{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T01:34:44Z","timestamp":1792805684883,"version":"4.5.0"},"reference-count":118,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100004837","name":"Ministerio de Ciencia e Innovaci\u00f3n","doi-asserted-by":"publisher","award":["CEX2021-001189-S-20-1"],"award-info":[{"award-number":["CEX2021-001189-S-20-1"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004837","name":"Ministerio de Ciencia e Innovaci\u00f3n","doi-asserted-by":"publisher","award":["CEX2021-001189-S\/ MCIN\/AEI \/ 10.13039\/501100011033"],"award-info":[{"award-number":["CEX2021-001189-S\/ MCIN\/AEI \/ 10.13039\/501100011033"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004837","name":"Ministerio de Ciencia e Innovaci\u00f3n","doi-asserted-by":"publisher","award":["PID2022-139328OA-I00"],"award-info":[{"award-number":["PID2022-139328OA-I00"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004837","name":"Ministerio de Ciencia e Innovaci\u00f3n","doi-asserted-by":"publisher","award":["CEX2021-001189-S\/ MCIN\/AEI \/ 10.13039\/501100011033"],"award-info":[{"award-number":["CEX2021-001189-S\/ MCIN\/AEI \/ 10.13039\/501100011033"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union\u2019s Horizon 2020","award":["898088"],"award-info":[{"award-number":["898088"]}]},{"DOI":"10.13039\/501100001602","name":"Science Foundation Ireland","doi-asserted-by":"publisher","award":["SFI\/12\/RC\/2273-P1 and SFI\/12\/RC\/2273-P2"],"award-info":[{"award-number":["SFI\/12\/RC\/2273-P1 and SFI\/12\/RC\/2273-P2"]}],"id":[{"id":"10.13039\/501100001602","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Wellcome Trust Investigator","award":["220876\/Z\/20\/Z"],"award-info":[{"award-number":["220876\/Z\/20\/Z"]}]},{"DOI":"10.13039\/501100023561","name":"Ministerio de Universidades","doi-asserted-by":"publisher","award":["Beatriz Galindo Junior Fellowship BG22\/00172"],"award-info":[{"award-number":["Beatriz Galindo Junior Fellowship BG22\/00172"]}],"id":[{"id":"10.13039\/501100023561","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","award":["639226"],"award-info":[{"award-number":["639226"]}],"id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["npj Biofilms Microbiomes"],"DOI":"10.1038\/s41522-025-00720-y","type":"journal-article","created":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T13:53:55Z","timestamp":1751378035000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["Mother-to-infant vertical transmission in early life: a systematic review and proportional meta-analysis of Bifidobacterium strain transmissibility"],"prefix":"10.1038","volume":"11","author":[{"given":"Eduard","family":"Flores Ventura","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mar\u00eda","family":"Esteban-Torres","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miguel","family":"Gueimonde","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Douwe","family":"van Sinderen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Omry","family":"Koren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lindsay J.","family":"Hall","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicola","family":"Segata","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mireia","family":"Valles-Colomer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Carmen","family":"Collado","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,7,1]]},"reference":[{"key":"720_CR1","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/5584_2018_312","volume":"1125","author":"M Selma-Royo","year":"2019","unstructured":"Selma-Royo, M. et al. Shaping Microbiota During the First 1000 Days of Life. Adv. Exp. Med. Biol. 1125, 3\u201324 (2019).","journal-title":"Adv. Exp. Med. Biol."},{"key":"720_CR2","doi-asserted-by":"publisher","unstructured":"Milani C., et al. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol. Mol. Biol. Rev. https:\/\/doi.org\/10.1128\/MMBR.00036-17 (2017).","DOI":"10.1128\/MMBR.00036-17"},{"key":"720_CR3","doi-asserted-by":"publisher","first-page":"4592","DOI":"10.1073\/pnas.1011383107","volume":"108","author":"O Koren","year":"2011","unstructured":"Koren, O. et al. Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proc. Natl. Acad. Sci. 108, 4592\u20134598 (2011).","journal-title":"Proc. Natl. Acad. Sci."},{"key":"720_CR4","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1038\/nrmicro2540","volume":"9","author":"A Spor","year":"2011","unstructured":"Spor, A., Koren, O. & Ley, R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat. Rev. Microbiol. 9, 279\u2013290 (2011).","journal-title":"Nat. Rev. Microbiol."},{"key":"720_CR5","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature11234","volume":"486","author":"Human Microbiome Project Consortium","year":"2012","unstructured":"Human Microbiome Project Consortium Structure, function and diversity of the healthy human microbiome. Nature 486, 207\u2013214 (2012).","journal-title":"Nature"},{"key":"720_CR6","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1016\/j.tim.2016.02.002","volume":"24","author":"A Moya","year":"2016","unstructured":"Moya, A. & Ferrer, M. Functional redundancy-induced stability of gut microbiota subjected to disturbance. Trends Microbiol. 24, 402\u2013413 (2016).","journal-title":"Trends Microbiol."