Analysis of the developing gut microbiota in young dairy calves-impact of colostrum microbiota and gut disturbances.

The aim of this study was to characterize the colostrum and fecal microbiota in calves and to investigate whether fecal microbiota composition was related to colostrum microbiota or factors associated with calf health. Colostrum samples were collected in buckets after hand milking of 76 calving cows from 38 smallholder dairy farms. Fecal samples were taken directly from the rectum of 76 calves at birth and at 14 days age. The bacterial community structure in colostrum and feces was analyzed by terminal restriction fragment length polymorphism for all samples, and the microbial composition was determined by 16S rRNA gene amplicon sequencing for a subset of the samples (8 colostrum, 40 fecal samples). There was a significant difference in fecal microbiota composition between day 0 and day 14 samples, but no associations between the microbiota and average daily gain, birth weight, or transfer of passive immunity. At 14 days of age, Faecalibacterium and Butyricicoccus were prevalent in higher relative abundances in the gut of healthy calves compared to calves with diarrhea that had been treated with antimicrobials. Colostrum showed great variation in composition of microbiota but no association to fecal microbiota. This study provides the first insights into the composition of colostrum and fecal microbiota of young dairy calves in southern Vietnam and can form the basis for future more detailed studies.

The Interactive Effects of Crude Oil and Corexit 9500 on Their Biodegradation in Arctic Seawater.

The risk of petroleum spills coupled with the potential application of chemical dispersants as a spill response strategy necessitates further understanding of the fate of oil and dispersants and their interactive effects during biodegradation. Using Arctic seawater mesocosms amended with either crude oil, Corexit 9500, or both together, we quantified the chemical losses of crude oil and Corexit 9500 and identified microbial taxa implicated in their biodegradation based on shifts in the microbial community structure over a 30-day time course. Chemical analyses included total petroleum hydrocarbons (TPH), n-alkanes, branched alkanes, and polycyclic aromatic hydrocarbons (PAHs) for oil loss and the surfactant components dioctyl sodium sulfosuccinate (DOSS), Span 80, Tween 80, Tween 85, and the DOSS metabolite ethylhexyl sulfosuccinate (EHSS) for Corexit loss. Changes to the microbial communities and identification of key taxa were determined by 16S rRNA gene amplicon sequencing. The nonionic surfactants of Corexit 9500 (Span 80 and Tweens 80 and 85) biodegraded rapidly, dropping to below the limits of detection within 5 days and prior to any detectable initiation of oil biodegradation. This resulted in no observable suppression of petroleum biodegradation in the presence of Corexit compared to that of oil alone. In contrast, biodegradation of DOSS was delayed in the presence of oil, based on the prolonged presence of DOSS and accumulation of the degradation intermediate EHSS that did not occur in the absence of oil. Microbial analyses revealed that oil and Corexit enriched different overall microbial communities, with the presence of both resulting in a community composition that shifted from one more similar to that of Corexit only to one reflecting the oil-only community over time, in parallel with the degradation of predominantly Corexit and then oil components. Some microbial taxa (Oleispira, Pseudofulvibacter, and Roseobacter) responded to either oil or Corexit, suggesting that some organisms may be capable of utilizing both substrates. Together, these findings reveal interactive effects of crude oil and Corexit 9500 on chemical losses and microbial communities as they biodegrade, providing further insight into their fate when copresent in the environment.IMPORTANCE Chemical dispersants such as Corexit 9500 are commonly used in oil spill response and are currently under consideration for use in the Arctic, where their fate and effects have not been well studied. This research was performed to determine the interactive effects of the copresence of crude oil and Corexit 9500 on the degradation of components from each mixture and the associated microbial community structure over time in Arctic seawater. These findings will help yield a better understanding of the biodegradability of dispersant components applied to an oil spill, the temporal microbial community response to dispersed oil, and the fundamental microbial ecology of organic contaminant biodegradation processes in the Arctic marine environment.

Dendrobium officinale Kimura et Migo and American ginseng mixture: A Chinese herbal formulation for gut microbiota modulation.

