Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life

Yassour, Moran, Jason, Eeva, Hogstrom, Larson J., Arthur, Timothy D., Tripathi, Surya, Siljander, Heli, Selvenius, Jenni, Oikarinen, Sami, Hyöty, Heikki, Virtanen, Suvi M., Ilonen, Jorma, Ferretti, Pamela, Pasolli, Edoardo, Tett, Adrian, Asnicar, Francesco, Segata, Nicola, Vlamakis, Hera, Lander, Eric S., Huttenhower, Curtis, Knip, Mikael, Xavier, Ramnik J.·2018·Cell Host & Microbe
DOI 10.1016/j.chom.2018.06.007

Cited by (472)

Items 401–472 of 472

  1. Additional file 3 of Understanding Horizontal Gene Transfer network in human gut microbiota
    Chen Li, Jiaxing Chen, Shuai Cheng Li · 2020 · Figshare
  2. Additional file 1 of Understanding Horizontal Gene Transfer network in human gut microbiota
    Chen Li, Jiaxing Chen, Shuai Cheng Li · 2020 · Figshare
  3. Additional file 2 of Strain-level analysis reveals the vertical microbial transmission during the life cycle of bumblebee
    Qinzhi Su, Wang, Qinglin, Xiaohuan Mu, Chen, Hao, Yujie Meng, Xue Zhang, Zheng Li, Hu, Xiaosong, Yifan Zhai, Hao Zheng · 2021 · Figshare
  4. GUT MICROBIOME STRUCTURE AND DYNAMICS IN HUMAN AND EXPERIMENTAL ANIMALS
    NINO KUKULADZE, ALEXANDER BAKHUTASHVILI · 2024 · EXPERIMENTAL & CLINICAL MEDICINE GEORGIA
  5. Role of gut microbes in shaping neonatal immunity and beyond
    Srijani Basu, Mohammad Aqdas, Mohammed Amir · 2024 · Elsevier eBooks
  6. Early life milk diets shape infant gut microbiota: evidence of microbial plasticity in response to breast and formula milk
    Melissa A. Lawson, Matthew J. Dalby, Shabhonam Caim, Larissa Richardson, Albert Koulman, Raymond Kiu, Gwénaëlle Le Gall, Lindsay J. Hall · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  7. Characterization of gut microbiomes in rural Honduras reveals novel species and associations with human genetic variation
    Francesco Beghini, Ilana Brito, Mark Gerstein, Nicholas A. Christakis · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  8. The role of cecal metabolites and DNA methylation in deciphering the effects of maternal genistein intake on white fat browning in adult female offspring
    Shunhua Li, Liyuan Zhou, Jing Ren, J. Y. Liu, Qian Zhang, Xinhua Xiao · 2025 · Food & Function
  9. The Impact of Maternal Antibiotic Consumption on the Development of Oral Thrush Infection in Breastfeeding Infants: A Quasi-Experimental Study
    Amal Mohamad Husein Mackawy, Basmah F. Alharbi, Ahmad Almatroudi, Mohsina Huq, Amal Hussain, Afshan Zeeshan Wasti, Manal F. Elharbi, Khaled S. Allemailem · 2025 · Breastfeeding Medicine
  10. Comprehensive Analysis of Maternal and Infant Microbiome Profiles: Maternal Microbial Transmission Shapes Offspring Somatic Growth Trajectory
    Keqing Wang, Qiangrong Zhai, Jinnan Liu, Xi Li, Junhong Chen, Leishen Wang, Fangyi Ren, Xiaomin Liu, Jing Wang, Bing Chen et al. · 2025 · SSRN Electronic Journal
  11. Unraveling the Potential Role of SIGNR1(CD209b) in Shaping Gut Microbiota During the Early Postnatal Life
    Nihal Hasan, Sizhe Zhu, Tie Chen · 2025 · Apmis
  12. Food and the Immune System: How Dietary Components Modulate Systemic Immunity Through Gut Microbiome Modifications
    Francesco Asnicar, Serena Manara · 2025 · The microbiomes of humans, animals, plants, and the environment
  13. Editorial: Breastfeeding's role in shaping infant gut microbiota for long-term health
    Rozeta Sokou, Aikaterini Konstantinidi, Stavroula Parastatidou · 2025 · Frontiers in Microbiology
  14. Exploring the Integrated Gut-Brain Metabolic Model for ADHD
    Ezgi Taş, Kutlu Ö. Ülgen · 2025 · Biochemical Genetics
  15. Mechanisms of maternal microbial vertical transmission on offspring health
