Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S, Belenky P
Journal
Microbiology spectrum
Year
2023
Keywords:
antibiotic-induced dysbiosis, dysbiosis, gut microbiome, microbiome
Antibiotic-induced gut microbiome dysbiosis (AID) is known to be influenced by host dietary composition. However, how and when diet modulates gut dysbiosis remains poorly characterized. Thus, here, we utilize a multi-omics approach to characterize how a diet supplemented with oats, a rich source of microbiota-accessible carbohydrates, or dextrose impacts amoxicillin-induced changes to gut microbiome structure and transcriptional activity. We demonstrate that oat administration during amoxicillin challenge provides greater protection from AID than the always oats or recovery oats diet groups. In particular, the group in which oats were provided at the time of antibiotic exposure induced the greatest protection against AID while the other oat diets saw greater effects after amoxicillin challenge. The oat diets likewise reduced amoxicillin-driven elimination of Firmicutes compared to the dextrose diet. Functionally, gut communities fed dextrose were carbohydrate starved and favored respiratory metabolism and consequent metabolic stress management while oat-fed communities shifted their transcriptomic profile and emphasized antibiotic stress management. The metabolic trends were exemplified when assessing transcriptional activity of the following two common gut commensal bacteria: Akkermansia muciniphila and Bacteroides thetaiotaomicron. These findings demonstrate that while host diet is important in shaping how antibiotics effect the gut microbiome composition and function, diet timing may play an even greater role in dietary intervention-based therapeutics. IMPORTANCE We utilize a multi-omics approach to demonstrate that diets supplemented with oats, a rich source of microbiota-accessible carbohydrates, are able to confer protection against antibiotic-induced dysbiosis (AID). Our findings affirm that not only is host diet important in shaping antibiotics effects on gut microbiome composition and function but also that the timing of these diets may play an even greater role in managing AID. This work provides a nuanced perspective on dietary intervention against AID and may be informative on preventing AID during routine antibiotic treatment.

Experiment 1


Needs review

Curated date: 2024/03/19

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Subjects

Location of subjects
United States of America
Host species Species from which microbiome was sampled. Contact us to have more species added.
Mus musculus
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
Response to diet Response to diet,response to diet
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Always Dextrose Day 5 Abx
Group 1 name Corresponds to the case (exposed) group for case-control studies
Prophylactic oats Day 5 Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Fecal pellets collected on day 5 from mice that were fed diet supplemented with oats as a preventive measure during amoxicillin 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
3
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
None

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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased

Signature 1

Needs review

Curated date: 2024/03/20

Curator: Barrakat

Revision editor(s): Barrakat

Source: Figure 3

Description: Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by DeSeq2

Abundance in Group 1: increased abundance in Prophylactic oats Day 5 Abx

NCBI Quality ControlLinks
Bacteroides faecichinchillae
Bacteroides ovatus
Bacteroides xylanisolvens
Staphylococcus xylosus
Thomasclavelia cocleata
borkfalkiaceae NOV MGBC 135946borkfalkiaceae NOV MGBC 135946
Bacteroides MGBC 111476Bacteroides MGBC 111476
Oscillospiraceae_NOV MGBC163448Oscillospiraceae_NOV MGBC163448
Oscillibacter MGBC000151Oscillibacter MGBC000151
Acutalibacter MGBC 115182Acutalibacter MGBC 115182
Lachnospiraceae_NOV MGBC 105353Lachnospiraceae_NOV MGBC 105353
Erysipelotrichaceae_NOV MGBC000147Erysipelotrichaceae_NOV MGBC000147
Eubacterium R MGBC120247Eubacterium R MGBC120247
Erysipelatoclostridiaceae_NOV MGBC 105353Erysipelatoclostridiaceae_NOV MGBC 105353
Erysipelotrichaceae_NOV MGBC163961Erysipelotrichaceae_NOV MGBC163961

Revision editor(s): Barrakat

Signature 2

Needs review

Curated date: 2024/03/20

Curator: Barrakat

Revision editor(s): Barrakat

Source: Figure 3

Description: Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by DeSeq2

Abundance in Group 1: decreased abundance in Prophylactic oats Day 5 Abx

NCBI Quality ControlLinks
Alistipes onderdonkii
Bacteroides congonensis
Bacteroides faecichinchillae
Bacteroides ovatus
Bacteroides thetaiotaomicron
Bacteroides xylanisolvens
Enterococcus asini
prevotella sp 900545525prevotella sp 900545525
prevotella MGBC 104324prevotella MGBC 104324
Bacteroides MGBC 143234Bacteroides MGBC 143234
Oscillibacter MGBC 104191Oscillibacter MGBC 104191
paraprevotella MGBC 133623paraprevotella MGBC 133623
paraprevotella MGBC 135601paraprevotella MGBC 135601
phocaiecola sp002493165phocaiecola sp002493165
phocaeicola MGBC 116964phocaeicola MGBC 116964

Revision editor(s): Barrakat

Experiment 2


Needs review

Curated date: 2024/03/20

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Always Dextrose Day 0 Abx
Group 1 name Corresponds to the case (exposed) group for case-control studies
Always Dextrose Day 5 Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Always Dextrose plus amoxicillin fecal pellets that were collected on day 5
Group 0 sample size Number of subjects in the control (unexposed) group
9
Group 1 sample size Number of subjects in the case (exposed) group
10

