ArticlemSystems2021
Integrative Transkingdom Analysis of the Gut Microbiome in Antibiotic Perturbation and Critical Illness.
Article in mSystems, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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.
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Who cites it
47 citing papers in PubMed, 73 citations in OpenAlex.
- Impact of fiber-containing enteral nutrition on microbial community dynamics in critically ill trauma patients: a pilot-randomized trial.BMC medicine · 2025Trial
- Gut microbiome remodeling and metabolomic profile improves in response to protein pacing with intermittent fasting versus continuous caloric restriction.Nature communications · 2024Trial
- 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
- Gut microecology in critical illness: mechanisms, biomarkers, and therapeutic strategies - a critical appraisal.Frontiers in gastroenterology (Lausanne, Switzerland) · 2026Review
- Retrospective analysis of intestinal flora alterations in adults with acute gastrointestinal injury.Frontiers in cellular and infection microbiology · 2026Article
- Decoding the reproductive microbiome: enabling clinical and biological insights through machine and deep learning.Frontiers in endocrinology · 2026Review
- Colonic biopsy-associated microbial signatures are predictive of response to anti-TNFα biological therapy in Crohn's disease.Frontiers in cellular and infection microbiology · 2026Article
- Friend or foe: the gut microbiota as a modulator of disease trajectory in trauma, surgery, and critical illness.Gut microbes · 2025Review
- The gastrointestinal microbiome in critical illness: A Clinician's guide to mechanisms, emerging tools, and therapeutic questions.Critical care and resuscitation : journal of the Australasian Academy of Critical Care Medicine · 2025Review
- Butyrate-producing gut bacteriumThe European respiratory journal · 2025Article
- Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson's disease.Microbiome · 2025Article
- Anti-Anaerobic Antibiotics, Gut Microbiota, and Sepsis-associated Acute Kidney Injury.American journal of respiratory and critical care medicine · 2025Article
- Integrated multi-omics of feces, plasma and urine can describe and differentiate pediatric active Crohn's Disease from remission.Communications medicine · 2025Article
- Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challenges.Frontiers in microbiology · 2025Review
- Multi-omics decodes host-specific and environmental microbiome interactions in sepsis.Frontiers in microbiology · 2025Review
- Semisynthetic simulation for microbiome data analysis.Briefings in bioinformatics · 2024Review
- Multi-omics analysis reveals regime shifts in the gastrointestinal ecosystem in chickens following anticoccidial vaccination andmSystems · 2024Article
- Intestinal microbiome dysbiosis increaseseLife · 2024Article
- The Gut Microbiome in Sepsis: From Dysbiosis to Personalized Therapy.Journal of clinical medicine · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
19 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial microbiota play a critical role in mediating local and systemic immunity, and shifts in these microbial communities have been linked to impaired outcomes in critical illness. Emerging data indicate that other intestinal organisms, including bacteriophages, viruses of eukaryotes, fungi, and protozoa, are closely interlinked with the bacterial microbiota and their host, yet their collective role during antibiotic perturbation and critical illness remains to be elucidated. We employed multi-omics factor analysis (MOFA) to systematically integrate the bacterial (16S rRNA), fungal (intergenic transcribed spacer 1 rRNA), and viral (virus discovery next-generation sequencing) components of the intestinal microbiota of 33 critically ill patients with and without sepsis and 13 healthy volunteers. In addition, we quantified the absolute abundances of bacteria and fungi using 16S and 18S rRNA PCRs and characterized the short-chain fatty acids (SCFAs) butyrate, acetate, and propionate using nuclear magnetic resonance spectroscopy. We observe that a loss of the anaerobic intestinal environment is directly correlated with an overgrowth of aerobic pathobionts and their corresponding bacteriophages as well as an absolute enrichment of opportunistic yeasts capable of causing invasive disease. We also observed a strong depletion of SCFAs in both disease states, which was associated with an increased absolute abundance of fungi with respect to bacteria. Therefore, these findings illustrate the complexity of transkingdom changes following disruption of the intestinal bacterial microbiome.
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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.