Rhodococcus spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids

Study information

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Reviewed Marked as Reviewed by Svetlana up on 2025-4-14

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

40032727

DOI Digital object identifier for electronic documents.

10.1080/19490976.2025.2469716

URI Uniform resource identifier for web resources.

https://pmc.ncbi.nlm.nih.gov/articles/PMC11881836/#sec26

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

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Curated date: 2025/03/31

Curator: Eniola

Revision editor(s): Eniola, Shulamite, KateRasheed

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

Total bacteria isolated before treatments + IgG isotype control pAb or the specific pAb + IgG isotype control pAb (T+C+N))

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

3

Group 1 sample size Number of subjects in the case (exposed) group

1

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).

relative abundances

Statistical test

LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

3

Signature 1

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Curated date: 2025/03/31

Curator: Shulamite

Revision editor(s): Shulamite, Eniola

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)

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Agrobacterium
Allobaculum
Brevibacterium
Pandoraea
Stenotrophomonas
Pseudomonas
Methylobacterium
Staphylococcus
Rhodococcus
Bulleidia
Chryseobacterium
Sphingomonas
Ochrobactrum
Rothia

Revision editor(s): Shulamite, Eniola

Signature 2

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Curated date: 2025/03/31

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Revision editor(s): Shulamite, Eniola

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)

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Candidatus Tremblayella

Revision editor(s): Shulamite, Eniola

Experiment 2

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Curated date: 2025/04/02

Curator: Shulamite

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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. (NoV)

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),

Group 0 sample size Number of subjects in the control (unexposed) group

1

Lab analysis

Statistical Analysis

Statistical test

Dunn's test

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

Not specified

Signature 1

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Curated date: 2025/04/02

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Source: Fig 1b and S2b

Description: Normalized counts of reads corresponding to Lactobacillus taiwanensis/johnsonii and Ligilactobacillus murinus/animalis and Abundance of Rhodococcustaxons. p<0.05 for Sidak's test comparing NoV subgroup with the rest of subgroups.

Abundance in Group 1: increased abundance in IgG isotype control pAb (C)

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Rhodococcus
Ligilactobacillus murinus/animalisLigilactobacillus murinus/animalis

Revision editor(s): Shulamite, Eniola

Experiment 3

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Curated date: 2025/04/02

Curator: Eniola

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

Isotype control antibody (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

Lab analysis

Statistical Analysis

Signature 1

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Curated date: 2025/04/03

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Source: Fig 1b and S2b

Description: Normalized counts of reads corresponding to Lactobacillus taiwanensis/johnsonii and Ligilactobacillus murinus/animalis and Abundance of Rhodococcus taxons. p<0.05 for Sidak's test comparing NoV subgroup with the rest of subgroups.

Abundance in Group 1: decreased abundance in Isotype control antibody (N)

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Rhodococcus
Ligilactobacillus murinus/animalisLigilactobacillus murinus/animalis

Revision editor(s): Shulamite, Eniola

Experiment 4

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Curated date: 2025/04/03

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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 recognised by the Anti-NoV GII.4 Sydney 2012 antibody. (NoV)

Lab analysis

Statistical Analysis

Signature 1

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Source: Fig 1b and S2b

Description: Normalized counts of reads corresponding to Lactobacillus taiwanensis/johnsonii and Ligilactobacillus murinus/animalis taxons and Abundance of Rhodococcus. 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)

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Rhodococcus
Ligilactobacillus murinus/animalisLigilactobacillus murinus/animalis

Revision editor(s): Shulamite

Experiment 5

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Curated date: 2025/04/11

Curator: Shulamite

Revision editor(s): Shulamite, KateRasheed

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 pAb + Total bacteria isolated before treatments + IgG isotype control pAb (NoV+T+C)

Group 1 name Corresponds to the case (exposed) group for case-control studies

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

Isotype control nor the specific pAb (N)

Group 0 sample size Number of subjects in the control (unexposed) group

3

Lab analysis

Statistical Analysis

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

3

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2025-4-14

Curated date: 2025/04/11

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Revision editor(s): Shulamite

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 Isotype control nor the specific pAb (N)

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Agrobacterium
Allobaculum
Brevibacterium
Pandoraea
Stenotrophomonas

Revision editor(s): Shulamite

Signature 2

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Reviewed Marked as Reviewed by Svetlana up on 2025-4-14

Curated date: 2025/04/11

Curator: Shulamite

Revision editor(s): Shulamite

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 Isotype control nor the specific pAb (N)

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Bulleidia
Candidatus Tremblayella
Chryseobacterium
Methylobacterium
Pseudomonas
Rhodococcus
Rothia
Sphingomonas
Staphylococcus
Ochrobactrum

Revision editor(s): Shulamite

Experiment 6

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Curated date: 2025/04/11

Curator: Shulamite

Revision editor(s): Shulamite, KateRasheed

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 pAb + isotype control nor the specific pAb + IgG isotype control pAb (NoV+N+C)

Group 1 name Corresponds to the case (exposed) group for case-control studies

Total bacteria isolated before treatments (T)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Total bacteria isolated before treatments

Lab analysis

Statistical Analysis

Statistical test

LEfSe

Signature 3

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Curated date: 2025/04/11

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Revision editor(s): Shulamite

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 Total bacteria isolated before treatments (T)

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Candidatus Tremblayella

Revision editor(s): Shulamite

Signature 4

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Reviewed Marked as Reviewed by Svetlana up on 2025-4-14

