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Kumari S, Choudhary G, Anu K, Devi S. Metagenomics insight into Puga geothermal geyser located in Himalayan Geothermal Belt (Trans-Himalayan Plateau) Ladakh, India. Braz J Microbiol 2024; 55:2321-2334. [PMID: 38874746 PMCID: PMC11405596 DOI: 10.1007/s42770-024-01408-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/25/2024] [Indexed: 06/15/2024] Open
Abstract
Puga geothermal geyser and surrounding area, located in the Himalayan Geothermal Belt of the Trans-Himalayan Plateau in Ladakh, India, are very geographically isolated and considered pristine and free of anthropogenic activities. In this study, we have conducted the first metagenomic investigation of the microbes in and around the geyser. The whole genome sequencing analysis showed the presence of a total of 44.8%, 39.7% and 41.4% bacterial phyla in the PugW, PugS, and PugSo samples respectively, 8.6% of archaeal phyla (in all the samples), unclassified (derived from other sequences, PugW: 27.6%, PugS: 27.6%, and PugSo: 15.5%) and unclassified (derived from bacteria, PugW: 12%, PugS: 13.8%, and PugSo: 13.8%). The majority of archaeal sequences were linked to Euryarchaeota (2.84%) while the majority of the bacterial communities that predominated in most geothermal locations were linked to Pseudomonadota (67.14%) and Bacteroidota (12.52%). The abundant bacterial strains at the species level included Dechloromonas aromatica, Acinetobacter baumannii, and Arcobacter butzleri, in all the samples while the most abundant archaeal species were Methanosaeta thermophile, Methanoregula boonei, and Methanosarcina berkeri. Further, this geothermal geyser metagenome has a large number of unique sequences linked to unidentified and unclassified lineages, suggesting a potential source for novel species of microbes and their products. The present study which only examined one of the many geothermal geysers and springs in the Puga geothermal area, should be regarded as a preliminary investigation of the microbiota that live in the geothermal springs on these remote areas. These findings suggest that further investigations should be undertaken to characterize the ecosystems of the Puga geothermal area, which serve as a repository for unidentified microbial lineages.
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Affiliation(s)
- Shalini Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box 06, Himachal Pradesh, Palampur, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Geetanjli Choudhary
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box 06, Himachal Pradesh, Palampur, 176061, India
| | - Kumari Anu
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box 06, Himachal Pradesh, Palampur, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sarita Devi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box 06, Himachal Pradesh, Palampur, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Choudhary G, Kumari S, Anu K, Devi S. Deciphering the microbial communities of alkaline hot spring in Panamik, Ladakh, India using a high-throughput sequencing approach. Braz J Microbiol 2024; 55:1465-1476. [PMID: 38662153 PMCID: PMC11153388 DOI: 10.1007/s42770-024-01346-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Due to their distinctive physicochemical characteristics, hot springs are extremely important. The whole genome metagenomic sequencing technology can be utilized to analyze the diverse microbial community that thrives in this habitat due to the particular selection pressure that prevails there. The current investigation emphasizes on culture-independent metagenomic study of the Panamik hot spring and its nearby areas from Ladakh, India. Based on different diversity indices, sequence analysis of the soil reservoir showed higher species richness and diversity in comparison to water and sediment samples. The mineral content and various physicochemical pameters like temperature, pH had an impact on the composition of the microbial community of the geothermal springs. The phyla Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacter, Firmicutes, and Verrucomicrobia in bacterial domain dominate the thermos-alkaline spring at Panamik in different concentrations. Economically significant microbes from the genera Actinobacter, Thermosynechoccus, Candidatus Solibacter, Chthoniobacter, Synechoccus, Pseudomonas and Sphingomonas, were prevalent in hot spring. In the archaeal domain, the most dominant phylum and genera were Euryarchaeota and Thermococcus in all the samples. Further, the most abundant species were Methanosarcina barkeri, Nitrospumilus maritimus and Methanosarcina acetivorans. The present study which only examined one of the several thermal springs present in the Himalayan geothermal area, should be regarded as a preliminary investigation of the microbiota that live in the hot springs on these remote areas. These findings suggest that further investigations should be undertaken to characterize the ecosystems of the Panamik hot spring, which serve as a repository for unidentified microbial lineages.
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Affiliation(s)
- Geetanjli Choudhary
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Shalini Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Kumari Anu
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sarita Devi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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He S, Deng X, Han Y, Gong Z, Wang J, Tao X, Tong H, Chen Y. Metabolites and metagenomic analysis reveals the quality of Pu-erh "tea head". Food Chem 2023; 429:136992. [PMID: 37516054 DOI: 10.1016/j.foodchem.2023.136992] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/17/2023] [Accepted: 07/23/2023] [Indexed: 07/31/2023]
Abstract
Tea head, a derivative product of Pu-erh tea, are tight tea lumps formed during pile-fermentation. The aim of this study was to reveal the differences of quality-related metabolites and microbial communities between ripened Pu-erh tea (PE-21) and tea heads (CT-21). Compared with PE-21, CT-21 showed a more mellow and smooth taste with slight bitterness and astringency, and can withstand multiple infusions. Metabolites analysis indicated CT-21 had more abundant water-soluble substances (47.39%) and showed significant differences with PE-21 in the main compositions of amino acids, catechins and saccharides which contributed to the viscosity of tea liquor, mellow taste and the tight tea lumps formation. Microbial communities and COG annotation analysis revealed CT-21 had lower abundance of Bacteria (84.05%), and higher abundance of Eukaryota (15.10%), carbohydrate transport and metabolism (8.28%) and glycoside hydrolases (37.36%) compared with PE-21. The different microbial communities may cause metabolites changes, forming distinct flavor of Pu-erh.
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Affiliation(s)
- Shiqiang He
- Department of Tea Science, College of Food Science, Southwest University, Chongqing 400715, China
| | - Xinyi Deng
- Department of Tea Science, College of Food Science, Southwest University, Chongqing 400715, China
| | - Yuxin Han
- Department of Tea Science, College of Food Science, Southwest University, Chongqing 400715, China
| | - Zhengli Gong
- Department of Tea Science, College of Food Science, Southwest University, Chongqing 400715, China
| | - Jian Wang
- Ice Island Mountain Tea Company, Mengku Town, Shuangjiang Autonomous County, Yunnan Province, China
| | - Xiaoqi Tao
- Department of Tea Science, College of Food Science, Southwest University, Chongqing 400715, China
| | - Huarong Tong
- Department of Tea Science, College of Food Science, Southwest University, Chongqing 400715, China
| | - Yingjuan Chen
- Department of Tea Science, College of Food Science, Southwest University, Chongqing 400715, China.
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Feng L, Gao S, Liu P, Wang S, Zheng L, Wang X, Teng J, Ye F, Gui A, Xue J, Zheng P. Microbial Diversity and Characteristic Quality Formation of Qingzhuan Tea as Revealed by Metagenomic and Metabolomic Analysis during Pile Fermentation. Foods 2023; 12:3537. [PMID: 37835190 PMCID: PMC10572444 DOI: 10.3390/foods12193537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
In order to analyze the changes in the microbial community structure during the pile fermentation of Qingzhuan tea and their correlation with the formation of quality compounds in Qingzhuan tea, this study carried out metagenomic and metabolomic analyses of tea samples during the fermentation process of Qingzhuan tea. The changes in the expression and abundance of microorganisms during the pile fermentation were investigated through metagenomic assays. During the processing of Qingzhuan tea, there is a transition from a bacterial dominated ecosystem to an ecosystem enriched with fungi. The correlation analyses of metagenomics and metabolomics showed that amino acids and polyphenol metabolites with relatively simple structures exhibited a significant negative correlation with target microorganisms, while the structurally complicated B-ring dihydroxy puerin, B-ring trihydroxy galloyl puerlin, and other compounds showed a significant positive correlation with target microorganisms. Aspergillus niger, Aspergillus glaucus, Penicillium in the Aspergillaceae family, and Talaromyces and Rasamsonia emersonii in Trichocomaceae were the key microorganisms involved in the formation of the characteristic qualities of Qingzhuan tea.
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Affiliation(s)
- Lin Feng
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (L.F.); (S.G.); (P.L.); (S.W.); (L.Z.); (X.W.); (J.T.); (F.Y.); (A.G.); (J.X.)
- Key Laboratory of Tea Resources Comprehensive Utilization, Ministry of Agriculture and Rural Affairs, Hubei Tea Engineering and Technology Research Centre, Wuhan 430064, China
| | - Shiwei Gao
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (L.F.); (S.G.); (P.L.); (S.W.); (L.Z.); (X.W.); (J.T.); (F.Y.); (A.G.); (J.X.)
- Key Laboratory of Tea Resources Comprehensive Utilization, Ministry of Agriculture and Rural Affairs, Hubei Tea Engineering and Technology Research Centre, Wuhan 430064, China
| | - Panpan Liu
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (L.F.); (S.G.); (P.L.); (S.W.); (L.Z.); (X.W.); (J.T.); (F.Y.); (A.G.); (J.X.)
- Key Laboratory of Tea Resources Comprehensive Utilization, Ministry of Agriculture and Rural Affairs, Hubei Tea Engineering and Technology Research Centre, Wuhan 430064, China
| | - Shengpeng Wang
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (L.F.); (S.G.); (P.L.); (S.W.); (L.Z.); (X.W.); (J.T.); (F.Y.); (A.G.); (J.X.)
- Key Laboratory of Tea Resources Comprehensive Utilization, Ministry of Agriculture and Rural Affairs, Hubei Tea Engineering and Technology Research Centre, Wuhan 430064, China
| | - Lin Zheng
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (L.F.); (S.G.); (P.L.); (S.W.); (L.Z.); (X.W.); (J.T.); (F.Y.); (A.G.); (J.X.)
