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References from Within-host evolution and transmission of a human gut symbiont across ecological scales. Local targets link to admitted publications; unresolved targets remain external evidence.
Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces
10.1128/aem.02340-06 · 2007 · External reference
Dominant and diet-responsive groups of bacteria within the human colonic microbiota
10.1038/ismej.2010.118 · 2011 · External reference
Diet rapidly and reproducibly alters the human gut microbiome
10.1038/nature12820 · 2014 · External reference
Diet dominates host genotype in shaping the murine gut microbiota
10.1016/j.chom.2014.11.010 · 2015 · External reference
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
10.1073/pnas.1000087107 · 2011 · External reference
Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile
10.1038/nature13828 · 2015 · External reference
Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability
10.1126/scitranslmed.aad0917 · 2016 · External reference
Recovery of gut microbiota of healthy adults following antibiotic exposure
10.1038/s41564-018-0257-9 · 2018 · External reference
Recovery of the gut microbiota after antibiotics depends on host diet, community context, and environmental reservoirs
10.1016/j.chom.2019.10.011 · 2019 · External reference
Adaptive evolution within gut microbiomes of healthy people
10.1016/j.chom.2019.03.007 · 2019 · External reference
Evolutionary dynamics of bacteria in the gut microbiome within and across hosts
10.1371/journal.pbio.3000102 · 2019 · External reference
Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation
10.1038/s41564-019-0625-0 · 2020 · External reference
Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment
10.1101/gr.265058.120 · 2021 · External reference
Rapid evolution and strain turnover in the infant gut microbiome
10.1101/gr.276306.121 · 2022 · External reference
Brief antibiotic use drives human gut bacteria towards low-cost resistance
10.1038/s41586-025-08781-x · 2025 · External reference
The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps
10.1371/journal.pgen.1004182 · 2014 · External reference
Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut
10.1111/mec.13851 · 2017 · External reference
Quantifying rapid bacterial evolution and transmission within the mouse intestine
10.1016/j.chom.2021.08.003 · 2021 · External reference
Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut
10.1073/pnas.1906958116 · 2019 · External reference
Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice
10.1016/j.chom.2021.02.001 · 2021 · External reference
Two modes of evolution shape bacterial strain diversity in the mammalian gut for thousands of generations
10.1038/s41467-022-33412-8 · 2022 · External reference
Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria
10.1038/ncomms9945 · 2015 · External reference
Specific Eco-evolutionary Contexts in the Mouse Gut Reveal Escherichia coli Metabolic Versatility
10.1016/j.cub.2020.01.050 · 2020 · External reference
Fluctuating selection on bacterial iron regulation in the mammalian gut
10.1016/j.cub.2022.06.017 · 2022 · External reference
The selective advantage of the lac operon for Escherichia coli is conditional on diet and microbiota composition
10.3389/fmicb.2021.709259 · 2021 · External reference
Long-term evolution of the natural isolate of Escherichia coli 536 in the mouse gut colonized after maternal transmission reveals convergence in the constitutive expression of the lactose operon
10.1111/mec.15232 · 2019 · External reference
Diet leaves a genetic signature in a keystone member of the gut microbiota
10.1016/j.chom.2022.01.002 · 2022 · External reference
Dynamic genetic adaptation of Bacteroides thetaiotaomicron during murine gut colonization
10.1016/j.celrep.2023.113009 · 2023 · External reference
The landscape of adaptive evolution of a gut commensal bacteria in aging mice
10.1016/j.cub.2020.01.037 · 2020 · External reference
Infection leaves a genetic and functional mark on the gut population of a commensal bacterium
10.1016/j.chom.2023.04.005 · 2023 · External reference
Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking
10.1038/s41467-024-45792-0 · 2024 · External reference
Trade-off between bile resistance and nutritional competence drives Escherichia coli diversification in the mouse gut
10.1371/journal.pgen.1002107 · 2011 · External reference
Gene-specific selective sweeps are pervasive across human gut microbiomes
10.1038/s41586-025-09798-y · 2026 · External reference
Dynamics of bacterial recombination in the human gut microbiome
10.1371/journal.pbio.3002472 · 2024 · External reference
Transmission modes of the mammalian gut microbiota
10.1126/science.aat7164 · 2018 · External reference
Dispersal strategies shape persistence and evolution of human gut bacteria
10.1016/j.chom.2021.05.008 · 2021 · External reference
Stable engraftment of Bifidobacterium longum AH1206 in the human gut depends on individualized features of the resident microbiome
10.1016/j.chom.2016.09.001 · 2016 · External reference
Microbiota-mediated colonization resistance: Mechanisms and regulation
10.1038/s41579-022-00833-7 · 2023 · External reference
Evolving perspectives on monopolization and priority effects
10.1016/j.tree.2015.12.009 · 2016 · External reference
Adaptive strategies of the candidate probiotic E. coli Nissle in the mammalian gut
10.1016/j.chom.2019.02.005 · 2019 · External reference
Bacterial adaptation is constrained in complex communities
10.1038/s41467-020-14570-z · 2020 · External reference
Diversity begets diversity under microbial niche construction
2022 · External reference
Does diversity beget diversity in microbiomes?
