Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/25
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Ye Y, Carlsson G, Agholme MB, Wilson JA, Roos A, Henriques-Normark B, Engstrand L, Modéer T, Pütsep K
Journal
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases
Year
2013
The role of oral bacteria in the development of chemotherapy-related oral mucositis has not been fully elucidated. This study aimed to investigate oral bacterial community diversity and dynamics in paediatric patients with malignancies in relation to the occurrence of oral mucositis. Patients with malignancies (n = 37) and reference individuals without known systemic disorders (n = 38) were recruited. For patients, oral bacterial samples were taken from mucosal surfaces both at the time of malignancy diagnosis and during chemotherapy. If oral mucositis occurred, samples were taken from the surface of the mucositis lesions. Oral mucosal bacterial samples were also taken from reference individuals. All samples were assessed using a 16S ribosomal RNA gene 454 pyrosequencing method. A lower microbial diversity (p < 0.01) and a higher intersubject variability (p < 0.001) were found in patients as compared with reference individuals. At the time of malignancy diagnosis (i.e. before chemotherapy) patients that later developed mucositis showed a higher microbial diversity (p < 0.05) and a higher intersubject variability (p < 0.001) compared with those without mucositis. The change of bacterial composition during chemotherapy was more pronounced in patients who later developed mucositis than those without mucositis (p < 0.01). In conclusion, we found a higher microbial diversity at the time of malignancy diagnosis in patients who later develop oral mucositis and that these patients had a more significant modification of the bacterial community by chemotherapy before the occurrence of mucositis. These findings may possibly be of clinical importance in developing better strategies for personalized preventive management.

Experiment 1


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/25

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, Rimsha, Claregrieve1

Subjects

Location of subjects
Sweden
Host species Species from which microbiome was sampled (if applicable)
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Buccal mucosa , Lower lip Buccal mucosa,Labium inferius oris,Lower jaw lip,Lower lip
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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
reference
Group 1 name Corresponds to the case (exposed) group for case-control studies
patients with newly diagnosed malignancies
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patients that are newly diagnosed with malignancies (before chemotherapy treatment) that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden)
Group 0 sample size Number of subjects in the control (unexposed) group
38
Group 1 sample size Number of subjects in the case (exposed) group
37

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

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
Matched on Factors on which subjects have been matched on in a case-control study
age, sex

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Rimsha on 2022/08/25

Curated date: 2020-06-23

Curator: William Lam

Revision editor(s): WikiWorks743

Source: Figure 1a, Supplemental Table S2

Description: Comparison of the oral bacterial community between reference individuals and patients at the time of malignancy diagnosis (before chemotherapy)

Abundance in Group 1: increased abundance in patients with newly diagnosed malignancies

NCBI Links
Abiotrophia
Lactococcus
Derxia

Revision editor(s): WikiWorks743

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/25

Curated date: 2020-06-23

Curator: William Lam

Revision editor(s): WikiWorks743

Source: Figure 1a, Supplemental Table S2

Description: Comparison of the oral bacterial community between reference individuals and patients at the time of malignancy diagnosis (before chemotherapy)

Abundance in Group 1: decreased abundance in patients with newly diagnosed malignancies

NCBI Links
Bifidobacteriaceae
Corynebacterium
Coriobacteriaceae
Paludibacter
Sphingobacteriia
Gemella
Lachnospiraceae
Fusobacterium
Shewanella
Halomonas
Actinobacillus

Revision editor(s): WikiWorks743

Experiment 2


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, Rimsha

Subjects

Location of subjects
Sweden
Host species Species from which microbiome was sampled (if applicable)
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Buccal mucosa , Lower lip Buccal mucosa,Labium inferius oris,Lower jaw lip,Lower lip
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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
no oral mucositis
Group 1 name Corresponds to the case (exposed) group for case-control studies
oral mucositis
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patients that are newly diagnosed with malignancies (before chemotherapy treatment) that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that has later developed oral mucositis (graded by the World Health Organization)
Group 0 sample size Number of subjects in the control (unexposed) group
12
Group 1 sample size Number of subjects in the case (exposed) group
25

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

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
Matched on Factors on which subjects have been matched on in a case-control study
age, sex

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26

Curated date: 2020-06-23

Curator: William Lam

Revision editor(s): WikiWorks743, Claregrieve1

Source: Table 2

Description: Comparison of the oral bacterial community at the time of malignancy diagnosis (before chemotherapy) in patients who later developed oral mucositis and those who did not develop oral mucositis

Abundance in Group 1: increased abundance in oral mucositis

NCBI Links
Capnocytophaga
Fusobacteriota
Lactococcus
Spirochaeta
Peptostreptococcaceae incertae sedis

