ArticleScientific reports2018
'Cyclical Bias' in Microbiome Research Revealed by A Portable Germ-Free Housing System Using Nested Isolation.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
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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.
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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
27 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Fecal microbiota transplantation from psychiatric patients to mice - systematic review of methodologies and a call for standardization.Translational psychiatry · 2026Pooled it
- Lactobacillus plantarum Attenuates Intestinal Inflammation and Prolongs Remission in Experimental Models of Crohn's Disease.Probiotics and antimicrobial proteins · 2026Article
- A Randomized Controlled Trial Comparing Soy-Pea Protein to Animal Protein in Adults with Crohn's Disease.medRxiv : the preprint server for health sciences · 2026Article
- Computational Quantification of Peristalsis in Preclinical Mouse Models Using Smartphone Videography.Neurogastroenterology and motility · 2026Article
- C9orf72 in myeloid cells prevents an inflammatory response to microbial glycogen.Cell reports · 2026Article
- Gut and faecal microbiota alterations in mice following infection with Arcobacter butzleri strains from a food processing plant.Scientific reports · 2025Article
- Gut microbiome and viral infections: A hidden nexus for immune protection.World journal of virology · 2025Review
- Leucine-Enriched Diet Reduces Fecal MPO but Does Not Protect Against DSS Colitis in a Mouse Model of Crohn's Disease-like Ileitis.International journal of molecular sciences · 2024Article
- The diversity of the microbiome impacts chronic lymphocytic leukemia development in mice and humans.Haematologica · 2024Article
- Anti-Inflammatory Effect of Dietary Pentadecanoic Fatty Acid Supplementation on Inflammatory Bowel Disease in SAMP1/YitFc Mice.Nutrients · 2024Article
- Rodent Gut Bacteria Coexisting with an Insect Gut Virus in Tapeworm Parasitic Cysts: Metagenomic Evidence of Microbial Selection in Extra-Intestinal Clinical Niches.Microorganisms · 2024Article
- Rodent Gut Bacteria Coexisting with an Insect Gut Virus in Parasitic Cysts: Metagenomic Evidence of Microbial Translocation and Co-adaptation in Spatially-Confined Niches.bioRxiv : the preprint server for biology · 2024Article
- Chronic stress induces colonic tertiary lymphoid organ formation and protection against secondary injury through IL-23/IL-22 signaling.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Parabacteroides distasonis induces depressive-like behavior in a mouse model of Crohn's disease.Brain, behavior, and immunity · 2021Article
- 'Statistical Irreproducibility' Does Not Improve with Larger Sample Size: How to Quantify and Address Disease Data Multimodality in Human and Animal Research.Journal of personalized medicine · 2021Article
- Replacing Animal Protein with Soy-Pea Protein in an "American Diet" Controls Murine Crohn Disease-Like Ileitis Regardless of Firmicutes: Bacteroidetes Ratio.The Journal of nutrition · 2021Article
- Use of Probiotics in Intravaginal Sponges in Sheep: A Pilot Study.Animals : an open access journal from MDPI · 2020Article
- Human Gut Microbiome Transplantation in Ileitis Prone Mice: A Tool for the Functional Characterization of the Microbiota in Inflammatory Bowel Disease Patients.Inflammatory bowel diseases · 2020Article
- Gut Microbiota Metabolite Fights Against Dietary Polysorbate 80-Aggravated Radiation Enteritis.Frontiers in microbiology · 2020Article
- Heterogeneity of CD4Frontiers in cell and developmental biology · 2020Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Germ-Free (GF) research has required highly technical pressurized HEPA-ventilation anchored systems for decades. Herein, we validated a GF system that can be easily implemented and portable using Nested Isolation (NesTiso). GF-standards can be achieved housing mice in non-HEPA-static cages, which only need to be nested 'one-cage-inside-another' resembling 'Russian dolls'. After 2 years of monitoring ~100,000 GF-mouse-days, NesTiso showed mice can be maintained GF for life (>1.3 years), with low animal daily-contamination-probability risk (1 every 867 days), allowing the expansion of GF research with unprecedented freedom and mobility. At the cage level, with 23,360 GF cage-days, the probability of having a cage contamination in NesTiso cages opened in biosafety hoods was statistically identical to that of opening cages inside (the 'gold standard') multi-cage pressurized GF isolators. When validating the benefits of using NesTiso in mouse microbiome research, our experiments unexpectedly revealed that the mouse fecal microbiota composition within the 'bedding material' of conventional SPF-cages suffers cyclical selection bias as moist/feces/diet/organic content ('soiledness') increases over time (e.g., favoring microbiome abundances of Bacillales, Burkholderiales, Pseudomonadales; and cultivable Enterococcus faecalis over Lactobacillus murinus and Escherichia coli), which in turn cyclically influences the gut microbiome dynamics of caged mice. Culture 'co-streaking' assays showed that cohoused mice exhibiting different fecal microbiota/hemolytic profiles in clean bedding (high-within-cage individual diversity) 'cyclically and transiently appear identical' (less diverse) as bedding soiledness increases, and recurs. Strategies are proposed to minimize this novel functional form of cyclical bedding-dependent microbiome selection bias.
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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.