10.7554/elife.58999 · 2020 · External reference
Predicting the first steps of evolution in randomly assembled communities
10.1038/s41467-024-52467-3 · 2024 · External reference
Highly-resolved within-species dynamics in the human facial skin microbiome
10.1016/j.chom.2025.04.010 · 2024 · External reference
Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation
2023 · External reference
The person-to-person transmission landscape of the gut and oral microbiomes
10.1038/s41586-022-05620-1 · 2023 · External reference
Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations
10.1073/pnas.1119910109 · 2012 · External reference
Quantitative evolutionary dynamics using high-resolution lineage tracking
10.1038/nature14279 · 2015 · External reference
Probabilistic invasion underlies natural gut microbiome stability
10.1016/j.cub.2017.05.034 · 2017 · External reference
Emergent evolutionary forces in spatial models of luminal growth and their application to the human gut microbiota
10.1073/pnas.2114931119 · 2022 · External reference
Shared evolutionary path in social microbiomes
10.1093/molbev/msad153 · 2023 · External reference
Rethinking gut microbiome residency and the Enterobacteriaceae in healthy human adults
10.1038/s41396-019-0435-7 · 2019 · External reference
Codiversification of gut microbiota with humans
10.1126/science.abm7759 · 2022 · External reference
Bacterial colonization factors control specificity and stability of the gut microbiota
10.1038/nature12447 · 2013 · External reference
Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes
10.1038/s41396-022-01208-9 · 2022 · External reference
Strain difference in coprophagous behavior in laboratory mice (Mus musculus)
1985 · External reference
Effect of water flow and chemical environment on microbiota growth and composition in the human colon
10.1073/pnas.1619598114 · 2017 · External reference
Within-host evolution of a gut pathobiont facilitates liver translocation
10.1038/s41586-022-04949-x · 2022 · External reference
Gut microbiota utilize immunoglobulin A for mucosal colonization
10.1126/science.aaq0926 · 2018 · External reference
Quantitative Imaging of Gut Microbiota Spatial Organization
10.1016/j.chom.2015.09.002 · 2015 · External reference
The Gut Microbiome: Connecting Spatial Organization to Function
10.1016/j.chom.2017.03.010 · 2017 · External reference
Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization
10.1038/s41467-023-39121-0 · 2023 · External reference
Profiling the human intestinal environment under physiological conditions
10.1038/s41586-023-05989-7 · 2023 · External reference
Biogeography of a human oral microbiome at the micron scale
10.1073/pnas.1522149113 · 2016 · External reference
Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont
10.1016/j.chom.2008.09.007 · 2008 · External reference
Characterization of four outer membrane proteins involved in binding starch to the cell surface of Bacteroides thetaiotaomicron
10.1128/jb.182.19.5365-5372.2000 · 2000 · External reference
Intragenic DNA inversions expand bacterial coding capacity
10.1038/s41586-024-07970-4 · 2023 · External reference
Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis
10.1093/nar/gkaa824 · 2020 · External reference
Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota
10.1016/j.chom.2021.12.008 · 2022 · External reference
Competitive species interactions constrain abiotic adaptation in a bacterial soil community
10.1002/evl3.83 · 2018 · External reference
Mechanism of the gut microbiota colonization resistance and enteric pathogen infection
10.3389/fcimb.2021.716299 · 2021 · External reference
Microbiome diversity protects against pathogens by nutrient blocking
10.1126/science.adj3502 · 2023 · External reference