- Key Laboratory of Tea Resources Comprehensive Utilization, Ministry of Agriculture and Rural Affairs, Hubei Tea Engineering and Technology Research Centre, Wuhan 430064, China
| | - Xueping Wang
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (L.F.); (S.G.); (P.L.); (S.W.); (L.Z.); (X.W.); (J.T.); (F.Y.); (A.G.); (J.X.)
- Key Laboratory of Tea Resources Comprehensive Utilization, Ministry of Agriculture and Rural Affairs, Hubei Tea Engineering and Technology Research Centre, Wuhan 430064, China
| | - Jing Teng
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (L.F.); (S.G.); (P.L.); (S.W.); (L.Z.); (X.W.); (J.T.); (F.Y.); (A.G.); (J.X.)
- Key Laboratory of Tea Resources Comprehensive Utilization, Ministry of Agriculture and Rural Affairs, Hubei Tea Engineering and Technology Research Centre, Wuhan 430064, China
| | - Fei Ye
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (L.F.); (S.G.); (P.L.); (S.W.); (L.Z.); (X.W.); (J.T.); (F.Y.); (A.G.); (J.X.)
- Key Laboratory of Tea Resources Comprehensive Utilization, Ministry of Agriculture and Rural Affairs, Hubei Tea Engineering and Technology Research Centre, Wuhan 430064, China
| | - Anhui Gui
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (L.F.); (S.G.); (P.L.); (S.W.); (L.Z.); (X.W.); (J.T.); (F.Y.); (A.G.); (J.X.)
- Key Laboratory of Tea Resources Comprehensive Utilization, Ministry of Agriculture and Rural Affairs, Hubei Tea Engineering and Technology Research Centre, Wuhan 430064, China
| | - Jinjin Xue
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (L.F.); (S.G.); (P.L.); (S.W.); (L.Z.); (X.W.); (J.T.); (F.Y.); (A.G.); (J.X.)
- Key Laboratory of Tea Resources Comprehensive Utilization, Ministry of Agriculture and Rural Affairs, Hubei Tea Engineering and Technology Research Centre, Wuhan 430064, China
| | - Pengcheng Zheng
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (L.F.); (S.G.); (P.L.); (S.W.); (L.Z.); (X.W.); (J.T.); (F.Y.); (A.G.); (J.X.)
- Key Laboratory of Tea Resources Comprehensive Utilization, Ministry of Agriculture and Rural Affairs, Hubei Tea Engineering and Technology Research Centre, Wuhan 430064, China
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Paul AK, Lim CL, Apu MAI, Dolma KG, Gupta M, de Lourdes Pereira M, Wilairatana P, Rahmatullah M, Wiart C, Nissapatorn V. Are Fermented Foods Effective against Inflammatory Diseases? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2481. [PMID: 36767847 PMCID: PMC9915096 DOI: 10.3390/ijerph20032481] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 01/21/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Fermented foods have been used over the centuries in various parts of the world. These foods are rich in nutrients and are produced naturally using various biological tools like bacteria and fungi. Fermentation of edible foods has been rooted in ancient cultures to keep food for preservation and storage for a long period of time with desired or enhanced nutritional values. Inflammatory diseases like rheumatoid arthritis, osteoarthritis, and chronic inflammatory pain are chronic disorders that are difficult to treat, and current treatments for these disorders fail due to various adverse effects of prescribed medications over a long period of time. Fermented foods containing probiotic bacteria and fungi can enhance the immune system, improve gastrointestinal health, and lower the risk of developing various inflammatory diseases. Foods prepared from vegetables by fermentation, like kimchi, sauerkraut, soy-based foods, or turmeric, lack proper clinical and translational experimental studies. The current review has focused on the effectiveness of various fermented foods or drinks used over centuries against inflammation, arthritis, and oxidative stress. We also described potential limitations on the efficacies or usages of these fermented products to provide an overarching picture of the research field.
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Affiliation(s)
- Alok K. Paul
- School of Pharmacy and Pharmacology, University of Tasmania, Hobart, TAS 7001, Australia
| | - Chooi Ling Lim
- Division of Applied Biomedical Science and Biotechnology, School of Health Sciences, International Medical University, Kuala Lumpur 57000, Malaysia
| | - Md. Aminul Islam Apu
- Department of Nutrition and Hospitality Management, The University of Mississippi, Oxford, MS 38677, USA
| | - Karma G. Dolma
- Department of Microbiology, Sikkim Manipal Institute of Medical Sciences, Sikkim Manipal University, Gangtok 737102, India
| | - Madhu Gupta
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Re-search University, New Delhi 110017, India
| | - Maria de Lourdes Pereira
- CICECO-Aveiro Institute of Materials & Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Mohammed Rahmatullah
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Lalmatia, Dhaka 1207, Bangladesh
| | - Christophe Wiart
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University Malaysia Sabah, Kota Kinabalu 88400, Malaysia
| | - Veeranoot Nissapatorn
- School of Allied Health Sciences, World Union for Herbal Drug Discovery (WUHeDD), and Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat 80160, Thailand
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Nurmilah S, Cahyana Y, Utama GL. Metagenomics Analysis of the Polymeric and Monomeric Phenolic Dynamic Changes Related to the Indigenous Bacteria of Black Tea Spontaneous Fermentation. BIOTECHNOLOGY REPORTS 2022; 36:e00774. [DOI: 10.1016/j.btre.2022.e00774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/19/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
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Expression of citrinin biosynthesis gene in Liupao tea and effect of Penicillium citrinum on tea quality. Fungal Genet Biol 2022; 163:103742. [PMID: 36108886 DOI: 10.1016/j.fgb.2022.103742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/19/2022] [Accepted: 09/08/2022] [Indexed: 01/06/2023]
Abstract
Similar to Pu-erh tea, Liupao tea is a post-fermented tea that is produced through natural fermentation by microorganisms. Penicillium citrinum is involved in multiple production processes of Liupao tea that can produce citrinin, a secondary metabolite with renal toxicity; however, the effect of P. citrinum on the quality of Liupao tea has not been investigated yet. Citrinin production is regulated by approximately 16 biosynthesis genes. However, little is known about the genetic background of citrinin in the complex Liupao tea system. In the present study, we cultured P. citrinum on potato dextrose agar and Liupao tea powder media and analyzed the changes of its nutritional components in Liupao tea. We selected six citrinin biosynthesis genes identified in Monascus exhibiting homology and high sequence similarity to those in P. citrinum and further analyzed the expression of citrinin biosynthesis genes in Liupao tea and the changes in citrinin yield. The results showed that the changes in nutritional components of Liupao tea were closely related to the growth and metabolism of P. citrinum and the quality of the tea. Decreases in the contents of soluble sugars (from 10.29% to 9.58%), soluble pectins (from 3.71% to 3.13%), free amino acids (from 3.84% to 3.14%), and tea polyphenols (from 22.84% to 18.78%) were noted. The Spearman's correlation analysis indicated that P. citrinum growth can improve the tea quality to some extent. Quantitative real-time PCR demonstrated that ctnA gene was a positive regulator of citrinin production regardless of the culture medium used. ctnA and orf5 expressions greatly influenced the metabolism of citrinin by P. citrinum in Liupao tea. In conclusion, the citrinin biosynthesis genes, ctnA and orf5, may be the promising targets for developing strategies to control P. citrinum infection and citrinin biosynthesis in Liupao tea.
