Intestinal Bacterial Composition Research Articles

Intestinal Bacterial Composition and Characteristics of Wintering Mandarin Duck ( Aix Galericulata ) in Shiqian Mandarin Duck Lake National Wetland Park, Guizhou Province

Intestinal Bacterial Composition and Characteristics of Wintering Mandarin Duck ( Aix Galericulata ) in Shiqian Mandarin Duck Lake National Wetland Park, Guizhou Province

High-throughput sequencing of 16S rRNA amplicons characterizes gut microbiota shift of juvenile sea cucumber Apostichopus japonicus feeding with three antibiotics

Sea cucumber Apostichopus japonicus is an important marine economic species in Asian countries due to its profound nutritional and medicinal value. So far, with the rapid development of intensified artificial aquaculture of sea cucumbers, the use of antibiotics is still an inexpensive and dispensable way to treat pathogenic infections, especially during the nursery phase. However, there is little information on the effects of antibiotics on the intestinal microbiota of sea cucumber. Therefore an Illumina based sequencing method was used to examine the intestinal bacterial composition of juvenile A. japonicas following diets with three typical antibiotics (tetracycline, erythromycin, and norfloxacin) under 15, 30, and 45 d. The findings reveal that different antibiotics have distinct effects on the growth performance of juvenile sea cucumbers. However, the richness and diversity of microbiota were barely affected by antibiotics but the community composition alterations indicated that the three antibiotics exhibited their respective patterns of reshaping the intestinal bacteria of juvenile sea cucumbers. In common, the abundance of some sensitive genera with helpful functions, such as Thalassotalea, Shewanella, Sulfitobacter, and Halomonas decreased significantly with exposure to antibiotics and the abundance of multiple potential pathogenic- and suspected antibiotic-resistant microorganisms like Arcobacter, Leucothrix, and Clostridium_sensu_stricto_1 was found increased significantly in the antibiotic groups. These results suggest that low doses of antibiotics could affect the composition of the intestinal microbiota of sea cucumbers and might increase the risk of infection of the hosts. This study could help us to explore how antibacterial compounds modify the gut microbiota of sea cucumbers and provide theoretical guidance in hatchery management by scientific antibiotic use in sea cucumber mariculture.

Microbiota and cancer immunotherapy: in search of microbial signals

The intestinal microbiota, a conglomerate of microorganisms comprising bacteria, viruses, archaea and fungi, has been recognised as an important component of host physiology through, for example, its influence on nutritional...

Fecal chromogranins and secretogranins are linked to the fecal and mucosal intestinal bacterial composition of IBS patients and healthy subjects

Altered fecal levels of chromogranins (Cg) and secretogranins (Sg) are demonstrated in irritable bowel syndrome (IBS), but their role in IBS pathophysiology remains unknown. This study aimed to determine if granins are associated with bacterial composition, immune activation and IBS symptoms. Protein levels of fecal granins (CgA, CgB, SgII and SgIII) were analysed with immunoassays. Mucosal mRNA expression of granins, TPH1 and immune markers were evaluated with RT-qPCR. 16S rRNA gene sequencing was performed on fecal and mucosal bacteria. The intestinal granin profile, based on fecal protein levels and mucosal mRNA expression, could not discriminate between IBS patients (n = 88) and healthy subjects (HS, n = 33). IBS patients dominated by high fecal or mucosal granin levels, respectively, did not differ in symptom or immune profiles. Fecal-dominated and mucosal-dominated granin clusters of IBS patients and HS, demonstrated separate fecal and mucosal bacterial profiles and high fecal abundance of granins were associated with a less diverse bacterial composition and the Bacteroides enterotype. The intestinal granin profiles of IBS patients and HS are linked to the intestinal bacterial composition, diversity and enterotypes. These findings suggest that granins may be one of several host-produced factors regulating the microbiota composition of the intestine.

