Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients

From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-7-24
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA, Zaura E
Journal
Scientific reports
Year
2019
The aim of this prospective, two center study was to investigate the dynamics of the microbial changes in relation to the development of ulcerative oral mucositis in autologous SCT (autoSCT) recipients. Fifty-one patients were diagnosed with multiple myeloma and treated with high-dose melphalan followed by autoSCT. They were evaluated before, three times weekly during hospitalization, and three months after autoSCT. At each time point an oral rinse was collected and the presence or absence of ulcerative oral mucositis (UOM) was scored (WHO scale). Oral microbiome was determined by using 16S rRNA amplicon sequencing and fungal load by qPCR. Twenty patients (39%) developed UOM. The oral microbiome changed significantly after autoSCT and returned to pre-autoSCT composition after three months. However, changes in microbial diversity and similarity were more pronounced and rapid in patients who developed UOM compared to patients who did not. Already before autoSCT, different taxa discriminated between the 2 groups, suggesting microbially-driven risk factors. Samples with high fungal load (>0.1%) had a significantly different microbial profile from samples without fungi. In conclusion, autoSCT induced significant and reversible changes in the oral microbiome, while patients who did not develop ulcerative oral mucositis had a more resilient microbial ecosystem.

Experiment 1


Reviewed Marked as Reviewed by Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, 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
Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Oral mucositis inflammation of the mouth,oral cavity mucosal damage,oral mucosa irritation,oral mucosal damage,oral mucosal injury,oral mucosal lesions,stomatitis,Oral mucositis,oral mucositis
Group 0 name Corresponds to the control (unexposed) group for case-control studies
no ulcerative oral mucositis
Group 1 name Corresponds to the case (exposed) group for case-control studies
ulcerative oral mucositis
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patient developed uclerative oral mucositis
Group 0 sample size Number of subjects in the control (unexposed) group
31
Group 1 sample size Number of subjects in the case (exposed) group
20

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
RT-qPCR

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
2


Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: William Lam

Revision editor(s): WikiWorks

Source: Figure 3

Description: Minimum entropy decomposition nodes (MEDs) that significantly discriminate multiple myeloma patients that did not develop uclerative oral mucositis and patients that did develop uclerative oral mucositis before auto stem cell transplant identified by LEfSe

Abundance in Group 1: increased abundance in ulcerative oral mucositis

NCBI Quality ControlLinks
Veillonella
Enterococcus
Streptococcus
Staphylococcus
Fusobacterium
Prevotella

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: William Lam

Revision editor(s): WikiWorks

Source: Figure 3

Description: Minimum entropy decomposition nodes (MEDs) that significantly discriminate multiple myeloma patients that did not develop uclerative oral mucositis and patients that did develop uclerative oral mucositis before auto stem cell transplant identified by LEfSe

Abundance in Group 1: decreased abundance in ulcerative oral mucositis

NCBI Quality ControlLinks
Streptococcus
Actinomyces

Revision editor(s): WikiWorks

Experiment 2


Reviewed Marked as Reviewed by Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
one and two weeks after stem cell transplant
Group 1 name Corresponds to the case (exposed) group for case-control studies
pre- and three month after auto stem cell transplant

Lab analysis

Statistical Analysis

Statistical test
PERMANOVA
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
Not specified

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: William Lam

Revision editor(s): WikiWorks, Atrayees

Source: text

Description: Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in non-uclerative oral mucositis group

Abundance in Group 1: increased abundance in pre- and three month after auto stem cell transplant

NCBI Quality ControlLinks
Veillonella atypica
Veillonella dispar
Actinomyces sp.
Actinomyces graevenitzii
Prevotella
Leptotrichia
Megasphaera micronuciformis
Veillonella sp.

Revision editor(s): WikiWorks, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: William Lam

Revision editor(s): WikiWorks, Atrayees

Source: text

Description: Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in non-uclerative oral mucositis group

Abundance in Group 1: decreased abundance in pre- and three month after auto stem cell transplant

NCBI Quality ControlLinks
Lactobacillus
Limosilactobacillus fermentum
Scardovia wiggsiae

Revision editor(s): WikiWorks, Atrayees

Experiment 3


Reviewed Marked as Reviewed by Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Differences from previous experiment shown

Subjects

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 Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: William Lam

Revision editor(s): WikiWorks, Atrayees

Source: text

Description: Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in uclerative oral mucositis group

Abundance in Group 1: increased abundance in pre- and three month after auto stem cell transplant

NCBI Quality ControlLinks
Streptococcus australis
Streptococcus parasanguinis
Veillonella atypica
Veillonella dispar
Actinomyces
Actinomyces graevenitzii
Gemella haemolysans
Gemella morbillorum
Gemella sanguinis

Revision editor(s): WikiWorks, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: William Lam

Revision editor(s): WikiWorks, Atrayees

Source: text

Description: Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in uclerative oral mucositis group

Abundance in Group 1: decreased abundance in pre- and three month after auto stem cell transplant

NCBI Quality ControlLinks
Staphylococcus aureus
Staphylococcus caprae
Staphylococcus epidermidis
Staphylococcus warneri
Scardovia wiggsiae
Enterococcus faecalis

Revision editor(s): WikiWorks, Atrayees

Experiment 4


Reviewed Marked as Reviewed by Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
low or no fungi load
Group 1 name Corresponds to the case (exposed) group for case-control studies
0.1% or higher fungi load

Lab analysis

Statistical Analysis

Statistical test
Mann-Whitney (Wilcoxon)


Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: William Lam

Revision editor(s): WikiWorks, Atrayees

Source: text

Description: Principle component analysis of salivary microbial profiles based on fungal load relative to bacterial 16s rDNA

Abundance in Group 1: increased abundance in 0.1% or higher fungi load

NCBI Quality ControlLinks
Scardovia
Staphylococcus
Lactobacillus

Revision editor(s): WikiWorks, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: William Lam

Revision editor(s): WikiWorks, Atrayees

Source: text

Description: Principle component analysis of salivary microbial profiles based on fungal load relative to bacterial 16s rDNA

Abundance in Group 1: decreased abundance in 0.1% or higher fungi load

NCBI Quality ControlLinks
Veillonella
Actinomyces
Prevotella
Leptotrichia
Megasphaera
Streptococcus

Revision editor(s): WikiWorks, Atrayees