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Huang R, Yu H, Dong C, Shen L, Qin Y, Liu Y, Jiang J, Song Y. Correlations between microbial diversity, monomeric phenols, and biological parameters during spontaneous fermentation of Cabernet Sauvignon grapes obtained from rain-shelter cultivation. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Multi-omics approach in tea polyphenol research regarding tea plant growth, development and tea processing: current technologies and perspectives. FOOD SCIENCE AND HUMAN WELLNESS 2022. [DOI: 10.1016/j.fshw.2021.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Chen R, Lai X, Xiang L, Li Q, Sun L, Lai Z, Li Z, Zhang W, Wen S, Cao J, Sun S. Aged green tea reduces high-fat diet-induced fat accumulation and inflammation via activating the AMP-activated protein kinase signaling pathway. Food Nutr Res 2022; 66:7923. [PMID: 35382381 PMCID: PMC8941417 DOI: 10.29219/fnr.v66.7923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 11/30/2021] [Accepted: 01/04/2022] [Indexed: 02/06/2023] Open
Abstract
Background Obesity is a global public health concern and increases the risk of metabolic syndrome and other diseases. The anti-obesity effects of various plant-derived bioactive compounds, such as tea extracts, are well-established. The mechanisms underlying the anti-obesity activity of Jinxuan green tea (JXGT) from different storage years are still unclear. Objective The aim of this study was to evaluate the effects of JXGTs from three different years on the high fat diet (HFD)-fed mouse model. Design The mice were divided into six groups, the control group received normal diet and the obese model group received HFD. We analyzed the effects of JXGTs from 2005, 2008, and 2016 on HFD-fed obese mice over a period of 7 weeks. Results The JXGTs reduced the body weight of the obese mice, and also alleviated fat accumulation and hepatic steatosis. Mechanistically, JXGTs increased the phosphorylation of AMP-activated protein kinase (p-AMPK)/AMP-activated protein kinase (AMPK) ratio, up-regulated carnitine acyl transferase 1A (CPT-1A), and down-regulated fatty acid synthase (FAS), Glycogen synthase kinase-3beta (GSK-3β), Peroxisome proliferator-activated receptor-gamma co-activator-1alpha (PGC-1α), Interleukin 6 (IL-6), and Tumour necrosis factor alpha (TNFα). Thus, JXGTs can alleviate HFD-induced obesity by inhibiting lipid biosynthesis and inflammation, thereby promoting fatty acid oxidation via the AMPK pathway. Discussion The anti-obesity effect of three aged JXGTs were similar. However, JXGT2016 exhibited a more potent activation of AMPK, and JXGT2005 and JXGT2008 exhibited a more potent inhibiting glycogen synthase and inflammation effect. Furthermore, the polyphenol (–)-epicatechin (EC) showed the strongest positive correlation with the anti-obesity effect of JXGT. Conclusions These findings demonstrate that JXGT treatment has a potential protection on HFD-induced obesity mice via activating the AMPK/CPT-1A and down-regulating FAS/GSK-3β/PGC-1α and IL-6/TNFα. Our study results also revealed that different storage time would not affect the anti-obesity and anti-inflammation effect of JXGT. Graphical abstract
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Affiliation(s)
- Ruohong Chen
- Tea Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, China
| | - Xingfei Lai
- Tea Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, China
| | - Limin Xiang
- Tea Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, China
| | - Qiuhua Li
- Tea Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, China
| | - Lingli Sun
- Tea Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, China
| | - Zhaoxiang Lai
- Tea Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, China
| | - Zhigang Li
- Tea Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, China
| | - Wenji Zhang
- Tea Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, China
| | - Shuai Wen
- Tea Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, China
| | - Junxi Cao
- Tea Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, China
| | - Shili Sun
- Tea Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, China
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Identification of characteristic flavor and microorganisms related to flavor formation in fermented common carp (Cyprinus carpio L.). Food Res Int 2022; 155:111128. [DOI: 10.1016/j.foodres.2022.111128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 01/20/2023]
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Ojeda-Linares CI, Solís-García IA, Casas A. Constructing Micro-Landscapes: Management and Selection Practices on Microbial Communities in a Traditional Fermented Beverage. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.821268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Colonche is a traditional beverage produced in Mexico by the fermentation of fruits of several cacti species. In the Meridional Central Plateau region of Mexico, where this study was conducted, it is mainly produced with fruits of Opuntia streptacantha; there, the producers perform spontaneous fermentation and/or fermentations through inoculums. Several factors can change the microbial community structure and dynamics through the fermentation process, but little attention has been directed to evaluate what type and extent of change the human practices have over the microbial communities. This study aims to assess the microbiota under spontaneous and inoculated fermentation techniques, the microorganisms present in the inoculums and containers, and the changes of microbiota during the process of producing colonche with different techniques. We used next-generation sequencing of the V3-V4 regions of the 16S rRNA gene and the ITS2, to characterize bacterial and fungal diversity associated with the different fermentation techniques. We identified 701 bacterial and 203 fungal amplicon sequence variants (ASVs) belonging to 173 bacterial and 187 fungal genera. The alpha and beta diversity analysis confirmed that both types of fermentation practices displayed differences in richness, diversity, and community structure. Richness of bacteria in spontaneous fermentation (0D = 136 ± 0.433) was higher than in the inoculated samples (0D = 128 ± 0.929), while fungal richness in the inoculated samples (0D = 32 ± 0.539) was higher than in spontaneous samples (0D = 19 ± 0.917). We identified bacterial groups like Lactobacillus, Leuconostoc, Pediococcus and the Saccharomyces yeast shared in ferments managed with different practices; these organisms are commonly related to the quality of the fermentation process. We identified that clay pots, where spontaneous fermentation is carried out, have an outstanding diversity of fungal and bacterial richness involved in fermentation, being valuable reservoirs of microorganisms for future fermentations. The inoculums displayed the lowest richness and diversity of bacterial and fungal communities suggesting unconscious selection on specific microbial consortia. The beta diversity analysis identified an overlap in microbial communities for both types of fermentation practices, which might reflect a shared composition of microorganisms occurring in the Opuntia streptacantha substrate. The variation in the spontaneous bacterial community is consistent with alpha diversity data, while fungal communities showed less differences among treatments, probably due to the high abundance and dominance of Saccharomyces. This information illustrates how traditional management guides selection and may drive changes in the microbial consortia to produce unique fermented beverages through specific fermentation practices. Although further studies are needed to analyze more specifically the advantages of each fermentation type over the quality of the product, our current analysis supports the role of traditional knowledge driving it and the relevance of plans for its conservation.
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An T, Chen M, Zu Z, Chen Q, Lu H, Yue P, Gao X. Untargeted and targeted metabolomics reveal changes in the chemical constituents of instant dark tea during liquid-state fermentation by Eurotium cristatum. Food Res Int 2021; 148:110623. [PMID: 34507767 DOI: 10.1016/j.foodres.2021.110623] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 11/26/2022]
Abstract
Instant green tea powder was used as raw material to prepare an instant dark tea via liquid-state fermentation by Eurotium cristatum. To understand how the chemical constituents present in fermented green tea develop during fermentation, samples were collected on different days during fermentation for qualitative analyses by ultra-performance liquid chromatography-Q Exactive Orbitrap/Mass spectrometry. Untargeted metabolomics analyses revealed that the levels of original secondary metabolites in the instant green tea changed significantly from day 3 to day 5 during fermentation. Targeted metabolomics indicated that the levels of galloylated catechins (GCs) and free amino acids (FAAs) significantly decreased, but the nongalloylated catechins (NGCs), alkaloids, thearubigins and theabrownins increased dramatically after fermentation. The changes in the contents of catechins, gallic acid and free amino acids in the instant dark tea samples were positively related to the DPPH radical scavenging activities in vitro, and the phenolic acids and FAAs were positively related to the inhibitory effects towards α-glucosidase. These results showed that fermentation by Eurotium cristatum is critical to the formation of certain qualities of instant dark tea.
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Affiliation(s)
- Tingting An
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Food Nutrition and Safety, Anhui Engineering Laboratory for Agro-products Processing, School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Mengxue Chen
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Food Nutrition and Safety, Anhui Engineering Laboratory for Agro-products Processing, School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Zhongqi Zu
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Food Nutrition and Safety, Anhui Engineering Laboratory for Agro-products Processing, School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Qi Chen
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Food Nutrition and Safety, Anhui Engineering Laboratory for Agro-products Processing, School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Hengqian Lu
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China
| | - Pengxiang Yue
- Shandong Tailory Agriculture Technology Co., Ltd., Taian 271400, Shandong, China
| | - Xueling Gao
- State Key Laboratory of Tea Plant Biology and Utilization, Key Laboratory of Food Nutrition and Safety, Anhui Engineering Laboratory for Agro-products Processing, School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, Anhui, China.
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Pino-Otín MR, Langa E, Val J, Mainar AM, Ballestero D. Impact of citronellol on river and soil environments using non-target model organisms and natural populations. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 287:112303. [PMID: 33714735 DOI: 10.1016/j.jenvman.2021.112303] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
Citronellol is an acyclic monoterpenoid with a wide range of pharmacological activities (antibacterial, antifungal, anti-lice, repellent, lipolytic, anti-allergic, anti-inflammatory, antispasmodic, antidiabetic, anti-cholesterol, among other) and potential to replace synthetic products. However, the impact of citronellol on the environment remains unknown. We analysed, for the first time, the environmental impact of citronellol on river and soil environments using non-target model organisms and natural populations. The acute toxicity of citronellol on the aquatic invertebrate Daphnia magna, the plant Allium cepa L and the earthworm Eisenia fetida was quantified. The effect of citronellol in a river ecosystem was analysed using river periphyton communities taxonomically characterised and a river microbial community characterised through 16 S rRNA gene sequencing. Finally, a microbial community from natural soil was used to monitor the effect of citronellol on the soil ecosystem. The results showed that E. fetida was most sensitive to citronellol (LC50 = 12.34 mg/L), followed by D. magna (LC50 = 14.11 mg/L). Citronellol affected the photosynthesis of the fluvial periphyton (LC50 = 94.10 mg/L) and was phytotoxic for A. cepa. Furthermore, citronellol modified the growth and metabolism of both fluvial (LC50 = 0.19% v/v) and edaphic (LC50 = 5.07% v/v) bacterial populations. The metabolism of the microorganisms in the soil and water exposed to citronellol decreased with respect to the control, especially their ability to metabolise carbohydrates. Our results show that citronellol has a negative impact on the environment. Although acute effects cannot be expected, it is necessary to quantify the environmental levels as well as the long-term and persistent effects of this monoterpene.
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Affiliation(s)
| | - Elisa Langa
- Universidad San Jorge, Villanueva de Gállego, 50830, Zaragoza, Spain.
| | - Jonatan Val
- Universidad San Jorge, Villanueva de Gállego, 50830, Zaragoza, Spain.
| | - Ana M Mainar
- I3A, Universidad de Zaragoza, c/ Mariano Esquillor s/n, 50018, Zaragoza, Spain.
| | - Diego Ballestero
- Universidad San Jorge, Villanueva de Gállego, 50830, Zaragoza, Spain.
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Meng Q, Wang S, Niu Q, Yan H, Li Q. The influences of illite/smectite clay on lignocellulose decomposition and maturation process revealed by metagenomics analysis during cattle manure composting. WASTE MANAGEMENT (NEW YORK, N.Y.) 2021; 127:1-9. [PMID: 33910097 DOI: 10.1016/j.wasman.2021.04.033] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/21/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
The purpose of this study was to analyze the effects of illite/smectite clay (I/S) on lignocellulosic degradation and humification process via metagenomics analysis during cattle manure composting. The test group (TG) with 10% I/S and the reference group (RG) were established. The results indicated that the addition of I/S made the degradation rate of cellulose, hemicellulose and lignin in TG (1.56%, 29.01%, 19.95%) was higher than that in RG (1.16%, 17.24%, 13.14%). Compared with RG, the abundance values of AA2, AA10, GH1 and GH10 in TG increased by 15.18%, 29.28%, 31.08%, 21.65%, respectively. Meanwhile, humic substance (HS) content was increased by 3.49% and 7.16% during RG and TG composting. Furthermore, the microbial community in TG changed, in which the relative abundance of Actinobacteria increased and Proteobacteria decreased. Redundancy analysis (RDA) showed that the temperature was positively correlated with the abundance of AA2, AA10, GH1 and GH10, whereas the organic matter content was negatively correlated. Overall, adding I/S to the composting could stimulate microbial activity, promote the degradation of lignocellulose and humification process.
