Dynamic changes of the luminal and mucosa-associated gut microbiota during and after antibiotic therapy with paromomycin

Gut microbiota play a key role in the host's health system. Broad antibiotic therapy is known to disrupt the microbial balance affecting pathogenic as well as host-associated microbes. The aim of the present study was to investigate the influence of antibiotic paromomycin on the luminal and mucosa-associated microbiota at the DNA (abundance) and RNA (potential activity) level as well as to identify possible differences. The influence of antibiotic treatment on intestinal microbiota was investigated in 5 healthy individuals (age range: 20–22 years). All participants received the antibiotic paromomycin for 3 d. Fecal samples as well as sigmoidal biopsies were collected before and immediately after cessation of antibiotic treatment as well as after a recovery phase of 42 d. Compartment- and treatment status-specific indicator operational taxonomic units (OTUs) as well as abundance- and activity-specific patterns were identified by 16S rRNA and 16S rRNA gene amplicon libraries and high-throughput pyrosequencing. Microbial composition of lumen and mucosa were significantly different at the DNA compared to the RNA level. Antibiotic treatment resulted in changes of the microbiota, affecting the luminal and mucosal bacteria in a similar way. Several OTUs were identified as compartment- and/or treatment status-specific. Abundance and activity patterns of some indicator OTUs differed considerably. The study shows fundamental changes in composition of gut microbiota under antibiotic therapy at both the potential activity and the abundance level at different treatment status. It may help to understand the complex processes of gut microbiota changes involved in resilience mechanisms and on development of antibiotic-associated clinical diseases.     

Alterations of gut microbiota and cytokines in elevated serum diamine oxidase disorder

The present study aimed to explore gut microbiota alterations and host cytokine responses in a population with elevated serum diamine oxidase (DAO) disorder. A total of 53 study participants were included in this study, segregated into 2 groups: subjects with high-level DAO (DAO-H, n = 22) subjects with normal DAO level (DAO-N, n = 31). We investigated the clinical and demographic parameters of study participants. The fecal bacterial communities and serum cytokines in 2 groups were assessed by 16S ribosomal RNA gene sequencing and immunoassay. High-pressure liquid chromatography was used to determine hemoglobin Alc. Flow cytometry was used to find the cytokine level in the blood serum. There is no difference in age, total cholesterol (TCHO), triglyceride (TG), high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C), hemoglobin Alc, fasting plasma glucose (FPG) and homocysteine between the 2 groups. No significant difference were found in α-diversity between the 2 groups, however, the gut microbiota of subjects in DAO-H were characterized by marked interindividual differences, decreased abundance of Phocaeicola, Lachnospira, Bacteroides, Alistipes, Agathobacter, Lachnospira and Bactetoides and increased abundances of Mediterraneibacter, Blautia, Faecallibacterium, Agathobacter, and Parasutterella. Furthermore, the cytokines were no related to the DAO level in both groups and exhibited no significant differences between DAO-H and DAO-N. This study adds a new dimension to our understanding of the DAO and gut microbiota, and revealed that an increase in the DAO level in the intestinal mucosa could alter the gut microbiota composition, which can cause gut-related complications. Research is needed to extensively evaluate downstream pathways and provide possible protective or treatment measures pertaining to relevant disorders.     

