Yiwen Cheng

Gut microbiota depletion from early adolescence in mice: Implications for brain and behaviour

BACKGROUND There is growing appreciation for the importance of bacteria in shaping brain development and behaviour. Adolescence and early adulthood are crucial developmental periods during which exposure to harmful environmental factors can have a permanent impact on brain function. Such environmental factors include perturbations of the gut bacteria that may affect gut-brain communication, altering the trajectory of brain development, and increasing vulnerability to psychiatric disorders. Here we assess the effects of gut bacterial depletion from weaning onwards on adult cognitive, social and emotional behaviours and markers of gut-brain axis dysfunction in mice. METHODS Mice were treated with a combination of antibiotics from weaning onwards and effects on behaviours and potential gut-brain axis neuromodulators (tryptophan, monoamines, and neuropeptides) and BDNF expression were assessed in adulthood. RESULTS Antibiotic-treatment depleted and restructured gut microbiota composition of caecal contents and decreased spleen weights in adulthood. Depletion of the gut microbiota from weaning onwards reduced anxiety, induced cognitive deficits, altered dynamics of the tryptophan metabolic pathway, and significantly reduced BDNF, oxytocin and vasopressin expression in the adult brain. CONCLUSIONS Microbiota depletion from weaning onwards by means of chronic treatment with antibiotics in mice impacts on anxiety and cognitive behaviours as well as key neuromodulators of gut-brain communication in a manner that is similar to that reported in germ-free mice. This model may represent a more amenable alternative for germ-free mice in the assessment of microbiota modulation of behaviour. Finally, these data suggest that despite the presence of a normal gut microbiome in early postnatal life, reduced abundance and diversity of the gut microbiota from weaning influences adult behaviours and key neuromodulators of the microbiota-gut-brain axis suggesting that dysregulation of this axis in the post-weaning period may contribute to the pathogenesis of disorders associated with altered anxiety and cognition.

Altered Fecal Microbiota Composition Associated with Food Allergy in Infants

ABSTRACT Increasing evidence suggests that perturbations in the intestinal microbiota composition of infants are implicated in the pathogenesis of food allergy (FA), while the actual structure and composition of the intestinal microbiota in human beings with FA remain unclear. Microbial diversity and composition were analyzed with parallel barcoded 454 pyrosequencing targeting the 16S rRNA gene hypervariable V1-V3 regions in the feces of 34 infants with FA (17 IgE mediated and 17 non-IgE mediated) and 45 healthy controls. Here, we showed that several key FA-associated bacterial phylotypes, but not the overall microbiota diversity, significantly changed in infancy fecal microbiota with FA and were associated with the development of FA. The proportion of abundant Bacteroidetes, Proteobacteria, and Actinobacteria phyla were significantly reduced, while the Firmicutes phylum was highly enriched in the FA group (P < 0.05). Abundant Clostridiaceae 1 organisms were prevalent in infants with FA at the family level (P = 0.016). FA-enriched phylotypes negatively correlated with interleukin-10, for example, the genera Enterococcus and Staphylococcus. Despite profound interindividual variability, levels of 20 predominant genera were significantly different between the FA and healthy control groups (P < 0.05). Infants with IgE-mediated FA had increased levels of Clostridium sensu stricto and Anaerobacter and decreased levels of Bacteroides and Clostridium XVIII (P < 0.05). A positive correlation was observed between Clostridium sensu stricto and serum-specific IgE (R = 0.655, P < 0.001). The specific microbiota signature could distinguish infants with IgE-mediated FA from non-IgE-mediated ones. Detailed microbiota analysis of a well-characterized cohort of infants with FA showed that dysbiosis of fecal microbiota with several FA-associated key phylotypes may play a pathogenic role in FA.

