Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking

被引:2
|
作者
Wong, Daniel P. G. H. [1 ]
Good, Benjamin H. [1 ,2 ,3 ]
机构
[1] Stanford Univ, Dept Appl Phys, Stanford, CA 94305 USA
[2] Stanford Univ, Dept Biol, Stanford, CA 94305 USA
[3] Chan Zuckerberg Biohub San Francisco, San Francisco, CA 94158 USA
基金
美国国家卫生研究院;
关键词
FITNESS; ADAPTATION; MICROBIOME; EVOLUTION; SYMBIONT; LEAVES;
D O I
10.1038/s41467-024-45792-0
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Gut microbiota can adapt to their host environment by rapidly acquiring new mutations. However, the dynamics of this process are difficult to characterize in dominant gut species in their complex in vivo environment. Here we show that the fine-scale dynamics of genome-wide transposon libraries can enable quantitative inferences of these in vivo evolutionary forces. By analyzing >400,000 lineages across four human Bacteroides strains in gnotobiotic mice, we observed positive selection on thousands of cryptic variants - most of which were unrelated to their original gene knockouts. The spectrum of fitness benefits varied between species, and displayed diverse tradeoffs over time and in different dietary conditions, enabling inferences of their underlying function. These results suggest that within-host adaptations arise from an intense competition between numerous contending variants, which can strongly influence their emergent evolutionary tradeoffs.
引用
收藏
页数:14
相关论文
共 50 条
  • [31] Adaptive optics for high-resolution imaging
    Nature Reviews Methods Primers, 1 (1):
  • [32] Adaptive optics for high-resolution imaging
    Karen M. Hampson
    Raphaël Turcotte
    Donald T. Miller
    Kazuhiro Kurokawa
    Jared R. Males
    Na Ji
    Martin J. Booth
    Nature Reviews Methods Primers, 1
  • [33] High-resolution structural imaging of volcanoes using improved muon tracking
    Bajou, R.
    Rosas-Carbajal, M.
    Tonazzo, A.
    Marteau, J.
    GEOPHYSICAL JOURNAL INTERNATIONAL, 2023, 235 (02) : 1138 - 1149
  • [34] High-resolution landscape of an antibiotic binding site
    Kevin B. Yang
    Maria Cameranesi
    Manjunath Gowder
    Criseyda Martinez
    Yosef Shamovsky
    Vitaliy Epshtein
    Zhitai Hao
    Thao Nguyen
    Eric Nirenstein
    Ilya Shamovsky
    Aviram Rasouly
    Evgeny Nudler
    Nature, 2023, 622 : 180 - 187
  • [35] Triggering the adaptive immune system with commensal gut bacteria protects against insulin resistance and dysglycemia
    Pomie, Celine
    Blasco-Baque, Vincent
    Klopp, Pascale
    Nicolas, Simon
    Waget, Aurelie
    Loubieres, Pascale
    Azalbert, Vincent
    Puel, Anthony
    Lopez, Frederic
    Dray, Cedric
    Valet, Philippe
    Lelouvier, Benjamin
    Servant, Florence
    Courtney, Michael
    Amar, Jacques
    Burcelin, Remy
    Garidou, Lucile
    MOLECULAR METABOLISM, 2016, 5 (06): : 392 - 403
  • [36] Quantifying bird migration by a high-resolution weather radar
    Nebuloni, Roberto
    Capsoni, Carlo
    Vigorita, Vittorio
    IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING, 2008, 46 (06): : 1867 - 1875
  • [37] Using high-resolution displays for high-resolution cardiac data
    Goodyer, Christopher
    Hodrien, John
    Wood, Jason
    Kohl, Peter
    Brodlie, Ken
    PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 2009, 367 (1898): : 2667 - 2677
  • [38] Quantifying Agulhas Leakage in a High-Resolution Climate Model
    Cheng, Yu
    Putrasahan, Dian
    Beal, Lisa
    Kirtman, Ben
    JOURNAL OF CLIMATE, 2016, 29 (19) : 6881 - 6892
  • [39] PROPOSAL FOR A SEMICONDUCTOR HIGH-RESOLUTION TRACKING DETECTOR
    REHAK, P
    NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH, 1983, 211 (2-3): : 323 - 329
  • [40] Tracking algorithm for high-resolution DOA estimation
    Zhou, Yunzhong
    Chen, Tianqi
    Huang, Xiangfu
    Dianzi Kexue Xuekan/Journal of Electronics, 1997, 19 (03): : 300 - 305