    Gaosheng Fan, Shuhuan Feng, Xiaohan Jiang, Baoqi Li, Shaoxuan Wang, Tiejun Li, Yulong Yin, Liuqin He · 2025 · Chinese Science Bulletin (Chinese Version)
  16. Additional file 2 of Using strain-resolved analysis to identify contamination in metagenomics data
    Yue Clare Lou, Jordan Hoff, Matthew R. Olm, West-Roberts, Jacob, Spencer Diamond, Brian Firek, Michael J. Morowitz, Jillian F. Banfield · 2023 · Figshare
  17. Additional file 3 of A genome catalog of the early-life human skin microbiome
    Zeyang Shen, Lukian Robert, Milan Stolpman, Che, You, Katrina Jane Allen, Saffery, Richard, Audrey Walsh, Young, Angela, Eckert, Jana, Clay Deming et al. · 2024 · Figshare
  18. Additional file 5 of Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life
    Anna Samarra, Raúl Cabrera‐Rubio, Cecilia Martínez‐Costa, Collado, Maria Carmen · 2024 · Figshare
  19. Additional file 3 of Strain-level analysis reveals the vertical microbial transmission during the life cycle of bumblebee
    Qinzhi Su, Wang, Qinglin, Xiaohuan Mu, Chen, Hao, Meng, Yujie, Zhang, Xue, Zheng, Li, Hu, Xiaosong, Yifan Zhai, Zheng, Hao · 2021 · Figshare
  20. Additional file 1 of Using strain-resolved analysis to identify contamination in metagenomics data
    Yue Clare Lou, Jordan Hoff, Matthew R. Olm, Jacob A. West-Roberts, Spencer Diamond, Brian Firek, Michael J. Morowitz, Jillian F. Banfield · 2023 · Figshare
  21. Additional file 6 of Longitudinal metagenomic study reveals the dynamics of fecal antibiotic resistome in pigs throughout the lifetime
    Ma, Lingyan, Song, Yuanyuan, Wentao Lyu, Chen, Qu, Xingning Xiao, Jin, Yuanxiang, Yang, Hua, Wang, Wen, Xiao, Yingping · 2024 · Figshare
  22. Additional file 2 of Remodeling of the maternal gut microbiome during pregnancy is shaped by parity
    Berry, Alexander S. F., Meghann K. Pierdon, Ana M. Misic, Megan C. Sullivan, O’Brien, Kevin, Chen, Ying, Murray, Samuel J., Lydia A. Ramharack, Baldassano, Robert N., Parsons, Thomas D. et al. · 2021 · Figshare
  23. Additional file 5 of Remodeling of the maternal gut microbiome during pregnancy is shaped by parity
    Berry, Alexander S. F., Meghann K. Pierdon, Ana M. Misic, Megan C. Sullivan, O’Brien, Kevin, Chen, Ying, Murray, Samuel J., Lydia A. Ramharack, Baldassano, Robert N., Parsons, Thomas D. et al. · 2021 · Figshare
  24. Additional file 8 of Remodeling of the maternal gut microbiome during pregnancy is shaped by parity
    Berry, Alexander S. F., Meghann K. Pierdon, Ana M. Misic, Megan C. Sullivan, O’Brien, Kevin, Chen, Ying, Murray, Samuel J., Lydia A. Ramharack, Baldassano, Robert N., Thomas D. Parsons et al. · 2021 · Figshare
  25. Additional file 4 of Longitudinal metagenomic study reveals the dynamics of fecal antibiotic resistome in pigs throughout the lifetime
    Ma, Lingyan, Song, Yuanyuan, Lyu, Wentao, Chen, Qu, Xingning Xiao, Jin, Yuanxiang, Yang, Hua, Wang, Wen, Xiao, Yingping · 2024 · Figshare
  26. Additional file 3 of Remodeling of the maternal gut microbiome during pregnancy is shaped by parity
    Berry, Alexander S. F., Meghann K. Pierdon, Ana M. Misic, Megan C. Sullivan, O’Brien, Kevin, Chen, Ying, Murray, Samuel J., Lydia A. Ramharack, Baldassano, Robert N., Parsons, Thomas D. et al. · 2021 · Figshare
  27. Additional file 1 of Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life
    Anna Samarra, Raúl Cabrera‐Rubio, Cecilia Martínez‐Costa, Maria Collado · 2024 · Figshare
  28. Additional file 5 of Understanding Horizontal Gene Transfer network in human gut microbiota
    Li, Chen, Jiaxing Chen, Li, Shuai Cheng · 2020 · Figshare
  29. Additional file 9 of Remodeling of the maternal gut microbiome during pregnancy is shaped by parity