Effects of a Commercial Microbial Agent on the Bacterial Communities in Shrimp Culture System

Commercial microbial agents (e.g., probiotics, microbial products, microorganism preparation et al.) have been widely applied for disease control in shrimp culture. However, the effect of these microbial agents (MA) on shrimp health is unstable and the underlying mechanism remains unclear. The effect of MA can probably be achieved by influencing the bacterial community of shrimp culture system. To test this hypothesis, we used 16S rRNA gene amplicon sequencing to investigate the dynamics of both planktonic and intestinal bacterial composition in shrimp culture ponds with or without commercial MA applied weekly. The results showed that MA application increased the temporal turnover rate of bacterioplankton community. Within 1 week, MA-treatment significantly drove bacterioplankton community composition to divert from that without MA-treatment at day 2 after MA application, but the deviation tended to vanish at days 4 and 7. At day 21, a significant difference was observed in shrimp intestinal bacterial community between two groups. The relative abundance of Rhodobacteraceae in shrimp intestine was significantly greater in the MA-treated group than that in the control. However, MA-treatment did not significantly improve the growth or survival ratio of shrimp. This study suggest that MA works in terms of accelerating bacterioplankton community turnover and shifting intestinal bacterial community, however, its effect on shrimp growth might vary greatly and might be improved by optimizing the method in activation and application and more investigation on the microbial ecological process of shrimp culture system is needed before we develop and apply probiotics more efficiently.

Gut microbiota relationships to lung function and adult asthma phenotype: a pilot study

IntroductionDespite strong evidence that maturation patterns of the gut microbiome in early life influence the risk for childhood asthma, very little is known about gut microbiota patterns in adults with...

Differences in bacterial composition of histamine intolerant patients

Rationale: Even though an impaired degradation of oral supplied histamine due to diamine oxidase (DAO) deficiency is assumed as leading cause for histamine intolerance (HIT), other factors including a deranged gut flora may contribute to an elevated histamine exposure. For this we aimed to determine the intestinal bacterial composition in patients (pts) with proven HIT in comparison to healthy persons and pts with other food intolerances.

Abstract 1264: Commensal microbiota is involved in anti-PD-1 mAb-mediated antitumor activity in a preclinical tumor model

Abstract Background: A number of studies have shown that the gut microbiome may influence anti-tumor immune responses via innate and adaptive immunity, and the recent work in mice has highlighted the key roles of the gut microbiota in mediating tumor responses to chemotherapeutic agents and immunotherapies targeting PD-L1, PD-1 or CTLA-4. Multiple studies have demonstrated that the gut microbiome can markedly influence the outcome of PD-1 blockade in mice and patients and several commensal have been proved to be associated with favorable clinical outcome. Considering complexity of intestinal micro-organisms, a larger panel or wider spectrum of microbiota species maybe involved in this process. Methods: Since compositional differences in the microbiome may influence cancer development and responses to therapies, we sought to determine whether intestinal bacterial composition and abundances of the tumor bearing mice were associated with a specific treatment outcome of immunotherapy. To test this, we analyzed and compared an enrichment of intestinal microbiota of CT26 syngeneic tumor bearing mice before and after a series of anti-PD-1 mAb treatment were given. Results The results demonstrating that some strains were robustly enriched and this enrichment was associated with tumor response to anti-PD 1 therapy, while as other strains were down regulated upon the checkpoint blockade. Conclusions: Upon further characterization and confirmation, these intriguing findings could lead to identification of one or more microbiota strains that could have biomarker potentials or therapeutic values for cancer immunotherapy. Citation Format: Fei Chen, Jian Ding, Xiangchao Gu, Juan Zhang, wenqing Yang, Qian Shi. Commensal microbiota is involved in anti-PD-1 mAb-mediated antitumor activity in a preclinical tumor model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1264.

Vitamin D administration leads to a shift of the intestinal bacterial composition in Crohn's disease patients, but not in healthy controls

