Genetic strategies for sex-biased persistence of gut microbes across human life

Chiara Tarracchini, Giulia Alessandri, Federico Fontana, Sonia Mirjam Rizzo, Gabriele Andrea Lugli, Massimiliano Giovanni Bianchi, Leonardo Mancabelli, Giulia Longhi, Chiara Argentini, Laura Maria Vergna, Rosaria Anzalone, Alice Viappiani, Francesca Turroni, Giuseppe Taurino, Martina Chiu, Silvia Arboleya, Miguel Gueimonde, Ovidio Bussolati, Douwe Sinderen, Christian Milani () and Marco Ventura ()
Additional contact information
Chiara Tarracchini: University of Parma
Giulia Alessandri: University of Parma
Federico Fontana: University of Parma
Sonia Mirjam Rizzo: University of Parma
Gabriele Andrea Lugli: University of Parma
Massimiliano Giovanni Bianchi: University of Parma
Leonardo Mancabelli: University of Parma
Giulia Longhi: University of Parma
Chiara Argentini: University of Parma
Laura Maria Vergna: University of Parma
Rosaria Anzalone: GenProbio srl
Alice Viappiani: GenProbio srl
Francesca Turroni: University of Parma
Giuseppe Taurino: University of Parma
Martina Chiu: University of Parma
Silvia Arboleya: Instituto de Productos Lácteos de Asturias, CSIC
Miguel Gueimonde: Instituto de Productos Lácteos de Asturias, CSIC
Ovidio Bussolati: University of Parma
Douwe Sinderen: National University of Ireland
Christian Milani: University of Parma
Marco Ventura: University of Parma

Nature Communications, 2023, vol. 14, issue 1, 1-16

Abstract: Abstract Although compositional variation in the gut microbiome during human development has been extensively investigated, strain-resolved dynamic changes remain to be fully uncovered. In the current study, shotgun metagenomic sequencing data of 12,415 fecal microbiomes from healthy individuals are employed for strain-level tracking of gut microbiota members to elucidate its evolving biodiversity across the human life span. This detailed longitudinal meta-analysis reveals host sex-related persistence of strains belonging to common, maternally-inherited species, such as Bifidobacterium bifidum and Bifidobacterium longum subsp. longum. Comparative genome analyses, coupled with experiments including intimate interaction between microbes and human intestinal cells, show that specific bacterial glycosyl hydrolases related to host-glycan metabolism may contribute to more efficient colonization in females compared to males. These findings point to an intriguing ancient sex-specific host-microbe coevolution driving the selective persistence in women of key microbial taxa that may be vertically passed on to the next generation.

Date: 2023
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DOI: 10.1038/s41467-023-39931-2

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