},{"key":"720_CR7","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1016\/j.cell.2014.09.053","volume":"159","author":"JK Goodrich","year":"2014","unstructured":"Goodrich, J. K. et al. Human genetics shape the gut microbiome. Cell 159, 789\u2013799 (2014).","journal-title":"Cell"},{"key":"720_CR8","doi-asserted-by":"publisher","first-page":"294","DOI":"10.1097\/MPG.0000000000000597","volume":"60","author":"PD Houghteling","year":"2015","unstructured":"Houghteling, P. D. & Walker, W. A. Why is initial bacterial colonization of the intestine important to infants\u2019 and children\u2019s health?. J. Pediatr. Gastroenterol. Nutr. 60, 294\u2013307 (2015).","journal-title":"J. Pediatr. Gastroenterol. Nutr."},{"key":"720_CR9","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.572921","volume":"11","author":"SK Dogra","year":"2020","unstructured":"Dogra, S. K., Dor\u00e9, J. & Damak, S. Gut Microbiota Resilience: Definition, Link to Health and Strategies for Intervention. Front. Microbiol. 11, 572921 (2020).","journal-title":"Front. Microbiol."},{"key":"720_CR10","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1038\/s41575-023-00864-2","volume":"21","author":"O Koren","year":"2024","unstructured":"Koren, O., Konnikova, L., Brodin, P., Mysorekar, I. U. & Collado, M. C. The maternal gut microbiome in pregnancy: implications for the developing immune system. Nat. Rev. Gastroenterol. Hepatol. 21, 35\u201345 (2024).","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"720_CR11","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1007\/s12223-020-00821-5","volume":"66","author":"RP Shastry","year":"2021","unstructured":"Shastry, R. P. & Rekha, P. D. Bacterial cross talk with gut microbiome and its implications: a short review. Folia Microbiol.66, 15\u201324 (2021).","journal-title":"Folia Microbiol."},{"key":"720_CR12","doi-asserted-by":"publisher","first-page":"492","DOI":"10.1038\/s41422-020-0332-7","volume":"30","author":"D Zheng","year":"2020","unstructured":"Zheng, D., Liwinski, T. & Elinav, E. Interaction between microbiota and immunity in health and disease. Cell Res. 30, 492\u2013506 (2020).","journal-title":"Cell Res."},{"key":"720_CR13","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-38694-0","volume":"14","author":"C Feehily","year":"2023","unstructured":"Feehily, C. et al. Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach. Nat. Commun. 14, 3015 (2023).","journal-title":"Nat. Commun."},{"key":"720_CR14","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1038\/s41586-019-1560-1","volume":"574","author":"Y Shao","year":"2019","unstructured":"Shao, Y. et al. Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature 574, 117\u2013121 (2019).","journal-title":"Nature"},{"key":"720_CR15","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/j.chom.2018.06.005","volume":"24","author":"P Ferretti","year":"2018","unstructured":"Ferretti, P. et al. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host Microbe 24, 133\u2013145.e5 (2018).","journal-title":"Cell Host Microbe"},{"key":"720_CR16","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1038\/nm.4272","volume":"23","author":"DM Chu","year":"2017","unstructured":"Chu, D. M. et al. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat. Med. 23, 314\u2013326 (2017).","journal-title":"Nat. Med."},{"key":"720_CR17","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1016\/j.chom.2015.04.004","volume":"17","author":"F B\u00e4ckhed","year":"2015","unstructured":"B\u00e4ckhed, F. et al. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 17, 690\u2013703 (2015).","journal-title":"Cell Host Microbe"},{"key":"720_CR18","doi-asserted-by":"publisher","unstructured":"Asnicar F., et al. Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling. mSystems. https:\/\/doi.org\/10.1128\/mSystems.00164-16 (2017).","DOI":"10.1128\/mSystems.00164-16"},{"key":"720_CR19","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1016\/j.chom.2018.06.007","volume":"24","author":"M Yassour","year":"2018","unstructured":"Yassour, M. et al. Strain-level analysis of mother-to-child bacterial transmission during the first few months of life. Cell Host Microbe 24, 146\u2013154.e4 (2018).","journal-title":"Cell Host Microbe"},{"key":"720_CR20","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2021.1911571","volume":"13","author":"S Wang","year":"2021","unstructured":"Wang, S. et al. Metagenomic analysis of mother-infant gut microbiome reveals global distinct and shared microbial signatures. Gut Microbes 13, 1911571 (2021).","journal-title":"Gut Microbes"},{"key":"720_CR21","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1016\/j.tim.2019.07.010","volume":"28","author":"S Wang","year":"2020","unstructured":"Wang, S. et al. Maternal vertical transmission affecting early-life microbiota development. Trends Microbiol. 28, 28\u201345 (2020).","journal-title":"Trends Microbiol."},{"key":"720_CR22","doi-asserted-by":"publisher","first-page":"365","DOI":"10.3920\/BM2021.0098","volume":"13","author":"CA Edwards","year":"2022","unstructured":"Edwards, C. A. et al. A systematic review of breast milk microbiota composition and the evidence for transfer to and colonisation of the infant gut. Benef. Microbes 13, 365\u2013381 (2022).","journal-title":"Benef. Microbes"},{"key":"720_CR23","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1016\/j.neures.2020.11.006","volume":"168","author":"S Tochitani","year":"2021","unstructured":"Tochitani, S. Vertical transmission of gut microbiota: points of action of environmental factors influencing brain development. Neurosci. Res. 168, 83\u201394 (2021).","journal-title":"Neurosci. Res."},{"key":"720_CR24","doi-asserted-by":"publisher","first-page":"438","DOI":"10.3345\/cep.2021.00955","volume":"65","author":"S Jeong","year":"2022","unstructured":"Jeong, S. Factors influencing development of the infant microbiota: from prenatal period to early infancy. Clin. Exp. Pediatr. 