Gut Bacterial Flora Research Articles

Stimulation of Tendon Healing With Delayed Dexamethasone Treatment Is Modified by the Microbiome

Background: The immune system reflects the microbiome (microbiota). Modulation of the immune system during early tendon remodeling by dexamethasone treatment can improve rat Achilles tendon healing. The authors tested whether changes in the microbiota could influence the effect of dexamethasone treatment. Hypothesis: A change in microbiome would influence the response to dexamethasone on regenerate remodeling, specifically tendon material properties (peak stress). Study Design: Controlled laboratory study. Methods: Specific opportunist and pathogen-free female rats were housed separately (n = 41) or together with specific pathogen-free rats carrying opportunistic microbes such as Staphylococcus aureus (n = 41). After 6 weeks, all co-housed rats appeared healthy but now carried S aureus. Changes in the gut bacterial flora were tested by API and RapID biochemical tests. All rats (clean and contaminated) underwent Achilles tendon transection under aseptic conditions. Flow cytometry was performed 8 days postoperatively on tendon tissue. Sixty rats received subcutaneous dexamethasone or saline injections on days 5 through 9 after transection. The tendons were tested mechanically on day 12. The predetermined primary outcome was the interaction between contamination and dexamethasone regarding peak stress, tested by 2-way analysis of variance. Results: Dexamethasone increased peak stress in all groups but more in contaminated rats (105%) than in clean rats (53%) (interaction, P = .018). A similar interaction was found for an estimate of elastic modulus (P = .021). Furthermore, dexamethasone treatment reduced transverse area but had small effects on peak force and stiffness. In rats treated with saline only, contamination reduced peak stress by 16% (P = .04) and elastic modulus by 35% (P = .004). Contamination led to changes in the gut bacterial flora and higher levels of T cells (CD3+CD4+) in the healing tendon (P < .05). Conclusion: Changes in the microbiome influence tendon healing and enhance the positive effects of dexamethasone treatment during the early remodeling phase of tendon healing. Clinical Relevance: The positive effect of dexamethasone on early tendon remodeling in rats is strikingly strong. If similar effects could be shown in humans, immune modulation by a few days of systemic corticosteroids, or more specific compounds, could open new approaches to rehabilitation after tendon injury.

Trial in progress: Multicenter observational study to evaluate the relationship between gut bacterial flora and their therapeutic or adverse effects in advanced non-small cell lung cancer patients treated with nivolumab.

TPS9114Background: Nivolumab is one of the standard therapies for pretreated advanced non-small cell lung cancer (NSCLC). A correlation between PD-L1 expression on tumor cells and antitumor effects...

Aerobic gut bacterial flora of Cydia pomonella (L.) (Lepidoptera: Tortricidae) and their virulence to the host

This study aimed to isolate and characterize bacteria from the codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae), and determine their virulence to its larvae. A total of 16 bacteria were isolated from larvae belonging to different instars. Based on morphological, biochemical, physiological, and molecular studies, the bacterial isolates were identified as Pseudomonas sp. (Cp1, 3, 5, and 13), Corynebacterium sp. (Cp2), Bacillus sp. (Cp4, 7, 9, 10, 12, and 15), Pectobacterium carotovorum (Cp6), Paenibacillus sp. (Cp8), Bacillus megaterium (Cp11), Bacillus pumilus (Cp14), and Terribacillus saccharophilus (Cp16). It was also determined the virulence of these isolates, where the highest potential activity was obtained by Bacillus sp. Cp9, with (76%) mortality. These results could be beneficial for future biocontrol programs of C. pomonella.

High salt intake increases plasma trimethylamine N-oxide (TMAO) concentration and produces gut dysbiosis in rats.