    Berry, Alexander S. F., Meghann K. Pierdon, Ana M. Misic, Megan C. Sullivan, O’Brien, Kevin, Chen, Ying, Murray, Samuel J., Lydia A. Ramharack, Baldassano, Robert N., Thomas D. Parsons et al. · 2021 · Figshare
  30. Additional file 10 of Remodeling of the maternal gut microbiome during pregnancy is shaped by parity
    Berry, Alexander S. F., Meghann K. Pierdon, Ana M. Misic, Megan C. Sullivan, O’Brien, Kevin, Chen, Ying, Murray, Samuel J., Lydia A. Ramharack, Baldassano, Robert N., Parsons, Thomas D. et al. · 2021 · Figshare
  31. Additional file 2 of Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life
    Anna Samarra, Raúl Cabrera‐Rubio, Cecilia Martínez‐Costa, Maria Collado · 2024 · Figshare
  32. Additional file 10 of Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome
    Emma K. Accorsi, Eric A. Franzosa, Tiffany Y. Hsu, Joice Cordy, Regina, Ayala Maayan‐Metzger, Hanaa Jaber, Aylana Reiss-Mandel, Kline, Madeleine, Casey R. DuLong, Marc Lipsitch et al. · 2020 · Figshare
  33. Additional file 1 of Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome
    Emma K. Accorsi, Eric A. Franzosa, Tiffany Y. Hsu, Joice Cordy, Regina, Ayala Maayan‐Metzger, Hanaa Jaber, Aylana Reiss-Mandel, Kline, Madeleine, Casey R. DuLong, Marc Lipsitch et al. · 2020 · Figshare
  34. Additional file 7 of Remodeling of the maternal gut microbiome during pregnancy is shaped by parity
    Berry, Alexander S. F., Meghann K. Pierdon, Ana M. Misic, Megan C. Sullivan, O’Brien, Kevin, Chen, Ying, Murray, Samuel J., Lydia A. Ramharack, Baldassano, Robert N., Parsons, Thomas D. et al. · 2021 · Figshare
  35. Additional file 4 of Remodeling of the maternal gut microbiome during pregnancy is shaped by parity
    Berry, Alexander S. F., Meghann K. Pierdon, Ana M. Misic, Megan C. Sullivan, O’Brien, Kevin, Chen, Ying, Murray, Samuel J., Lydia A. Ramharack, Baldassano, Robert N., Parsons, Thomas D. et al. · 2021 · Figshare
  36. Additional file 7 of Longitudinal metagenomic study reveals the dynamics of fecal antibiotic resistome in pigs throughout the lifetime
    Ma, Lingyan, Song, Yuanyuan, Wentao Lyu, Chen, Qu, Xingning Xiao, Jin, Yuanxiang, Yang, Hua, Wang, Wen, Xiao, Yingping · 2024 · Figshare
  37. Additional file 2 of Longitudinal metagenomic study reveals the dynamics of fecal antibiotic resistome in pigs throughout the lifetime
    Ma, Lingyan, Song, Yuanyuan, Wentao Lyu, Chen, Qu, Xingning Xiao, Jin, Yuanxiang, Yang, Hua, Wang, Wen, Xiao, Yingping · 2024 · Figshare
  38. Additional file 4 of Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life
    Anna Samarra, Raúl Cabrera‐Rubio, Cecilia Martínez‐Costa, Maria Collado · 2024 · Figshare
  39. Additional file 7 of Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
    Utter, Daniel R., Gary G. Borisy, Eren, A. Murat, Colleen M. Cavanaugh, Mark Welch, Jessica L. · 2020 · Figshare
  40. Additional file 1 of High-resolution strain-level microbiome composition analysis from short reads
    Liao, Herui, Yongxin Ji, Sun, Yanni · 2023 · Figshare
  41. Additional file 1 of Strain-level profiling with picodroplet microfluidic cultivation reveals host-specific adaption of honeybee gut symbionts
    Meng, Yujie, Li, Shuang, Zhang, Chong, Zheng, Hao · 2022 · Figshare
  42. Additional file 1 of Longitudinal metagenomic study reveals the dynamics of fecal antibiotic resistome in pigs throughout the lifetime
    Ma, Lingyan, Song, Yuanyuan, Wentao Lyu, Chen, Qu, Xingning Xiao, Jin, Yuanxiang, Yang, Hua, Wang, Wen, Xiao, Yingping · 2024 · Figshare
  43. Additional file 8 of Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
    Utter, Daniel R., Gary G. Borisy, Eren, A. Murat, Colleen M. Cavanaugh, Mark Welch, Jessica L. · 2020 · Figshare
