1. Biochemistry and Chemical Biology
  2. Microbiology and Infectious Disease
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A selective gut bacterial bile salt hydrolase alters host metabolism

  1. Lina Yao
  2. Sarah Craven Seaton
  3. Sula Ndousse-Fetter
  4. Arijit A Adhikari
  5. Nicholas DiBenedetto
  6. Amir I Mina
  7. Alexander S Banks
  8. Lynn Bry
  9. A Sloan Devlin  Is a corresponding author
  1. Harvard Medical School, United States
  2. Brigham and Women’s Hospital, United States
Research Article
Cite this article as: eLife 2018;7:e37182 doi: 10.7554/eLife.37182
9 figures, 1 table, 1 data set and 2 additional files

Figures

Enzymatic activity of gut bacterial bile salt hydrolase (BSH) enzymes.

(A) BSH cleave the amide bond linking primary bile acids to taurine or glycine. (B) Structures of the two most abundant murine-conjugated bile acids, tauro-β-muricholic acid (TβMCA) and tauro-cholic acid (TCA).

https://doi.org/10.7554/eLife.37182.003
Figure 2 with 3 supplements
Identification of selective BSH activity in the human gut bacterial phylum Bacteroidetes.

(A) Deconjugation ability of twenty prevalent Bacteroidetes strains and two Firmicutes strains found in the human gut represented as heat maps. Individual strains were incubated for 48 hr total with a group of glyco- or tauro-conjugated bile acids found in human and murine GI tracts. G (glyco-), T (tauro-), CA (cholic acid), CDCA (chenodeoxycholic acid), UDCA (ursodeoxycholic acid), DCA (deoxycholic acid), LCA (lithocholic acid), βMCA (β-muricholic acid). Assays were performed in biological duplicate. Group I (red): Bacteroidetes species that deconjugate primary bile acids based on steroidal core structure (C12 = H but not C12 = OH); Group II (gray): species that deconjugate based on amino acid conjugate; Group III (blue): species that deconjugate all bile acid substrates; Group IV (black): no deconjugation observed. (B) Representative UPLC-MS timecourses for deconjugation of TDCA and TLCA showing that steady state has been reached by 48 hr. (C) Representative UPLC-MS traces showing that Bacteroides thetaiotaomicron wild-type (Bt WT) and BtΔ1259 deconjugate TUDCA, whereas BtΔ2086 does not. BtΔ2086,2086 + recovered the deconjugation function while the BtΔ2086,CTRL +control strain containing an empty pNBU2 vector did not, demonstrating that BT2086 is responsible for bile salt hydrolase activity in Bt. (D) Representative UPLC-MS traces showing that Bt WT deconjugates the murine primary bile acid TβMCA but not TCA, whereas BTΔ2086 (Bt KO) does not deconjugate either bile acid.

https://doi.org/10.7554/eLife.37182.004
Figure 2—figure supplement 1
Biological duplicates of percent deconjugation at 48 hr, glyco-conjugated bile acids.
https://doi.org/10.7554/eLife.37182.005
Figure 2—figure supplement 2
Biological duplicates of percent deconjugation at 48 hr, tauro-conjugated bile acids.
https://doi.org/10.7554/eLife.37182.006
Figure 2—figure supplement 3
Deconjugation heat maps, 24 hr timepoint.

Assays were performed in biological duplicate. Group I (red): Bacteroidetes species that deconjugate primary bile acids based on steroidal core structure (C12 = H but not C12 = OH); Group II (gray): species that deconjugate based on amino acid conjugate; Group III (blue): species that deconjugate all bile acid substrates; Group IV (black): no deconjugation observed.

https://doi.org/10.7554/eLife.37182.007
Homology-based classification of Bacteroidetes strains and putative BSH genes.

(A) Phylogenetic tree of 20 Bacteroidetes strains using alignment-based whole proteome phylogeny (PhyloPhlAn). Bacteroidetes strains from Group II (gray; deconjugation based on amino acid) form a partial clade, while Group I (red) and Group III (blue) strains do not separate into distinct clades. (B) Phlyogenetic tree of candidate Bacteroidetes BSH genes. A search for BLAST-P matches of BT2086 identified an ortholog in 19 of the 20 Bacteroidetes species assayed. Numbers next to the branches represent the percentage of replicate trees in which this topology was reached in a bootstrap test of 1000 replicates. No significant clustering of Bacteroidetes strains into clades based on enzymatic activity was observed. Scale bars represent number of nucleotide substitutions per site.

https://doi.org/10.7554/eLife.37182.008
Figure 4 with 2 supplements
Monocolonization of GF mice with BT WT and Bt KO results in predictably altered bile acid pools.

