Analysis of Interactions between Endobiotics and Human Gut Microbiota Using In Vitro Bath Fermentation Systems

Yunfei Hu; Huahai Chen; Ping Li; Baiyuan Li; Linyan Cao; Changhui Zhao; Qing Gu; Yeshi Yin

doi:10.3791/59725

JoVE Journal > Immunology and Infection

Immunologie et infection

Analysis of Interactions between Endobiotics and Human Gut Microbiota Using In Vitro Bath Fermentation Systems

Published: August 23, 2019

doi:

10.3791/59725

Yunfei Hu¹, Huahai Chen¹, Ping Li², Baiyuan Li¹, Linyan Cao¹, Changhui Zhao¹, Qing Gu², Yeshi Yin¹

¹Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, College of Chemistry and Bioengineering,Hunan University of Science and Engineering, ²College of Food and Biological Engineering,Zhejiang Gongshang University

Summary

Described here is a protocol to investigate the interactions between endobiotics and human gut microbiota using in vitro batch fermentation systems.

Abstract

Human intestinal microorganisms have recently become an important target of research in promoting human health and preventing diseases. Consequently, investigations of interactions between endobiotics (e.g., drugs and prebiotics) and gut microbiota have become an important research topic. However, in vivo experiments with human volunteers are not ideal for such studies due to bioethics and economic constraints. As a result, animal models have been used to evaluate these interactions in vivo. Nevertheless, animal model studies are still limited by bioethics considerations, in addition to differing compositions and diversities of microbiota in animals vs. humans. An alternative research strategy is the use of batch fermentation experiments that allow evaluation of the interactions between endobiotics and gut microbiota in vitro. To evaluate this strategy, bifidobacterial (Bif) exopolysaccharides (EPS) were used as a representative xenobiotic. Then, the interactions between Bif EPS and human gut microbiota were investigated using several methods such as thin-layer chromatography (TLC), bacterial community compositional analysis with 16S rRNA gene high-throughput sequencing, and gas chromatography of short-chain fatty acids (SCFAs). Presented here is a protocol to investigate the interactions between endobiotics and human gut microbiota using in vitro batch fermentation systems. Importantly, this protocol can also be modified to investigate general interactions between other endobiotics and gut microbiota.

Introduction

Gut microbiota play an important role in the functioning of human intestines and in host health. Consequently, gut microbiota have recently become an important target for disease prevention and therapy¹. Moreover, gut bacteria interact with host intestinal cells and regulate fundamental host processes, including metabolic activities, nutrient availabilities, immune system modulation, and even brain function and decision-making²^,³. Endobiotics have considerable potential to influence the bacterial composition and diversity of gut microbiota. Thus, interactions between endobiotics and human gut microbiota have attracted increasing research attention⁴^,⁵^,⁶^,⁷^,⁸^,⁹.

It is difficult to evaluate interactions between endobiotics and human gut microbiota in vivo due to bioethics and economic constraints. For example, experiments investigating the interactions between endobiotics and human gut microbiota cannot be performed without permission of the Food and Drug Administration, and recruitment of volunteers is expensive. Consequently, animal models are often used for such investigations. However, the use of animal models is limited due to different microbiota compositions and diversity in animal- vs. human-associated communities. An alternative in vitro method to explore the interactions between endobiotics and human gut microbiota is through the use of batch culture experiments.

Exopolysaccharides (EPSs) are prebiotics that significantly contribute to the maintenance of human health¹⁰. Distinct EPSs that consist of different monosaccharide compositions and structures can exhibit distinct functions. Previous analyses have determined the composition of Bif EPSs, which are the representative xenobiotic targeted in the current study¹¹. However, host-associated metabolic effects have not been considered with regard to EPS composition and diversity.

The protocol described here uses the fecal microbiota from 12 volunteers to ferment Bif EPSs. Thin-layer chromatography (TLC), 16S rRNA gene high-throughput sequencing, and gas chromatography (GC) are then used in combination to investigate the interactions between EPSs and human gut microbiota. Distinct advantages of this protocol compared to in vivo experiments are its low cost and avoidance of interfering effects from the host’s metabolism. Furthermore, the described protocol can be used in other studies that investigate interactions between endobiotics and human gut microbiota.