Impacts of infection with different toxigenic Clostridium difficile strains on faecal microbiota in children

Increasing evidence suggests that altered intestinal microbial composition and function result in an increased risk of Clostridium difficile-associated diarrhoea (CDAD); however, the specific changes of intestinal microbiota in children suffering from CDAD and their associations with C. difficile strain toxigenicity are poorly understood. High-throughput pyrosequencing showed that reduced faecal bacterial diversity and dramatic shifts of microbial composition were found in children with CDAD. The Firmicutes/Bacteroidetes ratio was increased significantly in patients with CDAD, which indicated that dysbiosis of faecal microbiota was closely associated with CDAD. C. difficile infection resulted in an increase in lactate-producing phylotypes, with a corresponding decrease in butyrate-producing bacteria. The decrease in butyrate and lactate buildup impaired intestinal colonisation resistance, which increased the susceptibility to C. difficile colonisation. Strains of C. difficile which were positive for both toxin A and toxin B reduced faecal bacterial diversity to a greater degree than strains that were only toxin B-positive, and were associated with unusually abundant Enterococcus, which implies that the C. difficile toxins have different impacts on the faecal microbiota of children. Greater understanding of the relationships between disruption of the normal faecal microbiota and colonisation with C. difficile that produces different toxins might lead to improved treatment.

Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population.

The available evidence suggests that alterations in gut microbiota may be tightly linked to the increase in microbial translocation and systemic inflammation in patients with human immunodeficiency virus 1 (HIV-1) infection. We profiled the fecal microbiota as a proxy of gut microbiota by parallel barcoded 454-pyrosequencing in 67 HIV-1-infected patients (32 receiving highly active antiretroviral therapy [HAART] and 35 HAART naïve) and 16 healthy controls from a Chinese population. We showed that α-diversity indices did not differ significantly between the healthy control and HIV-1-infected patients. The ratio of Firmicutes/Bacteroidetes increased significantly in HIV-1-infected patients. Several key bacterial phylotypes, including Prevotella, were prevalent in HIV-1-infected patients; whereas Phascolarctobacterium, Clostridium XIVb, Dialister and Megamonas were significantly correlated with systemic inflammatory cytokines. After short-term, effective HAART, the viral loads of HIV-1 were reduced; however, the diversity and composition of the fecal microbiota were not completely restored. and the dysbiosis remained among HIV-1-infected subjects undergoing HAART. Our detailed analysis demonstrated that dysbiosis of fecal microbiota might play an active role in HIV-1 infection. Thus, new insights may be provided into therapeutics that target the microbiota to attenuate the progression of HIV disease and to reduce the risk of gut-linked disease in HIV-1-infected patients.

Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project.

Increasing evidence suggests that altered gut microbiota is implicated in the pathogenesis of hepatitis B virus-induced chronic liver disease (HBV-CLD). However, the structure and composition of the oral microbiota of patients with HBV-CLD remains unclear. High-throughput pyrosequencing showed that decreased oral bacterial diversity was found in patients with HBV-CLD. The Firmicutes/Bacteroidetes ratio was increased significantly, which indicated that dysbiosis of the oral microbiota participated in the process of HBV-CLD development. However, the changing patterns of the oral microbiota in patients with HBV-induced liver cirrhosis (LC) were almost similar to patients with chronic hepatitis B (CHB). HBV infection resulted in an increase in potential H2S- and CH3SH-producing phylotypes such as Fusobacterium, Filifactor, Eubacterium, Parvimonas and Treponema, which might contribute to the increased oral malodor. These key oral-derived phylotypes might invade into the gut as opportunistic pathogens and contribute to altering the composition of the gut microbiota. This study provided important clues that dysbiosis of the oral microbiota might be involved in the development of HBV-CLD. Greater understanding of the relationships between the dysbiosis of oral microbiota and the development of HBV-CLD might facilitate the development of non-invasive differential diagnostic procedures and targeted treatments of HBV-CLD patients harbouring specific oral phylotypes.

Clostridium butyricum Combined with Bifidobacterium infantis Probiotic Mixture Restores Fecal Microbiota and Attenuates Systemic Inflammation in Mice with Antibiotic-Associated Diarrhea

Antibiotic-associated diarrhea (AAD) is one of the most common complications of most types of antibiotics. Our aim was to determine the efficacy of Clostridium butyricum, Bifidobacterium infantis, and their mixture for AAD treatment in mice. AAD models were administered with single probiotic strain and probiotic mixture for short term and long term to evaluate the changes of the composition and diversity of intestinal microbiota, histopathology of the colon, and the systemic inflammation. Our data indicated that long-term probiotic therapy, but not short-term course, exerted beneficial effects on the restoration of the intestinal microbiota, the recovery of the tissue architecture, and attenuation of systemic inflammation. All predominant fecal bacteria reached normal level after the long-term probiotic mixture treatment, while IL-10, IFN-γ, and TNF-α also returned to normal level. However, the efficacy for AAD was time dependent and probiotic strain specific. Short-term administration of probiotic strains or mixture showed no apparent positive effects for AAD. In addition, the beneficial effects of C. butyricum combined with B. infantis probiotic mixture were superior to their single strain. This research showed that supplementation with C. butyricum combined with B. infantis probiotic mixture may be a simple and effective method for AAD treatment.