65, 438\u2013447 (2022).","journal-title":"Clin. Exp. Pediatr."},{"key":"720_CR25","doi-asserted-by":"publisher","first-page":"7078","DOI":"10.1128\/AEM.02037-15","volume":"81","author":"C Milani","year":"2015","unstructured":"Milani, C. et al. Exploring vertical transmission of bifidobacteria from mother to child. Appl. Environ. Microbiol. 81, 7078\u20137087 (2015).","journal-title":"Appl. Environ. Microbiol."},{"key":"720_CR26","doi-asserted-by":"publisher","DOI":"10.1016\/j.xcrm.2021.100393","volume":"2","author":"YC Lou","year":"2021","unstructured":"Lou, Y. C. et al. Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition. Cell Rep. Med. 2, 100393 (2021).","journal-title":"Cell Rep. Med."},{"key":"720_CR27","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1038\/s41564-021-00970-4","volume":"6","author":"MF Laursen","year":"2021","unstructured":"Laursen, M. F. et al. Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut. Nat. Microbiol 6, 1367\u20131382 (2021).","journal-title":"Nat. Microbiol"},{"key":"720_CR28","doi-asserted-by":"publisher","first-page":"1855","DOI":"10.3390\/microorganisms8121855","volume":"8","author":"H Kumar","year":"2020","unstructured":"Kumar, H. et al. The bifidogenic effect revisited\u2014ecology and health perspectives of bifidobacterial colonization in early life. Microorganisms 8, 1855 (2020).","journal-title":"Microorganisms"},{"key":"720_CR29","doi-asserted-by":"publisher","first-page":"619","DOI":"10.1016\/j.earlhumdev.2015.09.001","volume":"91","author":"L Bode","year":"2015","unstructured":"Bode, L. The functional biology of human milk oligosaccharides. Early Hum. Dev. 91, 619\u2013622 (2015).","journal-title":"Early Hum. Dev."},{"key":"720_CR30","doi-asserted-by":"crossref","unstructured":"Lordan C., et al. Linking human milk oligosaccharide metabolism and early life gut microbiota: bifidobacteria and beyond. Microbiol Mol Biol Rev. e0009423 (2024).","DOI":"10.1128\/mmbr.00094-23"},{"key":"720_CR31","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-02573-2","volume":"9","author":"J Stokholm","year":"2018","unstructured":"Stokholm, J. et al. Maturation of the gut microbiome and risk of asthma in childhood. Nat. Commun. 9, 141 (2018).","journal-title":"Nat. Commun."},{"key":"720_CR32","doi-asserted-by":"publisher","first-page":"1187","DOI":"10.1038\/nm.4176","volume":"22","author":"KE Fujimura","year":"2016","unstructured":"Fujimura, K. E. et al. Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nat. Med 22, 1187\u20131191 (2016).","journal-title":"Nat. Med"},{"key":"720_CR33","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1038\/nature09646","volume":"469","author":"S Fukuda","year":"2011","unstructured":"Fukuda, S. et al. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 469, 543\u2013547 (2011).","journal-title":"Nature"},{"key":"720_CR34","doi-asserted-by":"publisher","first-page":"2415","DOI":"10.3390\/microorganisms9122415","volume":"9","author":"S Saturio","year":"2021","unstructured":"Saturio, S. et al. Role of bifidobacteria on infant health. Microorganisms 9, 2415 (2021).","journal-title":"Microorganisms"},{"key":"720_CR35","doi-asserted-by":"publisher","first-page":"278","DOI":"10.3390\/microorganisms10020278","volume":"10","author":"GA Stuivenberg","year":"2022","unstructured":"Stuivenberg, G. A., Burton, J. P., Bron, P. A. & Reid, G. Why are bifidobacteria important for infants?. Microorganisms 10, 278 (2022).","journal-title":"Microorganisms"},{"key":"720_CR36","doi-asserted-by":"publisher","unstructured":"Samarra A., Cabrera-Rubio R., Mart\u00ednez-Costa C., Collado M. C. The role of bifidobacterium genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life. Gut Microbes. https:\/\/doi.org\/10.1080\/19490976.2024.2357176.","DOI":"10.1080\/19490976.2024.2357176"},{"key":"720_CR37","doi-asserted-by":"publisher","first-page":"629","DOI":"10.3390\/ph5060629","volume":"5","author":"K Mikami","year":"2012","unstructured":"Mikami, K., Kimura, M. & Takahashi, H. Influence of maternal bifidobacteria on the development of gut bifidobacteria in infants. Pharmaceuticals 5, 629\u2013642 (2012).","journal-title":"Pharmaceuticals"},{"key":"720_CR38","doi-asserted-by":"publisher","first-page":"79","DOI":"10.12938\/bmfh.18-011","volume":"37","author":"H Makino","year":"2018","unstructured":"Makino, H. Bifidobacterial strains in the intestines of newborns originate from their mothers. Biosci. Microbiota Food Health 37, 79\u201385 (2018).","journal-title":"Biosci. Microbiota Food Health"},{"key":"720_CR39","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1038\/s41586-022-05620-1","volume":"614","author":"M Valles-Colomer","year":"2023","unstructured":"Valles-Colomer, M. et al. The person-to-person transmission landscape of the gut and oral microbiomes. Nature 614, 125\u2013135 (2023).","journal-title":"Nature"},{"key":"720_CR40","unstructured":"PRISMA 2020 explanation and elaboration: updated guidance and exemplars for reporting systematic reviews. BMJ. https:\/\/www.bmj.com\/content\/372\/bmj.n160 Accessed 21 Sep 2023."},{"key":"720_CR41","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1016\/j.jclinepi.2016.01.021","volume":"75","author":"J McGowan","year":"2016","unstructured":"McGowan, J. et al. PRESS peer review of electronic search strategies: 2015 guideline statement. J. Clin. Epidemiol. 75, 40\u201346 (2016).","journal-title":"J. Clin. Epidemiol."},{"key":"720_CR42","doi-asserted-by":"publisher","DOI":"10.1186\/s13643-016-0384-4","volume":"5","author":"M Ouzzani","year":"2016","unstructured":"Ouzzani, M., Hammady, H., Fedorowicz, Z. & Elmagarmid, A. Rayyan\u2014a web and mobile app for systematic reviews. Syst. Rev. 5, 210 (2016).","journal-title":"Syst. Rev."