Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling
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Abstract
Abstract The gut microbiome starts to be shaped in the first days of life and continues to increase its diversity during the first months. Several investigations are assessing the link between the configuration of the infant gut microbiome and infant health, but a comprehensive strain-level assessment of vertically transmitted microbes from mother to infant is still missing. We longitudinally collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life, and applied shotgun metagenomic sequencing followed by strain-level profiling. We observed several specific strains including those from Bifidobacterium bifidum , Coprococcus comes , and Ruminococcus bromii , that 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 the in vivo expression of vertically transmitted microbes, for example Bacteroides vulgatus and Bifidobacterium spp., thus suggesting that transmitted strains are functionally active in the two rather different environments of the adult and infant guts. By combining longitudinal microbiome sampling and newly developed computational tools for strain-level microbiome analysis, we showed that it is possible to track vertical transmission of members of the microbiome from mother to infants and characterize their transcriptional activity. Our work poses the basis for surveying at larger scale the sources of microbial diversity in the infants and starts associating these transmissions with the subsequent longer-term development of a healthy or dysbiotic microbiome. Importance Early infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support that the maternal microbial reservoir is a key route of microbial transmission, yet much is inferred from the observation of shared species in mother and infant. Common species, per se , does not necessarily equate vertical transmission as species exhibit considerable strain heterogeneity and it is therefore imperative to identify shared strains. We demonstrate here the potential of shotgun metagenomics and strain-level resolution to identify vertical transmission events via the maternal source. Combined with a metatranscriptomic approach, we show the potential not only to identify and track the fate of microbes in the early infant microbiome but also identify the metabolically active members. These approaches will ultimately provide important insights into the acquisition, development and community dynamics of the infant microbiome.
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Escherichia coli and Bifidobacterium species (B. uniformis, B. bifidum, B. breve, B. catenulatum) have been found to be highly transmitted from mother to child in several studies.
“that have been found to be highly transmitted from mother to child in several studies10,15,16,17,41 and that are also present but not shared in pairs from non-westernized populations (Figure 2C).”
From Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population (2023) · cites this paper as [15]
Escherichia coli and Bifidobacterium spp. are the most shared within European mother-infant pairs.
“While Escherichia coli and Bifidobacterium spp. are the most shared within the European pairs, as previously described,10,15,16,17,41”
From Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population (2023) · cites this paper as [15]
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Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303 · see citing works
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- Authors
- Asnicar, F., Manara, S., Zolfo, M., Truong, D. T., Scholz, M., Armanini, F., Ferretti, P., Gorfer, V., Pedrotti, A., Tett, A., & Segata, N.
- Affiliations
- University of Trento (IT)
- Provincia Autonoma di Trento (IT)
- Corresponding author
- Tett, Adrian
- Segata, Nicola
- ORCID
- Venue
- mSystems
- Publisher
- American Society for Microbiology
- Published
- 2017-02-28
- Volume
- 2
- Issue
- 1
- ISSN
- 2379-5077 (ISSN-L)
- PMC
- PMC5264247
- OpenAlex
- W2951579468
- Cited by
- 445
- References
- 89
- Citations by year
- 2026: 24 · 2025: 45 · 2024: 37 · 2023: 48 · 2022: 62 · 2021: 61 · 2020: 72 · 2019: 51 · 2018: 27 · 2017: 16 · 2016: 1
- FWCI
- 18.55
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- mSystems (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Iris (University of Trento) (submittedVersion, cc-by-nc)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Fondazione Caritro (Rif.Int.2013.0239, Rif.int.2014.0325)
- European Union, Marie Curie Actions (PCIG13-GA-2013-618833)
- MIUR - Futuro in Ricerca (RBFR13EWWI_001)
- Leo Pharma Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- vertical transmission, infant microbiome, strain heterogeneity, microbial transmission, metatranscriptomics, microbial community dynamics
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