The microbiome in urogenital schistosomiasis and induced bladder pathologies

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study design
case-control
Citation
PMID PubMed identifier for scientific articles.
28793309
DOI Digital object identifier for electronic documents.
https://doi.org/10.1371/journal.pntd.0005826
URI
Authors
Adebayo AS, Suryavanshi MV, Bhute S, Agunloye AM, Isokpehi RD, Anumudu CI, Shouche YS
Journal
PLoS neglected tropical diseases
Year
2017
BACKGROUND: Human schistosomiasis is a highly prevalent neglected tropical disease (NTD) caused by Schistosoma species. Research on the molecular mechanisms influencing the outcomes of bladder infection by Schistosoma haematobium is urgently needed to develop new diagnostics, therapeutics and infection prevention strategies. The objective of the research study was to determine the microbiome features and changes in urine during urogenital schistosomiasis and induced bladder pathologies. METHODOLOGY: Seventy participants from Eggua, southwestern Nigeria provided morning urine samples and were screened for urogenital schistosomiasis infection and bladder pathologies in a cross-sectional study. Highthroughput NGS sequencing was carried out, targeting the 16S V3 region. Filtered reads were processed and analyzed in a bioinformatics pipeline. PRINCIPAL FINDINGS: The study participants (36 males and 34 females, between ages 15 and 65) were categorized into four groups according to status of schistosomiasis infection and bladder pathology. Data analytics of the next-generation sequencing reads revealed that Proteobacteria and Firmicutes dominated and had influence on microbiome structure of both non-infected persons and persons with urogenital schistosomiasis. Furthermore, gender and age influenced taxa abundance independent of infection or bladder pathology. Several taxa distinguished urogenital schistosomiasis induced bladder pathologies from urogenital schistosomiasis infection alone and from healthy persons, including known immune-stimulatory taxa such as Fusobacterium, Sphingobacterium and Enterococcus. Some of these significant taxa, especially Sphingobacterium were projected as markers of infection, while several genera including potentially beneficial taxa such as Trabulsiella and Weissella, were markers of the non-infected. Finally, expected changes in protein functional categories were observed to relate to cellular maintenance and lipid metabolism. CONCLUSION: The urinary microbiome is a factor to be considered in developing biomarkers, diagnostic tools, and new treatment for urogenital schistosomiasis and induced bladder pathologies.

Experiment 1


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Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu

Subjects

Location of subjects
Nigeria
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
Urine Urine,urine
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Urinary schistosomiasis bladder Schistosomiasis,bladder schistosomiasis,cystitis with bilharziasis,cystitis with bilharziasis (disorder),Schistosoma haematobium,Schistosoma haematobium (& vesical schistosomiasis),Schistosoma haematobium infection,Schistosoma Hematobium Infection,Schistosoma hematobium infection,Schistosoma hematobium infection (disorder),Schistosoma hematobium infectious disease,Schistosomiasis due to schistosoma haematobium,schistosomiasis due to Schistosoma haematobium,Schistosomiasis haematobia,schistosomiasis of bladder,Schistosomiasis of bladder [Ambiguous],urinary bladder schistosomiasis,urinary schistosomiasis,urinary schistosomiasis (disorder),vesical schistosomiasis,Vesical schistosomiasis NOS,Urinary schistosomiasis
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy Control
Group 1 name Corresponds to the case (exposed) group for case-control studies
Infection-Only
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Urine samples infected with urogenital schistosomiasis
Group 0 sample size Number of subjects in the control (unexposed) group
13
Group 1 sample size Number of subjects in the case (exposed) group
25
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Recent use of Antibiotics

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Ion Torrent

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Mann-Whitney (Wilcoxon)
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

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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Curated date: 2024/04/25

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu

Source: Figure 6B

Description: Differentially abundant microbiome between urogenital schistosomiasis (infection-only) and healthy controls

Abundance in Group 1: increased abundance in Infection-Only

NCBI Quality ControlLinks
Aerococcus   
Chryseobacterium   
Facklamia   
Klebsiella   
Pseudomonas   
Shewanella   
unclassified Carnobacteriaceae   
unclassified Planococcaceae   
Staphylococcus   
unclassified Moraxellaceae   
Acinetobacter   

