“Delivery Mode Shapes the Acquisition and Structure of the Initial Microbiota across Multiple Body Habitats in Newborns” (2010), by Maria G. Dominguez-Bello, Elizabeth K. Costello, Monica Contreras, Magda Magris, Glida Hidalgo, Noah Fierer, and Rob Knight

In 2010, Maria Dominguez-Bello, Elizabeth Costello, Monica Contreras, and colleagues published “Delivery Mode Shapes the Acquisition and Structure of the Initial Microbiota Across Multiple Body Habitats in Newborns,” hereafter “Delivery Mode” in the journal Proceedings of the National Academy of Sciences. The term microbiota, which the authors use interchangeably with the term microbiome, refers to the collection of microorganisms, including bacteria, fungi, and viruses, found in and on the human body. The development of the microbiome, which begins at birth when a newborn is first exposed to the mother’s microbiota, impacts the development of the immune system, and how a person’s body responds to disease. Though researchers in the early 2000s were aware of a connection between delivery mode and the neonatal gut microbiome, they knew little about how delivery mode affects a neonate’s microbiome beyond the gut. Dominguez-Bello and associates’ experiment was one of the first to show that a neonate’s microbial community is uniform across their body and elaborate on the differences in microbiomes across delivery methods, which can make neonates born via c-section more susceptible to conditions such as asthma.

1. Background
2. Article Contents
3. Impacts

Background

In their article, Dominguez-Bello and colleagues report on experiments evaluating the connection between the mother’s microbiome and their neonate’s. Each person has a unique microbiome, and in the gut, there are ten times more microbes than there are human cells. The microbial community begins developing when a neonate is first exposed to microbes. That happens during and after birth, from contact with the mother’s skin and the mother’s vaginal canal. The microbiome continues developing afterwards, depending on the environments the neonate is exposed to and the microbes within those environments. The immune system initially develops in response to the microbes in the gut, some of which are harmful, and some of which are not. After the immune system is first exposed to harmful microbes, it will be able to recognize those microbes in the future and respond to them. The authors investigated whether different methods of delivering a fetus, which expose it to different kinds of bacteria, would alter its subsequently forming microbiome and immune system. The main delivery modes they investigated were vaginal birth and cesarean section, hereafter c-section, which is a delivery procedure during which a doctor removes a neonate through an incision in a pregnant person’s abdomen.

The authors of “Delivery Mode” collaborated internationally to conduct their study in Amazonas State, Venezuela. At the time of publication, Dominguez-Bello was in the Department of Biology, University of Puerto Rico in San Juan, Puerto Rico. Costello was in the Department of Microbiology and Immunology at Stanford University at Stanford Medicine in Stanford, California. Contreras was with the Center of Biophysics and Biochemistry at Venezuelan Institute for Scientific Research in Caracas, Venezuela. Magris and Hidalgo were with the Amazonic Center for Research and Control of Tropical Diseases in Puerto Ayacucho, Amazonas, Venezuela. Fierer was with the Department of Ecology and Evolutionary Biology, and the Cooperative Institute for Research in Environmental Sciences, at the University of Colorado in Boulder, Colorado. And Knight was with the Department of Chemistry and Biochemistry at the University of Colorado in Boulder, Colorado and was an Investigator of the Howard Hughes Medical Institute.

In the early 2000s, scientists were aware of a connection between delivery mode and a neonate’s gut microbiome, but there was little research on how the microbiome differs across different areas of the neonate's body. A 1999 study was one of the first to research the connection between delivery mode and the gut microbiome. The researchers of that study compared fecal microbiota, which reflect the microbiota in the gut, of neonates born by c-section and neonates born vaginally. The researchers found that infants born by c-sections have different gut microbiota than infants born vaginally, and that their gut microbiota can remain different for around six months, as compared to the original gut bacterial community of newborns born vaginally.

