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Khoramipour K, Rajizadeh MA, Akbari Z, Arjmand M. The effect of high-intensity interval training on type 2 diabetic muscle: A metabolomics-based study. Heliyon 2024; 10:e34917. [PMID: 39170342 PMCID: PMC11336285 DOI: 10.1016/j.heliyon.2024.e34917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 08/23/2024] Open
Abstract
Background This study aimed to investigate the effect of eight weeks of high-intensity interval training (HIIT) on muscle metabolism in rats with type 2 diabetes (T2D) using metabolomics approaches. Methods 20 male Wistar rats at the age of 8 weeks-were assigned to four groups of five, each in the group randomly: control (CTL), type 2 diabetes (DB), HIIT (EX), and type 2 diabetes + HIIT (DBX). T2D was induced by two months of a high-fat diet plus a single dose of streptozotocin (35 mg/kg). Rats in the EX and DBX groups performed eight weeks of HIIT (running at 80-100 % of Vmax, 4-10 intervals). NMR spectroscopy was used to determine the changes in the muscle metabolome profile after training. Results Changes in metabolite abundance following exercise revealed distinct clustering in multivariate analysis. The essential metabolite changes between the DB and CTL groups were arginine metabolism, purine metabolism, phosphate pathway, amino sugar metabolism, glutathione metabolism, and aminoacyl-tRNA biosynthesis. However, Arginine biosynthesis, pyrimidine metabolism, aminoacyl-tRNA biosynthesis, and alanine, aspartate, and glutamate metabolism were altered between the DBX and DB groups. Conclusion These results suggest that eight weeks of HIIT could reverse metabolic changes induced by T2D in rat muscles, contributing to reduced FBG and HOMA-IR levels.
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Affiliation(s)
- Kayvan Khoramipour
- Endocrinology and Metabolism Research Center, Kerman University of Medical Sciences Kerman, Iran
- i+HeALTH Strategic Research Group, Department of Health Sciences, Miguel de Cervantes European University (UEMC), 47012 Valladolid, Spain
| | - Mohammad Amin Rajizadeh
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Ziba Akbari
- Metabolomics Lab, Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Arjmand
- Metabolomics Lab, Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran
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Liu N, Qin L, Zeng H, Wen A, Miao S. Integrative proteomic-transcriptomic analysis revealed the lifestyles of Lactobacillus paracasei H4-11 and Kluyveromyces marxianus L1-1 under co-cultivation conditions. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2023.03.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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López-García E, Benítez-Cabello A, Tronchoni J, Arroyo-López FN. Understanding the transcriptomic response of Lactiplantibacillus pentosus LPG1 during Spanish-style green table olive fermentations. Front Microbiol 2023; 14:1264341. [PMID: 37808291 PMCID: PMC10556671 DOI: 10.3389/fmicb.2023.1264341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
Lactiplantibacillus pentosus (Lbp. pentosus) is a species of lactic acid bacteria with a great relevance during the table olive fermentation process, with ability to form non-pathogenic biofilms on olive epidermis. The objective of this work is to deepen into the genetic mechanisms of adaptation of Lpb. pentosus LPG1 during Spanish-style green table olive fermentations, as well as to obtain a better understanding of the mechanisms of adherence of this species to the fruit surface. For this purpose, we have carried out a transcriptomic analysis of the differential gene expression of this bacterium during 60 days of fermentation in both brine and biofilms ecosystems. In brines, it was noticed that a total of 235 genes from Lpb. pentosus LPG1 were differentially expressed during course of fermentation and grouped into 9 clusters according to time-course analysis. Transport and metabolism of carbohydrates and amino acids, energy production, lactic acid and exopolysaccharide synthesis genes increased their expression in the planktonic cells during course of fermentation. On the other hand, expression of genes associated to stress response, bacteriocin synthesis and membrane protein decreased. A total of 127 genes showed significant differential expression between Lpb. pentosus LPG1 planktonic (brine) and sessile (biofilms) cells at the end of fermentation process (60 days). Among the 64 upregulated genes in biofilms, we found genes involved in adhesion (strA), exopolysaccharide production (ywqD, ywqE, and wbnH), cell shape and elongation (MreB), and well as prophage excision. Deeping into the genetic bases of beneficial biofilm formation by Lpb. pentosus strains with probiotic potential will help to turn this fermented vegetable into a carrier of beneficial microorganisms to the final consumers.
