Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/23
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
de Steenhuijsen Piters WA, Huijskens EG, Wyllie AL, Biesbroek G, van den Bergh MR, Veenhoven RH, Wang X, Trzciński K, Bonten MJ, Rossen JW, Sanders EA, Bogaert D
Journal
The ISME journal
Year
2016
Bacterial pneumonia is a major cause of morbidity and mortality in elderly. We hypothesize that dysbiosis between regular residents of the upper respiratory tract (URT) microbiome, that is balance between commensals and potential pathogens, is involved in pathogen overgrowth and consequently disease. We compared oropharyngeal microbiota of elderly pneumonia patients (n=100) with healthy elderly (n=91) by 16S-rRNA-based sequencing and verified our findings in young adult pneumonia patients (n=27) and young healthy adults (n=187). Microbiota profiles differed significantly between elderly pneumonia patients and healthy elderly (PERMANOVA, P<0.0005). Highly similar differences were observed between microbiota profiles of young adult pneumonia patients and their healthy controls. Clustering resulted in 11 (sub)clusters including 95% (386/405) of samples. We observed three microbiota profiles strongly associated with pneumonia (P<0.05) and either dominated by lactobacilli (n=11), Rothia (n=51) or Streptococcus (pseudo)pneumoniae (n=42). In contrast, three other microbiota clusters (in total n=183) were correlated with health (P<0.05) and were all characterized by more diverse profiles containing higher abundances of especially Prevotella melaninogenica, Veillonella and Leptotrichia. For the remaining clusters (n=99), the association with health or disease was less clear. A decision tree model based on the relative abundance of five bacterial community members in URT microbiota showed high specificity of 95% and sensitivity of 84% (89% and 73%, respectively, after cross-validation) for differentiating pneumonia patients from healthy individuals. These results suggest that pneumonia in elderly and young adults is associated with dysbiosis of the URT microbiome with bacterial overgrowth of single species and absence of distinct anaerobic bacteria. Whether the observed microbiome changes are a cause or a consequence of the development of pneumonia or merely coincide with disease status remains a question for future research.

Experiment 1


Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/23

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Rimsha, Claregrieve1, ChiomaBlessing, Victoria

Subjects

Location of subjects
Netherlands
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
Mucosa of oropharynx Mucosa of oral part of pharynx,Mucosa of organ of oral part of pharynx,Mucosa of organ of oropharynx,Mucous membrane of oral part of pharynx,Mucous membrane of oropharynx,Oral part of pharynx mucosa,Oral part of pharynx mucosa of organ,Oral part of pharynx mucous membrane,Oral part of pharynx organ mucosa,Organ mucosa of oral part of pharynx,Organ mucosa of oropharynx,Oropharynx mucosa,Oropharynx mucosa of organ,Oropharynx mucous membrane,Oropharynx organ mucosa,Mucosa of oropharynx,mucosa of oropharynx
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Pneumonia acute pneumonia,chest infection due to pneumonia,pneumonia,Pneumonia (disorder),Pneumonia (disorder) [Ambiguous],Pneumonia due to other specified organism,Pneumonia due to other specified organisms,Pneumonia due to other specified organisms (disorder),Pneumonia NOS,Pneumonia NOS (disorder),pneumonia with infectious disease,Pneumonitis,Pneumonitis (disorder),Pneumonia
Group 0 name Corresponds to the control (unexposed) group for case-control studies
elderly controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
elderly pneumonia patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patients >= 60 years of age with pneumonia
Group 0 sample size Number of subjects in the control (unexposed) group
91
Group 1 sample size Number of subjects in the case (exposed) group
100
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
3 months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V5-V7
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
raw counts
Statistical test
T-Test
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
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, smoking behavior, comorbidity

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Richness Number of species
decreased

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/23

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 2

Description: Differential microbial abundance between elderly controls and elderly pneumonia patients

Abundance in Group 1: increased abundance in elderly pneumonia patients

NCBI Quality ControlLinks
Lactobacillus
Rothia
Streptococcus pseudopneumoniae

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/23

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Claregrieve1, Merit, WikiWorks

Source: Figure 2

Description: Differential microbial abundance between elderly controls and elderly pneumonia patients

Abundance in Group 1: decreased abundance in elderly pneumonia patients

NCBI Quality ControlLinks
Leptotrichia
Parascardovia
Prevotella melaninogenica
Veillonella dispar

Revision editor(s): Claregrieve1, Merit, WikiWorks

Experiment 2


Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/23

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Rimsha, Claregrieve1, ChiomaBlessing, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
adult controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
adult pneumonia patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patients <60 years of age with pneumonia
Group 0 sample size Number of subjects in the control (unexposed) group
187
Group 1 sample size Number of subjects in the case (exposed) group
27

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/23

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 2

Description: Differential microbial abundance between healthy adult controls and pneumonia patients

Abundance in Group 1: increased abundance in adult pneumonia patients

NCBI Quality ControlLinks
Lactobacillus
Rothia
Streptococcus pseudopneumoniae

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/23

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 2

Description: Differential microbial abundance between healthy adult controls and pneumonia patients

Abundance in Group 1: decreased abundance in adult pneumonia patients

NCBI Quality ControlLinks
Bacilli
Haemophilus
Leptotrichia
Neisseria
Prevotella melaninogenica
Veillonella dispar

Revision editor(s): Claregrieve1, WikiWorks