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References from Breastfeeding and maternal microbial reservoirs are associated with infant gut phageome development during the first year of life. Local targets link to admitted publications; unresolved targets remain external evidence.
Microbial transmission, colonisation and succession: from pregnancy to infancy
10.1136/gutjnl-2022-328970 · 2023 · External reference
Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year
10.1016/j.chom.2024.05.005 · 2024 · External reference
Microbial beginnings: determinants and disruptions of the neonatal microbiome
10.3389/fmicb.2025.1672780 · 2025 · External reference
Patterns of Early-Life Gut Microbial Colonization during Human Immune Development: An Ecological Perspective
10.3389/fimmu.2017.00788 · 2017 · External reference
Maternal-infant antibiotic resistance genes transference: what do we know?
10.1080/19490976.2023.2194797 · 2023 · External reference
Horizontal Gene Exchange in Environmental Microbiota
10.3389/fmicb.2011.00158 · 2011 · External reference
Lysogeny in nature: mechanisms, impact and ecology of temperate phages
10.1038/ismej.2017.16 · 2017 · External reference
When bacteria are phage playgrounds: interactions between viruses, cells, and mobile genetic elements
10.1016/j.mib.2022.102230 · 2022 · External reference
The Human Gut Phage Community and Its Implications for Health and Disease
10.3390/v9060141 · 2017 · External reference
Transmission and dynamics of mother-infant gut viruses during pregnancy and early life
10.1038/s41467-024-45257-4 · 2024 · External reference
Longitudinal comparison of the developing gut virome in infants and their mothers
10.1016/j.chom.2023.01.003 · 2023 · External reference
Interactions between bacterial and phage communities in natural environments
10.1038/s41579-021-00602-y · 2022 · External reference
Role of vertical and horizontal microbial transmission of antimicrobial resistance genes in early life: insights from maternal-infant dyads
10.1016/j.mib.2023.102424 · 2024 · External reference
Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life
10.1186/s12941-024-00725-z · 2024 · External reference
The role of Bifidobacterium genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life
10.1080/19490976.2024.2357176 · 2024 · External reference
Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome
10.1038/s41467-025-61154-w · 2025 · External reference
Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome
10.1016/j.chom.2018.06.005 · 2018 · External reference
Selective maternal seeding and environment shape the human gut microbiome
10.1101/gr.233940.117 · 2018 · External reference
Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements
10.1038/s41467-018-06393-w · 2018 · External reference
Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth
10.1038/s41586-019-1560-1 · 2019 · External reference
A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning
10.1016/j.cell.2022.10.011 · 2022 · External reference
Early-life development of the gut virome and plasmidome: A longitudinal study in cesarean-born infants
10.1016/j.celrep.2025.115731 · 2025 · External reference
Phage diversity in human breast milk: a systematic review
10.1007/s00431-025-06173-x · 2025 · External reference
Role of Human Milk Bioactives on Infants’ Gut and Immune Health
10.3389/fimmu.2021.604080 · 2021 · External reference
Human Milk Oligosaccharides and Immune System Development
10.3390/nu10081038 · 2018 · External reference
Functional effects of human milk oligosaccharides (HMOs)
10.1080/19490976.2023.2186115 · 2023 · External reference
Shaping the Gut Microbiota by Breastfeeding: The Gateway to Allergy Prevention?
10.3389/fped.2019.00047 · 2019 · External reference
Can breastfeeding protect against antimicrobial resistance?
