Characteristics of Intestinal Microecology during Mesenchymal Stem Cell-Based Therapy for Mouse Acute Liver Injury

Background The mechanisms of mesenchymal stem cell (MSC) transplantation to protect against acute liver injury have been well studied within the liver. However, the associated changes in the intestinal microbiota during this process are poorly understood. Methods In this study, compact bone-derived MSCs were injected into mice after carbon tetrachloride (CCl4) administration. Potential curative effect of MSC was evaluated by survival rate and biochemical and pathological results. Overall structural changes of microbial communities and alterations in the intestinal microbiota were assessed by sequenced 16S rRNA amplicon libraries from the contents of the cecum and colon. Results MSCs significantly reduced the serum levels of aspartate transaminase and alanine transaminase and improved the histopathology and survival rate. Lower expression and discontinuous staining of zonula occludens, as well as disrupted tight junctions, were observed in CCl4-treated mice at 48 h compared with MSC-transplanted mice. Moreover, MSC transplantation to the liver leads to intestinal microbiota changes that were reflected in the decreased abundance of Bacteroidetes S24-7 and Bacteroidaceae and increased abundance of Firmicutes Clostridiales, Ruminococcaceae, and Lactobacillus at the initial time point compared with that in CCl4-treated mice. In addition, phylogenetic investigation of communities by the reconstruction of unobserved states (PICRUSt) based on the Greengenes database revealed functional biomarkers of MSC-transplanted mice involved in cell motility, signal transduction, membrane transport, transcription, and metabolism of lipids, cofactors, vitamins, terpenoids, and polyketides, as well as xenobiotics. Conclusion The initial alterations in the Firmicutes/Bacteroidetes ratio, which resulted from MSC infusion to the liver, maintain intestinal mucosal biology and homeostasis that may be beneficial to liver repair.

Signals from the gut microbiota have been associated with maintenance of healthy host functions and various diseases, including nonalcoholic fatty liver disease/nonalcoholic steatohepatitis (NAFLD/NASH), type 1/2 diabetes, obesity, inflammatory bowel disease, and autism [16]. For liver diseases, microbial dysbiosis, exposing the gut mucosal cells to potentially harmful substances, including enteric bacterial pathogens [17], lipopolysaccharide (LPS), and endotoxins, as well as secreted cytokines (e.g., tumor necrosis factor-α) [18], can disrupt TJs and increase intestinal permeability and expose the liver to potentially proinflammatory bacterial products that may promote hepatic steatosis [19,20]. However, the role of gut microbiota in MSC therapy of acute liver injury remains unknown. This is the first study to reveal the gut microbiome and its related pathways, as well as intestinal epithelial TJs, following MSC treatment of CCl 4 -induced acute liver injury.

Materials and Methods
2.1. Animals. Eight-week-old male wild-type C57BL/6 mice (weight, 20-25 g) (Shanghai SLAC Laboratory Animal Co. Ltd., Shanghai, China) were used for the induction of acute liver injury, and inbred 2-week-old green fluorescent protein (GFP) transgenic mice (male and female, C57BL/6 background, Nanjing Biomedical Research Institute of Nanjing University, Nanjing, China) were used for the isolation and culture of MSCs. Wild-type C57BL/6 mice were housed in a barrier environment, and GFP transgenic mice were housed in an insulated environment. All animals received humane care, and all procedures were approved by the Animal Care Ethics Committee of the First Affiliated Hospital, Zhejiang University.

Cells.
The isolation and culture of mouse MSCs from compact bone were performed as previously described [21]. The cells were cultured in an MSC medium (OriCell™ C57BL/6 MSC complete medium; Cyagen Biosciences, Guangzhou, China) at 37°C in a 5% CO 2 incubator (HERA-cell®150; Thermo Fisher Scientific Inc., Waltham, MA, USA). MSCs from passages 5 and 7 were used throughout the experiments. The phenotype and multipotential differentiation of infused MSCs were investigated (Supplementary Figure S1 online).