High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals

Background: The intestinal microbiota is associated with human health and diseases. The luminal microbiota (LM) and the mucosal-associated microbiota (MAM) are 2 distinct ecosystems with different metabolic and immunological functions. Aim: To characterize the intestinal LM and MAM in humans using high throughput sequencing of the 16S rRNA gene. Methods: Fresh fecal samples and distal colonic mucosal biopsies collected from 24 healthy subjects before (fecal) and during (mucosa) a flexible sigmoidoscopy of an un-prepared bowel. High throughput sequencing of the 16S rRNA gene was used to characterize bacterial communities. Sequences were processed using the QIIME pipeline. Results: LM and MAM populations were significantly different (ANOSIM: R = 0.49, P = 0.001). The LM displayed tighter clustering compared to the MAM (average weighted UniFrac distances 0.27 ± 0.05 vs. 0.43 ± 0.09, P < 0.001, respectively), and showed higher diversity (Shannon diversity index: 4.96 ± 0.37 vs 4.14 ± 0.56, respectively, P < 0.001). The dominant phyla in the LM and MAM were significantly different: Firmicutes (41.4% vs. 29.1%, FDR < 0.0001, respectively), Bacteroidetes (20.2% vs. 26.3%, FDR < 0.05, respectively), Actinobacteria (22% vs. 12.6%, FDR < 0.0001, respectively) and Proteobacteria (9.3% vs. 19.3%, FDR < 0.0001, respectively). The abundance of 56 genera differed significantly (FDR < 0.1) between the 2 niches. All of the genera in the fecal microbiota were present in the MAM while 10 genera were found to be unique to the MAM. Conclusion: The LM and MAM are distinct microbial ecosystems that differ significantly from each other in microbial diversity and composition. These two microbial niches should be investigated independently to better understand the role of the intestinal microbiota in health and disease.     

High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals

Background: The intestinal microbiota is associated with human health and diseases. The luminal microbiota (LM) and the mucosal-associated microbiota (MAM) are 2 distinct ecosystems with different metabolic and immunological functions. Aim: To characterize the intestinal LM and MAM in humans using high throughput sequencing of the 16S rRNA gene. Methods: Fresh fecal samples and distal colonic mucosal biopsies collected from 24 healthy subjects before (fecal) and during (mucosa) a flexible sigmoidoscopy of an un-prepared bowel. High throughput sequencing of the 16S rRNA gene was used to characterize bacterial communities. Sequences were processed using the QIIME pipeline. Results: LM and MAM populations were significantly different (ANOSIM: R = 0.49, P = 0.001). The LM displayed tighter clustering compared to the MAM (average weighted UniFrac distances 0.27 ± 0.05 vs. 0.43 ± 0.09, P < 0.001, respectively), and showed higher diversity (Shannon diversity index: 4.96 ± 0.37 vs 4.14 ± 0.56, respectively, P < 0.001). The dominant phyla in the LM and MAM were significantly different: Firmicutes (41.4% vs. 29.1%, FDR < 0.0001, respectively), Bacteroidetes (20.2% vs. 26.3%, FDR < 0.05, respectively), Actinobacteria (22% vs. 12.6%, FDR < 0.0001, respectively) and Proteobacteria (9.3% vs. 19.3%, FDR < 0.0001, respectively). The abundance of 56 genera differed significantly (FDR < 0.1) between the 2 niches. All of the genera in the fecal microbiota were present in the MAM while 10 genera were found to be unique to the MAM. Conclusion: The LM and MAM are distinct microbial ecosystems that differ significantly from each other in microbial diversity and composition. These two microbial niches should be investigated independently to better understand the role of the intestinal microbiota in health and disease.     

The development of gut microbiota in critically ill extremely low birth weight infants assessed with 16S rRNA gene based sequencing

Objective: An increasing number of studies that are using high-throughput molecular methods are rapidly extending our knowledge of gut microbial colonization in preterm infants whose immaturity and requirement for extensive treatment may result in altered colonization process. We aimed to describe the profile of gut microbiota in 50 extremely low birth weight (&lt;1200 g) critically ill infants at three different time points during the first two months of life by using 16S rRNA gene specific sequencing.   Patients and Methods: Stool samples were collected at the age of one week, one month and two months. Bacterial community profiling was done using universal amplification of 16S rRNA gene and 454 pyrosequencing. Results: The diversity of gut microbiota in preterm neonates in the first week of life was low but increased significantly over two months. The gut microbiota was dominated by facultative anaerobic bacteria (Staphylococcus spp. and Enterobacteriaceae) and lacked colonization with bacteria known to provide resistance against pathogens (Bacteroides, Bifidobacterium, and Lactobacillus) throughout the study. Colonization of Escherichia coli and uncultured Veillionella was positively correlated with maturity. Infants born to mothers with chorioamnionitis had significantly higher bacterial diversity than those without. Conclusions: High prevalence and abundance of potentially pathogenic Enterobacteriaceae and Staphylococcaceae with low prevalence and abundance of colonization resistance providing taxa bifidobacteria, Bacteroides and lactobacilli may lead to high infection risk via microbial translocation from the gut. Additionally, our data suggest that maternal chorioamnionitis may have an effect on the diversity of infants’ gut microbiota; however, the mechanisms involved remain to be elucidated.     