A high-salt diet is considered a cardiovascular risk factor; however, the mechanisms are not clear. Research suggests that gut bacteria-derived metabolites such as trimethylamine N-oxide (TMAO) are markers of cardiovascular diseases. We evaluated the effect of high salt intake on gut bacteria and their metabolites plasma level. Sprague Dawley rats ages 12-14 wk were maintained on either water (controls) or 0.9% or 2% sodium chloride (NaCl) water solution (isotonic and hypertonic groups, respectively) for 2 wk. Blood plasma, urine, and stool samples were analyzed for concentrations of trimethylamine (TMA; a TMAO precursor), TMAO, and indoxyl sulfate (indole metabolite). The gut-blood barrier permeability to TMA and TMA liver clearance were assessed at baseline and after TMA intracolonic challenge test. Gut bacterial flora was analyzed with a 16S ribosomal ribonucleic acid (rRNA) gene sequence analysis. The isotonic and hypertonic groups showed a significantly higher plasma TMAO and significantly lower 24-hr TMAO urine excretion than the controls. However, the TMA stool level was similar between the groups. There was no significant difference between the groups in gut-blood barrier permeability and TMA liver clearance. Plasma indoxyl concentration and 24-hr urine indoxyl excretion were similar between the groups. There was a significant difference between the groups in gut bacteria composition. High salt intake increases plasma TMAO concentration, which is associated with decreased TMAO urine excretion. Furthermore, high salt intake alters gut bacteria composition. These findings suggest that salt intake affects an interplay between gut bacteria and their host homeostasis.

Mining the Virome for Insights into Type 1 Diabetes

Type 1 diabetes (T1D) is characterized by the autoimmune destruction of insulin-producing pancreatic beta cells. Although environmental factors interplay with genetic susceptibility to promote immune dysregulation and disease, it remains unclear as to which potential environmental factors are causative and not simply correlative. Despite many hints that the microbiome can have a profound effect on T1D, significant changes in bacterial gut flora and diversity appear to emerge only after the detection of early signs of T1D. Surprisingly, we recently found significant differences in the gut virome preceding the initial signs of T1D, raising the tantalizing possibility that the state of the virome may influence or predict whether susceptible individuals progress on the path to disease. The challenge will be to discern whether there is likely a causative relationship between detected virome differences and T1D.

The Neurodevelopmental Perspective of Surgical Necrotizing Enterocolitis: The Role of the Gut-Brain Axis.

This state-of-the-art review article aims to highlight the most recent evidence about the therapeutic options of surgical necrotizing enterocolitis, focusing on the molecular basis of the gut-brain axis in relevance to the neurodevelopmental outcomes of primary peritoneal drainage and primary laparotomy. Current evidence favors primary laparotomy over primary peritoneal drainage as regards neurodevelopment in the surgical treatment of necrotizing enterocolitis. The added exposure to inhalational anesthesia in infants undergoing primary laparotomy is an additional confounding variable but requires further study. The concept of the gut-brain axis suggests that bowel injury initiates systemic inflammation potentially affecting the developing central nervous system. Signals about microbes in the gut are transduced to the brain and the limbic system via the enteric nervous system, autonomic nervous system, and hypothalamic-pituitary axis. Preterm infants with necrotizing enterocolitis have significant differences in the diversity of the microbiome compared with preterm controls. The gut bacterial flora changes remarkably prior to the onset of necrotizing enterocolitis with a predominance of pathogenic organisms. The type of initial surgical approach correlates with the length of functional gut and microbiome equilibrium influencing brain development and function through the gut-brain axis. Existing data favor patients who were treated with primary laparotomy over those who underwent primary peritoneal drainage in terms of neurodevelopmental outcomes. We propose that this is due to the sustained injurious effect of the remaining diseased and necrotic bowel on the developing newborn brain, in patients treated with primary peritoneal drainage, through the gut-brain axis and probably not due to the procedure itself.

Immucillins in Infectious Diseases.

