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.
“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
The Results and Discussion report that C-section mothers’ skin communities were no more similar to their own babies’ microbiota than to that of other C-section babies. But the authors say nonmaternal exposures could contribute and explicitly note that their data do not identify specific sources; they do not demonstrate that colonization originates from nonmaternal sources. Page numbers are not provided in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measuredThe infant and child microbiota is susceptible to a range of environmental influences, including birth mode, birth location, diet, maternal gestational diet and weight gain, pet ownership, physical illness, antibiotic use, and stress.
“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
The Results and Discussion (page not specified in our copy) identify delivery mode as the primary determinant of the newborns’ initial bacterial communities and mention a suggested effect of breastfeeding. The paper does not establish effects of home versus hospital birth or formula versus breastfeeding, so it supports only part of the environmental-influences claim attributed to this citation. (LLM, conf=0.86)
Experimental — accuracy not yet measuredA seminal study has shown 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.
“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
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.
“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
C-section born babies have a higher risk of developing neonatal infections by methicillin-resistant Staphylococcus aureus or C. difficile.
“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
Vaginally born infants are initially colonized by vaginal taxa such as Lactobacillus and Prevotella, whereas Cesarean-born infants are initially colonized by skin microbiota.
“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]
Significant gut colonization begins immediately after delivery, and bacteria can be found in an infant's first meconium.
“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]
Mode of birth drives the initial seeding of the infant microbiome, such that babies delivered vaginally can be discriminated from those delivered by C-section based on their microbiome.
“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]
Delivery mode impacts the composition of the initial microbiota across multiple body habitats.
“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]
C-section-delivered infants have a microbiota resembling adult skin, with Streptococci as a dominant species.
“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]
During the first hours of life, a wide range of microorganisms can be detected in the upper respiratory tract of healthy term neonates.
“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]
There are long-term compositional differences in gut microbiota by mode of birth, with differences observed up until age seven.
“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]
Several factors are known to influence microbial composition at different stages of life, including genetic factors, mode of delivery, gestational age, exercise, medication use, living environment, and diet.
“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]
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.
“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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Cites
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227 · see citing works
Self-citationBacterial Community Variation in Human Body Habitats Across Space and Time
Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I., & Knight, R. (2009) · Science · doi:10.1126/science.1177486 · Cited by 3,231 · see citing works
Self-citationMechanisms underlying the resistance to diet-induced obesity in germ-free mice
Bäckhed, F., Manchester, J. K., Semenkovich, C. F., & Gordon, J. I. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605374104 · Cited by 2,615 · see citing works
Samuel, B. S., Shaito, A., Motoike, T., Rey, F. E., Backhed, F., Manchester, J. K., Hammer, R. E., Williams, S. C., Crowley, J., Yanagisawa, M., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808567105 · Cited by 1,564 · see citing works
Cesarean Delivery May Affect the Early Biodiversity of Intestinal Bacteria1,
Biasucci, G., Benenati, B., Morelli, L., Bessi, E., & Boehm, G. (2008) · The Journal of Nutrition · doi:10.1093/jn/138.9.1796s · Cited by 458 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [34]Coppa GV, Zampini L, Galeazzi T, Gabrielli O (2006) Prebiotics in human milk: A review. Dig Liver Dis 38(Suppl 2):S291 -S294.