In contrast to the 1999 study, Dominguez-Bello and colleagues aimed to compare multiple areas of the body of neonates born vaginally and by c-section to determine if each neonate’s microbiota was uniform across their entire body, or if different areas of the neonates’ bodies had different microbiota, as adults do. Dominguez-Bello and colleagues also looked to find if the microbiome of neonates born by c-section is representative of their mothers’ skin microbiota, similar to how the bacterial community of neonates born vaginally reflect the mother’s vaginal microbiome. The authors of “Delivery Mode” followed a group of nine women at a hospital in Venezuela and collected samples of their bacterial communities before birth, and their neonates’ bacterial communities right after birth to study the differences between microbiota in infants born vaginally and those born by c-section.

Article Contents

The authors organized “Delivery Mode,” into three main parts: an untitled introductory section, followed by a “Results and Discussion” section, and ending with a “Methods” section. In the untitled introduction section, the authors explain that while scientists were aware of a connection between delivery mode and the gut microbiome prior to their study, the goal of their study was to understand the development of the entire neonatal microbiome across different areas of the body and how it differs based on the delivery mode. In “Results and Discussion” the authors explain that their study found that the neonatal microbiome is uniform across all areas of the body regardless of the delivery method. The team continues the section by explaining that neonates born by c-section develop bacterial communities most similar to that of their mother’s skin, and the lack of vaginal bacteria may lead to allergies and asthma, while neonates born vaginally develop bacterial communities most similar to that of their mother’s vagina. In “Methods,” the authors discuss their collection methods for swabbing the mothers and neonates near the time of delivery, and the sequencing methods that allowed them to understand and compare the dominant bacteria they found in the different areas of the body of mothers, and across the neonatal microbiome.

In the unnamed introductory section, Dominguez-Bello and colleagues introduce the idea that neonates born by different delivery modes are exposed to different initial microbiota. The authors explain how the bacteria encountered immediately during and after birth colonize the neonate’s microbiome. The team notes that microbiome development and initial bacterial colonization impacts immune function and long-term health. The researchers discuss that, prior to their study, most other publications focused on the impact of microbiome colonization in the gut, not necessarily the entire body. The authors describe that the goal of the study is to characterize and understand the development of the bacterial communities present in neonates born vaginally and by c-section across different areas of the neonate’s body. According to the authors, their findings are important for understanding the development of the human microbiome based on delivery mode, and how the development can impact neonatal and infantile health.

In the “Results and Discussion” section, the authors explain that they used nine patients from a hospital in Venezuela to determine that delivery mode affected the vertical transmission of bacteria from mother to newborn. Five of the women gave birth via c-section, and four delivered vaginally. The authors note that they gathered samples from the mother’s skin, mouth, and vagina an hour before delivery. The team gathered samples from the neonate’s oral lining, skin, and upper respiratory passage within five minutes of delivery, and the neonate’s first stool within twenty-four hours of delivery. They explain that, to identify the dominant bacteria present across different areas of the body, they used polymerase chain reaction, or PCR, which is a technique used by scientists to create many copies of DNA or RNA sequences from a small sample that they can then study in further detail and identify the bacteria that those sequences belong to. They explain that their findings show that each of the areas of the mothers’ bodies, including skin, mouth, and vagina, had different dominant bacterial strains, but those strains were typical to that region. The dominant bacterial strains in the vagina varied among the mothers. The authors discuss that each of the neonates had the same dominant bacteria present across all areas of their bodies. Furthermore, the microbiome of neonates delivered vaginally had dominant bacteria that reflected the bacteria present in their mother’s vagina. The microbiome of neonates delivered via c-section lacked bacteria present in the vagina, and had bacteria that was similar to that of their mother’s skin.