Dendrobium officinale Kimura et Migo (D. officinale) is a famous traditional Chinese medicine (TCM). A mixture of D. officinale and American ginseng has been shown to enhance cell-mediated immunity, humoral immunity, and monocyte/macrophage functions in mice. Here, the effects of a D. officinale and American ginseng mixture on the structure of gut microbial community in dogs were examined using high-throughput 16S rRNA gene amplicon sequencing. The data revealed that while the mixture did not change the diversity of gut microbial community significantly, differences among individuals were significantly reduced. Furthermore, the mixture-responsive operational taxonomic units (OTUs) exhibited a phase-dependent expression pattern. Fifty-five OTUs were found to exhibit a mixture-induced expression pattern, among which one third were short-chain fatty acid (SCFA)-producing genera and the others were probiotic genera included Lactobacillus spp., Sutterella, Alistipes, Anaerovorax, Bilophila, Coprococcus, Gordonibacter, Oscillibacter, among others. By contrast, 36% of the OTUs exhibiting a mixture-repressed expression pattern were disease-associated microorganisms, and six genera, namely Actinomyces, Escherichia/Shigella, Fusobacterium, Slackia, Streptococcus and Solobacterium, were associated with cancer. In addition, five genera were closely associated with diabetes, namely Collinsella, Rothia, Howardella, Slackia and Intestinibacter. Our results indicate that this D. officinale and American ginseng mixture may be used as a prebiotic agent to enhance SCFA-producing genera and prevent gut dysbiosis.

Response of gastrointestinal fermentative activity and colonic microbiota to protected sodium butyrate and protected sodium heptanoate in weaned piglets challenged with ETEC F4.

This study aimed to evaluate the potential of two new fat-protected butyrate or heptanoate salts to improve gut health and control post-weaning colibacillosis in weaning piglets challenged with enterotoxigenic Escherichia coli (ETEC) F4+, particularly focusing on their impact on intestinal microbiota and fermentative activity along the gastrointestinal tract (GIT). Seventy-two 21-d-old pigs were fed a plain diet (CTR) or supplemented with sodium butyrate (BUT) or sodium heptanoate (HPT), both at 0.3%. After a week of adaptation, animals were orally challenged at days 8 and 9 with 5.8 · 109 and 6.6 · 1010 cfu, respectively, and were euthanised on d 4 and d 8 post-inoculation (PI) (n = 8) to collect blood, digesta and tissue samples and characterise microbial groups, pathogen loads (qPCR), fermentation, ileal histomorphometry and immune markers. Colonic microbiota was analysed by 16S rRNA gene MiSeq sequencing. Supplementing both acid salts did not compensate clinical challenge effects nor performance impairments and neither histomorphometry nor serum biomarkers. Changes in the gastric fermentative activity were registered, BUT reducing lactic acid concentrations (day 8 PI), and with HPT fewer animals presenting detectable concentrations of propionic, butyric and valeric acids. At ileum BUT increased acetic acid concentration (day 8 PI), and both additives reduced short-chain fatty acids (SCFA) in the colon. Increases in enterobacteria and coliforms counts in ileal digesta (day 4 PI, p < 0.10) and mucosa scrapes (p < 0.05) were registered although E. coli F4 gene copies were unaffected. Regarding changes in the colonic microbiota (day 4 PI), Prevotellaceae and Prevotella were promoted with BUT supplementation whereas only minor groups were modified in HPT-treated animals. Summarising, although the pathogen loads or inflammatory mediators remained unresponsive, butyrate and heptanoate showed a significant impact on microbial fermentation along the whole GIT, being able to modify different bacterial groups at the colon. It could be hypothesised that these effects might be mediated by a carry-over effect of the changes observed in gastric fermentation, but possibly also to a better nutrient digestion in the foregut as a result of the reduced colonic SCFA concentrations.

Ecotoxicity of a new biopesticide produced by Lavandula luisieri on non-target soil organisms from different trophic levels.

