ArticleGenome research2013
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 258 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
258 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis.Microbiome · 2017Pooled it
- Microbiota dynamics in a randomized trial of gut decontamination during allogeneic hematopoietic cell transplantation.JCI insight · 2022Trial
- Trial
- Eukaryotic metagenome-assembled genomes recovered from deep metagenomic sequencing of the seagrass,Microbial genomics · 2026Article
- Protecting Newborns from Multidrug-Resistant Infections: The Emerging Role of Bacteriophages.Viruses · 2026Review
- Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics.Cell genomics · 2025Article
- Large diversity in the O-chain biosynthetic cluster within populations of Pelagibacterales.mBio · 2025Article
- A review of neural networks for metagenomic binning.Briefings in bioinformatics · 2025Review
- Essential nucleic acid omics: a theoretical foundation for early-stage users.Frontiers in bioinformatics · 2025Review
- Constructing phylogenetic trees for microbiome data analysis: A mini-review.Computational and structural biotechnology journal · 2024Review
- 4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs.Nucleic acids research · 2024Article
- Metaproteogenomics resolution of a high-COMicrobiome · 2024Article
- A Proteogenomic Approach to Unveiling the Complex Biology of the Microbiome.International journal of molecular sciences · 2024Review
- PUPpy: a primer design pipeline for substrain-level microbial detection and absolute quantification.mSphere · 2024Article
- AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides.BMC bioinformatics · 2024Article
- VirGrapher: a graph-based viral identifier for long sequences from metagenomes.Briefings in bioinformatics · 2024Article
- Infant gut DNA bacteriophage strain persistence during the first 3 years of life.Cell host & microbe · 2024Article
- High niche specificity and host genetic diversity of groundwater viruses.The ISME journal · 2024Article
- Dysbiosis of lower respiratory tract microbiome are associated with proinflammatory states in non-small cell lung cancer patients.Thoracic cancer · 2024Article
- The Diversity of Bacteriophages in the Human Gut.Methods in molecular biology (Clifton, N.J.) · 2024Article
198 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
The gastrointestinal microbiome undergoes shifts in species and strain abundances, yet dynamics involving closely related microorganisms remain largely unknown because most methods cannot resolve them. We developed new metagenomic methods and utilized them to track species and strain level variations in microbial communities in 11 fecal samples collected from a premature infant during the first month of life. Ninety six percent of the sequencing reads were assembled into scaffolds of >500 bp in length that could be assigned to organisms at the strain level. Six essentially complete (∼99%) and two near-complete genomes were assembled for bacteria that comprised as little as 1% of the community, as well as nine partial genomes of bacteria representing as little as 0.05%. In addition, three viral genomes were assembled and assigned to their hosts. The relative abundance of three Staphylococcus epidermidis strains, as well as three phages that infect them, changed dramatically over time. Genes possibly related to these shifts include those for resistance to antibiotics, heavy metals, and phage. At the species level, we observed the decline of an early-colonizing Propionibacterium acnes strain similar to SK137 and the proliferation of novel Propionibacterium and Peptoniphilus species late in colonization. The Propionibacterium species differed in their ability to metabolize carbon compounds such as inositol and sialic acid, indicating that shifts in species composition likely impact the metabolic potential of the community. These results highlight the benefit of reconstructing complete genomes from metagenomic data and demonstrate methods for achieving this goal.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.