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Affiliation(s)
- Qingran Meng
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Susu Wang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Qiuqi Niu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Hailong Yan
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Qunliang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China.
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16
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Effects of Polyphenols in Tea (Camellia sinensis sp.) on the Modulation of Gut Microbiota in Human Trials and Animal Studies. GASTROENTEROLOGY INSIGHTS 2021. [DOI: 10.3390/gastroent12020018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A diet high in polyphenols is associated with a diversified gut microbiome. Tea is the second most consumed beverage in the world, after water. The health benefits of tea might be attributed to the presence of polyphenol compounds such as flavonoids (e.g., catechins and epicatechins), theaflavins, and tannins. Although many studies have been conducted on tea, little is known of its effects on the trillions of gut microbiota. Hence, this review aimed to systematically study the effect of tea polyphenols on the stimulation or suppression of gut microbiota in humans and animals. It was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol. Articles were retrieved from PubMed and Scopus databases, and data were extracted from 6 human trials and 15 animal studies. Overall, large variations were observed in terms of microbiota composition between humans and animals. A more consistent pattern of diversified microbiota was observed in animal studies. Tea alleviated the gut microbiota imbalance caused by high-fat diet-induced obesity, diabetes, and ultraviolet-induced damage. The overall changes in microbiota composition measured by beta diversity analysis showed that tea had shifted the microbiota from the pattern seen in animals that received tea-free intervention. In humans, a prebiotic-like effect was observed toward the gut microbiota, but these results appeared in lower-quality studies. The beta diversity in human microbiota remains intact despite tea intervention; supplementation with different teas affects different types of bacterial taxa in the gut. These studies suggest that tea polyphenols may have a prebiotic effect in disease-induced animals and in a limited number of human interventions. Further intervention is needed to identify the mechanisms of action underlying the effects of tea on gut microbiota.
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17
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Maske BL, de Melo Pereira GV, da Silva Vale A, Marques Souza DS, De Dea Lindner J, Soccol CR. Viruses in fermented foods: are they good or bad? Two sides of the same coin. Food Microbiol 2021; 98:103794. [PMID: 33875222 PMCID: PMC7992106 DOI: 10.1016/j.fm.2021.103794] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/21/2021] [Indexed: 12/23/2022]
Abstract
The emergence of Coronavirus disease 2019 as a global pandemic has increased popular concerns about diseases caused by viruses. Fermented foods containing high loads of viable fungi and bacteria are potential sources for virus contamination. The most common include viruses that infect bacteria (bacteriophage) and yeasts reported in fermented milks, sausages, vegetables, wine, sourdough, and cocoa beans. Recent molecular studies have also associated fermented foods as vehicles for pathogenic human viruses. Human noroviruses, rotavirus, and hepatitis virus have been identified in different fermented foods through multiple routes. No severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) virus or close members were found in fermented foods to date. However, the occurrence/persistence of other pathogenic viruses reveals a potential vulnerability of fermented foods to SARS-CoV-2 contamination. On the other side of the coin, some bacteriophages are being suggested for improving the fermentation process and food safety, as well as owing potential probiotic properties in modern fermented foods. This review will address the diversity and characteristics of viruses associated with fermented foods and what has been changed after a short introduction to the most common next-generation sequencing platforms. Also, the risk of SARS-CoV-2 transmission via fermented foods and preventive measures will be discussed.
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Affiliation(s)
- Bruna Leal Maske
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | | | - Alexander da Silva Vale
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Doris Sobral Marques Souza
- Department of Food Science and Technology, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil; Applied Virology Laboratory, UFSC, Florianópolis, SC, Brazil
| | - Juliano De Dea Lindner
- Department of Food Science and Technology, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Carlos Ricardo Soccol
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
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Balkir P, Kemahlioglu K, Yucel U. Foodomics: A new approach in food quality and safety. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2020.11.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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19
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Leech J, Cabrera-Rubio R, Walsh AM, Macori G, Walsh CJ, Barton W, Finnegan L, Crispie F, O'Sullivan O, Claesson MJ, Cotter PD. Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants. mSystems 2020; 5:e00522-20. [PMID: 33172966 PMCID: PMC7657593 DOI: 10.1128/msystems.00522-20] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
Fermented foods have been the focus of ever greater interest as a consequence of purported health benefits. Indeed, it has been suggested that consumption of these foods helps to address the negative consequences of "industrialization" of the human gut microbiota in Western society. However, as the mechanisms via which the microbes in fermented foods improve health are not understood, it is necessary to develop an understanding of the composition and functionality of the fermented-food microbiota to better harness desirable traits. Here, we considerably expand the understanding of fermented-food microbiomes by employing shotgun metagenomic sequencing to provide a comprehensive insight into the microbial composition, diversity, and functional potential (including antimicrobial resistance and carbohydrate-degrading and health-associated gene content) of a diverse range of 58 fermented foods from artisanal producers from a number of countries. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity. From the combined data set, 127 high-quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species of Acetobacter, Acidisphaera, Gluconobacter, Companilactobacillus, Leuconostoc, and Rouxiella, were generated. Potential health promoting attributes were more common in fermented foods than nonfermented equivalents, with water kefirs, sauerkrauts, and kvasses containing the greatest numbers of potentially health-associated gene clusters. Ultimately, this study provides the most comprehensive insight into the microbiomes of fermented foods to date and yields novel information regarding their relative health-promoting potential.IMPORTANCE Fermented foods are regaining popularity worldwide due in part to a greater appreciation of the health benefits of these foods and the associated microorganisms. Here, we use state-of-the-art approaches to explore the microbiomes of 58 of these foods, identifying the factors that drive the microbial composition of these foods and potential functional benefits associated with these populations. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity and, notably, potential health promoting attributes were more common in fermented foods than nonfermented equivalents. The information provided here will provide significant opportunities for the further optimization of fermented-food production and the harnessing of their health-promoting potential.
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Affiliation(s)
- John Leech
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | - Guerrino Macori
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Calum J Walsh
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Wiley Barton
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
| | - Laura Finnegan
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Orla O'Sullivan
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Marcus J Claesson
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
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20
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Zhou B, Ma C, Ren X, Xia T, Zheng C, Liu X. Correlation analysis between filamentous fungi and chemical compositions in a pu-erh type tea after a long-term storage. Food Sci Nutr 2020; 8:2501-2511. [PMID: 32405406 PMCID: PMC7215201 DOI: 10.1002/fsn3.1543] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/03/2020] [Accepted: 03/09/2020] [Indexed: 01/11/2023] Open
Abstract
Storage environment caused the difference between Jinhua Pu-erh tea (JPT) and General Pu-erh tea. In this study, fungal flora and chemical compositions were analyzed. The results showed that storage environment caused significant (p < .05) differences of theaflavins (TF), theabrownins (TB), tea polyphenols (TP), and water-soluble sugars (WSS), and a highly significant (p < .01) difference of thearubigins (TR). Aspergillus niger, Aspergillus pallidofulvus, Aspergillus sesamicola, Penicillium manginii, and Aspergillus tamarii were isolated from Pu-erh teas and identified based on colony characteristics and ITS, β-tubulin, and calmodulin gene sequences, respectively. A. pallidofulvus, A. sesamicola, and P. manginii were dominant fungi in JPT and generated macroscopic yellow cleistothecia after a long-term storage. Correlation analysis showed that dominant fungi exhibited significantly (p < .05 or p < .01) positive or negative corrections with TF, TB, TP, WSS, TR, and gallic acid. This study revealed dominant fungi including A. pallidofulvus, A. sesamicola, and P. manginii and their effects on given chemical compositions.
