in

Reply to: Erroneous predictions of auxotrophies by CarveMe

[adace-ad id="91168"]
  • Machado, D. et al. Polarization of microbial communities between competitive and cooperative metabolism. Nat. Ecol. Evol. 5, 195–203 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Thompson, L. R. et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Price, M. Erroneous predictions of auxotrophies by CarveMe. https://doi.org/10.1038/s41559-022-01936-3 (2022).

  • Machado, D., Andrejev, S., Tramontano, M. & Patil, K. R. Fast automated reconstruction of genome-scale metabolic models for microbial species and communities. Nucleic Acids Res. 46, 7542–7553 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Price, M. N., Deutschbauer, A. M. & Arkin, A. P. GapMind: automated annotation of amino acid biosynthesis. mSystems 5, e00291-20 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mee, M. T., Collins, J. J., Church, G. M. & Wang, H. H. Syntrophic exchange in synthetic microbial communities. Proc. Natl. Acad. Sci. USA 111, E2149–E2156 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ponomarova, O. et al. Yeast creates a niche for symbiotic lactic acid bacteria through nitrogen overflow. Cell Syst. 5, 345–357.e6 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zengler, K. & Zaramela, L. S. The social network of microorganisms—how auxotrophies shape complex communities. Nat. Rev. Microbiol. 16, 383–390 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Giri, S. et al. Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria. Curr. Biol. 31, 5547–5557.e6 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Morris, J. J., Lenski, R. E. & Zinser, E. R. The black queen hypothesis: evolution of dependencies through adaptive gene loss. mBio 3, e00036-12 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Campbell, K. et al. Self-establishing communities enable cooperative metabolite exchange in a eukaryote. eLife 4, e09943 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • D’Souza, G. & Kost, C. Experimental evolution of metabolic dependency in bacteria. PLOS Genet. 12, e1006364 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ziesack, M. et al. Engineered interspecies amino acid cross-feeding increases population evenness in a synthetic bacterial consortium. mSystems 4, e00352-19 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ryback, B., Bortfeld-Miller, M. & Vorholt, J. A. Metabolic adaptation to vitamin auxotrophy by leaf-associated bacteria. ISME J. https://doi.org/10.1038/s41396-022-01303-x (2022).


  • Source: Ecology - nature.com

    Comparison of the effects of litter decomposition process on soil erosion under simulated rainfall

    World leaders must step up to put biodiversity deal on path to success