REFERENCES

1. Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell. 2014;157:121-41.

2. David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505:559-63.

3. Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457:480-4.

4. Qin J, Li R, Raes J, et al; MetaHIT Consortium. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59-65.

5. Eckburg PB, Bik EM, Bernstein CN, et al. Diversity of the human intestinal microbial flora. Science. 2005;308:1635-8.

6. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207-14.

7. Slavin J. Fiber and prebiotics: mechanisms and health benefits. Nutrients. 2013;5:1417-35.

8. Gibson GR, Hutkins R, Sanders ME, et al. Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol. 2017;14:491-502.

9. Davani-Davari D, Negahdaripour M, Karimzadeh I, et al. Prebiotics: definition, types, sources, mechanisms, and clinical applications. Foods. 2019;8:92.

10. Holscher HD. Dietary fiber and prebiotics and the gastrointestinal microbiota. Gut Microbes. 2017;8:172-84.

11. Dion C, Chappuis E, Ripoll C. Does larch arabinogalactan enhance immune function? A review of mechanistic and clinical trials. Nutr Metab. 2016;13:28.

12. Uauy R. The assessment of dietary adequacy based on nutrient intake data is a complex issue. Foreword. Br J Nutr. 2009;101 Suppl 2:S1.

13. Gibson GR, Roberfroid MB. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr. 1995;125:1401-12.

14. Wang Y, LaPointe G. Arabinogalactan utilization by Bifidobacterium longum subsp. longum NCC 2705 and Bacteroides caccae ATCC 43185 in monoculture and coculture. Microorganisms. 2020;8:1703.

15. Kim K, Kim CY. Rheological properties of arabinogalactan solutions related to the carbohydrate composition of different legumes. Korean J Food Preserv. 2023;30:785-96.

16. Rakhmanberdyeva RK, Zhauynbayeva KS, Senchenkova SN, Shashkov AS, Bobakulov KM. Structure of arabinogalactan and pectin from the Silybum marianum. Carbohydr Res. 2019;485:107797.

17. Wang M, Wichienchot S, He X, Fu X, Huang Q, Zhang B. In vitro colonic fermentation of dietary fibers: fermentation rate, short-chain fatty acid production and changes in microbiota. Trends Food Sci Technol. 2019;88:1-9.

18. Sun Y, Hu J, Zhang S, et al. Prebiotic characteristics of arabinogalactans during in vitro fermentation through multi-omics analysis. Food Chem Toxicol. 2021;156:112522.

19. Victoria Obayomi O, Folakemi Olaniran A, Olugbemiga Owa S. Unveiling the role of functional foods with emphasis on prebiotics and probiotics in human health: a review. J Funct Foods. 2024;119:106337.

20. Wang Y, Liu Y, Ivusic Polic I, Chandran Matheyambath A, Lapointe G. Modulation of human gut microbiota composition and metabolites by arabinogalactan and Bifidobacterium longum subsp. longum BB536 in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®). J Funct Foods. 2021;87:104820.

21. Sasaki Y, Horigome A, Odamaki T, et al. Novel 3-O-α-D-Galactosyl-α-L-arabinofuranosidase for the assimilation of gum arabic arabinogalactan protein in Bifidobacterium longum subsp. longum. Appl Environ Microbiol. 2021;87:e02690-20.

22. Onumpai C, Kolida S, Bonnin E, Rastall RA. Microbial utilization and selectivity of pectin fractions with various structures. Appl Environ Microbiol. 2011;77:5747-54.

23. Lindstad LJ, Lo G, Leivers S, et al. Human gut faecalibacterium prausnitzii deploys a highly efficient conserved system to cross-feed on β-mannan-derived oligosaccharides. mBio. 2021;12:e0362820.

24. Culp EJ, Goodman AL. Cross-feeding in the gut microbiome: ecology and mechanisms. Cell Host Microbe. 2023;31:485-99.

25. Cartmell A, Muñoz-Muñoz J, Briggs JA, et al. A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation. Nat Microbiol. 2018;3:1314-26.

26. Wang S, Mu L, Yu C, et al. Microbial collaborations and conflicts: unraveling interactions in the gut ecosystem. Gut Microbes. 2024;16:2296603.

27. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42:D490-5.

28. Shi E, Nie M, Wang X, et al. Polysaccharides affect the utilization of β-carotene through gut microbiota investigated by in vitro and in vivo experiments. Food Res Int. 2023;174:113592.

29. Holmes ZC, Villa MM, Durand HK, et al. Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake. Microbiome. 2022;10:114.

30. Falony G, Joossens M, Vieira-Silva S, et al. Population-level analysis of gut microbiome variation. Science. 2016;352:560-4.

31. Wang Q, Spenkelink B, Boonpawa R, Rietjens IMCM, Beekmann K. Use of physiologically based kinetic modeling to predict rat gut microbial metabolism of the isoflavone daidzein to S-equol and its consequences for ERα activation. Mol Nutr Food Res. 2020;64:e1900912.