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Affiliation(s)
- Binxing Zhou
- College of Long Run Pu‐erh TeaYunnan Agricultural UniversityKunmingChina
| | - Cunqiang Ma
- College of Long Run Pu‐erh TeaYunnan Agricultural UniversityKunmingChina
- Kunming Dapu Tea CO., LTDKunmingChina
| | - Xiaoying Ren
- College of Long Run Pu‐erh TeaYunnan Agricultural UniversityKunmingChina
- Liaocheng Senior Financial Vocational SchoolLiaochengChina
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefeiChina
| | - Chengqin Zheng
- College of Long Run Pu‐erh TeaYunnan Agricultural UniversityKunmingChina
| | - Xiaohui Liu
- College of Long Run Pu‐erh TeaYunnan Agricultural UniversityKunmingChina
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21
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Microbial bioconversion of the chemical components in dark tea. Food Chem 2020; 312:126043. [PMID: 31896450 DOI: 10.1016/j.foodchem.2019.126043] [Citation(s) in RCA: 185] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/26/2019] [Accepted: 12/09/2019] [Indexed: 02/06/2023]
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22
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Xue J, Yang L, Yang Y, Yan J, Ye Y, Hu C, Meng Y. Contrasting microbiomes of raw and ripened Pu-erh tea associated with distinct chemical profiles. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109147] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Li Z, Huang L, Xia N, Teng J, Wei B, Peng D. Amount of
Eurotium
sp. in Chinese Liupao tea and its relationship with tea quality. J Appl Microbiol 2020; 128:1658-1668. [DOI: 10.1111/jam.14589] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 01/03/2020] [Accepted: 01/06/2020] [Indexed: 01/07/2023]
Affiliation(s)
- Z. Li
- Institute of Light Industry and Food Engineering Guangxi University Nanning China
| | - Li Huang
- Institute of Light Industry and Food Engineering Guangxi University Nanning China
| | - N. Xia
- Institute of Light Industry and Food Engineering Guangxi University Nanning China
| | - J. Teng
- Institute of Light Industry and Food Engineering Guangxi University Nanning China
| | - B. Wei
- Institute of Light Industry and Food Engineering Guangxi University Nanning China
| | - D. Peng
- Institute of Light Industry and Food Engineering Guangxi University Nanning China
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LIU XF, LIU CJ, ZENG XQ, ZHANG HY, LUO YY, LI XR. Metagenomic and metatranscriptomic analysis of the microbial community structure and metabolic potential of fermented soybean in Yunnan Province. FOOD SCIENCE AND TECHNOLOGY 2020. [DOI: 10.1590/fst.01718] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Xiao-Feng LIU
- Kunming University of Science and Technology, China; Chinese Academy of Agricultural Sciences, China
| | | | - Xue-Qin ZENG
- Kunming University of Science and Technology, China
| | | | - Yi-Yong LUO
- Kunming University of Science and Technology, China
| | - Xiao-Ran LI
- Kunming University of Science and Technology, China
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25
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Production of theophylline via aerobic fermentation of pu-erh tea using tea-derived fungi. BMC Microbiol 2019; 19:261. [PMID: 31771506 PMCID: PMC6878699 DOI: 10.1186/s12866-019-1640-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 11/14/2019] [Indexed: 11/21/2022] Open
Abstract
Background Caffeine is one of the most abundant methylxanthines in tea, and it remains stable in processing of general teas. In the secondary metabolism of microorganism, theophylline is the main conversion product in caffeine catabolism through demethylation. Microorganisms, involved in the solid-state fermentation of pu-erh tea, have a certain impact on caffeine level. Inoculating an appropriate starter strain that is able to convert caffeine to theophylline would be an alternative way to obtain theophylline in tea. The purpose of this study was to isolate and identify the effective strain converting caffeine to theophylline in pu-erh tea, and discuss the optimal conditions for theophylline production. Results Caffeine content was decreased significantly (p < 0.05) and theophylline content was increased significantly (p < 0.05) during the aerobic fermentation of pu-erh tea. Five dominant fungi were isolated from the aerobic fermentation and identified as Aspergillus niger, Aspergillus sydowii, Aspergillus pallidofulvus, Aspergillus sesamicola and Penicillium mangini, respectively. Especially, A. pallidofulvus, A. sesamicola and P. mangini were detected in pu-erh tea for the first time. All isolates except A. sydowii TET-2, enhanced caffeine content and had no significant influence on theophylline content. In the aerobic fermentation of A. sydowii TET-2, 28.8 mg/g of caffeine was degraded, 93.18% of degraded caffeine was converted to theophylline, and 24.60 mg/g of theophylline was produced. A. sydowii PET-2 could convert caffeine to theophylline significantly, and had application potential in the production of theophylline. The optimum conditions of theophylline production in the aerobic fermentation were 1) initial moisture content of 35% (w/w), 2) inoculation quantity of 8%, and 3) incubation temperature at 35 °C. Conclusions For the first time, we find that A. sydowii PET-2 could convert caffeine to theophylline, and has the potential value in theophylline production through aerobic fermentation.
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Weckx S, Van Kerrebroeck S, De Vuyst L. Omics approaches to understand sourdough fermentation processes. Int J Food Microbiol 2019; 302:90-102. [DOI: 10.1016/j.ijfoodmicro.2018.05.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 05/12/2018] [Accepted: 05/28/2018] [Indexed: 12/31/2022]
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27
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Verce M, De Vuyst L, Weckx S. Shotgun Metagenomics of a Water Kefir Fermentation Ecosystem Reveals a Novel Oenococcus Species. Front Microbiol 2019; 10:479. [PMID: 30918501 PMCID: PMC6424877 DOI: 10.3389/fmicb.2019.00479] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/25/2019] [Indexed: 12/29/2022] Open
Abstract
Water kefir is a fruity, sour, slightly alcoholic and carbonated beverage, which is made by fermentation of an aqueous sucrose solution in the presence of dried figs and water kefir grains. These polysaccharide grains contain lactic acid bacteria (LAB), yeasts, and sometimes bifidobacteria and/or acetic acid bacteria, which consume sucrose to produce exopolysaccharides, lactic acid, acetic acid, ethanol, and carbon dioxide. Shotgun metagenomic sequencing was used to examine the microbial species diversity present at two time points during water kefir fermentation in detail, both in the water kefir liquor and on the water kefir grains, hence representing four samples. Lactobacillus harbinensis, Lactobacillus hilgardii, Lactobacillus nagelii, Lactobacillus paracasei, and a Lactobacillus species similar to Lactobacillus hordei/mali were present in the water kefir examined, along with Bifidobacterium aquikefiri and two yeast species, namely Saccharomyces cerevisiae and Dekkera bruxellensis. In addition, evidence for a novel Oenococcus species related to Oenococcus oeni and Oenococcus kitaharae was found. Its genome was derived from the metagenome and made available under the name of Candidatus Oenococcus aquikefiri. Through functional analysis of the four metagenomic data sets, it was possible to link the production of lactic acid, acetic acid, ethanol, and carbon dioxide to subgroups of the microbial species found. In particular, the production of mannitol from fructose was linked to L. hilgardii, Candidatus O. aquikefiri, and B. aquikefiri, whereas glycerol production was associated with S. cerevisiae. Also, there were indications of cross-feeding, for instance in the case of amino acid supply. Few bacterial species could synthesize a limited number of cofactors, making them reliant on the figs or S. cerevisiae. The LAB species in turn were found to be capable of contributing to water kefir grain growth, as dextransucrase-encoding genes were attributed to L. hilgardii, L. hordei/mali, and Candidatus O. aquikefiri.
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Affiliation(s)
- Marko Verce
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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Pan SA, Sun Y, Li M, Deng WW, Zhang ZZ. Guanine deaminase provides evidence of the increased caffeine content during the piling process of pu'erh tea. RSC Adv 2019; 9:36136-36143. [PMID: 35540571 PMCID: PMC9075041 DOI: 10.1039/c9ra05655f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/31/2019] [Indexed: 12/17/2022] Open
Abstract
Wet piling is a key process for producing pu'erh tea because various components change under the action of microorganisms. Among these components, caffeine content is increased. Evidence has indicated a salvage pathway for caffeine biosynthesis in microbes, in which xanthine is methylated in the order of N-3 → N-1 → N-7. In addition, guanine can be used to synthesize xanthine through guanine deaminase (EC: 3.5.4.3). In this study, we investigated the variation in caffeine content during piling fermentation with supplementary guanine, 15N-labeled guanine and xanthine. We cloned the guanine deaminase gene (GUD1) from Saccharomyces cerevisiae (one dominant strain in piling fermentation). The results revealed that [15N]xanthine could be synthesized from [15N]guanine, and [15N]caffeine was also detected during piling with supplementary [15N]xanthine. Furthermore, ScGUD1 could catalyze the conversion of guanine to xanthine, which is likely to be methylated for caffeine synthesis under microorganism action. The obtained results revealed the mechanism underlying the increased caffeine content during piling of pu'erh tea. Wet piling is a key process for producing pu'erh tea because various components change under the action of microorganisms.![]()
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Affiliation(s)
- Si-an Pan
- State Key Laboratory of Tea Plant Biology and Utilization
- Anhui Agricultural University
- Hefei
- China
| | - Ying Sun
- State Key Laboratory of Tea Plant Biology and Utilization
- Anhui Agricultural University
- Hefei
- China
| | - Mengmeng Li
- State Key Laboratory of Tea Plant Biology and Utilization
- Anhui Agricultural University
- Hefei
- China
| | - Wei-Wei Deng
- State Key Laboratory of Tea Plant Biology and Utilization
- Anhui Agricultural University
- Hefei
- China
| | - Zheng-Zhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization
- Anhui Agricultural University
- Hefei
- China
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Revealing the influence of microbiota on the quality of Pu-erh tea during fermentation process by shotgun metagenomic and metabolomic analysis. Food Microbiol 2018; 76:405-415. [DOI: 10.1016/j.fm.2018.07.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 06/27/2018] [Accepted: 07/01/2018] [Indexed: 11/17/2022]
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Munir S, He P, Wu Y, He P, Khan S, Huang M, Cui W, He P, He Y. Huanglongbing Control: Perhaps the End of the Beginning. MICROBIAL ECOLOGY 2018; 76:192-204. [PMID: 29196843 DOI: 10.1007/s00248-017-1123-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/23/2017] [Indexed: 05/25/2023]
Abstract
Huanglongbing (HLB) is one of the most destructive citrus plant diseases worldwide. It is associated with the fastidious phloem-limited α-proteobacteria 'Candidatus Liberibacter asiaticus', 'Ca. Liberibacter africanus' and 'Ca. Liberibacter americanus'. In recent years, HLB-associated Liberibacters have extended to North and South America. The causal agents of HLB have been putatively identified, and their transmission pathways and worldwide population structure have been extensively studied. However, very little is known about the epidemiologic relationships of Ca. L. asiaticus, which has limited the scope of HLB research and especially the development of control strategies. HLB-affected plants produce damaged fruits and die within several years. To control the disease, scientists have developed new compounds and screened existing compounds for their antibiotic and antimicrobial activities against the disease. These compounds, however, have very little or even no effect on the disease. The aim of the present review was to compile and compare different methods of HLB disease control with newly developed integrative strategies. In light of recent studies, we also describe how to control the vectors of this disease and the biological control of other citrus plant pathogens. This work could steer the attention of scientists towards integrative control strategies.
