Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome

Study information

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study design

laboratory experiment

Citation

PMID PubMed identifier for scientific articles.

39235366

DOI Digital object identifier for electronic documents.

https://doi.org/10.1128/msystems.00788-24

URI

Authors

Liu L, Ma L, Liu H, Zhao F, Li P, Zhang J, Lü X, Zhao X, Yi Y

Journal

mSystems

Year

2024

Keywords:

gut inflammation, gut microbiome remodeling, in vitro screening, systemic inflammation response syndrome

Systemic inflammatory response syndrome (SIRS) is a severe inflammatory response that can lead to organ dysfunction and death. Modulating the gut microbiome is a promising therapeutic approach for managing SIRS. This study assesses the therapeutic potential of the Xuanfei Baidu (XFBD) formula in treating SIRS. The results showed that XFBD administration effectively reduced mortality rates and inflammation in SIRS mice. Using 16S rRNA sequencing and fecal microbiota transplantation (FMT), we substantiated that the therapeutic effects of XFBD are partly attributed to gut microbiota modulation. We conducted in vitro experiments to accurately assess the gut microbiome remodeling effects of 51 compounds isolated from XFBD. These compounds exhibited varying abilities to induce a microbial structure that closely resembles that of the healthy control group. By quantifying their impact on microbial structure and clustering their regulatory patterns, we devised multiple gut microbiome remodeling compound (GMRC) cocktails. GMRC cocktail C, comprising aucubin, gentiopicroside, syringic acid, gallic acid, p-hydroxybenzaldehyde, para-hydroxybenzoic acid, and isoimperatorin, demonstrated superior efficacy in treating SIRS compared to a single compound or to other cocktails. Finally, in vitro experiments showcased that GMRC cocktail C effectively rebalanced bacteria composition in SIRS patients. This study underscores XFBD's therapeutic potential in SIRS and highlights the importance of innovative treatment approaches for this disease by targeting the gut microbiota.IMPORTANCEDeveloping effective treatment strategies for systemic inflammatory response syndrome (SIRS) is crucial due to its severe and often life-threatening nature. While traditional treatments like dexamethasone have shown efficacy, they also come with significant side effects and limitations. This study makes significant strides by demonstrating that the Xuanfei Baidu (XFBD) formula can substantially reduce mortality rates and inflammation in SIRS mice through effective modulation of the gut microbiota. By quantitatively assessing the impact of 51 compounds derived from XFBD on the gut microbiome, we developed a potent gut microbiome remodeling compound cocktail. This cocktail outperformed individual compounds and other mixtures in efficacy against SIRS. These findings highlight the potential of XFBD as a therapeutic solution for SIRS and underscore the critical role of innovative strategies targeting the gut microbiota in addressing this severe inflammatory condition.

Experiment 1

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Subjects

Location of subjects

China

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

Systemic inflammatory response syndrome Inflammatory Response Syndrome, Systemic,Sepsis Syndrome,SIRS,Systemic inflammatory response syndrome,systemic inflammatory response syndrome

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Control Group

Group 1 name Corresponds to the case (exposed) group for case-control studies

LPS-induced SIRS (systemic inflammatory response syndrome) group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Lipopolysaccharide-induced SIRS group represent the disease model receiving treatment. They serve as the primary target for testing the efficacy of therapeutic interventions aimed at reducing inflammation and restoring gut microbiota balance.

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

6

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

V3-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).

relative abundances

Statistical test

ANOVA

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.05

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

decreased

Experiment 2

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

LPS-induced SIRS (systemic inflammatory response syndrome) group

Group 1 name Corresponds to the case (exposed) group for case-control studies

FMT-L Group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

The (Xuanfei Baidu)XFBD-fed group containing live microbiota

Lab analysis

Statistical Analysis

Alpha Diversity

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

increased

Chao1 Abundance-based estimator of species richness

increased

Signature 1

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Source: Figure S2D

Description: Specific genus variations used for Fecal Microbiota Transplantation effects of SIRS mice.

Abundance in Group 1: decreased abundance in FMT-L Group

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unclassified Oscillospiraceae

Revision editor(s): Ifeanyisam

Experiment 3

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Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

FMT-L Group

Group 1 name Corresponds to the case (exposed) group for case-control studies

FMT-HK Group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

The (Xuanfei Baidu)XFBD-fed group containing heat-killed microbiota

Lab analysis

Statistical Analysis

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

decreased

Signature 1

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Source: Figure S2A

Description: Specific genus variations used for the Fecal Microbiota Transplantation effects on microbiota in SIRS mice.

