1
|
Zhang N, Kandalai S, Zhou X, Hossain F, Zheng Q. Applying multi-omics toward tumor microbiome research. IMETA 2023; 2:e73. [PMID: 38868335 PMCID: PMC10989946 DOI: 10.1002/imt2.73] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/30/2022] [Accepted: 11/28/2022] [Indexed: 06/14/2024]
Abstract
Rather than a "short-term tenant," the tumor microbiome has been shown to play a vital role as a "permanent resident," affecting carcinogenesis, cancer development, metastasis, and cancer therapies. As the tumor microbiome has great potential to become a target for the early diagnosis and treatment of cancer, recent research on the relevance of the tumor microbiota has attracted a wide range of attention from various scientific fields, resulting in remarkable progress that benefits from the development of interdisciplinary technologies. However, there are still a great variety of challenges in this emerging area, such as the low biomass of intratumoral bacteria and unculturable character of some microbial species. Due to the complexity of tumor microbiome research (e.g., the heterogeneity of tumor microenvironment), new methods with high spatial and temporal resolution are urgently needed. Among these developing methods, multi-omics technologies (combinations of genomics, transcriptomics, proteomics, and metabolomics) are powerful approaches that can facilitate the understanding of the tumor microbiome on different levels of the central dogma. Therefore, multi-omics (especially single-cell omics) will make enormous impacts on the future studies of the interplay between microbes and tumor microenvironment. In this review, we have systematically summarized the advances in multi-omics and their existing and potential applications in tumor microbiome research, thus providing an omics toolbox for investigators to reference in the future.
Collapse
Affiliation(s)
- Nan Zhang
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Shruthi Kandalai
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Xiaozhuang Zhou
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Farzana Hossain
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Qingfei Zheng
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
- Department of Biological Chemistry and Pharmacology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
| |
Collapse
|
2
|
Boness HVM, de Sá HC, Dos Santos EKP, Canuto GAB. Sample Preparation in Microbial Metabolomics: Advances and Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:149-183. [PMID: 37843809 DOI: 10.1007/978-3-031-41741-2_7] [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: 10/17/2023]
Abstract
Microbial metabolomics has gained significant interest as it reflects the physiological state of microorganisms. Due to the great variability of biological organisms, in terms of physicochemical characteristics and variable range of concentration of metabolites, the choice of sample preparation methods is a crucial step in the metabolomics workflow and will reflect on the quality and reliability of the results generated. The procedures applied to the preparation of microbial samples will vary according to the type of microorganism studied, the metabolomics approach (untargeted or targeted), and the analytical platform of choice. This chapter aims to provide an overview of the sample preparation workflow for microbial metabolomics, highlighting the pre-analytical factors associated with cultivation, harvesting, metabolic quenching, and extraction. Discussions focus on obtaining intracellular and extracellular metabolites. Finally, we introduced advanced sample preparation methods based on automated systems.
Collapse
Affiliation(s)
- Heiter V M Boness
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Hanna C de Sá
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Emile K P Dos Santos
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Gisele A B Canuto
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil.
| |
Collapse
|
3
|
Kim SH, Singh D, Son SY, Lee S, Suh DH, Lee NR, Park GS, Kang J, Lee CH. Characterization and temporal dynamics of the intra- and extracellular environments of Lactiplantibacillus plantarum using multi-platform metabolomics. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
4
|
Insights into the Metabolic Response of Lactiplantibacillus plantarum CCFM1287 upon Patulin Exposure. Int J Mol Sci 2022; 23:ijms231911652. [PMID: 36232948 PMCID: PMC9570479 DOI: 10.3390/ijms231911652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Patulin (PAT) is a common mycotoxin in the food industry, and is found in apple products in particular. Consumption of food or feed contaminated with PAT can cause acute or chronic toxicity in humans and animals. Lactiplantibacillus plantarum CCFM1287 is a probiotic strain that effectively degrades PAT in PBS and food systems. In this study, it was found that the concentration of PAT (50 mg/L) in MRS medium decreased by 85.09% during the first stages of CCFM1287 growth, and this change was consistent with the first-order degradation kinetic model. Meanwhile, the regulation of oxidative stress by L. plantarum CCFM1287 in response to PAT exposure and metabolic changes that occur during PAT degradation were investigated. The degree of intracellular damage was attenuated after 16 h of exposure compared to 8 h. Meanwhile, metabolomic data showed that 30 and 29 significantly different metabolites were screened intracellularly in the strain after 8 h and 16 h of PAT stress at 50 mg/L, respectively. The results of pathway enrichment analysis suggested that the purine metabolic pathway was significantly enriched at both 8 h and 16 h. However, as is consistent with the performance of the antioxidant system, the changes in Lactiplantibacillus diminished with increasing time of PAT exposure. Therefore, this study helps to further explain the mechanism of PAT degradation by L. plantarum CCFM1287.
