# Effect of Different Polymerized Xylooligosaccharides on the Metabolic Pathway inBifidobacterium adolescentis

Authors: Di Yao; Mengna Wu; Xiaoyu Wang; Lei Xu; Xiqun Zheng
Journal: Journal of Food Quality
 (2022)

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## Abstract

Metabolic pathway analysis ofBifidobacterium adolescent (B. adolescentis) grown on either xylobiose and xylotriose (X2/X3) or xylopentaose (X5) and identifying key regulatory-related genes and metabolites from RNA-seq and UHPLC system was performed. Compared with X5, X2/X3 highly promoted the growth of B. adolescentis. Also, the transcriptome analysis showed that a total of 268 differentially expressed genes (DEGs) of B. adolescentis cultured with X2/X3 and X5 were screened, including 163 upregulated and 105 downregulated genes (X2/X3 vs. X5), which mainly were ABC transporters. Furthermore, the qRT-PCR results of 16 DGEs validated the accuracy of the RNA-seq data. Meanwhile, metabolomics analysis showed that 192 differential metabolites noted on MS2 included 127 upregulated and 65 downregulated metabolites; mainly, metabolites were amino acids and organic acids. The abundance difference of specific genes and metabolites highlighted regulatory mechanisms involved in utilizing different polymerized xylooligosaccharides by B. adolescentis.


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## Body

## 1. Introduction

Bifidobacterium is believed to play an important role in maintaining and promoting human health by eliciting a number of beneficial properties, such as improvement of gastrointestinal health [1] and immune function [2,3]. Bifidobacteria can utilize a diverse range of dietary carbohydrates that escape degradation in the upper parts of the intestine, many of which are plant-derived oligosaccharides [4–6]. Therefore, the plant-derived oligosaccharides can be used as a kind of prebiotics [7]. Accumulating evidence on probiotic and prebiotic interventions has demonstrated promising effects on promoting gastrointestinal health by modulating the microbiota toward the enrichment of beneficial microorganisms [8]. The effects of both probiotics and prebiotics on immune function have been well described in a range of studies including in vitro assessment studies, animal models, and human trials [2].As a prebiotic candidate, xylooligosaccharides (XOS) have recently been shown to have promising effects on beneficial commensal microbes and health outcomes [3]. The most informative studies on XOS are those carried out by Okazaki et al. [9]. A volunteer trial involving feeding XOS to healthy humans showed significant increases in bifidobacteria. There was also a significant increase in the concentration of organic acids in the faeces. Additional studies have demonstrated that XOS stimulate the growth of caecal and faecal bifidobacteria at higher levels than the prebiotic fructooligosaccharide (FOS) [6,10]. Therefore, XOS have attracted more attention due to the highly selective proliferation effect on bifidobacteria.Different bifidobacterial strains may possess different carbohydrate utilizing abilities. However,B.adolescentis is able to efficiently utilize XOS [11]. The genome of some species of bifidobacteria from humans and animal origin demonstrates a high presence of genes involved in the metabolism of complex oligosaccharides [12, 13]. Five gene clusters involved in the utilization of XOS have been identified [14]. In most cases, the genes encoding the transporter components and the associated catabolic enzymes for carbohydrates within a range of degrees of polymerization, similar monosaccharide constituents, or linkage are clustered in conserved modules and coregulated as single operons [15]. In addition, Crittenden suggested that bifidobacteria were able to utilize XOS but not xylan [16]. In fact, bifidobacteria are unable to grow on xylan, owing to the extracellular xylan-degrading activity, thereby allowing efficient uptake of the produced XOS by a dedicated ABC transporter encoded by bifidobacteria [17]. Based on the XOS catabolic pathway, XOS (DP of 2 to 6) transported via the ABC system were hydrolyzed by endo-1,4-β-xylanases and β-xylosidases [18].Although our previous studies have elucidated the utilization and metabolism of XOS inB. adolescentis 15703 and identified the key regulatory-related genes and metabolites. However, to date, no work has been carried out on the regulatory mechanisms that control the expression of the genes and metabolites involved in the metabolic pathways on different polymerized XOS. To address this issue, we performed combined transcriptome and metabolome analyses to elucidate the molecular mechanism for utilization and metabolism of different polymerized XOS in B. adolescentis.


## 2. Materials and Methods

### 2.1. Separation and Preparation of Different Polymerized XOS

Sephadex G-10 (Sigma, Saint Louis, MO, USA) was selected as a separation medium using preparative chromatography technology; xylobiose, xylotriose mixture (X2/X3), and xylopentaose (X5) from XOS were separated. The sample loading was 2 mL, the elution flow rate was 1.0 mL/min, and the injection concentration was 30%. On the basis of ensuring purity, X2/X3 and X5 were prepared using continuous preparative chromatography equipment and then were analyzed by HPLC. Chromatographic conditions were as follows: SUGAR KS-802 column, ultrapure water as mobile phase, the flow rate of 0.6 mL/min, and column temperature of 81 °C.


### 2.2. Cultivation ofB. adolescentis 15703

B. adolescentis 15703 (General Microbiological Culture Collection Center, Beijing, China) was resuscitated and precultivated twice using MRS Broth (Hope Bio, China). Then, cells were harvested and suspended as 2% inoculation into an MRS medium containing X2/X3 or X5 and a control medium without carbohydrate and incubated at 37°C under anaerobic conditions [19]. Cell growth was determined by measuring the optical density at 600 nm (OD600).


### 2.3. RNA-Seq Analysis

Cell pellets ofB. adolescentis 15703 were harvested by centrifugation. The cells were used for extracting total RNA following the manufacturer’s recommendations of the QIAGEN 74524 kit. After the concentration and purity of extracted RNA were qualified, the mRNA was enriched by removing rRNA using Ribo-ZeroTM Magnetic Kit (Epicentre). The mRNA was reverse-transcripted into cDNA; then, second strands were synthesized using DNA polymerase I, RNase H, and dNTP. The obtained cDNA fragments were purified, end-repaired, poly(A)-added, and ligated to Illumina sequencing adapters [19]. The ligation products size were chosen, amplified, and sequenced using Illumina HiSeqTM 2500. The sequenced reads were mapped to a reference genome by TopHat2; then, the transcripts were merged from multiple groups into a finally comprehensive set of transcripts for further downstream differential expression analysis. Gene abundance was quantified by the RSEM software. The gene expression level was normalized with the FPKM method and the edgeR package was used to identify DEGs across groups. In comparison to significant DEGs, FDR <0.01 and Fold Change (FC) ≥2 were used as screening criteria. DEGs between X2/X3 and X5 treatments were conducted using the DEseq package. DEGs were subjected to enrichment analysis of KEGG pathways.


### 2.4. Quantitative Real-Time PCR

Total RNA was isolated as described above. Then the cDNA synthesis was performed using reverse transcriptase. The primers sequence are listed in Supplementary Table1 and each reaction (20 μL mixture) contained 2 μL cDNA, 10 μL 2× SYBR Green qPCR Master Mix, 0.5 μL the forward and reverse primers, and 7.0 μL ddH2O. All qRT-PCR analyses were performed in ABI StepOnePlus and performed in two steps: first, predenaturation for 3 min and 45 cycles of denaturation for 3 s at 95, then annealing/extension for 30 s at 58°C. Gene expression was normalized by the 2-ΔΔCt method, and the 16S rRNA gene was used as the normalized standard [20].


### 2.5. Metabolites’ Extraction

The sample of 100μL was accurately removed and placed in an EP tube, 300 μL methanol was added to start extraction, and 20 μL of internal standard substances was added, followed by vortex for 30 s. Then, the mixture tube was immersed into the ultrasonic bath with ice water and ultrasonically incubated in ice water for 10 min and incubated for 1 h at −20°C to precipitate proteins. Then the mixture was centrifuged at 13000 rpm for 15 min at 4°C. Moreover, 200 μL of the supernatant sample was transferred to a fresh 2 mL LC/MS glass vial, 20 μL from the supernatant of each sample was marked as QC samples, and another supernatant was used for the UHPLC-QTOF-MS analysis. All experiments were carried out in triplicate.