Cited by
Sorted by citations
Breastfeeding in the 21st century: epidemiology, mechanisms, and lifelong effect
Victora, C. G., Bahl, R., Barros, A. J. D., França, G. V. A., Horton, S., Krasevec, J., Murch, S., Sankar, M. J., Walker, N., & Rollins, N. C. (2016) · The Lancet · doi:10.1016/s0140-6736(15)01024-7 · Cited by 8,040 · see citing works
Human gut microbiome viewed across age and geography
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815 · see citing works
Self-citationDiversity, stability and resilience of the human gut microbiota
Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012) · Nature · doi:10.1038/nature11550 · Cited by 5,533 · see citing works
Self-citationCryan, J. F., O'Riordan, K. J., Cowan, C. S. M., Sandhu, K. V., Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. V., et al. (2019) · Physiological Reviews · doi:10.1152/physrev.00018.2018 · Cited by 5,286 · see citing works
Host-gut microbiota metabolic interactions
Nicholson, J. K., Holmes, E., Kinross, J., Burcelin, R., Gibson, G., Jia, W., & Pettersson, S. (2012) · Science · doi:10.1126/science.1223813 · Cited by 4,760 · see citing works
Proteobacteria: Microbial signature of dysbiosis in gut microbiota
Shin, N.-R., Whon, T. W., & Bae, J.-W. (2015) · Trends in Biotechnology · doi:10.1016/j.tibtech.2015.06.011 · Cited by 3,954 · see citing works
Interaction between microbiota and immunity in health and disease
Zheng, D., Liwinski, T., & Elinav, E. (2020) · Cell Research · doi:10.1038/s41422-020-0332-7 · Cited by 3,947 · see citing works
Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
Ridaura, V. K., Faith, J. J., Rey, F. E., Cheng, J., Duncan, A. E., Kau, A. L., Griffin, N. W., Lombard, V., Henrissat, B., Bain, J. R., et al. (2013) · Science · doi:10.1126/science.1241214 · Cited by 3,788 · see citing works
Self-citationThe gut microbiota--masters of host development and physiology
Sommer, F., & Bäckhed, F. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro2974 · Cited by 3,681 · see citing works
The impact of the gut microbiota on human health: an integrative view
Clemente, J. C., Ursell, L. K., Parfrey, L. W., & Knight, R. (2012) · Cell · doi:10.1016/j.cell.2012.01.035 · Cited by 3,710 · see citing works
Self-citationThe Human Intestinal Microbiome in Health and Disease
Lynch, S. V., & Pedersen, O. (2016) · New England Journal of Medicine · doi:10.1056/nejmra1600266 · Cited by 3,637 · see citing works
Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life
Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., Li, Y., Xia, Y., Xie, H., Zhong, H., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.004 · Cited by 3,315 · see citing works
Rinninella, E., Raoul, P., Cintoni, M., Franceschi, F., Miggiano, G. A. D., Gasbarrini, A., & Mele, M. C. (2019) · Microorganisms · doi:10.3390/microorganisms7010014 · Cited by 3,462 · see citing works
Grice, E. A., & Segre, J. A. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2537 · Cited by 3,143 · see citing works
The Role of Short-Chain Fatty Acids From Gut Microbiota in Gut-Brain Communication
Silva, Y. P., Bernardi, A., & Frozza, R. L. (2020) · Frontiers in Endocrinology · doi:10.3389/fendo.2020.00025 · Cited by 3,043 · see citing works
“Furthermore, delivery mode (47) and early-life occurrences such as feeding changes, infection, and antibiotics treatment (48, 49) have a huge effect on the gutmicrobiota composition with a long-term impact on brain and behavior (9, 29).”
BackgroundRole of the normal gut microbiota
Jandhyala, S. M. (2015) · World Journal of Gastroenterology · doi:10.3748/wjg.v21.i29.8787 · Cited by 3,001 · see citing works
Byrd, A. L., Belkaid, Y., & Segre, J. A. (2018) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.157 · Cited by 2,806 · see citing works
The Placenta Harbors a Unique Microbiome