(A) Male germ-free C57BL/6 mice were monocolonized with either Bt WT or BT KO and fed a high-fat diet (HFD) for 4 weeks (monocolonization experiment). In a second experiment, monocolonized mice (Bt WT or Bt KO) or GF mice were fed a HFD for 4 weeks and transferred to CLAMS during the 4th week to monitor metabolic inputs and outputs (CLAMS experiment). (B) Bile acid profiling using UPLC-MS revealed that Bt KO-colonized mice displayed higher levels of TβMCA in cecal contents than Bt WT-colonized mice while the levels of TCA remained the same between the two groups. βMCA levels were significantly higher in Bt WT-colonized animals and no CA was detected in any group (red boxes). (C–D) Similar changes were observed in feces (C) and distal ileum (D), although no βMCA was observed in any group in the distal ileum. Data are presented as mean ± SEM. BA (bile acid). For the monocolonization experiment, n = 12 mice per group, Welch’s t test. For the CLAMS experiment, n = 7–8 mice per group, one-way ANOVA followed by Tukey’s multiple comparisons test. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001.

https://doi.org/10.7554/eLife.37182.009
Figure 4—figure supplement 1
Confirmation of in vivo expression of Bt BSH.

(A) Bt BSH qRT-PCR results from mouse cecal contents from CLAMS experiment on day 32, using 16S ribosomal RNA as the housekeeping gene. (B) Gel electroporation results of the same qRT-PCR products. Lane 1–8, amplification of 16S ribosomal RNA qPCR fragment from eight Bt WT-colonized mice; lane 9–16, amplification of 16S ribosomal RNA qPCR fragment from eight Bt KO-colonized mice; lane 17–24, amplification of Bt BSH qPCR fragment from eight Bt WT-colonized mice; lane 25–32, amplification of Bt BSH qPCR fragment from eight Bt KO-colonized mice.

https://doi.org/10.7554/eLife.37182.010
Figure 4—figure supplement 2
Bile acid composition in the liver and plasma.

No significant differences in bile acid pool composition were noted in the liver (A) or plasma (B). Data are presented as mean ± SEM. BA (bile acid). For the monocolonization experiment, n = 12 mice per group, Welch’s t test.

https://doi.org/10.7554/eLife.37182.011
Bt BSH colonization status affects weight gain and lipid profiles.

(A) Weight-matched, male, germ-free C57BL/6 mice monocolonized with Bt KO gained less weight during a 4-week diet challenge than Bt WT-colonized mice. n = 12 mice per group, multiple t test analysis using the FDR method (Q = 1%), ***p<0.001 (FDR-corrected). (B) Microbial biomass did not differ between the Bt WT and Bt KO strains in GF mice. For the monocolonization experiment, frozen feces (day 2 post-colonization) were plated to determine colony-forming units per gram. For the CLAMS experiment, fresh feces (day 2) were plated. Cecal contents collected at sacrifice (day 32) were also plated to confirm maintenance of monocolonized status throughout the experiment. No CFU were detected in the GF group. n = 6 samples per group, Mann-Whitney test. (C–D) Lipid levels in plasma and blood, monocolonization experiment. (C) Triglyceride, free fatty acid, and cholesterol levels were lower in the plasma of Bt KO-colonized mice. (D) Levels of triglycerides were reduced in Bt KO-colonized mice. No significant differences in liver free fatty acids, liver cholesterol, or liver cholesterol esters were observed. n = 12 mice per group, Welch’s t test. (E) Representative H and E staining of liver sections (monocolonization experiment). Bt KO-colonized mice displayed decreased liver steatosis. Scale bars, 100 μm. Yellow arrows indicate representative white lipid droplets. n = 4 mice per group. All data are presented as mean ± SEM. *p<0.05, **p<0.01.

https://doi.org/10.7554/eLife.37182.012
Figure 6 with 1 supplement
Bt WT-colonized, Bt KO-colonized, and GF mice display distinct metabolic phenotypes.

