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Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, Armanini F, Truong DT, Manara S, Zolfo M, Beghini F, Bertorelli R, De Sanctis V, Bariletti I, Canto R, Clementi R, Cologna M, Crifò T, Cusumano G, Gottardi S, Innamorati C, Masè C, Postai D, Savoi D, Duranti S, Lugli GA, Mancabelli L, Turroni F, Ferrario C, Milani C, Mangifesta M, Anzalone R, Viappiani A, Yassour M, Vlamakis H, Xavier R, Collado CM, Koren O, Tateo S, Soffiati M, Pedrotti A, Ventura M, Huttenhower C, Bork P, Segata N. Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome. Cell Host Microbe 2018; 24:133-145.e5. [PMID: 30001516 PMCID: PMC6716579 DOI: 10.1016/j.chom.2018.06.005] [Citation(s) in RCA: 640] [Impact Index Per Article: 106.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/17/2018] [Accepted: 06/14/2018] [Indexed: 02/08/2023]
Abstract
The acquisition and development of the infant microbiome are key to establishing a healthy host-microbiome symbiosis. The maternal microbial reservoir is thought to play a crucial role in this process. However, the source and transmission routes of the infant pioneering microbes are poorly understood. To address this, we longitudinally sampled the microbiome of 25 mother-infant pairs across multiple body sites from birth up to 4 months postpartum. Strain-level metagenomic profiling showed a rapid influx of microbes at birth followed by strong selection during the first few days of life. Maternal skin and vaginal strains colonize only transiently, and the infant continues to acquire microbes from distinct maternal sources after birth. Maternal gut strains proved more persistent in the infant gut and ecologically better adapted than those acquired from other sources. Together, these data describe the mother-to-infant microbiome transmission routes that are integral in the development of the infant microbiome.
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Affiliation(s)
- Pamela Ferretti
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy; European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Edoardo Pasolli
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Adrian Tett
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesco Asnicar
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | | | - Sabina Fedi
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Federica Armanini
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Duy Tin Truong
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Serena Manara
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Moreno Zolfo
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesco Beghini
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Roberto Bertorelli
- NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Veronica De Sanctis
- NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | | | - Rosarita Canto
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | | | - Marina Cologna
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Tiziana Crifò
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | | | | | | | - Caterina Masè
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Daniela Postai
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Daniela Savoi
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; GenProbio srl, 43124 Parma, Italy
| | - Rosaria Anzalone
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | | | - Moran Yassour
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carmen Maria Collado
- Institute of Agrochemistry and Food Technology, National Research Council, Paterna, 46980 Valencia, Spain
| | - Omry Koren
- Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
| | - Saverio Tateo
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | | | - Anna Pedrotti
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy.
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Duranti S, Lugli GA, Mancabelli L, Armanini F, Turroni F, James K, Ferretti P, Gorfer V, Ferrario C, Milani C, Mangifesta M, Anzalone R, Zolfo M, Viappiani A, Pasolli E, Bariletti I, Canto R, Clementi R, Cologna M, Crifò T, Cusumano G, Fedi S, Gottardi S, Innamorati C, Masè C, Postai D, Savoi D, Soffiati M, Tateo S, Pedrotti A, Segata N, van Sinderen D, Ventura M. Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission. Microbiome 2017; 5:66. [PMID: 28651630 PMCID: PMC5485682 DOI: 10.1186/s40168-017-0282-6] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/05/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND The correct establishment of the human gut microbiota represents a crucial development that commences at birth. Different hypotheses propose that the infant gut microbiota is derived from, among other sources, the mother's fecal/vaginal microbiota and human milk. RESULTS The composition of bifidobacterial communities of 25 mother-infant pairs was investigated based on an internal transcribed spacer (ITS) approach, combined with cultivation-mediated and genomic analyses. We identified bifidobacterial strains/communities that are shared between mothers and their corresponding newborns. Notably, genomic analyses together with growth profiling assays revealed that bifidobacterial strains that had been isolated from human milk are genetically adapted to utilize human milk glycans. In addition, we identified particular bacteriophages specific of bifidobacterial species that are common in the viromes of mother and corresponding child. CONCLUSIONS This study highlights the transmission of bifidobacterial communities from the mother to her child and implies human milk as a potential vehicle to facilitate this acquisition. Furthermore, these data represent the first example of maternal inheritance of bifidobacterial phages, also known as bifidophages in infants following a vertical transmission route.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | | | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Kieran James
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Pamela Ferretti
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | | | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | | | - Rosaria Anzalone
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Moreno Zolfo
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | | | - Edoardo Pasolli
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | | | - Rosarita Canto
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | | | - Marina Cologna
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | - Tiziana Crifò
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | | | - Sabina Fedi
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | | | | | - Caterina Masè
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | - Daniela Postai
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | - Daniela Savoi
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | | | - Saverio Tateo
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | - Anna Pedrotti
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
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