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Affiliation(s)
- Elio López-García
- Department of Food Biotechnology, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, Seville, Spain
| | - Antonio Benítez-Cabello
- Department of Food Biotechnology, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, Seville, Spain
| | - Jordi Tronchoni
- Universidad Internacional de Valencia, Comunidad Valencia, Spain
| | - Francisco Noé Arroyo-López
- Department of Food Biotechnology, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, Seville, Spain
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Li K, Gao N, Tang J, Ma H, Jiang J, Duan Y, Li Z. A Study on the Formation of Flavor Substances by Bacterial Diversity in the Fermentation Process of Canned Bamboo Shoots in Clear Water. Foods 2023; 12:3478. [PMID: 37761186 PMCID: PMC10529733 DOI: 10.3390/foods12183478] [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: 08/06/2023] [Revised: 09/09/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Canned bamboo shoots in clear water could produce a unique flavor through bacterial diversity via the fermentation process. Weissella, Streptococcus, Leuconostoc, Acinetobacter, Lactococcus and Lactobacillus were the main microorganisms. Tyrosine was the most abundant free amino acid (FAA), which had a negative correlation with Lactococcus. Ten kinds of flavor substances, such as 3-methyl-1-butanol, acetic acid, 2-phenylethyl ester, benzene acetaldehyde, benzoic acid and ethyl ester, were important influential factors in the flavor of fermented bamboo shoots. Through the verification test of tyrosine and phenylalanine decarboxylase, it was found that Lactococcus lactis TJJ2 could decompose tyrosine and phenylalanine to produce benzaldehyde and benzene acetaldehyde, which provided the fermented bamboo shoots with a grassy aroma.
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Affiliation(s)
- Ke Li
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China; (K.L.); (N.G.); (J.T.); (H.M.); (J.J.); (Y.D.)
- Hunan Province Key Laboratory of Food Science and Biotechnology, Changsha 410128, China
| | - Ning Gao
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China; (K.L.); (N.G.); (J.T.); (H.M.); (J.J.); (Y.D.)
| | - Jiaojiao Tang
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China; (K.L.); (N.G.); (J.T.); (H.M.); (J.J.); (Y.D.)
| | - Huiqin Ma
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China; (K.L.); (N.G.); (J.T.); (H.M.); (J.J.); (Y.D.)
| | - Jiayan Jiang
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China; (K.L.); (N.G.); (J.T.); (H.M.); (J.J.); (Y.D.)
| | - Yufan Duan
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China; (K.L.); (N.G.); (J.T.); (H.M.); (J.J.); (Y.D.)
| | - Zongjun Li
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China; (K.L.); (N.G.); (J.T.); (H.M.); (J.J.); (Y.D.)
- Hunan Province Key Laboratory of Food Science and Biotechnology, Changsha 410128, China
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Zhao H, Ji R, Zha X, Xu Z, Lin Y, Zhou S. Investigation of the bactericidal mechanism of Penicilazaphilone C on Escherichia coli based on 4D label-free quantitative proteomic analysis. Eur J Pharm Sci 2022; 179:106299. [PMID: 36179970 DOI: 10.1016/j.ejps.2022.106299] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/16/2022] [Accepted: 08/27/2022] [Indexed: 11/03/2022]
Abstract
There is an urgent need to find new antibiotics to fight against the increasing drug resistance of microorganisms. A novel natural compound, Penicilazaphilone C (PAC), was isolated from a marine-derived fungus. It has displayed broad bactericidal activities against Gram-negative and Gram-positive bacteria. However, its bactericidal mechanism is still unknown. Herein, time-kill assays verified that PAC is a fast and efficient bactericidal agent. Furthermore, data from 4D label-free quantitative proteome assays revealed that PAC significantly influences over 898 proteins in Escherichia coli. Combining the results of biofilm formation, β-galactosidase measurement, TEM observation, soft agar plate swimming, reactive oxygen species measurement, qRT-PCR, and west-blotting, the mode of PAC action against E. coli was to block respiration, inhibit assimilatory nitrate reduction and dissimilar sulfur reduction, facilitate assimilatory sulfate reduction, suppress cysteine and methionine biosynthesis, down-regulate antioxidant protein expression and induced intracellular ROS accumulation, weaken bacterial chemotaxis, destroy flagellar assembly, etc., and finally cause the bacteria's death. Our findings suggest that PAC could have a multi-target regulatory effect on E. coli and could be used as a new antibiotic in medicine.