Dysbiosis is a common feature in the pathogenesis of inflammatory bowel diseases (IBD). Environmental factors, such as vitamin D deficiency, seem to play a role in the intestinal inflammation of IBD. The aim of this study was to investigate whether vitamin D administration has an impact on the bacterial composition in Crohn's disease (CD) compared to healthy controls (HC). A prospective, longitudinal, controlled interventional analysis was conducted in seven patients with CD in clinical remission and 10 HC to investigate the effect of orally administrated vitamin D on the intestinal bacterial composition using 16S ribosomal RNA gene amplicon sequencing. Clinical parameters were assessed. In contrast to HC, microbial communities of CD patients changed significantly during early vitamin D administration. However, a further increase in vitamin D level was associated with a reversal of this effect and additionally with a decrease in the bacterial richness in the CD microbiome. Specific species with a high abundancy were found during vitamin D administration in CD, but not in HC; the abundancy of Alistipes, Barnesiella, unclassified Porphyromonadaceae (both Actinobacteria), Roseburia, Anaerotruncus, Subdoligranulum and an unclassified Ruminococaceae (all Firmicutes) increased significantly after 1-week vitamin D administration in CD. Vitamin D has a specific influence on the bacterial communities in CD, but not in HC. Administration of vitamin D may have a positive effect in CD by modulating the intestinal bacterial composition and also by increasing the abundance of potential beneficial bacterial strains.

Gut Microbiota-Regulated Pharmacokinetics of Berberine and Active Metabolites in Beagle Dogs After Oral Administration.

Berberine (BBR) is considered a multi-target drug that has significant advantages. In contrast to its significant pharmacological effects in clinic, the plasma level of BBR is very low. Our previous work revealed that dihydroberberine (dhBBR) could be an absorbable form of BBR in the intestine, and butyrate is an active metabolite that is generated by gut bacteria in rats. In this study, for the first time we describe gut microbiota-regulated pharmacokinetics in beagle dogs after oral administration of BBR by single (50 mg/kg) or multiple doses (50 mg/kg/d) for 7 days. GC-MS, GC, LC-MS/MS, and LC/MSn-IT-TOF were used to detect dhBBR, butyrate and BBR as well as its Phase I and II metabolites, respectively. The results showed that dhBBR was not detected in dog plasma but was excreted in small amounts in the feces of dogs examined on days 3 and 7. Butyrate was generated by gut bacteria and increased by 1.3- and 1.2-fold in plasma or feces, respectively, after 7 days of BBR treatment compared to the levels before treatment. Changes of intestinal bacterial composition were analyzed by 16S rRNA genes analysis. The results presented that dogs treated with BBR for 7 days increased both the abundance of the butyrate- and the nitroreductases- producing bacteria. We also identified chemical structures of the Phase I and II metabolites and analyzed their contents in beagle dogs. Eleven metabolites were detected in plasma and feces after BBR oral administration (50 mg/kg) to dogs, including 8 metabolites of Phase I and III metabolites of Phase II. The pharmacokinetic profile indicated that the concentration of BBR in plasma was low, with a Cmax value of 36.88 ± 23.45 ng/mL. The relative content of glucuronic acid conjugates (M11) was higher than those of other metabolites (M1, M2, M12, and M14) in plasma. BBR was detected in feces, with high excreted amounts on day 3 (2625.04 ± 1726.94 μg/g) and day 7 (2793.43 ± 488.10 μg/g). In summary, this is the first study to describe gut microbiota-regulated pharmacokinetics in beagle dogs after oral administration of BBR, which is beneficial for discovery of drugs with poor absorption but good therapeutic efficacy.

Dietary lipid levels could improve growth and intestinal microbiota of juvenile swimming crab, Portunus trituberculatus

An 8 week feeding trial was conducted to evaluate the effects of dietary lipid levels on growth and intestinal microbiota of juvenile swimming crab. Three isonitrogenous (47% crude protein) diets were formulated to contain 5.8%, 9.9% and 15.1% crude lipid levels, respectively. Three groups of swimming crab (n = 60 per group) were randomly assigned to each diet. An Illumina-based sequencing method was used to analyze the intestinal bacterial composition of the crabs. The results indicated that swimming crab fed the diets containing 5.8% and 9.9% lipid had significantly higher weight gain and survival than those fed the 15.1% lipid diet. Proteobacteria, Fusobacteria and Tenericutes were dominant in the intestines of swimming crab regardless of the diet; the relative abundance of Fusobacteria decreased while Proteobacteria increased with increase of dietary lipid levels. Swimming crab fed the diets containing 9.9% and 15.1% lipid had a higher abundance of pathogenic bacteria than those fed the 5.8% lipid diet. These results indicate that dietary lipid levels could affect the composition of the intestinal microbiota; also, higher dietary lipid levels have a negative impact and increase the potential risk of disease in swimming crab.