Abundance in Group 1: increased abundance in FMT-HK Group

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Bacteroides

Revision editor(s): Ifeanyisam

Experiment 4

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Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

LPS-induced SIRS (systemic inflammatory response syndrome) group

Lab analysis

Statistical Analysis

Signature 1

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Source: Figure S2A

Description: Specific genus variations used for the Fecal Microbiota Transplantation effects on microbiota in SIRS mice.

Abundance in Group 1: increased abundance in FMT-HK Group

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Bacteroides

Revision editor(s): Ifeanyisam

Signature 2

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Source: Figure S2D

Description: Specific genus variations used for the Fecal Microbiota Transplantation effects on microbiota in SIRS mice.

Abundance in Group 1: decreased abundance in FMT-HK Group

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unclassified Oscillospiraceae

Revision editor(s): Ifeanyisam

Experiment 5

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Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

N (uncultured control)

Group 1 name Corresponds to the case (exposed) group for case-control studies

M (Uncultured Model)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

SIRS fecal sample before in vitro culture

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

Statistical Analysis

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

unchanged

Experiment 6

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Curated date: 2024/10/22

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

M (Uncultured Model Group)

Group 1 name Corresponds to the case (exposed) group for case-control studies

MD (Cultured Model Group)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Microbial composition from the fecal content of LPS-induced SIRS mice after the in vitro culturing process.

Lab analysis

Statistical Analysis

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

decreased

Experiment 7

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Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

ND (cultured control)

Group 1 name Corresponds to the case (exposed) group for case-control studies

MD (cultured model)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Microbial composition from the fecal content of LPS-induced SIRS mice after the in vitro culturing process

Lab analysis

Statistical Analysis

Signature 2

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Source: Figure S5D

Description: The relative abundance in genus levels after cocktail treatment

Abundance in Group 1: increased abundance in MD (cultured model)

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Bacteroides
Enterobacter
Enterococcus
Escherichia/Shigella sp.

Revision editor(s): Ifeanyisam

Experiment 8

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Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

MD (cultured model)

Group 1 name Corresponds to the case (exposed) group for case-control studies

C4 (Compound 4)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

XFBD (Xuanfei Baidu) derived compounds

Lab analysis

Statistical Analysis

Experiment 9

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Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

C50 (Compound 50)

Lab analysis

Statistical Analysis

Experiment 10

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Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

N

Group 1 name Corresponds to the case (exposed) group for case-control studies

M

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Cultured Model

Lab analysis

Statistical Analysis

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

raw counts

Statistical test

DESeq2

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

decreased

Chao1 Abundance-based estimator of species richness

decreased

Signature 1

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Source: Figure 5B

Description: A waterfall plot of significantly altered genus between model and control showing consistent trend in uncultured groups.

Abundance in Group 1: increased abundance in M

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Bacteroides
Proteus
Butyricimonas
Escherichia/Shigella sp.
Parabacteroides
Bilophila
Enterococcus
Clostridium
Asaccharospora
Thomasclavelia

Revision editor(s): Ifeanyisam

Signature 2

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Source: Figure 5B

Description: A waterfall plot of significantly altered genus between model and control showing consistent trend in uncultured groups

Abundance in Group 1: decreased abundance in M

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Allobaculum
Candidatus Saccharimonas
Ruminiclostridium
Turicibacter
uncultured Oscillospiraceae bacterium
ruminococcus 1ruminococcus 1
lachnospiraceae UCG-001lachnospiraceae UCG-001

Revision editor(s): Ifeanyisam

Experiment 11

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Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

ND

Group 1 name Corresponds to the case (exposed) group for case-control studies

MD

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Cultured model

Lab analysis

Statistical Analysis

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

relative abundances

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

Not specified

Signature 1

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Source: Figure 5B

Description: A waterfall plot of significantly altered genus between model and control showing consistent trend in cultured groups

Abundance in Group 1: increased abundance in MD

NCBI	Quality Control	Links
Bacteroides
Proteus
Butyricimonas
Escherichia/Shigella sp.
Parabacteroides
Clostridium
Bilophila
Enterococcus
Asaccharospora
Thomasclavelia

Revision editor(s): Ifeanyisam

Signature 2

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Source: Figure 5B

Description: A waterfall plot of significantly altered genus between model and control showing consistent trend in cultured groups

Abundance in Group 1: decreased abundance in MD

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Ruminiclostridium
ruminococcus 1ruminococcus 1
Allobaculum
Turicibacter
Candidatus Saccharimonas
uncultured Oscillospiraceae bacterium
lachnospiraceae UCG-001lachnospiraceae UCG-001