Curated date: 2025/04/11

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Revision editor(s): Shulamite

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 Total bacteria isolated before treatments (T)

NCBI	Quality Control	Links
Methylobacterium
Staphylococcus
Stenotrophomonas
Rhodococcus
Bulleidia
Allobaculum
Rothia
Ochrobactrum
Sphingomonas
Agrobacterium
Chryseobacterium
Brevibacterium
Pseudomonas
Pandoraea

Revision editor(s): Shulamite

Experiment 7

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Curated date: 2025/04/11

Curator: Shulamite

Revision editor(s): Shulamite, KateRasheed

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 pAb + Isotype control nor the specific pAb +Total bacteria isolated before treatments (NoV+N+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 recognized by the IgG isotype control antibody

Lab analysis

Statistical Analysis

Signature 1

EditHistoryDelete

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Reviewed Marked as Reviewed by Svetlana up on 2025-4-14

Curated date: 2025/04/11

Curator: Shulamite

Revision editor(s): Shulamite

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 IgG isotype control pAb (C)

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Rhodococcus
Rothia
Bulleidia
Ochrobactrum
Candidatus Tremblayella
Sphingomonas
Staphylococcus
Methylobacterium
Chryseobacterium
Pseudomonas

Revision editor(s): Shulamite

Signature 2

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Reviewed Marked as Reviewed by Svetlana up on 2025-4-14

Curated date: 2025/04/11

Curator: Shulamite

Revision editor(s): Shulamite

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 IgG isotype control pAb (C)

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Brevibacterium
Agrobacterium
Stenotrophomonas
Allobaculum
Pandoraea

Revision editor(s): Shulamite

Experiment 8

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Curated date: 2025/04/11

Curator: Shulamite

Revision editor(s): Shulamite

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 pAb + Total bacteria isolated before treatments + IgG isotype control pAb (NoV+T+C)

Group 1 name Corresponds to the case (exposed) group for case-control studies

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 unreactive to any antibodies

Lab analysis

Statistical Analysis

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

2

Signature 1

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Curated date: 2025/04/11

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Revision editor(s): Shulamite, KateRasheed

Source: Fig. S2A

Description: LEfSe analysis of different subsamples (N, NoV, T and C) at the species level.

Abundance in Group 1: increased abundance in Isotype control nor the specific pAb (N)

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Ligilactobacillus murinus/animalisLigilactobacillus murinus/animalis
Lactobacillus taiwanensis/johnsoniiLactobacillus taiwanensis/johnsonii

Revision editor(s): Shulamite, KateRasheed

Signature 2

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Source: Fig. S2A

Description: LEfSe analysis of different subsamples (N, NoV, T and C) at the species level.

Abundance in Group 1: decreased abundance in Isotype control nor the specific pAb (N)

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Rhodococcus erythropolis

Revision editor(s): Shulamite

Experiment 9

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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 pAb + Isotype control nor the specific pAb +Total bacteria isolated before treatments (NoV+N+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 recognized by the IgG isotype control antibody

Lab analysis

Statistical Analysis

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2025-4-14

Curated date: 2025/04/11

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Revision editor(s): Shulamite

Source: Fig. S2A

Description: LEfSe analysis of different subsamples (N, NoV, T and C) at the species level

Abundance in Group 1: increased abundance in IgG isotype control pAb (C)

NCBI	Quality Control	Links
Rhodococcus erythropolis

Revision editor(s): Shulamite

Signature 2

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Curated date: 2025/04/12

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Revision editor(s): Shulamite

Source: Fig. S2A

Description: LEfSe analysis of different subsamples (N, NoV, T and C) at the species level.

Abundance in Group 1: decreased abundance in IgG isotype control pAb (C)

NCBI	Quality Control	Links
Ligilactobacillus murinus/animalisLigilactobacillus murinus/animalis
Lactobacillus taiwanensis/johnsoniiLactobacillus taiwanensis/johnsonii

Revision editor(s): Shulamite

Experiment 10

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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. (NoV) + IgG isotype control pAb (C) + isotype control antibody nor the specific antibody (N)

Group 1 name Corresponds to the case (exposed) group for case-control studies

Total bacteria (T)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Total bacteria isolated before treatments

Lab analysis

Statistical Analysis

Signature 1

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Source: Fig. S2A

Description: LEfSe analysis of different subsamples (N, NoV, T and C) at the species level

Abundance in Group 1: decreased abundance in Total bacteria (T)

NCBI	Quality Control	Links
Lactobacillus taiwanensis/johnsoniiLactobacillus taiwanensis/johnsonii
Ligilactobacillus murinus/animalisLigilactobacillus murinus/animalis
Rhodococcus erythropolis

Revision editor(s): Shulamite

Experiment 11

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Curated date: 2025/04/11

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Total bacteria isolated before treatments + IgG isotype control pAb or the specific pAb + IgG isotype control pAb (T+C+N)

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

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2025-4-14

Curated date: 2025/04/11

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Revision editor(s): Shulamite

Source: Fig. S2A

Description: LEfSe analysis of different subsamples (N, NoV, T and C) at the species level.

Abundance in Group 1: increased abundance in Anti-NoV GII.4 Sydney 2012 antibody. (NoV)

NCBI	Quality Control	Links
Ligilactobacillus murinus/animalisLigilactobacillus murinus/animalis
Lactobacillus taiwanensis/johnsoniiLactobacillus taiwanensis/johnsonii
Rhodococcus erythropolis

Revision editor(s): Shulamite