研究报告

不同富营养培养基对人肠道菌群的体外培养效果比较分析

  • 路婧 ,
  • 夏雪娟 ,
  • 黄骏楠 ,
  • 陈泫羽 ,
  • 周璐 ,
  • 董庆利
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  • (上海理工大学 健康科学与工程学院,上海,200093)
第一作者:硕士研究生(董庆利教授为通信作者,E-mail:dongqingli@126.com)

收稿日期: 2024-01-15

  修回日期: 2024-03-01

  网络出版日期: 2024-12-30

基金资助

上海市浦江人才计划(23PJ1409600);上海理工大学创新创业训练计划项目(XJ2023328)

Comparative analysis of in vitro cultivation effects of different rich media on human intestinal microbiota

  • LU Jing ,
  • XIA Xuejuan ,
  • HUANG Junnan ,
  • CHEN Xuanyu ,
  • ZHOU Lu ,
  • DONG Qingli
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  • (School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China)

Received date: 2024-01-15

  Revised date: 2024-03-01

  Online published: 2024-12-30

摘要

以富含营养的培养基(rich media,RM)为关键组成部分的培养组学技术的兴起为肠道菌群与宿主互作的机制研究提供了重要保障。为了探究不同RM对人肠道菌群的体外培养效果,采用平板计数法以及16S rDNA高通量测序技术分析YCFA培养基(yeast extract-casein hydrolysate-fatty acid medium)、GAM培养基(gifu anaerobic medium)和一种具有专利保护的ZJ培养基对人肠道菌群的体外培养效果。平板计数法显示在不同培养基中培养不同时间(0~7 d)后菌落总数多呈先上升后下降的趋势,经3种培养基培养后肠道菌群的菌落总数的最高值为:ZJ(9.88 lg CFU/mL)>GAM(9.79 lg CFU/mL)>YCFA(9.68 lg CFU/mL)。高通量测序结果显示体外培养后细菌多样性降低,各培养基会选择性富集不同菌株,其中ZJ培养基培养后群落多样性下降最为明显。β-多样性分析结果显示GAM培养基培养后肠道菌群的组成更接近于未培养时的菌群组成。因此,与YCFA和ZJ培养基相比,GAM培养基是一种更优的适合肠道菌群体外培养的RM培养基。

本文引用格式

路婧 , 夏雪娟 , 黄骏楠 , 陈泫羽 , 周璐 , 董庆利 . 不同富营养培养基对人肠道菌群的体外培养效果比较分析[J]. 食品与发酵工业, 2024 , 50(24) : 201 -211 . DOI: 10.13995/j.cnki.11-1802/ts.038595

Abstract

The emergence of culturomics, with rich media (RM) as a crucial component, provides a significant foundation for studying the mechanisms of interaction between the gut microbiota and the host.To explore the in vitro cultivation effects of different RMs on the human gut microbiota, the plate counting method and high-throughput 16S rDNA sequencing technology were employed to analyze the cultivation effects of Yeast extract-casein hydrolysate-fatty acid medium (YCFA medium), Gifu anaerobic medium (GAM medium), and a patented ZJ medium on the human gut microbiota.Plate counting results showed that the total colony count of gut microbiota exhibited a trend of initially increasing and then decreasing after cultivation for different durations (0-7 days) in various culture media.The highest colony count values for the gut microbiota after cultivation in three different media were as follows:ZJ (9.88 lg CFU/mL) > GAM (9.79 lg CFU/mL) > YCFA (9.68 lg CFU/mL).The high-throughput sequencing results revealed a decrease in bacterial diversity after in vitro cultivation, with each culture medium selectively enriching different strains.Among them, the ZJ medium exhibited the most significant decrease in community diversity after cultivation.The β-diversity analysis indicated that the gut microbiota’s composition after cultivation in the GAM medium was closer to the composition observed in the uncultivated state.Therefore, compared to YCFA and ZJ media, GAM medium is a more optimal RM medium for the in vitro cultivation of the gut microbiota.