Altered diversity and composition of gut microbiota in Chinese patients with chronic pancreatitis

Background/ObjectivesGut microbiota alterations in chronic pancreatitis (CP) are seldomly described systematically. It is unknown whether pancreatic exocrine insufficiency (PEI) and different etiologies in patients with CP are associated with gut microbiota dysbiosis.MethodsThe fecal microbiota of 69 healthy controls (HCs) and 71 patients with CP were compared to investigate gut microbiome alterations in CP and the relationship among gut microbiome dysbiosis, PEI and different etiologies. Fecal microbiomes were analyzed through 16S ribosomal RNA gene profiling, based on next-generation sequencing. Pancreatic exocrine function was evaluated by determining fecal elastase 1 activity.ResultsPatients with CP showed gut microbiota dysbiosis with decreased diversity and richness, and taxa-composition changes. On the phylum level, the gut microbiome of the CP group showed lower Firmicutes and Actinobacteria abundances than the HC group and higher Proteobacteria abundances. The abundances of Escherichia-Shigella and other genera were high in gut microbiomes in the CP group, whereas that of Faecalibacterium was low. Kyoto Encyclopedia of Genes and Genomes pathways (lipopolysaccharide biosynthesis and bacterial invasion of epithelial cells) were predicted to be enriched in the CP group. Among the top 5 phyla and 8 genera (in terms of abundance), only Fusobacteria and Eubacterium rectale group showed significant differences between CP patients, with or without PEI. Correlation analysis showed that Bifidobacterium and Lachnoclostridium correlated positively with fecal elastase 1 (r = 0.2616 and 0.2486, respectively, P < 0.05).ConclusionsThe current findings indicate that patients with CP have gut microbiota dysbiosis that is partly affected by pancreatic exocrine function.     

Procyanidin B2 protects against diet-induced obesity and non-alcoholic fatty liver disease via the modulation of the gut microbiota in rabbits

BACKGROUND Procyanidins have beneficial effects on metabolic syndrome and antimicrobial activity,but the mechanisms underlying these effects are unclear.AIM To investigate the effects of procyanidin B2(PB2)on non-alcoholic fatty liver disease and to explore the possible mechanism.METHODS Thirty male New Zealand white rabbits were randomized into three groups.All of them were fed either a high-fat-cholesterol diet(HCD)or chow diet.HCD-fed rabbits were treated with vehicle or PB2 daily for 12 wk.Body weight and food intake were evaluated once a week.Serum biomarkers,such as total cholesterols,triglycerides,and aspartate transaminase,were detected.All rabbits were sacrificed and histological parameters of liver were assessed by hematoxylin and eosin-stained sections.Moreover,several lipogenic genes and gut microbiota(by 16S rRNA sequencing)were investigated to explore the possible mechanism.RESULTS The HCD group had higher body weight,liver index,serum lipid profile,insulin resistance,serum glucose,and hepatic steatosis compared to the CHOW group.PB2 treatment prevented HCD-induced increases in body weight and hypertriglyceridemia in association with triglyceride accumulation in the liver.PB2 also ameliorated low-grade inflammation,which was reflected by serum lipopolysaccharides and improved insulin resistance.In rabbit liver,PB2 prevented the upregulation of steroid response element binding protein 1c and fatty acid synthase and the downregulation of carnitine palmitoyltransferase,compared to the HCD group.Moreover,HCD led to a decrease of Bacteroidetes in gut microbiota.PB2 significantly improved the proportions of Bacteroidetes at the phylum level and Akkermansia at the genus level.CONCLUSION Our results indicate the possible mechanism of PB2 to improve HCD-induced features of metabolic syndrome and provide a new dietary supplement.     