The intestinal microbiota: antibiotics, colonization resistance, and enteric pathogens
10.1111/imr.12563 · 2017 · External reference
Design, construction, and in vivo augmentation of a complex gut microbiome
10.1016/j.cell.2022.08.003 · 2022 · External reference
The impact of iron and heme availability on the healthy human gut microbiome in vivo and in vitro
10.1016/j.chembiol.2022.12.001 · 2023 · External reference
Single nucleotide mapping of trait space reveals Pareto fronts that constrain adaptation
10.1038/s41559-019-0993-0 · 2019 · External reference
Mutant phenotypes for thousands of bacterial genes of unknown function
10.1038/s41586-018-0124-0 · 2018 · External reference
Identifying genetic determinants needed to establish a human gut symbiont in its habitat
10.1016/j.chom.2009.08.003 · 2009 · External reference
Within-host evolution of the gut microbiome
10.1016/j.mib.2022.102258 · 2023 · External reference
Beneficial mutation–selection balance and the effect of linkage on positive selection
10.1534/genetics.106.067678 · 2007 · External reference
An exclusive metabolic niche enables strain engraftment in the gut microbiota
10.1038/s41586-018-0092-4 · 2018 · External reference
Tunable Expression Tools Enable Single-Cell Strain Distinction in the Gut Microbiome
10.1016/j.cell.2017.03.041 · 2017 · External reference
Copy number change: evolving views on gene amplification
10.2217/fmb.13.53 · 2013 · External reference
“Gene accordions” cause genotypic and phenotypic heterogeneity in clonal populations of Staphylococcus aureus
10.1038/s41467-020-17277-3 · 2020 · External reference
Evolution of symbiotic bacteria in the distal human intestine
10.1371/journal.pbio.0050156 · 2007 · External reference
Fitness variation across subtle environmental perturbations reveals local modularity and global pleiotropy of adaptation
10.7554/elife.61271 · 2020 · External reference
Inducible transposon mutagenesis for genome-scale forward genetics
2024 · External reference
High-resolution lineage tracking reveals travelling wave of adaptation in laboratory yeast
10.1038/s41586-019-1749-3 · 2019 · External reference
Multiplex recording of cellular events over time on CRISPR biological tape
10.1126/science.aao0958 · 2017 · External reference
Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms
10.1186/s12864-018-4703-0 · 2018 · External reference
Quality filtering of Illumina index reads mitigates sample cross-talk
10.1186/s12864-016-3217-x · 2016 · External reference
Bartender: a fast and accurate clustering algorithm to count barcode reads
10.1093/bioinformatics/btx655 · 2018 · External reference
Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq
2014 · External reference
DADA2: High-resolution sample inference from Illumina amplicon data
10.1038/nmeth.3869 · 2016 · External reference
QIIME allows analysis of high-throughput community sequencing data
10.1038/nmeth.f.303 · 2010 · External reference
EMBOSS: the European molecular biology open software suite
10.1016/s0168-9525(00)02024-2 · 2000 · External reference
A one pot, one step, precision cloning method with high throughput capability
10.1371/journal.pone.0003647 · 2008 · External reference
Optimization of the 16S rRNA sequencing analysis pipeline for studying in vitro communities of gut commensals
10.1016/j.isci.2022.103907 · 2022 · External reference
Reducing chimera formation during PCR amplification to ensure accurate genotyping
10.1016/j.gene.2010.08.009 · 2010 · External reference
Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota
10.7554/elife.81212 · 2023 · External reference
The dynamics of molecular evolution over 60,000 generations
10.1038/nature24287 · 2017 · External reference
Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq
10.1186/1471-2164-15-1039 · 2014 · External reference