Aagaard, K., Ma, J., Antony, K. M., Ganu, R., Petrosino, J., & Versalovic, J. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3008599 · Cited by 2,494 · see citing works
Population-level analysis of gut microbiome variation
Falony, G., Joossens, M., Vieira-Silva, S., Wang, J., Darzi, Y., Faust, K., Kurilshikov, A., Bonder, M. J., Valles-Colomer, M., Vandeputte, D., et al. (2016) · Science · doi:10.1126/science.aad3503 · Cited by 2,400 · see citing works
Gut biogeography of the bacterial microbiota
Donaldson, G. P., Lee, S. M., & Mazmanian, S. K. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro3552 · Cited by 2,535 · see citing works
How colonization by microbiota in early life shapes the immune system
Gensollen, T., Iyer, S. S., Kasper, D. L., & Blumberg, R. S. (2016) · Science · doi:10.1126/science.aad9378 · Cited by 2,044 · see citing works
Serotonin, tryptophan metabolism and the brain-gut-microbiome axis
O’Mahony, S. M., Clarke, G., Borre, Y. E., Dinan, T. G., & Cryan, J. F. (2015) · Behavioural Brain Research · doi:10.1016/j.bbr.2014.07.027 · Cited by 2,012 · see citing works
Milani, C., Duranti, S., Bottacini, F., Casey, E., Turroni, F., Mahony, J., Belzer, C., Delgado Palacio, S., Arboleya Montes, S., Mancabelli, L., et al. (2017) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00036-17 · Cited by 1,950 · see citing works
Cox, L. M., Yamanishi, S., Sohn, J., Alekseyenko, A. V., Leung, J. M., Cho, I., Kim, S. G., Li, H., Gao, Z., Mahana, D., et al. (2014) · Cell · doi:10.1016/j.cell.2014.05.052 · Cited by 1,859 · see citing works
Lloyd-Price, J., Abu-Ali, G., & Huttenhower, C. (2016) · Genome Medicine · doi:10.1186/s13073-016-0307-y · Cited by 1,891 · see citing works
Dysbiosis and the immune system
Levy, M., Kolodziejczyk, A. A., Thaiss, C. A., & Elinav, E. (2017) · Nature Reviews Immunology · doi:10.1038/nri.2017.7 · Cited by 1,769 · see citing works
Reciprocal interactions of the intestinal microbiota and immune system
Maynard, C. L., Elson, C. O., Hatton, R. D., & Weaver, C. T. (2012) · Nature · doi:10.1038/nature11551 · Cited by 1,598 · see citing works
Unravelling the effects of the environment and host genotype on the gut microbiome
Spor, A., Koren, O., & Ley, R. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2540 · Cited by 1,509 · see citing works
The Application of Ecological Theory Toward an Understanding of the Human Microbiome
Costello, E. K., Stagaman, K., Dethlefsen, L., Bohannan, B. J. M., & Relman, D. A. (2012) · Science · doi:10.1126/science.1224203 · Cited by 1,437 · see citing works
Self-citationOdamaki, T., Kato, K., Sugahara, H., Hashikura, N., Takahashi, S., Xiao, J.-Z., Abe, F., & Osawa, R. (2016) · BMC Microbiology · doi:10.1186/s12866-016-0708-5 · Cited by 1,521 · see citing works
Short-chain fatty acids: Linking diet, the microbiome and immunity
Mann, E. R., Lam, Y. K., & Uhlig, H. H. (2024) · Nature reviews. Immunology · doi:10.1038/s41577-024-01014-8 · Cited by 1,595 · see citing works
The central nervous system and the gut microbiome
Sharon, G., Sampson, T. R., Geschwind, D. H., & Mazmanian, S. K. (2016) · Cell · doi:10.1016/j.cell.2016.10.027 · Cited by 1,513 · see citing works
An insight into gut microbiota and its functionalities
Adak, A., & Khan, M. R. (2019) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-018-2943-4 · Cited by 1,485 · see citing works
Antibiotics, birth mode, and diet shape microbiome maturation during early life
Bokulich, N. A., Chung, J., Battaglia, T., Henderson, N., Jay, M., Li, H., D. Lieber, A., Wu, F., Perez-Perez, G. I., Chen, Y., et al. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aad7121 · Cited by 1,469 · see citing works
Self-citationKang, D.-W., Adams, J. B., Gregory, A. C., Borody, T., Chittick, L., Fasano, A., Khoruts, A., Geis, E., Maldonado, J., McDonough-Means, S., et al. (2017) · Microbiome · doi:10.1186/s40168-016-0225-7 · Cited by 1,391 · see citing works
