliation(s)
- Jiahua Gu
- Single-cell BioEngineering Group, State Key Laboratory of Marine Resource Utilization in South China Sea, School of Marine Biology and Fisheries, Hainan University, Haikou, 570228, China
| | - Yuan Xiao
- Single-cell BioEngineering Group, State Key Laboratory of Marine Resource Utilization in South China Sea, School of Marine Biology and Fisheries, Hainan University, Haikou, 570228, China
| | - Mingcan Wu
- Single-cell BioEngineering Group, State Key Laboratory of Marine Resource Utilization in South China Sea, School of Marine Biology and Fisheries, Hainan University, Haikou, 570228, China
| | - Aoqi Wang
- Single-cell BioEngineering Group, State Key Laboratory of Marine Resource Utilization in South China Sea, School of Marine Biology and Fisheries, Hainan University, Haikou, 570228, China
| | - Xinyu Cui
- Single-cell BioEngineering Group, State Key Laboratory of Marine Resource Utilization in South China Sea, School of Marine Biology and Fisheries, Hainan University, Haikou, 570228, China
| | - Yi Xin
- Single-cell BioEngineering Group, State Key Laboratory of Marine Resource Utilization in South China Sea, School of Marine Biology and Fisheries, Hainan University, Haikou, 570228, China
| | - Kalyanee Paithoonrangsarid
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Yandu Lu
- Single-cell BioEngineering Group, State Key Laboratory of Marine Resource Utilization in South China Sea, School of Marine Biology and Fisheries, Hainan University, Haikou, 570228, China.
- Hainan Provincial Key Laboratory of Tropical Hydrobiotechnology, Hainan University, Haikou, China.
- Haikou Technology Innovation Center for Research and Utilization of Algal Bioresources, Hainan University, Haikou, China.
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Tran TH, Roberts AQ, Escapa IF, Gao W, Segre JA, Kong HH, Conlan S, Kelly MS, Lemon KP. Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543719. [PMID: 37333201 PMCID: PMC10274666 DOI: 10.1101/2023.06.05.543719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. Based on the prevalence of these species, at least two likely coexist in the nasal microbiota of 82% of adults. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the functional protein repertoire and metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the U.S. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution across Africa and North America. All four species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent (core) compared to the accessory genome of each species indicating limited strain-level variability in metabolic capacity. Moreover, core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in the Botswanan clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.
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Affiliation(s)
- Tommy H. Tran
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Ari Q. Roberts
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Isabel F. Escapa
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Wei Gao
- The Forsyth Institute (Microbiology), Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Julie A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Heidi H. Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthew S. Kelly
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Katherine P. Lemon
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Division of Infectious Diseases, Texas Children’s Hospital, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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Westenberg R, Peralta-Yahya P. Toward implementation of carbon-conservation networks in nonmodel organisms. Curr Opin Biotechnol 2023; 81:102949. [PMID: 37172422 DOI: 10.1016/j.copbio.2023.102949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/10/2023] [Indexed: 05/15/2023]
Abstract
Decarboxylation - the release of carbon dioxide (CO2) from a substrate - reduces the carbon yield of bioproduced chemicals. When overlaid onto central carbon metabolism, carbon-conservation networks (CCNs) that reroute flux around CO2 release can theoretically achieve higher carbon yields for products derived from intermediates that traditionally require CO2 release, such as acetyl-CoA. Recently, CCNs have started to be implemented in model organisms to produce compounds at higher carbon yields. However, implementation of CCNs in nonmodel hosts may have the greatest impact given their ability to assimilate a larger array of feedstocks, greater environmental tolerance, and unique biosynthetic pathways, ultimately enabling access to a wider range of products. Here, we review recent advances in CCNs with a focus on their application to nonmodel organisms. The differences in central carbon metabolism among different nonmodel hosts reveal opportunities to engineer and apply new CCNs.
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Affiliation(s)
- Ray Westenberg
- Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Pamela Peralta-Yahya
- Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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