Mark W. Sumarah

Accelerated Biodegradation of Veterinary Antibiotics in Agricultural Soil following Long-Term Exposure, and Isolation of a Sulfamethazine-degrading sp.

The World Health Organization has identified antibiotic resistance as one of the top three threats to global health. There is concern that the use of antibiotics as growth promoting agents in livestock production contributes to the increasingly problematic development of antibiotic resistance. Many antibiotics are excreted at high rates, and the land application of animal manures represents a significant source of environmental exposure to these agents. To evaluate the long-term effects of antibiotic exposure on soil microbial populations, a series of field plots were established in 1999 that have since received annual applications of a mixture of sulfamethazine (SMZ), tylosin (TYL), and chlortetracycline (CTC). During the first 6 yr (1999-2004) soils were treated at concentrations of 0, 0.01 0.1, and 1.0 mg kg soil, in subsequent years at concentrations of 0, 0.1, 1.0, and 10 mg kg soil. The lower end of this concentration range is within that which would result from an annual application of manure from medicated swine. Following ten annual applications, the fate of the drugs in the soil was evaluated. Residues of SMZ and TYL, but not CTC were removed much more rapidly in soil with a history of exposure to 10 mg/kg drugs than in untreated control soil. Residues of C-SMZ were rapidly and thoroughly mineralized to CO in the historically treated soils, but not in the untreated soil. A SMZ-degrading sp. was isolated from the treated soil. Overall, these results indicate that soil bacteria adapt to long-term exposure to some veterinary antibiotics resulting in sharply reduced persistence. Accelerated biodegradation of antibiotics in matrices exposed to agricultural, wastewater, or pharmaceutical manufacturing effluents would attenuate environmental exposure to antibiotics, and merits investigation in the context of assessing potential risks of antibiotic resistance development in environmental matrices.

Secondary metabolites from anti-insect extracts of endophytic fungi isolated from Picea rubens

The extracts of a selection of 150 foliar fungal endophytes isolated from Picea rubens (red spruce) needles were screened by LC-MS and assayed for toxicity. Three of these strains that were toxic to the forest pest Choristoneura fumiferana (eastern spruce budworm) in dietary bioassays were selected for further study. Their culture extracts were analyzed by LC-NMR spectroscopy, and the major metabolites were isolated by LC-MS-SPE or PTLC/column chromatography and characterized. The structures were elucidated by spectroscopic analyses including 2D NMR, HRMS and by comparison to literature data. Compounds 1 and 5-7 are hitherto unknown whereas compounds 2 and 3 are natural products described for the first time. Compound 4 is reported for the first time as a fungal metabolite and 8-9 were identified as known fungal metabolites in genera.

Effect of a Rugulosin-producing Endophyte in Picea glauca on Choristoneura fumiferana

Disease-free second instar Choristoneura fumiferana (eastern spruce budworm) were placed on trees infected with a rugulosin-producing needle endophyte in two experiments. They were allowed to grow to sixth instar when survivors were collected. First, by using 3-yr old trees, a comparison was made of budworm growth on infected and uninfected trees. A second experiment used 4-yr old trees to study the effect of rugulosin content in the needle on growth. This permitted an examination of a dose response in relation to growth, and allowed us to eliminate the potential for differences in environment or foliar chemistry affecting the results. At sixth instar, budworms feeding on infected trees that contained rugulosin were smaller than those on uninfected trees. At needle concentrations above the dietary low observed effect level of rugulosin for C. fumerana >0.5xa0μg g−1, a dose response was seen. For the first time, this demonstrates an inverse effect in outdoor nursery experiments between budworm weight and rugulosin concentration.

