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Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns
Open accessAbstract
Upon delivery, the neonate is exposed for the first time to a wide array of microbes from a variety of sources, including maternal bacteria. Although prior studies have suggested that delivery mode shapes the microbiota's establishment and, subsequently, its role in child health, most researchers have focused on specific bacterial taxa or on a single body habitat, the gut. Thus, the initiation stage of human microbiome development remains obscure. The goal of the present study was to obtain a community-wide perspective on the influence of delivery mode and body habitat on the neonate's first microbiota. We used multiplexed 16S rRNA gene pyrosequencing to characterize bacterial communities from mothers and their newborn babies, four born vaginally and six born via Cesarean section. Mothers' skin, oral mucosa, and vagina were sampled 1 h before delivery, and neonates' skin, oral mucosa, and nasopharyngeal aspirate were sampled <5 min, and meconium <24 h, after delivery. We found that in direct contrast to the highly differentiated communities of their mothers, neonates harbored bacterial communities that were undifferentiated across multiple body habitats, regardless of delivery mode. Our results also show that vaginally delivered infants acquired bacterial communities resembling their own mother's vaginal microbiota, dominated by Lactobacillus, Prevotella, or Sneathia spp., and C-section infants harbored bacterial communities similar to those found on the skin surface, dominated by Staphylococcus, Corynebacterium, and Propionibacterium spp. These findings establish an important baseline for studies tracking the human microbiome's successional development in different body habitats following different delivery modes, and their associated effects on infant health.
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“in that study there was no relation between the specific skin microbiota of the mother and the microbiota of their C-section born infants, demonstrating that bacterial colonization originates from non-maternal sources.”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Dominguez-Bello et al., 2010
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“The infant and child microbiota is susceptible to a range of environmental influences, from birth mode (vaginal vs C-section), and birth location (home vs hospital) , to diet, (including breastfeeding versus formula feeding) (Azad et al., 2013;Biasucci et al., 2010;Dominguez-Bello et al., 2010;Ho et al., 2018), maternal gestational diet and weight gain (Baumann-Dudenhoeffer et al., 2018;Seppo et”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Dominguez-Bello et al., 2010
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Infants born vaginally are exposed to maternal vaginal and intestinal microbiota, including Lactobacillus, Bacteroides, and Bifidobacterium species.”
From Elective cesarean section versus vaginal delivery: A comparative analysis of maternal and neonatal outcomes (2026) · cites this paper as Dominguez-Bello et al., 2010
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Cesarean-born infants tend to show delayed colonization by maternal commensal bacteria and increased colonization by skin and environmental microorganisms, especially when antibiotic prophylaxis, delayed breastfeeding, or neonatal intensive care admission occurs (Dominguez-Bello et al., 2010).”
From Elective cesarean section versus vaginal delivery: A comparative analysis of maternal and neonatal outcomes (2026) · cites this paper as Dominguez-Bello et al., 2010
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
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“A seminal study has shown that there is vertical transmission of bacteria from the mother to the newborn, with the microbiota of vaginally-delivered babies closely resembling the vaginal microbiota of their mothers (Dominguez-Bello et al., 2010).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Dominguez-Bello et al., 2010
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In the citing paper
“the initial colonization of bacteria in C-section delivered babies seems to be dominated by bacteria typically present on the skin and in the environment, with increased levels of Staphylococcus spp.(Dominguez-Bello et al., 2010).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Dominguez-Bello et al., 2010
The cited source says what the claim attributes to it.
In the citing paper
“C-section born babies also have a higher risk of developing neonatal infections by methicillin-resistant Staphylococcus aureus, (Dominguez-Bello et al., 2010) or C. difficile (Penders et al., 2006).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Dominguez-Bello et al., 2010
In the citing paper
“Infants born vaginally are initially colonized by bacterial taxa found in the vagina, such as Lactobacillus and Prevotella, whereas infants who are born by Cesarean section are initially colonized by bacteria found in the skin microbiota2.”
From Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease (2014) · cites this paper as [2]
In the citing paper
“Significant colonization of the gut begins immediately after delivery although, remarkably, bacteria can be found in an infant's first meconium2.”
From Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease (2014) · cites this paper as [2]
In the citing paper
“Mode of birth, whether through natural birthing process or Caesarean section (C-section), drives the initial seeding of the infant microbiome, such that babies delivered via the vaginal canal can be discriminated from those delivered by C-section based on their microbiome (102–104).”
From Emerging Roles for the Gut Microbiome in Autism Spectrum Disorder (2017) · cites this paper as [102]
In the citing paper
“Multiple modulators impact this initial colonization, including delivery mode that impacts on the composition of the initial microbiota across multiple body habitats.27”
From Interaction between microbiota and immunity in health and disease (2020) · cites this paper as [27]
In the citing paper
“the microbiota of C-section delivered infants resembles that populating the skin of adults, with Streptococci being a dominant species [85].”
From Antibiotic-Induced Changes in the Intestinal Microbiota and Disease (2016) · cites this paper as [85]
In the citing paper
“During the first hours of life, a wide range of microorganisms can be detected in the URT of healthy term neonates19,20.”
From The microbiota of the respiratory tract: gatekeeper to respiratory health (2017) · cites this paper as [19]
In the citing paper
“The result is long-term compositional differences in gut microbiota by mode of birth20–24, with differences observed up until age seven24.”
From The relation between cesarean birth and child cognitive development (2017) · cites this paper as [21]
In the citing paper
“Several factors are known to influence microbial composition at different stages of life, including genetic factors, mode of delivery [vaginal birth or Caesarean section (C-section)], gestational age, exercise, medication use, living environment, and diet (237-240).”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [237]
In the citing paper
“Thus, naturally born infants are exposed to the mother's vaginal bacteria, whereas babies born by C-section are first introduced to bacteria of the mother's skin, the hospital environment, or the healthcare workers (237).”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [237]
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“Importantly, the gut microbiota of vaginally born infants closely resembles the microbial compositions of the mothers’ vagina, while newborns delivered via cesarean section are enriched with microbes found on human skin and in the surrounding environment [25].”
BackgroundGut microbiome and liver diseases
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“92 Factors associated with allergy such as birth delivery mode (caesarean section vs vaginal delivery), 93 antibiotic use in the newborn and infant, and non-breast-milk diets are also associated with shifts in the gut microbiota.”
BackgroundChapter 12: Human Microbiome Analysis
Morgan, X. C., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002808 · Cited by 496
Metadata
- Authors
- Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R.
- Affiliations
- Department of Biology, University of Puerto Rico, San Juan, Puerto Rico 00931;
- University of Colorado Boulder (US)
- Center of Biophysics and Biochemistry, Venezuelan Institute for Scientific Research, Caracas 1020A, Venezuela;
- Amazonic Center for Research and Control of Tropical Diseases, Puerto Ayacucho 7101, Amazonas, Venezuela; and
- Cooperative Institute for Research in Environmental Sciences (US)
- Howard Hughes Medical Institute (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2010-06-21
- Volume
- 107
- Issue
- 26
- Pages
- 11971-11975
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC2900693
- OpenAlex
- W2023506796
- Cited by
- 4,774
- References
- 7
- Citations by year
- 2026: 202 · 2025: 292 · 2024: 285 · 2023: 338 · 2022: 403 · 2021: 419 · 2020: 437 · 2019: 415 · 2018: 378 · 2017: 359 · 2016: 339 · 2015: 252 · 2014: 226 · 2013: 186 · 2012: 125
- FWCI
- 54.29
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Crohn's and Colitis Foundation
- National Human Genome Research Institute (R01HG004872)
- 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 › Immunology and Microbiology › Microbiology › Reproductive tract infections research
- Keywords
- mode of delivery, vaginal delivery, cesarean section, neonatal microbiome, skin microbiome, oral microbiota, vaginal microbiota, meconium, maternal microbiota, Lactobacillus, Prevotella, Sneathia, Staphylococcus, Corynebacterium, Propionibacterium, microbial colonization
- MeSH terms
- Adult, Bacteria, Base Sequence, Cesarean Section, Female, Humans, Infant, Newborn, Male, Mouth Mucosa, Nasopharynx, Pregnancy, RNA, Bacterial, RNA, Ribosomal, 16S, Skin, Vagina, Venezuela, Ecosystem, DNA Primers, Delivery, Obstetric, Metagenome, Young Adult
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