Vital Members in the More Dysbiotic Oropharyngeal Microbiotas in H7N9-Infected Patients

Characteristics of the gut microbiota in Bifidobacterium catenulatum LI10 pre-treated rats with lower levels of D-galactosamine-induced liver damage

AIMS

Liver damage has caused great illness in human beings. Bifidobacterium catenulatum LI10 has been determined with protective effect against D-galactosamine-induced liver damage. However, due to the sample limitation, the individual difference in its protective effect was not determined. The current study was designed to characterise the gut microbiota of LI10-pretreated rats with lower levels of liver damage.

METHODS AND RESULTS

A series of experiments and bioinformatic analyses were carried out. Two rat cohorts with different levels of liver damage were determined, i.e., Non-Severe and Severe cohorts. Six out of the seven measured liver function variables were lower in the Non-Severe cohort, while four cytokine variables also yielded differences between the two cohorts. The Non-Severe and Severe cohorts were determined with distinct gut microbiota, among which, ASV14_Parabacteroides and ASV7_Bacteroides were most associated with Non-Severe and Severe cohorts, respectively. Five phylotypes were determined as structural gatekeepers in the microbiota network of Non-Severe cohort, ASV135_Lachnospiraceae_NK4A136 of which contributed most to the stability of the network.

CONCLUSIONS

The relevant findings suggest that some gut bacteria could benefit the protective effect of LI10 on lowering the severity of rat liver damage.

SIGNIFICANCE AND IMPACT OF THE STUDY

The bacteria benefiting the protective effects of potential probiotics could be further investigated for future clinical application.

Characterising the Intestinal Bacterial and Fungal Microbiome Associated With Different Cytokine Profiles in Two Bifidobacterium strains Pre-Treated Rats With D-Galactosamine-Induced Liver Injury

Multiple probiotics have protective effects against different types of liver injury. Different intestinal microbes could be beneficial to the protective effects of the probiotics on the treated cohorts in different aspects. The current study was designed to determine the intestinal bacterial and fungal microbiome associated with different cytokine profiles in the Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10 pretreated rats with D-galactosamine-induced liver injury. In this study, partition around medoids clustering analysis determined two distinct cytokine profiles (i.e., CP1 and CP2) comprising the same 11 cytokines but with different levels among the LI09, LI10, positive control (PC), and negative control (NC) cohorts. All rats in PC and NC cohorts were determined with CP1 and CP2, respectively, while the rats with CP1 in LI09 and LI10 cohorts had more severe liver injury than those with CP2, suggesting that CP2 represented better immune status and was the “better cytokine profile” in this study. PERMANOVA analyses showed that the compositions of both bacterial and fungal microbiome were different in the LI10 cohorts with different cytokine profiles, while the same compositions were similar between LI09 cohorts with different cytokine profiles. The phylotype abundances of both bacteria and fungi were different in the rats with different cytokine profiles in LI09 or LI10 cohorts according to similarity percentage (SIMPER) analyses results. At the composition level, multiple microbes were associated with different cytokine profiles in LI09 or LI10 cohorts, among which Flavonifractor and Penicillium were the bacterium and fungus most associated with LI09 cohort with CP2, while Parabacteroides and Aspergillus were the bacterium and fungus most associated with LI10 cohort with CP2. These microbes were determined to influence the cytokine profiles of the corresponding cohorts. At the structure level, Corynebacterium and Cephalotrichiella were determined as the two most powerful gatekeepers in the microbiome networks of LI09 cohort CP2, while Pseudoflavonifractor was the most powerful gatekeeper in LI10 cohort with CP2. These identified intestinal microbes were likely to be beneficial to the effect of probiotic Bifidobacterium on the immunity improvement of the treated cohorts, and they could be potential microbial biomarkers assisting with the evaluation of immune status of probiotics-treated cohorts.