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Affiliation(s)
- Huange Zhao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Disease Control, Hainan Provincial Key Laboratory of Tropical Medicine, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199
| | - Rong Ji
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Disease Control, Hainan Provincial Key Laboratory of Tropical Medicine, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199
| | - Xiangru Zha
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Disease Control, Hainan Provincial Key Laboratory of Tropical Medicine, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199
| | - Zhen Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Disease Control, Hainan Provincial Key Laboratory of Tropical Medicine, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199
| | - Yingying Lin
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Disease Control, Hainan Provincial Key Laboratory of Tropical Medicine, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199
| | - Songlin Zhou
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Disease Control, Hainan Provincial Key Laboratory of Tropical Medicine, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199.
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Loss of the Rhodobacter capsulatus Serine Acetyl Transferase Gene, cysE1, Impairs Gene Transfer by Gene Transfer Agents and Biofilm Phenotypes. Appl Environ Microbiol 2022; 88:e0094422. [PMID: 36098534 PMCID: PMC9552610 DOI: 10.1128/aem.00944-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biofilms are widespread in the environment, where they allow bacterial species to survive adverse conditions. Cells in biofilms are densely packed, and this proximity is likely to increase the frequency of horizontal gene transfer. Gene transfer agents (GTAs) are domesticated viruses with the potential to spread any gene between bacteria. GTA production is normally restricted to a small subpopulation of bacteria, and regulation of GTA loci is highly coordinated, but the environmental conditions that favor GTA production are poorly understood. Here, we identified a serine acetyltransferase gene, cysE1, in Rhodobacter capsulatus that is required for optimal receipt of GTA DNA, accumulation of extracellular polysaccharide, and biofilm formation. The cysE1 gene is directly downstream of the core Rhodobacter-like GTA (RcGTA) structural gene cluster and upregulated in an RcGTA overproducer strain, although it is expressed on a separate transcript. The data we present suggest that GTA production and biofilm are coregulated, which could have important implications for the study of rapid bacterial evolution and understanding the full impact of GTAs in the environment. IMPORTANCE Direct exchange of genes between bacteria leads to rapid evolution and is the major factor underlying the spread of antibiotic resistance. Gene transfer agents (GTAs) are an unusual but understudied mechanism for genetic exchange that are capable of transferring any gene from one bacterium to another, and therefore, GTAs are likely to be important factors in genome plasticity in the environment. Despite the potential impact of GTAs, our knowledge of their regulation is incomplete. In this paper, we present evidence that elements of the cysteine biosynthesis pathway are involved in coregulation of various phenotypes required for optimal biofilm formation by Rhodobacter capsulatus and successful infection by the archetypal RcGTA. Establishing the regulatory mechanisms controlling GTA-mediated gene transfer is a key stepping stone to allow a full understanding of their role in the environment and wider impact.
