Amelioration of Colitis by a Gut Bacterial Consortium Producing Anti-Inflammatory Secondary Bile Acids

From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-6-4
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Zhou C, Wang Y, Li C, Xie Z, Dai L
Journal
Microbiology spectrum
Year
2023
Keywords:
bacterial consortium, colitis, gut microbiome, metabolomics, secondary bile acids, targeted metabolomics
The Integrative Human Microbiome Project and other cohort studies have indicated that inflammatory bowel disease is accompanied by dysbiosis of gut microbiota, decreased production of secondary bile acids, and increased levels of primary bile acids. Secondary bile acids, such as ursodeoxycholic acid (UDCA) and lithocholic acid (LCA), have been reported to be anti-inflammatory, yet it remains to be studied whether introducing selected bacteria strains to restore bile acid metabolism of the gut microbiome can alleviate intestinal inflammation. In this study, we screened human gut bacterial strains for bile acid metabolism and designed a consortium of three species, including Clostridium AP sp000509125, Bacteroides ovatus, and Eubacterium limosum, and named it BAC (bile acid consortium). We showed that the three-strain gut bacterial consortium BAC is capable of converting conjugated primary bile acids taurochenodeoxycholic acid and glycochenodeoxycholic acid to secondary bile acids UDCA and LCA in vitro. Oral gavage treatment with BAC in mice resulted in protective effects against dextran sulfate sodium (DSS)-induced colitis, including reduced weight loss and increased colon length. Furthermore, BAC treatment increased the fecal level of bile acids, including UDCA and LCA. BAC treatment enhanced intestinal barrier function, which may be attributed to the increased activation of the bile acid receptor TGR5 by secondary bile acids. Finally, we examined the remodeling of gut microbiota by BAC treatment. Taken together, the three-strain gut bacterial consortium BAC restored the dysregulated bile acid metabolism and alleviated DSS-induced colitis. Our study provides a proof-of-concept demonstration that a rationally designed bacterial consortium can reshape the metabolism of the gut microbiome to treat diseases. IMPORTANCE Secondary bile acids have been reported to be anti-inflammatory, yet it remains to be studied whether introducing selected bacteria strains to restore bile acid metabolism of the gut microbiome can alleviate intestinal inflammation. To address this gap, we designed a consortium of human gut bacterial strains based on their metabolic capacity to produce secondary bile acids UDCA and LCA, and we evaluated the efficacy of single bacterial strains and the bacterial consortium in treating the murine colitis model. We found that oral gavage of the bacterial consortium to mice restored secondary bile acid metabolism to increase levels of UDCA and LCA, which induced the activation of TGR5 to improve gut-barrier integrity and reduced the inflammation in murine colitis. Overall, our study demonstrates that rationally designed bacterial consortia can reshape the metabolism of the gut microbiome and provides novel insights into the application of live biotherapeutics for treating IBD.

Experiment 1


Reviewed Marked as Reviewed by Svetlana up on 2024-6-4

Curated date: 2024/03/15

Curator: Victoria

Revision editor(s): Victoria

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
Colitis Colitides,colitis,colitis (disease),colon inflammation,inflammation of colon,Colitis
Group 0 name Corresponds to the control (unexposed) group for case-control studies
DSS Group (Day 7)
Group 1 name Corresponds to the case (exposed) group for case-control studies
DSS + BAC Group (Day 7)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Mice were given dextran sulfate sodium (DSS) to induce Colitis and then treated with Bile Acid Consortium (BAC).
Group 0 sample size Number of subjects in the control (unexposed) group
7
Group 1 sample size Number of subjects in the case (exposed) group
7

Lab analysis

Sequencing type
WMS
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
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
LEfSe
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
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2


Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-6-4

Curated date: 2024/03/15

Curator: Victoria

Revision editor(s): Victoria

Source: Figure 5C

Description: Bacterial taxa identified as differentially abundant between the untreated group (DSS) and the BAC treatment group (DSS + BAC) by LEfSe. Green indicates bacterial taxa whose abundance was higher in the DSS + BAC group; red indicates otherwise.

Abundance in Group 1: increased abundance in DSS + BAC Group (Day 7)

NCBI Quality ControlLinks
Bacilli
Bacteroidales
Bacteroides ovatus
Bacteroidia
Bacteroidota
Barnesiella viscericola
Barnesiellaceae
Bifidobacterium animalis
Lactobacillales
Muribaculaceae
Muribaculum intestinale
Lactobacillaceae
Ligilactobacillus murinus

Revision editor(s): Victoria

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-6-4

Curated date: 2024/03/15

Curator: Victoria

Revision editor(s): Victoria

Source: Figure 5C

Description: Bacterial taxa identified as differentially abundant between the untreated group (DSS) and the BAC treatment group (DSS + BAC) by LEfSe. Green indicates bacterial taxa whose abundance was higher in the DSS + BAC group; red indicates otherwise.

Abundance in Group 1: decreased abundance in DSS + BAC Group (Day 7)

NCBI Quality ControlLinks
Alistipes finegoldii
Alistipes shahii
Bacillota
Betaproteobacteria
Bifidobacterium pseudolongum
Burkholderiales bacterium YL45
Clostridia
Clostridiaceae
Clostridiales bacterium CCNA10
Clostridioides difficile
Enterocloster bolteae
Erysipelotrichaceae
Erysipelotrichales
Erysipelotrichia
Faecalibacterium prausnitzii
Faecalibaculum rodentium
Flavonifractor plautii
Intestinimonas butyriciproducens
Lachnoclostridium phocaeense
Lachnospiraceae
Lachnospiraceae bacterium GAM79
Oscillibacter sp. PEA192
Peptostreptococcaceae
Pseudoflavonifractor
Pseudomonadota
Rikenellaceae
Roseburia hominis
Salmonella enterica
Eubacteriales
Oscillospiraceae

Revision editor(s): Victoria