Protocol

This protocol follows the guidelines of the ethics committee of Hunan University of Science and Engineering (Hunan, China), and the Zhejiang Gongshang University (Zhejiang, China).

1. Preparation of bacteria

Preparation of bifidobacterium medium broth
1. Combine the following components in 950 mL of distilled water: meat extract, 5 g/L; yeast extract, 5 g/L; casein peptone, 10 g/L; soytone, 5 g/L; glucose, 10 g/L; K₂HPO₄, 2.04 g/L; MgSO₄·7H₂O, 0.22 g/L; MnSO₄.H₂0, 0.05 g/L; NaCl, 5 g/L; Tween 80, 1 mL; salt solution, 40 mL (CaCl₂.2H₂O, 0.25 g/L; KH₂PO₄, 1 g/L; NaHCO₃, 10 g/L; NaCl, 2 g/L); and resazurin, 0.4 mL (2.5 mg/L). Adjust the pH to 6.8 with 2 M NaOH.
2. Autoclave at 121 °C for 15 min and allow the broth to cool to room temperature (RT) under anaerobic conditions (10% H₂, 10% CO₂, 80% N₂). Add filter-sterilized cysteine-HCl (0.5 g/L) and mupirocin (5 mg/L) to the medium.
Add an aliquot (50 μL) of frozen Bifidobacterium longum to a culture tube with 5 mL of bifidobacterium medium broth under anaerobic conditions, then culture in an anaerobic incubator for 24 h at 37 °C.

2. Preparation of bifidobacterial EPSs

Preparation of PYG agar medium
1. Combine the following: peptone, 20 g/L; yeast extract, 10 g/L; glucose, 5 g/L; NaCl, 0.08 g/L; CaCl₂, 0.008 g/L; MgSO₄·7H₂O, 0.008 g/L; K₂HPO₄, 0.04 g/L; KH₂PO₄, 0.04 g/L; NaHCO₃, 0.4 g/L; agar, 12 g/L. Adjust the pH to 7.2 using 10 M NaOH.
2. Autoclave the media at 121 °C for 15 min and cool to ~50 °C. Then, per 1 L of medium, add 0.5 mL of filter-sterilized vitamin K₁ solution (1 g of vitamin K₁ dissolved in 99 mL of 99% ethanol), 5 mL of haemin solution (0.5 g of haemin dissolved in 1 mL of 1 mol/L NaOH, then brought up to 100 mL with distilled water), and 0.5 g of cysteine-HCl.
3. Before pouring the PYG plates, add filter-sterilized 5-bromo-4-chloro-3-indolyl β-D-galactopyranoside (X-Gal, 0.06 g/L), LiCl·3H₂O (5.7 g/L) and mupirocin (5 mg/L) to the medium.
  NOTE: X-Gal and LiCl.3H₂O allow the identification of B. longum colonies on plates via coloration changes.
Inoculate 20 μL of B. longum strains (step 1.2) to PYG plates and place in an anaerobic incubator at 37 °C for 72 h.
Collect mucoid bacterial colonies from the PYG plates using a weighing scoop, then completely resuspend in 10 mL of phosphate-buffered saline (PBS) using a vortex oscillator.
NOTE: The bacterial and EPS mixtures should be resuspended completely by vortexing or pipetting up and down repeatedly until the fibers are completely dissolved in PBS.
Centrifuge the suspension at 6,000 x g for 5 min.
Carefully transfer the supernatants to a new centrifuge tube and mix completely with three volumes of cold 99% ethanol by repeated inversion and blending.
Centrifuge the mixture at 6,000 x g for 5 min and completely remove the supernatants.
Remove the precipitates from the centrifuge tubes by scraping and drying the EPS extracts overnight using a speed vacuum.

