Toward defining the autoimmune microbiome for type 1 diabetes
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Giongo A, Gano KA, Crabb DB, Mukherjee N, Novelo LL, Casella G, Drew JC, Ilonen J, Knip M, Hyöty H, Veijola R, Simell T, Simell O, Neu J, Wasserfall CH, Schatz D, Atkinson MA, Triplett EW
Journal
The ISME journal
Year
2011
Several studies have shown that gut bacteria have a role in diabetes in murine models. Specific bacteria have been correlated with the onset of diabetes in a rat model. However, it is unknown whether human intestinal microbes have a role in the development of autoimmunity that often leads to type 1 diabetes (T1D), an autoimmune disorder in which insulin-secreting pancreatic islet cells are destroyed. High-throughput, culture-independent approaches identified bacteria that correlate with the development of T1D-associated autoimmunity in young children who are at high genetic risk for this disorder. The level of bacterial diversity diminishes overtime in these autoimmune subjects relative to that of age-matched, genotype-matched, nonautoimmune individuals. A single species, Bacteroides ovatus, comprised nearly 24% of the total increase in the phylum Bacteroidetes in cases compared with controls. Conversely, another species in controls, represented by the human firmicute strain CO19, represented nearly 20% of the increase in Firmicutes compared with cases overtime. Three lines of evidence are presented that support the notion that, as healthy infants approach the toddler stage, their microbiomes become healthier and more stable, whereas, children who are destined for autoimmunity develop a microbiome that is less diverse and stable. Hence, the autoimmune microbiome for T1D may be distinctly different from that found in healthy children. These data also suggest bacterial markers for the early diagnosis of T1D. In addition, bacteria that negatively correlated with the autoimmune state may prove to be useful in the prevention of autoimmunity development in high-risk children.
Experiment 1
Needs review
Subjects
- Location of subjects
- Finland
- 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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Autoimmune disease Autoimmune disease,autoimmune disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control 1
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Case 1
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples from children diagnosed with autoimmunity, determined by the appearance of at least two autoantibodies at four months after birth.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
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
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- Chi-Square
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- 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, Matched on: "HLA-DQ genotype" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.HLA-DQ genotype
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Table 3, 4, S2, S3, S4, S5
Description: Mean percent of total reads for six taxonomic levels identified in the case and control samples.
Abundance in Group 1: increased abundance in Case 1
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Table 3, 4, S2, S3, S4, S5
Description: Mean percent of total reads for six taxonomic levels identified in the case and control samples.
Abundance in Group 1: decreased abundance in Case 1
Revision editor(s): Aleru Divine
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control 2
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Case 2
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples from children diagnosed with autoimmunity, determined by the appearance of at least two autoantibodies at 1 year after birth.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Table 3, 4, S2, S3, S4, S5
Description: Mean percent of total reads for six taxonomic levels identified in the case and control samples.
Abundance in Group 1: increased abundance in Case 2
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Table 3, 4, S2, S3, S4, S5
Description: Mean percent of total reads for six taxonomic levels identified in the case and control samples.
Abundance in Group 1: decreased abundance in Case 2
Revision editor(s): Aleru Divine
Experiment 3
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control 3
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Case 3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples from children diagnosed with autoimmunity, determined by the appearance of at least two autoantibodies at 2 years after birth.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Needs review
Source: Table 3, 4, S2, S3, S4, S5
Description: Mean percent of total reads for six taxonomic levels identified in the case and control samples.
Abundance in Group 1: increased abundance in Case 3
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Table 3, 4, S2, S3, S4, S5
Description: Mean percent of total reads for six taxonomic levels identified in the case and control samples.
Abundance in Group 1: decreased abundance in Case 3
Revision editor(s): Aleru Divine
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