### 2.6. Metabolites’ Analysis by LC-MS/MS

The UHPLC system (1290, Agilent Technologies) with a UPLC BEH Amide column (1.7μm 2.1∗100 mm, Waters) coupled with Triple TOF 5600 (Q-TOF, AB Sciex) was used for LC-MS/MS analyses. Then, 25 mM NH4OAc and 25 mM NH4OH in water (pH = 9.75) (A) and acetonitrile (B) were used as the mobile phase. The elution gradient was as follows: 0 min, 95% B; 7 min, 65% B; 9 min, 40% B; 9.1 min, 95% B; 12 min, 95% B. The flow rate of the mobile phase was 0.5 mL min-1. The injection volume of the analytical solution was 3 μL. The Triple-TOF-MS was used for its ability to acquire MS/MS spectra on an information-dependent basis (IDA) during an LC/MS experiment. In this mode, the full scan survey MS data collect and trigger the acquisition of MS/MS spectra depending on preselected criteria surveyed by the acquisition software (Analyst TF 1.7, AB Sciex) [21]. In each cycle, 12 precursor ions with intensity greater than 100 were chosen for fragmentation at collision energy (CE) of 30 V (15 MS/MS events with product ion accumulation time of 50 msec each). ESI source conditions were set as follows: ion source gas 1, 60 Psi; ion source gas 2, 60 Psi; curtain gas, 35 Psi; source temperature, 650°C; ion spray voltage floating (ISVF), 5000 V or -4000 V in positive or negative modes, respectively.The mzXML format was obtained using ProteoWizard to convert MS raw data files and processed byR package XCMS (version 3.2). The processed results generated a data matrix consisting of retention time (RT), mass-to-charge ratio (m/z) values, and peak intensity. R package CAMERA was used for peak annotation after XCMS data processing [22]. The metabolites were identified by the in-house MS2 database.


## 2.1. Separation and Preparation of Different Polymerized XOS

Sephadex G-10 (Sigma, Saint Louis, MO, USA) was selected as a separation medium using preparative chromatography technology; xylobiose, xylotriose mixture (X2/X3), and xylopentaose (X5) from XOS were separated. The sample loading was 2 mL, the elution flow rate was 1.0 mL/min, and the injection concentration was 30%. On the basis of ensuring purity, X2/X3 and X5 were prepared using continuous preparative chromatography equipment and then were analyzed by HPLC. Chromatographic conditions were as follows: SUGAR KS-802 column, ultrapure water as mobile phase, the flow rate of 0.6 mL/min, and column temperature of 81 °C.


## 2.2. Cultivation ofB. adolescentis 15703

B. adolescentis 15703 (General Microbiological Culture Collection Center, Beijing, China) was resuscitated and precultivated twice using MRS Broth (Hope Bio, China). Then, cells were harvested and suspended as 2% inoculation into an MRS medium containing X2/X3 or X5 and a control medium without carbohydrate and incubated at 37°C under anaerobic conditions [19]. Cell growth was determined by measuring the optical density at 600 nm (OD600).


## 2.3. RNA-Seq Analysis

Cell pellets ofB. adolescentis 15703 were harvested by centrifugation. The cells were used for extracting total RNA following the manufacturer’s recommendations of the QIAGEN 74524 kit. After the concentration and purity of extracted RNA were qualified, the mRNA was enriched by removing rRNA using Ribo-ZeroTM Magnetic Kit (Epicentre). The mRNA was reverse-transcripted into cDNA; then, second strands were synthesized using DNA polymerase I, RNase H, and dNTP. The obtained cDNA fragments were purified, end-repaired, poly(A)-added, and ligated to Illumina sequencing adapters [19]. The ligation products size were chosen, amplified, and sequenced using Illumina HiSeqTM 2500. The sequenced reads were mapped to a reference genome by TopHat2; then, the transcripts were merged from multiple groups into a finally comprehensive set of transcripts for further downstream differential expression analysis. Gene abundance was quantified by the RSEM software. The gene expression level was normalized with the FPKM method and the edgeR package was used to identify DEGs across groups. In comparison to significant DEGs, FDR <0.01 and Fold Change (FC) ≥2 were used as screening criteria. DEGs between X2/X3 and X5 treatments were conducted using the DEseq package. DEGs were subjected to enrichment analysis of KEGG pathways.


## 2.4. Quantitative Real-Time PCR

Total RNA was isolated as described above. Then the cDNA synthesis was performed using reverse transcriptase. The primers sequence are listed in Supplementary Table1 and each reaction (20 μL mixture) contained 2 μL cDNA, 10 μL 2× SYBR Green qPCR Master Mix, 0.5 μL the forward and reverse primers, and 7.0 μL ddH2O. All qRT-PCR analyses were performed in ABI StepOnePlus and performed in two steps: first, predenaturation for 3 min and 45 cycles of denaturation for 3 s at 95, then annealing/extension for 30 s at 58°C. Gene expression was normalized by the 2-ΔΔCt method, and the 16S rRNA gene was used as the normalized standard [20].


## 2.5. Metabolites’ Extraction

The sample of 100μL was accurately removed and placed in an EP tube, 300 μL methanol was added to start extraction, and 20 μL of internal standard substances was added, followed by vortex for 30 s. Then, the mixture tube was immersed into the ultrasonic bath with ice water and ultrasonically incubated in ice water for 10 min and incubated for 1 h at −20°C to precipitate proteins. Then the mixture was centrifuged at 13000 rpm for 15 min at 4°C. Moreover, 200 μL of the supernatant sample was transferred to a fresh 2 mL LC/MS glass vial, 20 μL from the supernatant of each sample was marked as QC samples, and another supernatant was used for the UHPLC-QTOF-MS analysis. All experiments were carried out in triplicate.


## 2.6. Metabolites’ Analysis by LC-MS/MS

The UHPLC system (1290, Agilent Technologies) with a UPLC BEH Amide column (1.7μm 2.1∗100 mm, Waters) coupled with Triple TOF 5600 (Q-TOF, AB Sciex) was used for LC-MS/MS analyses. Then, 25 mM NH4OAc and 25 mM NH4OH in water (pH = 9.75) (A) and acetonitrile (B) were used as the mobile phase. The elution gradient was as follows: 0 min, 95% B; 7 min, 65% B; 9 min, 40% B; 9.1 min, 95% B; 12 min, 95% B. The flow rate of the mobile phase was 0.5 mL min-1. The injection volume of the analytical solution was 3 μL. The Triple-TOF-MS was used for its ability to acquire MS/MS spectra on an information-dependent basis (IDA) during an LC/MS experiment. In this mode, the full scan survey MS data collect and trigger the acquisition of MS/MS spectra depending on preselected criteria surveyed by the acquisition software (Analyst TF 1.7, AB Sciex) [21]. In each cycle, 12 precursor ions with intensity greater than 100 were chosen for fragmentation at collision energy (CE) of 30 V (15 MS/MS events with product ion accumulation time of 50 msec each). ESI source conditions were set as follows: ion source gas 1, 60 Psi; ion source gas 2, 60 Psi; curtain gas, 35 Psi; source temperature, 650°C; ion spray voltage floating (ISVF), 5000 V or -4000 V in positive or negative modes, respectively.The mzXML format was obtained using ProteoWizard to convert MS raw data files and processed byR package XCMS (version 3.2). The processed results generated a data matrix consisting of retention time (RT), mass-to-charge ratio (m/z) values, and peak intensity. R package CAMERA was used for peak annotation after XCMS data processing [22]. The metabolites were identified by the in-house MS2 database.


## 3. Results and Discussion

### 3.1. Growth Characteristics ofB. adolescentis on X2/X3 and X5

The HPLC analysis of the prepared X2/X3 and X5 was shown in Supplementary Figure1. According to the results of the composition analysis, the purity of X2/X3 and X5 was 87.29% and 90.05%, respectively. Then, the X2/X3 and X5 were used as a carbon source to cultivate B. adolescentis. As shown in Figure 1, the growth of B. adolescentis on different polymerized XOS was significantly higher than that of the blank control group without a carbon source. The OD value of cultures of B. adolescentis with X2/X3 as the carbon source is the highest, X5 is the second, and xylose is the lowest; however, the lag and logarithmic phase is the shortest. Also, a rapid growth rate was observed at 8–20 h. The growth yield (stable phase) on X2/X3 was about 1.3-fold greater than that on X5, indicating that XOS at a lower degree of polymerization was more preferred by B. adolescentis. Bifidobacterium can preferentially hydrolyze XOS with a low degree of polymerization and then use monosaccharides for further metabolism. This result is consistent with the conclusion reported by Okazaki that oligosaccharides are more easily absorbed and utilized by bifidobacteria than by polysaccharides and corresponding monosaccharides [9]. The composition of X2 and X3 is entirely composed of xylose units and does not contain arabinosyl groups and substituents such as methoxy and acetyl groups, while X5 often contains arabinosyl isomers, which should firstly be degraded by arabinosidase [23]; this higher complexity may lead to a significant difference in the proliferation effect of X2/X3 and X5 on B. adolescentis.Figure 1
Growth ofB. adolescentis on different polymerized XOS and control medium (no carbohydrate).


