ArticleMolecular systems biology2015
Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics.
Article in Molecular systems biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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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.
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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.
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Who cites it
22 citing papers in PubMed, 33 citations in OpenAlex.
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- Dual membrane-spanning anti-sigma 2 controls OMV biogenesis and colonization fitness inJournal of bacteriology · 2026Article
- Recent progress in microbial production and consumption of nitrous oxide in agricultural soils.World journal of microbiology & biotechnology · 2025Review
- Design and regulation of engineered bacteria for environmental release.Nature microbiology · 2025Review
- Plasmid Library Construction From Genomic DNA.Current protocols · 2025Article
- Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance.Nature communications · 2024Article
- A Brief History of Microbial Study and Techniques for Exploring the Gastrointestinal Microbiome.Clinics in colon and rectal surgery · 2023Review
- Systems and synthetic biology-driven engineering of live bacterial therapeutics.Frontiers in bioengineering and biotechnology · 2023Review
- Programmable CRISPR-Cas transcriptional activation in bacteria.Molecular systems biology · 2020Article
- Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria.Nature communications · 2019Article
- Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities.Biochemistry · 2019Review
- Tracking of Engineered Bacteria In Vivo Using Nonstandard Amino Acid Incorporation.ACS synthetic biology · 2018Article
- Review
- Metagenomic Approaches for Understanding New Concepts in Microbial Science.International journal of genomics · 2018Review
- Diversity and functions of the sheep faecal microbiota: a multi-omic characterization.Microbial biotechnology · 2017Article
- The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation.Genome medicine · 2016Review
- Manipulating Bacterial Communities by in situ Microbiome Engineering.Trends in genetics : TIG · 2016Review
- On the Origins and Control of Community Types in the Human Microbiome.PLoS computational biology · 2016Article
- Review
- High-throughput bacterial functional genomics in the sequencing era.Current opinion in microbiology · 2015Review
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
Elucidating functions of commensal microbial genes in the mammalian gut is challenging because many commensals are recalcitrant to laboratory cultivation and genetic manipulation. We present Temporal FUnctional Metagenomics sequencing (TFUMseq), a platform to functionally mine bacterial genomes for genes that contribute to fitness of commensal bacteria in vivo. Our approach uses metagenomic DNA to construct large-scale heterologous expression libraries that are tracked over time in vivo by deep sequencing and computational methods. To demonstrate our approach, we built a TFUMseq plasmid library using the gut commensal Bacteroides thetaiotaomicron (Bt) and introduced Escherichia coli carrying this library into germfree mice. Population dynamics of library clones revealed Bt genes conferring significant fitness advantages in E. coli over time, including carbohydrate utilization genes, with a Bt galactokinase central to early colonization, and subsequent dominance by a Bt glycoside hydrolase enabling sucrose metabolism coupled with co-evolution of the plasmid library and E. coli genome driving increased galactose utilization. Our findings highlight the utility of functional metagenomics for engineering commensal bacteria with improved properties, including expanded colonization capabilities in vivo.
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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.