Respiratory and Gut Microbiome Modification during Respiratory Syncytial Virus Infection: A Systematic Review
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Sources and Search Strategy
2.2. Eligibility Criteria
2.3. Date Extraction and Quality Assessment
2.4. Date Synthesis and Analysis
3. Results
3.1. Study Selection
3.2. Quality of Studies
3.3. Main Study Characteristics
3.4. Changes in Microbial Composition in the Respiratory Tract Associated with RSV Infection
3.4.1. Respiratory Tract Microbiome Compared to Healthy Controls
3.4.2. Respiratory Tract Microbiome Compared to Patients Other Than Healthy Controls
3.5. RSV Infection-Associated Changes in Microbial Composition in the Gut
3.6. Microbial Diversity in the Respiratory Tract Associated with RSV Infection
3.6.1. Alpha Diversity
3.6.2. Beta Diversity
3.7. Microbial Diversity in the Gut Associated with RSV Infection
3.7.1. Alpha Diversity
3.7.2. Beta Diversity
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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First Author (Year) | Country | Age Category | Number of Patients with RSV Infection | Number of Controls | Types of Samples | Diagnostic Method for RSV Infection | Microbiome Approach, Pipeline, and Database |
---|---|---|---|---|---|---|---|
Alba C et al. (2021) [29] | Spain | <2 years | 54 | 14 (Healthy control) | Nasal wash | PCR DFA | 16S rRNA (V3–V4) QIIME v. 1.9.1 [40] |
Rajagopala SV et al. (2021) [36] | USA | <3 years | 43 | 22 (Healthy control) | Nasal swab | PCR | Metagenomics Trimmomatic v. 0.39 [41] SILVA [42] |
Grier A et al. (2020) [32] | USA | <1 year | 89 (For the longitudinal cohort, 12) | 102 (Healthy control) (For the longitudinal cohort, 12) | Nasal swab | PCR | 16S rRNA (V1–V3) QIIME 2 [43] Greengenes [44] |
Schippa S et al. (2020) [39] | Italy | <6 months | 48 (RSV positive) | 28 (Negative to other respiratory viruses) | Nasopharyngeal wash | PCR | 16S rRNA (V3–V4) Mothur v. 1.39.5 [45] SILVA v. 1.19 [42] |
Ederveen THA et al. (2018) [31] | Netherlands | <6 months | 54 | 21 (Healthy control) | Nasopharyngeal aspirate | PCR | 16S rRNA (V3–V4) QIIME v.1.8 [40] RDP classifier v. 2.3 [46] |
de Steenhuijsen Piters WAA et al. (2016) [30] | USA | <2 years | 106 (Outpatients, 22; Inpatients, 84) | 26 (Healthy control) | Nasopharyngeal swab | PCR Rapid antigen | 16S rRNA (V5–V7) QIIME v.1.8 [40] Greengenes [44] |
First Author (Year) | Country | Age Category | Number of Patients with RSV Infection | Number of Controls | Samples | Diagnostic Method for RSV Infection | Microbiome Approach, Pipeline, and Database |
---|---|---|---|---|---|---|---|
Russell MM et al. (2022) [38] | USA | <4 months | 20 | 9 (Healthy control) | Feces (peri-anal swab) | PCR | 16S rRNA (V4) SILVA release 102 [42] |
Alba C et al. (2021) [29] | Spain | <2 years | 46 | 17 | Feces | PCR DFA | 16S rRNA (V3–V4) QIIME v. 1.9.1 [40] |
Harding JN et al. (2020) [33] | USA | <1 year | 58 | 37 | Feces | PCR | 16S rRNA (V4) QIIME 2 [43] Greengenes [44] |
Phylum | Class | Order | Family | Genus | Species |
---|---|---|---|---|---|
Pseudomonadota corrig. phyl. nov. (Proteobacteria) ↑↑ Bacillota corrig. phyl. nov.(Firmicutes) ↓↓↑ Actinomycetota corrig. phyl. nov. (Actinobacteria) ↓↑ Phylum level → Bacteroidota corrig. phyl. nov. (Bacteroidetes) ↑ | Alphaproteobacteria ↑ Gammaproteobacteria ↑ Betaproteobacteria ↑ | Pseudomonadales ↑ Burkholderiales ↑ | Haemophilus ↑↑↑ Moraxella ↑ Streptococcus ↑ Corynebacterium ↓ Mannheimia ↑ Staphylococcus ↓ Pseudomonas ↑ Gluconacetobacter ↑ Alistipes ↓ Bacteroides ↓ Kineothrix ↓ Oscillibacter ↓ Pseudoflavonifractor ↓ Klebsiella Achromobacter ↑ | Haemophilus influenzae (Haemophilus sp.) ↑↑↑ Moraxella catarrhalis ↑ Streptococcus pneumoniae ↑↑ Delftia sp. ↑ Cutibacterium acnes ↑ [Eubacterium] Sireum ↓ Alistipes putredinis ↓ Bamasiella intestinihominis ↓ Kineothrix alysoides ↓ Oscillibacter ruminantium ↓ Prevotella oralis ↓ Pseudoflavonifractor phocaeensis ↓ Roseburia intestinalis ↓ Staphylococcus aureus ↑ |
Phylum | Class | Order | Family | Genus | Species |
---|---|---|---|---|---|
S24_7 ↑ Odoribacteraceae ↑ Clostridiales ↑ Lactobacillaceae ↑ Actinomyces ↑ | Bifidobacterium ↑ Enterobactericeae unclassified ↑ Lachnospiraceae incertae sedis↑ Enterococcus ↑ Clostridiales Unclassified ↓ Porphyromonas ↓ Eggerthella ↑ Staphylococcus ↓ Haemophilus ↓ S24_7 ↑ Odoribacter ↑ |
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Yagi, K.; Lukacs, N.W.; Huffnagle, G.B.; Kato, H.; Asai, N. Respiratory and Gut Microbiome Modification during Respiratory Syncytial Virus Infection: A Systematic Review. Viruses 2024, 16, 220. https://doi.org/10.3390/v16020220
Yagi K, Lukacs NW, Huffnagle GB, Kato H, Asai N. Respiratory and Gut Microbiome Modification during Respiratory Syncytial Virus Infection: A Systematic Review. Viruses. 2024; 16(2):220. https://doi.org/10.3390/v16020220
Chicago/Turabian StyleYagi, Kazuma, Nicholas W. Lukacs, Gary B. Huffnagle, Hideo Kato, and Nobuhiro Asai. 2024. "Respiratory and Gut Microbiome Modification during Respiratory Syncytial Virus Infection: A Systematic Review" Viruses 16, no. 2: 220. https://doi.org/10.3390/v16020220
APA StyleYagi, K., Lukacs, N. W., Huffnagle, G. B., Kato, H., & Asai, N. (2024). Respiratory and Gut Microbiome Modification during Respiratory Syncytial Virus Infection: A Systematic Review. Viruses, 16(2), 220. https://doi.org/10.3390/v16020220