CCl 4 -Induced Acute Liver Injury and Sample Collection.
The solution of CCl 4 (Sigma-Aldrich, St. Louis, MO, USA) and olive oil (Sigma-Aldrich) at a ratio of 1 : 1 and dose of 3 mL/kg body weight was administered intraperitoneally (i.p.) in a single dose. Control mice were administered an i.p. injection of an equal volume of olive oil (3 mL/kg) only. Next, 5 × 10 5 MSCs in 100 μL of phosphate-buffered saline (PBS) or 100 μL of PBS were injected into the mice via the caudal vein 6 h after CCl 4 administration.
The mice were anesthetized by i.p. injection of 4% chloral hydrate (Sangon Biotech, Shanghai, China) at a dose of 10 μL/g body weight, and blood samples were drawn from the inferior vena cava at 48 h, 1 week (w), and 2 w after CCl 4 administration. Following exsanguination, the liver, small intestinal segments, and cecum and colon contents were precisely dissected and harvested, snap frozen in liquid nitrogen, and stored at -80°C until further analysis. Portions of the liver and ileum were immediately fixed in 10% neutral buffered formalin for histopathologic examination.

Liver Biochemistry and Intestinal and Liver
Histology. For histopathologic analysis, formalin-fixed liver and ileum samples were paraffin-embedded, sectioned (5 μm thickness), and stained with hematoxylin and eosin. The sections were randomly numbered prior to reading and observed by an experienced pathologist. Images were acquired using a NanoZoomer 2.0-RS scanner (Hamamatsu Photonics KK, Hamamatsu City, Japan) equipped with scanner software. Terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) staining (Roche Diagnostics GmbH, Mannheim, Germany) was performed following the manufacturer's instruction and counterstained with 4 ′ , 6-diamidino-2-phenylindole (DAPI). The alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities of serum samples were measured using a dry chemistry analyzer (FUJI DRI-CHEM 4000ie; Fujifilm Corporation, Tokyo, Japan) according to the manufacturer's instructions.
2.8. Bacterial DNA Sequencing. Following homogenization of the mouse cecum and colon contents using glass beads in a Precellys 24 homogenizer (Bertin Technologies, Montigny, France), bacterial DNA was extracted using the QIAamp DNA Stool Mini Kit (Qiagen). Primers 319F (5 ′ -ACTCCTACGGGAGGCAGCAG-3 ′ ) and 806R (5 ′ -GGAC TACHVGGGTWTCTAAT-3 ′ ) were used to amplify the V3-V4 domain of the 16S ribosomal RNA (rRNA) gene. PCR was performed as described previously [22]. The cycling parameters were as follows: 30 s of denaturation at 98°C, followed by 30 cycles of 15 s at 98°C, annealing for 15 s at 58°C, and elongation for 15 s at 72°C, with a final extension at 72°C for 60 s. The amplicons were then subjected to normalization, pooling, and pyrosequencing using the Illumina Miseq desktop sequencer (2 × 300 bp paired-end run). QIIME (version 1.9.0, http://qiime.org) was used to perform sequence read processing, quality trimming, demultiplexing, and taxonomic assignments [23]. The alpha diversity, including the indexes of Shannon, Simpson, phylogenetic diversity-(PD-) whole tree, Chao1, and observed species, was calculated using QIIME. Weighted UniFrac principal coordinate analysis (PCoA) was performed using QIIME. Functional profiling of microbial communities was predicted by the phylogenetic investigation of communities by the reconstruction of unobserved states (PICRUSt) based on the Greengenes database [24]. The linear discriminant analysis (LDA) effect size (LEfSe) was conducted to estimate the effect size of each taxon with significant differential abundance [25]. The output file was further analyzed using statistical analysis of metagenomic profile (STAMP) software [26].
2.9. Statistical Analysis. We carried out two groups' comparisons by t-test (normal distribution and equal variance) or White's nonparametric t-test (nonnormal distribution) using SPSS (version 21.0; IBM Corp., Armonk, NY, USA). All the data are expressed as means ± standard deviation. A p value < 0.05 was deemed to indicate statistical significance.