3. Preparation of fermentation medium

Preparation of basic culture medium VI
1. Combine the following: peptone, 3 g/L; tryptone, 3 g/L; yeast extract, 4.5 g/L; mucin, 0.5 g/L; bile salts No. 3, 0.4 g/L; NaCl, 4.5 g/L; KCl, 2.5 g/L; MgCl₂·6H₂O, 4.5 g/L; 1 mL Tween 80; CaCl₂.6H₂O, 0.2 g/L; KH₂PO₄, 0.4 g/L; MgSO₄·7H₂O, 3.0 g/L; MnCl₂·4H₂O, 0.32 g/L; FeSO₄·7H2O, 0.1 g/L; CoSO₄·7H₂O, 0.18 g/L; CaCl₂·2H₂O, 0.1 g/L; ZnSO₄·7H₂O, 0.18 g/L; CuSO₄·5H₂O, 0.01 g/L; and NiCl₂·6H₂O, 0.092 g/L. Adjust the pH to 6.5 with 1 M HCl.
2. Prepare haemin and cysteine as done in section 2.1 and add after autoclaving and cooling.
Prepare culture media that contains different carbon sources with a VI base media. Prior to autoclaving, add 8 g/L of Bif EPS fibers to medium VI, comprising group VI_Bif. In addition, add 8 g/L starch to medium VI to represent group VI_Starch. Finally, medium VI without addition of a carbon source is used as the control (group VI).
NOTE: Bif EPS and starch are first dissolved in hot water using a magnetic agitator, then mixed with prepared VI medium.
Autoclave all media at 121 °C for 15 min and allow to cool to RT.
Transfer a subsample (5 mL) of each medium to culture tubes in an anaerobic incubator, and store the remaining media at 4 °C.

4. Human fecal sample preparation

Collect fresh fecal samples immediately following fresh defecation from healthy adult human volunteers using feces containers, and subsequently use for slurry preparation.
NOTE: Prior to sample collection, all the volunteers should be screened to ensure no receiving of antibiotics, probiotics, or prebiotic treatments for at least 3 months prior to donating samples. In addition, all donors must provide informed, written consent.
Transfer a fresh fecal sample (1 g) to 10 mL of 0.1 M anaerobic PBS (pH 7.0) into glass beakers, then use glass rods to prepare a 10% (w/v) slurry.
Use a 0.4 mM sieve to filter the fecal slurry. Then, use a subsample of the filtered slurry to inoculate batch culture fermentation experiments, and store the remainder at -80 °C for further analyses.
NOTE: Steps 4.2–4.3 are conducted in an anaerobic chamber.

5. In vitro batch fermentation

Add filtered fecal slurry (500 μL) to the fermentation medium prepared in step 3.2 within an anaerobic chamber, then incubate at 37 °C.
Collect 2 mL of fermented samples at 24 h and 48 h in the anaerobic chamber and then centrifuge outside of the chamber at 6,000 x g for 3 min.
Carefully transfer the supernatants to a new centrifuge tube that will be used for polysaccharide degradation analysis and short-chain fatty acids (SCFAs) measurements.
Store the centrifugation pellets at -80 °C and subsequently use for bacterial genomic DNA extraction.

6. EPS degradation by human fecal microbiota

Load 0.2 μL of fermented supernatants onto pre-coated silica gel-60 TLC aluminum plates, then dry using a hair drier.
Develop the plates in 20 mL of a formic acid/n-butanol/water (6:4:1, v:v:v) solution and dry using a hair drier.
Soak the plates in the orcinol reagent to dye, then dry using a hair drier.
1. Prepare orcinol reagents by dissolving 900 mg of Lichenol in 25 mL of distilled water then adding 375 mL of ethanol. Subsequently, concentrated sulfuric acid should be slowly added and the solution thoroughly mixed.
Heat plates at 120 °C for 3 min in a baking oven and evaluate degradation of EPS by measuring TLC bands.