The role of gut microbiota in immune homeostasis and autoimmunity
Wu, H.-J., & Wu, E. (2012) · Gut Microbes · doi:10.4161/gmic.19320 · Cited by 1,426 · see citing works
The microbiota of the respiratory tract: gatekeeper to respiratory health
Man, W. H., de Steenhuijsen Piters, W. A. A., & Bogaert, D. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.14 · Cited by 1,384 · see citing works
The Integrative Human Microbiome Project
The Integrative HMP (iHMP) Research Network Consortium, Proctor, L. M., Creasy, H. H., Fettweis, J. M., Lloyd-Price, J., Mahurkar, A., Zhou, W., Buck, G. A., Snyder, M. P., Strauss, J. F., et al. (2019) · Nature · doi:10.1038/s41586-019-1238-8 · Cited by 1,381 · see citing works
Ferretti, P., Pasolli, E., Tett, A., Asnicar, F., Gorfer, V., Fedi, S., Armanini, F., Truong, D. T., Manara, S., Zolfo, M., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.06.005 · Cited by 1,292 · see citing works
Ursell, L. K., Metcalf, J. L., Parfrey, L. W., & Knight, R. (2012) · Nutrition Reviews · doi:10.1111/j.1753-4887.2012.00493.x · Cited by 1,255 · see citing works
Self-citationPaneth cells, antimicrobial peptides and maintenance of intestinal homeostasis
Bevins, C. L., & Salzman, N. H. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2546 · Cited by 1,238 · see citing works
The first 1000 cultured species of the human gastrointestinal microbiota
Rajilić-Stojanović, M., & de Vos, W. M. (2014) · FEMS Microbiology Reviews · doi:10.1111/1574-6976.12075 · Cited by 1,182 · see citing works
The microbiome in early life: Implications for health outcomes
Tamburini, S., Shen, N., Wu, H. C., & Clemente, J. C. (2016) · Nature Medicine · doi:10.1038/nm.4142 · Cited by 1,213 · see citing works
Minireview: Gut microbiota: The neglected endocrine organ
Clarke, G., Stilling, R. M., Kennedy, P. J., Stanton, C., Cryan, J. F., & Dinan, T. G. (2014) · Molecular Endocrinology · doi:10.1210/me.2014-1108 · Cited by 1,192 · see citing works
Perez-Muñoz, M. E., Arrieta, M.-C., Ramer-Tait, A. E., & Walter, J. (2017) · Microbiome · doi:10.1186/s40168-017-0268-4 · Cited by 1,096 · see citing works
Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth
Shao, Y., Forster, S. C., Tsaliki, E., Vervier, K., Strang, A., Simpson, N., Kumar, N., Stares, M. D., Rodger, A., Brocklehurst, P., et al. (2019) · Nature · doi:10.1038/s41586-019-1560-1 · Cited by 1,088 · see citing works
Kelly, J. R., Kennedy, P. J., Cryan, J. F., Dinan, T. G., Clarke, G., & Hyland, N. P. (2015) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2015.00392 · Cited by 1,110 · see citing works
Microbiota and neurodevelopmental windows: implications for brain disorders
Borre, Y. E., O’Keeffe, G. W., Clarke, G., Stanton, C., Dinan, T. G., & Cryan, J. F. (2014) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2014.05.002 · Cited by 1,089 · see citing works
Yassour, M., Vatanen, T., Siljander, H., Hämäläinen, A.-M., Härkönen, T., Ryhänen, S. J., Franzosa, E. A., Vlamakis, H., Huttenhower, C., Gevers, D., et al. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aad0917 · Cited by 1,043 · see citing works
Chu, D. M., Ma, J., Prince, A. L., Antony, K. M., Seferovic, M. D., & Aagaard, K. M. (2017) · Nature Medicine · doi:10.1038/nm.4272 · Cited by 1,063 · see citing works
The resilience of the intestinal microbiota influences health and disease
Sommer, F., Anderson, J. M., Bharti, R., Raes, J., & Rosenstiel, P. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.58 · Cited by 1,058 · see citing works
Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer
Dominguez-Bello, M. G., De Jesus-Laboy, K. M., Shen, N., Cox, L. M., Amir, A., Gonzalez, A., Bokulich, N. A., Song, S. J., Hoashi, M., Rivera-Vinas, J. I., et al. (2016) · Nature Medicine · doi:10.1038/nm.4039 · Cited by 1,014 · see citing works
