Research Progress on the Impact of Gut Microbial “Dark Matter” and Dietary Nutrition on Human Health

Yangyang CHU; Yilin ZHANG; Chunping YOU

doi:10.13386/j.issn1002-0306.2022100047

Volume 44 Issue 13

Jun. 2023

Turn off MathJax

Article Contents

Abstract

References

Science and Technology of Food Industry > 2023 > 44(13): 474-482. > DOI: 10.13386/j.issn1002-0306.2022100047

CHU Yangyang, ZHANG Yilin, YOU Chunping. Research Progress on the Impact of Gut Microbial “Dark Matter” and Dietary Nutrition on Human Health[J]. Science and Technology of Food Industry, 2023, 44(13): 474−482. (in Chinese with English abstract). doi: 10.13386/j.issn1002-0306.2022100047.

Citation:

PDF (1616 KB)

Research Progress on the Impact of Gut Microbial “Dark Matter” and Dietary Nutrition on Human Health

1.
State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai 200436, China
2.
College of Food Sciences & Technology, Shanghai Ocean University, Shanghai 201306, China

More Information

Received Date: October 08, 2022
Available Online: April 21, 2023

Graphical Abstract

Abstract

Abstract

Gut microbial "dark matter" refers to the microorganism that exists in low or rare abundance in the gastrointestinal tract and affects human health, without a clear disclosure of its influence and the related mechanism. Most current studies on the relationship among diet, gut microbiota, and host health have focused on the high-abundance gut microbiota, while the role of gut microbial "dark matter" has often been neglected. Therefore, this paper reviews the interactions among dietary nutrition, gut microbial "dark matter", and host health, as well as the new advances in microbiomics technologies, discusses the importance of exploring the acting mechanisms of microbial "dark matter" on human health, and provides new ideas for future dietary interventions to influence gut microbiota for preventing or even improving human diseases.
- microbial "dark matter",
- low abundance microbiota,
- host health,
- dietary nutrition,
- microbiomics

FullText(HTML)

References (58)