7. Effects of EPS on human intestinal microbiota

Freeze-thaw the original fecal samples prepared in step 4.3 and fermented samples prepared in step 5.4.
Extract bacterial genomic DNA (gDNA) from all the samples using a stool bacterial genomic DNA extraction kit following the manufacturer’s instructions.
Determine DNA concentrations, integrities, and size distributions using a micro-spectrophotometer and agar gel electrophoresis.
Conduct PCR of bacterial 16S rRNA genes from the extracted gDNA using the following previously described forward and reverse primers¹²:
-forward primer (barcoded primer 338F): ACTCCTACGGGAGGCAGCA
-reverse primer (806R): GGACTACHVGGGTWTCTAAT
Use the following thermal cycler conditions:
1. 94 °C for 5 min.
2. 94 °C for 30 s.
3. 55 °C for 30 s.
4. 72 °C for 1 min.
5. Repeat 2–4 for 35 cycles
6. 72 °C for 5 min.
7. 4 °C hold until removal from thermal cycler.
Conduct high-throughput sequencing of PCR products at a DNA sequencing company using ultra-high throughput microbial community analysis.
Obtain clean, high quality sequences using the Quantitative Insights into Microbial Ecology (QIIME) sequence analysis pipeline¹³.
Define operational taxonomic units (OTUs) for 16S rRNA gene sequences with greater than 97% nucleotide similarity using bioinformatics tools such as the Mothur software suite¹⁴.
Choose a representative sequence from each OTU and use the RDP classifier along with the SILVA taxonomic database to classify representative sequences¹⁵.
Calculate Good’s coverage, alpha diversity metrics (including Simpson and Shannon index), and richness (observed number of OTUs) using bioinformatics tools¹⁶.

8. Effects of EPS on SCFA production by human intestinal microbiota

Add fermented supernatants (1 mL) prepared in step 5.3 to 2 mL centrifuge tubes.
Add 0.2 mL of 25% (w/v) metaphosphoric acid to each of the samples and thoroughly mix the solutions by vortexing.
Centrifuge the mixtures at 13,000 x g for 20 min and transfer the supernatants to fresh tubes.
Concomitantly, prepare solutions of 120 mM acetic, propionic, butyric, isobutyric, valeric and isovaleric acids. Then, add 1 mL of each prepared acid to 1.2 mL of 25% (w/v) metaphosphoric acid and use as the standard cocktails.
Filter the samples using a 0.22 μM membrane.
Detect SCFA concentrations using high performance gas chromatography according to previously described protocols¹¹^,¹⁷.
NOTE: An InertCap FFAP column (0.25 mM x 30 m x 0.25 μM) is used for gas chromatography (GC). SCFA concentrations are then quantified based on peak areas using the single-point internal standard method in the GC Solution software package.

Representative Results

The production of mucoid EPS could be observed in B. longum cultures on PYG plates after anaerobic incubation for 72 h (Figure 1A). Centrifugation of culture scrapes, followed by ethanol precipitation and drying, resulted in the collection of cellulose-like EPS (Figure 1B). Dried EPS and soluble starch were then used as carbon sources for fermentation cultures. TLC was used for oligosaccharide separation and purity analysis due to its low cost and rapid results turnaround¹⁸. Although the degradation rate of starch by human fecal microbiota was faster than that of Bif EPS (Figure 2), Bif EPS degradation was clearly observed for some EPS-inoculated samples.

Community compositional analysis via 16S rRNA gene high-throughput sequencing and principal coordinate analysis (PCoA) was then performed to investigate the effects of Bif EPS on human gut microbiota. Samples from the VI_Bif and VI_Starch groups clustered separately from each other in the PCoA analysis (Figure 3A), indicating that EPS and starch availability differentially shape human fecal bacterial communities. Linear discriminant analysis effect size (LEfSe) was further used to distinguish the specific bacterial taxa that differed between the VI_Bif and VI_Starch treatments. The genera Collinsella, Coprococcus, Parabacteroides, and Rhodopseudomonas were significantly more abundant in the VI_Bif samples than in the VI_Starch samples (Figure 3B). Furthermore, GC measurements were made for several SCFAs to evaluate their production following the addition of different carbon sources. SCFAs that were measured from fermentation cultures included acetic, propionic, isobutyric, butyric, isovaleric, and valeric acids. Following fermentation for 24 h and 48 h, five of the six aforementioned SCFA concentrations were similar among treatments and not statistically different between the VI_Bif, VI_Starch, and VI groups. However, propionic acid concentrations were significantly higher in the VI_Bif group than in the VI_Starch group (Figure 4).