Association between serum vitamin D and severity of liver fibrosis in chronic hepatitis C patients: a systematic meta-analysis

To conduct a systematic review of group studies assessing the association of serum vitamin D status with the severity of liver fibrosis in chronic hepatitis C patients using meta-analysis. The relevant research literatures were identified by searching PubMed and EMBASE databases prior to October 2013 with no restrictions. We included group studies that reported odds ratio (OR) estimates with 95% confidence intervals (CIs) or a mean with standard deviation (SD) for the association between serum vitamin D status and the severity of liver fibrosis in chronic hepatitis C patients. Approximately 8321 participants from several countries were included in this analysis. Six studies on serum vitamin D status and the severity of liver fibrosis were included in this meta-analysis. ORs with 95% CIs were extracted from four studies and the pooled ORs were 0.866 (95% CI, 0.649 to 1.157). The means with SDs were extracted from three studies and the pooled means were −0.487 (95% CI, −0.659 to −0.315). There was statistically significant heterogeneity among the mean data extracted studies (P=0.029; I2=71.8%) but not among the OR data extracted studies (P=0.061; I2=55.6%). Finally, results from the mean data extracted studies suggest that lower serum vitamin D is a risk factor for the severity of liver fibrosis in chronic hepatitis C patients. However, there is no conclusive evidence on this association because of inconsistencies between the OR data extracted studies and the mean data extracted studies.概要研究目的利用meta 分析方法来探索慢性丙型肝炎患者低血清维生素D 水平与严重肝纤维化相关性。创新要点丙型病毒性肝炎病人的低血清维生素D 水平与严重肝纤维化并不一定有相关性。研究方法结合已发表的临床研究数据, 采用荟萃分析方法, 定量分析低血清维生素D 水平与慢性丙型肝炎患者严重肝纤维化相关性(图2; 表2)。重要结论此荟萃分析对于认识丙型肝炎病人低血清维生素D 水平与肝纤维化严重程度的相关性有重要意义, 对未来相关临床研究具有指导意义。

Comparative genomic study of three species within the genus Ornithinibacillus, reflecting the adaption to different habitats.

In the present study, we report the whole genome sequences of two species, Ornithinibacillus contaminans DSM22953(T) isolated from human blood and Ornithinibacillus californiensis DSM 16628(T) isolated from marine sediment, in genus Ornithinibacillus. Comparative genomic study of the two species was conducted together with their close relative Ornithinibacillus scapharcae TW25(T), a putative pathogenic bacteria isolated from dead ark clam. The comparisons showed O. contaminans DSM22953(T) had the smallest genome size of the three species indicating that it has a relatively more stable habitat. More stress response and heavy metal resistance genes were found in the genome of O. californiensis DSM 16628(T) reflecting its adaption to the complex marine environment. O. scapharcae TW25(T) contained more antibiotic resistance genes and virus factors in the genome than the other two species, which revealed its pathogen potential.

Blood microbiota as a potential noninvasive diagnostic biomarker for liver fibrosis in severely obese patients: Choose carefully