Plant-based biopesticides have become an eco-friendly alternative to synthetic pesticides by reducing the undesired environmental impacts and side-effects on human health. However, their effects on the environment and especially on non-target organisms have been little studied. This study analyses the ecotoxicological effects of the extract of Lavandula luisieri on soil non-target organisms from different trophic levels: the earthworm Eisenia fetida, the plant Allium cepa and a natural-soil microbial community whose taxonomy was analysed through 16S rRNA gene sequencing. The extract tested is the hydrolate -product from a semi industrial steam distillation process- of a Spanish pre-domesticated variety of L. luisieri. This hydrolate has been recently shown to have bionematicide activity against the root-knot nematode Meloidogyne javanica. A previous study showed that the main components of the hydrolate are camphor and 2,3,4,4-Tetramethyl-5-methylidenecyclopent-2-en-1-one. Hydrolate caused acute toxicity (LC50 2.2% v/v) on A. cepa, while only a slight toxicity on E. fetida (LC50 > 0.4 mL/g). All the concentrations tested (from 1 to 100% v/v) caused a significant decrease in bacterial growth (LC50 9.8% v/v after 120 h of exposure). The physiological diversity of the community was also significantly altered, except in the case of the lowest concentration of hydrolate (1% v/v). The ability of soil microbial communities to use a variety of carbon sources increased for all substrates at the highest concentrations. These results show that both the plants and bacterial communities of the soil can be affected by the application of biopesticides based on these hydrolates, which highlights the need for a more detailed risk assessment during the development of plant-based products.

Bacterial Community of the Digestive Tract of the European Medicinal Leech (Hirudo verbana) from the Danube River.

The digestive tract of medicinal leeches from commercial suppliers has been investigated previously and comprises of a relatively simple bacterial community. However, the microbiome of medicinal leeches collected directly from the natural habitat has not been examined. In this study, we characterized the bacterial community in the digestive tract (anterior crop, posterior crop, and intestine) of the European medicinal leech, Hirudo verbana, collected from the Danube river using culture-independent and culture-dependent approaches. Culture-independent approach confirmed that the digestive tract of H. verbana carries a relatively simple bacterial community with species richness in the individual samples ranging from 43 to164. The dominant bacterial taxon was Mucinivorans sp. (49.7% of total reads), followed by Aeromonas sp. (18.7% of total reads). Several low abundance taxa, new for H. verbana, such as Phreatobacter, Taibaiella, Fluviicola, Aquabacterium, Burkholderia, Hydrogenophaga, Wolinella, and unidentified Chitinophagia, were also detected. The aerobic culturing approach showed Aeromonas veronii (Proteobacteria), the known leech symbiont, as the most dominant taxon followed by several Pseudomonas and Acidovorax spp. No significant differences in the bacterial community composition were detected among different parts of the digestive tract of individual leeches. However, the overall composition of the bacterial community among individual specimen varied significantly and this is possibly due to differences in leech age, feeding status, and blood source. Our results showed that the core bacterial community of H. verbana collected from the natural habitat is similar to that reported from the digestive tract of commercially supplied leeches maintained in the laboratory.

Land use shapes the resistance of the soil microbial community and the C cycling response to drought in a semi-arid area.

The aim of this study was to understand the responses of the microbial community of soil under different land uses to drought in a semi-arid Mediterranean area. In a laboratory incubation, soil samples from different land uses (natural forest, drip-irrigated orchard, rain-fed almond tree cultivation and abandoned area) were maintained at 20% and 60% of the WHC. The microbial biomass and potential enzyme activities were determined after four and fifty days of soil incubation. The diversity and composition of the microbial community were studied after 50 days of incubation. The total mineralisation of soil organic C (SOC), as well as, the mineralisation of fresh organic matter (FOM) and the "priming effect" were analysed after addition of 13C-enriched plant tissue. Both land use and drought had significant effects in the soil microbial community, but the effect of land use was stronger than that of drought. The PLFA content (microbial biomass) of the forests soil was greater under drought. After 50 days of soil incubation, the microbial biomass and most of potential enzyme activities of the almond tree and abandoned soil samples were not significantly affected by drought contrary to those in orchard soil. The total and FOM mineralisation were on average lower in soil under drought than under optimal moisture for all land uses. However, the responses of the priming effect to drought were dependent on the land use. Overall, we conclude that the resistance to drought of the soil microbial community from an agroecosystem having a semi-arid climate is strongly influenced by the previous land use.

16S ribosomal RNA sequencing reveals a modulation of intestinal microbiome and immune response by dietary L-theanine supplementation in broiler chickens.