Figure 1: EPS produced by B. longum.
Frozen B. longum was restored in Bifidobacterium medium broth and then streaked onto PYG plates, followed by anaerobic incubation at 37 °C for 72 h (A). The EPS produced by bacterial cultures were scraped from plate cultures, precipitated using ethanol, and dried overnight using a speed vacuum (B). Please click here to view a larger version of this figure.

Figure 2: TLC analysis of in vitro EPS and starch degradation by human gut microbiota.
TLC analysis was conducted on 0.2 μL samples collected at 24 h and 48 h from each fermentation culture grown under anaerobic conditions. VI, VI_Starch, and VI_Bif indicate VI media, VI media + starch supplement, and VI media + EPS supplement, respectively. The numbers 1–12 indicate fecal bacterial samples from the 12 volunteers that were used to inoculate the fermentation experiments. The control group represents treatment without additional carbon supplements. This figure is modified from Yin et al.¹¹. Please click here to view a larger version of this figure.

Figure 3: Effects of Bif EPS availability on human gut microbiota communities.
(A) PCoA plot of gut microbiota community compositional dissimilarities based on the unweighted UniFrac metric. (B) LEfSE analysis of bacterial taxa that were differentially abundant among treatment groups. A cutoff of p < 0.05 was used to assess the statistical significance of bacterial taxonomic differences among groups. Ori indicates the gut microbiota of the volunteer fecal samples. VI_Bif and VI_Starch indicate the gut microbiota from fermentation samples using VI media with EPS and starch as carbon substrates, respectively. VI represents the control group with gut microbiota inoculated fermentations in VI media without supplementation of other carbohydrates. This figure is modified from Yin et al.¹¹ Please click here to view a larger version of this figure.

Figure 4: Effects of EPS availability on SCFA production after 24 h and 48 h of fermentation.
Acetic, propionic, isobutyric, butyric, isovaleric, and valeric acids were detected using gas chromatography. VI_Bif, VI_Starch, and VI indicate the samples that were collected after cultivation using VI media + EPS, VI media + starch, and VI media, respectively. All samples were measured in triplicate. The figures were generated using GraphPad Prism Version 5.01. Panels represent organic acid concentrations within each fermented sample for A, acetic acid; B, propionic acid; C, isobutyric acid; D, butyric acid; E, isovaleric acid; and F, valeric acid. This figure is modified from Yin et al.¹¹ Please click here to view a larger version of this figure.

Discussion

Significant progress has been made towards understanding human gut microbiota composition and activities over the last decade. As a consequence of these studies, the holobiont concept has emerged, which represents the interactions between hosts and associated microbial communities, such as in between humans and their gut microbiota¹⁹^,²⁰. Furthermore, humans are even now regarded as superorganisms²¹, wherein the gut microbiota have been recognized as one of the functional organs in humans²²^,²³. The human body hosts a complex microbial ecosystem, consisting of approximately 10¹³ microbial cells²⁴. Moreover, the genomes of gut microbiota are considered auxiliary genomes from humans that encode numerous metabolic-related genes that expand the host’s metabolic capabilities⁴. However, xenobiotics, including therapeutic drugs and diet-derived bioactive compounds, can potentially alter the gut microbiome community structure and associated functions⁵. Increasing numbers of studies have indicated that interactions between gut microbiota and xenobiotics play important roles in mediating chemical toxicity and causing, or otherwise exacerbating, human diseases⁶^,⁷. Thus, investigations of the interactions between xenobiotics and the human gut microbiota have recently garnered significant research attention.

