ArticlePLoS computational biology2015
High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 211 papers, 2 of them syntheses that pooled it.
What it found
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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.
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
211 citing papers in PubMed, 2 syntheses or guidelines pooled it, 360 citations in OpenAlex.
- Pooled it
- Systematic review of human gut resistome studies revealed variable definitions and approaches.Gut microbes · 2020Pooled it
- Probiotic intervention not beneficial to prevent antibiotic-associated diarrhea in absence of antibiotic-induced microbiome disruption.Scientific reports · 2026Trial
- Multi-omic profiling a defined bacterial consortium for treatment of recurrent Clostridioides difficile infection.Nature medicine · 2025Trial
- Maternal antibiotic prophylaxis during cesarean section has a limited impact on the infant gut microbiome.Cell host & microbe · 2024Trial
- Impact of a Purified Microbiome Therapeutic on Abundance of Antimicrobial Resistance Genes in Patients With Recurrent Clostridioides difficile Infection.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2024Trial
- Trial
- Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study.Genome medicine · 2021Trial
- Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients.mSphere · 2021Trial
- Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial.Microbiome · 2020Trial
- Human gut flagellome profiling using FlaPro reveals TLR5-related phenotype-specific alterations in IBD.Gut microbes · 2026Article
- K-MARVEL: K-Mer-based antimicrobial resistance virtual exploration lab.Nature communications · 2026Article
- A geroprotective probiotic and its functional metabolite counteract inflammaging to extend healthspan.Nature aging · 2026Article
- Computational Genomics for Resistome Characterization: Current Advancements and Future Challenges Under a One Health Perspective.Antibiotics (Basel, Switzerland) · 2026Review
- Microbiome features associated with persistent intestinal carriages of Escherichia coli ST131 in a Southeast Asian cohort study.Nature communications · 2026Article
- From gene detection to resistome ecology: targeted hybrid capture in AMR surveillance.mSphere · 2026Article
- Gut microbiome associations with acute malnutrition relapse in South Sudan.Microbiology spectrum · 2026Article
- Metabolic reprogramming of the infant gut by bifidobacteria-based probiotics drives exclusion of antibiotic-resistant pathobionts.Cell reports. Medicine · 2026Article
- Exploring alterations in the gut resistome in medically treated inflammatory bowel disease patients.BMC microbiology · 2026Article
- Gut microbial community structure, metabolic signature, and resistome in dyslipidemia: implications for cardiovascular disease management.Microbiology spectrum · 2026Article
151 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 at 3 institutions in 2 countries.
Funding
Abstract
Profiling microbial community function from metagenomic sequencing data remains a computationally challenging problem. Mapping millions of DNA reads from such samples to reference protein databases requires long run-times, and short read lengths can result in spurious hits to unrelated proteins (loss of specificity). We developed ShortBRED (Short, Better Representative Extract Dataset) to address these challenges, facilitating fast, accurate functional profiling of metagenomic samples. ShortBRED consists of two components: (i) a method that reduces reference proteins of interest to short, highly representative amino acid sequences ("markers") and (ii) a search step that maps reads to these markers to quantify the relative abundance of their associated proteins. After evaluating ShortBRED on synthetic data, we applied it to profile antibiotic resistance protein families in the gut microbiomes of individuals from the United States, China, Malawi, and Venezuela. Our results support antibiotic resistance as a core function in the human gut microbiome, with tetracycline-resistant ribosomal protection proteins and Class A beta-lactamases being the most widely distributed resistance mechanisms worldwide. ShortBRED markers are applicable to other homology-based search tasks, which we demonstrate here by identifying phylogenetic signatures of antibiotic resistance across more than 3,000 microbial isolate genomes. ShortBRED can be applied to profile a wide variety of protein families of interest; the software, source code, and documentation are available for download at http://huttenhower.sph.harvard.edu/shortbred.
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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.