Mice were monitored in metabolic cages during the final week of the CLAMS experiment and continued on a HFD. Mice were allowed to acclimate to cages for 24 hr prior to the start of data acquisition. (A) Respiratory exchange ratio (RER). One-way ANOVA followed by Tukey’s multiple comparisons test, *p<0.05. (B–C) Oxygen consumption and (B) carbon dioxide production (C). ANCOVA with lean body mass as the covariate, *p<0.05. (D) Regression plot of energy expenditure as a function of lean mass. Energy expenditure (EE) is given by EE = CV x VO2, where CV = 3.815 + 1.232(RER). For the Bt WT-colonized group, *p=0.0168, indicating the slope is significantly non-zero. For the Bt KO-colonized and GF groups, p=0.6806 and p=0.6930, respectively. For (A–C), data are represented as mean ± SEM, where the number of samples is the number of mice. For Bt WT-colonized group, n = 7 mice, and for Bt KO-colonized and GF groups, n = 8 mice per group.

https://doi.org/10.7554/eLife.37182.013
Figure 6—figure supplement 1
Locomotor activity.

(A) Locomotor activity was measured by the number of beam breaks. Each dot represents the mean for a given mouse. Data are represented as mean ± SEM, where the number of samples is the number of mice. (B) Hourly plot in which each dot represents the mean for a group of mice (Bt WT-colonized, Bt KO-colonized, or GF) at a given time point and error bars are omitted for clarity. For Bt WT-colonized group, n = 7 mice, and for Bt KO-colonized and GF groups, n = 8 mice per group.

https://doi.org/10.7554/eLife.37182.014
Detergent properties of ileal bile acid pools do not significantly differ.

(A) Bile acid pools were reconstituted in vitro using the mean values measured from the distal ileum of Bt KO- and Bt WT-colonized mice (CLAMS experiment). Pools were added to four different concentrations of a mixture of fats representative of lipolysis products in the small intestine and incubated under physiologically relevant conditions (37˚C, pH 6.3). SDS (sodium dodecyl sulfate) was used as a positive control at its critical micelle concentration (8.2 mM). No significant differences in solubilization effects as measured by OD400 were observed at 5 hr and 24 hr time points. n = 3 biological replicates per condition, one-way ANOVA followed by Tukey’s multiple comparisons test. (B) No significant differences were observed in energy content of feces collected from Bt KO-colonized, Bt WT-colonized, or GF mice (CLAMS experiment). Feces were collected from CLAMS cages. n = 7–8 mice per group, one-way ANOVA followed by Tukey’s multiple comparisons test. Each data point represents the mean of two calorimetry experiments per mouse. All data are presented as mean ± SEM.

https://doi.org/10.7554/eLife.37182.015
Figure 8 with 2 supplements
Global transcription analysis revealed changes in metabolism, circadian rhythm, immune response, and histone modification pathways in the distal ileum of Bt KO- vs.

Bt WT-colonized mice (monocolonization experiment). (A) Log2-transformed fold change in normalized RNA-seq gene counts in the distal ileum of GF mice colonized with Bt KO relative to mice colonized with Bt WT. MA plot showing the relationship between average concentration (logCPM) and fold-change (logFC) across the genes. Each gene is represented by a black dot. Significant differentially expressed genes are colored in red. The blue lines represent logFC ±0.5 threshold. (B) Multidimensional scaling (MDS) plot of two monocolonized groups (S1-S6: Bt WT-colonized mice; S7-S12: Bt KO-colonized mice) derived from RNA-Seq normalized gene counts, showing that samples segregate based on colonization status (Bt WT vs. Bt KO). (C) Changes in the host distal ileum transcriptome between Bt WT- and Bt KO-colonized conditions. Heatmap shows statistically significant fold changes of genes identified using differential expression analysis (FDR ≤ 0.05 and absolute Log2 fold-change ≥0.5). n = 6 samples for each group. (D–E) Gene expression in the distal ileum as measured by qPCR. Data are presented as mean ± SEM; n = 12 mice/group; *p<0.05, Welch’s t test.

https://doi.org/10.7554/eLife.37182.016
Figure 8—figure supplement 1
RNA-seq workflow.
https://doi.org/10.7554/eLife.37182.017
Figure 8—figure supplement 2
RNA-seq, biological coefficient of variation.

Low variation within biological replicates was observed.

https://doi.org/10.7554/eLife.37182.018
Bt BSH status affects transcription of genes in FXR-dependent and FXR-independent pathways.