Revision editor(s): Ifeanyisam

Experiment 12

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

MD (cultured model)

Group 1 name Corresponds to the case (exposed) group for case-control studies

A2.1 (gut microbiome remodeling compound)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula

Lab analysis

Statistical Analysis

Statistical test

ANOVA

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

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Source: Figure S5D

Description: The relative abundance in genus levels after cocktail treatment

Abundance in Group 1: increased abundance in A2.1 (gut microbiome remodeling compound)

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Enterococcus

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Signature 2

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Source: Figure S5D

Description: The relative abundance in genus levels after cocktail treatment

Abundance in Group 1: decreased abundance in A2.1 (gut microbiome remodeling compound)

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Bacteroides
Enterobacter
Escherichia/Shigella sp.

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Experiment 13

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Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

A2.2(gut microbiome remodeling compound)

Lab analysis

Statistical Analysis

Alpha Diversity

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

increased

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

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Source: Figure S5D

Description: The relative abundance in genus levels after cocktail treatment

Abundance in Group 1: decreased abundance in A2.2(gut microbiome remodeling compound)

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Bacteroides
Enterobacter
Escherichia/Shigella sp.
Enterococcus

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Experiment 14

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

B2.1 (gut microbiome remodeling compound)

Lab analysis

Statistical Analysis

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

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Source: Figure S5D

Description: The relative abundance in genus levels after cocktail treatment

Abundance in Group 1: increased abundance in B2.1 (gut microbiome remodeling compound)

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Enterococcus

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Signature 2

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Source: Figure S5D

Description: The relative abundance in genus levels after cocktail treatment

Abundance in Group 1: decreased abundance in B2.1 (gut microbiome remodeling compound)

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Bacteroides
Enterobacter
Escherichia/Shigella sp.

Revision editor(s): Ifeanyisam

Experiment 15

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Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

PD1 (Patient sample 1 with DMSO)

Group 1 name Corresponds to the case (exposed) group for case-control studies

PC1 (Patient sample 1 treated with cocktail c)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Patient sample treated with cocktail c

Lab analysis

Statistical Analysis

Alpha Diversity

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

increased

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

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Source: Figure S6A

Description: The relative abundance in Phylum Levels

Abundance in Group 1: decreased abundance in PC1 (Patient sample 1 treated with cocktail c)

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Bacillota
Enterobacter

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Signature 2

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Source: Figure S6A

Description: The relative abundance in Phylum Levels

Abundance in Group 1: increased abundance in PC1 (Patient sample 1 treated with cocktail c)

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Pseudomonadota

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Experiment 16

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Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

PD2 (Patient sample 2 with DMSO)

Group 1 name Corresponds to the case (exposed) group for case-control studies

PC2 (Patient sample 2 treated with cocktail c)

Lab analysis

Statistical Analysis

Alpha Diversity

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

unchanged

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

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Source: Figure S6A and S6C

Description: The relative abundance in Phylum and genera levels

Abundance in Group 1: decreased abundance in PC2 (Patient sample 2 treated with cocktail c)

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Bacteroides
Bacteroidia
Parabacteroides
Pseudomonadota

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Signature 2

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Source: Figure S6A

Description: The relative abundance level in Phylum levels

Abundance in Group 1: increased abundance in PC2 (Patient sample 2 treated with cocktail c)

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Bacillota

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Experiment 17

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

PD4 (Patient sample 4 with DMSO)

Group 1 name Corresponds to the case (exposed) group for case-control studies

PC4 (Patient sample 4 treated with cocktail c)

Lab analysis

Statistical Analysis

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

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Source: Figure S6A and S6C

Description: the relative abundance in Phylum and genera levels

Abundance in Group 1: decreased abundance in PC4 (Patient sample 4 treated with cocktail c)

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Bacteroides
Enterobacter
Pseudomonadota
Bacteroidia

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Signature 2

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Source: figure S6A and S6C

Description: The relative abundance in Phylum and genera levels

Abundance in Group 1: increased abundance in PC4 (Patient sample 4 treated with cocktail c)

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Bacillota
Escherichia/Shigella sp.