References

[1]	MILANI C, DURANTI S, BOTTACINI F, et al. The first microbial colonizers of the human gut: Composition, activities, and health implications of the infant gut microbiota[J]. Microbiology and Molecular Biology Reviews,2017,81(4):e00036−17.
[2]	BARRATT M J, LEBRILLA C, SHAPIRO H Y, et al. The gut microbiota, food science, and human nutrition: A timely marriage[J]. Cell Host & Microbe,2017,22(2):134−141.
[3]	GILBERT J A, BLASER M J, CAPORASO J G, et al. Current understanding of the human microbiome[J]. Nature Medicine,2018,24(4):392−400. doi: 10.1038/nm.4517
[4]	YANBEI W, JIAWEI W, CHOE U, et al. Interactions between food and gut microbiota: Impact on human health[J]. Annual Review of Food Science and Technology,2019,10:389−408. doi: 10.1146/annurev-food-032818-121303
[5]	IEBBA V, TOTINO V, GAGLIARDI A, et al. Eubiosis and dysbiosis: The two sides of the microbiota[J]. New Microbiologica,2016,39(1):1−12.
[6]	BOKULICH N A, CHUNG J, BATTAGLIA T, et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life[J]. Science Translational Medicine,2016,8(343):34382.
[7]	张烽, 张晨虹. 膳食营养与肠道微生物组[J]. 生命科学,2017,29(7):695−706. [ZHANG F, ZHANG C H. Dietary nutrition and gut microbiota[J]. Chinese Bulletin of Life Sciences,2017,29(7):695−706. doi: 10.13376/j.cbls/2017094 ZHANG F, ZHANG C H. Dietary nutrition and gut microbiota[J]. Chinese Bulletin of Life Sciences, 2017, 29(7): 695-706. doi: 10.13376/j.cbls/2017094
[8]	HAJISHENGALLIS G, DARVEAU R P, CURTIS M A. The keystone-pathogen hypothesis[J]. Nature Reviews Microbiology,2012,10(10):717−725. doi: 10.1038/nrmicro2873
[9]	SHRIKANT S B, SAROJ S G, YOGESH S S. Rare biosphere in human gut: A less explored component of human gut microbiota and its association with human health[J]. Mining of Microbial Wealth and Meta Genomics,2017:133−142.
[10]	BENJAMINO J, LINCOLN S, SRIVASTAVA R, et al. Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration[J]. Microbiome,2018,6(1):86. doi: 10.1186/s40168-018-0469-5
[11]	晁伟, 王力. 暗物质研究进展[J]. 中国科学:物理学、力学、天文学,2022,52(7):39−54. [CHAO W, WANG L. Progress of dark matter research[J]. Scientia Sinica:Physica, Mechanica & Astronomica,2022,52(7):39−54. CHAO W, WANG L. Progress of dark matter research[J]. Scientia Sinica: Physica, Mechanica & Astronomica, 2022, 52(7): 39-54.
[12]	DE CENA J A, ZHANG J, DENG D, et al. Low-abundant microorganisms: The human microbiome's dark matter, a scoping review[J]. Frontiers in Cellular and Infection Microbiology,2021,11:689197. doi: 10.3389/fcimb.2021.689197
[13]	RANJAN R, RANI A, FINN P W, et al. Multiomic strategies reveal diversity and important functional aspects of human gut microbiome[J]. Biomed Research International,2018,2018:6074918.
[14]	DANNESKIOLD-SAMSOE N B, DE FREITAS QUEIROZ BARROS H D, SANTOS R, et al. Interplay between food and gut microbiota in health and disease[J]. Food Research International,2019,115:23−31. doi: 10.1016/j.foodres.2018.07.043
[15]	VERNOCCHI P, DEL CHIERICO F, PUTIGNANI L. Gut microbiota metabolism and interaction with food components[J]. International Journal of Molecular Sciences,2020,21(10):3688. doi: 10.3390/ijms21103688
[16]	MIA C T, YONG JUN G, KRISTIAN FOG N, et al. Lactobacillus acidophilus metabolizes dietary plant glucosides and externalizes their bioactive phytochemicals[J]. mBio,2017,8(6):e01421−17.
[17]	ROTHSCHILD D, WEISSBROD O, BARKAN E, et al. Environment dominates over host genetics in shaping human gut microbiota[J]. Nature,2018,555(7695):210−215. doi: 10.1038/nature25973
[18]	SHANG Y, KHAFIPOUR E, DERAKHSHANI H, et al. Short term high fat diet induces obesity-enhancing changes in mouse gut microbiota that are partially reversed by cessation of the high fat diet[J]. Lipids,2017,52(6):499−511. doi: 10.1007/s11745-017-4253-2
[19]	HEINKEN A, THIELE I. Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework[J]. Gut Microbes,2015,6(2):120−130. doi: 10.1080/19490976.2015.1023494
[20]	TROSVIK P, DE MUINCK E J. Ecology of bacteria in the human gastrointestinal tract-identification of keystone and foundation taxa[J]. Microbiome,2015,12(3):44.