### 3.2. Annotation and Analysis of Differentially Expressed Genes (DEGs) ofB. adolescentis on X2/X3 and X5

A total of 268 DEGs were identified forB. adolescentis grown on X2/X3 and X5, including 163 upregulated genes and 105 downregulated genes (Supplementary Figure 2). The DEGs involved in biological functions were further analyzed by KEGG, and 20 pathways were predicted (Figure 2). ABC transporters, starch and sucrose metabolism, pyrimidine metabolism, and galactose metabolism are the highly represented categories. Among these pathways, the QValue of ABC transporters is the lowest (red color), suggesting the different encoding genes of ABC transporters is the most.Figure 2
KEGG pathway enrichment analysis of DEGs (X2/X3 vs. X5). The vertical axis indicates the name of the KEGG pathway, and the horizontal axis indicates the rich factor. The dot size indicates the number of differentially expressed genes in the pathway, and the color of the dots corresponds to differentQ values.The DEGs involved in the ABC transporters are shown in Table1. In the ABC transporter pathway, 33 genes were significantly upregulated. Genes BAD_RS00340 and BAD_RS07050 encoded ABC transporter. Genes BAD_RS01000, BAD_RS07410, BAD_RS02260, BAD_RS04685, BAD_RS00815, BAD_RS00810, BAD_RS08280, BAD_RS02545, BAD_RS06685, BAD_RS08205, BAD_RS08275, BAD_RS03705, BAD_RS06690, and BAD_RS08210 encoded ABC transporter permease. Genes BAD_RS02255, BAD_RS07415, BAD_RS01495, BAD_RS00805, BAD_RS00390, BAD_RS08285, BAD_RS08340, BAD_RS00990, and BAD_RS06680 encoded ABC transporter substrate-binding protein. Genes BAD_RS08285, BAD_RS00805, and BAD_RS02355 encoded solute-binding protein. Genes BAD_RS04090, BAD_RS00495, BAD_RS01005, BAD_RS03710, and BAD_RS00520 encoded ABC transporter ATP-binding protein. Five genes (BAD_RS02355, BAD_RS05605, BAD_RS03210, BAD_RS03215, and BAD_RS05655), which are ABC transporter-related genes, were significantly downregulated after X5 treatment.Table 1
DEGs involved in the related ABC transporter during the growth ofB. adolescentis on X5 compared to X2/X3 assessed by RNA-seq.
Gene no.aLog2 (Fc)bP valueFDRSymbolAnnotationcLinear FMPK valuedX2/X3X5BAD_RS022553.01↑00yurOSugar ABC transporter substrate-binding protein989.287940.17BAD_RS074152.79↑4.47E − 861.40E − 84mdxEABC transporter, solute-binding protein51.88360.4BAD_RS074102.75↑2.30E − 191.78E − 18amyDABC transporter permease16.53111.24BAD_RS022652.57↑00yurMThiamine ABC transporter ATP-binding protein514.593056.15BAD_RS022602.57↑00malFSugar ABC transporter permease4662759.99BAD_RS014952.51↑2.51E − 2612.23E − 259TP_0034ABC transporter substrate-binding protein319.831819.21BAD_RS008052.17↑00yurOSolute-binding protein of ABC transporter system618.732790.2BAD_RS046851.87↑0.00720.0164-ABC transporter permease6.8425.03BAD_RS003851.75↑0.01190.0254livFABC-type branched-chain amino acid transport systems ATPase component5.217.55BAD_RS003901.74↑0.00120.0031BR1785Branched-chain amino acid ABC transporter substrate-binding protein6.0520.15BAD_RS008151.58↑3.35E − 738.39E − 72araQSugar ABC transporter permease326.41974.92BAD_RS070501.56↑00lipOABC transporter3361.719912.7BAD_RS008101.53↑2.70E − 625.55E − 61yurNSugar ABC transporter permease278.86804.48BAD_RS082801.51↑3.55E − 1001.18E − 98msmFSugar ABC transporter permease491.141401.37BAD_RS082851.51↑7.82E − 1934.82E − 191ugpBABC transporter, solute-binding protein686.941954.61BAD_RS040901.51↑0.00080.0022TM_0352Macrolide ABC transporter ATP-binding protein15.4243.86BAD_RS004951.46↑1.94E − 312.32E − 30MT1311Multidrug ABC transporter ATP-binding protein81.69225.1BAD_RS010051.39↑0.02420.0478fbpCABC transporter ATP-binding protein6.0715.95BAD_RS083401.36↑1.22E − 074.99E − 07msmESugar ABC transporter substrate-binding protein27.5970.62BAD_RS009901.31↑0.00090.0024-ABC transporter substrate-binding protein13.9134.5BAD_RS037101.30↑9.00E − 050.0002lolDABC transporter ATP-binding protein26.5365.31BAD_RS082101.27↑1.50E − 1075.58E − 106amyDPermease of ABC transporter possibly for oligosaccharides933.342256.42BAD_RS005201.27↑4.19E − 183.02E − 17TpdAmino acid ABC transporter substrate-binding protein173.12416.3BAD_RS025451.25↑0.00800.0178gsiCABC transporter permease11.6527.77BAD_RS033251.22↑2.33E − 101.15E − 09MJ1508ABC transporter ATP-binding protein85.46198.92BAD_RS066801.17↑2.10E − 262.13E − 25yxeMAmino acid ABC transporter substrate-binding protein228.62513.46BAD_RS066851.15↑3.29E − 172.29E − 16tcyLABC transporter permease196.97437.68BAD_RS082051.15↑2.91E − 565.54E − 55amyCSugar ABC transporter permease603.51334.63BAD_RS082751.13↑1.22E − 401.82E − 39amyCABC transporter permease413.73903.85BAD_RS037051.11↑5.91E − 061.98E − 05-ABC transporter permease35.9577.6BAD_RS003401.10↑1.30E − 311.61E − 30PipABC transporter109.76235.38BAD_RS066901.03↑2.25E − 057.07E − 05patMABC transporter permease65.13133.26BAD_RS023551.35↓5.99E − 143.50E − 13braCSolute-binding protein of ABC transporter for branched-chain amino acids171.3167.28BAD_RS056051.53↓4.01E − 122.20E − 11-Sugar ABC transporter substrate-binding protein247.0285.73BAD_RS032102.07↓1.34E − 442.10E − 43lolDPeptide ABC transporter ATP-binding protein496.58118.13BAD_RS032152.76↓4.00E − 1862.37E − 184macBABC transporter permease480.9171.17BAD_RS056552.93↓8.53E − 062.81E − 05bceAABC transporter ATP-binding protein31.994.2aGene number referenced as B. adolescentis being alphabet and a five-digit number. bSignificance of fold change data is judged by having a P value of no more than 0.01. cGene annotations were blasted against Swiss-Prot. dFPKM (fragments per kilobase of exon per million fragments mapped) values for cultures on media with X2/X3 or X5 treatment.The DEGs involved in carbohydrate metabolism are shown in Table2. Compared to X2/X3 treatment, five genes (BAD_RS06400, BAD_RS07395, BAD_RS07400, BAD_RS08325, and BAD_RS08455) encoded beta-galactosidase and two genes (BAD_RS08195 and BAD_RS08270) encoded alpha-amylase related to starch and sucrose metabolism (ko00500), galactose metabolism pathway (ko00052), glycan degradation (ko00511), and sphingolipid metabolism (ko00600) were significantly upregulated after X5 treatment. The beta-xylosidase that encoded gene BAD_RS02270 was involved in amino sugar and nucleotide sugar metabolism (ko00520) and starch and sucrose metabolism (ko00500). Moreover, two genes (BAD_RS06365 and BAD_RS08480) encoded beta-glucosidase related to starch and sucrose metabolism (ko00500). Two genes (BAD_RS06360 and BAD_RS08405) encoded glycoside hydrolase involved in starch and sucrose metabolism (ko00500). In addition, gene BAD_RS01050 coded shikimate kinase, BAD_RS05480 coded mannan endo-1,4-beta-mannosidase, BAD_RS01040 coded 6-phosphogluconate dehydrogenase, BAD_RS02150 coded lactaldehyde reductase, BAD_RS07445 coded L-ribulose-5-phosphate 4-epimerase, BAD_RS01580 coded UDP-N-acetylenolpyruvoylglucosamine reductase, which was involved in the biosynthesis of antibiotics (ko01130), peptidoglycan biosynthesis (ko00550), microbial metabolism in diverse environments (ko01120), carbon metabolism (ko01200), fructose and mannose metabolism (ko00051), pentose phosphate pathway (ko00030), glyoxylate and dicarboxylate metabolism (ko00630), propanoate metabolism (ko00640), and pentose and glucuronate interconversions (ko00040), which was significantly upregulated after X5 treatment. Only one gene, BAD_RS07575, encoded alpha-1,4-glucan-maltose-1-phosphate maltosyltransferase, which was significantly downregulated after X5 treatment.Table 2
DEGs involved in related carbohydrate metabolism in the KEGG pathway during the growth ofB. adolescentis on X5 compared to X2/X3 assessed by RNA-seq.
Gene no.Log2 (Fc)p valueFDRSymbolAnnotationLinear FMPK valueKEGG pathwayX2/X3X5BAD_RS064001.04↑4.00E − 050.0001bgaBBeta-galactosidase19.7940.65ko00052BAD_RS073951.07↑1.12E − 188.34E − 18bgaBBeta-galactosidase I84.64177.96ko00052BAD_RS074002.10↑7.31E − 185.21E − 17BGAL16Beta-galactosidase13.0656.17ko00052/ko00600/ko00511BAD_RS081951.78↑00malLAlpha-amylase733.052512.17ko00500/ko00052BAD_RS082701.36↑1.8E − 1489.3E − 147malLAlpha-amylase493.041264.3ko00500/ko00052BAD_RS083251.62↑1.75E − 231.54E − 22lacZBeta-galactosidase25.277.45ko00052/ko00600/ko00511BAD_RS084551.04↑3.10E − 354.07E − 34lacZBeta-galactosidase126.46259.45ko00052/ko00600/ko00511BAD_RS022702.22↑5.69E − 2474.56E − 245xynBBeta-xylosidase251.31174.15ko01100/ko00500/ko00520BAD_RS063601.08↑2.76E − 565.32E − 55xynBGlycoside hydrolase 43 family protein362.57764.37ko01100/ko00500/ko00520BAD_RS063651.52↑2.76E − 1231.23E − 121exgABeta-glucosidase475.021358.67ko00500BAD_RS075751.18↓1.84E − 1127.20E − 111glgEAlpha-1,4-glucan--maltose-1-phosphate maltosyltransferase1093.58481.27ko01100/ko00500/BAD_RS084051.03↑4.88E − 061.64E − 05bglBGlycosyl hydrolase21.7244.24ko01100/ko01110/ko00500/ko00460BAD_RS084801.11↑2.43E − 181.79E − 17bglBBeta-glucosidase66.25142.54ko01100/ko01110/ko00500/ko00460BAD_RS054801.31↑4.84E − 082.04E − 07BAD_1030Mannan endo-1,4-beta-mannosidase13.7934.24ko00051BAD_RS015801.05↑6.05E − 123.28E − 11murBUDP-N-acetylenolpyruvoylglucosamine reductase93.71194.42ko01100/ko00520/ko00550BAD_RS074451.38↑5.29E − 306.09E − 29ulaFL-ribulose-5-phosphate 4-epimerase229.09594.72ko01100/ko00040BAD_RS010402.09↑6.41E − 245.84E − 23Gnd6-Phosphogluconate dehydrogenase45.07192.09ko01100/ko01110/ko01130/ko01120/ko01200/ko00480BAD_RS010503.46↑2.25E − 231.97E − 22IdnkShikimate kinase15.68172.02ko01100/ko01110/ko01130/ko01120/ko01200/ko00030BAD_RS021501.69↑00fucOLactaldehyde reductase1795.215803.32ko01120/ko00630/ko00640