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Subspecies Classification and Comparative Genomic Analysis of Lactobacillus kefiranofaciens HL1 and M1 for Potential Niche-Specific Genes and Pathways. Microorganisms 2022; 10:microorganisms10081637. [PMID: 36014054 PMCID: PMC9415760 DOI: 10.3390/microorganisms10081637] [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: 07/23/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Strains HL1 and M1, isolated from kefir grains, have been tentatively identified, based on their partial 16S rRNA gene sequences, as Lactobacillus kefiranofaciens. The two strains demonstrated different health benefits. Therefore, not only the genetic factors exerting diverse functionalities in different L. kefiranofaciens strains, but also the potential niche-specific genes and pathways among the L. kefiranofaciens strains, should be identified. (2) Methods: Phenotypic and genotypic approaches were employed to identify strains HL1 and M1 at the subspecies level. For the further characterization of the probiotic properties of both strains, comparative genomic analyses were used. (3) Results: Both strains were identified as L. kefiranofaciens subsp. kefirgranum. According to the COG function category, dTDP-rhamnose and rhamnose-containing glycans were specifically detected in the L. kefiranofaciens subsp. Kefirgranum genomes. Three unique genes (epsI, epsJ, and epsK) encoding glycosyltransferase in the EPS gene cluster, and the ImpB/MucB/SamB family protein encoding gene were found in HL1 and M1. The specific ability to degrade arginine via the ADI pathway was found in HL1. The presence of the complete glycogen metabolism (glg) operon in the L. kefiranofaciens strains suggested the importance of glycogen synthesis to enable colonization in kefir grains and extend survival under environmental stresses. (4) Conclusions: The obtained novel information on the potential genes and pathways for polysaccharide synthesis and other functionalities in our HL1 and M1 strains could be applied for further functionality predictions for potential probiotic screening.
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Yang M, Ma L, Yang X, Li L, Chen S, Qi B, Wang Y, Li C, Yang S, Zhao Y. Bioinformatic Prediction and Characterization of Proteins in Porphyra dentata by Shotgun Proteomics. Front Nutr 2022; 9:924524. [PMID: 35873412 PMCID: PMC9301277 DOI: 10.3389/fnut.2022.924524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Porphyra dentata is an edible red seaweed with high nutritional value. It is widely cultivated and consumed in East Asia and has vast economic benefits. Studies have found that P. dentata is rich in bioactive substances and is a potential natural resource. In this study, label-free shotgun proteomics was first applied to identify and characterize different harvest proteins in P. dentata. A total of 13,046 different peptides were identified and 419 co-expression target proteins were characterized. Bioinformatics was used to study protein characteristics, functional expression, and interaction of two important functional annotations, amino acid, and carbohydrate metabolism. Potential bioactive peptides, protein structure, and potential ligand conformations were predicted, and the results suggest that bioactive peptides may be utilized as high-quality active fermentation substances and potential targets for drug production. Our research integrated the global protein database, the first time bioinformatic analysis of the P. dentata proteome during different harvest periods, improves the information database construction and provides a framework for future research based on a comprehensive understanding.
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Affiliation(s)
- Mingchang Yang
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- College of Food Science and Bioengineering, Tianjin Agricultural University, Tianjin, China
- Co-innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China
| | - Lizhen Ma
- College of Food Science and Bioengineering, Tianjin Agricultural University, Tianjin, China
| | - Xianqing Yang
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Co-innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Laihao Li
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Co-innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Shengjun Chen
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Co-innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China
| | - Bo Qi
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Co-innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China
| | - Yueqi Wang
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Co-innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China
| | - Chunsheng Li
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Shaoling Yang
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Co-innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China
| | - Yongqiang Zhao
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Co-innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
- *Correspondence: Yongqiang Zhao,
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Liang J, Quan Z, Zhu J, Gan M, Shen P. A functional promoter from the archaeon Halobacterium salinarum is also transcriptionally active in E. coli. BMC Microbiol 2022; 22:79. [PMID: 35331139 PMCID: PMC8943987 DOI: 10.1186/s12866-022-02489-y] [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: 04/20/2021] [Accepted: 02/25/2022] [Indexed: 11/18/2022] Open
Abstract
Background Archaea form a third domain of life that is distinct from Bacteria and Eukarya. So far, many scholars have elucidated considerable details about the typical promoter architectures of the three domains of life. However, a functional promoter from the archaeon Halobacterium salinarum has never been studied in Escherichia coli. Results This paper found that the promoter of Halobacterium salinarum showed a promoter function in Escherichia coli. This Escherichia coli promoter structure contains − 10 box, -10 box extension and − 29 elements, however, no -35 box. The − 29 element is exercised by the TATA box in archaea. And we isolated the RM10 fragment that possessed the fusion characteristics of bacteria and archaea, which was overlapped with functionality of TATA box and − 29 elements. Conclusions The − 29 element reflects the evolutionary relationship between the archaeal promoter and the bacterial promoter. The result possibly indicated that there may be a certain internal connection between archaea and bacteria. We hypothesized that it provided a new viewpoint of the evolutionary relationship of archaea and other organisms. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02489-y.