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
decreased

Experiment 3


Needs review

Curated date: 2024/03/20

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Always Dextrose Day 9 Post Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Always Dextrose without amoxicillin fecal pellets that were collected on day 9
Group 1 sample size Number of subjects in the case (exposed) group
3

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Experiment 4


Needs review

Curated date: 2024/03/20

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Always Dextrose Day 14 Post Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Always Dextrose without amoxicillin fecal pellets that were collected on day 14
Group 1 sample size Number of subjects in the case (exposed) group
7

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Experiment 5


Needs review

Curated date: 2024/03/20

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Always Dextrose Day 5 Abx
Group 1 name Corresponds to the case (exposed) group for case-control studies
Always Dextrose Day 9 Post A Pbx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Always Dextrose without amoxicillin fecal pellets that were collected on day 9
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
3

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
decreased

Experiment 6


Needs review

Curated date: 2024/03/20

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Always Dextrose Day 14 Post Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Always Dextrose without amoxicillin fecal pellets that were collected on day 14
Group 1 sample size Number of subjects in the case (exposed) group
7

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Experiment 7


Needs review

Curated date: 2024/03/20

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Always Dextrose Day 9 Post Abx
Group 0 sample size Number of subjects in the control (unexposed) group
3

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Experiment 8


Needs review

Curated date: 2024/03/20

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Always Oats Day 0 Abx
Group 1 name Corresponds to the case (exposed) group for case-control studies
Always oats Day 5 Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Always Oats with amoxicillin fecal pellets that were collected on day 5
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
6

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
decreased

Experiment 9


Needs review

Curated date: 2024/03/20

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Always oats Day 11 Post Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Always oats without amoxicillin fecal pellets that were collected on day 11
Group 1 sample size Number of subjects in the case (exposed) group
3

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Experiment 10


Needs review

Curated date: 2024/03/20

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Always oats Day 14 Post Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Always oats without amoxicillin fecal pellets that were collected on day 14
Group 1 sample size Number of subjects in the case (exposed) group
4

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Experiment 11


Needs review

Curated date: 2024/03/20

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Always Oats Day 5 Abx
Group 1 name Corresponds to the case (exposed) group for case-control studies
Always Oats Day 11 Post Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Always oats without amoxicillin fecal pellets that were collected on day 11
Group 0 sample size Number of subjects in the control (unexposed) group
6
Group 1 sample size Number of subjects in the case (exposed) group
3

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Experiment 12


Needs review

Curated date: 2024/03/20

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Always oats Day 5 Abx
Group 1 name Corresponds to the case (exposed) group for case-control studies
Always oats Day 14 Post Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Always oats without amoxicillin fecal pellets that were collected on day 14
Group 1 sample size Number of subjects in the case (exposed) group
4

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Experiment 13


Needs review

Curated date: 2024/03/20

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Always oats Day 11 Post Abx
Group 0 sample size Number of subjects in the control (unexposed) group
3

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Experiment 14


Needs review

Curated date: 2024/03/21

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Prophylactic oats Day 0 Abx
Group 1 name Corresponds to the case (exposed) group for case-control studies
Prophylactic oats Day 6 Post Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Prophylactic oats without amoxicillin fecal pellets that were collected on day 6
Group 0 sample size Number of subjects in the control (unexposed) group
9
Group 1 sample size Number of subjects in the case (exposed) group
3

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Experiment 15


Needs review

Curated date: 2024/03/21

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Prophylactic oats Day 14 Post Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Prophylactic oats without amoxicillin fecal pellets that were collected on day 14

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Experiment 16


Needs review

Curated date: 2024/03/21

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Prophylactic oats Day 6 Post Abx
Group 0 sample size Number of subjects in the control (unexposed) group
3

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Experiment 17


Needs review

Curated date: 2024/03/21

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Recovery oats Day 0 Abx
Group 1 name Corresponds to the case (exposed) group for case-control studies
Recovery oats Day 5 Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Recovery oats with amoxicillin fecal pellets that were collected on day 5
Group 0 sample size Number of subjects in the control (unexposed) group
6
Group 1 sample size Number of subjects in the case (exposed) group
10

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
decreased

Experiment 18


Needs review

Curated date: 2024/03/21

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Recovery oats Day 7 Post Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Recovery oats without amoxicillin fecal pellets that were collected on day 7
Group 1 sample size Number of subjects in the case (exposed) group
4

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Experiment 19


Needs review

Curated date: 2024/03/21

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Recovery oats Day 14 Post Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Recovery oats without amoxicillin fecal pellets that were collected on day 14

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Experiment 20


Needs review

Curated date: 2024/03/21

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Recovery oats Day 5 Abx
Group 1 name Corresponds to the case (exposed) group for case-control studies
Recovery oats Day 7 Post Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Recovery oats without amoxicillin fecal pellets that were collected on day 7
Group 0 sample size Number of subjects in the control (unexposed) group
10

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased

Experiment 21


Needs review

Curated date: 2024/03/21

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Recovery oats Day 14 Post Abx
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Recovery oats without amoxicillin fecal pellets that were collected on day 14

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased

Experiment 22


Needs review

Curated date: 2024/03/21

Curator: Barrakat

Revision editor(s): Barrakat, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Recovery oats Day 7 Post Abx
Group 0 sample size Number of subjects in the control (unexposed) group
4

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
decreased