### 3.3. Validation of Transcript Abundance Using qRT-PCR

To verify the RNA-seq results, the mRNA expressions of 16 selected candidate genes (eight upregulated and eight downregulated) were measured by qRT-PCR. The normalized fold expressions of 16 DEGs are shown in Figure3(a); the results showed that the upregulated and downregulated levels of these genes are consistent with RNA-seq. Furthermore, the expression levels of 16 DEGs with qRT-PCR were compared to those of DEGs with RNA-seq by the linear fitting. A significant correlation (R2 = 0.98642) was found between RNA-seq and qRT-PCR (Figure 3(b)). The qRT-PCR results are consistent with their transcript abundance in RNA-seq, which verified the accuracy of the DEGs from RNA-seq analyses.Figure 3
Results of expression profiles (a) and the linear fitting (b) of DEGs by qRT-PCR. Black column: upregulated; blank column: downregulated.
(a)(b)


### 3.4. Metabolite Profile and KEGG Mapping of Metabolites

The metabolites profiling ofB. adolescentis was performed using LC-MS. The primary metabolites are amino acids, organic acids, fatty acids, polyhydroxy acids, sugars, polyols, and N-compounds. A total of 192 different metabolites (MS2) were identified for X2/X3 and X5 treatments (p < 0.05, log2FC > 1), including 127 upregulated metabolites and 65 downregulated metabolites. The different metabolites were annotated in 50 KEGG pathways. ABC transporters and the phosphotransferase system (PTS) were classified as environmental information processing. Aminoacyl-tRNA biosynthesis was included in genetic information processing. The remaining 47 pathways belong to metabolism processing, microbial metabolism in diverse environments, and biosynthesis of secondary metabolites, which are the most highly represented in metabolism processing (Figure 4).Figure 4
The annotated and classified results of the differential metabolite in the KEGG pathway.Different metabolites involved in carbohydrate transport and metabolism are shown in Table3. Compared to X2/X3 treatment, ten metabolites (meta_15, meta_376, meta_166, meta_1695, meta_651, meta_246, meta_219, meta_527, meta_82, and meta_991), which are glycerol, D-ribose, D-mannose, maltotriose, D-biotin, D-mannitol, L-arginine, L-cystine, L-isoleucine, and cellobiose, are significantly different in the ABC transporters pathway (ko02010) for X5 treatment. Also, eight metabolites, including D-mannose, cellobiose, D-mannitol-1-phosphate (meta_759), L-ascorbic acid (meta_312), D-sorbitol-6-phosphate (meta_761), N-acetyl-D-glucosamine-6-phosphate (meta_754), D-mannitol, and pyruvate (meta_8) are significantly different in the phosphotransferase system (PTS) (ko02060) for X5 compared to X2/X3 treatment. In addition, these metabolites, such as D-mannitol, D-mannose, D-mannitol-1-phosphate, and D-sorbitol-6-phosphate, were involved in fructose and mannose metabolism (ko00051). D-Ribose, pyruvate, and D-ribose-5-phosphate are involved in the pentose phosphate pathway (ko00030). However, galactinol, stachyose, and glycerol are involved in galactose metabolism (ko00052). Among all the metabolites, pyruvate (meta_8) is involved in most pathways, including pyruvate metabolism (ko00620), pantothenate and CoA biosynthesis (ko00770), glycolysis/gluconeogenesis (ko00010), and citrate cycle (ko00020).Table 3
Metabolites involved in related carbohydrate transport and metabolism in the KEGG pathway during the growth ofB. adolescentis on X5 compared to X2/X3 assessed by metabolome.
Meta IDLog2 (Fc)MS2 namemzmedrtmedKEGG_pathway_annotationmeta_151.591↑Glycerol91.042107.553ko00052/ko00040/ko02010/ko01100/ko00561meta_3762.919↓D-Ribose209.070204.675ko02010/ko00030/ko02030meta_1661.701↑D-Mannose161.048418.573ko00520/ko02060ko00052/ko00051/ko02010/ko01100meta_16951.226↑Maltotriose563.190430.279ko02010meta_6511.260↑D-Biotin260.109104.804ko00780/ko02010/ko01100meta_2461.362↑D-Mannitol182.077282.069ko02010/ko00051/ko02060meta_2191.027↑L-Arginine173.106380.973ko00261/ko00970/ko01100/ko00472/ko01130/ko00331/ko00220/ko02010/ko01110/ko00330/ko01230/meta_5271.820↑L-Cystine239.020413.417ko02010/ko00270meta_821.306↑L-Isoleucine130.089221.442ko02010/ko01230/ko00970/ko01130/ko00290/ko00280/ko00460/ko01210/ko01110meta_9911.647↑Cellobiose341.113281.354ko00500/ko02060/ko02010/ko01100meta_7591.072↑D-Mannitol-1-phosphate283.125138.928ko00051/ko02060meta_3124.861↓L-Ascorbic acid197.00545.633ko01100/ko01120/ko02060/ko00053/ko01110/ko00480meta_7614.397↑D-Sorbitol-6-phosphate283.12844.744ko02060/ko00051meta_7541.046↑N-Acetyl-D-glucosamine 6-phosphate282.034128.662ko01100/ko02060/ko01130/ko00520meta_20042.193↑Galactinol683.235370.331ko00052meta_20961.645↑Stachyose725.246464.357ko00052meta_81.198↓Pyruvate87.01154.515ko00440/ko00760/ko00900/ko01220/ko00630/ko01120/ko00622/ko01210/ko00040/ko00620/ko00770/ko00362/ko01130/ko00270/ko00010/ko00020/ko01110/ko00250//ko01100/ko00730/ko00330/ko00290/ko02060/ko00680/ko01230/ko00360/ko01200/ko01502/ko00710/ko00720/ko00030meta_18161.128↑UDP-N-acetylglucosamine606.0818147409.813ko00524/ko00520/ko00550/ko00540/ko01130/ko01502/ko01100meta_2931.293↓Citrate191.022376.386ko01130/ko01100/ko00720/ko01230/ko02020/ko00020/ko01110/ko01210/ko00250/ko01200/ko01120/ko00630meta_2112.899↑Isocitrate173.012478.821ko01230/ko01110/ko00020/ko01210/ko01200/ko01120/ko00630/ko01130/ko01100/ko00720meta_3651.042↑Alpha-ketoglutarate205.039396.502ko00720/ko01100/ko00053/ko00660/ko00430/ko00250/ko00365/ko00650/ko01200/ko00020/ko01110/ko01230/ko00340/ko00471/ko01130/ko01120/ko00220/ko00630/ko01210/ko00040/ko00300meta_852.181↑D-Xylulose131.037357.043ko00040/ko01100meta_1301.709↓D-Lyxose149.049301.108ko00040meta_1353.108↑Ribitol151.064232.243ko00740/ko01100/ko00040meta_11.551↓Dihydroxyacetone71.016198.357ko01100/ko01200/ko01120/ko00561/ko00680meta_41.205↓Glycolate75.010262.283ko00361/ko01110/ko00625/ko01120/ko01200/ko00630/ko01130/ko01100meta_741.033↓Citraconic acid129.02273.135ko00630/ko01200/ko01210/ko01100/ko00290/ko00660meta_7891.496↑D-Ribose 5-phosphate289.037442.521ko00440/ko01110/ko01230/ko01120/ko01200/ko00230/ko01130/ko00710/ko00030/ko01100