},{"key":"720_CR43","unstructured":"Create Elegant Data Visualisations Using the Grammar of Graphics https:\/\/ggplot2.tidyverse.org\/ Accessed 5 Oct 2023."},{"key":"720_CR44","unstructured":"Deckmyn OS. code by RAB and ARWR version by RBE by TPM and A (2022) maps: Draw Geographical Maps."},{"key":"720_CR45","unstructured":"Brownrigg O. S. code by RAB and ARWR version by R (2022) mapdata: Extra Map Databases."},{"key":"720_CR46","unstructured":"Wickham H., et al. dplyr: A Grammar of Data Manipulation (2023)"},{"key":"720_CR47","unstructured":"R: The R Project for Statistical Computing. https:\/\/www.r-project.org\/ Accessed 14 Sep 2023."},{"key":"720_CR48","doi-asserted-by":"publisher","first-page":"626","DOI":"10.1101\/gr.216242.116","volume":"27","author":"DT Truong","year":"2017","unstructured":"Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C. & Segata, N. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res. 27, 626\u2013638 (2017).","journal-title":"Genome Res."},{"key":"720_CR49","doi-asserted-by":"publisher","first-page":"1045","DOI":"10.1038\/nbt.3319","volume":"33","author":"C Luo","year":"2015","unstructured":"Luo, C. et al. ConStrains identifies microbial strains in metagenomic datasets. Nat. Biotechnol. 33, 1045\u20131052 (2015).","journal-title":"Nat. Biotechnol."},{"key":"720_CR50","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1038\/s41587-020-00797-0","volume":"39","author":"MR Olm","year":"2021","unstructured":"Olm, M. R. et al. InStrain enables population genomic analysis from metagenomic data and sensitive detection of shared microbial strains. Nat. Biotechnol. 39, 727\u2013736 (2021).","journal-title":"Nat. Biotechnol."},{"key":"720_CR51","doi-asserted-by":"publisher","first-page":"1686","DOI":"10.21105\/joss.01686","volume":"4","author":"H Wickham","year":"2019","unstructured":"Wickham, H. et al. Welcome to the Tidyverse. J. Open Source Softw. 4, 1686 (2019).","journal-title":"J. Open Source Softw."},{"key":"720_CR52","doi-asserted-by":"publisher","unstructured":"Viechtbauer W. Conducting meta-analyses in R with the metafor Package. J Stat Softw. https:\/\/doi.org\/10.18637\/jss.v036.i03 (2010).","DOI":"10.18637\/jss.v036.i03"},{"key":"720_CR53","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1136\/ebmental-2019-300117","volume":"22","author":"S Balduzzi","year":"2019","unstructured":"Balduzzi, S., R\u00fccker, G. & Schwarzer, G. How to perform a meta-analysis with R: a practical tutorial. Evid. Based Ment. Health 22, 153\u2013160 (2019).","journal-title":"Evid. Based Ment. Health"},{"key":"720_CR54","unstructured":"JBI Manual for Evidence Synthesis\u2014JBI Global Wiki. https:\/\/jbi-global-wiki.refined.site\/space\/MANUAL Accessed 11 Jul 2023."},{"key":"720_CR55","doi-asserted-by":"publisher","first-page":"962","DOI":"10.1080\/19490976.2020.1730294","volume":"11","author":"I Garc\u00eda-Mantrana","year":"2020","unstructured":"Garc\u00eda-Mantrana, I. et al. Distinct maternal microbiota clusters are associated with diet during pregnancy: impact on neonatal microbiota and infant growth during the first 18 months of life. Gut Microbes 11, 962\u2013978 (2020).","journal-title":"Gut Microbes"},{"key":"720_CR56","doi-asserted-by":"publisher","first-page":"763","DOI":"10.3920\/BM2017.0064","volume":"8","author":"O Sakwinska","year":"2017","unstructured":"Sakwinska, O. et al. Does the maternal vaginal microbiota play a role in seeding the microbiota of neonatal gut and nose?. Benef. Microbes 8, 763\u2013778 (2017).","journal-title":"Benef. Microbes"},{"key":"720_CR57","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.3390\/metabo12111136","volume":"12","author":"J Ding","year":"2022","unstructured":"Ding, J. et al. Effect of breastmilk microbiota and sialylated oligosaccharides on the colonization of infant gut microbial community and fecal metabolome. Metabolites 12, 1136 (2022).","journal-title":"Metabolites"},{"key":"720_CR58","first-page":"e31419","volume":"101","author":"K Karampatsas","year":"2022","unstructured":"Karampatsas, K. et al. Gastrointestinal, vaginal, nasopharyngeal, and breast milk microbiota profiles and breast milk metabolomic changes in Gambian infants over the first two months of lactation: a prospective cohort study. Medicines101, e31419 (2022).","journal-title":"Medicines"},{"key":"720_CR59","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1007\/s00284-015-0843-5","volume":"71","author":"M Schanche","year":"2015","unstructured":"Schanche, M. et al. High-resolution analyses of overlap in the microbiota between mothers and their children. Curr. Microbiol. 71, 283\u2013290 (2015).","journal-title":"Curr. Microbiol."},{"key":"720_CR60","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2023.1144254","volume":"13","author":"SJ Dos Santos","year":"2023","unstructured":"Dos Santos, S. J. et al. Maternal vaginal microbiome composition does not affect development of the infant gut microbiome in early life. Front. Cell Infect. Microbiol. 13, 1144254 (2023).","journal-title":"Front. Cell Infect. Microbiol."},{"key":"720_CR61","doi-asserted-by":"publisher","first-page":"2804","DOI":"10.3390\/ijms23052804","volume":"23","author":"AS Cheema","year":"2022","unstructured":"Cheema, A. S. et al. Exclusively breastfed infant microbiota develops over time and is associated with human milk oligosaccharide intakes. Int. J. Mol. Sci. 23, 2804 (2022).","journal-title":"Int. J. Mol. Sci."