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Affiliation(s)
- Shahzad Munir
- Faculty of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Pengfei He
- Faculty of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Yixin Wu
- Faculty of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Pengbo He
- Faculty of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Sehroon Khan
- World Agroforestry Centre, East and Central Asia, 132 Lanhei Rd, Heilongtan, Kunming, Yunnan, 650201, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Min Huang
- Faculty of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Agriculture College and Urban Modern Agriculture Engineering Research Center, Kunming University, Kunming, 650214, China
| | - Wenyan Cui
- Faculty of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Pengjie He
- Faculty of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Yueqiu He
- Faculty of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
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Zhou B, Ma C, Wang H, Xia T. Biodegradation of caffeine by whole cells of tea-derived fungi Aspergillus sydowii, Aspergillus niger and optimization for caffeine degradation. BMC Microbiol 2018; 18:53. [PMID: 29866035 PMCID: PMC5987490 DOI: 10.1186/s12866-018-1194-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 05/23/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pu-erh tea is a traditional Chinese tea and produced by natural solid-state fermentation. Several studies show that the natural microbiota influence caffeine level in pu-erh tea. Our previous research also found that the caffeine declined significantly (p < 0.05) in the fermentation, which suggested that the caffeine level could be influenced by specific strains. The purpose of this study was to isolate and identify microorganisms for caffeine degradation, and this research explored the degradation products from caffeine and optimal condition for caffeine degradation. RESULTS 11 Fungi were isolated from pu-erh tea fermentation and 7 strains could survive in caffeine solid medium. Two superior strains were identified as Aspergillus niger NCBT110A and Aspergillus sydowii NRRL250 by molecular identification. In the substrate tests with caffeine, A. niger NCBT110A could use caffeine as a potential carbon source while glucose is absent, A. sydowii NRRL250 could degrade 600 mg/L caffeine completely in a liquid medium. During the degradation product analysis of A. sydowii NRRL250, theophylline and 3-methlxanthine were detected, and the level of theophylline and 3-methlxanthine increased significantly (p < 0.05) with the degradation of caffeine. The single factor analysis showed that the optimum conditions of caffeine degradation were 1) substrate concentration of 1200 mg/L, 2) reaction temperature at 30 °C, and 3) pH of 6. In the submerged fermentation of tea infusion by A. sydowii NRRL250, 985.1 mg/L of caffeine was degraded, and 501.2 mg/L of theophylline was produced. CONCLUSIONS Results from this research indicate that Aspergillus sydowii NRRL250 was an effective strain to degrade caffeine. And theophylline and 3-methlxanthine were the main caffeine degradation products.
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Affiliation(s)
- Binxing Zhou
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China. .,College of Long Run Pu-erh Tea, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
| | - Cunqiang Ma
- Henan Key Laboratory of Tea Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University, Xinyang, 464000, Henan, China. .,College of Long Run Pu-erh Tea, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
| | - Hongzhen Wang
- College of Long Run Pu-erh Tea, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China.
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Li H, Li M, Yang X, Gui X, Chen G, Chu J, He X, Wang W, Han F, Li P. Microbial diversity and component variation in Xiaguan Tuo Tea during pile fermentation. PLoS One 2018; 13:e0190318. [PMID: 29462204 PMCID: PMC5819769 DOI: 10.1371/journal.pone.0190318] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/12/2017] [Indexed: 11/29/2022] Open
Abstract
Xiaguan Tuo Tea is largely consumed by the Chinese, but there is little research into the microbial diversity and component changes during the fermentation of this tea. In this study, we first used fluorescence in situ hybridization (FISH), next-generation sequencing (NGS) and chemical analysis methods to determine the microbial abundance and diversity and the chemical composition during fermentation. The FISH results showed that the total number of microorganisms ranges from 2.3×102 to 4.0×108 cells per gram of sample during fermentation and is mainly dominated by fungi. In the early fermentation stages, molds are dominant (0.6×102~2.8×106 cells/g, 0~35 d). However, in the late stages of fermentation, yeasts are dominant (3.6×104~9.6×106 cells/g, 35~56 d). The bacteria have little effect during the fermentation of tea (102~103 cells/g, <1% of fungus values). Of these fungi, A. niger (Aspergillus niger) and B. adeninivorans (Blastobotrys adeninivorans) are identified as the two most common strains, based on Next-generation Sequencing (NGS) analysis. Peak diversity in tea was observed at day 35 of fermentation (Shannon–Weaver index: 1.195857), and lower diversity was observed on days 6 and 56 of fermentation (Shannon–Weaver index 0.860589 and 1.119106, respectively). During the microbial fermentation, compared to the unfermented tea, the tea polyphenol content decreased by 54%, and the caffeine content increased by 59%. Theanine and free amino acid contents were reduced during fermentation by 81.1 and 92.85%, respectively.
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Affiliation(s)
- Haizhou Li
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Min Li
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xinrui Yang
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xin Gui
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Guofeng Chen
- Yunnan Xiaguan Tuo Tea (Group) Co., Ltd, Dali, Yunnan, China
| | - Jiuyun Chu
- Yunnan Xiaguan Tuo Tea (Group) Co., Ltd, Dali, Yunnan, China
| | - Xingwang He
- Yunnan Xiaguan Tuo Tea (Group) Co., Ltd, Dali, Yunnan, China
| | - Weitao Wang
- Yunnan Xiaguan Tuo Tea (Group) Co., Ltd, Dali, Yunnan, China
| | - Feng Han
- College of Architecture and Urban Planning, Tongji University, Shanghai, China
| | - Ping Li
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- * E-mail:
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Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas. BMC SYSTEMS BIOLOGY 2017; 11:131. [PMID: 29322917 PMCID: PMC5763296 DOI: 10.1186/s12918-017-0503-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Anti-microbial peptides (AMPs), naturally encoded by genes and generally containing 12–100 amino acids, are crucial components of the innate immune system and can protect the host from various pathogenic bacteria and viruses. In recent years, the widespread use of antibiotics has resulted in the rapid growth of antibiotic-resistant microorganisms that often induce critical infection and pathogenesis. Recently, the advent of high-throughput technologies has led molecular biology into a data surge in both the amount and scope of data. For instance, next-generation sequencing technology has been applied to generate large-scale sequencing reads from foods, water, soil, air, and specimens to identify microbiota and their functions based on metagenomics and metatranscriptomics, respectively. In addition, oolong tea is partially fermented and is the most widely produced tea in Taiwan. Many studies have shown the benefits of oolong tea in inhibiting obesity, reducing dental plaque deposition, antagonizing allergic immune responses, and alleviating the effects of aging. However, the microbes and their functions present in oolong tea remain unknown. Results To understand the relationship between Taiwanese oolong teas and bacterial communities, we designed a novel bioinformatics scheme to identify AMPs and their functional types based on metagenomics and metatranscriptomic analysis of high-throughput transcriptome data. Four types of oolong teas (Dayuling tea, Alishan tea, Jinxuan tea, and Oriental Beauty tea) were subjected to 16S ribosomal DNA and total RNA extraction and sequencing. Metagenomics analysis results revealed that Oriental Beauty tea exhibited greater bacterial diversity than other teas. The most common bacterial families across all tea types were Bacteroidaceae (21.7%), Veillonellaceae (22%), and Fusobacteriaceae (12.3%). Metatranscriptomics analysis results revealed that the dominant bacteria species across all tea types were Escherichia coli, Bacillus subtilis, and Chryseobacterium sp. StRB126, which were subjected to further functional analysis. A total of 8194 (6.5%), 26,220 (6.1%), 5703 (5.8%), and 106,183 (7.8%) reads could be mapped to AMPs. Conclusion We found that the distribution of anti-gram-positive and anti-gram-negative AMPs is highly correlated with the distribution of gram-positive and gram-negative bacteria in Taiwanese oolong tea samples. Electronic supplementary material The online version of this article (10.1186/s12918-017-0503-4) contains supplementary material, which is available to authorized users.
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He GQ, Liu TJ, Sadiq FA, Gu JS, Zhang GH. Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches. J Zhejiang Univ Sci B 2017; 18:289-302. [PMID: 28378567 DOI: 10.1631/jzus.b1600148] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Chinese traditional fermented foods have a very long history dating back thousands of years and have become an indispensable part of Chinese dietary culture. A plethora of research has been conducted to unravel the composition and dynamics of microbial consortia associated with Chinese traditional fermented foods using culture-dependent as well as culture-independent methods, like different high-throughput sequencing (HTS) techniques. These HTS techniques enable us to understand the relationship between a food product and its microbes to a greater extent than ever before. Considering the importance of Chinese traditional fermented products, the objective of this paper is to review the diversity and dynamics of microbiota in Chinese traditional fermented foods revealed by HTS approaches.