### 3.5. Effects of Specific Genes and Metabolites on XOS Transportation and Metabolism

Numerous carbohydrate uptake systems [24], especially ATP-binding cassette (ABC) importers, are encoded by bifidobacteria [25]. The affinity and specificity of ABC importers are defined largely by the extracellular solute-binding proteins (SBP) in bifidobacteria [26]. Compared to X2/X3, the gene expression of substrate-binding proteins (BAD_RS02255 and BAD_RS08340) and solute-binding proteins (BAD_RS07415, BAD_RS00805, and BAD_RS08285) was upregulated in the X5 treatment group, while one substrate-binding protein BAD_RS05605 was downregulated. The upregulation of binding protein indicates that XOS with higher polymerized degree indicated that required higher expression of binding proteins in B. adolescentis to better bind substrate. After the initial capture by SBPs, oligosaccharide ligands are released into the permease of the transporter, which is formed by two transmembrane domains (TMD), and the translocation is coupled to ATP-hydrolysis by cytoplasmic nucleotide-binding domains [27,28]. Compared with the X2/X3, the gene expression of ABC transporter permease (BAD_RS08280, BAD_RS02260, BAD_RS08210, BAD_RS08275, and BAD_RS08205) was upregulated in X5 treatment, while gene BAD_RS03215 was downregulated. Genes BAD_RS01005, BAD_RS08375, BAD_RS03325, and BAD_RS05655 may activate ATP-binding protein to participate in transportation. Compared with X2/X3, except that gene expression of BAD_RS05655 was downregulated, the remaining three ATP-binding proteins were upregulated (Table 1 and Figure 5). Therefore, high-polymerized XOS require highly expressed permease and ATP-binding protein to transport substrates into cells in B. adolescentis.Figure 5
Proposed model for the catabolism of different polymerized XOS inB. adolescents. The numbers indicated the respective genes in the genome of B. adolescents, omitting the “BAD_RS.”After entering the cell through cell membrane, XOS are degraded by endo-1,4-beta-xylanase (xylA) andβ-xylosidase (xynB). In general, xylA randomly cleaves β-1,4 glycosidic bond of XOS, while xynB degrades XOS at the nonreducing end to release D-xylose [29]. Compared to X2/X3, the gene expressions of xynA (BAD_RS08020) and xynB (BAD_RS02270 and BAD_RS06360) in X5 treatment were upregulated (Table 2 and Figure 5). Both xylanase and xylosidase belong to glycoside hydrolase 43 family protein, for which the higher expression is conducive to the degradation of XOS [30]. In the present study, the gene expression related to transport and degradation of different polymerized XOS in B. adolescentis had a considerable difference, consistent with their functional association.After XOS were degraded to D-xylose, D-xylose was isomerized to D-xylulose using xylose isomerase (xylA). Compared to the X2/X3, the expression of gene encoding xylose isomerase (BAD_RS02240) was not significantly different, while the content of D-xylulose (meta_85) was significantly increased in X5 treatment (Table3 and Figure 5). Xylulose was further phosphorylated to xylulose-5-phosphate by xylulose kinase, but the xylulose kinase coding gene (BAD_RS06130) between the two treatment groups was not significantly different. Hereafter, xylulose 5-phosphate is converted to glyceraldehyde 3-phosphate using xylulose-5-phosphate phosphoketolase (XPPKT) [31, 32]. Compared to the X2/X3 treatment, the expression of gene encoding XPPKT (BAD_RS03665) was downregulated in the X5 treatment, but the difference was not significant. Glyceraldehyde 3-phosphate produces diphosphoglyceric acid under the action of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Diphosphoglyceric acid continues to generate phosphoenolpyruvate using phosphoglycerate kinase (PGK). Compared with X2/X3, the expression of gene GAPDH (BAD_RS05735) and PGK (BAD_RS04470) was slightly downregulated in X5 treatment, but the difference was not significant. Phosphoenolpyruvate is converted to pyruvate after dephosphorylation (Figure 5). Metabolome analysis showed that phosphoenolpyruvate (meta_183) and pyruvate (meta_8) were downregulated in the X5 treatment group compared with X2/X3 (Table 3). The pyruvate is furtherly metabolized to different organic acids, such as lactic acid. The catabolic pathway of XOS is consistent with the pathway of B. adolescentis LMG10502 studied by Lagaert et al. [33], but it is different from the metabolic pathway of B. longum, which degrades XOS outside the cell by xylanase and then transports the degraded xylose into the cell for further metabolism [4].


## 3.1. Growth Characteristics ofB. adolescentis on X2/X3 and X5

The HPLC analysis of the prepared X2/X3 and X5 was shown in Supplementary Figure1. According to the results of the composition analysis, the purity of X2/X3 and X5 was 87.29% and 90.05%, respectively. Then, the X2/X3 and X5 were used as a carbon source to cultivate B. adolescentis. As shown in Figure 1, the growth of B. adolescentis on different polymerized XOS was significantly higher than that of the blank control group without a carbon source. The OD value of cultures of B. adolescentis with X2/X3 as the carbon source is the highest, X5 is the second, and xylose is the lowest; however, the lag and logarithmic phase is the shortest. Also, a rapid growth rate was observed at 8–20 h. The growth yield (stable phase) on X2/X3 was about 1.3-fold greater than that on X5, indicating that XOS at a lower degree of polymerization was more preferred by B. adolescentis. Bifidobacterium can preferentially hydrolyze XOS with a low degree of polymerization and then use monosaccharides for further metabolism. This result is consistent with the conclusion reported by Okazaki that oligosaccharides are more easily absorbed and utilized by bifidobacteria than by polysaccharides and corresponding monosaccharides [9]. The composition of X2 and X3 is entirely composed of xylose units and does not contain arabinosyl groups and substituents such as methoxy and acetyl groups, while X5 often contains arabinosyl isomers, which should firstly be degraded by arabinosidase [23]; this higher complexity may lead to a significant difference in the proliferation effect of X2/X3 and X5 on B. adolescentis.Figure 1
Growth ofB. adolescentis on different polymerized XOS and control medium (no carbohydrate).


