ArticlemSystems
Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease.
Article in mSystems. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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
34 citing papers in PubMed, 65 citations in OpenAlex.
- Gut metaproteomics reveals activated arginine catabolism and impaired arginine biosynthesis in systemic lupus erythematosus.mSystems · 2026Article
- Predicted meta-omics: A potential solution to multi-omics data scarcity in microbiome studies.PloS one · 2026Article
- A Proteogenomic Approach to Unveiling the Complex Biology of the Microbiome.International journal of molecular sciences · 2024Review
- Integrating multi-omics to unravel host-microbiome interactions in inflammatory bowel disease.Cell reports. Medicine · 2024Review
- Interpretable metric learning in comparative metagenomics: The adaptive Haar-like distance.PLoS computational biology · 2024Article
- Advances in multi-omics integrated analysis methods based on the gut microbiome and their applications.Frontiers in microbiology · 2024Review
- Article
- Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota.NPJ biofilms and microbiomes · 2023Article
- Gut Microbiome Proteomics in Food Allergies.International journal of molecular sciences · 2023Review
- Increasing taxonomic and functional characterization of host-microbiome interactions by DIA-PASEF metaproteomics.Frontiers in microbiology · 2023Article
- Metaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits.The ISME journal · 2022Article
- Towards standardized and reproducible research in skin microbiomes.Environmental microbiology · 2022Review
- Article
- Crohn's disease in endoscopic remission, obesity, and cases of high genetic risk demonstrates overlapping shifts in the colonic mucosal-luminal interface microbiome.Genome medicine · 2022Article
- The gut metagenomics and metabolomics signature in patients with inflammatory bowel disease.Gut pathogens · 2022Article
- Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research.Toxicological sciences : an official journal of the Society of Toxicology · 2022Review
- Article
- Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity.Nature microbiology · 2022Article
- Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes.PLoS pathogens · 2021Article
- Berberine and its structural analogs have differing effects on functional profiles of individual gut microbiomes.Gut microbes · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although genetic approaches are the standard in microbiome analysis, proteome-level information is largely absent. This discrepancy warrants a better understanding of the relationship between gene copy number and protein abundance, as this is crucial information for inferring protein-level changes from metagenomic data. As it remains unknown how metaproteomic systems evolve during dynamic disease states, we leveraged a 4.5-year fecal time series using samples from a single patient with colonic Crohn's disease. Utilizing multiplexed quantitative proteomics and shotgun metagenomic sequencing of eight time points in technical triplicate, we quantified over 29,000 protein groups and 110,000 genes and compared them to five protein biomarkers of disease activity. Broad-scale observations were consistent between data types, including overall clustering by principal-coordinate analysis and fluctuations in Gene Ontology terms related to Crohn's disease. Through linear regression, we determined genes and proteins fluctuating in conjunction with inflammatory metrics. We discovered conserved taxonomic differences relevant to Crohn's disease, including a negative association of
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.