Revision editor(s): WikiWorks743, Claregrieve1

Experiment 3


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, Rimsha

Subjects

Location of subjects
Sweden
Host species Species from which microbiome was sampled (if applicable)
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Buccal mucosa , Lower lip Buccal mucosa,Labium inferius oris,Lower jaw lip,Lower lip
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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
at malignancy diagnosis
Group 1 name Corresponds to the case (exposed) group for case-control studies
during chemotherapy
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patients that are newly diagnosed with malignancies that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that has later developed oral mucositis (graded by the World Health Organization) during chemotherapy treatment
Group 0 sample size Number of subjects in the control (unexposed) group
12
Group 1 sample size Number of subjects in the case (exposed) group
12

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

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
Matched on Factors on which subjects have been matched on in a case-control study
age, sex


Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26

Curated date: 2020-06-23

Curator: William Lam

Revision editor(s): WikiWorks743, Claregrieve1

Source: Table 3

Description: Differential microbial abundance between the malignancy diagnosis (pre-chemotherapy) timepoint and during chemotherapy timepoint in those who have oral mucositis

Abundance in Group 1: increased abundance in during chemotherapy

NCBI Links
Staphylococcus

Revision editor(s): WikiWorks743, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26

Curated date: 2020-06-23

Curator: William Lam

Revision editor(s): WikiWorks743, Claregrieve1

Source: Table 3

Description: Differential microbial abundance between the malignancy diagnosis (pre-chemotherapy) timepoint and during chemotherapy timepoint in those who have oral mucositis

Abundance in Group 1: decreased abundance in during chemotherapy

NCBI Links
Derxia
Pseudomonadota

Revision editor(s): WikiWorks743, Claregrieve1

Experiment 4


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, Rimsha

Subjects

Location of subjects
Sweden
Host species Species from which microbiome was sampled (if applicable)
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Buccal mucosa , Lower lip Buccal mucosa,Labium inferius oris,Lower jaw lip,Lower lip
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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
at malignancy diagnosis
Group 1 name Corresponds to the case (exposed) group for case-control studies
during chemotherapy
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patients that are newly diagnosed with malignancies that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that did not develop oral mucositis (graded by the World Health Organization) during chemotherapy treatment
Group 0 sample size Number of subjects in the control (unexposed) group
10
Group 1 sample size Number of subjects in the case (exposed) group
10

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

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
Matched on Factors on which subjects have been matched on in a case-control study
age, sex


Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26

Curated date: 2020-06-23

Curator: William Lam

Revision editor(s): WikiWorks743, Claregrieve1

Source: Table 3

Description: Differential microbial abundance between the malignancy diagnosis (pre-chemotherapy) timepoint and during chemotherapy timepoint in those who do not have oral mucositis

Abundance in Group 1: increased abundance in during chemotherapy

NCBI Links
Xanthomonas

Revision editor(s): WikiWorks743, Claregrieve1

Experiment 5


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, Rimsha, Claregrieve1

Subjects

Location of subjects
Sweden
Host species Species from which microbiome was sampled (if applicable)
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Buccal mucosa , Lower lip Buccal mucosa,Labium inferius oris,Lower jaw lip,Lower lip
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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
all samples
Group 1 name Corresponds to the case (exposed) group for case-control studies
mucositis lesions
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
samples from mucositis lesions
Group 0 sample size Number of subjects in the control (unexposed) group
97
Group 1 sample size Number of subjects in the case (exposed) group
27

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

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
Matched on Factors on which subjects have been matched on in a case-control study
age, sex


Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26

Curated date: 2020-06-23

Curator: William Lam

Revision editor(s): WikiWorks743, Claregrieve1

Source: Supplemental Table S4, Figure S1, S2

Description: Relative abundance (%) of taxa with different levels between all mucosal samples from lip and bucca and samples from mucositis lesions

Abundance in Group 1: increased abundance in mucositis lesions

NCBI Links
Abiotrophia
Actinomyces
Bacillus
Erysipelotrichaceae
Lactococcus
Rikenellaceae
Scardovia
Staphylococcus
candidate phylum NAG2
Lactobacillus
Peptostreptococcus
Stenotrophomonas
Mycoplasmatota
Mycoplasma

Revision editor(s): WikiWorks743, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26

Curated date: 2020-06-23

Curator: William Lam

Revision editor(s): WikiWorks743, Claregrieve1

Source: Supplemental Table S4, Figure S1, S2

Description: Relative abundance (%) of taxa with different levels between all mucosal samples from lip and bucca and samples from mucositis lesions

Abundance in Group 1: decreased abundance in mucositis lesions

NCBI Links
Actinobacillus
Aggregatibacter
Haemophilus

Revision editor(s): WikiWorks743, Claregrieve1