},{"key":"720_CR62","doi-asserted-by":"publisher","first-page":"780","DOI":"10.1007\/s12275-022-1641-y","volume":"60","author":"P Li","year":"2022","unstructured":"Li, P. et al. Dynamic colonization of gut microbiota and its influencing factors among the breast-feeding infants during the first two years of life. J. Microbiol. 60, 780\u2013794 (2022).","journal-title":"J. Microbiol."},{"key":"720_CR63","doi-asserted-by":"publisher","first-page":"1225","DOI":"10.1128\/jcm.28.6.1225-1228.1990","volume":"28","author":"GW Tannock","year":"1990","unstructured":"Tannock, G. W., Fuller, R., Smith, S. L. & Hall, M. A. Plasmid profiling of members of the family Enterobacteriaceae, lactobacilli, and bifidobacteria to study the transmission of bacteria from mother to infant. J. Clin. Microbiol. 28, 1225\u20131228 (1990).","journal-title":"J. Clin. Microbiol."},{"key":"720_CR64","doi-asserted-by":"publisher","first-page":"1740","DOI":"10.3390\/foods12091740","volume":"12","author":"K Wang","year":"2023","unstructured":"Wang, K. et al. Microbial diversity and correlation between breast milk and the infant gut. Foods 12, 1740 (2023).","journal-title":"Foods"},{"key":"720_CR65","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1007\/s00248-021-01758-z","volume":"83","author":"JT Wallenborn","year":"2022","unstructured":"Wallenborn, J. T., Gunier, R. B., Pappas, D. J., Chevrier, J. & Eskenazi, B. Breastmilk, stool, and meconium: bacterial communities in South Africa. Micro. Ecol. 83, 246\u2013251 (2022).","journal-title":"Micro. Ecol."},{"key":"720_CR66","doi-asserted-by":"publisher","first-page":"902","DOI":"10.1093\/jn\/nxy299","volume":"149","author":"JE Williams","year":"2019","unstructured":"Williams, J. E. et al. Strong multivariate relations exist among milk, oral, and fecal microbiomes in mother-infant dyads during the first six months postpartum. J. Nutr. 149, 902\u2013914 (2019).","journal-title":"J. Nutr."},{"key":"720_CR67","doi-asserted-by":"publisher","first-page":"965","DOI":"10.1128\/AEM.02063-08","volume":"75","author":"R Mart\u00edn","year":"2009","unstructured":"Mart\u00edn, R. et al. Isolation of bifidobacteria from breast milk and assessment of the bifidobacterial population by pcr-denaturing gradient gel electrophoresis and quantitative real-time PCR. Appl. Environ. Microbiol. 75, 965\u2013969 (2009).","journal-title":"Appl. Environ. Microbiol."},{"key":"720_CR68","doi-asserted-by":"publisher","unstructured":"Department of Food Science and Nutrition, Faculty of Science and Technology, Prince of Songkla University, Pattani Campus, Pattani, Thailand, Azis L, Wichienchot S, Center of Excellence in Functional Foods and Gastronomy, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai Campus, Hat Yai, Thailand, Pinkaew S, Department of Food Science and Nutrition, Faculty of Science and Technology, Prince of Songkla University, Pattani Campus, Pattani, Thailand The correlations between gut microbiota of Muslim Thai lactating women and their dietary intake and gut microbiota of breastfed infants. Malays J Nutr. https:\/\/doi.org\/10.31246\/mjn-2021-0019 (2021).","DOI":"10.31246\/mjn-2021-0019"},{"key":"720_CR69","doi-asserted-by":"publisher","first-page":"1155","DOI":"10.3390\/microorganisms10061155","volume":"10","author":"EC Davis","year":"2022","unstructured":"Davis, E. C., Wang, M. & Donovan, S. M. Microbial interrelationships across sites of breastfeeding mothers and infants at 6 weeks postpartum. Microorganisms 10, 1155 (2022).","journal-title":"Microorganisms"},{"key":"720_CR70","doi-asserted-by":"publisher","DOI":"10.1186\/s13099-020-00370-9","volume":"12","author":"C Li","year":"2020","unstructured":"Li, C., Chen, J. & Li, S. C. Understanding Horizontal Gene Transfer network in human gut microbiota. Gut Pathog. 12, 33 (2020).","journal-title":"Gut Pathog."},{"key":"720_CR71","doi-asserted-by":"publisher","first-page":"1995","DOI":"10.3390\/microorganisms9091995","volume":"9","author":"M Ding","year":"2021","unstructured":"Ding, M. et al. The species-level composition of the fecal bifidobacterium and lactobacillus genera in indonesian children differs from that of their mothers. Microorganisms 9, 1995 (2021).","journal-title":"Microorganisms"},{"key":"720_CR72","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1097\/MPG.0b013e31827a964b","volume":"56","author":"F Tuzun","year":"2013","unstructured":"Tuzun, F., Kumral, A., Duman, N. & Ozkan, H. Breast milk jaundice: effect of bacteria present in breast milk and infant feces. J. Pediatr. Gastroenterol. Nutr. 56, 328\u2013332 (2013).","journal-title":"J. Pediatr. Gastroenterol. Nutr."},{"key":"720_CR73","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1007\/s10517-010-1069-y","volume":"150","author":"EV Kulagina","year":"2010","unstructured":"Kulagina, E. V. et al. Molecular genetic study of species and strain variability in bifidobacteria population in intestinal microflora of breast-fed infants and their mothers. Bull. Exp. Biol. Med. 150, 61\u201364 (2010).","journal-title":"Bull. Exp. Biol. Med."},{"key":"720_CR74","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1016\/j.micpath.2017.08.014","volume":"111","author":"M Eshaghi","year":"2017","unstructured":"Eshaghi, M. et al. Bifidobacterium obtained from mother\u2019s milk and their infant stool; a comparative genotyping and antibacterial analysis. Micro. Pathog. 111, 94\u201398 (2017).","journal-title":"Micro. Pathog."},{"key":"720_CR75","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1097\/MPG.0b013e3181f0e032","volume":"51","author":"H Takahashi","year":"2010","unstructured":"Takahashi, H. et al. Comparative analysis of the properties of bifidobacterial isolates from fecal samples of mother\u2013infant pairs. J. Pediatr. Gastroenterol. Nutr. 51, 653\u2013660 (2010).","journal-title":"J. Pediatr. Gastroenterol. Nutr."