The Immucillins are chemically stable analogues that mimic the ribocation and leaving-group features of N-ribosyltransferase transition states. Infectious disease agents often rely on ribosyltransferase chemistry in pathways involving precursor synthesis for nucleic acids, salvage of nucleic acid precursors, or synthetic pathways with nucleoside intermediates. Here, we review three infectious agents and the use of the Immucillins to taget enzymes essential to the parasites. First, DADMe-Immucillin-G is a purine nucleoside phosphorylase (PNP) inhibitor that blocks purine salvage and shows clinical potential for treatment for the malaria parasite Plasmodium falciparum, a purine auxotroph requiring hypoxanthine for purine nucleotide synthesis. Inhibition of the PNPs in the host and in parasite cells leads to apurinic starvation and death. Second, Helicobacter pylori, a causative agent of human ulcers, synthesizes menaquinone, an essential electron transfer agent, in a pathway requiring aminofutalosine nucleoside hydrolysis. Inhibitors of the H.pylori methylthioadenosine nucleosidase (MTAN) are powerful antibiotics for this organism. Synthesis of menaquinone by the aminofutalosine pathway does not occur in most bacteria populating the human gut microbiome. Thus, MTAN inhibitors provide high-specificity antibiotics for H.pylori and are not expected to disrupt the normal gut bacterial flora. Third, Immucillin-A was designed as a transition state analogue of the atypical PNP from Trichomonas vaginalis. In antiviral screens, Immucillin-A was shown to act as a prodrug. It is active against filoviruses and flaviviruses. In virus-infected cells, Immucillin-A is converted to the triphosphate, is incorporated into the viral transcript, and functions as an atypical chain-terminator for RNA-dependent RNA polymerases. Immucillin-A has entered clinical trials for use as an antiviral. We also summarize other Immucillins that have been characterized in successful clinical trials for T-cell lymphoma and gout. The human trials support the potential development of the Immucillins in infectious diseases.

Effect of probiotics and synbiotics consumption on serum concentrations of liver function test enzymes: a systematic review and meta-analysis.

The gut-liver interaction suggests that modification of gut bacterial flora using probiotics and synbiotics may improve liver function. This systematic review and meta-analysis aimed to clarify the effect of probiotics and synbiotics consumption on the serum concentration of liver function enzymes. PubMed (MEDLINE), Cumulative Index to Nursing and Allied Health Literature, and Cochrane Library (Central) were searched from 1980 to August 2017 for studies where adults consumed probiotics and/or synbiotics in controlled trials and changes in liver function enzymes were examined. A total of 17 studies (19 trials) were included in the meta-analysis. Random effects meta-analyses were applied. Probiotics and synbiotics significantly reduced serum alanine aminotransferase [-8.05IU/L, 95% confidence interval (CI) -13.07 to -3.04; p = 0.002]; aspartate aminotransferase (-7.79IU/L, 95% CI: -13.93 to -1.65; p = 0.02) and gamma-glutamyl transpeptidase (-8.40IU/L, 95% CI -12.61 to -4.20; p < 0.001). Changes in the serum concentration of alkaline phosphatase and albumin did not reach a statistically significant level. Changes to bilirubin levels were in favour of the control group (0.95μmol/L, 95% CI 0.48-1.42; p < 0.001). Subgroup analysis suggested the existence of liver disease at baseline, synbiotics supplementation and duration of supplementation ≥ 8 weeks resulted in more pronounced improvement in liver function enzymes than their counterparts. Probiotics and synbiotics may be suggested as supplements to improve serum concentration of liver enzymes, especially when synbiotics administered for a period ≥ 8 weeks and in individuals with liver disease.

Midgut Bacterial Diversity of Wild Populations of Phlebotomus (P.) papatasi, the Vector of Zoonotic Cutaneous Leishmaniasis (ZCL) in Turkey

Phlebotomine sand flies are hematophagous insects that harbor bacterial, viral and parasitic agents like Bartonella sp., Phleboviruses and Leishmania spp., respectively. There are few reports on bacterial microbiota of Phlebotomus (P.) papatasi but no data available for natural populations of Turkey, where leishmaniasis is endemic. Therefore, we aimed to investigate the midgut bacterial flora of different populations of P. papatasi. Sand flies were collected from different towns (Karaburun, Urla, Ayvacik and Başçayır) located in the western part of Turkey. Laboratory reared P. papatasi were included in the study as an insectarium population. After sterile washing steps, sand flies were dissected and guts were separated. Three pools, (males, unfed females and blood-fed females) were generated for each population. Prokaryotic 16 S rRNA gene was amplified and DGGE was performed. Fourteen different organisms belonging to two Phylum (Proteobactericea and Furmicutes) were identified according to sequence results in the studied pools. The presence of Wolbachia sp. was shown for the first time in the wild-caught sand fly populations of Turkey. This is the first report of gut bacterial flora of wild-caught P. papatasi collected in an endemic area for leishmaniasis in Turkey. Microbiome profiling of wild-caught sand flies will be of great help in the investigating of possible vector control candidates for paratransgenic control approach.