Overall Structural Changes of Microbial Communities
following CCl 4 and MSC Treatment. After the generation of multiplexed reads based on the nucleotide barcode of each sample and filtering the sequence reads for quality using QIIME, 2,132,586 high-quality sequences were acquired from all samples, with an average of 50,776 (range: 30,927-70,878) sequences per sample used for downstream statistical analysis. Specifically, 319,780 sequences were obtained from the olive oil control; 291,936, 314,004, and 313,643 sequences were obtained from the CCl 4 -treated groups (48 h, 1 w, and 2 w after CCl 4 treatment, respectively); and 347,219, 273,154, and 272,850 sequences were obtained from the MSC-transplanted groups (48 h, 1 w, and 2 w after CCl 4 treatment, respectively). All the sequences were clustered into 1517 operational taxonomic units (OTUs) using QIIME based on 97% sequence similarity and classified into 249 bacterial groups at the genus level. Each sample and group OTU number were calculated using QIIME. Specifically, there were 586 species-level OTUs in the olive oil control; 656, 896, and 794 OTUs in the CCl 4 -treated groups (48 h, 1 w, and 2 w after CCl 4 treatment, respectively); and 713, 596, and 668 OTUs in the MSC-transplanted groups (48 h, 1 w, and 2 w after CCl 4 treatment, respectively). Good coverage of all samples and groups was more than 99.5%, indicating sufficient community coverage. Details are shown in Table 1 and Table S1. At 48 h, compared with the CCl 4 -treated group, the MSC-transplanted group had a higher Shannon index (4.9732 vs. 5.3811) and lower Simpson index (0.9336 vs. 0.9279), and there were no statistically significant differences (p = 0 055 and p = 0 680, respectively). However, there were significant differences (p = 0 009) between the two groups at 48 h for the PD whole-tree index (15.8604 vs. 19.0074). The richness indices Chao1 (347.88065 vs. 459.8725) and observed species (280 vs. 374) between the two groups at 48 h showed no significant differences (p = 0 067 and p = 0 055). At 1 and 2 w, there were no significant differences between the CCl 4 -treated and MSC-transplanted groups for alpha diversity measures (Shannon and Simpson indices), PD whole-tree index, and richness indices Chao1 and observed species (Figure 1(a)).
Interestingly, the CCl 4 -treated groups showed steadily increased alpha diversity values (Shannon and Simpson indices) and richness indices (Chao1 and observed species) over time. The MSC-transplanted groups showed increased alpha diversity values (Shannon and Simpson indices) but decreased richness indices (Chao1 and observed species) over time (Table 1). Rarefaction curves for the observed species approached a plateau, indicating that the sequencing effort was sufficient in all samples for coverage of all OTUs ( Figure 1