Collapse
|
5
|
Ye D, Li X, Shen J, Xia X. Microbial metabolomics: From novel technologies to diversified applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
6
|
Abstract
Metabolomics is a powerful tool that can systematically describe global changes in the metabolome of microbes, thus improving our understanding of the mechanisms of action of antibiotics and facilitating the development of next-generation antibacterial therapies. However, current sample preparation methods are not efficient or reliable for studying the effects of antibiotics on microbes. In the present study, we reported a novel sample preparation approach using cold methanol/ethylene glycol for quenching Escherichia coli, thus overcoming the loss of intracellular metabolites caused by cell membrane damage. After evaluating the extraction efficiency of several extraction methods, we employed the optimized workflow to profile the metabolome of E. coli exposed to cephalexin. In doing so, we proved the utility of the proposed approach and provided insights into the comprehensive metabolic alterations associated with antibiotic treatment. IMPORTANCE The emergence and global spread of multidrug-resistant bacteria and genes are a global problem. It is critical to understand the interactions between antibiotics and bacteria and find alternative treatments for infections when we are moving closer to a postantibiotic era. It has been demonstrated that the bacterial metabolic environment plays an important role in the modulation of antibiotic susceptibility and efficacy. In the present study, we proposed a novel metabolomic approach for intracellular metabolite profiling of E. coli, which can be used to investigate the metabolite alterations of bacteria caused by antibiotic treatment. Further understanding of antibiotic-induced perturbations of bacterial metabolism would facilitate the discovery of new therapeutic targets and pathways.
Collapse
|
7
|
Close K, Marques R, Carvalho VCF, Freitas EB, Reis MAM, Carvalho G, Oehmen A. The storage compounds associated with Tetrasphaera PAO metabolism and the relationship between diversity and P removal. WATER RESEARCH 2021; 204:117621. [PMID: 34500182 DOI: 10.1016/j.watres.2021.117621] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
In enhanced biological phosphorus removal (EBPR), Tetrasphaera can potentially be an abundant and important polyphosphate accumulating organism (PAO), however ongoing questions remain concerning its storage compounds, phosphorus (P) removal capabilities and metabolic behaviour. This study investigated each of these points in an enriched Tetrasphaera culture (95% biovolume). The enriched Tetrasphaera culture fermented amino acids, while also converting and storing diverse amino acids as aspartic and glutamic acid within cells. Subsequent intracellular consumption of these two amino acids during the aerobic phase supports their importance in the metabolism of Tetrasphaera. Polyhydroxyalkanoate (PHA) cycling was also observed in this study, in contrast to some previous studies on Tetrasphaera. While exhibiting anaerobic phosphorus release and aerobic uptake, the highly enriched Tetrasphaera culture was unable to completely remove phosphorus in sequencing batch reactors (SBR) cycles, with an average removal efficiency of 72.3 ± 7.8%. This is unlike a previous study containing both Tetrasphaera (70%) and Accumulibacter (22%), which regularly performed complete phosphorus removal under otherwise similar operational conditions, at efficiencies of > 99%. Notably, the phylodiversity of organisms belonging to Tetrasphaera was substantially different in the present work, consisting mainly of organisms within Clade 2, likely impacting PHA cycling. These results suggest that the contribution of Tetrasphaera towards P removal is highly dependent on the composition of its Clades within this microbial group and an observed higher abundance of Tetrasphaera in WWTPs does not necessarily imply overall higher P removal. This study improves our understanding of the role of Tetrasphaera within EBPR systems and key factors impacting its metabolism.
Collapse
Affiliation(s)
- Kylie Close
- School of Chemical Engineering, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Ricardo Marques
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Virginia C F Carvalho
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Elisabete B Freitas
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Maria A M Reis
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Gilda Carvalho
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Adrian Oehmen
- School of Chemical Engineering, The University of Queensland, St Lucia, Queensland, 4072, Australia; UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
| |
Collapse
|
8
|
Mei Y, Chen H, Yang B, Zhao J, Zhang H, Chen W. Linoleic Acid Triggered a Metabolomic Stress Condition in Three Species of Bifidobacteria Characterized by Different Conjugated Linoleic Acid-Producing Abilities. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11311-11321. [PMID: 34523917 DOI: 10.1021/acs.jafc.1c03752] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Abundant conjugated linoleic acid (CLA) producers exist among Bifidobacterium species. This CLA production is related to the mitigation of LA toxicity. However, there is still a lack of information on the metabolic response underlying this detoxification strategy. In this study, six bifidobacteria strains belonging to three different species were used to characterize growth and CLA accumulation in the presence of LA. A combination of non-targeted metabolomics techniques and biochemical indicators were used to explore metabolic profile changes in response to LA and the expression of important factors driving CLA production in Bifidobacterium species. The results suggested that free LA had growth inhibitory effects on bifidobacteria, resulting in a global metabolic stress response that caused metabolic reprogramming on all tested strains and promoted malondialdehyde production, inducing a redox imbalance. In particular, a strong decrease in reduced glutathione level was observed in Bifidobacterium breve CCFM683 [log2(FC) = -3.29]. Furthermore, LA-induced oxidative stress is an important factor driving high CLA production in certain strains.
