Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota

Study information

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-26

study design

laboratory experiment

Citation

PMID PubMed identifier for scientific articles.

29483910

DOI Digital object identifier for electronic documents.

10.3389/fimmu.2018.00182

URI

Authors

Groves HT, Cuthbertson L, James P, Moffatt MF, Cox MJ, Tregoning JS

Journal

Frontiers in immunology

Year

2018

Keywords:

Bacteroidetes, Firmicutes, Mucin 5ac, gut microbiota, influenza, respiratory syncytial virus infections

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

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-26

Curated date: 2021/06/12

Curator: Claregrieve1

Revision editor(s): LGeistlinger, Claregrieve1, WikiWorks, Folakunmi

Subjects

Location of subjects

United Kingdom

Host species Species from which microbiome was sampled. Contact us to have more species added.

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,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Sampling time sampling_time_point,Sampling time,sampling time

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 with respiratory syncytial virus (RSV)

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

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-26

Curated date: 2021/06/13

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Folakunmi

Source: Figure 2A&2B, within results text (The Composition of the Gut Microbiota Is Altered following Lung Infection, paragraph 2)

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

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Bacillota
Lachnospiraceae
Lactobacillaceae

Revision editor(s): Claregrieve1, Folakunmi

Signature 2

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-26

Curated date: 2021/06/13

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Folakunmi

Source: Figure 2A&2B, within results text (The Composition of the Gut Microbiota Is Altered following Lung Infection, paragraph 2)

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	Quality Control	Links
Bacteroidaceae
Bacteroidia
Muribaculaceae

Revision editor(s): Claregrieve1, Folakunmi

Experiment 2

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-26

Curated date: 2021/06/15

Curator: Claregrieve1

Revision editor(s): LGeistlinger, Claregrieve1, WikiWorks, Folakunmi

Differences from previous experiment shown

Subjects

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

Statistical Analysis

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

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-26

Curated date: 2021/06/16

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Folakunmi

Source: Figure 4C, 4D

Description: Differential abundance of gut microbiota of influenza virus (H1N1) infected mice between Day 0 and Day 7 of infection

Abundance in Group 1: decreased abundance in Day 7

NCBI	Quality Control	Links
Bacillota

Revision editor(s): Claregrieve1, Folakunmi

Signature 2

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-26

Curated date: 2021/06/16

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Folakunmi

Source: Figure 4C, 4D

Description: Differential abundance of gut microbiota of influenza virus (H1N1) infected mice between Day 0 and Day 7 of infection

Abundance in Group 1: increased abundance in Day 7

NCBI	Quality Control	Links
Bacteroidota
Muribaculaceae
Porphyromonadaceae

Revision editor(s): Claregrieve1, Folakunmi

Experiment 3

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-26

Curated date: 2024/01/26

Curator: Folakunmi

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Differences from previous experiment shown

Subjects

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 phosphate-buffered saline (PBS).

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

raw counts

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

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-26

Curated date: 2024/01/26

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: Figure 2A&2B, within results text (The Composition of the Gut Microbiota Is Altered following Lung Infection, paragraph 2)

Description: Differential abundance of gut microbiota of phosphate-buffered saline (PBS) infected mice between Day 0 and Day 7 of infection

Abundance in Group 1: increased abundance in Day 7

NCBI	Quality Control	Links
Bacillota
Lachnospiraceae

Revision editor(s): Folakunmi

Signature 2

EditHistoryDelete

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-26

Curated date: 2024/01/26

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: Figure 2A&2B, within results text (The Composition of the Gut Microbiota Is Altered following Lung Infection, paragraph 2)

Description: Differential abundance of gut microbiota of phosphate-buffered saline (PBS) infected mice between Day 0 and Day 7 of infection

Abundance in Group 1: decreased abundance in Day 7

NCBI	Quality Control	Links
Bacteroidia

Revision editor(s): Folakunmi