Mouse models have been the most widely used methods to investigate interactions between microbiota and hosts. However, differences in composition and activities between the gut microbiota of humans and mice²⁵ may result in inadequate modeling of human interactions through studies of mice. Nevertheless, bioethics considerations require minimal use of mice. An alternative to the above in vivo models is batch fermentation, which can be used to simulate human gut microbiota in vitro²⁶. Consequently, fermentation experiments have been used to investigate the interactions between xenobiotics and human gut microbiota. For example, Yin et al.¹⁷ have used batch fermentation experiments to investigate the interactions between polysaccharides and human gut microbiota. The results from this study indicate that some polysaccharides can be metabolized by the human gut microbiota, and that polysaccharides modulate the human bacterial community and metabolites that they produce in vitro, including SCFAs. However, some methodological considerations are critical for use of this protocol. For example, fecal samples should be collected as soon as possible, and an anaerobic chamber should be used to ensure the growth of obligate anaerobes. The latter consideration is particularly critical, because oxygen exposure can lead to the death of some gut bacterial populations and thus, alteration of the bacterial community. In addition, xenobiotics are metabolized in the upper digestive system. Consequently, modeling the interactions between xenobiotics and the lower digestive system microbiota is an important consideration for in vivo modeling.

Batch fermentation experiments have clear advantages over in vivo human and animal studies because they are more economically feasible and convenient. Moreover, they can be used to investigate interindividual variation of human gut microbiota responses to xenobiotic exposure. Moreover, batch fermentation can be easily applied to manipulate microbiota communities and evaluate their associated metabolic functions. However, batch fermentation systems suffer from the limitation of static state dynamics. Future investigations could implement bioreactor chemostats that allow the dynamic modulation of pH, temperature, and peristalsis, while maintaining a steady supply of nutrients and the continuous removal of waste. Such activities would allow experiments to better mimic in vivo intestinal tracts and provide new insights to supplement those from batch fermentation experiments. An additional limitation of batch fermentation experiments is that they remove all microbiome-host tissue interactions. This could be a particularly important consideration, as some xenobiotics (e.g., methamphetamine) can be co-metabolized by human cells and gut microbiota²⁷. Moreover, recent studies have indicated that gut metagenome (GM) can indirectly regulate xenobiotic metabolism via regulating host gene expression regulation⁸.

Although developments of batch fermentation systems are still needed, these systems can be widely used for high-throughput and rapid screening of interactions between xenobiotics and human gut microbiota. Elucidating the mechanisms underlying xenobiotic resistance and metabolism in active human gut microbiomes will provide important insights into unexplained patient-to-patient variation in drug efficacy and toxicity⁸^,⁹. Furthermore, a more detailed understanding of how diets and specific food components alter microbial metabolisms and consequently effect host health is the first step towards realizing the goal of personalized medicine via microbiota modulation.

Divulgations

The authors have nothing to disclose.

Acknowledgements

This study was funded by the National Nature Science Foundation of China (No. 31741109), the Hunan Natural Science Foundation (No. 2018JJ3200), and the construct program of applied characteristic discipline in Hunan University of Science and Engineering. We thank LetPub (www.letpub.com) for its linguistic assistance during the preparation of this manuscript.