(A) Plasma glucose and hormone levels, CLAMS experiment. Mice were fasted for 4 hr prior to terminal blood draw. n = 7–8 mice per group, data are presented as mean ± SEM, one-way ANOVA followed by Tukey’s multiple comparisons test, *p<0.05, **p<0.01. (B) Expression of genes in FXR-mediated pathways in the distal ileum was not significantly different between Bt KO- and Bt WT-colonized mice as measured by qPCR. (C) Gene expression in the liver as measured by qPCR. Genes in both FXR-mediated pathways (Nr0b2/Shp, Cyp7a1, Apoc2) and pathways not known to be mediated by FXR (Cd36, Tnf/Tnfα, Adgre1/Emr1, Sphk2) were significantly affected by Bt BSH status. (B–C) Data are presented as mean ± SEM; n = 12 mice/group; *p<0.05, **p<0.001, ns - not significant, Welch’s t test.

https://doi.org/10.7554/eLife.37182.019

Tables

Key resources table
Reagent type (species)
or resource
DesignationSource or referenceIdentifiersAdditional information
Strain, strain background
(Bacteroides thetaiotaomicron)
VPI 5482 [CIP 104206T,
E50, NCTC 10582]
ATCCATCC 29148
Strain, strain background
(Bacteroides caccae)
VPI 3452A
[CIP 104201T, JCM 9498]
ATCCATCC 43185
Strain, strain background
(Bacteroides ovatus)
[NCTC 11153]ATCCATCC 8483
Strain, strain background
(Bacteroides vulgatus)
[NCTC 11154]ATCCATCC 8482
Strain, strain background
(Bacteroides uniformis)
Not applicableATCCATCC 8492
Strain, strain background
(Parabacteroides distasonis)
[NCTC 11152]ATCCATCC 8503
Strain, strain background
(Bacteroides fragilis)
VPI 2553
[EN-2; NCTC 9343]
ATCCATCC 25285
Strain, strain background
(Parabacteroides merdae)
VPI T4-1
[CIP 104202T, JCM 9497]
ATCCATCC 43184
Strain, strain background
(Bacteroides eggerthii)
Not applicableDSMZDSM-20697
Strain, strain background
(Bacteroides finegoldii)
199DSMZDSM-17565
Strain, strain background
(Bacteroides dorei)
175DSMZDSM-17855
Strain, strain background
(Bacteroides dorei)
5_1_36/D4BEIHM-29
Strain, strain background
(Bacteroides sp.)
1_1_6BEIHM-23
Strain, strain background
(Bacteroides sp.)
9_1_42FAABEIHM-27
Strain, strain background
(Bacteroides sp.)
D2BEIHM-28
Strain, strain background
(Bacteroides sp.)
3_1_19BEIHM-19
Strain, strain background
(Bacteroides sp.)
2_1_16BEIHM-58
Strain, strain background
(Parabacteroides sp.)
20_3 (Deposited as
Bacteroides sp., Strain 20_3)
BEIHM-166
Strain, strain background
(Bacteroides sp.)
2_1_22BEIHM-18
Strain, strain background
(Bacteroides fragilis)
638ROtherGift from Seth
Rakoff-Nahoum, Boston
Children's Hospital
Strain, strain background
(Lactobacillus plantarum)
NCIMB 8826
[Hayward 3A, WCFS1]
ATCCBAA-793
Strain, strain background
(Clostridium perfringens)
NCTC 8237 [ATCC 19408,
CIP 103 409, CN 1491,
NCIB 6125, NCTC 6125, S 107]
ATCCATCC 13124
Strain, strain background
(Escherichia coli S17-1 λ pir)
E. coli S17-1 λ pirOtherGift from Michael Fischbach,
Stanford University
Strain, strain background
(B. thetaiotaomicron
VPI-5482 Δtdk)
Bt WTOtherGift from Michael Fischbach,
Stanford University
Strain, strain background
(B. thetaiotaomicron
VPI-5482 ΔtdkΔ2086)
BtΔ2086This paperSee Materials and methods,
‘Construction of Bacteroides
thetaiotaomicron
knockout mutants’
Strain, strain background
(B. thetaiotaomicron
VPI-5482 ΔtdkΔ1259)
BtΔ1259This paperSee Materials and methods,
‘Construction of Bacteroides
thetaiotaomicron
knockout mutants’
Strain, strain background
(B. thetaiotaomicron
VPI-5482 Δtdk Δ2086
pNBU2_erm_us1311_BT2086)