Collapse
Affiliation(s)
- Yongchao Mei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, Jiangsu 214122, P. R. China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| |
Collapse
|
9
|
Yang B, Gao H, Qi H, Chen Y, Ross RP, Stanton C, Zhao J, Zhang H, Chen H, Chen W. Linoleate Isomerase Complex Contributes to Metabolism and Remission of DSS-Induced Colitis in Mice of Lactobacillus plantarum ZS2058. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8160-8171. [PMID: 34281339 DOI: 10.1021/acs.jafc.1c02944] [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: 06/13/2023]
Abstract
A linoleate isomerase complex including myosin-cross-reactive antigen, short-chain dehydrogenase/oxidoreductase, and acetoacetate decarboxylase has been confirmed as the pivotal factor for conjugated linoleic acid (CLA) production in Lactobacillus plantarum. However, its role in the metabolism and health-associated benefits of Lactobacillus remain unclear. In the current study, the mild type, knockout, and complemented mutants of the linoleate isomerase complex of L. plantarum ZS2058 were used to investigate those putative effects. The metabonomic results showed that a linoleate isomerase complex could significantly influence the glycol-metabolism, lipid metabolism, and antioxidant compounds. Especially, with the stress of linoleic acid, linoleate isomerase complex knockout mutants induced the increase of several antioxidant compounds, such as glutamic acid, glycine, l-cysteine, glycerol, and l-sorbosone. Moreover, the linoleate isomerase complex played a pivotal role in ameliorating DSS-induced colitis. The knockout mutants showed effects similar to those in the DSS group, whereas complementation of the corresponding gene in the knockout mutants could restore the anti-inflammatory activity, wherein the integrity of a mucus layer was repaired, the level of pro-inflammatory cytokines decreased, and the amount of anti-inflammatory cytokines increased significantly. All the results indicated that the linoleate isomerase complex plays a key role in CLA production and metabolism as well as the health-associated benefits of L. plantarum ZS2058. These results are conducive to promote clinical trials and product development of probiotics for colitis.
Collapse
Affiliation(s)
- Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - He Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hui Qi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yang Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - R Paul Ross
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi 214122, Jiangsu, China
- APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland
| | - Catherine Stanton
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi 214122, Jiangsu, China
- APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland
- Teagasc Food Research Centre, Moorepark, Co. Cork P61 C996, Ireland
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
10
|
Gao H, Yang B, Stanton C, Ross RP, Zhang H, Chen H, Chen W. Linoleic acid induces different metabolic modes in two Bifidobacterium breve strains with different conjugated linoleic acid-producing abilities. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.110974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
11
|
Chen X, Wang T, Jin M, Tan Y, Liu L, Liu L, Li C, Yang Y, Du P. Metabolomics analysis of growth inhibition of
Lactobacillus plantarum
under ethanol stress. Int J Food Sci Technol 2020. [DOI: 10.1111/ijfs.14677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xiaoqian Chen
- Key Laboratory of Dairy Sciences College of Food Science Northeast Agricultural University Harbin150030China
| | - Tingting Wang
- Key Laboratory of Dairy Sciences College of Food Science Northeast Agricultural University Harbin150030China
| | - Man Jin
- National Dairy Quality Supervision and Inspection Center Harbin150028China
| | - Ying Tan
- Key Laboratory of Dairy Sciences College of Food Science Northeast Agricultural University Harbin150030China
| | - Libo Liu
- Key Laboratory of Dairy Sciences College of Food Science Northeast Agricultural University Harbin150030China
| | - Lihua Liu
- Institute of Animal Science (IAS) Chinese Academy of Agricultural Sciences (CAAS) Beijing100193China
| | - Chun Li
- Key Laboratory of Dairy Sciences College of Food Science Northeast Agricultural University Harbin150030China
| | - Yuzhuo Yang
- Heilongjiang Academy of Green Food Science Harbin150030China
| | - Peng Du
- Key Laboratory of Dairy Sciences College of Food Science Northeast Agricultural University Harbin150030China
| |
Collapse
|
12
|
Sake CL, Newman DM, Boyle NR. Evaluation of quenching methods for metabolite recovery in photoautotrophic Synechococcus sp. PCC 7002. Biotechnol Prog 2020; 36:e3015. [PMID: 32388924 DOI: 10.1002/btpr.3015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/07/2020] [Accepted: 05/05/2020] [Indexed: 12/29/2022]