Temporal and spatial variation of the human microbiota during pregnancy

Despite the critical role of the human microbiota in health, our understanding of microbiota compositional dynamics during and after pregnancy is incomplete. We conducted a case-control study of 49 pregnant women, 15 of whom delivered preterm. From 40 of these women, we analyzed bacterial taxonomic composition of 3,767 specimens collected prospectively and weekly during gestation and monthly after delivery from the vagina, distal gut, saliva, and tooth/gum. Linear mixed-effects modeling, medoid-based clustering, and Markov chain modeling were used to analyze community temporal trends, community structure, and vaginal community state transitions. Microbiota community taxonomic composition and diversity remained remarkably stable at all four body sites during pregnancy (P > 0.05 for trends over time). Prevalence of a Lactobacillus-poor vaginal community state type (CST 4) was inversely correlated with gestational age at delivery (P = 0.0039). Risk for preterm birth was more pronounced for subjects with CST 4 accompanied by elevated Gardnerella or Ureaplasma abundances. This finding was validated with a set of 246 vaginal specimens from nine women (four of whom delivered preterm). Most women experienced a postdelivery disturbance in the vaginal community characterized by a decrease in Lactobacillus species and an increase in diverse anaerobes such as Peptoniphilus, Prevotella, and Anaerococcus species. This disturbance was unrelated to gestational age at delivery and persisted for up to 1 y. These findings have important implications for predicting premature labor, a major global health problem, and for understanding the potential impact of a persistent, altered postpartum microbiota on maternal health, including outcomes of pregnancies following short interpregnancy intervals.The human body harbors diverse, complex, and abundant microbiota whose composition is determined largely by body site but also by host genetics, environmental exposures, and time (1, 2). The microbiota plays critical roles in health and in disease, including nutrient acquisition, immune programming, and protection from pathogens (3). Normal pregnancy represents a unique, transient, and dynamic state of altered anatomy, physiology, and immune function. Preterm birth, i.e., before 37 wk of gestation, occurs in 11% of pregnancies and is the leading cause of neonatal death (4). In both term and preterm pregnancies, the interplay between the microbiota and the host remains poorly understood.Approximately 25% of preterm births are associated with occult microbial invasion of the amniotic cavity (5). Evidence suggests that the most common source of invading microbes is the host microbiota. In studies of amniotic fluid from women with preterm labor and either intact or ruptured membranes, 16S ribosomal RNA (rRNA) sequences of known vaginal, gut, and oral indigenous bacterial species have been recovered in 15–50% of cases, and their relative abundances have correlated directly with markers of inflammation and inversely with time to delivery (6–9). Preterm birth also is associated with bacterial vaginosis, a community-wide alteration of the vaginal microbiota (10, 11) that increases the risk of preterm birth approximately twofold (12, 13).Several studies have examined the vaginal microbiota during pregnancy using cultivation-independent techniques (14–19). Collectively, these studies found the vaginal communities of pregnant women to be dominated by Lactobacillus species and characterized by lower richness and diversity than in nonpregnant women but with higher stability. Of the two studies that evaluated pregnancy outcomes, one found preterm birth to be linked with higher intracommunity (alpha) diversity in the vagina (16), but the other found no significant association between preterm birth and any specific community type or microbial taxon (17).Other (nonvaginal) body sites have been even less well studied in the setting of pregnancy. The subgingival crevice has been investigated only with cultivation (20, 21) or with taxon-specific molecular approaches (22). Two studies of the fecal microbiota reported differences in bacterial community structure between the first and third trimesters (23, 24); in each study, however, samples were collected at only two time points. These limited findings support the need for longitudinal investigations of the microbiota at multiple body sites during pregnancy.As part of a larger ongoing study, we examined a total of 49 women who were divided into two groups, each of which included controls (term deliveries) and cases (preterm deliveries). We characterized the temporal dynamics of microbiota composition based on prospective weekly sampling during pregnancy from four body sites: vagina, distal gut (stool), saliva, and tooth/gum, as well as after delivery. Our data reveal microbiota compositional stability during pregnancy at all body sites, a diverse vaginal community state early during pregnancy in women who subsequently delivered prematurely, and a dramatic shift in vaginal microbiota composition at the time of delivery that in some cases persisted for the maximum duration of postpartum sampling (1 y).     