Integration of the TGx-28.65 genomic biomarker with the flow cytometry micronucleus test to assess the genotoxicity of disperse orange and 1,2,4-benzenetriol in human TK6 cells

In vitro gene expression signatures to predict toxicological responses can provide mechanistic context for regulatory testing. We previously developed the TGx-28.65 genomic biomarker from a database of gene expression profiles derived from human TK6 cells exposed to 28 well-known compounds. The biomarker comprises 65 genes that can classify chemicals as DNA damaging or non-DNA damaging. In this study, we applied the TGx-28.65 genomic biomarker in parallel with the in vitro micronucleus (MN) assay to determine if two chemicals of regulatory interest at Health Canada, disperse orange (DO: the orange azo dye 3-[[4-[(4-Nitrophenyl)azo]phenyl] benzylamino]propanenitrile) and 1,2,4-benzenetriol (BT: a metabolite of benzene) are genotoxic or non-genotoxic. Both chemicals caused dose-dependent declines in relative survival and increases in apoptosis. A strong significant increase in MN induction was observed for all concentrations of BT; the top two concentrations of DO also caused a statistically significant increase in MN, but these increases were <2-fold above controls. TGx-28.65 analysis classified BT as genotoxic at all three concentrations and DO as genotoxic at the mid and high concentrations. Thus, although DO only caused a small increase in MN, this response was sufficient to induce a cellular DNA damage response. Benchmark dose modeling confirmed that BT is much more potent than DO. The results strongly suggest that follow-up work is required to assess whether DO and BT are also genotoxic in vivo. This is particularly important for DO, which may require metabolic activation by bacterial gut flora to fully induce its genotoxic potential. Our previously published data and this proof of concept study suggest that the TGx-28.65 genomic biomarker has the potential to add significant value to existing approaches used to assess genotoxicity.

Characterization of gut bacterial flora of Apis mellifera from north-west Pakistan.

Gut microbiota has been recognized to play a beneficial role in honey bees (Apis mellifera). Present study was designed to characterize the gut bacterial flora of honey bees in north-west Pakistan. Total 150 aerobic and facultative anaerobic bacteria from guts of 45 worker bees were characterized using biochemical assays and 16S rDNA sequencing followed by bioinformatics analysis. The gut isolates were classified into three bacterial phyla of Firmicutes (60%), Proteobacteria (26%) and Actinobacteria (14%). Most of the isolates belonged to genera and families of Staphylococcus, Bacillus, Enterococcus, Ochrobactrum, Sphingomonas, Ralstonia, Enterobacteriaceae, Corynebacterium and Micrococcineae. Many of these bacteria were tolerant to acidic environments and fermented sugars, hence considered beneficial gut inhabitants and involved the maintenance of a healthy microbiota. However, several opportunistic commensals that proliferate in the hive environment including members Staphylococcus haemolyticus group and Sphingomonas paucimobilis were also identified. This is the first report on bee gut microbiota from north-west Pakistan geographically situated at the crossroads of Indian subcontinent and central Asia.

Conserved nature of Helicoverpa armigera gut bacterial flora on different host plants and in vitro interactions with PI proteins advocates role in host digestive physiology

Abstract Helicoverpa armigera is anxious insect pest of agricultural crops. Array of defensive molecules in host plants and extensive use of chemical insecticides are unable to cease the attack incidences. Gut bacterial communities are found to contribute in various physiological activities in most of the arthropods. In the current study the bacterial communities were isolated from gut of H. armigera feeding on three host plants (Pigeonpea, Chickpea and Cotton) by culture dependent and culture independent methods. Predominant bacterial communities were identified by terminal restriction fragment length polymorphism (TRFLP). Three dominant phylotypes namely proteobacteria, actinobacteria and firmicutes were identified by TRFLP and found to conserve on different host plant selected. Five Bacillus species namely Bacillus sp. JR14, Bacillus sp. YP1, Bacillus safensis CG1, Bacillus subtillis KAVK2 and Bacillus megaterium 47N were purified by culture dependent method and identified by 16S rRNA sequencing. Among all identified Bacillus, Bacillus sp. YP1 strain was found to be potent protease producer as assisted by dot-blot assay and in vitro solution assays. The in vitro interactions of these proteases with host plant PIs were studied by reverse zymography and gel X-ray contact print (GXCP) analysis. Reduction in activity of PIs and degradation pattern of PI bands on gels in presence of trypsin and protease extract of Bacillus sp. YP1 indicates inactivation of PIs. Thus, conserved nature and in vitro response to PI proteins advocates role of gut bacterial flora in H. armigera digestive physiology.