## 3.2. Annotation and Analysis of Differentially Expressed Genes (DEGs) ofB. adolescentis on X2/X3 and X5

A total of 268 DEGs were identified forB. adolescentis grown on X2/X3 and X5, including 163 upregulated genes and 105 downregulated genes (Supplementary Figure 2). The DEGs involved in biological functions were further analyzed by KEGG, and 20 pathways were predicted (Figure 2). ABC transporters, starch and sucrose metabolism, pyrimidine metabolism, and galactose metabolism are the highly represented categories. Among these pathways, the QValue of ABC transporters is the lowest (red color), suggesting the different encoding genes of ABC transporters is the most.Figure 2
KEGG pathway enrichment analysis of DEGs (X2/X3 vs. X5). The vertical axis indicates the name of the KEGG pathway, and the horizontal axis indicates the rich factor. The dot size indicates the number of differentially expressed genes in the pathway, and the color of the dots corresponds to differentQ values.The DEGs involved in the ABC transporters are shown in Table1. In the ABC transporter pathway, 33 genes were significantly upregulated. Genes BAD_RS00340 and BAD_RS07050 encoded ABC transporter. Genes BAD_RS01000, BAD_RS07410, BAD_RS02260, BAD_RS04685, BAD_RS00815, BAD_RS00810, BAD_RS08280, BAD_RS02545, BAD_RS06685, BAD_RS08205, BAD_RS08275, BAD_RS03705, BAD_RS06690, and BAD_RS08210 encoded ABC transporter permease. Genes BAD_RS02255, BAD_RS07415, BAD_RS01495, BAD_RS00805, BAD_RS00390, BAD_RS08285, BAD_RS08340, BAD_RS00990, and BAD_RS06680 encoded ABC transporter substrate-binding protein. Genes BAD_RS08285, BAD_RS00805, and BAD_RS02355 encoded solute-binding protein. Genes BAD_RS04090, BAD_RS00495, BAD_RS01005, BAD_RS03710, and BAD_RS00520 encoded ABC transporter ATP-binding protein. Five genes (BAD_RS02355, BAD_RS05605, BAD_RS03210, BAD_RS03215, and BAD_RS05655), which are ABC transporter-related genes, were significantly downregulated after X5 treatment.Table 1
DEGs involved in the related ABC transporter during the growth ofB. adolescentis on X5 compared to X2/X3 assessed by RNA-seq.
Gene no.aLog2 (Fc)bP valueFDRSymbolAnnotationcLinear FMPK valuedX2/X3X5BAD_RS022553.01↑00yurOSugar ABC transporter substrate-binding protein989.287940.17BAD_RS074152.79↑4.47E − 861.40E − 84mdxEABC transporter, solute-binding protein51.88360.4BAD_RS074102.75↑2.30E − 191.78E − 18amyDABC transporter permease16.53111.24BAD_RS022652.57↑00yurMThiamine ABC transporter ATP-binding protein514.593056.15BAD_RS022602.57↑00malFSugar ABC transporter permease4662759.99BAD_RS014952.51↑2.51E − 2612.23E − 259TP_0034ABC transporter substrate-binding protein319.831819.21BAD_RS008052.17↑00yurOSolute-binding protein of ABC transporter system618.732790.2BAD_RS046851.87↑0.00720.0164-ABC transporter permease6.8425.03BAD_RS003851.75↑0.01190.0254livFABC-type branched-chain amino acid transport systems ATPase component5.217.55BAD_RS003901.74↑0.00120.0031BR1785Branched-chain amino acid ABC transporter substrate-binding protein6.0520.15BAD_RS008151.58↑3.35E − 738.39E − 72araQSugar ABC transporter permease326.41974.92BAD_RS070501.56↑00lipOABC transporter3361.719912.7BAD_RS008101.53↑2.70E − 625.55E − 61yurNSugar ABC transporter permease278.86804.48BAD_RS082801.51↑3.55E − 1001.18E − 98msmFSugar ABC transporter permease491.141401.37BAD_RS082851.51↑7.82E − 1934.82E − 191ugpBABC transporter, solute-binding protein686.941954.61BAD_RS040901.51↑0.00080.0022TM_0352Macrolide ABC transporter ATP-binding protein15.4243.86BAD_RS004951.46↑1.94E − 312.32E − 30MT1311Multidrug ABC transporter ATP-binding protein81.69225.1BAD_RS010051.39↑0.02420.0478fbpCABC transporter ATP-binding protein6.0715.95BAD_RS083401.36↑1.22E − 074.99E − 07msmESugar ABC transporter substrate-binding protein27.5970.62BAD_RS009901.31↑0.00090.0024-ABC transporter substrate-binding protein13.9134.5BAD_RS037101.30↑9.00E − 050.0002lolDABC transporter ATP-binding protein26.5365.31BAD_RS082101.27↑1.50E − 1075.58E − 106amyDPermease of ABC transporter possibly for oligosaccharides933.342256.42BAD_RS005201.27↑4.19E − 183.02E − 17TpdAmino acid ABC transporter substrate-binding protein173.12416.3BAD_RS025451.25↑0.00800.0178gsiCABC transporter permease11.6527.77BAD_RS033251.22↑2.33E − 101.15E − 09MJ1508ABC transporter ATP-binding protein85.46198.92BAD_RS066801.17↑2.10E − 262.13E − 25yxeMAmino acid ABC transporter substrate-binding protein228.62513.46BAD_RS066851.15↑3.29E − 172.29E − 16tcyLABC transporter permease196.97437.68BAD_RS082051.15↑2.91E − 565.54E − 55amyCSugar ABC transporter permease603.51334.63BAD_RS082751.13↑1.22E − 401.82E − 39amyCABC transporter permease413.73903.85BAD_RS037051.11↑5.91E − 061.98E − 05-ABC transporter permease35.9577.6BAD_RS003401.10↑1.30E − 311.61E − 30PipABC transporter109.76235.38BAD_RS066901.03↑2.25E − 057.07E − 05patMABC transporter permease65.13133.26BAD_RS023551.35↓5.99E − 143.50E − 13braCSolute-binding protein of ABC transporter for branched-chain amino acids171.3167.28BAD_RS056051.53↓4.01E − 122.20E − 11-Sugar ABC transporter substrate-binding protein247.0285.73BAD_RS032102.07↓1.34E − 442.10E − 43lolDPeptide ABC transporter ATP-binding protein496.58118.13BAD_RS032152.76↓4.00E − 1862.37E − 184macBABC transporter permease480.9171.17BAD_RS056552.93↓8.53E − 062.81E − 05bceAABC transporter ATP-binding protein31.994.2aGene number referenced as B. adolescentis being alphabet and a five-digit number. bSignificance of fold change data is judged by having a P value of no more than 0.01. cGene annotations were blasted against Swiss-Prot. dFPKM (fragments per kilobase of exon per million fragments mapped) values for cultures on media with X2/X3 or X5 treatment.The DEGs involved in carbohydrate metabolism are shown in Table2. Compared to X2/X3 treatment, five genes (BAD_RS06400, BAD_RS07395, BAD_RS07400, BAD_RS08325, and BAD_RS08455) encoded beta-galactosidase and two genes (BAD_RS08195 and BAD_RS08270) encoded alpha-amylase related to starch and sucrose metabolism (ko00500), galactose metabolism pathway (ko00052), glycan degradation (ko00511), and sphingolipid metabolism (ko00600) were significantly upregulated after X5 treatment. The beta-xylosidase that encoded gene BAD_RS02270 was involved in amino sugar and nucleotide sugar metabolism (ko00520) and starch and sucrose metabolism (ko00500). Moreover, two genes (BAD_RS06365 and BAD_RS08480) encoded beta-glucosidase related to starch and sucrose metabolism (ko00500). Two genes (BAD_RS06360 and BAD_RS08405) encoded glycoside hydrolase involved in starch and sucrose metabolism (ko00500). In addition, gene BAD_RS01050 coded shikimate kinase, BAD_RS05480 coded mannan endo-1,4-beta-mannosidase, BAD_RS01040 coded 6-phosphogluconate dehydrogenase, BAD_RS02150 coded lactaldehyde reductase, BAD_RS07445 coded L-ribulose-5-phosphate 4-epimerase, BAD_RS01580 coded UDP-N-acetylenolpyruvoylglucosamine reductase, which was involved in the biosynthesis of antibiotics (ko01130), peptidoglycan biosynthesis (ko00550), microbial metabolism in diverse environments (ko01120), carbon metabolism (ko01200), fructose and mannose metabolism (ko00051), pentose phosphate pathway (ko00030), glyoxylate and dicarboxylate metabolism (ko00630), propanoate metabolism (ko00640), and pentose and glucuronate interconversions (ko00040), which was significantly upregulated after X5 treatment. Only one gene, BAD_RS07575, encoded alpha-1,4-glucan-maltose-1-phosphate maltosyltransferase, which was significantly downregulated after X5 treatment.Table 2
DEGs involved in related carbohydrate metabolism in the KEGG pathway during the growth ofB. adolescentis on X5 compared to X2/X3 assessed by RNA-seq.
Gene no.Log2 (Fc)p valueFDRSymbolAnnotationLinear FMPK valueKEGG pathwayX2/X3X5BAD_RS064001.04↑4.00E − 050.0001bgaBBeta-galactosidase19.7940.65ko00052BAD_RS073951.07↑1.12E − 188.34E − 18bgaBBeta-galactosidase I84.64177.96ko00052BAD_RS074002.10↑7.31E − 185.21E − 17BGAL16Beta-galactosidase13.0656.17ko00052/ko00600/ko00511BAD_RS081951.78↑00malLAlpha-amylase733.052512.17ko00500/ko00052BAD_RS082701.36↑1.8E − 1489.3E − 147malLAlpha-amylase493.041264.3ko00500/ko00052BAD_RS083251.62↑1.75E − 231.54E − 22lacZBeta-galactosidase25.277.45ko00052/ko00600/ko00511BAD_RS084551.04↑3.10E − 354.07E − 34lacZBeta-galactosidase126.46259.45ko00052/ko00600/ko00511BAD_RS022702.22↑5.69E − 2474.56E − 245xynBBeta-xylosidase251.31174.15ko01100/ko00500/ko00520BAD_RS063601.08↑2.76E − 565.32E − 55xynBGlycoside hydrolase 43 family protein362.57764.37ko01100/ko00500/ko00520BAD_RS063651.52↑2.76E − 1231.23E − 121exgABeta-glucosidase475.021358.67ko00500BAD_RS075751.18↓1.84E − 1127.20E − 111glgEAlpha-1,4-glucan--maltose-1-phosphate maltosyltransferase1093.58481.27ko01100/ko00500/BAD_RS084051.03↑4.88E − 061.64E − 05bglBGlycosyl hydrolase21.7244.24ko01100/ko01110/ko00500/ko00460BAD_RS084801.11↑2.43E − 181.79E − 17bglBBeta-glucosidase66.25142.54ko01100/ko01110/ko00500/ko00460BAD_RS054801.31↑4.84E − 082.04E − 07BAD_1030Mannan endo-1,4-beta-mannosidase13.7934.24ko00051BAD_RS015801.05↑6.05E − 123.28E − 11murBUDP-N-acetylenolpyruvoylglucosamine reductase93.71194.42ko01100/ko00520/ko00550BAD_RS074451.38↑5.29E − 306.09E − 29ulaFL-ribulose-5-phosphate 4-epimerase229.09594.72ko01100/ko00040BAD_RS010402.09↑6.41E − 245.84E − 23Gnd6-Phosphogluconate dehydrogenase45.07192.09ko01100/ko01110/ko01130/ko01120/ko01200/ko00480BAD_RS010503.46↑2.25E − 231.97E − 22IdnkShikimate kinase15.68172.02ko01100/ko01110/ko01130/ko01120/ko01200/ko00030BAD_RS021501.69↑00fucOLactaldehyde reductase1795.215803.32ko01120/ko00630/ko00640