Characterization of Polyketide Metabolites from Foliar Endophytes of Picea glauca

A collection of 250 foliar endophytes of Picea glauca (white spruce) yielded several isolates that produced metabolites toxic to Choristoneura fumiferana (spruce budworm). Three of these strains were selected for further study based on their ability to be cultured and produce secondary metabolites under laboratory conditions. The culture filtrate of each was extracted and analyzed by LC-MS and LC-NMR, and the major metabolites were isolated and characterized. Structures were elucidated by spectroscopic analyses including 2D NMR and HRMS and by comparison to literature data. In some cases the extract was methylated in order to facilitate separation, but the original natural structure was determined by comparing the NMR data of the isolated methylated product with that of the stop-flow NMR of the underivatized extract (i.e., 2a, 2b, and 4). Two of these metabolites, 1 and 2a, are new structures, 3 and 4 are reported here for the first time as fungal metabolites, and 5- 10 as known fungal metabolites from other species. Tyrosol (10) was the only common metabolite found in all three extracts but did not account for the observed toxicity to C. fumiferana.

Spread and persistence of a rugulosin-producing endophyte in Picea glauca seedlings.

We have studied Picea glauca (white spruce) endophyte colonization and its affect on the growth of Choristoneura fumiferana (spruce budworm). Here we examine the spread and persistence of a rugulosin-producing endophyte and rugulosin in needles from trees maintained in the nursery, as well as in trees planted in a test field site. Additionally, we report toxicity of rugulosin against three P. glauca needle herbivores: C. fumiferana, Lambdina fiscellaria (hemlock looper) and Zeiraphera canadensis (spruce budmoth). Reduction in body weight for both the C. fumiferana and L. fiscellaria were observed at 25 and 50mum, respectively, and head capsules were reduced at 100 and 150 microm. Z. canadensis larvae did not perform as well in tests due to an Aspergillus fumigatus infection, but were shown to be lighter when tested with 100 and 150 microm compared with controls. The endophyte and its toxin were shown to spread throughout the nursery-grown seedlings. After 3.5 and 4.5 y post-inoculation (one and two years in the test site), the inoculated endophyte and its toxin had remained present with an average rugulosin concentration of 1 microg g(-1).

Isolation and metabolite production by Penicillium roqueforti, P. paneum and P. crustosum isolated in Canada

Penicillium roqueforti, P. crustosum and P. paneum grow on ensiled grain and recycled feed unless properly treated. The former two species occur also on cut lumber in Canada. These are known to produce a number of secondary metabolites including roquefortine. In cooler dairy production areas, including Scandinavia and North America, cattle toxicosis has been associated with silage contaminated by these fungi. We collected strains associated with cow or cattle toxicoses. The principal metabolites were determined making use of a new extraction method and analysis combining HPLC, LC/MS/MS, and LC/NMR. Penicillium roqueforti and P. crustosum required amino acid nitrogen for metabolite formation and their toxins were formed under conditions of low oxygen (20–30% saturation). Production of roquefortine C occurred on depletion of the available nitrogen and penitrem A on depletion of carbon source. Yield was reduced by excess carbon. Medium osmotic tension (aw) affected metabolite production by the two species differently. Penicillium paneum was associated with ill-thrift of dairy cows and P. roqueforti was associated with more serious symptoms. Our data suggest a physiological basis for the common occurrence of roquefortine C in silage without serious consequences and the alternative, the presence of roquefortine C and toxicoses. The strain isolated from lumber was the best producer of the toxins studied. This is the first report of the toxigenic potential of P. roqueforti and P. paneum from Canada.

Antifungal metabolites from fungal endophytes of Pinus strobus.

The extracts of five foliar fungal endophytes isolated from Pinus strobus (eastern white pine) that showed antifungal activity in disc diffusion assays were selected for further study. From these strains, the aliphatic polyketide compound 1 and three related sesquiterpenes 2-4 were isolated and characterized. Compound 2 is reported for the first time as a natural product and the E/Z conformational isomers 3 and 4 were hitherto unknown. Additionally, the three known macrolides; pyrenophorol (5), dihydropyrenophorin (6), and pyrenophorin (7) were isolated and identified. Their structures were elucidated by spectroscopic analyses including 2D NMR, HRMS and by comparison to literature data where available. The isolated compounds 1, 2, and 5 were antifungal against both the rust Microbotryum violaceum and Saccharomyces cerevisae.