参考文献

[1] ABDUL-HUSSEIN Z R, ATIA S S.Antimicrobial effect of pyocyanin extracted from Pseudomonas aeroginosa[J].European Journal of Experimental Biology, 2016, 6(6):1-4.
[2] SAUS E, IRAOLA-GUZMÁN S, WILLIS J R, et al.Microbiome and colorectal cancer:Roles in carcinogenesis and clinical potential[J].Molecular Aspects of Medicine, 2019, 69:93-106.
[3] LIU R X, HONG J, XU X Q, et al.Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention[J].Nature Medicine, 2017, 23(7):859-868.
[4] NAKATSU G, LI X C, ZHOU H K, et al.Gut mucosal microbiome across stages of colorectal carcinogenesis[J].Nature Communications, 2015, 6:8727.
[5] NAYFACH S, POLLARD K S.Toward accurate and quantitative comparative metagenomics[J].Cell, 2016, 166(5):1103-1116.
[6] LAGIER J C, ARMOUGOM F, MILLION M, et al.Microbial culturomics:Paradigm shift in the human gut microbiome study[J].Clinical Microbiology and Infection, 2012, 18(12):1185-1193.
[7] LAGIER J C, DUBOURG G, MILLION M, et al.Culturing the human microbiota and culturomics[J].Nature Reviews Microbiology, 2018, 16:540-550.
[8] 余中节, 赵洁, 孙志宏.多组学技术在自然发酵乳中的应用[J].生物产业技术, 2019(4):63-68.
YU Z J, ZHAO J, SUN Z H.Application of multi-omics technology in naturally fermented milk[J].Biotechnology & Business, 2019(4):63-68.
[9] TIDJANI ALOU M, NAUD S, KHELAIFIA S, et al.State of the art in the culture of the human microbiota:New interests and strategies[J].Clinical Microbiology Reviews, 2020, 34(1):e00 129-19.
[10] BROWNE H P, FORSTER S C, ANONYE B O, et al.Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation[J].Nature, 2016, 533(7604):543-546.
[11] FORSTER S C, KUMAR N, ANONYE B O, et al.A human gut bacterial genome and culture collection for improved metagenomic analyses[J].Nature Biotechnology, 2019, 37(2):186-192.
[12] GOTOH A, NARA M, SUGIYAMA Y, et al.Use of Gifu Anaerobic Medium for culturing 32 dominant species of human gut microbes and its evaluation based on short-chain fatty acids fermentation profiles[J].Bioscience, Biotechnology, and Biochemistry,2017, 81(10):2009-2017.
[13] 曾令聪, 胡犁涛.一种从人体粪便中分离肠道菌群的方法技术:中国, CN201510840354.1[P].2015-11-27.
ZENG L C, HU L T.A method technology for separating intestinal flora from human feces:China, CN201510840354.1[P].2015-11-27.
[14] CHEN C C, WU W K, CHANG C M, et al.Comparison of DNA stabilizers and storage conditions on preserving fecal microbiota profiles[J].Journal of the Formosan Medical Association, 2020, 119(12):1791-1798.
[15] 常宇骁. 人类肠道微生物培养组优化及肠道菌库构建与应用[D].北京:军事科学院, 2020.
CHANG Y X.Optimization of human intestinal microbial culture group and construction and application of intestinal bacterial library[D].Beijing:Academy of Military Science, 2020.
[16] LIU C, DU M X, ABUDUAINI R, et al.Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank[J].Microbiome, 2021, 9(1):119.
[17] 伍灵怡, 唐黎, 张静, 等.胆汁淤积性肝病患者肠道菌群特征及其临床相关性研究[J].第三军医大学学报, 2020, 42(22):2251-2258.
WU L Y, TANG L, ZHANG J, et al.Characteristics of gut microbiota and their correlation with clinical parameters in patients with cholestatic liver disease[J].Journal of Third Military Medical University, 2020, 42(22):2251-2258.
[18] LIU L X, WANG H Y, ZHANG H P, et al.Toward a deeper understanding of gut microbiome in depression:The promise of clinical applicability[J].Advanced Science, 2022, 9(35):e2203707.
[19] LI Z, LIANG H F, HU Y Y, et al.Gut bacterial profiles in Parkinson′s disease:A systematic review[J].CNS Neuroscience & Therapeutics, 2023, 29(1):140-157.
[20] MILLION M, DIALLO A, RAOULT D.Gut microbiota and malnutrition[J].Microbial Pathogenesis, 2017, 106:127-138.
[21] CHE Q M, AKAO T, HATTORI M, et al.Isolation of a human intestinal bacterium capable of transforming barbaloin to Aloe-emodin anthrone[J].Planta Medica, 1991, 57(1):15-19.
[22] GAVZY S J, KENSISKI A, LEE Z L, et al.Bifidobacterium mechanisms of immune modulation and tolerance[J].Gut Microbes, 2023, 15(2):2291164.
[23] MABWI H A, HITAYEZU E, MAULIASARI I R, et al.Simulation of the mucosal environment in the re-construction of the synthetic gut microbial ecosystem[J].Journal of Microbiological Methods, 2021, 191:106351.
[24] KAVITAKE D, DEVI P B, DELATTRE C, et al.Exopolysaccharides produced by Enterococcus genus-An overview[J].International Journal of Biological Macromolecules, 2023, 226:111-120.
[25] SISTI D, PAZIENZA V, PICCINI F, et al.A proposal for the reference intervals of the Italian microbiota “scaffold” in healthy adults[J].Scientific Reports, 2022, 12:3952.
[26] RESENDE A S, LEITE G S F, LANCHA JUNIOR A H.Changes in the gut bacteria composition of healthy men with the same nutritional profile undergoing 10-week aerobic exercise training:A randomized controlled trial[J].Nutrients, 2021, 13(8):2839.
[27] ARANDA-DÍAZ A, NG K M, THOMSEN T, et al.Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota[J].Cell Host & Microbe, 2022, 30(2):260-272.e5.
[28] WAN C, WU K Z, LU X Y, et al.Integrative analysis of the gut microbiota and metabolome for in vitro human gut fermentation modeling[J].Journal of Agricultural and Food Chemistry, 2021, 69(50):15414-15424.
[29] ZHANG N, JIN M L, WANG K M, et al.Functional oligosaccharide fermentation in the gut:Improving intestinal health and its determinant factors-a review[J].Carbohydrate Polymers, 2022, 284:119043.
[30] 刘莎, 陈从英.肠道微生物培养的研究进展及应用[J].微生物学报,2023, 63(3):881-899.
LIU S, CHEN C Y.Research progress and application of gut microorganism culture[J].Acta Microbiologica Sinica, 2023, 63(3):881-899.
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