ArticleProceedings of the National Academy of Sciences of the United States of America2013
Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 133 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
133 citing papers in PubMed, 243 citations in OpenAlex.
- The protease code of the bacterial gut microbiota: ecological regulation, barrier disruption, and rewiring host defense and signaling.Gut microbes · 2026Review
- Gut microbiota-derived taurolithocholic acid modulates myofiber-type switching via p38 MAPK/PGC-1α signaling underlying breed differences between Arbor Acres and Taoyuan chickens.Poultry science · 2026Article
- A Comprehensive Review of the Gut-Microbiota-Brain Axis in Alzheimer's Disease: From Pathophysiology to Potential Therapies.Pathogens (Basel, Switzerland) · 2026Review
- The Gut-Brain Axis in Post-Traumatic Stress Disorder: From Biological Mechanisms to Microbiome-Based Therapeutic Strategies-A Narrative Review.Microorganisms · 2026Review
- Triple-emulsion microfluidic Core-Shell hydrogel microcapsules for oral pentoxifylline Delivery: Ameliorating colitis and rebalancing gut microbiome.Materials today. Bio · 2026Article
- Investigating Salmonella biofilm responses to antibiotic treatment using optical photothermal infrared spectroscopy.Communications biology · 2026Article
- Breaking down barriers: is intestinal mucus degradation byInfection and immunity · 2025Review
- Preparation ofLife (Basel, Switzerland) · 2025Article
- Biological properties, synthetic pathways and anti-aging mechanisms of nicotinamide mononucleotide (NMN): Research progress and challenges.Biogerontology · 2025Review
- Host-pathobiont interactions in Crohn's disease.Nature reviews. Gastroenterology & hepatology · 2025Review
- Gut Feelings: How Microbes, Diet, and Host Immunity Shape Disease.Biomedicines · 2025Review
- HEX-1 reduces colitis-driven colorectal cancer via inactivating the prolyl isomerase PIN1 sensitization and remodeling the gut microbiota.Discover oncology · 2025Article
- Bifidobacterium breve synergizes with Akkermansia muciniphila and Bacteroides ovatus to antagonize Clostridioides difficile.The ISME journal · 2025Article
- Metaproteomics-based stable isotope fingerprinting links intestinal bacteria to their carbon source and captures diet-induced substrate switching.The ISME journal · 2025Article
- Metabolic modeling of host-microbe interactions.Computational and structural biotechnology journal · 2025Review
- Diagnosing and engineering gut microbiomes.EMBO molecular medicine · 2024Review
- Goblet cells: guardians of gut immunity and their role in gastrointestinal diseases.eGastroenterology · 2024Article
- A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation.Signal transduction and targeted therapy · 2024Review
- Spatial host-microbiome sequencing reveals niches in the mouse gut.Nature biotechnology · 2024Article
- Tissue-resident bacteria in metabolic diseases: emerging evidence and challenges.Nature metabolism · 2024Review
73 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
12 authors at 4 institutions in 3 countries.
Funding
Abstract
The animal and human intestinal mucosa secretes an assortment of compounds to establish a physical barrier between the host tissue and intestinal contents, a separation that is vital for health. Some pathogenic microorganisms as well as members of the commensal intestinal microbiota have been shown to be able to break down these secreted compounds. Our understanding of host-compound degradation by the commensal microbiota has been limited to knowledge about simplified model systems because of the difficulty in studying the complex intestinal ecosystem in vivo. In this study, we introduce an approach that overcomes previous technical limitations and allows us to observe which microbial cells in the intestine use host-derived compounds. We added stable isotope-labeled threonine i.v. to mice and combined fluorescence in situ hybridization with high-resolution secondary ion mass spectrometry imaging to characterize utilization of host proteins by individual bacterial cells. We show that two bacterial species, Bacteroides acidifaciens and Akkermansia muciniphila, are important host-protein foragers in vivo. Using gnotobiotic mice we show that microbiota composition determines the magnitude and pattern of foraging by these organisms, demonstrating that a complex microbiota is necessary in order for this niche to be fully exploited. These results underscore the importance of in vivo studies of intestinal microbiota, and the approach presented in this study will be a powerful tool to address many other key questions in animal and human microbiome research.
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.