Publisher Correction: Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study

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: Type II diabetes mellitus adult onset diabetes,Adult-Onset Diabetes,adult-onset diabetes,Adult-Onset Diabetes Mellitus,diabetes mellitis type 2,diabetes mellitis type II,DIABETES MELLITUS TYPE 02,diabetes mellitus type 2,Diabetes Mellitus, Adult Onset,Diabetes Mellitus, Adult-Onset,Diabetes Mellitus, Ketosis Resistant,Diabetes Mellitus, Ketosis-Resistant,Diabetes Mellitus, Maturity Onset,Diabetes Mellitus, Maturity-Onset,Diabetes Mellitus, Non Insulin Dependent,Diabetes Mellitus, Non-Insulin-Dependent,Diabetes Mellitus, Noninsulin Dependent,diabetes mellitus, noninsulin-dependent,Diabetes Mellitus, Slow Onset,Diabetes Mellitus, Slow-Onset,Diabetes Mellitus, Stable,Diabetes Mellitus, Type 2,diabetes mellitus, type 2,diabetes mellitus, type 2, protection against,Diabetes Mellitus, Type II,Diabetes, Type 2,diabetes, type 2,insulin resistance, susceptibility to,Ketosis-Resistant Diabetes Mellitus,Maturity Onset Diabetes Mellitus,maturity-onset diabetes,Maturity-Onset Diabetes Mellitus,MODY,NIDDM,Non-Insulin Dependent Diabetes,non-insulin dependent diabetes,Non-Insulin Dependent Diabetes Mellitus,non-insulin dependent diabetes mellitus,non-insulin-dependent diabetes mellitus,noninsulin dependent diabetes,noninsulin-dependent diabetes mellitus,Slow-Onset Diabetes Mellitus,Stable Diabetes Mellitus,T2DM - Type 2 Diabetes mellitus,T2DM - type 2 diabetes mellitus,Type 2 Diabetes,type 2 diabetes,Type 2 Diabetes Mellitus,type 2 diabetes mellitus,Type 2 Diabetes Mellitus Non-Insulin Dependent,type 2 diabetes mellitus non-insulin dependent,Type II Diabetes,type II diabetes,type II diabetes mellitus,Type II diabetes mellitus

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-T2DM controls (healthy individuals)

Group 1 name Corresponds to the case (exposed) group for case-control studies: T2DM individuals (subjects with Type 2 Diabetes)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Native Emirati subjects diagnosed with T2DM, attending the endocrinology clinic.

Group 0 sample size Number of subjects in the control (unexposed) group: 25

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): 3 months

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: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: raw counts

Statistical test: DESeq2

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: Confounders controlled for: "disease state" 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.disease state

Alpha Diversity

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

Richness Number of species: unchanged

Signature 1

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Reviewed Marked as Reviewed by Folakunmi on 2024-11-4

Curated date: 2024/10/15

Curator: Sproff

Revision editor(s): Sproff, Tosin

Source: Figure 1G and within result text.

Description: Prokaryotic profiling of gut microbiome - Barplot of log2 fold changes in taxonomic feature abundances between health controls and T2DM.

Abundance in Group 1: increased abundance in T2DM individuals (subjects with Type 2 Diabetes)

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Phascolarctobacterium
Mogibacterium
Acidaminococcus
unclassified Victivallaceae

Revision editor(s): Sproff, Tosin

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Reviewed Marked as Reviewed by Folakunmi on 2024-11-4

Curated date: 2024/10/15

Curator: Sproff

Revision editor(s): Sproff, Tosin

Source: Figure1G and within result text

Description: Prokaryotic profiling of gut microbiome - Barplot of log2 fold changes in taxonomic feature abundances between health controls and T2DM

Abundance in Group 1: decreased abundance in T2DM individuals (subjects with Type 2 Diabetes)

NCBI	Quality Control	Links
Odoribacter
Lactococcus

Revision editor(s): Sproff, Tosin

Experiment 2

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Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Folakunmi on 2024-11-4

Curated date: 2024/10/21

Curator: Tosin

Revision editor(s): Tosin

Differences from previous experiment shown

Subjects

Lab analysis

Sequencing type: ITS / ITS2

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, Confounders controlled for: "disease state" 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.disease state