Self-citationJakobsson, H. E., Abrahamsson, T. R., Jenmalm, M. C., Harris, K., Quince, C., Jernberg, C., Björkstén, B., Engstrand, L., & Andersson, A. F. (2014) · Gut · doi:10.1136/gutjnl-2012-303249 · Cited by 1,011 · see citing works
The Microbiome and the Respiratory Tract
Dickson, R. P., Erb-Downward, J. R., Martinez, F. J., & Huffnagle, G. B. (2016) · Annual Review of Physiology · doi:10.1146/annurev-physiol-021115-105238 · Cited by 953 · see citing works
Exploring the bovine rumen bacterial community from birth to adulthood
Jami, E., Israel, A., Kotser, A., & Mizrahi, I. (2013) · The ISME Journal · doi:10.1038/ismej.2013.2 · Cited by 963 · see citing works
From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways
Rogers, G. B., Keating, D. J., Young, R. L., Wong, M.-L., Licinio, J., & Wesselingh, S. (2016) · Molecular Psychiatry · doi:10.1038/mp.2016.50 · Cited by 969 · see citing works
Towards standards for human fecal sample processing in metagenomic studies
Costea, P. I., Zeller, G., Sunagawa, S., Pelletier, E., Alberti, A., Levenez, F., Tramontano, M., Driessen, M., Hercog, R., Jung, F.-E., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3960 · Cited by 893 · see citing works
Antibiotic-Induced Changes in the Intestinal Microbiota and Disease
Becattini, S., Taur, Y., & Pamer, E. G. (2016) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2016.04.003 · Cited by 901 · see citing works
Intestinal microbiota in functional bowel disorders: a Rome foundation report
Simrén, M., Barbara, G., Flint, H. J., Spiegel, B. M. R., Spiller, R. C., Vanner, S., Verdu, E. F., Whorwell, P. J., & Zoetendal, E. G. (2013) · Gut · doi:10.1136/gutjnl-2012-302167 · Cited by 939 · see citing works
Microbiota: a key orchestrator of cancer therapy
Roy, S., & Trinchieri, G. (2017) · Nature Reviews Cancer · doi:10.1038/nrc.2017.13 · Cited by 883 · see citing works
Effects of gut microbes on nutrient absorption and energy regulation
Krajmalnik‐Brown, R., Ilhan, Z., Kang, D., & DiBaise, J. K. (2012) · Nutrition in Clinical Practice · doi:10.1177/0884533611436116 · Cited by 852 · see citing works
Cabrera-Rubio, R., Collado, M. C., Laitinen, K., Salminen, S., Isolauri, E., & Mira, A. (2012) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.112.037382 · Cited by 886 · see citing works
Bäckhed, F., Fraser, C. M., Ringel, Y., Sanders, M. E., Sartor, R. B., Sherman, P. M., Versalovic, J., Young, V., & Finlay, B. B. (2012) · Cell Host & Microbe · doi:10.1016/j.chom.2012.10.012 · Cited by 836 · see citing works
The microbiome of uncontacted Amerindians
Clemente, J. C., Pehrsson, E. C., Blaser, M. J., Sandhu, K., Gao, Z., Wang, B., Magris, M., Hidalgo, G., Contreras, M., Noya-Alarcón, Ó., et al. (2015) · Science Advances · doi:10.1126/sciadv.1500183 · Cited by 851 · see citing works
Self-citationMicrobiota and Host Nutrition across Plant and Animal Kingdoms
Hacquard, S., Garrido-Oter, R., González, A., Spaepen, S., Ackermann, G., Lebeis, S., McHardy, A. C., Dangl, J. L., Knight, R., Ley, R., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.009 · Cited by 779 · see citing works
Self-citationExercise alters gut microbiota composition and function in lean and obese humans
ALLEN, J. M., MAILING, L. J., NIEMIRO, G. M., MOORE, R., COOK, M. D., WHITE, B. A., HOLSCHER, H. D., & WOODS, J. A. (2018) · Medicine & Science in Sports & Exercise · doi:10.1249/mss.0000000000001495 · Cited by 820 · see citing works
Gut instincts: microbiota as a key regulator of brain development, ageing and neurodegeneration
Dinan, T. G., & Cryan, J. F. (2017) · The Journal of Physiology · doi:10.1113/jp273106 · Cited by 813 · see citing works
The human microbiome: Our second genome
