Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

Pamela Ferretti,Roberto Bertorelli,Francesco Asnicar,Stefania Gottardi,Gabriele Andrea Lugli,Rosarita Canto,Hera Vlamakis,Veronica De Sanctis,Moran Yassour,Duy Tin Truong,Francesca Turroni,Sabina Fedi,Rosaria Anzalone,Marina Cologna,Giuseppina Cusumano,Tiziana Crifò,Edoardo Pasolli,Ilaria Bariletti,Valentina Gorfer,Curtis Huttenhower,Marta Mangifesta,Omry Koren,Serena Manara,Daniela Postai,Chiara Ferrario,Peer Bork,Alice Viappiani,Leonardo Mancabelli,Claudia Innamorati,Adrian Tett,Federica Armanini,Christian Milani,Rosanna Clementi,Daniela Savoi,Francesco Beghini,Moreno Zolfo,Massimo Soffiati,Nicola Segata,Marco Ventura,Saverio Tateo,Sabrina Duranti,Anna Pedrotti,Caterina Masè,María Carmen Collado ,Ramnik J Xavier

doi:10.1016/j.chom.2018.06.005

Abstract

SummaryThe 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.

Highlights

To use strain-level profiling to identify and quantify the instances of transmission from external sources to the infant. This has been shown for a limited number of cultivable species (Makino et al, 2011; Milani et al, 2015), and we previously demonstrated that the maternal microbial reservoir is an important source in the early acquisition of microbial species and strains in the infant gut (Asnicar et al, 2017; Korpela et al, 2018)
When looking at strain identity within the shared oral-gut species, we found that S. salivarius (Figure 5C) and R. mucilaginosa (Figure 5B) were the species with the highest number of shared strains (Table S5E)
These results suggest that S. salivarius and R. mucilaginosa might have an increased capacity to survive in both the oral cavity and the gut, at least for a limited time

Summary

Methods

METHOD DETAILSSample Collection The samples collection procedure was based on HMP sampling guidelines (Human Microbiome Project Consortium, 2012b). After pre-moistening with 2 ml SCF-1 buffer (50 mM Tris buffer, pH 7.6, 1mM EDTA, pH 8.0, and 0.5% Tween-20) (Human Microbiome Project Consortium, 2012b) contained in a 15 ml sterile screw top collection tube (Sarstedt, Nu€mbrecht, Germany), the swab head was rubbed back and forth for approximately 30 seconds over the area (repeating twice) before the swab was returned to the buffered solution. The swab was rubbed 5 times, with a circular motion, in the vaginal introitus and the swab head was placed in a 15 ml sterile screw top collection tube containing 2 ml SCF-1 buffer. Stool samples from the mother were collected during or shortly after the delivery by the hospital staff, using collection tubes specific for faecal material (Sarstedt, Nu€mbrecht, Germany). Normally three days after delivery, the mothers performed the collection of the infants’ stool samples at home and put the samples immediately at -20C, which were delivered to the hospital staff within 12 hours

Results

Discussion

Conclusion