Gut microbiota alterations in response to sleep length among African-origin adults
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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
Fei N, Choo-Kang C, Reutrakul S, Crowley SJ, Rae D, Bedu-Addo K, Plange-Rhule J, Forrester TE, Lambert EV, Bovet P, Riesen W, Korte W, Luke A, Layden BT, Gilbert JA, Dugas LR
Journal
PloS one
Year
2021
Sleep disorders are increasingly being characterized in modern society as contributing to a host of serious medical problems, including obesity and metabolic syndrome. Changes to the microbial community in the human gut have been reportedly associated with many of these cardiometabolic outcomes. In this study, we investigated the impact of sleep length on the gut microbiota in a large cohort of 655 participants of African descent, aged 25-45, from Ghana, South Africa (SA), Jamaica, and the United States (US). The sleep duration was self-reported via a questionnaire. Participants were classified into 3 sleep groups: short (<7hrs), normal (7-<9hrs), and long (≥9hrs). Forty-seven percent of US participants were classified as short sleepers and 88% of SA participants as long sleepers. Gut microbial composition analysis (16S rRNA gene sequencing) revealed that bacterial alpha diversity negatively correlated with sleep length (p<0.05). Furthermore, sleep length significantly contributed to the inter-individual beta diversity dissimilarity in gut microbial composition (p<0.01). Participants with both short and long-sleep durations exhibited significantly higher abundances of several taxonomic features, compared to normal sleep duration participants. The predicted relative proportion of two genes involved in the butyrate synthesis via lysine pathway were enriched in short sleep duration participants. Finally, co-occurrence relationships revealed by network analysis showed unique interactions among the short, normal and long duration sleepers. These results suggest that sleep length in humans may alter gut microbiota by driving population shifts of the whole microbiota and also specific changes in Exact Sequence Variants abundance, which may have implications for chronic inflammation associated diseases. The current findings suggest a possible relationship between disrupted sleep patterns and the composition of the gut microbiota. Prospective investigations in larger and more prolonged sleep researches and causally experimental studies are needed to confirm these findings, investigate the underlying mechanism and determine whether improving microbial homeostasis may buffer against sleep-related health decline in humans.
Experiment 1
Needs review
Subjects
- Location of subjects
- Ghana
- Jamaica
- South Africa
- United States of America
- 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 , Saliva 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,Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sleep duration Sleep duration,sleep duration
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Sleepers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Short Sleepers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants of African descent aged 22 to 45 years who sleep for less than 7 hours daily
- Group 0 sample size Number of subjects in the control (unexposed) group
- 250
- Group 1 sample size Number of subjects in the case (exposed) group
- 154
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
- Chi-Square
- 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)?
- No
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, Confounders controlled for: "Country" 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.Country, Confounders controlled for: "gender" 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.gender
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Needs review
Source: FIGURE 1(D)
Description: Differential ESV abundance among short, normal and long sleepers adjusted for BMI, age, gender and countries. ESV with relative abundance ≥ 1% in at least one group shown.
Abundance in Group 1: increased abundance in Short Sleepers
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Bacteroides |
Revision editor(s): AishatBolarinwa
Signature 2
Needs review
Source: FIGURE 1(D)
Description: Differential ESV abundance among short, normal and long sleepers adjusted for BMI, age, gender and countries. ESV with relative abundance ≥ 1% in at least one group shown.
Abundance in Group 1: decreased abundance in Short Sleepers
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella |
Revision editor(s): AishatBolarinwa
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Long Sleepers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants of African descent aged 22 to 45 years who sleep for longer than 9 hours daily
- Group 1 sample size Number of subjects in the case (exposed) group
- 248
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Needs review
Source: FIGURE 1(D)
Description: Differential ESV abundance among short, normal and long sleepers adjusted for BMI, age, gender and countries. ESV with relative abundance ≥ 1% in at least one group shown.
Abundance in Group 1: increased abundance in Long Sleepers
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Prevotella | ||
| Erysipelotrichaceae | ||
| Oscillospira | ||
| Oscillospiraceae | ||
| Catenibacterium |
Revision editor(s): AishatBolarinwa
Experiment 3
Needs review
Differences from previous experiment shown
Subjects
- Location of subjects
- Ghana
- South Africa
- Jamaica
- United States of America
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Short sleepers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 154
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "country" 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.country, age, Confounders controlled for: "gender" 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.gender, body mass index
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: FIGURE 1(D)
Description: Differential ESV abundance among short, normal and long sleepers adjusted for BMI, age, gender and countries. ESV with relative abundance ≥ 1% in at least one group shown.
Abundance in Group 1: increased abundance in Long Sleepers
| NCBI | Quality Control | Links |
|---|---|---|
| Erysipelotrichaceae | ||
| Oscillospiraceae | ||
| Oscillospira | ||
| Catenibacterium |
Revision editor(s): AishatBolarinwa
Signature 2
Needs review
Source: FIGURE 1(D)
Description: Differential ESV abundance among short, normal and long sleepers adjusted for BMI, age, gender and countries. ESV with relative abundance ≥ 1% in at least one group shown.
Abundance in Group 1: decreased abundance in Long Sleepers
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides |
Revision editor(s): AishatBolarinwa
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