Grice, E. A., & Segre, J. A. (2012) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090711-163814 · Cited by 759 · see citing works
The microbiome in infectious disease and inflammation
Honda, K., & Littman, D. R. (2012) · Annual Review of Immunology · doi:10.1146/annurev-immunol-020711-074937 · Cited by 791 · see citing works
Dietary metabolism, the gut microbiome, and heart failure
Tang, W. H. W., Li, D. Y., & Hazen, S. L. (2019) · Nature Reviews Cardiology · doi:10.1038/s41569-018-0108-7 · Cited by 789 · see citing works
Low gut microbiota diversity in early infancy precedes asthma at school age
Abrahamsson, T. R., Jakobsson, H. E., Andersson, A. F., Björkstén, B., Engstrand, L., & Jenmalm, M. C. (2014) · Clinical & Experimental Allergy · doi:10.1111/cea.12253 · Cited by 750 · see citing works
Gut microbiome and aging: physiological and mechanistic insights
Nagpal, R., Mainali, R., Ahmadi, S., Wang, S., Singh, R., Kavanagh, K., Kitzman, D. W., Kushugulova, A., Marotta, F., & Yadav, H. (2018) · Nutrition and Healthy Aging · doi:10.3233/nha-170030 · Cited by 670 · see citing works
Our gut microbiome: The evolving inner self
Kundu, P., Blacher, E., Elinav, E., & Pettersson, S. (2017) · Cell · doi:10.1016/j.cell.2017.11.024 · Cited by 633 · see citing works
Martínez, I., Kim, J., Duffy, P. R., Schlegel, V. L., & Walter, J. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015046 · Cited by 645 · see citing works
The role of the microbiome in cancer development and therapy
Bhatt, A. P., Redinbo, M. R., & Bultman, S. J. (2017) · CA A Cancer Journal for Clinicians · doi:10.3322/caac.21398 · Cited by 653 · see citing works
Maturation of the gut microbiome and risk of asthma in childhood
Stokholm, J., Blaser, M. J., Thorsen, J., Rasmussen, M. A., Waage, J., Vinding, R. K., Schoos, A.-M. M., Kunøe, A., Fink, N. R., Chawes, B. L., et al. (2018) · Nature Communications · doi:10.1038/s41467-017-02573-2 · Cited by 614 · see citing works
Development of the gut microbiota in infancy and its impact on health in later life
Tanaka, M., & Nakayama, J. (2017) · Allergology International · doi:10.1016/j.alit.2017.07.010 · Cited by 639 · see citing works
Microbial genes, brain & behaviour – epigenetic regulation of the gut–brain axis
Stilling, R. M., Dinan, T. G., & Cryan, J. F. (2014) · Genes, Brain and Behavior · doi:10.1111/gbb.12109 · Cited by 637 · see citing works
Review article: dietary fibre-microbiota interactions
Simpson, H. L., & Campbell, B. J. (2015) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.13248 · Cited by 602 · see citing works
Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease
Albenberg, L. G., & Wu, G. D. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.01.058 · Cited by 606 · see citing works
Interaction of dietary compounds, especially polyphenols, with the intestinal microbiota: a review
Duda-Chodak, A., Tarko, T., Satora, P., & Sroka, P. (2015) · European Journal of Nutrition · doi:10.1007/s00394-015-0852-y · Cited by 599 · see citing works
Emerging Roles for the Gut Microbiome in Autism Spectrum Disorder
Vuong, H. E., & Hsiao, E. Y. (2017) · Biological Psychiatry · doi:10.1016/j.biopsych.2016.08.024 · Cited by 595 · see citing works
Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans
Hagan, T., Cortese, M., Rouphael, N., Boudreau, C., Linde, C., Maddur, M. S., Das, J., Wang, H., Guthmiller, J., Zheng, N.-Y., et al. (2019) · Cell · doi:10.1016/j.cell.2019.08.010 · Cited by 572 · see citing works
A wave of regulatory T cells into neonatal skin mediates tolerance to commensal microbes
Scharschmidt, T. C., Vasquez, K. S., Truong, H.-A., Gearty, S. V., Pauli, M. L., Nosbaum, A., Gratz, I. K., Otto, M., Moon, J. J., Liese, J., et al. (2015) · Immunity · doi:10.1016/j.immuni.2015.10.016 · Cited by 586 · see citing works
Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort