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Affiliation(s)
- Jinye Liang
- Key laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Zhenghui Quan
- College of Life Sciences, Wuhan University, 430000, Wuhan, China
| | - Jianyu Zhu
- Key laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China. .,College of Life Sciences, Wuhan University, 430000, Wuhan, China.
| | - Min Gan
- Key laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China.
| | - Ping Shen
- College of Life Sciences, Wuhan University, 430000, Wuhan, China.
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Wang Y, Wu J, Lv M, Shao Z, Hungwe M, Wang J, Bai X, Xie J, Wang Y, Geng W. Metabolism Characteristics of Lactic Acid Bacteria and the Expanding Applications in Food Industry. Front Bioeng Biotechnol 2021; 9:612285. [PMID: 34055755 PMCID: PMC8149962 DOI: 10.3389/fbioe.2021.612285] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/16/2021] [Indexed: 12/31/2022] Open
Abstract
Lactic acid bacteria are a kind of microorganisms that can ferment carbohydrates to produce lactic acid, and are currently widely used in the fermented food industry. In recent years, with the excellent role of lactic acid bacteria in the food industry and probiotic functions, their microbial metabolic characteristics have also attracted more attention. Lactic acid bacteria can decompose macromolecular substances in food, including degradation of indigestible polysaccharides and transformation of undesirable flavor substances. Meanwhile, they can also produce a variety of products including short-chain fatty acids, amines, bacteriocins, vitamins and exopolysaccharides during metabolism. Based on the above-mentioned metabolic characteristics, lactic acid bacteria have shown a variety of expanded applications in the food industry. On the one hand, they are used to improve the flavor of fermented foods, increase the nutrition of foods, reduce harmful substances, increase shelf life, and so on. On the other hand, they can be used as probiotics to promote health in the body. This article reviews and prospects the important metabolites in the expanded application of lactic acid bacteria from the perspective of bioengineering and biotechnology.
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Affiliation(s)
- Yaqi Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Jiangtao Wu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Mengxin Lv
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Zhen Shao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Meluleki Hungwe
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Jinju Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaojia Bai
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Jingli Xie
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yanping Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Weitao Geng
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
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Levante A, Lazzi C, Vatsellas G, Chatzopoulos D, Dionellis VS, Makrythanasis P, Neviani E, Folli C. Genome Sequencing of five Lacticaseibacillus Strains and Analysis of Type I and II Toxin-Antitoxin System Distribution. Microorganisms 2021; 9:microorganisms9030648. [PMID: 33800997 PMCID: PMC8003834 DOI: 10.3390/microorganisms9030648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/10/2021] [Accepted: 03/18/2021] [Indexed: 11/16/2022] Open
Abstract
The analysis of bacterial genomes is a potent tool to investigate the distribution of specific traits related to the ability of surviving in particular environments. Among the traits associated with the adaptation to hostile conditions, toxin–antitoxin (TA) systems have recently gained attention in lactic acid bacteria. In this work, genome sequences of Lacticaseibacillus strains of dairy origin were compared, focusing on the distribution of type I TA systems homologous to Lpt/RNAII and of the most common type II TA systems. A high number of TA systems have been identified spread in all the analyzed strains, with type I TA systems mainly located on plasmid DNA. The type II TA systems identified in these strains highlight the diversity of encoded toxins and antitoxins and their organization. This study opens future perspectives on the use of genomic data as a resource for the study of TA systems distribution and prevalence in microorganisms of industrial relevance.
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Affiliation(s)
- Alessia Levante
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (C.L.); (E.N.)
- Correspondence: (A.L.); (C.F.); Tel.: +39-0521-906524 (A.L.); +39-0521-905174 (C.F.)
| | - Camilla Lazzi
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (C.L.); (E.N.)
| | - Giannis Vatsellas
- Biomedical Research Foundation of the Academy of Athens (BRFAA), 115 27 Athens, Greece; (G.V.); (D.C.); (V.S.D.); (P.M.)
| | - Dimitris Chatzopoulos
- Biomedical Research Foundation of the Academy of Athens (BRFAA), 115 27 Athens, Greece; (G.V.); (D.C.); (V.S.D.); (P.M.)
| | - Vasilis S. Dionellis
- Biomedical Research Foundation of the Academy of Athens (BRFAA), 115 27 Athens, Greece; (G.V.); (D.C.); (V.S.D.); (P.M.)
- Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Periklis Makrythanasis
- Biomedical Research Foundation of the Academy of Athens (BRFAA), 115 27 Athens, Greece; (G.V.); (D.C.); (V.S.D.); (P.M.)
| | - Erasmo Neviani
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (C.L.); (E.N.)
| | - Claudia Folli
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (C.L.); (E.N.)
- Correspondence: (A.L.); (C.F.); Tel.: +39-0521-906524 (A.L.); +39-0521-905174 (C.F.)
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Gallardo-Benavente C, Campo-Giraldo JL, Castro-Severyn J, Quiroz A, Pérez-Donoso JM. Genomics Insights into Pseudomonas sp. CG01: An Antarctic Cadmium-Resistant Strain Capable of Biosynthesizing CdS Nanoparticles Using Methionine as S-Source. Genes (Basel) 2021; 12:187. [PMID: 33514061 PMCID: PMC7912247 DOI: 10.3390/genes12020187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/23/2022] Open
Abstract
Here, we present the draft genome sequence of Pseudomonas sp. GC01, a cadmium-resistant Antarctic bacterium capable of biosynthesizing CdS fluorescent nanoparticles (quantum dots, QDs) employing a unique mechanism involving the production of methanethiol (MeSH) from methionine (Met). To explore the molecular/metabolic components involved in QDs biosynthesis, we conducted a comparative genomic analysis, searching for the genes related to cadmium resistance and sulfur metabolic pathways. The genome of Pseudomonas sp. GC01 has a 4,706,645 bp size with a 58.61% G+C content. Pseudomonas sp. GC01 possesses five genes related to cadmium transport/resistance, with three P-type ATPases (cadA, zntA, and pbrA) involved in Cd-secretion that could contribute to the extracellular biosynthesis of CdS QDs. Furthermore, it exhibits genes involved in sulfate assimilation, cysteine/methionine synthesis, and volatile sulfur compounds catabolic pathways. Regarding MeSH production from Met, Pseudomonas sp. GC01 lacks the genes E4.4.1.11 and megL for MeSH generation. Interestingly, despite the absence of these genes, Pseudomonas sp. GC01 produces high levels of MeSH. This is probably associated with the metC gene that also produces MeSH from Met in bacteria. This work is the first report of the potential genes involved in Cd resistance, sulfur metabolism, and the process of MeSH-dependent CdS QDs bioproduction in Pseudomonas spp. strains.
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Affiliation(s)
- Carla Gallardo-Benavente
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, 4780000 Temuco, Chile;
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, 4780000 Temuco, Chile
| | - Jessica L. Campo-Giraldo
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8320000 Santiago, Chile;
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, 1240000 Antofagasta, Chile;
| | - Andrés Quiroz
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, 4780000 Temuco, Chile
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, 4780000 Temuco, Chile
| | - José M. Pérez-Donoso
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8320000 Santiago, Chile;
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Neamah WH, Busbee PB, Alghetaa H, Abdulla OA, Nagarkatti M, Nagarkatti P. AhR Activation Leads to Alterations in the Gut Microbiome with Consequent Effect on Induction of Myeloid Derived Suppressor Cells in a CXCR2-Dependent Manner. Int J Mol Sci 2020; 21:ijms21249613. [PMID: 33348596 PMCID: PMC7767008 DOI: 10.3390/ijms21249613] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/27/2020] [Accepted: 12/12/2020] [Indexed: 02/06/2023] Open
Abstract
Aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a potent ligand for AhR and a known carcinogen. While AhR activation by TCDD leads to significant immunosuppression, how this translates into carcinogenic signal is unclear. Recently, we demonstrated that activation of AhR by TCDD in naïve C57BL6 mice leads to massive induction of myeloid derived-suppressor cells (MDSCs). In the current study, we investigated the role of the gut microbiota in TCDD-mediated MDSC induction. TCDD caused significant alterations in the gut microbiome, such as increases in Prevotella and Lactobacillus, while decreasing Sutterella and Bacteroides. Fecal transplants from TCDD-treated donor mice into antibiotic-treated mice induced MDSCs and increased regulatory T-cells (Tregs). Injecting TCDD directly into antibiotic-treated mice also induced MDSCs, although to a lesser extent. These data suggested that TCDD-induced dysbiosis plays a critical role in MDSC induction. Interestingly, treatment with TCDD led to induction of MDSCs in the colon and undetectable levels of cysteine. MDSCs suppressed T cell proliferation while reconstitution with cysteine restored this response. Lastly, blocking CXC chemokine receptor 2 (CXCR2) impeded TCDD-mediated MDSC induction. Our data demonstrate that AhR activation by TCDD triggers dysbiosis which, in turn, regulates, at least in part, induction of MDSCs.