BtΔ2086,2086+This paperSee Materials and methods,
‘Construction of Bacteroides
thetaiotaomicron
complementation strains’
Strain, strain background
(B. thetaiotaomicron
VPI-5482 Δtdk Δ2086
pNBU2_erm_us1311_CTRL)
BtΔ2086,CTRL+This paperSee Materials and methods, ‘
Construction of Bacteroides
thetaiotaomicron
complementation strains’
Recombinant DNA reagentpExchange-tdk
(plasmid)
PMID: 18611383
Recombinant DNA reagentpNBU2_erm_us1311
(plasmid)
PMID: 25574022
Sequence-based
reagent (knockout primer pairs)
BT2086_UFEurofins GenomicsGAA AGA AGA TAA CAT TCG AGT
CGA CAT CCA AAC CCA GTG
TGA ACT
Sequence-based
reagent (knockout primer pairs)
BT2086_UREurofins GenomicsCAT ATT ACT TCC AAA TTA AAT
AGT TGA TAC TC
Sequence-based
reagent (knockout primer pairs)
BT2086_DFEurofins GenomicsGAG TAT CAA CTA TTT AAT TTG
GAA GTA ATA TGT AGT CGA TAG
TTA GTT ATG TGG TAA G
Sequence-based
reagent (knockout primer pairs)
BT2086_DREurofins GenomicsCCA CCG CGG TGG CGG CCG
CTC TAG AAG CAG ACG TTA TCC
TGG TTT C
Sequence-based
reagent
(knockout primer pairs)
BT1259_UFEurofins GenomicsGAA AGA AGA TAA CAT TCG AGT
CGA CGG ATG ATT ATT GCC CCA
TTT TG
Sequence-based
reagent
(knockout primer pairs)
BT1259_UREurofins GenomicsCGT ACA CAT AAT TTC GAT TTT
TAG TTA TAG
Sequence-based
reagent
(knockout primer pairs)
BT1259_DFEurofins GenomicsCTA TAA CTA AAA ATC GAA ATT
ATG TGT ACG TAA ATT GAT AGC
AGC TTG CTG C
Sequence-based
reagent
(knockout primer pairs)
BT1259_DREurofins GenomicsCCA CCG CGG TGG CGG CCG
CTC TAG ACG TTT TTC TAC CGG
ACG AAT C
Sequence-based
reagent (complementation
primer pairs)
us1311-BT-For-NdeIEurofins GenomicsGGG TCC ATA TGA AGA AAA AAC
TTA CGG GTG TTG C
Sequence-based reagent
(complementation
primer pairs)
BT-Rev-XbaIEurofins GenomicsCTA GTC TAG ACT ACA TCA CCG
GAG TTT CGA A
Sequence-based
reagent (diagnostic primer)
pExchange_seq_UFEurofins GenomicsCGG TGA TCT GGC ATC TTT CT
Sequence-based
reagent (diagnostic primer)
pExchange_seq_DREurofins GenomicsAAC GCA CTG AGA AGC CCT TA
Sequence-based
reagent (diagnostic primer)
BT2086_seq_F1Eurofins GenomicsCAA CTG TCC GGG TGA ATA TAA AG
Sequence-based
reagent (diagnostic primer)
BT2086_seq_F2Eurofins GenomicsGAA GTT TTC GTT GGG TGA ATG
Sequence-based
reagent (diagnostic primer)
BT1259_seq_F1Eurofins GenomicsAGA AGG TAC ATC GCC TGT AC
Sequence-based
reagent (diagnostic primer)
BT1259_seq_F2Eurofins GenomicsTAC TAT TCA CGC ACC ACA CC
Sequence-based
reagent (diagnostic primer)
pNBU2_UNIV-FEurofins GenomicsTAA CGG TTG TGG ACA ACA AG
Sequence-based
reagent (diagnostic primer)
pNBU2_UNIV-REurofins GenomicsCAC AAT ATG AGC AAC AAG GAA TCC
Sequence-based
reagent (qRT-PCR primer)
qBTBSH_FEurofins GenomicsGCGTGCGGGACACAATAAAG
Sequence-based
reagent (qRT-PCR primer)
qBTBSH_REurofins GenomicsTAGCCTGTTGCGATTACGCT
Sequence-based
reagent (qRT-PCR primer)
qBT16s_FEurofins GenomicsGTGAGGTAACGGCTCACCAA
Sequence-based
reagent (qRT-PCR primer)
qBT16s_REurofins GenomicsCTGCCTCCCGTAGGAGTTTG

Data availability

RNA-Seq data are deposited in the Gene Expression Omnibus (GEO) database (accession GSE112571). All other data generated or analyzed during this study are included in the manuscript and supporting files.

The following data sets were generated
  1. 1
    A selective gut bacterial bile salt hydrolase alters host metabolism
    1. Yao L
    2. Devlin AS
    (2018)
    Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE112571).

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