## 3.3. Validation of Transcript Abundance Using qRT-PCR

To verify the RNA-seq results, the mRNA expressions of 16 selected candidate genes (eight upregulated and eight downregulated) were measured by qRT-PCR. The normalized fold expressions of 16 DEGs are shown in Figure3(a); the results showed that the upregulated and downregulated levels of these genes are consistent with RNA-seq. Furthermore, the expression levels of 16 DEGs with qRT-PCR were compared to those of DEGs with RNA-seq by the linear fitting. A significant correlation (R2 = 0.98642) was found between RNA-seq and qRT-PCR (Figure 3(b)). The qRT-PCR results are consistent with their transcript abundance in RNA-seq, which verified the accuracy of the DEGs from RNA-seq analyses.Figure 3
Results of expression profiles (a) and the linear fitting (b) of DEGs by qRT-PCR. Black column: upregulated; blank column: downregulated.
(a)(b)


## 3.4. Metabolite Profile and KEGG Mapping of Metabolites

The metabolites profiling ofB. adolescentis was performed using LC-MS. The primary metabolites are amino acids, organic acids, fatty acids, polyhydroxy acids, sugars, polyols, and N-compounds. A total of 192 different metabolites (MS2) were identified for X2/X3 and X5 treatments (p < 0.05, log2FC > 1), including 127 upregulated metabolites and 65 downregulated metabolites. The different metabolites were annotated in 50 KEGG pathways. ABC transporters and the phosphotransferase system (PTS) were classified as environmental information processing. Aminoacyl-tRNA biosynthesis was included in genetic information processing. The remaining 47 pathways belong to metabolism processing, microbial metabolism in diverse environments, and biosynthesis of secondary metabolites, which are the most highly represented in metabolism processing (Figure 4).Figure 4
The annotated and classified results of the differential metabolite in the KEGG pathway.Different metabolites involved in carbohydrate transport and metabolism are shown in Table3. Compared to X2/X3 treatment, ten metabolites (meta_15, meta_376, meta_166, meta_1695, meta_651, meta_246, meta_219, meta_527, meta_82, and meta_991), which are glycerol, D-ribose, D-mannose, maltotriose, D-biotin, D-mannitol, L-arginine, L-cystine, L-isoleucine, and cellobiose, are significantly different in the ABC transporters pathway (ko02010) for X5 treatment. Also, eight metabolites, including D-mannose, cellobiose, D-mannitol-1-phosphate (meta_759), L-ascorbic acid (meta_312), D-sorbitol-6-phosphate (meta_761), N-acetyl-D-glucosamine-6-phosphate (meta_754), D-mannitol, and pyruvate (meta_8) are significantly different in the phosphotransferase system (PTS) (ko02060) for X5 compared to X2/X3 treatment. In addition, these metabolites, such as D-mannitol, D-mannose, D-mannitol-1-phosphate, and D-sorbitol-6-phosphate, were involved in fructose and mannose metabolism (ko00051). D-Ribose, pyruvate, and D-ribose-5-phosphate are involved in the pentose phosphate pathway (ko00030). However, galactinol, stachyose, and glycerol are involved in galactose metabolism (ko00052). Among all the metabolites, pyruvate (meta_8) is involved in most pathways, including pyruvate metabolism (ko00620), pantothenate and CoA biosynthesis (ko00770), glycolysis/gluconeogenesis (ko00010), and citrate cycle (ko00020).Table 3
Metabolites involved in related carbohydrate transport and metabolism in the KEGG pathway during the growth ofB. adolescentis on X5 compared to X2/X3 assessed by metabolome.
Meta IDLog2 (Fc)MS2 namemzmedrtmedKEGG_pathway_annotationmeta_151.591↑Glycerol91.042107.553ko00052/ko00040/ko02010/ko01100/ko00561meta_3762.919↓D-Ribose209.070204.675ko02010/ko00030/ko02030meta_1661.701↑D-Mannose161.048418.573ko00520/ko02060ko00052/ko00051/ko02010/ko01100meta_16951.226↑Maltotriose563.190430.279ko02010meta_6511.260↑D-Biotin260.109104.804ko00780/ko02010/ko01100meta_2461.362↑D-Mannitol182.077282.069ko02010/ko00051/ko02060meta_2191.027↑L-Arginine173.106380.973ko00261/ko00970/ko01100/ko00472/ko01130/ko00331/ko00220/ko02010/ko01110/ko00330/ko01230/meta_5271.820↑L-Cystine239.020413.417ko02010/ko00270meta_821.306↑L-Isoleucine130.089221.442ko02010/ko01230/ko00970/ko01130/ko00290/ko00280/ko00460/ko01210/ko01110meta_9911.647↑Cellobiose341.113281.354ko00500/ko02060/ko02010/ko01100meta_7591.072↑D-Mannitol-1-phosphate283.125138.928ko00051/ko02060meta_3124.861↓L-Ascorbic acid197.00545.633ko01100/ko01120/ko02060/ko00053/ko01110/ko00480meta_7614.397↑D-Sorbitol-6-phosphate283.12844.744ko02060/ko00051meta_7541.046↑N-Acetyl-D-glucosamine 6-phosphate282.034128.662ko01100/ko02060/ko01130/ko00520meta_20042.193↑Galactinol683.235370.331ko00052meta_20961.645↑Stachyose725.246464.357ko00052meta_81.198↓Pyruvate87.01154.515ko00440/ko00760/ko00900/ko01220/ko00630/ko01120/ko00622/ko01210/ko00040/ko00620/ko00770/ko00362/ko01130/ko00270/ko00010/ko00020/ko01110/ko00250//ko01100/ko00730/ko00330/ko00290/ko02060/ko00680/ko01230/ko00360/ko01200/ko01502/ko00710/ko00720/ko00030meta_18161.128↑UDP-N-acetylglucosamine606.0818147409.813ko00524/ko00520/ko00550/ko00540/ko01130/ko01502/ko01100meta_2931.293↓Citrate191.022376.386ko01130/ko01100/ko00720/ko01230/ko02020/ko00020/ko01110/ko01210/ko00250/ko01200/ko01120/ko00630meta_2112.899↑Isocitrate173.012478.821ko01230/ko01110/ko00020/ko01210/ko01200/ko01120/ko00630/ko01130/ko01100/ko00720meta_3651.042↑Alpha-ketoglutarate205.039396.502ko00720/ko01100/ko00053/ko00660/ko00430/ko00250/ko00365/ko00650/ko01200/ko00020/ko01110/ko01230/ko00340/ko00471/ko01130/ko01120/ko00220/ko00630/ko01210/ko00040/ko00300meta_852.181↑D-Xylulose131.037357.043ko00040/ko01100meta_1301.709↓D-Lyxose149.049301.108ko00040meta_1353.108↑Ribitol151.064232.243ko00740/ko01100/ko00040meta_11.551↓Dihydroxyacetone71.016198.357ko01100/ko01200/ko01120/ko00561/ko00680meta_41.205↓Glycolate75.010262.283ko00361/ko01110/ko00625/ko01120/ko01200/ko00630/ko01130/ko01100meta_741.033↓Citraconic acid129.02273.135ko00630/ko01200/ko01210/ko01100/ko00290/ko00660meta_7891.496↑D-Ribose 5-phosphate289.037442.521ko00440/ko01110/ko01230/ko01120/ko01200/ko00230/ko01130/ko00710/ko00030/ko01100