Revision editor(s): Adenike Oladimeji-Kasumu

Signature 2

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Source: Figure 6B

Description: Differentially abundant microbiome between urogenital schistosomiasis (infection-only) and healthy controls

Abundance in Group 1: decreased abundance in Infection-Only

NCBI Quality ControlLinks
Enterobacter   
Edwardsiella   
Erwinia   
Mycoplana   
Photorhabdus   
Hafnia   
Limnobacter   
Weissella   
Gardnerella   
Psychrobacter   
Acinetobacter   
unclassified Moraxellaceae   
unclassified Bifidobacteriaceae   
unclassified Aeromonadales   
unclassified Enterobacteriaceae   
unclassified Pseudoalteromonadaceae   

Revision editor(s): Adenike Oladimeji-Kasumu

Experiment 2


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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Advanced
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Urine samples infected with urogenital schistosomiasis induced bladder pathology.
Group 1 sample size Number of subjects in the case (exposed) group
22

Lab analysis

Statistical Analysis

Alpha Diversity

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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Needs review

Curated date: 2024/04/29

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu

Source: Figure 6A

Description: Differentially abundant microbiome between urogenital schistosomiasis induced bladder pathology (advanced) and healthy controls.

Abundance in Group 1: increased abundance in Advanced

NCBI Quality ControlLinks
Bacteroides   
Jeotgalicoccus   
Prevotella   
Fusobacterium   
Veillonella   
Aerococcus   
Granulicatella   
Facklamia   
Brevibacterium   
Peptoniphilus   
Caulobacter   
Lactobacillus   
Staphylococcus   
Acinetobacter   
unclassified Cardiobacteriales   

Revision editor(s): Adenike Oladimeji-Kasumu

Signature 2

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Source: Figure 6A

Description: Differentially abundant microbiome between urogenital schistosomiasis induced bladder pathology (advanced) and healthy controls.

Abundance in Group 1: decreased abundance in Advanced

NCBI Quality ControlLinks
unclassified Enterococcaceae   
unclassified Bifidobacteriaceae   
unclassified Pseudoalteromonadaceae   
unclassified Enterobacteriaceae   
unclassified Moraxellaceae   
unclassified Aeromonadales   
Enterobacter   
Edwardsiella   
Weissella   
Erwinia   
Photorhabdus   
Hafnia   
Pseudomonas   
Staphylococcus   
Acinetobacter   

Revision editor(s): Adenike Oladimeji-Kasumu

Experiment 3


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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Non-Infected
Group 1 name Corresponds to the case (exposed) group for case-control studies
Infected
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Infected with urogenital schistosomiasis
Group 0 sample size Number of subjects in the control (unexposed) group
24
Group 1 sample size Number of subjects in the case (exposed) group
46

Lab analysis

Statistical Analysis

Alpha Diversity

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

EditHistoryDelete
Mark reviewed
Your review change was submitted
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Curated date: 2024/04/30

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu

Source: Figure 5A, 5B

Description: Differentially abundant microbiome genera in urogenital schistosomiasis (infected) and controls (non-infected).

Abundance in Group 1: increased abundance in Infected

NCBI Quality ControlLinks
Acinetobacter   
Aerococcaceae   
Aerococcus   
Bacteroidaceae   
Bacteroides   
Brevibacteriaceae   
Brevibacterium   
Carnobacteriaceae   
Chryseobacterium   
Enterococcaceae   
Enterococcus   
Facklamia   
Fusobacteriaceae   
Fusobacterium   
Granulicatella   
Jeotgalicoccus   
Lactobacillaceae   
Lactobacillus   
Lactococcus   
Melissococcus   
Moraxellaceae   
Peptoniphilus   
Prevotella   
Prevotellaceae   
Staphylococcaceae   
Staphylococcus   
Streptococcaceae   
Tissierellaceae   
Veillonella   
Veillonellaceae   
Weeksellaceae   
unclassified Cardiobacteriales   
unclassified Carnobacteriaceae   

Revision editor(s): Adenike Oladimeji-Kasumu

Signature 2

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Curated date: 2024/04/30

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Revision editor(s): Adenike Oladimeji-Kasumu

Source: Figure 5A, 5B

Description: Differentially abundant microbiome genera in urogenital schistosomiasis (infected) and controls (non-infected).