Despite the availability of abundant literature on green tea, studies on the use of L-theanine (an amino acid found only in green tea) as a feed additive in poultry especially broiler are limited. So, this study was conducted to explore the effects of L-theanine on the intestinal microbiome and immune response in a broiler. A total of 400-d-old chicks were randomly divided into four treatment groups (A, B, C, and D) using a complete randomized design. Treatments were as follows: A, control (basal diet); B, basal diet + 100 mg L-theanine/kg diet; C, basal diet + 200 mg L-theanine/kg diet; and D, basal diet + 300 mg L-theanine/kg diet. Mucosal samples from ileum and jejunum of broiler chicken were extracted at 21 and 42 d of age. Extraction of genomic DNA was followed by amplification of V3 and V4 hypervariable regions of 16S ribosomal RNA. After Illumina sequencing, results revealed that treatment with L-theanine significantly increased the population of Lactobacillus in ileum and jejunum as compared to a control group, but the higher population was observed in jejunum at both 21 and 42 d of age. The overall diversity of the jejunum microbiome in the treatment group was significantly lower than that of the ileum and control group (P < 0.05). Results of this study revealed that mRNA expression of TLRs (TLR-2 and TLR-4) and cytokines (TNF-α, IFN-γ, and IL-2) was decreased in response to treatment with L-theanine. Moreover, the negative correlation of abundance of Lactobacillus was observed with expression of IL-2 and IFN-γ in the intestine and these effects were highly significant (P < 0.01). In summary, our finding revealed that dietary supplementation of L-theanine exhibited a positive influence on intestinal bacteria by supporting beneficial microbes like Lactobacillus while decreasing harmful microbes like Clostridium.

Effects of glucose oxidase on growth performance, gut function, and cecal microbiota of broiler chickens.

A study was conducted to study the effects of glucose oxidase (GOD) supplement on the growth performance, gut function, and cecal microbiota in broiler chickens from 1 to 42 d, and further evaluate the use of GOD as an antibiotic substitution. A total of 525 1-d-old healthy Arbor Acres broilers were randomly assigned to five treatments, including control group, antibiotic growth promoters (AGP) supplement group, and three GOD supplement groups, with seven replicates per treatment and 15 birds per replicate. Growth performance, gut function including digestive ability and gut barrier, and cecal microbiota were determined. Compared with the control group, the increased daily body weight gain, improved meat quality, and enhanced digestive ability that indicated from the nutrients apparent digestibility and digestive enzymes were identified in GOD supplement groups, which could have a similar effect with the AGP supplement. The content of secreted immunoglobulin A and the transepithelial electrical resistance were also increased with the GOD supplement, which indicated an enhanced gut barrier. Additionally, 16S rRNA gene of cecal contents was sequenced by high-throughput sequencing. Sequencing data indicated that the Firmicutes phylum, Ruminococcaceae and Rikenellaceae families, Faecalibacterium genus, and F. prausnitzii species were significantly altered. Especially, combined with previous studies, our results indicated that the significantly increased F. prausnitzii, Ruminococcaceae, and Firmicutes could be involved in the effect of GOD on gut function and growth performance of broilers. Our results indicated that dietary GOD supplement could improve the growth performance of broilers in two main ways: by enhancing the digestive function of gut, which concluded from the improved nutrients apparent digestibility and digestive enzyme, and by increasing the abundance of beneficial bacterium, such as F. prausnitzii, Ruminococcaceae, and Firmicutes, which could be further served as an important regulator to improve the growth performance and the gut health.

Phenotype and RNA-seq-Based transcriptome profiling of Staphylococcus aureus biofilms in response to tea tree oil.

Staphylococcus aureus (S. aureus) is a Gram-positive bacterium that causes a wide range of diseases, including food poisoning. Tea tree oil (TTO), an essential oil distilled from Melaleuca alternifolia, is well-known for its antibacterial activities. TTO effectively inhibited all 19 tested strains of S. aureus biofilm and planktonic cells. Phenotype analyses of S. aureus biofilm cells exposed to TTO were performed by biofilm adhesion assays, eDNA detection and PIA release. RNA sequencing (RNA-seq) was used in our study to elucidate the mechanism of TTO as a potential antibacterial agent to evaluate differentially expressed genes (DEGs) and the functional network in S. aureus ATCC 29213 biofilms. TTO significantly changed (greater than a 2- or less than a 2-fold change) the expression of 304 genes in S. aureus contained in biofilms. The levels of genes related to the glycine, serine and threonine metabolism pathway, purine metabolism pathway, pyrimidine metabolism pathway and amino acid biosynthesis pathway were dramatically changed in the biofilm exposed to TTO. Furthermore, the expression changes identified by RNA-seq analysis were verified by real-time RT-PCR. To the best of our knowledge, this research is the first study to report the phenotype and expression profiles of S. aureus in biofilms exposed to TTO.