What Effects do Silver Nanoparticles Have on Drosophila melanogaster Larvae with Respect to Stress Response and Microbial Intestinal Composition?

Silver nanoparticles (AgNPs) have been shown to be highly toxic to certain organisms and can induce stress in cells. The purpose of this study is twofold: first, to examine the stress response to AgNP exposure on Drosophila melanogaster (fruit fly) larvae, and secondly, to determine if exposure to AgNPs alters the intestinal bacterial composition. To answer these questions, fruit flies were grown on food mixed with AgNPs. Larvae were monitored for their ability to escape from heat stress and their climbing ability before metamorphosis into pupae. Larval wandering behaviour was examined by devising a test to determine if they could crawl their way back to food. In order to examine the flora in the digestive tract, DNA was isolated from dissected larval intestines, purified and then a relatively conserved portion of the bacterial DNA was amplified. These samples were then sent for pyrosequencing, which is a technique that will allow us to examine the composition of the intestinal microbial population. Preliminary results have been mixed. There has been some suggestion of a stress response, but this has not been very consistent. Therefore, more experiments need to be done. However, the bacterial population of the gut does seem to change after the treatment, indicating that AgNP exposure results in altered microbial composition in D. melanogaster intestines. It is hoped that this research will help elucidate our understanding of the impact NPs have on organisms, which is highly relevant because of the high prevalence of NPs in consumer and medicinal materials.

Hand-in-hand — colorectal cancer metastasizes with microorganisms

Increased relative abundance of Fusobacterium species contributes to the difference in intestinal bacterial composition between healthy individuals and patients with colorectal cancer (CRC). A new study now reveals that live Fusobacterium originating from primary CRC associate with liver metastasis, suggesting a potentially important function for this bacterial genus in metastatic tumour growth.

Molecular Alteration Analysis of Human Gut Microbial Composition in Graves' disease Patients.

The gut microbial association with host co-existence is critical for body homeostasis and pathogenicity. Graves' disease (GD) is an autoimmune disease manifested with hyperthyroidism and ophthalmopathy. However, we hypothesized that gut bacteria could affect an important role in GD pathogenicity. The current study aim was to characterize and investigate the intestinal bacterial composition of GD qualitatively and quantitatively. 27 GD and 11 healthy controls were enrolled for fecal sample collection. The PCR-DGGE of 16S rRNA gene by targeting V3 region and Real-time PCR for Lactobacillus, Bifidobacterium, Bacteroides vulgatus and Clostridium leptum, were performed. High-throughput sequencing of 16S rRNA gene with the V3+V4 site was perormed on Hiseq2500 platform on randomly 20 selected samples. The relative analysis of richness indices and diversity illustrated lesser diversification of intestinal bacteria in GD patients in contrast to controls. The data statistics shows the alteration in phyla of GD as compared to control. At the family taxonomic level, the relative abundance of Prevotellaceae and Pasteurellaceae were significantly higher in patients, while Enterobacteriaceae, Veillonellaceae, and Rikenellaceae were significantly lower in the diseased group as compared to control. At the genus level, a significant raised in genera count of the diseased group were Prevotella_9 and Haemophilus, while significantly decreased in the genera of the GD group were Alistipes and Faecalibacterium. The modulation in intestinal bacterial composition was checked at species level particularly H. parainfluenza abundance was raised in GD. The outcomes of the current study are aligned with the proposed hypothesis of gut microbial dysbiosis in GD. Statistically, alpha indices and differential abundance analyses of each intestinal bacterial community were significantly changed in GD. Therefore, the current study may provide a new insight into the GD pathogenesis and, in turn, explore its contribution in possible treatments.