Changes in gut microbiota composition and diversity associated with post-cholecystectomy diarrhea

BACKGROUNDPost-cholecystectomy diarrhea (PCD) frequently occurs in patients following gallbladder removal. PCD is part of the post-cholecystectomy (PC) syndrome, and is difficult to treat. After cholecystectomy, bile enters the duodenum directly, independent of the timing of meals. The interaction between the bile acids and the intestinal microbes is changed. Therefore, the occurrence of PCD may be related to the change in microbiota. However, little is known about the relationship between the gut microbiota and PCD.AIMTo better understand the role of the gut microbiota in PCD patients.METHODSFecal DNA was isolated. The diversity and profiles of the gut microbiota were analyzed by performing high-throughput 16S rRNA gene sequencing. The gut microbiota were characterized in a healthy control (HC) group and a PC group. Subsequently, the PC group was further divided into a PCD group and a post-cholecystectomy non-diarrhea group (PCND) according to the patients’ clinical symptoms. The composition, diversity and richness of microbial communities were determined and compared.RESULTSIn the PC and HC groups, 720 operational taxonomic units (OTUs) were identified. The PC group had fewer OTUs than the HC group. β-diversity was decreased in the PC group. This indicated decreased microbial diversity in the PC group. Fifteen taxa with differential abundance between the HC and PC groups were identified. In the PCD group compared to the PCND group, significant decreases in microbial diversity, Firmicutes/Bacteroidetes ratio, and richness of probiotic microbiota (Bifidobacterium and Lactococcus), and an increase in detrimental microbiota (Prevotella and Sutterella) were observed. Moreover, a negative correlation was found between Prevotella and Bifidobacterium. Using a Kyoto Encyclopedia of Genes and Genomes functional analysis, it was found that the abundances of gut microbiota involved in lipid metabolism pathways were markedly lower in the PCD group compared to the PCND group.CONCLUSIONThis study demonstrated that gut dysbiosis may play a critical role in PCD, which provides new insights into therapeutic options for PCD patients.     

基于微生物16S rDNA测序技术研究高脂血症豚鼠肠道菌群的变化

目的利用微生物16S rDNA测序技术研究高脂血症豚鼠肠道菌群的变化情况。方法豚鼠随机分为对照组和模型组,每组10只。高脂喂养8周复制高脂血症模型。第8周末测定豚鼠血清总胆固醇(TC)、甘油三酯(TG)、低密度脂蛋白胆固醇(LDLC)和高密度脂蛋白胆固醇(HDLC)水平;剖取肝脏、主动脉和结肠,HE染色观察肝脏、主动脉和结肠组织形态学变化; 16S rDNA测序检测豚鼠肠道内容物微生物组成和比例的变化情况。结果与对照组相比,模型组豚鼠血清TC、TG、LDLC和HDLC水平均显著升高(P0.01);组织形态学显示,模型组豚鼠均出现重度脂肪肝病变,但仅1只模型组豚鼠出现少量泡沫细胞聚集。16S rDNA基因序列分析显示,与对照组相比,在门分类学水平上,模型组豚鼠肠道互养菌门细菌比例显著增加(P0.05);在属分类学水平上,模型组豚鼠肠道毛螺旋菌NK4A136、瘤胃球菌、幽门螺杆菌、Odoribacter、Allobaculum和Caldicoprobacter细菌比例显著降低(P0.05),依赖杆菌、毛螺旋菌XPB1014、锥形杆菌和Enterorhabdus细菌比例明显升高(P0.05)。结论高脂血症豚鼠肠道菌群的组成及比例发生了明显变化。该实验结果为基于肠道菌群研究高脂血症作用机制奠定了理论基础。     