},{"key":"720_CR76","doi-asserted-by":"publisher","first-page":"669","DOI":"10.1203\/PDR.0b013e31819ed7a8","volume":"65","author":"K Mikami","year":"2009","unstructured":"Mikami, K. et al. Influence of maternal bifidobacteria on the establishment of bifidobacteria colonizing the gut in infants. Pediatr. Res. 65, 669\u2013674 (2009).","journal-title":"Pediatr. Res."},{"key":"720_CR77","doi-asserted-by":"publisher","first-page":"6788","DOI":"10.1128\/AEM.05346-11","volume":"77","author":"H Makino","year":"2011","unstructured":"Makino, H. et al. Transmission of intestinal bifidobacterium longum subsp. longum strains from mother to infant, determined by multilocus sequencing typing and amplified fragment length polymorphism. Appl Environ. Microbiol.77, 6788\u20136793 (2011).","journal-title":"Appl Environ. Microbiol."},{"key":"720_CR78","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.1007\/s10534-014-9762-3","volume":"27","author":"P Mastromarino","year":"2014","unstructured":"Mastromarino, P. et al. Correlation between lactoferrin and beneficial microbiota in breast milk and infant\u2019s feces. BioMetals 27, 1077\u20131086 (2014).","journal-title":"BioMetals"},{"key":"720_CR79","doi-asserted-by":"publisher","first-page":"196","DOI":"10.3390\/nu9030196","volume":"9","author":"S Jinno","year":"2017","unstructured":"Jinno, S. et al. Maternal prebiotic ingestion increased the number of fecal bifidobacteria in pregnant women but not in their neonates aged one month. Nutrients 9, 196 (2017).","journal-title":"Nutrients"},{"key":"720_CR80","doi-asserted-by":"publisher","first-page":"2891","DOI":"10.1111\/1462-2920.12238","volume":"16","author":"T Jost","year":"2014","unstructured":"Jost, T., Lacroix, C., Braegger, C. P., Rochat, F. & Chassard, C. Vertical mother-neonate transfer of maternal gut bacteria via breastfeeding: mother-neonate bacterial transfer. Environ. Microbiol 16, 2891\u20132904 (2014).","journal-title":"Environ. Microbiol"},{"key":"720_CR81","doi-asserted-by":"publisher","DOI":"10.1038\/srep40597","volume":"7","author":"K Murphy","year":"2017","unstructured":"Murphy, K. et al. The composition of human milk and infant faecal microbiota over the first three months of life: a pilot study. Sci. Rep. 7, 40597 (2017).","journal-title":"Sci. Rep."},{"key":"720_CR82","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-04848-1","volume":"12","author":"T Vatanen","year":"2022","unstructured":"Vatanen, T. et al. Transcription shifts in gut bacteria shared between mothers and their infants. Sci. Rep. 12, 1276 (2022).","journal-title":"Sci. Rep."},{"key":"720_CR83","doi-asserted-by":"publisher","first-page":"9873","DOI":"10.3390\/ijms23179873","volume":"23","author":"M Ding","year":"2022","unstructured":"Ding, M. et al. Shared and non-shared siga-coated and -uncoated bacteria in intestine of mother\u2013infant pairs. Int J. Mol. Sci. 23, 9873 (2022).","journal-title":"Int J. Mol. Sci."},{"key":"720_CR84","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.664407","volume":"12","author":"N Amenyogbe","year":"2021","unstructured":"Amenyogbe, N. et al. Bacterial and fungal gut community dynamics over the first 5 years of life in predominantly rural communities in Ghana. Front Microbiol 12, 664407 (2021).","journal-title":"Front Microbiol"},{"key":"720_CR85","doi-asserted-by":"publisher","first-page":"e78331","DOI":"10.1371\/journal.pone.0078331","volume":"8","author":"H Makino","year":"2013","unstructured":"Makino, H. et al. Mother-to-infant transmission of intestinal bifidobacterial strains has an impact on the early development of vaginally delivered infant\u2019s microbiota. PLoS ONE 8, e78331 (2013).","journal-title":"PLoS ONE"},{"key":"720_CR86","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2021.1908100","volume":"13","author":"B Yang","year":"2021","unstructured":"Yang, B. et al. Development of gut microbiota and bifidobacterial communities of neonates in the first 6 weeks and their inheritance from mother. Gut Microbes 13, 1908100 (2021).","journal-title":"Gut Microbes"},{"key":"720_CR87","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1039\/D1FO03131G","volume":"13","author":"C Qi","year":"2022","unstructured":"Qi, C. et al. Lactation-dependent vertical transmission of natural probiotics from the mother to the infant gut through breast milk. Food Funct. 13, 304\u2013315 (2022).","journal-title":"Food Funct."},{"key":"720_CR88","doi-asserted-by":"publisher","first-page":"11543","DOI":"10.1039\/D2FO01244H","volume":"13","author":"C Qi","year":"2022","unstructured":"Qi, C. et al. Widespread vertical transmission of secretory immunoglobulin A coated trace bacterial variants from the mother to infant gut through breastfeeding. Food Funct. 13, 11543\u201311554 (2022).","journal-title":"Food Funct."},{"key":"720_CR89","doi-asserted-by":"publisher","first-page":"279","DOI":"10.3390\/nu8050279","volume":"8","author":"C Martin","year":"2016","unstructured":"Martin, C., Ling, P.-R. & Blackburn, G. Review of infant feeding: key features of breast milk and infant formula. Nutrients 8, 279 (2016).","journal-title":"Nutrients"},{"key":"720_CR90","doi-asserted-by":"publisher","first-page":"e0219633","DOI":"10.1371\/journal.pone.0219633","volume":"15","author":"K Kordy","year":"2020","unstructured":"Kordy, K. et al. Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve. PLoS ONE 15, e0219633 (2020).","journal-title":"PLoS ONE"},{"key":"720_CR91","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-017-0282-6","volume":"5","author":"S Duranti","year":"2017","unstructured":"Duranti, S. et al. Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission. Microbiome 5, 66 (2017).","journal-title":"Microbiome"},{"key":"720_CR92","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07631-x","volume":"9","author":"L Wampach","year":"2018","unstructured":"Wampach, L. et al. Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential. Nat. Commun. 9, 5091 (2018).","journal-title":"Nat. Commun."},{"key":"720_CR93","doi-asserted-by":"publisher","first-page":"1214","DOI":"10.3389\/fmicb.2017.01214","volume":"8","author":"E Biagi","year":"2017","unstructured":"Biagi, E. et al. The bacterial ecosystem of mother\u2019s milk and infant\u2019s mouth and gut. Front. Microbiol. 8, 1214 (2017).","journal-title":"Front. Microbiol."},{"key":"720_CR94","doi-asserted-by":"publisher","first-page":"2539","DOI":"10.3390\/nu12092539","volume":"12","author":"MD Babakobi","year":"2020","unstructured":"Babakobi, M. D. et al. Effect of maternal diet and milk lipid composition on the infant gut and maternal milk microbiomes. Nutrients 12, 2539 (2020).","journal-title":"Nutrients"},{"key":"720_CR95","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.669442","volume":"12","author":"W Yan","year":"2021","unstructured":"Yan, W., Luo, B., Zhang, X., Ni, Y. & Tian, F. Association and occurrence of bifidobacterial phylotypes between breast milk and fecal microbiomes in mother\u2013infant dyads during the first 2 years of life. Front. Microbiol. 12, 669442 (2021).","journal-title":"Front. Microbiol."},{"key":"720_CR96","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1038\/s43705-021-00021-3","volume":"1","author":"MF Laursen","year":"2021","unstructured":"Laursen, M. F. et al. Maternal milk microbiota and oligosaccharides contribute to the infant gut microbiota assembly. ISME Commun. 1, 21 (2021).","journal-title":"ISME Commun."},{"key":"720_CR97","doi-asserted-by":"publisher","first-page":"1939","DOI":"10.1016\/j.cub.2023.04.011","volume":"33","author":"S Manara","year":"2023","unstructured":"Manara, S. et al. Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population. Curr. Biol. 33, 1939\u20131950.e4 (2023).","journal-title":"Curr. Biol."},{"key":"720_CR98","unstructured":"Selma-Royo, M. et al. Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year. Cell Host Microbe (In press) (2025)."},{"key":"720_CR99","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1128\/AEM.02359-12","volume":"79","author":"E Avershina","year":"2013","unstructured":"Avershina, E. et al. Bifidobacterial succession and correlation networks in a large unselected cohort of mothers and their children. Appl. Environ. Microbiol. 79, 497\u2013507 (2013).","journal-title":"Appl. Environ. Microbiol."},{"key":"720_CR100","doi-asserted-by":"publisher","first-page":"280","DOI":"10.1111\/1574-6941.12223","volume":"87","author":"E Avershina","year":"2014","unstructured":"Avershina, E. et al. Major faecal microbiota shifts in composition and diversity with age in a geographically restricted cohort of mothers and their children. FEMS Microbiol. Ecol. 87, 280\u2013290 (2014).","journal-title":"FEMS Microbiol. Ecol."},{"key":"720_CR101","doi-asserted-by":"publisher","unstructured":"Nayfach S., Rodriguez-Mueller B., Garud N., Pollard K. S. An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria. https:\/\/doi.org\/10.1101\/031757 (2015).","DOI":"10.1101\/031757"},{"key":"720_CR102","doi-asserted-by":"publisher","first-page":"3489","DOI":"10.1111\/all.14877","volume":"76","author":"AE Seppo","year":"2021","unstructured":"Seppo, A. E. et al. Infant gut microbiome is enriched with Bifidobacterium longum ssp. infantis in Old Order Mennonites with traditional farming lifestyle. Allergy 76, 3489\u20133503 (2021).","journal-title":"Allergy"},{"key":"720_CR103","doi-asserted-by":"publisher","DOI":"10.1016\/j.xcrm.2020.100156","volume":"1","author":"CM Mitchell","year":"2020","unstructured":"Mitchell, C. M. et al. Delivery mode affects stability of early infant gut microbiota. Cell Rep. Med. 1, 100156 (2020).","journal-title":"Cell Rep. Med."},{"key":"720_CR104","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1016\/j.chom.2020.06.009","volume":"28","author":"K Fehr","year":"2020","unstructured":"Fehr, K. et al. Breastmilk feeding practices are associated with the co-occurrence of bacteria in mothers\u2019 milk and the infant gut: the CHILD cohort study. Cell Host Microbe 28, 285\u2013297.e4 (2020).","journal-title":"Cell Host Microbe"},{"key":"720_CR105","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2021.663513","volume":"11","author":"Y Cheng","year":"2022","unstructured":"Cheng, Y. et al. Influence of geographical location on maternal-infant microbiota: study in two populations from Asia and Europe. Front. Cell Infect. Microbiol. 11, 663513 (2022).","journal-title":"Front. Cell Infect. Microbiol."},{"key":"720_CR106","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1177\/0890334411424729","volume":"28","author":"V Mart\u00edn","year":"2012","unstructured":"Mart\u00edn, V. et al. Sharing of bacterial strains between breast milk and infant feces. J. Hum. Lact. 28, 36\u201344 (2012).","journal-title":"J. Hum. Lact."},{"key":"720_CR107","doi-asserted-by":"publisher","first-page":"779","DOI":"10.3945\/an.114.007229","volume":"5","author":"JM Rodr\u00edguez","year":"2014","unstructured":"Rodr\u00edguez, J. M. The origin of human milk bacteria: is there a bacterial entero-mammary pathway during late pregnancy and lactation?. Adv. Nutr. 5, 779\u2013784 (2014).","journal-title":"Adv. Nutr."