Dysbiosis of the Gut Microbiota on the Inflammatory Background due to Lack of Suppressor of Cytokine Signalling-1 in Mice

Background: Both environmental and genetic factors have been implicated in the induction of autoimmune disease. Therefore, it is important to understand the pathophysiological significance of the gut microbiota and host genetic background that contribute to an autoimmune disease such as inflammatory bowel disease (IBD). We have previously reported that mice deficient for suppressor of cytokine signaling-1 (SOCS1), in which SOCS1 expression was restored in T and B cells on an SOCS1^–/– background (SOCS1^–/–Tg mice), developed systemic autoimmune diseases accompanied by spontaneous colitis. Methods: To investigate whether the proinflammatory genetic background affects the gut microbiota, we used SOCS1^–/–Tg mice as a model of spontaneous chronic colitis. Fecal samples were collected from SOCS1^–/–Tg mice and SOCS1^+/+Tg (control) mice at 1 and 6 months of age, and the fecal bacterial 16S ribosomal RNA genes were sequenced using the Illumina MiSeq platform. Results: Gut microbial diversity was significantly reduced and the intestinal bacterial community composition changed in SOCS1^–/–Tg mice in comparison with the control mice. Interestingly, the population of Prevotella species, which is known to be elevated in ulcerative colitis and colorectal cancer patients, was significantly increased in SOCS1^–/–Tg mice regardless of age. Conclusion: Taken together, these results suggest that the proinflammatory genetic background owing to SOCS1 deficiency causes dysbiosis of the gut microbiota, which in turn generates a procolitogenic environment.

Hydrogen-water ameliorates radiation-induced gastrointestinal toxicity via MyD88\u2019s effects on the gut microbiota

Although radiation therapy is a cornerstone of modern management of malignancies, various side effects are inevitably linked to abdominal and pelvic cancer after radiotherapy. Radiation-mediated gastrointestinal (GI) toxicity impairs the life quality of cancer survivors and even shortens their lifespan. Hydrogen has been shown to protect against tissue injuries caused by oxidative stress and excessive inflammation, but its effect on radiation-induced intestinal injury was previously unknown. In the present study, we found that oral gavage with hydrogen-water increased the survival rate and body weight of mice exposed to total abdominal irradiation (TAI); oral gavage with hydrogen-water was also associated with an improvement in GI tract function and the epithelial integrity of the small intestine. Mechanistically, microarray analysis revealed that hydrogen-water administration upregulated miR-1968-5p levels, thus resulting in parallel downregulation of MyD88 expression in the small intestine after TAI exposure. Additionally, high-throughput sequencing showed that hydrogen-water oral gavage resulted in retention of the TAI-shifted intestinal bacterial composition in mice. Collectively, our findings suggested that hydrogen-water might be used as a potential therapeutic to alleviate intestinal injury induced by radiotherapy for abdominal and pelvic cancer in preclinical settings.

Rifaximin has minor effects on bacterial composition, inflammation, and bacterial translocation in cirrhosis: A randomized trial.

Decompensated cirrhosis is characterized by disturbed hemodynamics, immune dysfunction, and high risk of infections. Translocation of viable bacteria and bacterial products from the gut to the blood is considered a key driver in this process. Intestinal decontamination with rifaximin may reduce bacterial translocation (BT) and decrease inflammation. A randomized, placebo-controlled trial investigated the effects of rifaximin on inflammation and BT in decompensated cirrhosis. Fifty-four out-patients with cirrhosis and ascites were randomized, mean age 56years (±8.4), and model for end-stage liver disease score 12 (±3.9). Patients received rifaximin 550-mg BD (n=36) or placebo BD (n=18). Blood and fecal (n=15) sampling were conducted at baseline and after 4weeks. Bacterial DNA in blood was determined by real-time qPCR 16S rRNA gene quantification. Bacterial composition in feces was analyzed by 16S rRNA gene sequencing. Circulating markers of inflammation, including tumor necrosis factor alpha, interleukins 6, 10, and 18, stromal cell-derived factor 1-α, transforming growth factor β-1, and high sensitivity C-reactive protein, were unaltered by rifaximin treatment. Rifaximin altered abundance of bacterial taxa in blood marginally, only a decrease in Pseudomonadales was observed. In feces, rifaximin decreased bacterial richness, but effect on particular species was not observed. Subgroup analyses on patients with severely disturbed hemodynamics (n=34) or activated lipopolysaccharide binding protein (n=37) revealed no effect of rifaximin. Four weeks of treatment with rifaximin had no impact on the inflammatory state and only minor effects on BT and intestinal bacterial composition in stable, decompensated cirrhosis (NCT01769040).

Bacteriological and Immunological Profiling of Meconium and Fecal Samples from Preterm Infants: A Two-Year Follow-Up Study.

