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Effect of in vitro cultivation on human gut microbiota composition using 16S rDNA amplicon sequencing and metabolomics approach. Sci Rep 2023; 13:3026. [PMID: 36810418 PMCID: PMC9945476 DOI: 10.1038/s41598-023-29637-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/08/2023] [Indexed: 02/23/2023] Open
Abstract
Gut microbiota (GM) plays many key functions and helps maintain the host's health. Consequently, the development of GM cultivation under in vitro stimulating physiological conditions has gained extreme interest in different fields. In this study, we evaluated the impact of four culture media: Gut Microbiota Medium (GMM), Schaedler Broth (SM), Fermentation Medium (FM), and Carbohydrate Free Basal Medium (CFBM) on preserving the biodiversity and metabolic activity of human GM in batch in vitro cultures using PMA treatment coupled with 16S rDNA sequencing (PMA-seq) and LC-HR-MS/MS untargeted metabolomics supplemented with GC-MS SCFA profiling. Before the experiments, we determined the possibility of using the pooled faecal samples (MIX) from healthy donors (n = 15) as inoculum to reduce the number of variables and ensure the reproducibility of in vitro cultivation tests. Results showed the suitability of pooling faecal samples for in vitro cultivation study. Non-cultured MIX inoculum was characterized by higher α-diversity (Shannon effective count, and Effective microbial richness) compared to inocula from individual donors. After 24 h of cultivation, a significant effect of culture media composition on GM taxonomic and metabolomic profiles was observed. The SM and GMM had the highest α-diversity (Shannon effective count). The highest number of core ASVs (125) shared with non-cultured MIX inoculum and total SCFAs production was observed in the SM. These results might contribute to the development of standardized protocols for human GM in vitro cultivation by preventing methodological bias in the data.
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Chen S, Luan L, Zhang Y, Liu F, Ye X, Hou Z. A comparison study on polysaccharides extracted from Rosa sterilis S.D.Shi using different methods: Structural and in vitro fermentation characterizations. Food Chem X 2022; 17:100533. [PMID: 36506785 PMCID: PMC9732117 DOI: 10.1016/j.fochx.2022.100533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 10/27/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
In this study, the structural and in vitro fermentation characterizations of Rosa sterilis S.D.Shi polysaccharides (RSP), extracted by hot water (HW), acid (AA), alkali (AK) and enzyme (EM) were investigated for the first time. The results indicated that extraction methods exhibited significant effects on the structure of RSPs, thus resulting in different probiotic effects. HW-RSP and AA-RSP had high contents of Gal, Glc and GalA, while AK-RSP and EM-RSP mainly contained Ara, Gal and GalA. EM-RSP was rich in RG-I and its size of average side chain were the largest. Moreover, HW-RSP and AK-RSP exhibited the smallest (57.55 kDa) and largest (922.20 kDa) molecular weights, respectively. All RSPs promoted the production of total SCFAs and the growth of beneficial bacteria like Bifidobacterium, Bacteroides, Faecalibacterium and Paraclostrium to varying degrees, but inhibited the growth of pathogenic bacteria such as Escherichia-shigella, thereby regulating the composition of gut microbiota. Furthermore, the function prediction results showed that EM-RSP had the most special metabolic pathways. Collectively, our findings provide new insights into the relationship between the structure and probiotic function of RSPs, and offer theoretical basis for the development of functional products of Rosa sterilis S.D.Shi.
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Affiliation(s)
- Shiguo Chen
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang Engineering Laboratory of Food Technology and Equipment, Zhejiang University, Hangzhou 310058, China,Zhejiang University Zhongyuan Institute, Zhengzhou 450000, China,Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314102, China,Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linli 276000, China,Fuli Institute of Food Science, Zhejiang University, Hangzhou 310058, China,Ningbo Research Institute, Zhejiang University, Hangzhou 315100, China
| | - Luqin Luan
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang Engineering Laboratory of Food Technology and Equipment, Zhejiang University, Hangzhou 310058, China
| | - Yanru Zhang
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang Engineering Laboratory of Food Technology and Equipment, Zhejiang University, Hangzhou 310058, China
| | - Feifei Liu
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang Engineering Laboratory of Food Technology and Equipment, Zhejiang University, Hangzhou 310058, China
| | - Xingqian Ye
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang Engineering Laboratory of Food Technology and Equipment, Zhejiang University, Hangzhou 310058, China,Zhejiang University Zhongyuan Institute, Zhengzhou 450000, China,Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314102, China,Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linli 276000, China,Fuli Institute of Food Science, Zhejiang University, Hangzhou 310058, China,Ningbo Research Institute, Zhejiang University, Hangzhou 315100, China
| | - Zhiqiang Hou
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang Engineering Laboratory of Food Technology and Equipment, Zhejiang University, Hangzhou 310058, China,Corresponding author.