Materials

0.22 µm membrane filters	Millipore	SLGP033RB	Use to filter samples
0.4-mm Sieve	Thermo Fischer	308080-99-1	Use to prepare human fecal samples
5-bromo-4-chloro-3-indolyl β-D-galactopyranoside (X-Gal)	Solarbio	X1010	Use to prepare color plate
Acetic	Sigma-Aldrich	71251	Standard sample for SCFA
Agar	Solarbio	YZ-1012214	The component of medium
Anaerobic chamber	Electrotek	AW 400SG	Bacteria culture and fermentation
Autoclave	SANYO	MLS-3750	Use to autoclave
Bacto soytone	Sigma-Aldrich	70178	The component of medium
Baking oven	Shanghai Yiheng Scientific Instruments Co., Ltd	DHG-9240A	Use to heat and bake
Beef Extract	Solarbio	G8270	The component of medium
Bifidobacterium longum Reuter	ATCC	ATCC® 51870™	Bacteria
Bile Salts	Solarbio	YZ-1071304	The component of medium
Butyric	Sigma-Aldrich	19215	Standard sample for SCFA
CaCl₂	Solarbio	C7250	Salt solution of medium
Capillary column	SHIMADZU-GL	InertCap FFAP (0.25 mm × 30 m × 0.25 μm)	Used to SCFA detection
Casein Peptone	Sigma-Aldrich	39396	The component of medium
Centrifuge	Thermo Scientific	Sorvall ST 8	Use for centrifugation
CoSO₄.7H₂O	Solarbio	C7490	The component of medium
CuSO₄.5H₂O	Solarbio	203165	The component of medium
Cysteine-HCl	Solarbio	L1550	The component of medium
Ethanol	Sigma-Aldrich	E7023	Use to prepare vitamin K₁
FeSO₄.7H₂O	Solarbio	YZ-111614	The component of medium
Formic Acid	Sigma-Aldrich	399388	Used to TLC
Gas chromatography	Shimadzu Corporation	GC-2010 Plus	Used to SCFA detection
Glass beaker	Fisher Scientific	FB10050	Used for slurry preparation
Glucose	Solarbio	G8760	The component of medium
Haemin	Solarbio	H8130	The component of medium
HCl	Sigma-Aldrich	30721	Basic solution used to adjust the pH of the buffers
Isobutyric	Sigma-Aldrich	46935-U	Standard sample for SCFA
Isovaleric Acids	Sigma-Aldrich	129542	Standard sample for SCFA
K₂HPO₄	Solarbio	D9880	Salt solution of medium
KCl	Solarbio	P9921	The component of medium
KH₂PO₄	Solarbio	P7392	Salt solution of medium
LiCl.3H₂O	Solarbio	C8380	Use to prepare color plate
Meat Extract	Sigma-Aldrich-Aldrich	70164	The component of medium
Metaphosphoric Acid	Sigma-Aldrich	B7350	Standard sample for SCFA
MgCl₂.6H₂O	Solarbio	M8160	The component of medium
MgSO₄.7H₂O	Solarbio	M8300	Salt solution of medium
MISEQ	Illumina	MiSeq 300PE system	DNA sequencing
MnSO₄.H₂0	Sigma-Aldrich	M8179	Salt solution of medium
Mupirocin	Solarbio	YZ-1448901	Antibiotic
NaCl	Solarbio	YZ-100376	Salt solution of medium
NaHCO₃	Sigma-Aldrich	792519	Salt solution of medium
NanoDrop ND-2000	NanoDrop Technologies	ND-2000	Determine DNA concentrations
NaOH	Sigma-Aldrich	30620	Basic solution used to adjust the pH of the buffers
n-butanol	ChemSpider	71-36-3	Used to TLC
NiCl₂	Solarbio	746460	The component of medium
Orcinol	Sigma-Aldrich	447420	Used to prepare orcinol reagents
Propionic	Sigma-Aldrich	94425	Standard sample for SCFA
QIAamp DNA Stool Mini Kit	QIAGEN	51504	Extract bacterial genomic DNA
Ready-to-use PBS powder	Sangon Biotech (Shanghai) Co., Ltd.	A610100-0001	Used to prepare the lipid suspension
Resazurin	Solarbio	R8150	Anaerobic Equipment
Speed Vacuum Concentrator	LABCONCO	CentriVap	Use to prepare EPSs
Starch	Solarbio	YZ-140602	Use to the carbon source
Sulfuric Acid	Sigma-Aldrich	150692	Used to prepare orcinol reagents
T100 PCR	BIO-RAD	1861096	PCR amplification
TLC aluminium sheets	MerckMillipore	116835	Used to TLC
Trypticase Peptone	Sigma-Aldrich	Z699209	The component of medium
Tryptone	Sigma-Aldrich	T7293	The component of medium
Tween 80	Solarbio	T8360	Salt solution of medium
Valeric	Sigma-Aldrich	75054	Standard sample for SCFA
Vitamin K₁	Sigma-Aldrich	V3501	The component of medium
Vortex oscillator	Scientific Industries	Vortex.Genie2	Use to vortexing
Yeast Extract	Sigma-Aldrich	Y1625	The component of medium
ZnSO₄.7H₂O	Sigma-Aldrich	Z0251	The component of medium

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Hu, Y., Chen, H., Li, P., Li, B., Cao, L., Zhao, C., Gu, Q., Yin, Y. Analysis of Interactions between Endobiotics and Human Gut Microbiota Using In Vitro Bath Fermentation Systems. J. Vis. Exp. (150), e59725, doi:10.3791/59725 (2019).