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Dietary carbohydrates alter immune-modulatory functionalities and DNA inversions in Bacteroides thetaiotaomicron

Author

Listed:
  • Noa Gal-Mandelbaum

    (Technion-Israel Institute of Technology)

  • Shaqed Carasso

    (Technion-Israel Institute of Technology)

  • Alon Kedem

    (Technion-Israel Institute of Technology)

  • Tamar Ziv

    (Technion-Israel Institute of Technology)

  • Roni Keshet-David

    (Technion-Israel Institute of Technology)

  • Roberto Abboud

    (Technion-Israel Institute of Technology)

  • Rawan Zaatry

    (Technion-Israel Institute of Technology)

  • Tal Gefen

    (Technion-Israel Institute of Technology)

  • Naama Geva-Zatorsky

    (Technion-Israel Institute of Technology
    CIFAR)

Abstract

The gut bacteria environment is highly dynamic. Environmental conditions were shown to affect microbial composition. Yet, their influences on bacterial functionality (e.g., immune-modulation activity) are mostly overlooked. Distinct strains of the same species, and even the same bacterial strain, may have different effects on the immune system depending on their growth environment. Therefore, studying the functionality of strains under different conditions is crucial. We analyzed functional alterations in the gut symbiont Bacteroides thetaiotaomicron (B. theta) under different dietary components consumption in humans, upon white sugar consumption in mice, and in response to 190 different carbon sources in vitro. Dietary alterations affected the orientation of phase variable regions in B. theta in humans, in vivo, and in vitro, and altered B. theta’s proteome and immune-modulatory functionality. Studying the effects of dietary components on the immune-modulatory functionalities of key members of the gut microbiota will allow for personalized dietary recommendations.

Suggested Citation

  • Noa Gal-Mandelbaum & Shaqed Carasso & Alon Kedem & Tamar Ziv & Roni Keshet-David & Roberto Abboud & Rawan Zaatry & Tal Gefen & Naama Geva-Zatorsky, 2025. "Dietary carbohydrates alter immune-modulatory functionalities and DNA inversions in Bacteroides thetaiotaomicron," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-60202-9
    DOI: 10.1038/s41467-025-60202-9
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    1. Koji Atarashi & Takeshi Tanoue & Kenshiro Oshima & Wataru Suda & Yuji Nagano & Hiroyoshi Nishikawa & Shinji Fukuda & Takuro Saito & Seiko Narushima & Koji Hase & Sangwan Kim & Joëlle V. Fritz & Paul W, 2013. "Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota," Nature, Nature, vol. 500(7461), pages 232-236, August.
    2. Sarkis K. Mazmanian & June L. Round & Dennis L. Kasper, 2008. "A microbial symbiosis factor prevents intestinal inflammatory disease," Nature, Nature, vol. 453(7195), pages 620-625, May.
    3. Koji Atarashi & Junichi Nishimura & Tatsuichiro Shima & Yoshinori Umesaki & Masahiro Yamamoto & Masaharu Onoue & Hideo Yagita & Naoto Ishii & Richard Evans & Kenya Honda & Kiyoshi Takeda, 2008. "ATP drives lamina propria TH17 cell differentiation," Nature, Nature, vol. 455(7214), pages 808-812, October.
    4. Rachael B. Chanin & Patrick T. West & Jakob Wirbel & Matthew O. Gill & Gabriella Z. M. Green & Ryan M. Park & Nora Enright & Arjun M. Miklos & Angela S. Hickey & Erin F. Brooks & Krystal K. Lum & Ilea, 2024. "Intragenic DNA inversions expand bacterial coding capacity," Nature, Nature, vol. 634(8032), pages 234-242, October.
    5. Corinna M. Krinos & Michael J. Coyne & Katja G. Weinacht & Arthur O. Tzianabos & Dennis L. Kasper & Laurie E. Comstock, 2001. "Extensive surface diversity of a commensal microorganism by multiple DNA inversions," Nature, Nature, vol. 414(6863), pages 555-558, November.
    6. Neeraj K. Surana & Dennis L. Kasper, 2018. "Erratum: Moving beyond microbiome-wide associations to causal microbe identification," Nature, Nature, vol. 554(7692), pages 392-392, February.
    7. Mingming Sun & Wei Wu & Liang Chen & Wenjing Yang & Xiangsheng Huang & Caiyun Ma & Feidi Chen & Yi Xiao & Ye Zhao & Chunyan Ma & Suxia Yao & Victor H. Carpio & Sara M. Dann & Qihong Zhao & Zhanju Liu , 2018. "Microbiota-derived short-chain fatty acids promote Th1 cell IL-10 production to maintain intestinal homeostasis," Nature Communications, Nature, vol. 9(1), pages 1-15, December.
    8. Yukihiro Furusawa & Yuuki Obata & Shinji Fukuda & Takaho A. Endo & Gaku Nakato & Daisuke Takahashi & Yumiko Nakanishi & Chikako Uetake & Keiko Kato & Tamotsu Kato & Masumi Takahashi & Noriko N. Fukuda, 2013. "Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells," Nature, Nature, vol. 504(7480), pages 446-450, December.
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