Is it bowel-associated dermatosis-arthritis syndrome induced by small intestinal bacteria overgrowth?

IntroductionBowel-associated dermatosis-arthritis syndrome is rare systemic diseases characterized by a prodrome of fever, chills, and influenza-like symptoms with subsequent skin eruptions, myalgias, and polyarthralgias. It is reported to be occurred in Intestinal bypass surgery and inflammatory bowel disease.Case descriptionHerein, we described a 29-years-old man with Bowel-associated dermatosis-arthritis syndrome. He had no history of gastrointestinal surgery and inflammatory bowel disease. Distribution of the gut bacterial flora showed small intestinal bacterial overgrowth.Discussion and EvaluationIt is rarely form as Non-intestinal bypass road and non-inflammatory bowel disease was induced by small intestinal bacteria overgrowth.ConclusionsWe concluded that Immuno-inflammatory response to overgrowth of intestinal bacterial antigen induce the clinical symptoms of bowel-associated dermatosis-arthritis syndrome.

Effects of different carbohydrates on the simulation of human intestinal bacterial flora with in vitro culture

To investigate the optimal growth condition of human fecal bacterial flora in vitro by comparing the effect of different carbohydrates as cultural media. Three fecal samples (1, 2, 3) were collected and inoculated into a single-stage chemostat system, in which starch medium (VI) and starch polysaccharide medium(XP) were used. Samples were collected for bacterial genomic DNA extraction and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis. Bacterial composition and short chain fatty acid (SCFA) were then analyzed. The single stage chemostat system reached steady after operating 8 days, when evaluated by the PCR-DGGE. Bacterial 16s rRNA high-throughput sequencing showed that the intestinal bacteria of these three volunteers was mainly composed of four bacterial phyla, namely, Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria. When the influence of bacterial abundance was considered, the similarity of bacterial composition between the original fecal samples to the harvested flora after culture was 0.847, 0.825, 0.968 in VI medium and 0.927, 0.926, 0.836 in XP medium, respectively. The similarity was decreased to 0.553, 0.580, 0.623 with VI medium and 0.617, 0.520, 0.574 with XP medium, when the number of bacterial species was considered. The variation of host individual also influenced the simulation. VI medium favored fecal sample 3, while XP medium more benefited sample 1 and 2. Bacteroides and Lachnospiraceae_incertae_sedis grew in both VI and XP medium. However, some species were only detected in VI medium and some were specifically found in the XP medium. The SCFA concentration in fermenters was 15-35 mmol/L, mainly propionate and butyrate. The chemostat system works for stimulating human gut bacterial flora in vitro. The bacterial composition is affected by different carbohydrate in the culture medium yet with close simulation higher than 80%.

Effect of Overgrowth or Decrease in Gut Microbiota on Health and Disease

Context: The composition and function of the gut microbiota develop with their host from birth. The human microbiome, especially the gut microbiota, plays a critical role in a myriad of health and normal activities. However, the increase or decrease in number of gut bacteria may cause several disorders. This review aimed to assess the importance of human gut microflora and their roles in the health and possible diseases caused by fluctuations in the number of these bacteria. Evidence Acquisition: For the current review, we searched for the terms “bacterial gut flora”, “role,” “number,” and “increase” and “decrease” on the Google scholar, PubMed, Science Direct, SciVerse, and Scopus search engines and databases. The exclusion criteria were “genetic factors,” “veterinary flora,” “protozoal flora,” “mold,” “fungal,” and “yeast flora”. Results: The gut microbiota is accompanied by the regulation of several host metabolic pathways, giving rise to interactive host-microbiota signaling, metabolic, and immune-inflammatory responses that physiologically connect the gut, muscle, liver, and brain. A more thorough understanding of these axes is an early essential for reaching therapeutic strategies to use the gut microbiota for combating disease and improving health. Bacterial species of Bacteroides, Clostridia, and Bifidobacterium consist of a large proportion of the gut bacterial flora. Increase in the proportion of these genera in the gut could cause abscess formation, sepsis, inflammatory bowel disease (IBD), Crohn’s disease, toxicity, infection, and malnutrition. However, the decrease in the proportion of these species is accompanied by allergies in infants, inflammation, malabsorption syndrome, carbohydrate/fiber intolerance, atopic eczema, and IBD. Conclusions: The results showed that although the human gut microbiome plays a pivotal role in health in a normal concentration, fluctuation in their number (increase or decrease) is a possible factor in the appearance of major diseases.