  44. Additional file 6 of Remodeling of the maternal gut microbiome during pregnancy is shaped by parity
    Berry, Alexander S. F., Meghann K. Pierdon, Ana M. Misic, Megan C. Sullivan, O’Brien, Kevin, Chen, Ying, Murray, Samuel J., Lydia A. Ramharack, Baldassano, Robert N., Parsons, Thomas D. et al. · 2021 · Figshare
  45. Additional file 2 of A genome catalog of the early-life human skin microbiome
    Zeyang Shen, Lukian Robert, Milan Stolpman, Che, You, Katrina Jane Allen, Saffery, Richard, Audrey Walsh, Young, Angela, Eckert, Jana, Clay Deming et al. · 2024 · Figshare
  46. Additional file 5 of Longitudinal metagenomic study reveals the dynamics of fecal antibiotic resistome in pigs throughout the lifetime
    Ma, Lingyan, Song, Yuanyuan, Wentao Lyu, Chen, Qu, Xingning Xiao, Jin, Yuanxiang, Yang, Hua, Wang, Wen, Xiao, Yingping · 2024 · Figshare
  47. Additional file 1 of Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
    Utter, Daniel R., Gary G. Borisy, Eren, A. Murat, Colleen M. Cavanaugh, Mark Welch, Jessica L. · 2020 · Figshare
  48. Additional file 3 of Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life
    Anna Samarra, Raúl Cabrera‐Rubio, Cecilia Martínez‐Costa, Maria Collado · 2024 · Figshare
  49. Additional file 1 of SNV-FEAST: microbial source tracking with single nucleotide variants
    Leah Briscoe, Halperin, Eran, Nandita R. Garud · 2024 · Figshare
  50. Additional file 2 of SNV-FEAST: microbial source tracking with single nucleotide variants
    Leah Briscoe, Halperin, Eran, Nandita R. Garud · 2024 · Figshare
  51. Additional file 1 of A genome catalog of the early-life human skin microbiome
    Zeyang Shen, Lukian Robert, Milan Stolpman, Che, You, Katrina Jane Allen, Richard Saffery, Audrey Walsh, Young, Angela, Eckert, Jana, Clay Deming et al. · 2024 · Figshare
  52. Additional file 3 of Longitudinal metagenomic study reveals the dynamics of fecal antibiotic resistome in pigs throughout the lifetime
    Ma, Lingyan, Song, Yuanyuan, Wentao Lyu, Chen, Qu, Xingning Xiao, Jin, Yuanxiang, Yang, Hua, Wang, Wen, Xiao, Yingping · 2024 · Figshare
  53. Additional file 1 of Mother-to-infant transmission of the carcinogenic colibactin-producing bacteria
    Tsunematsu, Yuta, Koji Hosomi, Kunisawa, Jun, Michio Sato, Noriko Shibuya, Saito, Emiko, Murakami, Haruka, Yuko Yoshikawa, Yuji Iwashita, Noriyuki Miyoshi et al. · 2021 · Figshare
  54. Copper intake influences offspring growth, Cu excretion, microbiota, and antibiotic resistance genes via vertical transmission in pigeons
    D.Y. Zhang, Yuxin Shao, Yifang Cui, Bo Zhang, Jing Li, Jianguo Huang, Ashraful Kabir, Fuzhou Xu, Hui Liu, Yangping Wang et al. · 2026 · Agriculture Communications
  55. Motif Analysis of the Horizontal Gene Transfer Networks in Human Gut Microbiota
    Zhangdi Song, Haoran Sun, Yufan Li, Runze Zhang, Jiaxing Chen · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  56. Pregnancy and Early-Life Gut Virome in the Lifelines NEXT cohort: Origin, Persistence, Influencing Factors and Health Implications
    Asier Fernández-Pato, Anastasia A. Gulyaeva, Nataliia Kuzub, Trishla Sinha, Siobhan Brushett, Johanne E. Spreckels, Milla F. Brandao Gois, Archontis Goumagias, Angel Jonathan Ruiz-Moreno, Antoni Pedro Camargo et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  57. Contribution of Host Genetics and Maternal Inflammatory Bowel Disease to Fecal Calprotectin and Microbiota Composition During Early Life
    Paola Nicoletti, W. H. Lee, Adam Cantor, Leonid Tarassishin, Samreen Zafer, Jianzhong Hu, Mellissa Picker, Alexa P. Rendon, Anketse Debebe, Isabella Nguyen et al. · 2026 · JCC Plus
  58. Novel insights into how gestational diet affects maternal-infant microbiota: a cross-sectional causal mediation analysis at one month postpartum