Abundance in Group 1: decreased abundance in Infected

NCBI Quality ControlLinks
Acinetobacter   
Bacillaceae   
Bacillus   
Bifidobacteriaceae   
Caulobacteraceae   
Chryseobacterium   
Edwardsiella   
Enhydrobacter   
Enterobacter   
Enterobacteriaceae   
Erwinia   
Gardnerella   
Hafnia   
Janthinobacterium   
Limnobacter   
Moraxellaceae   
Mycoplana   
Oxalobacteraceae   
Photorhabdus   
Pseudoalteromonadaceae   
Psychrobacter   
Staphylococcaceae   
Staphylococcus   
Weeksellaceae   
Weissella   
unclassified Aeromonadales   
unclassified Bifidobacteriaceae   
unclassified Pseudoalteromonadaceae   

Revision editor(s): Adenike Oladimeji-Kasumu

Experiment 4


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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pathology only
Group 1 name Corresponds to the case (exposed) group for case-control studies
Advanced
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Urogenital schistosomiasis induced bladder pathology.
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
22

Lab analysis

Statistical Analysis

Alpha Diversity

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

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2024/04/30

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu

Source: Figure 5D

Description: Differentially abundant microbiome genera in non-infected bladder pathology (pathology-only) and urogenital schistosomiasis induced bladder pathology (advanced).

Abundance in Group 1: increased abundance in Advanced

NCBI Quality ControlLinks
Bacteroides   
Prevotella   
Jeotgalicoccus   
Wautersiella   
Veillonella   
Fusobacterium   
Comamonas   
unclassified Cardiobacteriales   
Aerococcus   
Peptoniphilus   
unclassified Pseudomonadaceae   
Brevibacterium   
Facklamia   
Weeksella   
Granulicatella   
Sphingobacterium   
Hylemonella sp.   
Lactobacillus   
Acinetobacter   

Revision editor(s): Adenike Oladimeji-Kasumu

Signature 2

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Curated date: 2024/04/30

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu

Source: Figure 5D

Description: Differentially abundant microbiome genera in non-infected bladder pathology (pathology-only) and urogenital schistosomiasis induced bladder pathology (advanced).

Abundance in Group 1: decreased abundance in Advanced

NCBI Quality ControlLinks
Edwardsiella   
unclassified Pseudoalteromonadaceae   
Hafnia   
unclassified Aeromonadales   
unclassified Enterobacteriaceae   
Staphylococcus   
unclassified Planococcaceae   
Enhydrobacter   
Pseudomonas   
Chryseobacterium   
Bacillus   
Janthinobacterium   
Acinetobacter   

Revision editor(s): Adenike Oladimeji-Kasumu

Experiment 5


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Revision editor(s): Adenike Oladimeji-Kasumu

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Infection Only
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
urogenital schistosomiasis induced bladder pathology.
Group 0 sample size Number of subjects in the control (unexposed) group
25

Lab analysis

Statistical Analysis

Alpha Diversity

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

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2024/04/30

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu

Source: Figure 5C

Description: Differential microbiome genera between urogenital schistosomiasis (infection-only) and urogenital schistosomiasis induced bladder pathology (advanced).

Abundance in Group 1: increased abundance in Advanced

NCBI Quality ControlLinks
unclassified Pseudomonadaceae   
Bacteroides   
Prevotella   
Jeotgalicoccus   
unclassified Moraxellaceae   
unclassified Cardiobacteriales   
Psychrobacter   
Fusobacterium   
Veillonella   
Granulicatella   
Facklamia   
Brevibacterium   
Peptoniphilus   
unclassified Bifidobacteriaceae   
Caulobacter   
Gardnerella   
Sphingobacterium   
Wautersiella   
Limnobacter   
Weeksella   
Lactobacillus   
Mycoplana   
Acinetobacter   
Staphylococcus   

Revision editor(s): Adenike Oladimeji-Kasumu

Signature 2

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Your review change was submitted
Needs review

Curated date: 2024/04/30

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu

Source: Figure 5C

Description: Differential microbiome genera between urogenital schistosomiasis (infection-only) and urogenital schistosomiasis induced bladder pathology (advanced).

