Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Groves HT, Cuthbertson L, James P, Moffatt MF, Cox MJ, Tregoning JS
Journal
Frontiers in immunology
Year
2018
Alterations in the composition of the gut microbiota have profound effects on human health. Consequently, there is great interest in identifying, characterizing, and understanding factors that initiate these changes. Despite their high prevalence, studies have only recently begun to investigate how viral lung infections have an impact on the gut microbiota. There is also considerable interest in whether the gut microbiota could be manipulated during vaccination to improve efficacy. In this highly controlled study, we aimed to establish the effect of viral lung infection on gut microbiota composition and the gut environment using mouse models of common respiratory pathogens respiratory syncytial virus (RSV) and influenza virus. This was then compared to the effect of live attenuated influenza virus (LAIV) vaccination. Both RSV and influenza virus infection resulted in significantly altered gut microbiota diversity, with an increase in Bacteroidetes and a concomitant decrease in Firmicutes phyla abundance. Although the increase in the Bacteroidetes phylum was consistent across several experiments, differences were observed at the family and operational taxonomic unit level. This suggests a change in gut conditions after viral lung infection that favors Bacteroidetes outgrowth but not individual families. No change in gut microbiota composition was observed after LAIV vaccination, suggesting that the driver of gut microbiota change is specific to live viral infection. Viral lung infections also resulted in an increase in fecal lipocalin-2, suggesting low-grade gut inflammation, and colonic Muc5ac levels. Owing to the important role that mucus plays in the gut environment, this may explain the changes in microbiota composition observed. This study demonstrates that the gut microbiota and the gut environment are altered following viral lung infections and that these changes are not observed during vaccination. Whether increased mucin levels and gut inflammation drive, or are a result of, these changes is still to be determined.

Experiment 1


Needs review

Curated date: 2021/06/12

Curator: Claregrieve1

Revision editor(s): WikiWorks753, LGeistlinger, Claregrieve1

Subjects

Location of subjects
United Kingdom
Host species Species from which microbiome was sampled (if applicable)
Mus musculus
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
viral pneumonia Pneumonia, Viral,viral pneumonia,Viruses caused pneumonia,Viruses pneumonia
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Day 0
Group 1 name Corresponds to the case (exposed) group for case-control studies
Day 7
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Mice assessed 7 days after infection

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
ANOVA
DESeq2
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)?
Yes


Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
unchanged

Signature 1

Needs review

Curated date: 2021/06/13

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 2a

Description: Differential abundance of gut microbiota of respiratory syncytial virus (RSV) infected mice between Day 0 and Day 7 of infection

Abundance in Group 1: decreased abundance in Day 7

NCBI Links
Bacillota

Revision editor(s): Claregrieve1

Signature 2

Needs review

Curated date: 2021/06/13

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 2a

Description: Differential abundance of gut microbiota of respiratory syncytial virus (RSV) infected mice between Day 0 and Day 7 of infection

Abundance in Group 1: increased abundance in Day 7

NCBI Links
Bacteroidota

Revision editor(s): Claregrieve1

Experiment 2


Needs review

Curated date: 2021/06/15

Curator: Claregrieve1

Revision editor(s): WikiWorks753, LGeistlinger, Claregrieve1

Subjects

Location of subjects
United Kingdom
Host species Species from which microbiome was sampled (if applicable)
Mus musculus
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
viral pneumonia Pneumonia, Viral,viral pneumonia,Viruses caused pneumonia,Viruses pneumonia
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Day 0
Group 1 name Corresponds to the case (exposed) group for case-control studies
Day 7
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Day 7 of infection for mice infected with influenza virus (H1N1)

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
ANOVA
DESeq2
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)?
Yes


Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
unchanged

Signature 1

Needs review

Curated date: 2021/06/16

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 4c

Description: Differential abundance of gut microbiota of respiratory syncytial virus (RSV) infected mice between Day 0 and Day 7 of infection

Abundance in Group 1: decreased abundance in Day 7

NCBI Links
Bacillota

Revision editor(s): Claregrieve1

Signature 2

Needs review

Curated date: 2021/06/16

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 4c

Description: Differential abundance of gut microbiota of respiratory syncytial virus (RSV) infected mice between Day 0 and Day 7 of infection

Abundance in Group 1: increased abundance in Day 7

NCBI Links
Bacteroidota

Revision editor(s): Claregrieve1