[21]	PRAZDNOVA E V, GOROVTSOV A V, VASILCHENKO N G, et al. Quorum-sensing inhibition by gram-positive bacteria[J]. Microorganisms,2022,10(2):350. doi: 10.3390/microorganisms10020350
[22]	BINDA C, LOPETUSO L R, RIZZATTI G, et al. Actinobacteria: A relevant minority for the maintenance of gut homeostasis[J]. Digestive and Liver Disease,2018,50(5):421−428. doi: 10.1016/j.dld.2018.02.012
[23]	GOLDSTEIN J L, BROWN M S. A century of cholesterol and coronaries: From plaques to genes to statins[J]. Cell,2015,161(1):161−172. doi: 10.1016/j.cell.2015.01.036
[24]	KENNY D J, PLICHTA D R, SHUNGIN D, et al. Cholesterol metabolism by uncultured human gut bacteria influences host cholesterol level[J]. Cell Host & Microbe,2020,28(2):245−257.
[25]	HOFFMANN C, DOLLIVE S, GRUNBERG S, et al. Archaea and fungi of the human gut microbiome: Correlations with diet and bacterial residents[J]. Plos One,2013,8(6):e66019. doi: 10.1371/journal.pone.0066019
[26]	BRUGERE J F, BORREL G, GACI N, et al. Archaebiotics proposed therapeutic use of archaea to prevent trimethylaminuria and cardiovascular disease[J]. Gut Microbes,2014,5(1):5−10. doi: 10.4161/gmic.26749
[27]	TOMOVA A, BUKOVSKY I, REMBERT E, et al. The effects of vegetarian and vegan diets on gut microbiota[J]. Frontiers in Nutrition,2019,6:47. doi: 10.3389/fnut.2019.00047
[28]	SHEFLIN A M, MELBY C L, CARBONERO F, et al. Linking dietary patterns with gut microbial composition and function[J]. Gut Microbes,2017,8(2):113−129. doi: 10.1080/19490976.2016.1270809
[29]	韩嘉明, 高中山, 段豪亮, 等. 氧化三甲胺在冠心病中的研究进展[J]. 中国心血管病研究,2022,20(7):643−649. [HAN J M, GAO Z S, DUAN H L, et al. Research progress of TMAO in coronary heart disease[J]. Chinese Journal of Cardiovascular Research,2022,20(7):643−649. doi: 10.3969/j.issn.1672-5301.2022.07.010 HAN J M, GAO Z S, DUAN H L, et al. Research progress of TMAO in coronary heart disease[J]. Chinese Journal of Cardiovascular Research, 2022, 20(7): 643-649. doi: 10.3969/j.issn.1672-5301.2022.07.010
[30]	FAITH J J, GURUGE J L, CHARBONNEAU M, et al. The long-term stability of the human gut microbiota[J]. Science,2013,341(6141):1237439. doi: 10.1126/science.1237439
[31]	MEDICINE S I J N E J O. Weight loss with a low-carbohydrate, Mediterranean, or low-fat diet[J]. Fleischwirtschaft,2008,359(3):229−241.
[32]	RINOTT E, MEIR A Y, TSABAN G, et al. The effects of the Green-Mediterranean diet on cardiometabolic health are linked to gut microbiome modifications: A randomized controlled trial[J]. Genome Medicine,2022,14(1):29. doi: 10.1186/s13073-022-01015-z
[33]	ALAMMAR N, WANG L, SABERI B, et al. The impact of peppermint oil on the irritable bowel syndrome: A meta-analysis of the pooled clinical data[J]. Bmc Complementary and Alternative Medicine,2019,19(1):21. doi: 10.1186/s12906-018-2409-0
[34]	HAWRELAK J A, WOHLMUTH H, PTATINSON M, et al. Western herbal medicines in the treatment of irritable bowel syndrome: A systematic review and meta-analysis[J]. Complementary Therapies in Medicine,2020,48:102233. doi: 10.1016/j.ctim.2019.102233
[35]	THAPA S, LUNA R A, CHUMPITAZI B P, et al. Peppermint oil effects on the gut microbiome in children with functional abdominal pain[J]. Cts-Clinical and Translational Science,2022,15(4):1036−1049. doi: 10.1111/cts.13224
[36]	YADAV M, VERMA M K, CHAUHAN N S. A review of metabolic potential of human gut microbiome in human nutrition[J]. Archives of Microbiology,2018,200(2):203−217. doi: 10.1007/s00203-017-1459-x
[37]	NEEDHAM B D, FUNABASHI M, ADAME M D, et al. A gut-derived metabolite alters brain activity and anxiety behaviour in mice[J]. Nature,2022,602(7898):647−653. doi: 10.1038/s41586-022-04396-8
[38]	HAN N D, CHENG J, DELANNOY-BRUNO O, et al. Microbial liberation of N-methylserotonin from orange fiber in gnotobiotic mice and humans[J]. Cell,2022,185(14):2495−2509(e11). doi: 10.1016/j.cell.2022.06.004
[39]	SERGER E, LUENGO-GUTIERREZ L, CHADWICK J S, et al. The gut metabolite indole-3 propionate promotes nerve regeneration and repair[J]. Nature,2022,607(7919):585−592. doi: 10.1038/s41586-022-04884-x