An abnormal colonization pattern of the preterm gut may affect immune maturation and exert a long-term influence on the intestinal bacterial composition and host health. However, follow-up studies assessing the evolution of the fecal microbiota of infants that were born preterm are very scarce. In this work, the bacterial compositions of fecal samples, obtained from sixteen 2-year-old infants were evaluated using a phylogenetic microarray; subsequently, the results were compared with those obtained in a previous study from samples of meconium and feces collected from the same infants while they stayed in the neonatal intensive care unit (NICU). In parallel, the concentration of a wide range of cytokines, chemokines, growth factors and immunoglobulins were determined in meconium and fecal samples. Globally, a higher bacterial diversity and a lower interindividual variability were observed in 2-year-olds’ feces, when compared to the samples obtained during their first days of life. Hospital-associated fecal bacteria, that were dominant during the NICU stay, seemed to be replaced, two years later, by genera, which are usually predominant in the healthy adult microbiome. The immune profile of the meconium and fecal samples differed, depending on the sampling time, showing different immune maturation statuses of the gut.

Fecal bacteria from treatment-naive Crohn's disease patients can skew helper T cell responses

Many studies have demonstrated that the inflamed mucosa of Crohn's disease (CD) patients presented a disturbed gut commensal community, and the shift in microbial composition and species variety is associated with disease severity. To establish a link between changes in the intestinal bacterial composition and the alteration of inflammation, we obtained fecal bacteria from CD patients and non-CD controls. The bacteria were then used to stimulate the peripheral blood mononuclear cells (PBMCs) from one non-CD individual. We found that the frequency of IFN-γ- and IL-17-expressing CD4 T cells was significantly higher after stimulation with CD bacteria than with non-CD bacteria, while the frequency of IL-4- and IL-10-expressing CD4 T cells was significantly decreased after stimulation with CD bacteria. A similar trend was observed in the level of cytokine expression and transcription expression. However, this difference was not clear-cut, as overlapping regions were observed between the two groups. With longer stimulation using CD bacteria, the skewing toward Th1/Th17 responses were further increased. This increase depended on the presence of monocytes/macrophages. Interestingly, we also found that B cells presented an inhibitory effect in CD bacteria-mediated skewing toward Th1/Th17 cells and promoted IL-10 secretion in CD bacteria-stimulated PBMCs. Together, our results demonstrated that CD bacteria could promote Th1/Th17 inflammation in a host factor-independent fashion.

Intestinal Microbiota of White Shrimp Penaeus vannamei Under Intensive Cultivation Conditions in Ecuador.

The goal of the study was to characterize the intestinal tract bacterial microbiota composition of Penaeus vannamei in intensive commercial ponds in Ecuador, comparing two shrimp-farming phases: nursery and harvest. Bacterial microbiota was examined by sequencing amplicons V2-V3 of the 16S rRNA using Ion Torrent technology. Archaea sequences were detected in both phases. Sequence analyses revealed quantitative and qualitative differences between the nursery phase and the harvest phase in shrimp intestinal microbiota composition. The main differences were observed at the phylum level during the nursery phase, and the prevailing phyla were CKC4 (37.3%), Proteobacteria (29.8%), Actinobacteria (11.6%), and Firmicutes (10.1%). In the harvest phase, the prevailing phyla were Proteobacteria (28.4%), Chloroflexi (19.9%), and Actinobacteria (15.1%). At the genus level, microbiota from the nursery phase showed greater relative abundances of CKC4 uncultured bacterium (37%) and Escherichia-Shigella (18%). On the contrary, in the microbiota of harvested shrimp, the prevailing genera were uncultured Caldilinea (19%) and Alphaproteobacteria with no other assigned rate (10%). The analysis of similarity ANOSIM test (beta diversity) indicated significant differences between the shrimp microbiota for these two farming phases. Similarly, alfa-diversity analysis (Chao1) indicated that the microbiota at harvest was far more diverse than the microbiota during the nursery phase, which showed a homogeneous composition. These results suggest that shrimp microbiota diversify their composition during intensive farming. The present work offers the most detailed description of the microbiota of P. vannamei under commercial production conditions to date.