Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods

Авторы: Bulygin Ivan, Shatov Vladislav, Rykachevskiy Anton, Raiko Arsenii, Bernstein Alexander, Burnaev Evgeny, Gelfand Mikhail S.
Журнал: PeerJ
Том: 11
Год издания: 2023
Издательство: PeerJ
Местоположение издательства: San Francisco
Номер статьи: e15838
DOI: 10.7717/peerj.15838
Аннотация: Enterotypes of the human gut microbiome have been proposed to be a powerful prognostic tool to evaluate the correlation between lifestyle, nutrition, and disease. However, the number of enterotypes suggested in the literature ranged from two to four. The growth of available metagenome data and the use of exact, non-linear methods of data analysis challenges the very concept of clusters in the multidimensional space of bacterial microbiomes. Using several published human gut microbiome datasets of variable 16S rRNA regions, we demonstrate the presence of a lower-dimensional structure in the microbiome space, with high-dimensional data concentrated near a low-dimensional non-linear submanifold, but the absence of distinct and stable clusters that could represent enterotypes. This observation is robust with regard to diverse combinations of dimensionality reduction techniques and clustering algorithms.
Добавил в систему: Шатов Владислав Михайлович

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