The impact of in utero HIV exposure on gut microbiota,inflammation, and microbial translocation

ABSTRACT

HIV-exposed but uninfected (HEU) children represent a growing population and show a significantly higher number of infectious diseases, several immune alterations, compromised growth, and increased mortality rates when compared to HIV-unexposed children. Considering the impact that the gut microbiota has on general host homeostasis and immune system development and modulation, we hypothesized that HEU children present altered gut microbiota that is linked to the increased morbidity and the immune system disorders faced by them. Our experiments revealed no differences in beta and alpha diversity of the gut microbiota between HEU and unexposed children or between HIV-infected and uninfected mothers. However, there were differences in the abundance of several taxa from the gut microbiota between HEU and unexposed children and between HIV-infected and uninfected mothers. Functional prediction based on 16S rRNA sequences also indicated differences between HEU and unexposed children and between infected and uninfected mothers. In addition, we detected no differences between HEU and unexposed children in relation to weight, weight-for-age z scores, albumin serum levels, or microbial translocation and inflammation markers. In summary, HIV-infected mothers and their HIV-exposed children present alterations in the abundance of several taxa in the gut microbiome and the predicted functional metagenome when compared to uninfected mothers and unexposed children. Knowledge about the gut microbiome of HEU children in different settings is essential in order to determine better treatments for this susceptible population.     

Vasopressin deletion is associated with sex-specific shifts in the gut microbiome

Brattleboro rats harbor a spontaneous deletion of the arginine-vasopressin (Avp) gene. In addition to diabetes insipidus, these rats exhibit low levels of anxiety and depressive behaviors. Recent work on the gut-brain axis has revealed that gut microbiota can influence anxiety behaviors. Therefore, we studied the effects of Avp gene deletion on gut microbiota. Since Avp gene expression is sexually different, we also examined how Avp deletion affects sex differences in gut microbiota. Males and females show modest but differentiated shifts in taxa abundance across 3 separate Avp deletion genotypes: wildtype (WT), heterozygous (Het) and AVP-deficient Brattleboro (KO) rats. For each sex, we found examples of taxa that have been shown to modulate anxiety behavior, in a manner that correlates with anxiety behavior observed in homozygous knockout Brattleboro rats. One prominent example is Lactobacillus, which has been reported to be anxiolytic: Lactobacillus was found to increase in abundance in inverse proportion to increasing gene dosage (most abundant in KO rats). This genotype effect of Lactobacillus abundance was not found when females were analyzed independently. Therefore, Avp deletion appears to affect microbiota composition in a sexually differentiated manner.     

Temporal and region-specific effects of sleep fragmentation on gut microbiota and intestinal morphology in Sprague Dawley rats

ABSTRACT

Sleep is a fundamental biological process, that when repeatedly disrupted, can result in severe health consequences. Recent studies suggest that both sleep fragmentation (SF) and dysbiosis of the gut microbiome can lead to metabolic disorders, though the underlying mechanisms are largely unclear. To better understand the consequences of SF, we investigated the effects of acute (6 days) and chronic (6 weeks) SF on rats by examining taxonomic profiles of microbiota in the distal ileum, cecum and proximal colon, as well as assessing structural and functional integrity of the gastrointestinal barrier. We further assayed the impact of SF on a host function by evaluating inflammation and immune response. Both acute and chronic SF induced microbial dysbiosis, more dramatically in the distal ileum (compared to other two regions studied), as noted by significant perturbations in alpha- and beta-diversity; though, specific microbial populations were significantly altered throughout each of the three regions. Furthermore, chronic SF resulted in increased crypt depth in the distal ileum and an increase in the number of villi lining both the cecum and proximal colon. Additional changes were noted with chronic SF, including: decreased microbial adhesion and penetration in the distal ileum and cecum, elevation in serum levels of the cytokine KC/GRO, and depressed levels of corticotropin. Importantly, our data show that perturbations to microbial ecology and intestinal morphology intensify in response to prolonged SF and these changes are habitat specific. Together, these results reveal consequences to gut microbiota homeostasis and host response following acute and chronic SF in rats.