Alterations in the Intestinal Microbiota in Response to
Acute Liver Injury and Administration of MSCs. To characterize changes in the intestinal microbiota associated with CCl 4 -induced acute liver injury and administration of MSCs, we established and sequenced 16S rRNA amplicon libraries from the contents of the cecum and colon. Mice receiving an equal volume of olive oil followed by sacrifice at 48 h were used as controls. At the phylum level, the proportion of the five dominant bacterial phyla (Bacteroidetes, Firmicutes, Proteobacteria, Deferribacteres, and Verrucomicrobia) accounted for >95% of all sequences in all the groups (Figure 2(a)). Interestingly, the groups treated with CCl 4 showed a steady increase in Firmicutes abundance but a reciprocal decrease in Bacteroidetes over time. The groups intravenously injected with MSCs exhibited opposite results, exhibiting a gradual increase in Bacteroidetes abundance but an inverse decrease in Firmicutes and Proteobacteria over time.
To characterize the specific bacterial taxa at 48 h, 1 w, and 2 w after CCl 4 treatment and MSC transplantation, the LEfSe algorithm was used. The cladograms that displayed the predominant bacterial taxa in the CCl 4 -treated and MSC-transplanted groups at different times are shown in Figure 3. The LEfSe analysis separately discovered 24, 25, and 12 discriminative features (LDA score > 2). The MSC-transplanted groups at 48 h and 1 w mainly showed the members of bacterial taxa in the Firmicutes phylum; those in the Bacteroidetes phylum were enriched in the CCl 4 -treated group at 48 h, whereas Verrucomicrobia, Deferribacteres, and Proteobacteria were enriched in the CCl 4 -treated groups at 48 h, 1 w, and 2 w, respectively (Figure 3), findings that were consistent with the above results. Interestingly, we found that the predominant families or genera did not always have high LDA scores, suggesting that the superimposed effect of some nonpredominant microflora may not be overlooked. At 48 h, Sutterella, Dehalobacterium, and Lactobacillus were most abundant in the MSC-transplanted group, and f_S24-7, Bacteroides, Enterococcus, and Akkermansia were most abundant in the CCl 4 -treated group. At 1 w, Oscillospira and Dehalobacterium were most abundant in the MSC-transplanted group, and Proteus, Mucispirillum, Prevotella, Odoribacter, Dysgonomonas, AF12, Anaerostipes, Eubacterium, and Enterococcus were most abundant in the CCl 4 -treated group. At 2 w, f_Helicobacteraceae, f_Bradyhizobiaceae, Dehalobacterium, and Allobacullum were most abundant only in the CCl 4 -treated group. In addition, the microbiota difference within different stages (48 h, 1 w, and 2 w) of the MSC-transplanted groups was also analyzed (48 h vs. 1 w; 48 h vs. 2 w). Some bacteria (Prevotella, Flexispira, Holdemania, Ruminococcus, Sutterella, Anaerostipes, Eubacterium, Dysgonomonas, and Coprobacillus) with high LDA scores were found in the MSC-transplanted group at 48 h. However, only o_Burkholderiales, f_Alcaligenaceae, and g_Sutterella were significantly changed in the MSC-transplanted group at 48 h, compared with the CCl 4 -treated group, suggesting that Sutterella may be more important to the MSC-transplanted group in the above mentioned bacteria.  [24]. In addition, LEfSe was applied to study the effect size of each KEGG pathway with significant differential abundance. Figure 4 shows 44, 54, and 3 biomarkers found at pathway level_3 in the CCl 4 -treated groups, and 12, 12, and 1 in the MSC-transplanted groups, at 48 h, 1 w, and 2 w, respectively. At 48 h, 27 metabolic pathways were          In addition, the highest discriminating nonmetabolic pathway was "pore ion channels" under the cellular processes and signaling category. Furthermore, "cell division" was also noted. However, in the MSC-transplanted group, the three highest discriminatory powers of pathways were "bacterial motility proteins," "flagellar assembly," and "bacterial chemotaxis" under the cell motility category, followed by signal transduction and membrane transport categories. Three metabolic pathways were detected in the MSCtransplanted group under lipid metabolism, metabolism of cofactors and vitamins, xenobiotic biodegradation, and metabolism categories (Figure 4(a)). At 1 w, the pathway with the highest discriminatory power in the CCl 4 -treated group was the "lipopolysaccharide biosynthesis proteins" under the glycan biosynthesis and metabolism category. In addition, "lipopolysaccharide biosynthesis," "glycosyltransferases," and "N-glycan biosynthesis" were noted. The second discriminating pathway was "membrane and intracellular structural molecules" under the cellular processes and signaling category that also contains "pore ion channels," "other ion-coupled transporters," "inorganic ion transport  and metabolism," "cell motility and secretion," and "electron transfer carrier" pathways in this group. Again, pathways in this group were mainly classified under the metabolism category (55.6%; 30 of 54 pathways). In the MSC-transplanted group, the two highest discriminatory powers of pathways were "transporters" and "ABC transporters" under the membrane transport category, followed by "sporulation (unclassified)," "transcription factors," and "bacterial chemotaxis" pathways under the sporulation, transcription, and cell motility categories, respectively. Six metabolic pathways were detected in the MSC-transplanted group under the metabolism of other amino acids, lipid metabolism, metabolism of terpenoids and polyketides, xenobiotic biodegradation, and metabolism categories (Figure 4(b)). At 2 w, three pathways were found in the CCl 4 -treated group, and only one was detected in the MSCtransplanted group, indicating that the two groups tended to be consistent (Figure 4(c)). To evaluate epithelial tight junctions (TJs), we examined the expression and distribution of ZO-1, a protein that interacts directly with transmembrane TJ proteins [27], by qPCR and immunofluorescence analysis. At 48 h, MSC transplantation increased ZO-1 mRNA (m vs. c; p = 0 013; t-test) in the ileum but decreased ZO-1 mRNA (c vs. o, p = 0 029, t-test) in the CCl 4 -treated group. At 1 and 2 w, there were no significant differences between these groups, although ZO-1 expression was lower in the CCl 4 -treated groups ( Figure 5(b)). Accordingly, immunofluorescence performed on ileal sections displayed discontinuous staining for ZO-1 at the apical cellular border [28,29] at 48 h in the CCl 4 -treated group, suggesting a destroyed network of TJ proteins. Additionally, at 48 h, MSC transplantation improved epithelial TJs. At 1 and 2 w, both the CCl 4 -treated and MSC-transplanted groups showed intact epithelial TJs ( Figure 5(c)). Because the TJ is a multiprotein complex, TEM was used in ultrathin sections to validate the ZO-1 results. The lower electron density of TJs was only evident in the CCl 4 -treated group at 48 h ( Figure 5(d)).