The authors also found that delivery mode affects how similar the mother’s microbiota is to the neonate’s microbiota. In neonates born vaginally, the mother’s vaginal bacterial community was significantly more similar to her neonate’s microbiota than to the other neonates delivered vaginally. The team explained that because the mother-child pair is similar and unique to each pair, the vaginal delivery method has a large impact in establishing the neonate’s microbiota via vertical transmission from the mother to child. In neonates born by c-section, the mother’s skin bacteria were no more similar to her own neonate’s bacterial community than to the microbiota of other neonates born by c-section. The authors suggest that incidental exposure to bacteria in the hospital environment could contribute to establishing the initial microbiome of infants delivered by c-section.

Finally, in “Results and Discussion,” Dominguez-Bello and colleagues reference other studies to show that a lack of vaginal exposure during birth could result in higher susceptibility to allergies and asthma. The authors explain that other studies have found that certain bacterial communities develop much later, which may cause health issues. They cite other studies to show that lack of exposure to vaginal microbiota could result in higher risk of the neonate developing conditions like allergies and asthma. They conclude the section with the recommendation that further research would aid in understanding how the microbiome develops from one uniform microbiome into different microbiota in different areas of the body.

In “Methods,” the authors discuss the DNA extraction and sequencing procedures they employed to understand the dominant bacteria present in different body areas of the mothers and neonates. The authors split the methods section into eight sub-sections that explain the researcher’s procedures for gathering information. In the first subsection, “Subjects,” the authors detail the ethnicities of the participants, and that they informed the subjects about the details of the study in order to ensure that they were able to consent to their and their newborns’ involvement in the study. In the second subsection, “Sample Collection,” the authors discuss that they sampled the infants by swabbing their skin and mouth seconds after delivery, and their nasal passage within minutes of delivery. They explain that they sampled the mother’s skin, mouth, and vagina an hour before delivery, and the researchers froze all the samples to preserve the bacterial communities. In the third subsection, “DNA Extraction and Purification,” the authors describe the methods of extracting the DNA by placing the tips of the swabs in a solution in a test tube, incubating the solution, and then shaking the test tubes at high speeds to isolate the extracted DNA solution, which the researchers stored at negative twenty degrees Celsius for preservation. In the fourth, fifth, and sixth subsections, the authors explain their PCR and DNA sequence analysis process, by which they were able to understand what kinds of bacteria were present in different body areas of the mothers and neonates.

Next, in the seventh subsection, “Community Comparisons,” the authors explain that they used a computer program called UniFrac metric, which measures the evolutionary similarities of two bacteria, to determine the diversity between two bacterial communities. That process allowed them to compare the similarities between communities such as the mothers’ vaginal microbiota and the bacteria present on the neonate’s skin. In the eighth subsection, “Statistics,” the authors describe the statistical programs they used to help determine similarities among sample groups, which helped them to compare more than one group at a time. The programs allowed them to see the statistical differences to help determine which groups were most significantly different, and to compare the similarities of groups with the similarities of other groups. The example they provide for the comparison is between the similarities of bacterial communities in mothers with their own neonates compared to other neonates.

Impacts

“Delivery Mode” was one of the first articles to identify that after birth, a neonate’s microbiome is uniform across their entire body, and elaborate on how delivery mode impacts microbiome formation. As of 2024, the study has been cited over 56,000 times, and has informed further research on the role of the microbiome in immune development, with many publications focusing on the gut microbiome. “Delivery mode” has been cited in multiple articles finding a clear connection and information transfer through signaling between the gut microbiome and the brain. One of those articles, which researchers from the Oswaldo Cruz Institute in Rio de Janeiro, Brazil, published in 2020, found that the gut microbiota communicate with the brain through neural pathways, and that the gut microbiota can influence brain function. Another article citing “Delivery mode,” found that without proper communication between the microbiome and immune system, a person can be more susceptible to immune disorders.

Dominguez-Bello and colleagues’ research laid a foundation for future research aiming to uncover the relationship between c-sections and the development of health conditions related to the microbiota a neonate is first exposed to during and after birth. Understanding the initial microbial exposures of neonates can help researchers potentially prevent health conditions such as allergies and asthma later in life. The team’s research underscores the broader implications of delivery modes on long-term health outcomes, highlighting the importance of the microbiome in shaping our earliest defenses against disease.