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Affiliation(s)
- Guo-Qing He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Tong-Jie Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Faizan A Sadiq
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Jing-Si Gu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Guo-Hua Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
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Chen G, Chen C, Lei Z. Meta-omics insights in the microbial community profiling and functional characterization of fermented foods. Trends Food Sci Technol 2017. [DOI: 10.1016/j.tifs.2017.05.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Microbial Succession and the Dynamics of Chemical Compounds during the Solid-State Fermentation of Pu-erh Tea. APPLIED SCIENCES-BASEL 2017. [DOI: 10.3390/app7020166] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Assessment of bacterial superficial contamination in classical or ritually slaughtered cattle using metagenetics and microbiological analysis. Int J Food Microbiol 2016; 247:79-86. [PMID: 27756497 DOI: 10.1016/j.ijfoodmicro.2016.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 09/09/2016] [Accepted: 10/10/2016] [Indexed: 12/21/2022]
Abstract
The aim of this study was to investigate the influence of the slaughter technique (Halal vs Classical slaughter) on the superficial contamination of cattle carcasses, by using traditional microbiological procedures and 16S rDNA metagenetics. The purpose was also to investigate the neck area to identify bacteria originating from the digestive or the respiratory tract. Twenty bovine carcasses (10 from each group) were swabbed at the slaughterhouse, where both slaughtering methods are practiced. Two swabbing areas were chosen: one "legal" zone of 1600cm2 (composed of zones from rump, flank, brisket and forelimb) and locally on the neck area (200cm2). Samples were submitted to classical microbiology for aerobic Total Viable Counts (TVC) at 30°C and Enterobacteriaceae counts, while metagenetic analysis was performed on the same samples. The classical microbiological results revealed no significant differences between both slaughtering practices; with values between 3.95 and 4.87log CFU/100cm2 and 0.49 and 1.94log CFU/100cm2, for TVC and Enterobacteriaceae respectively. Analysis of pyrosequencing data showed that differences in the bacterial population abundance between slaughtering methods were mainly observed in the "legal" swabbing zone compared to the neck area. Bacterial genera belonging to the Actinobacteria phylum were more abundant in the "legal" swabbing zone in "Halal" samples, while Brevibacterium and Corynebacterium were encountered more in "Halal" samples, in all swabbing areas. This was also the case for Firmicutes bacterial populations (families of Aerococcaceae, Planococcaceae). Except for Planococcoceae, the analysis of Operational Taxonomic Unit (OTU) abundances of bacteria from the digestive or respiratory tract revealed no differences between groups. In conclusion, the slaughtering method does not influence the superficial microbiological pattern in terms of specific microbiological markers of the digestive or respiratory tract. However, precise analysis of taxonomy at the genus level taxonomy highlights differences between swabbing areas. Although not clearly proven in this study, differences in hygiene practices used during both slaughtering protocols could explain the differences in contamination between carcasses from both slaughtering groups.
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High-throughput sequencing-based analysis of endogenetic fungal communities inhabiting the Chinese Cordyceps reveals unexpectedly high fungal diversity. Sci Rep 2016; 6:33437. [PMID: 27625176 PMCID: PMC5022047 DOI: 10.1038/srep33437] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/26/2016] [Indexed: 11/23/2022] Open
Abstract
Chinese Cordyceps, known in Chinese as “DongChong XiaCao”, is a parasitic complex of a fungus (Ophiocordyceps sinensis) and a caterpillar. The current study explored the endogenetic fungal communities inhabiting Chinese Cordyceps. Samples were collected from five different geographical regions of Qinghai and Tibet, and the nuclear ribosomal internal transcribed spacer-1 sequences from each sample were obtained using Illumina high-throughput sequencing. The results showed that Ascomycota was the dominant fungal phylum in Chinese Cordyceps and its soil microhabitat from different sampling regions. Among the Ascomycota, 65 genera were identified, and the abundant operational taxonomic units showed the strongest sequence similarity to Ophiocordyceps, Verticillium, Pseudallescheria, Candida and Ilyonectria Not surprisingly, the genus Ophiocordyceps was the largest among the fungal communities identified in the fruiting bodies and external mycelial cortices of Chinese Cordyceps. In addition, fungal communities in the soil microhabitats were clustered separately from the external mycelial cortices and fruiting bodies of Chinese Cordyceps from different sampling regions. There was no significant structural difference in the fungal communities between the fruiting bodies and external mycelial cortices of Chinese Cordyceps. This study revealed an unexpectedly high diversity of fungal communities inhabiting the Chinese Cordyceps and its microhabitats.
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Zhang Y, Skaar I, Sulyok M, Liu X, Rao M, Taylor JW. The Microbiome and Metabolites in Fermented Pu-erh Tea as Revealed by High-Throughput Sequencing and Quantitative Multiplex Metabolite Analysis. PLoS One 2016; 11:e0157847. [PMID: 27337135 PMCID: PMC4918958 DOI: 10.1371/journal.pone.0157847] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/06/2016] [Indexed: 01/01/2023] Open
Abstract
Pu-erh is a tea produced in Yunnan, China by microbial fermentation of fresh Camellia sinensis leaves by two processes, the traditional raw fermentation and the faster, ripened fermentation. We characterized fungal and bacterial communities in leaves and both Pu-erhs by high-throughput, rDNA-amplicon sequencing and we characterized the profile of bioactive extrolite mycotoxins in Pu-erh teas by quantitative liquid chromatography-tandem mass spectrometry. We identified 390 fungal and 629 bacterial OTUs from leaves and both Pu-erhs. Major findings are: 1) fungal diversity drops and bacterial diversity rises due to raw or ripened fermentation, 2) fungal and bacterial community composition changes significantly between fresh leaves and both raw and ripened Pu-erh, 3) aging causes significant changes in the microbial community of raw, but not ripened, Pu-erh, and, 4) ripened and well-aged raw Pu-erh have similar microbial communities that are distinct from those of young, raw Ph-erh tea. Twenty-five toxic metabolites, mainly of fungal origin, were detected, with patulin and asperglaucide dominating and at levels supporting the Chinese custom of discarding the first preparation of Pu-erh and using the wet tea to then brew a pot for consumption.
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Affiliation(s)
- Yongjie Zhang
- School of Life Sciences, Shanxi University, Taiyuan, Shanxi, China
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Ida Skaar
- Section of Mycology, Norwegian Veterinary Institute, Oslo, Norway
| | - Michael Sulyok
- Center for Analytical Chemistry, Department of Agrobiotechnology, University of Natural Resources and Life Sciences, Tulln, Austria
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Mingyong Rao
- Bureau of Culture and Sports, Puer, Yunnan, China
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- * E-mail:
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Yang C, Powell CA, Duan Y, Shatters R, Fang J, Zhang M. Deciphering the Bacterial Microbiome in Huanglongbing-Affected Citrus Treated with Thermotherapy and Sulfonamide Antibiotics. PLoS One 2016; 11:e0155472. [PMID: 27171468 PMCID: PMC4865244 DOI: 10.1371/journal.pone.0155472] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/26/2016] [Indexed: 11/23/2022] Open
Abstract
Huanglongbing (HLB) is a serious citrus disease that threatens the citrus industry. In previous studies, sulfonamide antibiotics and heat treatment suppressed ‘Candidatus Liberibacter asiaticus’ (Las), but did not completely eliminate the Las. Furthermore, there are few reports studying the bacterial microbiome of HLB-affected citrus treated by heat and sulfonamide antibiotics. In this study, combinations of heat (45°C or 40°C) and sulfonamide treatment (sulfathiazole sodium–STZ, or sulfadimethoxine sodium—SDX) were applied to HLB-affected citrus. The bacterial microbiome of HLB-affected citrus following thermotherapy and/or chemotherapy was characterized by PhyloChipTMG3-based metagenomics. Our results showed that the combination of thermotherapy at 45°C and chemotherapy with STZ and SDX was more effective against HLB than thermotherapy alone, chemotherapy alone, or a combination of thermotherapy at 40°C and chemotherapy. The PhyloChipTMG3-based results indicated that 311 empirical Operational Taxonomic Units (eOTUs) were detected in 26 phyla. Cyanobacteria (18.01%) were dominant after thermo-chemotherapy. Thermotherapy at 45°C decreased eOTUs (64.43%) in leaf samples, compared with thermotherapy at 40°C (73.96%) or without thermotherapy (90.68%) and it also reduced bacterial family biodiversity. The eOTU in phylum Proteobacteria was reduced significantly and eOTU_28, representing “Candidatus Liberibacter,” was not detected following thermotherapy at 45°C. Following antibiotic treatment with SDX and STZ, there was enhanced abundance of specific eOTUs belonging to the families Streptomycetaceae, Desulfobacteraceae, Chitinophagaceae, and Xanthomonadaceae, which may be implicated in increased resistance to plant pathogens. Our study further develops an integrated strategy for combating HLB, and also provides new insight into the bacterial microbiome of HLB-affected citrus treated by heat and sulfonamide antibiotics.
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Affiliation(s)
- Chuanyu Yang
- State Key Lab for Conservation and Utilization of Subtropical Agro-biological Resources, Guangxi University, Nanning, 530005, China
- Indian River Research and Education Center, IFAS, University of Florida, Fort Pierce, FL, 34945, United States of America
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Charles A. Powell
- Indian River Research and Education Center, IFAS, University of Florida, Fort Pierce, FL, 34945, United States of America
| | - Yongping Duan
- Horticultural Research Lab, USDA-ARS, Fort Pierce, FL, 34945, United States of America
| | - Robert Shatters
- Horticultural Research Lab, USDA-ARS, Fort Pierce, FL, 34945, United States of America
| | - Jingping Fang
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agro-biological Resources, Guangxi University, Nanning, 530005, China
- Indian River Research and Education Center, IFAS, University of Florida, Fort Pierce, FL, 34945, United States of America
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- * E-mail:
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Delhalle L, Korsak N, Taminiau B, Nezer C, Burteau S, Delcenserie V, Poullet JB, Daube G. Exploring the Bacterial Diversity of Belgian Steak Tartare Using Metagenetics and Quantitative Real-Time PCR Analysis. J Food Prot 2016; 79:220-9. [PMID: 26818982 DOI: 10.4315/0362-028x.jfp-15-185] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Steak tartare is a popular meat dish in Belgium. It is prepared with raw minced beef and is eaten with sauce, vegetables, and spices. Because it contains raw meat, steak tartare is highly prone to bacterial spoilage. The objective of this study was to explore the diversity of bacterial flora in steak tartare in Belgium according to the source and to determine which bacteria are able to grow during shelf life. A total of 58 samples from butchers' shops, restaurants, sandwich shops, and supermarkets were collected. These samples were analyzed using 16S rDNA metagenetics, a classical microbiological technique, and quantitative real-time PCR (qPCR) targeting the Lactobacillus genus. Samples were analyzed at the beginning and at the end of their shelf life, except for those from restaurants and sandwich shops, which were analyzed only on the purchase date. Metagenetic analysis identified up to 180 bacterial species and 90 genera in some samples. But only seven bacterial species were predominant in the samples, depending on the source: Brochothrix thermosphacta, Lactobacillus algidus, Lactococcus piscium, Leuconostoc gelidum, Photobacterium kishitani, Pseudomonas spp., and Xanthomonas oryzae. With this work, an alternative method is proposed to evaluate the total flora in food samples based on the number of reads from metagenetic analysis and the results of qPCR. The degree of underestimation of aerobic plate counts at 30°C estimated with the classical microbiology method was demonstrated in comparison with the proposed culture-independent method. Compared with culture-based methods, metagenetic analysis combined with qPCR targeting Lactobacillus provides valuable information for characterizing the bacterial flora of raw meat.
