Rhodococcus spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Santiso-Bellón C, Randazzo W, Carmona-Vicente N, Peña-Gil N, Cárcamo-Calvo R, Lopez-Navarro S, Navarro-Lleó N, Yebra MJ, Monedero V, Buesa J, Gozalbo-Rovira R, Rodríguez-Díaz J
Journal
Gut microbes
Year
2025
Keywords:
Human norovirus, Rhodococcus, gut microbiota, histo-blood group antigens, human intestinal enteroids, stool samples
Viral infections, particularly human norovirus (NoV), are a leading cause of diarrheal diseases globally. To better understand NoV susceptibility, it is crucial to investigate both host glycobiology and the influence of the microbiota. Histo-blood group antigens (HBGA) displayed on surfaces of host cells act as NoV receptors, while certain bacteria express HBGA-like substances, facilitating virus-bacteria interactions. To identify bacterial species interacting with NoV during infection, stool samples from children infected with NoV GII.4 were analyzed. The samples were subjected to bacteria separation using anti-NoV GII.4 polyclonal antibodies coupled to magnetic beads, followed by microbiota profiling through 16S rDNA sequencing. This approach identified the genus Rhodococcus as enriched in samples captured with anti-NoV antibodies compared to controls. Electron microscopy confirmed the binding of NoV GII.4 Sydney 2012 viral-like particles (VLP) to five Rhodococcus strains from different species, which expressed HBGA-like substances on their surfaces, particularly from A and B blood groups. In human intestinal enteroids, Rhodococcus erythropolis reduced NoV GII.4 Sydney 2012 infection levels under displacement, exclusion and competitive exclusion settings. Extracellular polysaccharides (EPS) isolated from Rhodococcus strains bound VLP from both GII.4 and GII.6 genotypes. Blocking antibodies targeting A and B epitopes reduced the binding of the EPS from R. erythropolis to GII.6 VLP, while enhanced binding to GII.4 VLP was observed when A and B epitopes were blocked. These findings revealed the interaction of Rhodococcus to NoV in an in vitro setting and open new avenues for developing innovative antiviral strategies to prevent and treat NoV infections through the HBGA-like substances present in their EPS.
Experiment 1
Subjects
- Location of subjects
- Spain
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Viral disease infection, viral,infections, Viruses,viral disease,viral disorder,viral infection,viral infectious disease,virus infection,Viruses caused disease or disorder,Viruses disease or disorder,Viruses infection,Viruses infectious disease,Viral disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- IgG isotype control pAb (C)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- anti-NoV GII.4 Sydney 2012 pAb(NoV)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Bacteria captured by anti-NoV GII.4 Sydney 2012 pAb
- Group 0 sample size Number of subjects in the control (unexposed) group
- 2
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- log transformation
- Statistical test
- Kruskall-Wallis
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Signature 1
Source: Fig 1a
Description: LDA of bacterial genera quantified from clinical samples with NoV. The LDA score of 15 taxa with significant differences (p<0.05 in Kruskal-Wallis test, adjusted by FDR) in a LEfse analysis is presented.
Abundance in Group 1: increased abundance in anti-NoV GII.4 Sydney 2012 pAb(NoV)
| NCBI | Quality Control | Links |
|---|---|---|
| Agrobacterium | ||
| Allobaculum | ||
| Brevibacterium | ||
| Pandoraea | ||
| Stenotrophomonas |
Signature 2
Source: Fig 1a
Description: LDA of bacterial genera quantified from clinical samples with NoV. The LDA score of 15 taxa with significant differences (p<0.05 in Kruskal-Wallis test, adjusted by FDR) in a LEfse analysis is presented.
Abundance in Group 1: decreased abundance in anti-NoV GII.4 Sydney 2012 pAb(NoV)
| NCBI | Quality Control | Links |
|---|---|---|
| Bulleidia | ||
| Candidatus Tremblaya | ||
| Chryseobacterium | ||
| Methylobacterium | ||
| Ochrobactrum | ||
| Pseudomonas | ||
| Rhodococcus | ||
| Sphingomonas | ||
| Staphylococcus | ||
| Rothia |
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Total bacteria present in stools before experiment (T).
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Anti-NoV GII.4 Sydney 2012 antibody (NoV)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Bacteria recognized by the anti-NoV GII.4 Sydney 2012 antibody.
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Source: Fig S2b
Description: Normalized counts of reads corresponding to Lactobacillus taiwanensis/johnsonii and Ligilactobacillus murinus/animalis taxons. p<0.05 for Sidak's test comparing NoV subgroup with the rest of subgroups.
Abundance in Group 1: increased abundance in Anti-NoV GII.4 Sydney 2012 antibody (NoV)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus taiwanensis | ||
| Ligilactobacillus murinus |
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Anti-NoV GII.4 Sydney 2012 antibody.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Bacteria unreactive to any antibodies (neither the isotype control nor the specific pAb) (N)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Bacteria not recognized by the isotype control antibody nor the specific antibody (N)
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- log transformation
Signature 1
Source: Supplementary Fig S2b
Description: Normalized counts of reads corresponding to Lactobacillus taiwanensis/johnsonii and Ligilactobacillus murinus/animalis taxons. p<0.05 for Sidak's test comparing NoV subgroup with the rest of subgroups.
Abundance in Group 1: increased abundance in Bacteria unreactive to any antibodies (neither the isotype control nor the specific pAb) (N)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus taiwanensis | ||
| Ligilactobacillus murinus |
Experiment 4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Total bacteria present in stools before experiment (T)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IgG isotype control pAb (C),
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Bacteria captured by the IgG isotype control pAb (C),
Lab analysis
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
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