## 3.5. Effects of Specific Genes and Metabolites on XOS Transportation and Metabolism

Numerous carbohydrate uptake systems [24], especially ATP-binding cassette (ABC) importers, are encoded by bifidobacteria [25]. The affinity and specificity of ABC importers are defined largely by the extracellular solute-binding proteins (SBP) in bifidobacteria [26]. Compared to X2/X3, the gene expression of substrate-binding proteins (BAD_RS02255 and BAD_RS08340) and solute-binding proteins (BAD_RS07415, BAD_RS00805, and BAD_RS08285) was upregulated in the X5 treatment group, while one substrate-binding protein BAD_RS05605 was downregulated. The upregulation of binding protein indicates that XOS with higher polymerized degree indicated that required higher expression of binding proteins in B. adolescentis to better bind substrate. After the initial capture by SBPs, oligosaccharide ligands are released into the permease of the transporter, which is formed by two transmembrane domains (TMD), and the translocation is coupled to ATP-hydrolysis by cytoplasmic nucleotide-binding domains [27,28]. Compared with the X2/X3, the gene expression of ABC transporter permease (BAD_RS08280, BAD_RS02260, BAD_RS08210, BAD_RS08275, and BAD_RS08205) was upregulated in X5 treatment, while gene BAD_RS03215 was downregulated. Genes BAD_RS01005, BAD_RS08375, BAD_RS03325, and BAD_RS05655 may activate ATP-binding protein to participate in transportation. Compared with X2/X3, except that gene expression of BAD_RS05655 was downregulated, the remaining three ATP-binding proteins were upregulated (Table 1 and Figure 5). Therefore, high-polymerized XOS require highly expressed permease and ATP-binding protein to transport substrates into cells in B. adolescentis.Figure 5
Proposed model for the catabolism of different polymerized XOS inB. adolescents. The numbers indicated the respective genes in the genome of B. adolescents, omitting the “BAD_RS.”After entering the cell through cell membrane, XOS are degraded by endo-1,4-beta-xylanase (xylA) andβ-xylosidase (xynB). In general, xylA randomly cleaves β-1,4 glycosidic bond of XOS, while xynB degrades XOS at the nonreducing end to release D-xylose [29]. Compared to X2/X3, the gene expressions of xynA (BAD_RS08020) and xynB (BAD_RS02270 and BAD_RS06360) in X5 treatment were upregulated (Table 2 and Figure 5). Both xylanase and xylosidase belong to glycoside hydrolase 43 family protein, for which the higher expression is conducive to the degradation of XOS [30]. In the present study, the gene expression related to transport and degradation of different polymerized XOS in B. adolescentis had a considerable difference, consistent with their functional association.After XOS were degraded to D-xylose, D-xylose was isomerized to D-xylulose using xylose isomerase (xylA). Compared to the X2/X3, the expression of gene encoding xylose isomerase (BAD_RS02240) was not significantly different, while the content of D-xylulose (meta_85) was significantly increased in X5 treatment (Table3 and Figure 5). Xylulose was further phosphorylated to xylulose-5-phosphate by xylulose kinase, but the xylulose kinase coding gene (BAD_RS06130) between the two treatment groups was not significantly different. Hereafter, xylulose 5-phosphate is converted to glyceraldehyde 3-phosphate using xylulose-5-phosphate phosphoketolase (XPPKT) [31, 32]. Compared to the X2/X3 treatment, the expression of gene encoding XPPKT (BAD_RS03665) was downregulated in the X5 treatment, but the difference was not significant. Glyceraldehyde 3-phosphate produces diphosphoglyceric acid under the action of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Diphosphoglyceric acid continues to generate phosphoenolpyruvate using phosphoglycerate kinase (PGK). Compared with X2/X3, the expression of gene GAPDH (BAD_RS05735) and PGK (BAD_RS04470) was slightly downregulated in X5 treatment, but the difference was not significant. Phosphoenolpyruvate is converted to pyruvate after dephosphorylation (Figure 5). Metabolome analysis showed that phosphoenolpyruvate (meta_183) and pyruvate (meta_8) were downregulated in the X5 treatment group compared with X2/X3 (Table 3). The pyruvate is furtherly metabolized to different organic acids, such as lactic acid. The catabolic pathway of XOS is consistent with the pathway of B. adolescentis LMG10502 studied by Lagaert et al. [33], but it is different from the metabolic pathway of B. longum, which degrades XOS outside the cell by xylanase and then transports the degraded xylose into the cell for further metabolism [4].


## 4. Conclusions

From the present study, we can conclude thatlow-polymerized XOS promoted the growth of B. adolescentis than the high-polymerized one. When different polymerized XOS were used as a single carbon source, the related genes in annotated 51 metabolic pathways were significantly different, especially the ABC transporter pathway. Moreover, 192 differential metabolites were noted on MS2, and the mainly identified metabolites were organic acids. In summary, the expression of ABC transporter-related genes was significantly different during the process of different polymerized XOS transported into cells; however, the expression of most genes and metabolites related to XOS metabolism was not significantly different after entering the bifidus pathway, indicating the related proteins of ABC transport system played a key role on the process of B. adolescentis utilizing different polymerized XOS.



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*Source: 4412324-2022-03-07.xml*