ArticleFrontiers in microbiology2021
Hi-C Metagenomics in the ICU: Exploring Clinically Relevant Features of Gut Microbiome in Chronically Critically Ill Patients.
Article in Frontiers in microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.
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Who cites it
25 citing papers in PubMed, 1 synthesis or guideline pooled it, 33 citations in OpenAlex.
- Lower gastrointestinal tract dysbiosis in persistent critical illness: a systematic review.Journal of medical microbiology · 2024Pooled it
- Gut dysbiosis‑derived butyrate loss predicts feeding intolerance: Multiomics evidence guiding nurse‑driven microbiota‑supportive interventions (Review).Molecular medicine reports · 2026Review
- Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis.mSphere · 2026Article
- MetaFX: feature extraction from whole-genome metagenomic sequencing data.Bioinformatics (Oxford, England) · 2026Article
- Proof-of-concept of host attribution of antimicrobial resistance genes using wastewater Hi-C metagenome sequencing.Journal of water and health · 2026Article
- Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data.Genome biology · 2026Article
- An evaluation based on explainable machine learning: analysis of risk factors for enteral nutrition-related diarrhea in patients with severe stroke.Frontiers in nutrition · 2026Article
- GGut microbes · 2025Review
- Use of proximity ligation shotgun metagenomics to investigate the dynamics of plasmids and bacteriophages in the gut microbiome following fecal microbiota transplantation.Gut microbes · 2025Article
- Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking.PLoS biology · 2025Article
- Phages with a broad host range are common across ecosystems.Nature microbiology · 2025Article
- Synthetic community Hi-C benchmarking provides a baseline for virus-host inferences.bioRxiv : the preprint server for biology · 2025Article
- The prototypic crAssphage is a linear phage-plasmid.Cell host & microbe · 2025Article
- Microbiome and Microbial Profiling of Arctic Snow Using Whole Genome Sequencing, Psychrophilic Culturing, and Novel Sampling Techniques.Journal of biomolecular techniques : JBT · 2025Article
- Recent Insights into the Evolving Role of the Gut Microbiome in Critical Care.Critical care clinics · 2025Review
- Review
- Detection of rare plasmid hosts using a targeted Hi-C approach.ISME communications · 2025Article
- Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle.bioRxiv : the preprint server for biology · 2024Article
- Recovery of 52 bacterial genomes from the fecal microbiome of the domestic cat (Microbiology resource announcements · 2023Article
- Unraveling the Polysaccharide Biosynthesis Potential ofJournal of fungi (Basel, Switzerland) · 2023Article
Corrections and comments
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Authors and funding
12 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gut microbiome in critically ill patients shows profound dysbiosis. The most vulnerable is the subgroup of chronically critically ill (CCI) patients - those suffering from long-term dependence on support systems in intensive care units. It is important to investigate their microbiome as a potential reservoir of opportunistic taxa causing co-infections and a morbidity factor. We explored dynamics of microbiome composition in the CCI patients by combining "shotgun" metagenomics with chromosome conformation capture (Hi-C). Stool samples were collected at 2 time points from 2 patients with severe brain injury with different outcomes within a 1-2-week interval. The metagenome-assembled genomes (MAGs) were reconstructed based on the Hi-C data using a novel hicSPAdes method (along with the bin3c method for comparison), as well as independently of the Hi-C using MetaBAT2. The resistomes of the samples were derived using a novel assembly graph-based approach. Links of bacteria to antibiotic resistance genes, plasmids and viruses were analyzed using Hi-C-based networks. The gut community structure was enriched in opportunistic microorganisms. The binning using hicSPAdes was superior to the conventional WGS-based binning as well as to the bin3c in terms of the number, completeness and contamination of the reconstructed MAGs. Using
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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.