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Bottari B, Levante A, Neviani E, Gatti M. How the Fewest Become the Greatest. L. casei's Impact on Long Ripened Cheeses. Front Microbiol 2018; 9:2866. [PMID: 30524419 PMCID: PMC6262004 DOI: 10.3389/fmicb.2018.02866] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/07/2018] [Indexed: 12/23/2022] Open
Abstract
Members of the Lactobacillus casei group, including species classified currently as L. casei, L. paracasei, and L. rhamnosus, are among the most frequently found species in raw milk, hard cooked, long-ripened cheeses. Starting from very low numbers in raw milk, they become dominant in the cheese during ripening, selected by physical and chemical changes produced by cheese making and ripening. Their presence at different stages of cheese making and ripening is crucial in defining product features. For these reasons, the scientific community has been more and more interested in studying these “tiny but mighty microbes” and their implications during cheese making and ripening. The present paper reviews the current literature on the effect of L. casei in cheeses, with particular reference to the case of Parmigiano Reggiano and Grana Padano, two of the most famous PDO (Protected Designation of Origin) Italian cheeses. Recent advances regarding the selection of new wild strains able to persist until the end of ripening and carrying out slow but crucial activities resulting in specific aromatic features, are also presented.
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Affiliation(s)
| | - Alessia Levante
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Erasmo Neviani
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Monica Gatti
- Department of Food and Drug, University of Parma, Parma, Italy
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Wüthrich D, Irmler S, Berthoud H, Guggenbühl B, Eugster E, Bruggmann R. Conversion of Methionine to Cysteine in Lactobacillus paracasei Depends on the Highly Mobile cysK-ctl-cysE Gene Cluster. Front Microbiol 2018; 9:2415. [PMID: 30386310 PMCID: PMC6200037 DOI: 10.3389/fmicb.2018.02415] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/20/2018] [Indexed: 11/23/2022] Open
Abstract
Milk and dairy products are rich in nutrients and are therefore habitats for various microbiomes. However, the composition of nutrients can be quite diverse, in particular among the sulfur containing amino acids. In milk, methionine is present in a 25-fold higher abundance than cysteine. Interestingly, a fraction of strains of the species L. paracasei – a flavor-enhancing adjunct culture species – can grow in medium with methionine as the sole sulfur source. In this study, we focus on genomic and evolutionary aspects of sulfur dependence in L. paracasei strains. From 24 selected L. paracasei strains, 16 strains can grow in medium with methionine as sole sulfur source. We sequenced these strains to perform gene-trait matching. We found that one gene cluster – consisting of a cysteine synthase, a cystathionine lyase, and a serine acetyltransferase – is present in all strains that grow in medium with methionine as sole sulfur source. In contrast, strains that depend on other sulfur sources do not have this gene cluster. We expanded the study and searched for this gene cluster in other species and detected it in the genomes of many bacteria species used in the food production. The comparison to these species showed that two different versions of the gene cluster exist in L. paracasei which were likely gained in two distinct events of horizontal gene transfer. Additionally, the comparison of 62 L. paracasei genomes and the two versions of the gene cluster revealed that this gene cluster is mobile within the species.
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Affiliation(s)
- Daniel Wüthrich
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | | | | | | | - Elisabeth Eugster
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
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