We read with great interest the recent article by Lelouvier et al., who investigated the relationship between liver fibrosis in patients with severe obesity and blood microbiota. With well-characterized discovery and validation cohorts, the blood 16S ribosomal RNA concentration was shown to be increased in patients with liver fibrosis, whereas the bacterial diversity was decreased. Although specific bacterial taxa signatures in the discovery cohort were not confirmed in the validation cohort, the data nonetheless verified that blood dysbiosis was associated with liver fibrosis in obese patients, which could be used as a potential noninvasive biomarker. Obesity is one of the major predisposing factors for nonalcoholic fatty liver disease, and obesityassociated gut dysbiosis may contribute to increased intestinal permeability and bacterial translocation. The gut may be the major origin of blood microbiota; however, an oral source for blood microbiota cannot be ignored. Koren et al. suggested that the atherosclerotic plaque microbiota may at least in part be derived from the oral cavity. As an important risk factor for periodontal disease, obesity may also contribute to bacterial translocation from the oral cavity to the blood and participate in shaping the blood microbiota. Without excluding oral disease in the enrolled participants, a reliable correlation between blood microbiota and liver fibrosis cannot be established because specific bacterial signatures may also exist in patients with oral diseases but without liver fibrosis. Thus, the inclusion criteria should include the oral health status of the participants. Studying oral microbiota in addition to gut and blood microbiota may help clarify the role of key functional bacteria in liver fibrosis. In addition, bacterial fragments in blood cannot be equated with blood microbiota, which can be easily detected using sequencing techniques. However, the read numbers for each sample were not reported in the Lelouvier et al. study. Only one a-diversity index—the Shannon index—was used to define the decreased blood bacterial diversity, whereas other indices such as b-diversity and Good’s coverage were missing. Principal coordinates analysis can provide interindividual variations intuitively, whereas Good’s coverage estimator can evaluate the sequencing depth for blood microbiota. The operational taxonomic unit number and the overall composition in different taxonomic levels should also be provided to interpret the bacterial richness of blood microbiota and its taxonomic differences. The inclusion of all the aforementioned parameters will contribute to a comprehensive understanding of the overall structure and composition of blood microbiota. Moreover, blood microbiota in healthy participants should also be considered to exclude those commensal bacteria in the blood. In conclusion, blood microbiota analysis can be influenced by various factors, including the origin of the condition. Without considering these factors, it is impossible to demonstrate the relationship between blood microbiota and liver fibrosis, or arbitrarily use the specific blood taxonomic signatures as biomarkers.

Dysbiosis of the Urinary Microbiota Associated With Urine Levels of Proinflammatory Chemokine Interleukin-8 in Female Type 2 Diabetic Patients

Evidence has shown that dysbiosis of the urinary microbiota existed in female type 2 diabetes mellitus (T2DM) patients. Perturbations of intestinal microbiota are linked to proinflammatory chemokine interleukin-8 (IL-8); however, the correlations between urinary microbiota and IL-8 are not well studied. Here, we investigated the associations between the altered urinary microbiota and urinary IL-8 in female T2DM patients. A modified four-tube midstream urine technique was used to collect urine specimens from 70 female T2DM patients and 70 matched healthy controls (HCs). Bacterial genomic DNA from urine specimens was isolated using magnetic beads and the urinary microbiota was assessed using Illumina MiSeq platform targeting on the 16S rRNA gene V3–V4 region. Urinary IL-8 was determined by enzyme linked immunosorbent assay. Subsequently, the T2DM patients were separated into urine IL-8 detectable (WIL8) and undetectable (NIL8) groups, and the composition of urinary microbiota between the two groups was compared. Meanwhile, the levels of IL-8 between the “≥HCs” group (those specific bacterial genera were more than or equal to the HCs) and the “<HCs” group (those specific bacterial genera were less than the HCs) was also compared. Of 70 urine samples from T2DM patients without urinary tract infections, 46 patients had detectable IL-8 in their urine (64.31 ± 70.43 pg/mL), while 24 patients had undetectable IL-8. Compared to the NIL8 group, 11 bacterial genera increased in the WIL8 group, including Corynebacterium, Akkermansia, Enterococcus, etc., whereas 10 genera, such as Faecalibacterium, Bacteroides, and Pseudomonas decreased. One species of Lactobacillus, Lactobacillus iners, increased obviously in the WIL8 group. The “≥HCs” group showed 17 genera increased and 16 genera decreased. In addition, 18 genera contributed to the presence of urinary IL-8 in T2DM patients, which explained 95.60% of the total variance of urinary microbiota. Our study demonstrated that dysbiosis of the urinary microbiota with several key bacteria was associated with urinary IL-8 in female T2DM patients, which might be useful to explore the interactions between urinary microbiota and inflammatory responses and shed light on novel diagnosis and therapy for urinary microbiota associated with infections in T2DM patients.