MSCs Protect against CCl 4 -Induced Acute Liver Injury.
Mouse ALT and AST levels, hepatic histopathology, and survival curves were assayed to evaluate the therapeutic effect of MSCs. The results showed elevated serum levels of ALT and AST and widespread areas of hepatocellular necrosis and steatosis at 48 h in the CCl 4 -treated group, but significantly reduced serum levels of ALT and AST and the total size of necrosis and steatosis areas in the MSC transplantation group (Figures 6(a) and 6(b)). At 1 w, the CCl 4 -treated group showed normal biochemistry but punctate necrosis, while the MSC-transplanted group showed biochemical and histological recovery. At 2 w, both the CCl 4 -treated and MSC-transplanted groups showed normal biochemistry and liver histology. Furthermore, MSC transplantation ameliorated mouse survival significantly from 45.5% to 77.3% at 2 w (Figure 6(c)) and reduced apoptosis at 48 h (Figure 6(d)).

Discussion
Our study systematically analyzed gut microbial changes associated with MSC therapy for CCl 4 -induced acute liver injury. Functional KEGG pathway analysis demonstrated specific and distinct pathways of intestinal microbiota at designated times (48 h, 1 w, and 2 w) associated with liver injury and repair. Moreover, based on microbiota changes, ileum histopathology and epithelial TJs were assessed. Furthermore, the therapeutic effect of MSCs on CCl 4 -induced acute liver injury was reevaluated.
The effects of CCl 4 administration on liver cell injury have largely been studied in mice and, although the effects appear to be related to genetic strain determinants, C57BL/6 mice showed intermediate lesions between the more susceptible BALB/c strain, which shows histological recovery by 3 w, and the less susceptible SJL/J strain, which shows histological recovery by 1 w [30]. Accordingly, in the presented data, C57BL/6 mice exhibited normal biochemistry and liver histology 2 w after i.p. injection with 3 mL/kg 50% (v/v) CCl 4 . Moreover, transplantation with MSCs showed a significant therapeutic effect, with biochemical and histological recovery at 1 w. Although CCl 4 intoxication does not result in permanent liver damage, manifested as massive necrosis at 48 h followed by a period of repair [31], 66.7% (8/12) of mice died on day 6 or 7, indicating that other factors lead to sustained hepatic damage or death. Because the gut-liver axis plays a key role in hepatic disease [32], we assumed that gut microbiota also plays an important role in the outcome of this model. Indeed, the liver with transplantation of 5 × 10 5 MSCs showed a considerable effect on the composition of the microbial communities compared with no transplantation, despite no significant differences in the alpha diversity measurements except the PD whole-tree index between the groups, possibly because of the small sample sizes of both groups.
At 48 h and 1 w, higher Firmicutes abundance was linked to Clostridiales (unidentified family) and Ruminococcaceae, while Bacteroidetes contraction was linked to decreased S24-7 and Bacteroidaceae in the MSC-transplanted group. Firmicutes and Bacteroidetes are the most abundant bacterial phyla affecting host physiology in both humans and mice [33,34]. An imbalanced Firmicutes/Bacteroidetes ratio has been associated with various disease processes [35]. For instance, a high-fat diet and ob/ob mice have increased Firmicutes, and ob/ob mice also have lower Bacteroidetes over time compared with lean controls [36,37]. In addition, obese individuals have fewer Bacteroidetes and more Firmicutes than lean controls [38], and reduced Bacteroidetes, specifically the families S24-7 and Bacteroidaceae, were detected during the immune-priming phase of arthritis [39]. However, NASH patients have decreased abundance of the families Lachanospiraceae and Ruminococcaceae, which belong to the phylum Firmicutes, and increased abundance of the family Prevotellaceae and Enterobacteriaceae, which belong to the phylum Bacteroidetes and Proteobacteria, respectively [40]. In addition, diabetic mice have a lower Firmicutes/Bacteroidetes ratio [41], and a subset of Crohn's disease and ulcerative colitis patients is characterized by depletion of Firmicutes and Bacteroidetes with the relative expansion of Proteobacteria [42]. At 2 w, the most obvious difference in the gut microbiome between the CCl 4 -treated and MSC-transplanted groups was a relatively high proportion of the family Helicobacteraceae, which is generally associated with gastrointestinal tract diseases of animals belonging to the phylum Proteobacteria [43]. In addition, there was almost no evidence of the family Verrucomicrobiaceae, which only includes the genus Akkermansia, in the MSC-transplanted and