Abstract
The first step of many metabolomics studies is quenching, a technique vital for rapidly halting metabolism and ensuring that the metabolite profile remains unchanging during sample processing. The most widely used approach is to plunge the sample into prechilled cold methanol; however, this led to significant metabolite loss in Synecheococcus sp. PCC 7002. Here we describe our analysis of the impacts of cold methanol quenching on the model marine cyanobacterium Synechococcus sp. PCC 7002, as well as our brief investigation of alternative quenching methods. We tested several methods including cold methanol, cold saline, and two filtration approaches. Targeted central metabolites were extracted and metabolomic profiles were generated using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The results indicate that cold methanol quenching induces dramatic metabolite leakage in Synechococcus, resulting in a majority of central metabolites being lost prior to extraction. Alternatively, usage of a chilled saline quenching solution mitigates metabolite leakage and improves sample recovery without sacrificing rapid quenching of cellular metabolism. Finally, we illustrate that metabolite leakage can be assessed, and subsequently accounted for, in order to determine absolute metabolite pool sizes; however, our results show that metabolite leakage is inconsistent across various metabolite pools and therefore must be determined for each individually measured metabolite.
Collapse
Affiliation(s)
- Cara L Sake
- Chemical & Biological Engineering , Colorado School of Mines, Golden, Colorado, USA
| | - Darrian M Newman
- Chemical & Biological Engineering , Colorado School of Mines, Golden, Colorado, USA
| | - Nanette R Boyle
- Chemical & Biological Engineering , Colorado School of Mines, Golden, Colorado, USA
| |
Collapse
|
13
|
Distinct Gut Microbiota Induced by Different Fat-to-Sugar-Ratio High-Energy Diets Share Similar Pro-obesity Genetic and Metabolite Profiles in Prediabetic Mice. mSystems 2019; 4:4/5/e00219-19. [PMID: 31594827 PMCID: PMC6787563 DOI: 10.1128/msystems.00219-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Various types of diet can lead to type 2 diabetes. The gut microbiota in type 2 diabetic patients are also different. So, two questions arise: whether there are any commonalities between gut microbiota induced by different pro-obese diets and whether these commonalities lead to disease. Here we found that high-energy diets with two different fat-to-sugar ratios can both cause obesity and prediabetes but enrich different gut microbiota. Still, these different gut microbiota have similar genetic and metabolite compositions. The microbial metabolites in common between the diets modulate lipid accumulation and macrophage inflammation in vivo and in vitro. This work suggests that studies that only use 16S rRNA amplicon sequencing to determine how the microbes respond to diet and associate with diabetic state are missing vital information. Gut microbiota play important roles in host metabolism, especially in diabetes. However, why different diets lead to similar diabetic states despite being associated with different microbiota is not clear. Mice were fed two high-energy diets (HED) with the same energy density but different fat-to-sugar ratios to determine the associations between the microbiota and early-stage metabolic syndrome. The two diets resulted in different microbiota but similar diabetic states. Interestingly, the microbial gene profiles were not significantly different, and many common metabolites were identified, including l-aspartic acid, cholestan-3-ol (5β, 3α), and campesterol, which have been associated with lipogenesis and inflammation. Our study suggests that different metabolic-syndrome-inducing diets may result in different microbiota but similar microbiomes and metabolomes. This suggests that the metagenome and metabolome are crucial for the prognosis and pathogenesis of obesity and metabolic syndrome. IMPORTANCE Various types of diet can lead to type 2 diabetes. The gut microbiota in type 2 diabetic patients are also different. So, two questions arise: whether there are any commonalities between gut microbiota induced by different pro-obese diets and whether these commonalities lead to disease. Here we found that high-energy diets with two different fat-to-sugar ratios can both cause obesity and prediabetes but enrich different gut microbiota. Still, these different gut microbiota have similar genetic and metabolite compositions. The microbial metabolites in common between the diets modulate lipid accumulation and macrophage inflammation in vivo and in vitro. This work suggests that studies that only use 16S rRNA amplicon sequencing to determine how the microbes respond to diet and associate with diabetic state are missing vital information.
Collapse
|