Sources

1. Bokulich, Nicholas, Jennifer Chung, Thomas Battaglia, et al. “Antibiotics, Birth Mode, and Diet Shape Microbiome Maturation during Early Life.” Science Translational Medicine 8 (2016): 343ra82–343ra82. https://www.researchgate.net/publication/304006596_Antibiotics_birth_mode_and_diet_shape_microbiome_maturation_during_early_life (Accessed June 17, 2024).
2. Costello, Elizabeth, Daniel DiGiulio, Anna Robaczewska, et al. “Longitudinal Dynamics of the Human Vaginal Ecosystem across the Reproductive Cycle.” Nature Communications. https://www.biorxiv.org/content/10.1101/2022.11.20.517263v1 (Accessed July 3, 2024).
3. Dominguez-Bello, Maria G., Elizabeth K. Costello, Monica Contreras, et al. “Delivery Mode Shapes the Acquisition and Structure of the Initial Microbiota across Multiple Body Habitats in Newborns.” Proceedings of the National Academy of Sciences 107 (2010): 11971–5. https://doi.org/10.1073/pnas.1002601107 (Accessed June 17, 2024).
4. Fios Genomics. “Microbiome vs Microbiota.” Fios Genomics. https://www.fiosgenomics.com/microbiome-vs-microbiota/ (Accessed June 17, 2024).
5. Garcia-Amado, Maria, Hakdong Shin, Virginia Sanz D'Angelo, et al. “Comparison of Gizzard and Intestinal Microbiota of Wild Neotropical Birds.” PLOS ONE 13 (2018): e0194857. 10.1371/journal.pone.0194857 (Accessed June 17, 2024).
6. Grölund, Minna-Maija, Olli-Pekka Lehtonen, Erkki Eerola, et al. “Fecal Microflora in Healthy Infants Born by Different Methods of Delivery: Permanent Changes in Intestinal Flora After Cesarean Delivery.” Journal of Pediatric Gastroenterology and Nutrition 28 (1999): 19–25.
7. MedlinePlus. “Autoimmune Diseases” MedlinePlus. https://medlineplus.gov/autoimmunediseases.html (Accessed June 17, 2024).
8. National Human Genome Research Institute. “Polymerase Chain Reaction (PCR).” National Human Genome Research Institute. Last updated June 17, 2024. https://www.genome.gov/genetics-glossary/Polymerase-Chain-Reaction (Accessed June 17, 2024).
9. Rutgers Global Health Institute. “Maria Gloria Dominguez-Bello.” Rutgers Global Health Institute. https://globalhealth.rutgers.edu/directory/maria-gloria-dominguez-bello/ (Accessed June 17, 2024).
10. Silva, Ygor Parladore, Andressa Bernardi, Rudimar Luiz Frozza. “The Role of Short-Chain Fatty Acids from Gut Microbiota in Gut-Brain Communication.” Frontiers in Endocrinology 11 (2020): 25. 10.3389/fendo.2020.00025 (Accessed June 17, 2024).
11. Symul, Laura, Pratheepa Jeganathan, Elizabeth K Costello, et al. “Sub-Communities of the Vaginal Ecosystem in Pregnant and Non-Pregnant Women.” Proceedings. Biological Sciences 290 (2011): 20231461. 0.1098/rspb.2023.1461 (Accessed June 17, 2024).
12. Thursby, Elizabeth, and Nathalie Juge. “Introduction to the Human Gut Microbiota.” The Biochemical Journal 474 (2017): 1823–36. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5433529/ (Accessed June 17, 2024).
13. Zheng, Danping, Timur Liwinsk, Eran Elinav. “Interaction between Microbiota and Immunity in Health and Disease.” Cell Research 30 (2020): 492–506. https://doi.org/10.1038/s41422-020-0332-7 (Accessed June 17, 2024).