title: Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling.
abstract: The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during the first months. Links between the configuration of the infant gut microbiome and infant health are being shown, but a comprehensive strain-level assessment of microbes vertically transmitted from mother to infant is still missing. We collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life and applied shotgun metagenomic sequencing followed by computational strain-level profiling. We observed that several specific strains, including those ofBifidobacterium bifidum,Coprococcus comes, andRuminococcus bromii, were present in samples from the same mother-infant pair, while being clearly distinct from those carried by other pairs, which is indicative of vertical transmission. We further applied metatranscriptomics to study thein vivogene expression of vertically transmitted microbes and found that transmitted strains ofBacteroidesandBifidobacteriumspecies were transcriptionally active in the guts of both adult and infant. By combining longitudinal microbiome sampling and newly developed computational tools for strain-level microbiome analysis, we demonstrated that it is possible to track the vertical transmission of microbial strains from mother to infants and to characterize their transcriptional activity. Our work provides the foundation for larger-scale surveys to identify the routes of vertical microbial transmission and its influence on postinfancy microbiome development.IMPORTANCEEarly infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support for the idea that the maternal microbial reservoir is a key route of microbial transmission, and yet much is inferred from the observation of shared species in mother and infant. The presence of common species,per se, does not necessarily equate to vertical transmission, as species exhibit considerable strain heterogeneity. It is therefore imperative to assess whether shared microbes belong to the same genetic variant (i.e., strain) to support the hypothesis of vertical transmission. Here we demonstrate the potential of shotgun metagenomics and strain-level profiling to identify vertical transmission events. Combining these data with metatranscriptomics, we show that it is possible not only to identify and track the fate of microbes in the early infant microbiome but also to investigate the actively transcribing members of the community. These approaches will ultimately provide important insights into the acquisition, development, and community dynamics of the infant microbiome.
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Francesco
authors.identifier: 0000-0003-3732-1468
authors.initials: F
authors.lastname: Asnicar
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Serena
authors.initials: S
authors.lastname: Manara
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Moreno
authors.identifier: 0000-0001-6661-4046
authors.initials: M
authors.lastname: Zolfo
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Duy Tin
authors.initials: DT
authors.lastname: Truong
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Matthias
authors.identifier: 0000-0003-1414-5924
authors.initials: M
authors.lastname: Scholz
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Federica
authors.initials: F
authors.lastname: Armanini
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Pamela
authors.initials: P
authors.lastname: Ferretti
authors.affiliation: Azienda Provinciale per i Servizi Sanitari, Trento, Italy.
authors.forename: Valentina
authors.initials: V
authors.lastname: Gorfer
authors.affiliation: Azienda Provinciale per i Servizi Sanitari, Trento, Italy.
authors.forename: Anna
authors.initials: A
authors.lastname: Pedrotti
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Adrian
authors.initials: A
authors.lastname: Tett
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Nicola
authors.identifier: 0000-0002-1583-5794
authors.initials: N
authors.lastname: Segata
keywords: infant microbiome; metagenomics; microbial ecology; microbial genomics; vertical microbiome transmission