    Eduard Flores Ventura, Sergio Ruiz-Saavedra, Raúl Cabrera‐Rubio, Cecilia Martínez‐Costa, Sonia González, María Carmen Collado · 2026 · European Journal of Nutrition
  59. Isolation and Characterization of Bifidobacterium longum A1, an Isolate from Faeces of an Exclusively Breast-fed Infant with Probiotic Potential
    Lise Sanchez, Marcus Vinícius Canário Viana, Véronique Robert, Florian Chain, Sead Chadi, Vasco Ariston de Carvalho Azevedo, Alexis Mosca, Philippe Langella, Sylvie Binda, Rebeca Martín · 2026 · Probiotics and Antimicrobial Proteins
  60. Early-life acquisition of antimicrobial resistance genes and strain-level genomic concordance across maternal-infant compartments
    Jean Marc Mardirossian, Bahia Abdallah, Gavin M. Douglas, Jessy Barbour, B. Jesse Shapiro, Mira El Chaar · 2026 · Infection Genetics and Evolution
  61. Dual human milk oligosaccharide-fibre utilisation is a selection cue for the weaning gut microbiome
    Yunjeong So, Michael Jakob Pichler, Susanne Soendergaard Kappel, Chunsheng Jin, Carsten Eriksen, Ioanna Chatzigiannidou, Maria Haugaard Bohl Andersen, Vasileios Tsiamis, Marie Vestergaard Lukassen, Lea Eschen Skytthe et al. · 2026 · Nature Communications
  62. Impact of maternal fecal microbiota on the early development of neonatal gut microbial community
    Jae Youn Jo, In Ae Cho, Jin‐Su Jun, Ji Sook Park · 2026 · Frontiers in Pediatrics
  63. Probiotic formula intervention in infants leads to colonization and competitive strain displacement independent of IgA binding
    Michael Vig Merino, Svenja Weißenberger, Anastasia Ermolova, Elise Dhilly, Roan Spadazzi, Lior Levy, María Carmen Collado, Tomer Hertz, Hélène Omer, Vitor Heidrich et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  64. Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals
    Vitor Heidrich, Gloria Fackelmann, Liviana Ricci, Roan Spadazzi, Gabriel Baldanzi, Michal Punčochář, Giulia Naspi Catassi, Paolo Marchi, Monica Modesto, Gianmarco Piccinno et al. · 2026 · Cell Press Blue
  65. Gestational diabetes mellitus and maternal-infant microbiome axis: mechanistic insights and therapeutic interventions
    Jinjoo Choi, Jihyun Keum, Min‐Jin Kwak, Seung Hyun Kim, Jeong Kyu Hoh, Byong‐Hun Jeon, Hyun-kyung Park · 2026 · Journal of Translational Medicine
  66. Early-life microbiome trajectories as biomarkers to predict health outcomes
    Raphaela Joos, Aonghus Lavelle, Eugene Michael Dempsey, Catherine Stanton, R Paul Ross · 2026 · Microbiome Research Reports
  67. ZILA-SRM: a probabilistic framework with zero-inflated latent models for robust strain reconstruction from metagenomes
    Saidi Wang, Mintong Chen, Di Jiao · 2026 · Microbiology Spectrum
  68. Comparative genomics analysis of Lactobacillus helveticus identifies GH13 and GH36 as candidate markers for milk source-associated carbohydrate differentiation
    Runyu Yang, Lixia Zhao, Zhiyi Wu, Wenjun Liu · 2026 · Food Bioscience
  69. The who, how, and when of mother–infant microbial sharing
    Phoebe Crossley, Conor Feehily · 2026 · Trends in Microbiology
  70. A proposed framework for microbial inheritance in mammalian evolution: the apocrine-mammary-microbiota axis
    Andrew C. Retzinger · 2026 · Frontiers in Ecology and Evolution
  71. Gut microbiota and epigenetic mechanisms in brain physiology and disorders
    Gerard M. Moloney, GERARD CLARKE, John F. Cryan · 2026 · Handbook of clinical neurology
  72. From maternal microbial transmission to neonatal gut microbiota restoration: the potential and challenges of maternal fecal microbiota transplantation
    Xia Hu, Guangyu Ma, Jinbiao Han, 朱丽娟, Ying He, Dan Zhu · 2026 · Frontiers in Microbiology