32. Bénard MV, Arretxe I, Wortelboer K, et al. Anaerobic feces processing for fecal microbiota transplantation improves viability of obligate anaerobes. Microorganisms. 2023;11:2238.

33. Salonen A, Nikkilä J, Jalanka-Tuovinen J, et al. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Methods. 2010;81:127-34.

34. Pjevac P, Hausmann B, Schwarz J, et al. An economical and flexible dual barcoding, two-step PCR approach for highly multiplexed amplicon sequencing. Front Microbiol. 2021;12:669776.

35. Berry D, Mader E, Lee TK, et al. Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells. Proc Natl Acad Sci U S A. 2015;112:E194-203.

36. Eichorst SA, Strasser F, Woyke T, Schintlmeister A, Wagner M, Woebken D. Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils. FEMS Microbiol Ecol. 2015;91:fiv106.

37. Cui D, Kong L, Wang Y, Zhu Y, Zhang C. In situ identification of environmental microorganisms with Raman spectroscopy. Environ Sci Ecotechnol. 2022;11:100187.

38. Riva A, Rasoulimehrabani H, Cruz-Rubio JM, et al. Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting. Nat Commun. 2023;14:8210.

39. Henry DG, Jarvis I, Gillmore G, Stephenson M, Emmings JF. Assessing low-maturity organic matter in shales using Raman spectroscopy: effects of sample preparation and operating procedure. Int J Coal Geol. 2018;191:135-51.

40. Caro TA, Kashyap S, Brown G, Chen C, Kopf SH, Templeton AS. Single-cell measurement of microbial growth rate with Raman microspectroscopy. FEMS Microbiol Ecol. 2024;100:fiae110.

41. Stöckel S, Kirchhoff J, Neugebauer U, Rösch P, Popp J. The application of Raman spectroscopy for the detection and identification of microorganisms. J Raman Spectrosc. 2016;47:89-109.

42. Lee KS, Pereira FC, Palatinszky M, et al. Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions. Nat Protoc. 2021;16:634-76.

43. Lee KS, Palatinszky M, Pereira FC, et al. An automated Raman-based platform for the sorting of live cells by functional properties. Nat Microbiol. 2019;4:1035-48.

44. Wright ES, Yilmaz LS, Noguera DR. DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol. 2012;78:717-25.

45. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JA. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. 2007;35:W71-4.

46. R Studio Team. A language and environment for statistical computing. Available from: https://www.R-project.org. [Last accessed on 6 Aug 2025].

47. Valero-Mora PM. ggplot2: elegant graphics for data analysis. J Stat Softw. 2010.

48. Oksanen J, Simpson GL, Blanchet FG, et al. Package ‘vegan’. Available from: https://cran.r-project.org/web/packages/vegan/vegan.pdf. [Last accessed on 6 Aug 2025].

49. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Stat Methodol. 1995;57:289-300.

50. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.

51. Letunic I, Bork P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res. 2024;52:W78-82.

52. Kau AL, Ahern PP, Griffin NW, Goodman AL, Gordon JI. Human nutrition, the gut microbiome and the immune system. Nature. 2011;474:327-36.

53. Valdes AM, Walter J, Segal E, Spector TD. Role of the gut microbiota in nutrition and health. BMJ. 2018;361:k2179.

54. O’Callaghan A, van Sinderen D. Bifidobacteria and their role as members of the human gut microbiota. Front Microbiol. 2016;7:925.

55. Rinninella E, Raoul P, Cintoni M, et al. What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms. 2019;7:14.

56. Hill C, Guarner F, Reid G, et al. Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol. 2014;11:506-14.

57. Hughes RL, Alvarado DA, Swanson KS, Holscher HD. The prebiotic potential of inulin-type fructans: a systematic review. Adv Nutr. 2022;13:492-529.

58. Scott KP, Gratz SW, Sheridan PO, Flint HJ, Duncan SH. The influence of diet on the gut microbiota. Pharmacol Res. 2013;69:52-60.

59. Bindels LB, Delzenne NM, Cani PD, Walter J. Towards a more comprehensive concept for prebiotics. Nat Rev Gastroenterol Hepatol. 2015;12:303-10.

60. Xiao M, Zhang C, Duan H, et al. Cross-feeding of bifidobacteria promotes intestinal homeostasis: a lifelong perspective on the host health. NPJ Biofilms Microbiomes. 2024;10:47.

61. González R, Klaassens ES, Malinen E, de Vos WM, Vaughan EE. Differential transcriptional response of Bifidobacterium longum to human milk, formula milk, and galactooligosaccharide. Appl Environ Microbiol. 2008;74:4686-94.

62. Liu M, Liu Z, Zhang N, et al. Preparation of polysaccharides from Crepis tectorum Linn. and the regulation effects on intestinal microbiota. Process Biochem. 2023;130:50-66.