10.1186/s12916-020-01862-w · 2020 · External reference
The Impact of Cesarean Section Delivery on Intestinal Microbiota: Mechanisms, Consequences, and Perspectives—A Systematic Review
10.3390/ijms25021055 · 2024 · External reference
The Intestinal Microbiome in Early Life: Health and Disease
10.3389/fimmu.2014.00427 · 2014 · External reference
MAMI: a birth cohort focused on maternal-infant microbiota during early life
10.1186/s12887-019-1502-y · 2019 · External reference
Identification of mobile genetic elements with geNomad
10.1038/s41587-023-01953-y · 2024 · External reference
A core gut microbiome in obese and lean twins
10.1038/nature07540 · 2009 · External reference
10.1016/j.csbj.2020.08.028 · 2020 · Admitted local publication
BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains
10.7717/peerj.11396 · 2021 · External reference
iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria
10.1371/journal.pbio.3002083 · 2023 · External reference
The Aggregated Gut Viral Catalogue (AVrC): A unified resource for exploring the viral diversity of the human gut
10.1371/journal.pcbi.1012268 · 2025 · External reference
Piggyback-the-Winner in host-associated microbial communities
10.1038/npjbiofilms.2016.10 · 2016 · External reference
Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages
10.1080/19490976.2025.2507775 · 2025 · External reference
Expanding known viral diversity in the healthy infant gut
10.1038/s41564-023-01345-7 · 2023 · External reference
The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific
10.1016/j.chom.2019.09.009 · 2019 · External reference
Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota
10.1371/journal.pone.0158498 · 2016 · External reference
The Bifidogenic Effect Revisited—Ecology and Health Perspectives of Bifidobacterial Colonization in Early Life
10.3390/microorganisms8121855 · 2020 · External reference
Bifidobacterium Species Colonization in Infancy: A Global Cross-Sectional Comparison by Population History of Breastfeeding
10.3390/nu14071423 · 2022 · External reference
Long-read metagenomics reveals phage dynamics in the human gut microbiome
10.1038/s41586-025-09786-2 · 2026 · External reference
Phages in the infant gut: a framework for virome development during early life
10.1038/s41396-021-01090-x · 2022 · External reference
The influence of early life exposures on the infant gut virome
10.1080/19490976.2025.2501194 · 2025 · External reference
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
10.1101/gr.142315.112 · 2013 · External reference
Early life bifidobacterial mother–infant transmission: greater contribution from the infant gut to human milk revealed by microbiomic and culture-based methods
10.1128/msystems.00480-25 · 2025 · External reference
Enterobacteriaceae in the Human Gut: Dynamics and Ecological Roles in Health and Disease
10.3390/biology13030142 · 2024 · External reference
Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life
10.1016/j.chom.2015.04.004 · 2015 · External reference
Rebuilding the Gut Microbiota Ecosystem
10.3390/ijerph15081679 · 2018 · External reference
Effects of early-life antibiotics on the developing infant gut microbiome and resistome: a randomized trial
10.1038/s41467-022-28525-z · 2022 · External reference
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut
10.1016/j.chom.2020.08.003 · 2020 · External reference
The stepwise assembly of the neonatal virome is modulated by breastfeeding
10.1038/s41586-020-2192-1 · 2020 · External reference
Massive expansion of human gut bacteriophage diversity
10.1016/j.cell.2021.01.029 · 2021 · External reference
Shared and Distinct Features of Human Milk and Infant Stool Viromes
10.3389/fmicb.2018.01162 · 2018 · External reference
Prophage-encoded antibiotic resistance genes are enriched in human-impacted environments
10.1038/s41467-024-52450-y · 2024 · External reference
A metagenomic catalog of the early-life human gut virome
10.1038/s41467-024-45793-z · 2024 · External reference
Biases and complementarity in gut viromes obtained from bulk and virus-like particle-enriched metagenomic sequencing
2025 · External reference
FastQC: a quality control tool for high throughput sequence data Babraham
2010 · External reference
MultiQC: summarize analysis results for multiple tools and samples in a single report
10.1093/bioinformatics/btw354 · 2016 · External reference
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
10.1089/cmb.2012.0021 · 2012 · External reference
CheckV assesses the quality and completeness of metagenome-assembled viral genomes
10.1038/s41587-020-00774-7 · 2021 · External reference
Unresolved reference
2014 · External reference
taxMyPhage: Automated Taxonomy of dsDNA Phage Genomes at the Genus and Species Level
2025 · External reference
Multivariable association discovery in population-scale meta-omics studies
10.1371/journal.pcbi.1009442 · 2021 · External reference
Vegan: Community Ecology Package
2025 · External reference
ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics
2026 · External reference
lmerTest Package: Tests in Linear Mixed Effects Models
10.18637/jss.v082.i13 · 2017 · External reference
emmeans: Estimated Marginal Means, aka Least-Squares Means The Comprehensive
2026 · External reference
Unresolved reference
2020 · External reference
Layered Grammar for Alluvial Plots
10.21105/joss.02017 · 2020 · External reference
The Composer of Plots The Comprehensive
2025 · External reference
broom.mixed: Tidying Methods for Mixed Models The Comprehensive
2026 · External reference
Cluster-Robust (Sandwich) Variance Estimators with Small-Sample Corrections The Comprehensive
2026 · External reference
Unresolved reference
2025 · External reference
simr: an R package for power analysis of generalised linear mixed models by simulation
10.1111/2041-210x.12504 · 2016 · External reference
Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols
10.1261/rna.074922.120 · 2020 · External reference
Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere
10.1186/s40168-022-01371-3 · 2022 · External reference
Basic local alignment search tool
10.1016/s0022-2836(05)80360-2 · 1990 · External reference
Fitting Linear Mixed-Effects Models Using lme4
10.18637/jss.v067.i01 · 2015 · External reference
Unresolved reference
1988 · External reference