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Affiliation(s)
- L Delhalle
- University of Lìege, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, Department of Food Science, Sart-Tilman, B43bis, 4000 Liege, Belgium; Quality Partner, Belgium, Rue Hayeneux 62, 4040 Herstal, Belgium.
| | - N Korsak
- University of Lìege, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, Department of Food Science, Sart-Tilman, B43bis, 4000 Liege, Belgium
| | - B Taminiau
- University of Lìege, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, Department of Food Science, Sart-Tilman, B43bis, 4000 Liege, Belgium
| | - C Nezer
- Quality Partner, Belgium, Rue Hayeneux 62, 4040 Herstal, Belgium
| | - S Burteau
- Quality Partner, Belgium, Rue Hayeneux 62, 4040 Herstal, Belgium
| | - V Delcenserie
- University of Lìege, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, Department of Food Science, Sart-Tilman, B43bis, 4000 Liege, Belgium
| | - J B Poullet
- Quality Partner, Belgium, Rue Hayeneux 62, 4040 Herstal, Belgium
| | - G Daube
- University of Lìege, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, Department of Food Science, Sart-Tilman, B43bis, 4000 Liege, Belgium
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42
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Grangeteau C, Gerhards D, Terrat S, Dequiedt S, Alexandre H, Guilloux-Benatier M, von Wallbrunn C, Rousseaux S. FT-IR spectroscopy: A powerful tool for studying the inter- and intraspecific biodiversity of cultivable non-Saccharomyces yeasts isolated from grape must. J Microbiol Methods 2015; 121:50-8. [PMID: 26688103 DOI: 10.1016/j.mimet.2015.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 12/10/2015] [Accepted: 12/10/2015] [Indexed: 11/28/2022]
Abstract
The efficiency of the FT-IR technique for studying the inter- and intra biodiversity of cultivable non-Saccharomyces yeasts (NS) present in different must samples was examined. In first, the capacity of the technique FT-IR to study the global diversity of a given sample was compared to the pyrosequencing method, used as a reference technique. Seven different genera (Aureobasidium, Candida, Cryptococcus, Hanseniaspora, Issatchenkia, Metschnikowia and Pichia) were identified by FT-IR and also by pyrosequencing. Thirty-eight other genera were identified by pyrosequencing, but together they represented less than 6% of the average total population of 6 musts. Among the species identified, some of them present organoleptic potentials in winemaking, particularly Starmerella bacillaris (synonym Candidazemplinina). So in a second time, we evaluated the capacity of the FT-IR technique to discriminate the isolates of this species because few techniques were able to study intraspecific NS yeast biodiversity. The results obtained were validated by using a classic method as ITS sequencing. Biodiversity at strain level was high: 19 different strains were identified from 58 isolates. So, FT-IR spectroscopy seems to be an accurate and reliable method for identifying major genera present in the musts. The two biggest advantages of the FT-IR are the capacity to characterize intraspecific biodiversity of non-Saccharomyces yeasts and the possibility to discriminate a lot of strains.
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Affiliation(s)
- Cédric Grangeteau
- UMR Procédés Alimentaires et Microbiologiques, Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), AgroSup Dijon - Université de Bourgogne/Franche-Comté, IUVV, Rue Claude Ladrey, BP 27877, 21000 Dijon, France
| | - Daniel Gerhards
- Institut für Mikrobiologie und Biochemie Zentrum Analytische Chemie und Mikrobiologie - Hochschule Geisenheim University, Geisenheim, Germany
| | - Sebastien Terrat
- INRA, UMR 1347 Agroécologie-Plateforme Genosol, 17, rue Sully, BP 86510, 21000 Dijon, France
| | - Samuel Dequiedt
- INRA, UMR 1347 Agroécologie-Plateforme Genosol, 17, rue Sully, BP 86510, 21000 Dijon, France
| | - Hervé Alexandre
- UMR Procédés Alimentaires et Microbiologiques, Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), AgroSup Dijon - Université de Bourgogne/Franche-Comté, IUVV, Rue Claude Ladrey, BP 27877, 21000 Dijon, France
| | - Michèle Guilloux-Benatier
- UMR Procédés Alimentaires et Microbiologiques, Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), AgroSup Dijon - Université de Bourgogne/Franche-Comté, IUVV, Rue Claude Ladrey, BP 27877, 21000 Dijon, France
| | - Christian von Wallbrunn
- Institut für Mikrobiologie und Biochemie Zentrum Analytische Chemie und Mikrobiologie - Hochschule Geisenheim University, Geisenheim, Germany
| | - Sandrine Rousseaux
- UMR Procédés Alimentaires et Microbiologiques, Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), AgroSup Dijon - Université de Bourgogne/Franche-Comté, IUVV, Rue Claude Ladrey, BP 27877, 21000 Dijon, France.
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Kergourlay G, Taminiau B, Daube G, Champomier Vergès MC. Metagenomic insights into the dynamics of microbial communities in food. Int J Food Microbiol 2015; 213:31-9. [DOI: 10.1016/j.ijfoodmicro.2015.09.010] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 09/04/2015] [Accepted: 09/13/2015] [Indexed: 02/06/2023]
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Zhao M, Zhang DL, Su XQ, Duan SM, Wan JQ, Yuan WX, Liu BY, Ma Y, Pan YH. An Integrated Metagenomics/Metaproteomics Investigation of the Microbial Communities and Enzymes in Solid-state Fermentation of Pu-erh tea. Sci Rep 2015; 5:10117. [PMID: 25974221 PMCID: PMC4431464 DOI: 10.1038/srep10117] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 03/27/2015] [Indexed: 01/05/2023] Open
Abstract
Microbial enzymes during solid-state fermentation (SSF), which play important roles in the food, chemical, pharmaceutical and environmental fields, remain relatively unknown. In this work, the microbial communities and enzymes in SSF of Pu-erh tea, a well-known traditional Chinese tea, were investigated by integrated metagenomics/metaproteomics approach. The dominant bacteria and fungi were identified as Proteobacteria (48.42%) and Aspergillus (94.98%), through pyrosequencing-based analyses of the bacterial 16S and fungal 18S rRNA genes, respectively. In total, 335 proteins with at least two unique peptides were identified and classified into 28 Biological Processes and 35 Molecular Function categories using a metaproteomics analysis. The integration of metagenomics and metaproteomics data demonstrated that Aspergillus was dominant fungus and major host of identified proteins (50.45%). Enzymes involved in the degradation of the plant cell wall were identified and associated with the soft-rotting of tea leaves. Peroxiredoxins, catalase and peroxidases were associated with the oxidation of catechins. In conclusion, this work greatly advances our understanding of the SSF of Pu-erh tea and provides a powerful tool for studying SSF mechanisms, especially in relation to the microbial communities present.
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Affiliation(s)
- Ming Zhao
- 1] College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming 650201, Yunnan, China [2] Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Dong-Lian Zhang
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Xiao-Qin Su
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Shuang-Mei Duan
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Jin-Qiong Wan
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Wen-Xia Yuan
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Ben-Ying Liu
- Tea Research Institute of Yunnan Academy of Agricultural Science, Menghai 666201, China
| | - Yan Ma
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Ying-Hong Pan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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45
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Illeghems K, Weckx S, De Vuyst L. Applying meta-pathway analyses through metagenomics to identify the functional properties of the major bacterial communities of a single spontaneous cocoa bean fermentation process sample. Food Microbiol 2015; 50:54-63. [PMID: 25998815 DOI: 10.1016/j.fm.2015.03.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 03/01/2015] [Accepted: 03/24/2015] [Indexed: 11/15/2022]
Abstract
A high-resolution functional metagenomic analysis of a representative single sample of a Brazilian spontaneous cocoa bean fermentation process was carried out to gain insight into its bacterial community functioning. By reconstruction of microbial meta-pathways based on metagenomic data, the current knowledge about the metabolic capabilities of bacterial members involved in the cocoa bean fermentation ecosystem was extended. Functional meta-pathway analysis revealed the distribution of the metabolic pathways between the bacterial members involved. The metabolic capabilities of the lactic acid bacteria present were most associated with the heterolactic fermentation and citrate assimilation pathways. The role of Enterobacteriaceae in the conversion of substrates was shown through the use of the mixed-acid fermentation and methylglyoxal detoxification pathways. Furthermore, several other potential functional roles for Enterobacteriaceae were indicated, such as pectinolysis and citrate assimilation. Concerning acetic acid bacteria, metabolic pathways were partially reconstructed, in particular those related to responses toward stress, explaining their metabolic activities during cocoa bean fermentation processes. Further, the in-depth metagenomic analysis unveiled functionalities involved in bacterial competitiveness, such as the occurrence of CRISPRs and potential bacteriocin production. Finally, comparative analysis of the metagenomic data with bacterial genomes of cocoa bean fermentation isolates revealed the applicability of the selected strains as functional starter cultures.
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Affiliation(s)
- Koen Illeghems
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
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