[40]	BAE M, CASSILLY C D, LIU X, et al. Akkermansia muciniphila phospholipid induces homeostatic immune responses[J]. Nature,2022,608(7921):168−173. doi: 10.1038/s41586-022-04985-7
[41]	BARNETT C, NAZZAL L, GOLDFARB D S, et al. The presence of Oxalobacter formigenes in the microbiome of healthy young adults[J]. Journal of Urology,2016,195(2):499−506. doi: 10.1016/j.juro.2015.08.070
[42]	SIDHU H, ALLISON M J, CHOW J M, et al. Rapid reversal of hyperoxaluria in a rat model after probiotic administration of Oxalobacter formigenes[J]. Journal of Urology,2001,166(4):1487−1491.
[43]	ASSIMOS D G. Re: Oxalobacter formigenes: Opening the door to probiotic therapy for the treatment of hyperoxaluria editorial comment[J]. Journal of Urology,2015,194(2):424−425.
[44]	RAJILIC-STOJANOVIC M, DE VOS W M. The first 1000 cultured species of the human gastrointestinal microbiota[J]. Fems Microbiology Reviews,2014,38(5):996−1047. doi: 10.1111/1574-6976.12075
[45]	JAN G, BELZACQ A S, HAOUZI D, et al. Propionibacteria induce apoptosis of colorectal carcinoma cells via short-chain fatty acids acting on mitochondria[J]. Cell Death and Differentiation,2002,9(2):179−188. doi: 10.1038/sj.cdd.4400935
[46]	SUNG H, FERLAY J, SIEGEL R L, et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries[J]. Ca-a Cancer Journal for Clinicians,2021,71(3):209−249. doi: 10.3322/caac.21660
[47]	CASTELLARIN M, WARREN R L, FREEMAN J D, et al. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma[J]. Genome Research,2012,22(2):299−306. doi: 10.1101/gr.126516.111
[48]	KOSTIC A D, CHUN E, ROBERTSON L, et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment[J]. Cell Host & Microbe,2013,14(2):207−215.
[49]	ULSEMER P, TOUTOUNIAN K, KRESSEL G, et al. Impact of oral consumption of heat-treated Bacteroides xylanisolvens DSM 23964 on the level of natural TFα-specific antibodies in human adults[J]. Beneficial Microbes,2016,7(4):485−500. doi: 10.3920/BM2015.0143
[50]	YANAGIBASHI T, HOSONO A, OYAMA A, et al. IgA production in the large intestine is modulated by a different mechanism than in the small intestine: Bacteroides acidifaciens promotes IgA production in the large intestine by inducing germinal center formation and increasing the number of IgA(+) B cells[J]. Immunobiology,2013,218(4):645−651. doi: 10.1016/j.imbio.2012.07.033
[51]	DEVKOTA S, CHANG E B. Diet-induced expansion of pathobionts in experimental colitis[J]. Gut Microbes,2013,4(2):172−174. doi: 10.4161/gmic.23589
[52]	DEKABORUAH E, SURYAVANSHI M V, CHETTRI D, et al. Human microbiome: An academic update on human body site specific surveillance and its possible role[J]. Archives of Microbiology,2020,202(8):2147−2167. doi: 10.1007/s00203-020-01931-x
[53]	LANGILLE M G I, ZANEVELD J, CAPORASO J G, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences[J]. Nature Biotechnology,2013,31(9):814−821. doi: 10.1038/nbt.2676
[54]	张彦, 张双庆. 肠道微生物组与健康[M]. 北京: 中国轻工业出版社, 2021: 12. ZHANG Y, ZHANG S Q. Gut microbiome and health[M]. Beijing: China Light Industry Press, 2021: 12.
[55]	LIHAN W, JIAXIN Z, MENGYAO Z, et al. Evaluation of the effect of antibiotics on gut microbiota in early life based on culturomics, SMRT sequencing and metagenomics sequencing methods[J]. Analytical Methods:Advancing Methods and Applications,2021,13(43):5144−5156.
[56]	姚彩青, 鄂晶晶, 王俊国. 培养组学在人体肠道微生物研究中的应用[J]. 中国食品学报,2021,21(7):371−377. [YAO C Q, EE J J, WANG J G. Application of culturomics in human intestinal microbiota[J]. Journal of Chinese Institute of Food Science and Technology,2021,21(7):371−377. doi: 10.16429/j.1009-7848.2021.07.044 YAO C Q, EE J J, WANG J G. Application of culturomics in human intestinal microbiota[J]. Journal of Chinese Institute of Food Science and Technology, 2021, 21(7): 371-377. doi: 10.16429/j.1009-7848.2021.07.044
[57]	YESHI H, ZHIYUAN P, NI H, et al. Isolation and identification of cholesterol-degrading intestinal bacteria by culturomics and evaluation of their functions[J]. Chinese Journal of Biotechnology,2021,37(11):3734−3744.
[58]	LAGIER J C, DUBOURG G, MILLION M, et al. Culturing the human microbiota and culturomics[J]. Nature Reviews Microbiology,2018,16(9):540−550. doi: 10.1038/s41579-018-0041-0