Abundance in Group 1: decreased abundance in Advanced

NCBI Quality ControlLinks
unclassified Enterococcaceae   
unclassified Carnobacteriaceae   
Chryseobacterium   
Acinetobacter   
Staphylococcus   
Pseudomonas   
unclassified Planococcaceae   

Revision editor(s): Adenike Oladimeji-Kasumu

Experiment 6


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Revision editor(s): Adenike Oladimeji-Kasumu

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pathology Only
Group 1 name Corresponds to the case (exposed) group for case-control studies
Infection Only
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Urogenital schistosomiasis infection
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
25

Lab analysis

Statistical Analysis

Alpha Diversity

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

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2024/04/30

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu

Source: Figure S2B

Description: Differential abundance in the urine microbiome of persons with urogenital schistosomiasis infection without bladder pathology (infection-only) and pathology without schistosomiasis infection (pathology-only).

Abundance in Group 1: increased abundance in Infection Only

NCBI Quality ControlLinks
Aerococcus   
unclassified Pseudomonadaceae   
Comamonas   
Enterococcus   
Chryseobacterium   
Acinetobacter   

Revision editor(s): Adenike Oladimeji-Kasumu

Signature 2

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2024/04/30

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu

Source: Figure S2B

Description: Differential abundance in the urine microbiome of persons with urogenital schistosomiasis infection without bladder pathology (infection-only) and pathology without schistosomiasis infection (pathology-only).

Abundance in Group 1: decreased abundance in Infection Only

NCBI Quality ControlLinks
unclassified Pseudoalteromonadaceae   
Enterobacter   
Edwardsiella   
Erwinia   
Photorhabdus   
Caulobacter   
unclassified Enterobacteriaceae   
Staphylococcus   
Enhydrobacter   
Chryseobacterium   
Bacillus   
Janthinobacterium   
Psychrobacter   
unclassified Moraxellaceae   
Acinetobacter   

Revision editor(s): Adenike Oladimeji-Kasumu

Experiment 7


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Curated date: 2024/05/01

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Revision editor(s): Adenike Oladimeji-Kasumu

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Infected
Group 1 name Corresponds to the case (exposed) group for case-control studies
Non-Infected
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Not infected with urogenital schistosomiasis.
Group 0 sample size Number of subjects in the control (unexposed) group
46
Group 1 sample size Number of subjects in the case (exposed) group
24

Lab analysis

Statistical Analysis

Statistical test
LEfSe

Alpha Diversity

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

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2024/05/01

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu

Source: Figure 7

Description: Predicted microbial biomarkers in urogenital schistosomiasis cases (infected) and controls (non-infected).

Abundance in Group 1: increased abundance in Non-Infected

NCBI Quality ControlLinks
Leuconostocaceae bacterium   
Weissella   
unclassified Enterobacteriaceae   
Streptomycetaceae   
Peptostreptococcus   
Trabulsiella   
Peptostreptococcaceae   
Anaerococcus   
Xenorhabdus   

Revision editor(s): Adenike Oladimeji-Kasumu

Signature 2

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Curated date: 2024/05/01

Curator: Adenike Oladimeji-Kasumu

Revision editor(s): Adenike Oladimeji-Kasumu

Source: Figure 7

Description: Predicted microbial biomarkers in urogenital schistosomiasis cases (infected) and controls (non-infected).

Abundance in Group 1: decreased abundance in Non-Infected

NCBI Quality ControlLinks
Stenotrophomonas   
unclassified Bacillales   
Sphingobacteriaceae   
Sphingobacterium   
Sphingobacteriia   
Sphingobacteriales   

Revision editor(s): Adenike Oladimeji-Kasumu

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