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Kleigrewe K, Haack M, Baudin M, Ménabréaz T, Crovadore J, Masri M, Beyrer M, Andlauer W, Lefort F, Dawid C, Brück TB, Brück WM. Dietary Modulation of the Human Gut Microbiota and Metabolome with Flaxseed Preparations. Int J Mol Sci 2022; 23:ijms231810473. [PMID: 36142393 PMCID: PMC9499670 DOI: 10.3390/ijms231810473] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Flaxseeds are typically consumed either as whole flaxseed, ground flaxseed, flaxseed oil, partially defatted flaxseed meal, or as a milk alternative. They are considered a rich source of vitamins, minerals, proteins and peptides, lipids, carbohydrates, lignans, and dietary fiber, which have shown hypolipidemic, antiatherogenic, anticholesterolemic, and anti-inflammatory property activity. Here, an in vitro batch culture model was used to investigate the influence of whole milled flaxseed and partially defatted milled flaxseed press cake on the gut microbiota and the liberation of flaxseed bioactives. Microbial communities were profiled using 16S rRNA gene-based high-throughput sequencing with targeted mass spectrometry measuring lignan, cyclolinopeptide, and bile acid content and HPLC for short-chain fatty acid profiles. Flaxseed supplementation decreased gut microbiota richness with Firmicutes, Proteobacteria, and Bacteroidetes becoming the predominant phyla. Secoisolariciresinol, enterodiol, and enterolactone were rapidly produced with acetic acid, butyric acid, and propionic acid being the predominant acids after 24 h of fermentation. The flaxseed press cake and whole flaxseed were equivalent in microbiota changes and functionality. However, press cake may be superior as a functional additive in a variety of foods in terms of consumer acceptance as it would be more resistant to oxidative changes.
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Affiliation(s)
- Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Martina Haack
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich, Garching b., 85748 München, Germany
| | - Martine Baudin
- Institute of Life Technologies, School of Engineering, HES-SO University of Applied Sciences and Arts Western Switzerland Valais-Wallis, 1950 Sion, Switzerland
| | - Thomas Ménabréaz
- Institute of Life Technologies, School of Engineering, HES-SO University of Applied Sciences and Arts Western Switzerland Valais-Wallis, 1950 Sion, Switzerland
| | - Julien Crovadore
- Plants and Pathogens Group, Research Institute Land Nature and Environment, Geneva School of Engineering, Architecture and Landscape (HEPIA), HES-SO University of Applied Sciences and Arts Western Switzerland, 1254 Jussy, Switzerland
| | - Mahmoud Masri
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich, Garching b., 85748 München, Germany
| | - Michael Beyrer
- Institute of Life Technologies, School of Engineering, HES-SO University of Applied Sciences and Arts Western Switzerland Valais-Wallis, 1950 Sion, Switzerland
| | - Wilfried Andlauer
- Institute of Life Technologies, School of Engineering, HES-SO University of Applied Sciences and Arts Western Switzerland Valais-Wallis, 1950 Sion, Switzerland
| | - François Lefort
- Plants and Pathogens Group, Research Institute Land Nature and Environment, Geneva School of Engineering, Architecture and Landscape (HEPIA), HES-SO University of Applied Sciences and Arts Western Switzerland, 1254 Jussy, Switzerland
| | - Corinna Dawid
- Bavarian Center for Biomolecular Mass Spectrometry, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- Chair of Food Chemistry and Molecular Sensory Science, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Thomas B. Brück
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich, Garching b., 85748 München, Germany
| | - Wolfram M. Brück
- Institute of Life Technologies, School of Engineering, HES-SO University of Applied Sciences and Arts Western Switzerland Valais-Wallis, 1950 Sion, Switzerland
- Correspondence: ; Tel.: +41-58-606-86-64
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In Vitro Fecal Fermentation Patterns of Arabinoxylan from Rice Bran on Fecal Microbiota from Normal-Weight and Overweight/Obese Subjects. Nutrients 2021; 13:nu13062052. [PMID: 34203983 PMCID: PMC8232586 DOI: 10.3390/nu13062052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/01/2021] [Accepted: 06/10/2021] [Indexed: 01/01/2023] Open
Abstract
Arabinoxylan (AX) is a structural polysaccharide found in wheat, rice and other cereal grains. Diets high in AX-containing fiber may promote gut health in obesity through prebiotic function. Thus, the impact of soluble AX isolated from rice bran fiber on human gut microbiota phylogenetic composition and short-chain fatty acid (SCFA) production patterns from normal-weight and overweight/obese subjects was investigated through in vitro fecal fermentation. Results showed that rice bran arabinoxylan modified the microbiota in fecal samples from both weight classes compared to control, significantly increasing Collinsella, Blautia and Bifidobacterium, and decreasing Sutterella, Bilophila and Parabacteroides. Rice bran AX also significantly increased total and individual SCFA contents (p < 0.05). This study suggests that rice bran AX may beneficially impact gut health in obesity through prebiotic activities.
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