},{"key":"720_CR108","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-13036-1","volume":"10","author":"JS Johnson","year":"2019","unstructured":"Johnson, J. S. et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat. Commun. 10, 5029 (2019).","journal-title":"Nat. Commun."},{"key":"720_CR109","doi-asserted-by":"publisher","first-page":"4280","DOI":"10.1016\/j.cell.2022.10.011","volume":"185","author":"T Vatanen","year":"2022","unstructured":"Vatanen, T. et al. A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning. Cell 185, 4280\u20134297.e12 (2022).","journal-title":"Cell"},{"key":"720_CR110","doi-asserted-by":"publisher","first-page":"1220","DOI":"10.1126\/science.abj2972","volume":"376","author":"MR Olm","year":"2022","unstructured":"Olm, M. R. et al. Robust variation in infant gut microbiome assembly across a spectrum of lifestyles. Science 376, 1220\u20131223 (2022).","journal-title":"Science"},{"key":"720_CR111","doi-asserted-by":"publisher","first-page":"1472","DOI":"10.1016\/j.csbj.2021.03.006","volume":"19","author":"G Alessandri","year":"2021","unstructured":"Alessandri, G., van Sinderen, D. & Ventura, M. The genus Bifidobacterium: from genomics to functionality of an important component of the mammalian gut microbiota. Comput. Struct. Biotechnol. J. 19, 1472\u20131487 (2021).","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"720_CR112","doi-asserted-by":"publisher","first-page":"fiw056","DOI":"10.1093\/femsec\/fiw056","volume":"92","author":"C Ferrario","year":"2016","unstructured":"Ferrario, C. et al. Modulation of the eps-ome transcription of bifidobacteria through simulation of human intestinal environment. FEMS Microbiol. Ecol. 92, fiw056 (2016).","journal-title":"FEMS Microbiol. Ecol."},{"key":"720_CR113","doi-asserted-by":"publisher","first-page":"9797","DOI":"10.3390\/app12199797","volume":"12","author":"M Florczyk","year":"2022","unstructured":"Florczyk, M., Cydzik-Kwiatkowska, A., Ziembinska-Buczynska, A. & Ciesielski, S. Comparison of three DNA extraction kits for assessment of bacterial diversity in activated sludge, biofilm, and anaerobic digestate. Appl. Sci. 12, 9797 (2022).","journal-title":"Appl. Sci."},{"key":"720_CR114","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/s41579-020-0368-1","volume":"18","author":"T Van Rossum","year":"2020","unstructured":"Van Rossum, T., Ferretti, P., Maistrenko, O. M. & Bork, P. Diversity within species: interpreting strains in microbiomes. Nat. Rev. Microbiol. 18, 491\u2013506 (2020).","journal-title":"Nat. Rev. Microbiol."},{"key":"720_CR115","doi-asserted-by":"publisher","unstructured":"Segata N. (2018) On the road to strain-resolved comparative metagenomics. mSystems 3 :https:\/\/doi.org\/10.1128\/msystems.00190-17.","DOI":"10.1128\/msystems.00190-17"},{"key":"720_CR116","doi-asserted-by":"publisher","first-page":"e00148","DOI":"10.1128\/mSphere.00148-18","volume":"3","author":"SI Glassman","year":"2018","unstructured":"Glassman, S. I. & Martiny, J. B. H. Broadscale ecological patterns are robust to use of exact sequence variants versus operational taxonomic units. mSphere 3, e00148\u201318 (2018).","journal-title":"mSphere"},{"key":"720_CR117","doi-asserted-by":"publisher","DOI":"10.1172\/JCI154944","volume":"132","author":"CR Wensel","year":"2022","unstructured":"Wensel, C. R., Pluznick, J. L., Salzberg, S. L. & Sears, C. L. Next-generation sequencing: insights to advance clinical investigations of the microbiome. J. Clin. Investig. 132, e154944 (2022).","journal-title":"J. Clin. Investig."},{"key":"720_CR118","doi-asserted-by":"publisher","first-page":"e00520","DOI":"10.1128\/msphere.00520-23","volume":"8","author":"N Sirisaengtaksin","year":"2023","unstructured":"Sirisaengtaksin, N., O\u2019Donoghue, E. J., Jabbari, S., Roe, A. J. & Krachler, A. M. Bacterial outer membrane vesicles provide an alternative pathway for trafficking of Escherichia coli O157 type III secreted effectors to epithelial cells. mSphere 8, e00520\u201323 (2023).","journal-title":"mSphere"}],"container-title":["npj Biofilms and Microbiomes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41522-025-00720-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41522-025-00720-y","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41522-025-00720-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T14:51:52Z","timestamp":1751381512000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41522-025-00720-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,1]]},"references-count":118,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["720"],"URL":"https:\/\/doi.org\/10.1038\/s41522-025-00720-y","relation":{},"ISSN":["2055-5008"],"issn-type":[{"value":"2055-5008","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,7,1]]},"assertion":[{"value":"7 October 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 May 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 July 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"E.F.V., M.E.T., M.G., D.V.S., L.J.H., and M.V.C. declare no financial or non-financial competing interests. O.K. serves as Editors-in-Chief of this journal and had no role in the peer-review or decision to publish this manuscript. O.K. declares no financial competing interests. N.S. serves as Associate Editor of this journal and had no role in the peer-review or decision to publish this manuscript. N.S. declares no financial competing interests. M.C.C. serves as co-editor special issue \u201cWomen and their microbes\u201d of this journal and had no role in the peer-review or decision to publish this manuscript. M.C.C. declares no financial competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"121"}}