Hill, C. J., Lynch, D. B., Murphy, K., Ulaszewska, M., Jeffery, I. B., O’Shea, C. A., Watkins, C., Dempsey, E., Mattivi, F., Tuohy, K., et al. (2017) · Microbiome · doi:10.1186/s40168-016-0213-y · Cited by 573 · see citing works
Garcia-Mantrana, I., Selma-Royo, M., Alcantara, C., & Collado, M. C. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00890 · Cited by 574 · see citing works
Anxiety, depression, and the microbiome: A role for gut peptides
Lach, G., Schellekens, H., Dinan, T. G., & Cryan, J. F. (2018) · Neurotherapeutics · doi:10.1007/s13311-017-0585-0 · Cited by 573 · see citing works
Collective unconscious: How gut microbes shape human behavior
Dinan, T. G., Stilling, R. M., Stanton, C., & Cryan, J. F. (2015) · Journal of Psychiatric Research · doi:10.1016/j.jpsychires.2015.02.021 · Cited by 571 · see citing works
The Gut–Brain Axis and the Microbiome: Mechanisms and Clinical Implications
Osadchiy, V., Martin, C. R., & Mayer, E. A. (2019) · Clinical Gastroenterology and Hepatology · doi:10.1016/j.cgh.2018.10.002 · Cited by 555 · see citing works
Gut microbiota, obesity and diabetes
Patterson, E., Ryan, P. M., Cryan, J. F., Dinan, T. G., Ross, R. P., Fitzgerald, G. F., & Stanton, C. (2016) · Postgraduate Medical Journal · doi:10.1136/postgradmedj-2015-133285 · Cited by 552 · see citing works
Koren, O., Knights, D., Gonzalez, A., Waldron, L., Segata, N., Knight, R., Huttenhower, C., & Ley, R. E. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002863 · Cited by 508 · see citing works
Self-citationThe microbiome in patients with atopic dermatitis
Paller, A. S., Kong, H. H., Seed, P., Naik, S., Scharschmidt, T. C., Gallo, R. L., Luger, T., & Irvine, A. D. (2019) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2018.11.015 · Cited by 525 · see citing works
Diversity of the human skin microbiome early in life
Capone, K. A., Dowd, S. E., Stamatas, G. N., & Nikolovski, J. (2011) · Journal of Investigative Dermatology · doi:10.1038/jid.2011.168 · Cited by 532 · see citing works
The microbiome in autoimmune diseases
De Luca, F., & Shoenfeld, Y. (2018) · Clinical and Experimental Immunology · doi:10.1111/cei.13158 · Cited by 510 · see citing works
Lactobacillus species as biomarkers and agents that can promote various aspects of vaginal health
Petrova, M. I., Lievens, E., Malik, S., Imholz, N., & Lebeer, S. (2015) · Frontiers in Physiology · doi:10.3389/fphys.2015.00081 · Cited by 523 · see citing works
Gut microbiota and dysbiosis in Alzheimer's disease: Implications for pathogenesis and treatment
Liu, S., Gao, J., Zhu, M., Liu, K., & Zhang, H.-L. (2020) · Molecular Neurobiology · doi:10.1007/s12035-020-02073-3 · Cited by 516 · see citing works
Gut microbiome and liver diseases
Tilg, H., Cani, P. D., & Mayer, E. A. (2016) · Gut · doi:10.1136/gutjnl-2016-312729 · Cited by 525 · see citing works
An update on the use and investigation of probiotics in health and disease
Sanders, M. E., Guarner, F., Guerrant, R., Holt, P. R., Quigley, E. M., Sartor, R. B., Sherman, P. M., & Mayer, E. A. (2013) · Gut · doi:10.1136/gutjnl-2012-302504 · Cited by 503 · see citing works
Chapter 12: Human Microbiome Analysis
Morgan, X. C., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002808 · Cited by 496 · see citing works
Mode and place of delivery, gastrointestinal microbiota, and their influence on asthma and atopy
van Nimwegen, F. A., Penders, J., Stobberingh, E. E., Postma, D. S., Koppelman, G. H., Kerkhof, M., Reijmerink, N. E., Dompeling, E., van den Brandt, P. A., Ferreira, I., et al. (2011) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2011.07.027 · Cited by 493 · see citing works
- 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
- 5
- 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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