Detection of carboxylesterase and esterase activity in culturable gut bacterial flora isolated from diamondback moth, Plutella xylostella (Linnaeus), from India and its possible role in indoxacarb degradation.

Diamondback moth (DBM), Plutella xylostella (Linnaeus), is a notorious pest of brassica crops worldwide and is resistant to all groups of insecticides. The insect system harbors diverse groups of microbiota, which in turn helps in enzymatic degradation of xenobiotic-like insecticides. The present study aimed to determine the diversity of gut microflora in DBM, quantify esterase activity and elucidate their possible role in degradation of indoxacarb. We screened 11 geographic populations of DBM in India and analyzed them for bacterial diversity. The culturable gut bacterial flora underwent molecular characterization with 16S rRNA. We obtained 25 bacterial isolates from larvae (n = 13) and adults (n = 12) of DBM. In larval gut isolates, gammaproteobacteria was the most abundant (76%), followed by bacilli (15.4%). Molecular characterization placed adult gut bacterial strains into three major classes based on abundance: gammaproteobacteria (66%), bacilli (16.7%) and flavobacteria (16.7%). Esterase activity from 19 gut bacterial isolates ranged from 0.072 to 2.32 μmol/min/mg protein. Esterase bands were observed in 15 bacterial strains and the banding pattern differed in Bacillus cereus – KC985225 and Pantoea agglomerans – KC985229. The bands were characterized as carboxylesterase with profenofos used as an inhibitor. Minimal media study showed that B. cereus degraded indoxacarb up to 20%, so it could use indoxacarb for metabolism and growth. Furthermore, esterase activity was greater with minimal media than control media: 1.87 versus 0.26 μmol/min/mg protein. Apart from the insect esterases, bacterial carboxylesterase may aid in the degradation of insecticides in DBM.

Drosophila type IV collagen mutation associates with immune system activation and intestinal dysfunction

The basal lamina (BM) contains numerous components with a predominance of type IV collagens. Clinical manifestations associated with mutations of the human COL4A1 gene include perinatal cerebral hemorrhage and porencephaly, hereditary angiopathy, nephropathy, aneurysms and muscle cramps (HANAC), ocular dysgenesis, myopathy, Walker–Warburg syndrome and systemic tissue degeneration. In Drosophila, the phenotype associated with dominant temperature sensitive mutations of col4a1 include severe myopathy resulting from massive degradation of striated muscle fibers, and in the gut, degeneration of circular visceral muscle cells and epithelial cells following detachment from the BM. In order to determine the consequences of altered BM functions due to aberrant COL4A1 protein, we have carried out a series of tests using DrosophilaDTS-L3 mutants from our allelic series of col4a1 mutations with confirmed degeneration of various cell types and lowest survival rate among the col4a1 mutant lines at restrictive temperature. Results demonstrated epithelial cell degeneration in the gut, shortened gut, enlarged midgut with multiple diverticulae, intestinal dysfunction and shortened life span. Midgut immunohistochemistry analyses confirmed altered expression and distribution of BM components integrin PSI and PSII alpha subunits, laminin gamma 1, and COL4A1 both in larvae and adults. Global gene expression analysis revealed activation of the effector AMP genes of the primary innate immune system including Metchnikowin, Diptericin, DiptericinB, and edin that preceded morphological changes. Attacin::GFP midgut expression pattern further supported these changes. An increase in ROS production and changes in gut bacterial flora were also noted and may have further enhanced an immune response. The phenotypic features of Drosophila col4a1 mutants confirmed an essential role for type IV collagen in maintaining epithelial integrity, gut morphology and intestinal function and suggest that aberrant structure and function of the COL4A1 protein may also be a significant factor in modulating immunity.

Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria.