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Experiment 18

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Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

PD5 (Patient sample 5 with DMSO)

Group 1 name Corresponds to the case (exposed) group for case-control studies

PC5 (Patient sample 5 treated with cocktail c)

Lab analysis

Statistical Analysis

Alpha Diversity

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

unchanged

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

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Source: Figure S6A

Description: The relative abundance in phylum levels

Abundance in Group 1: decreased abundance in PC5 (Patient sample 5 treated with cocktail c)

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Bacillota

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Signature 2

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Source: Figure S6A

Description: The relative abundance in phylum levels

Abundance in Group 1: increased abundance in PC5 (Patient sample 5 treated with cocktail c)

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Pseudomonadota

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Experiment 19

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

PD6 (Patient sample 6 with DMSO)

Group 1 name Corresponds to the case (exposed) group for case-control studies

PC6 (Patient sample 6 treated with cocktail c)

Lab analysis

Statistical Analysis

Alpha Diversity

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

unchanged

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

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Curated date: 2024/10/23

Curator: Ifeanyisam

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Source: Figure S6A and S6C

Description: The relative abundance in Phylum and genera levels

Abundance in Group 1: decreased abundance in PC6 (Patient sample 6 treated with cocktail c)

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Pseudomonadota
Parabacteroides

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Source: Figure S6A

Description: The relative abundance in Phylum levels

Abundance in Group 1: increased abundance in PC6 (Patient sample 6 treated with cocktail c)

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Bacillota

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Experiment 20

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

PD8 (Patient sample 8 with DMSO)

Group 1 name Corresponds to the case (exposed) group for case-control studies

PC8 (Patient sample 8 treated with cocktail c)

Lab analysis

Statistical Analysis

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

decreased

Signature 1

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Curator: Ifeanyisam

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Source: Figure S6A and S6C

Description: The relative abundance in Phylum and genera levels

Abundance in Group 1: decreased abundance in PC8 (Patient sample 8 treated with cocktail c)

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Pseudomonadota
Escherichia/Shigella sp.

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Signature 2

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Source: Figure S6A and S6C

Description: The relative abundance in Phylum and genera levels

Abundance in Group 1: increased abundance in PC8 (Patient sample 8 treated with cocktail c)

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Bacillota
Bifidobacterium

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Experiment 21

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

H (Healthy Volunteers)

Group 1 name Corresponds to the case (exposed) group for case-control studies

P (Patients with SIRS)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Patients with SIRS

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

8

Lab analysis

Statistical Analysis

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Source: Figure 8C

Description: Abundance comparison of key genera between SIRS patients and healthy volunteers.

Abundance in Group 1: increased abundance in P (Patients with SIRS)

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Enterococcus
Lactobacillus
Bacteroides
Enterobacter
Lachnoclostridium
Escherichia/Shigella sp.
Akkermansia
Pseudomonas
Ralstonia
Dysgonomonas

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Source: Figure 8C

Description: Abundance comparison of key genera between SIRS patients and healthy volunteers

Abundance in Group 1: decreased abundance in P (Patients with SIRS)

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Bifidobacterium
Streptococcus
Blautia
Fusicatenibacter
Faecalibacterium
Dorea
Agathobacter
Romboutsia

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Experiment 22

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Curated date: 2024/10/24

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

MD (cultured model)

Group 1 name Corresponds to the case (exposed) group for case-control studies

B2.2 (gut microbiome remodeling compound)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Gut Microbiome Remodeling Compound cocktail concentrations simplified from XFBD formula

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

Statistical Analysis

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

unchanged

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Source: Figure S5D

Description: The relative abundance in genus levels after cocktail treatment

Abundance in Group 1: increased abundance in B2.2 (gut microbiome remodeling compound)

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Enterococcus

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Signature 2

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Source: Figure S5D

Description: The relative abundance in genus levels after cocktail treatment

Abundance in Group 1: decreased abundance in B2.2 (gut microbiome remodeling compound)

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Bacteroides
Escherichia/Shigella sp.
Enterobacter

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Experiment 23

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

C2.1 (gut microbiome remodeling compound)

Lab analysis

Statistical Analysis

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

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Curated date: 2024/10/24

Curator: Ifeanyisam

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Source: Figure S5C and S5D

Description: The ratio in Phylum levels of gut microbiome remodeling compounds cocktails and relative abundance in genus levels after cocktail treatment

Abundance in Group 1: increased abundance in C2.1 (gut microbiome remodeling compound)

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Bacillota
Bacteroidota
Enterococcus

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Source: Figure S5D

Description: The relative abundance in genus levels after cocktail treatment

Abundance in Group 1: decreased abundance in C2.1 (gut microbiome remodeling compound)

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Bacteroides
Escherichia/Shigella sp.
Enterobacter

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Experiment 24

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

C2.2 (gut microbiome remodeling compound)

Lab analysis

Statistical Analysis

Alpha Diversity

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

increased

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

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Curated date: 2024/10/24

Curator: Ifeanyisam

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Source: Figure S5D

Description: The relative abundance in genus levels after cocktail treatment

Abundance in Group 1: decreased abundance in C2.2 (gut microbiome remodeling compound)