63. Gao X, Xu F, Li T, et al. CAZymes-associated method to explore glycans that mitigate DSS-induced colitis via targeting Bacteroides cellulosilyticus. Int J Biol Macromol. 2024;258:128694.

64. Peterson CT, Sharma V, Iablokov SN, et al. 16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics. PLoS One. 2019;14:e0213869.

65. Aguirre M, Bussolo de Souza C, Venema K. The gut microbiota from lean and obese subjects contribute differently to the fermentation of arabinogalactan and inulin. PLoS One. 2016;11:e0159236.

66. He X, Zhao S, Li Y, Chen T. Faecalibacterium prausnitzii: a next-generation probiotic in gut disease improvement. Can J Infect Dis Med Microbiol. 2021;2021:1-10.

67. Fujita K, Sasaki Y, Kitahara K. Degradation of plant arabinogalactan proteins by intestinal bacteria: characteristics and functions of the enzymes involved. Appl Microbiol Biotechnol. 2019;103:7451-7.

68. Hirmas B, Gasaly N, Orellana G, et al. Metabolic modeling and bidirectional culturing of two gut microbes reveal cross-feeding interactions and protective effects on intestinal cells. mSystems. 2022;7:e0064622.

69. Steinert RE, Rehman A, Sadabad MS, et al. Microbial micronutrient sharing, gut redox balance and keystone taxa as a basis for a new perspective to solutions targeting health from the gut. Gut Microbes. 2025;17:2477816.

70. Ku S, Haque MA, Jang MJ, et al. The role of Bifidobacterium in longevity and the future of probiotics. Food Sci Biotechnol. 2024;33:2097-110.

71. Wong CB, Odamaki T, Xiao J. Beneficial effects of Bifidobacterium longum subsp. longum BB536 on human health: modulation of gut microbiome as the principal action. J Funct Foods. 2019;54:506-19.

72. Gossling J, Moore WEC. Gemmiger formicilis, n.gen., n.sp., an anaerobic budding bacterium from intestines. Int J Syst Bacteriol. 1975;25:202-7.

73. Salanitro JP, Muirhead PA, Goodman JR. Morphological and physiological characteristics of Gemmiger formicilis isolated from chicken ceca. Appl Environ Microbiol. 1976;32:623-32.

74. Zenner C, Hitch TCA, Riedel T, et al. Early-life immune system maturation in chickens using a synthetic community of cultured gut bacteria. mSystems. 2021;6:e01300-20.

75. Fitzgerald CB, Shkoporov AN, Sutton TDS, et al. Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa. BMC Genomics. 2018;19:931.

76. Guo W, Sun L, Yue H, et al. Associations of intermittent hypoxia burden with gut microbiota dysbiosis in adult patients with obstructive sleep apnea. Nat Sci Sleep. 2024;16:1483-95.

77. Qian L, Huang J, Qin H. Probiotics and dietary intervention modulate the colonic mucosa-associated microbiota in high-fat diet populations. Turk J Gastroenterol. 2020;31:295-304.

78. Arnold JW, Roach J, Fabela S, et al. The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut. Microbiome. 2021;9:31.

79. Alberto F, Bignon C, Sulzenbacher G, Henrissat B, Czjzek M. The three-dimensional structure of invertase (beta-fructosidase) from Thermotoga maritima reveals a bimodular arrangement and an evolutionary relationship between retaining and inverting glycosidases. J Biol Chem. 2004;279:18903-10.

80. Andersen JM, Barrangou R, Abou Hachem M, et al. Transcriptional analysis of oligosaccharide utilization by Bifidobacterium lactis Bl-04. BMC Genomics. 2013;14:312.

81. Fujita K, Tsunomachi H, Lixia P, et al. Bifidobacterial GH146 β-L-arabinofuranosidase for the removal of β1,3-L-arabinofuranosides on plant glycans. Appl Microbiol Biotechnol. 2024;108:199.

82. Fujita K, Sakamoto A, Kaneko S, Kotake T, Tsumuraya Y, Kitahara K. Degradative enzymes for type II arabinogalactan side chains in Bifidobacterium longum subsp. longum. Appl Microbiol Biotechnol. 2019;103:1299-310.

83. Fujita K, Takashi Y, Obuchi E, Kitahara K, Suganuma T. Characterization of a novel β-L-arabinofuranosidase in Bifidobacterium longum: functional elucidation of a DUF1680 protein family member. J Biol Chem. 2014;289:5240-9.

84. Xu J, Xu R, Jia M, Su Y, Zhu W. Metatranscriptomic analysis of colonic microbiota’s functional response to different dietary fibers in growing pigs. Anim Microbiome. 2021;3:45.

85. Li W, Lin X, Liang H, et al. Genomic and functional diversity of the human-derived isolates of Faecalibacterium. Front Microbiol. 2024;15:1379500.

86. Barlow JT, Bogatyrev SR, Ismagilov RF. A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities. Nat Commun. 2020;11:2590.

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