Multiple Intestinal Bacteria Associated with the Better Protective Effect of Bifidobacterium pseudocatenulatum LI09 against Rat Liver Injury

Bifidobacterium pseudocatenulatum LI09 could protect rats from D-galactosamine- (D-GalN-) induced liver injury. However, individual difference in the protective effects of LI09 on the liver injury remains poorly understood. The present study is aimed at determining the multiple intestinal bacteria associated with the better protective effect of LI09 against D-GalN-induced rat liver injury. Two rat cohorts, i.e., the nonsevere and severe cohorts, were divided based on their liver injury severity. Higher level of ALB and lower levels of ALT, AST, TBA, TB, IL-5, and MIP-3α were determined in the nonsevere cohort than the severe cohort. The alpha diversity indices (i.e., observed species, Shannon, and Pielou indices) did not yield significant differences between the intestinal microbiota of the nonsevere and severe cohorts. The intestinal microbiota composition was different between the two cohorts. Ten phylotypes assigned to Bacteroides, Clostridia_UCG-014, Clostridium Lachnospiraceae, Lachnospiraceae_NK4A136, and Parabacteroides were closely associated with the nonsevere cohort, among which, ASV8_Lachnospiraceae_NK4A136 was the most associated one. At the structure level, two groups of phylotypes with most correlations were determined in the intestinal microbiota networks of the two cohorts. Among them, ASV135_Lachnospiraceae_NK4A136 was the most powerful gatekeeper in the microbiota network of the nonsevere cohort. In conclusion, some intestinal bacteria, e.g., Lachnospiraceae_NK4A136, Parabacteroides, and Clostridium, were associated with the better protective effect of LI09 against D-GalN-induced rat liver injury. They were likely to enhance the effectiveness of LI09, and their clinical application deserves further investigation.

Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus

Type 2 diabetes mellitus (T2DM) influences the human health and can cause significant illnesses. The genitourinary microbiome profiles in the T2DM patients remain poorly understood. In the current study, a series of bioinformatic and statistical analyses were carried out to determine the multiple bacteria associated with the more dysbiotic genitourinary microbiomes (i.e., those with lower dysbiosis ratio) in T2DM patients, which were sequenced by Illumina-based 16S rRNA gene amplicon sequencing. All the genitourinary microbiomes from 70 patients with T2DM were clustered into three clusters of microbiome profiles, i.e., Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, with Cluster_3_T2DM at the most dysbiotic genitourinary microbial status. The three clustered T2DM microbiomes were determined with different levels of alpha diversity indices, and driven by distinct urinalysis variables. OTU12_Clostridiales and OTU28_Oscillospira were likely to drive the T2DM microbiomes to more dysbiotic status, while OTU34_Finegoldia could play a vital role in maintaining the least dysbiotic T2DM microbiome (i.e., Cluster_1_T2DM). The functional metabolites K08300_ribonuclease E, K01223_6-phospho-beta-glucosidase and K00029_malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) were most associated with Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, respectively. The characteristics and multiple bacteria associated with the more dysbiotic genitourinary microbiomes in T2DM patients may help with the better diagnosis and management of genitourinary dysbiosis in T2DM patients.

Recovery Dynamics of Intestinal Bacterial Communities of CCl4-Treated Mice with or without Mesenchymal Stem Cell Transplantation over Different Time Points

Liver injury has caused significant illness in humans worldwide. The dynamics of intestinal bacterial communities associated with natural recovery and therapy for CCl₄-treated liver injury remain poorly understood. This study was designed to determine the recovery dynamics of intestinal bacterial communities in CCl₄-treated mice with or without mesenchymal stem cell transplantation (i.e., MSC and CCl₄ groups) at 48 h, 1 week (w), and 2 w. MSCs significantly improved the histopathology, survival rate, and intestinal structural integrity in the treated mice. The gut bacterial communities were determined with significant changes in both the MSC and CCl₄ groups over time, with the greatest difference between the MSC and CCl₄ groups at 48 h. The liver injury dysbiosis ratio experienced a decrease in the MSC groups and a rise in the CCl₄ groups over time, suggesting the mice in the MSC group at 48 h and the CCl₄ group at two weeks were at the least gut microbial dysbiosis status among the corresponding cohorts. Multiple OTUs and functional categories were associated with each of the bacterial communities in the MSC and CCl₄ groups over time. Among these gut phylotypes, OTU1352_S24-7 was determined as the vital member in MSC-treated mice at 48 h, while OTU453_S24-7, OTU1213_Ruminococcaceae, and OTU841_Ruminococcus were determined as the vital phylotypes in CCl₄-treated mice at two weeks. The relevant findings could assist the diagnosis of the microbial dysbiosis status of intestinal bacterial communities in the CCl₄-treated cohorts with or without MSC transplantation.