NCBI	Quality Control	Links
Escherichia/Shigella sp.
Bacteroides
Enterobacter

Revision editor(s): Ifeanyisam

Signature 2

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Source: Figure S5D

Description: The relative abundance in genus levels after cocktail treatment

Abundance in Group 1: increased abundance in C2.2 (gut microbiome remodeling compound)

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Enterococcus

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Experiment 25

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

D2.1 (gut microbiome remodeling compound)

Lab analysis

Statistical Analysis

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

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Curated date: 2024/10/24

Curator: Ifeanyisam

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Source: Figure S5C and S5D

Description: The ratio in Phylum levels of gut microbiome remodeling compounds cocktails and relative abundance in genus levels after cocktail treatment

Abundance in Group 1: increased abundance in D2.1 (gut microbiome remodeling compound)

NCBI	Quality Control	Links
Bacillota
Bacteroidota
Enterococcus

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Source: Figure S5D

Description: the relative abundance in genus levels after cocktail treatment

Abundance in Group 1: decreased abundance in D2.1 (gut microbiome remodeling compound)

NCBI	Quality Control	Links
Bacteroides
Escherichia/Shigella sp.
Enterobacter

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Experiment 26

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

D2.2 (gut microbiome remodeling compound)

Lab analysis

Statistical Analysis

Alpha Diversity

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

increased

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

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Curated date: 2024/10/24

Curator: Ifeanyisam

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Source: Figure S5D

Description: The relative abundance in genus levels after cocktail treatment

Abundance in Group 1: increased abundance in D2.2 (gut microbiome remodeling compound)

NCBI	Quality Control	Links
Enterococcus

Revision editor(s): Ifeanyisam

Signature 2

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Curated date: 2024/10/24

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Source: Figure S5D

Description: The relative abundance in genus levels after cocktail treatment

Abundance in Group 1: decreased abundance in D2.2 (gut microbiome remodeling compound)

NCBI	Quality Control	Links
Bacteroides
Escherichia/Shigella sp.
Enterobacter

Revision editor(s): Ifeanyisam

Experiment 27

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

E2.1 (gut microbiome remodeling compound)

Lab analysis

Statistical Analysis

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

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Curated date: 2024/10/24

Curator: Ifeanyisam

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Source: figure S5C

Description: The ratio in Phylum levels of gut microbiome remodeling compound cocktails

Abundance in Group 1: increased abundance in E2.1 (gut microbiome remodeling compound)

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Bacillota
Bacteroidota

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Signature 2

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Source: Figure S5D

Description: The relative abundance in genus levels after cocktail treatment

Abundance in Group 1: decreased abundance in E2.1 (gut microbiome remodeling compound)

NCBI	Quality Control	Links
Escherichia/Shigella sp.
Bacteroides
Enterobacter

Revision editor(s): Ifeanyisam

Experiment 28

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

E2.2 (gut microbiome remodeling compound)

Lab analysis

Statistical Analysis

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

EditHistoryDelete

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Your review change was submitted

Needs review

Curated date: 2024/10/24

Curator: Ifeanyisam

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Source: Figure S5D

Description: the relative abundance in genus levels after cocktail treatment

Abundance in Group 1: decreased abundance in E2.2 (gut microbiome remodeling compound)

NCBI	Quality Control	Links
Escherichia/Shigella sp.
Bacteroides
Enterobacter

Revision editor(s): Ifeanyisam

Experiment 29

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

F2.1 (gut microbiome remodeling compound)

Lab analysis

Statistical Analysis

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

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Your review change was submitted

Needs review

Curated date: 2024/10/24

Curator: Ifeanyisam

Revision editor(s): Ifeanyisam

Source: Figure S5D

Description: The relative abundance in genus levels after cocktail treatment

Abundance in Group 1: decreased abundance in F2.1 (gut microbiome remodeling compound)

NCBI	Quality Control	Links
Escherichia/Shigella sp.
Bacteroides
Enterobacter

Revision editor(s): Ifeanyisam

Experiment 30

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

F2.2 (gut microbiome remodeling compound)

Lab analysis

Statistical Analysis

Alpha Diversity

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

unchanged

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

EditHistoryDelete

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Curated date: 2024/10/24

Curator: Ifeanyisam

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Source: Figure S5D

Description: The relative abundance in genus levels after cocktail treatment

Abundance in Group 1: decreased abundance in F2.2 (gut microbiome remodeling compound)

NCBI	Quality Control	Links
Escherichia/Shigella sp.
Bacteroides
Enterobacter

Revision editor(s): Ifeanyisam