olive oil control groups. A previous report revealed that the mean relative abundance values of Akkermansia in the gut microbiota of mice and healthy human adults are 0.003% and 0.744%, respectively [44]. The mucus-degrading bacteria Akkermansia, which initiate mucus degradation to produce oligosaccharides and acetate, resulting in colonized bacterial growth and resistance to pathogenic bacteria, are beneficial for mucus-associated microbiota composition [45]. Moreover, the mucuscolonizing microbes have been considered to contribute to the restoration of the microbiota [46]; in vitro, Akkermansia can adhere to the intestinal epithelium and strengthen enterocyte monolayer integrity [47]. Reactive growth of this bacterium may be one of the reasons for gut microflora self-recovery of the CCl 4 -treated groups. Interestingly, our data also demonstrated that the predominant families or genera do not always have high LDA scores. At 48 h and 1 w, Sutterella, Dehalobacterium, Lactobacillus (species reuteri), and Oscillospira were the most abundant genera in the MSC-transplanted groups. Lactobacillus reuteri can significantly increase the expression of TJ-associated proteins [48] and decrease bacterial translocation [49], as well as reduce serum triglycerides and increase the ratio of high-density lipoprotein to low-density lipoprotein [50]. It also has potent direct anti-inflammatory effects on epithelial cells by upregulating the anti-inflammatory molecule nerve growth factor and inhibiting nuclear factor κB (NF-κB) translocation to the nucleus [51]. It has been shown that Dehalobacterium and Oscillospira can prevent atherosclerosis, possibly through lipid metabolism [52]. However, little is known about the role of unclassified Sutterella in the intestinal tract. The gut microflora, as a forgotten organ, has collective metabolic and immunoregulation abilities that are relevant to host health and disease [53]. The potential functions of the gut microbiome in the MSC-transplanted groups differed significantly during liver injury and the repair phase, such as at 48 h and 1 w, compared with those in the CCl 4 -treated groups. At 48 h and 1 w, the microbiota in MSC-transplanted mice revealed biomarkers involved in cell motility, signal transduction, membrane transport, transcription, and metabolism of lipid, cofactors, vitamins, terpenoids, and polyketides, as well as xenobiotics, which are beneficial for maintaining the normal hepatic condition [35]. Especially at 48 h (liver injury phase), the MSCtransplanted group significantly enriched the functional genes involved in cell motility ("bacterial motility proteins," "flagellar assembly," and "bacterial chemotaxis"). This suggests that certain bacterial movements may be beneficial for adaptation and response to stimuli (such as changes in bile acids and/or systemic inflammatory factors). Because the above three pathways were significantly correlated with the ratio of Firmicutes/Bacteroidetes at 48 h (r > 0 9; p < 0 05; Spearman correlation analysis), it is possible that bacterial movements facilitate the growth and proliferation of some Firmicutes microorganisms, inhibit the proliferation of LPS-producing bacteria, and maintain the barrier integrity and homeostasis of the intestinal tract. Reducing the transfer of intestinal bacterial potentially proinflammatory products to the liver may be beneficial for liver repair. Surprisingly, at 48 h and 1 w, the highest discriminating nonmetabolic pathway of the gut microbiome in the CCl 4 -treated groups was the cellular processes and signaling category, followed by liver regeneration-associated gene expression [35], and the highest discriminating metabolic pathways, amino acid metabolism and glycan biosynthesis and metabolism, may also function in liver regeneration [35,54].

Conclusion
In summary, our data further indicate the extensive role of MSCs in rescuing acute liver injury induced by CCl 4 . It is possible that initial alterations in the Firmicutes/Bacteroidetes ratio maintain intestinal mucosal biology and homeostasis, which benefit liver repair.

Data Availability
All supporting data are included in the article and its additional files.
and family levels at 48 h, 1 w, and 2 w, respectively. Significant differences were determined using White's nonparametric t-test with an average abundance of taxon > 1%, p < 0 05 and 95% confidence intervals. c: CCl 4 -treated group; m: MSC-transplanted group. 48 h, 1 w, and 2 w indicate 48 hours, 1 week, and 2 weeks after CCl 4 treatment, respectively. Table S1: number of sequences and operational taxonomic units, good coverage estimation, and diversity index for each sample from the pyrosequencing analysis. (Supplementary Materials)