A multi-platform metabolomics approach identifies highly specific biomarkers of bacterial diversity in the vagina of pregnant and non-pregnant women.

Bacterial vaginosis (BV) increases transmission of HIV, enhances the risk of preterm labour, and is associated with malodour. Clinical diagnosis often relies on microscopy, which may not reflect the microbiota composition accurately. We use an untargeted metabolomics approach, whereby we normalize the weight of samples prior to analysis, to obtained precise measurements of metabolites in vaginal fluid. We identify biomarkers for BV with high sensitivity and specificity (AUCu2009=u20090.99) in a cohort of 131 pregnant and non-pregnant Rwandan women, and demonstrate that the vaginal metabolome is strongly associated with bacterial diversity. Metabolites associated with high diversity and clinical BV include 2-hydroxyisovalerate and γ-hydroxybutyrate (GHB), but not succinate, which is produced by both Lactobacillus crispatus and BV-associated anaerobes in vitro. Biomarkers associated with high diversity and clinical BV are independent of pregnancy status, and were validated in a blinded replication cohort from Tanzania (nu2009=u200945), where we predicted clinical BV with 91% accuracy. Correlations between the metabolome and microbiota identified Gardnerella vaginalis as a putative producer of GHB, and we demonstrate production by this species in vitro. This work illustrates how changes in community structure alter the chemical composition of the vagina, and identifies highly specific biomarkers for a common condition.

Effect of chemotherapy on the microbiota and metabolome of human milk, a case report

BackgroundHuman milk is an important source of bacteria for the developing infant and has been shown to influence the bacterial composition of the neonatal gut, which in turn can affect disease risk later in life. Human milk is also an important source of nutrients, influencing bacterial composition but also directly affecting the host. While recent studies have emphasized the adverse effects of antibiotic therapy on the infant microbiota, the effects of maternal chemotherapy have not been previously studied. Here we report the effects of drug administration on the microbiota and metabolome of human milk.MethodsMature milk was collected every two weeks over a four month period from a lactating woman undergoing chemotherapy for Hodgkin’s lymphoma. Mature milk was also collected from healthy lactating women for comparison. Microbial profiles were analyzed by 16S sequencing and the metabolome by gas chromatography–mass spectrometry.FindingsChemotherapy caused a significant deviation from a healthy microbial and metabolomic profile, with depletion of genera Bifidobacterium, Eubacterium, Staphylococcus and Cloacibacterium in favor of Acinetobacter, Xanthomonadaceae and Stenotrophomonas. The metabolites docosahexaenoic acid and inositol known for their beneficial effects were also decreased.ConclusionWith milk contents being critical for shaping infant immunity and development, consideration needs to be given to the impact of drugs administered to the mother and the long-term potential consequences for the health of the infant.

A systems biology approach investigating the effect of probiotics on the vaginal microbiome and host responses in a double blind, placebo-controlled clinical trial of post-menopausal women.

A lactobacilli dominated microbiota in most pre and post-menopausal women is an indicator of vaginal health. The objective of this double blinded, placebo-controlled crossover study was to evaluate in 14 post-menopausal women with an intermediate Nugent score, the effect of 3 days of vaginal administration of probiotic L. rhamnosus GR-1 and L. reuteri RC-14 (2.5×109 CFU each) on the microbiota and host response. The probiotic treatment did not result in an improved Nugent score when compared to when placebo. Analysis using 16S rRNA sequencing and metabolomics profiling revealed that the relative abundance of Lactobacillus was increased following probiotic administration as compared to placebo, which was weakly associated with an increase in lactate levels. A decrease in Atopobium was also observed. Analysis of host responses by microarray showed the probiotics had an immune-modulatory response including effects on pattern recognition receptors such as TLR2 while also affecting epithelial barrier function. This is the first study to use an interactomic approach for the study of vaginal probiotic administration in post-menopausal women. It shows that in some cases multifaceted approaches are required to detect the subtle molecular changes induced by the host to instillation of probiotic strains. Trial Registration ClinicalTrials.gov NCT02139839