Inflammatory bowel diseases (IBD), Crohn's disease and ulcerative colitis, are poorly understood disorders affecting the intestinal tract. The current model for disease suggests that genetically susceptible patients develop intolerance to gut microflora, and chronic inflammation develops as a result of environmental insults. Although interest has mainly focused on studying genetic variants and gut bacterial flora, little is known about the potential of viral infection to contribute to disease. Accordingly, we conducted a metagenomic analysis to document the baseline virome in colonic biopsy samples from patients with IBD in order to assess the contribution of viral infection to IBD. Libraries were generated from colon RNA to create approximately 2 GB sequence data per library. Using a bioinformatic pipeline designed to detect viral sequences, more than 1000 viral reads were derived directly from tissue without any coculture or isolation procedure. Herein, we describe the complexity and abundance of viruses, bacteria/bacteriophage, and human endogenous retroviral sequences from 10 patients with IBD and 5 healthy subjects undergoing surveillance colonoscopy. Differences in gut microflora and the abundance of mammalian viruses and human endogenous retroviruses were readily detected in the metagenomic analyses. Specifically, patients with herpesviridae sequences in their colon demonstrated increased expression of human endogenous viral sequences and differences in the diversity of their microbiome. This study provides a promising metagenomic approach to describe the colonic microbiome that can be used to better understand virus-host and phage-bacteria interactions in IBD.

Taxonomic and functional annotation of gut bacterial communities of Eisenia foetida and Perionyx excavatus

Epigeic earthworms can significantly hasten the decomposition of organic matter, which is known to be mediated by gut associated microflora. However, there is scanty information on the abundance and diversity of the gut bacterial flora in different earthworm genera fed with a similar diet, particularly Eisenia foetida and Perionyx excavatus. In this context, 16S rDNA based clonal survey of gut metagenomic DNA was assessed after growth of these two earthworms on lignocellulosic biomass. A set of 67 clonal sequences belonging to E. foetida and 75 to P. excavatus were taxonomically annotated using MG-RAST and RDP pipeline servers. Highest number of sequences were annotated to Proteobacteria (38–44%), followed by unclassified bacteria (14–18%) and Firmicutes (9.3–11%). Comparative analyses revealed significantly higher abundance of Actinobacteria and Firmicutes in the gut of P. excavatus. The functional annotation for the 16S rDNA clonal libraries of both the metagenomes revealed a high abundance of xylan degraders (12.1–24.1%). However, chitin degraders (16.7%), ammonia oxidizers (24.1%) and nitrogen fixers (7.4%) were relatively higher in E. foetida, while in P. excavatus; sulphate reducers and sulphate oxidizers (12.1–29.6%) were more abundant. Lignin degradation was detected in 3.7% clones of E. foetida, while cellulose degraders represented 1.7%. The gut microbiomes showed relative abundance of dehalogenators (17.2–22.2%) and aromatic hydrocarbon degraders (1.7–5.6%), illustrating their role in bioremediation. This study highlights the significance of differences in the inherent microbiome of these two earthworms in shaping the metagenome for effective degradation of different types of biomass under tropical conditions.

Decreased Plasma Myeloperoxidase Associated with Probiotic Therapy in Autistic Children

AIMTo assess plasma myeloperoxidase (MPO) levels in autistic children and to test the hypothesis that there is an association between decreased MPO concentration and probiotic therapy.SUBJECTS AND METHODSPlasma from 49 autistic children (39 males; mean age 11.4 years) (17 with diagnosed gastrointestinal (GI) disease – chronic diarrhea and/or constipation (10 of these GI patients were taking probiotics) and 26 receiving probiotic therapy) and 36 neurotypical controls (29 males; mean age 10.2 years; controls were not assessed for GI disease) were tested for MPO plasma concentration using Enzyme Linked Immunosorbent Assays (ELISAs). Plasma concentration of MPO in autistic individuals was compared to plasma concentration of copper and zinc.RESULTSWe found that individuals with autism, receiving no therapy, did not have significantly lower plasma MPO levels when compared to controls. In the autistic group, MPO levels were significantly lower in individuals taking probiotic therapy. In addition, plasma copper levels were significantly lower in autistic individuals taking probiotics compared to those not taking probiotics, but plasma zinc levels were not different in the probiotic group.DISCUSSIONThese results suggest a relationship between low MPO levels found in a group of autistic individuals and probiotic therapy. By possibly changing gut bacterial flora and thereby changing absorption properties in the gut, probiotic therapy was also associated with lower copper levels.