Pestalotiopsis-Like Species Causing Gray Blight Disease on Camellia sinensis in China.

Gray blight of tea, caused by several Pestalotiopsis-like species, is one of the most destructive foliar diseases in tea cultivation yet the characteristics of these pathogens have not been confirmed until now. With morphological and multigene phylogenetic analyses, we have identified the gray blight fungi as Pseudopestalotiopsis camelliae-sinensis, Neopestalotiopsis clavispora, and Pestalotiopsis camelliae. Phylogenetic analyses derived from the combined internal transcribed spacer, ß-tubulin, and translation elongation factor 1-α gene regions successfully resolved most of the Pestalotiopsis-like species used in this study with high bootstrap supports and revealed three major clusters representing these three species. Differences in colony appearance and conidia morphology (shape, size, septation, color and length of median cells, and length and number of apical and basal appendages) were consistent with the phylogenetic grouping. Pathogenicity tests validated that all three species isolated from tea leaves were causal agents of gray blight disease on tea plant (Camellia sinensis). This is the first description of the characteristics of the three species Pseudopestalotiopsis camelliae-sinensis, N. clavispora, and Pestalotiopsis camelliae as causal agents of tea gray blight disease in China.

Characterization of aerobic oil and grease-degrading bacteria in wastewater.

A bacterial consortium that degrades cooking oil (CO) has been isolated in wastewater (WW) samples, by enrichment in olive CO. This consortium could degrade 90% of CO within 7-9 days (from an initial 1% [w/v]), and it is more active at alkaline conditions. The 16S ribonucleic acid (RNA) gene analysis showed that it contains five bacterium species: Stenotrophomonas rhizophila, Sphingobacterium sp., Pseudomonas libanensis, Pseudomonas poae and Pseudomonas aeruginosa. This consortium can degrade the free fatty acids (FFA): palmitic, stearic, oleic, linoleic and linolenic acids; glycerol, glucose and amylose; and albumin, but could not efficiently degrade carboxymethyl-cellulose. Each strain could also degrade CO and FFAs. The level of bacterial crude-activity of extracellular lipases was found to be between 0.2 and 4U/ml. Using synthetic WW, the consortium could reduce 80% of the chemical oxygen demand [from 10550 ± 2828 mg/l], 80% of nitrogen (from 410 ± 78 mgl/l) and 57% of phosphorus (from 93 ± 25 mg/l). Thus, this consortium can be utilized in the removal of CO from WW.

Phylotype Dynamics of Bacterial P Utilization Genes in Microbialites and Bacterioplankton of a Monomictic Endorheic Lake.

Microbes can modulate ecosystem function since they harbor a vast genetic potential for biogeochemical cycling. The spatial and temporal dynamics of this genetic diversity should be acknowledged to establish a link between ecosystem function and community structure. In this study, we analyzed the genetic diversity of bacterial phosphorus utilization genes in two microbial assemblages, microbialites and bacterioplankton of Lake Alchichica, a semiclosed (i.e., endorheic) system with marked seasonality that varies in nutrient conditions, temperature, dissolved oxygen, and water column stability. We focused on dissolved organic phosphorus (DOP) utilization gene dynamics during contrasting mixing and stratification periods. Bacterial alkaline phosphatases (phoX and phoD) and alkaline beta-propeller phytases (bpp) were surveyed. DOP utilization genes showed different dynamics evidenced by a marked change within an intra-annual period and a differential circadian pattern of expression. Although Lake Alchichica is a semiclosed system, this dynamic turnover of phylotypes (from lake circulation to stratification) points to a different potential of DOP utilization by the microbial communities within periods. DOP utilization gene dynamics was different among genetic markers and among assemblages (microbialite vs. bacterioplankton). As estimated by the system's P mass balance, P inputs and outputs were similar in magnitude (difference was <10 %). A theoretical estimation of water column P monoesters was used to calculate the potential P fraction that can be remineralized on an annual basis. Overall, bacterial groups including Proteobacteria (Alpha and Gamma) and Bacteroidetes seem to be key participants in DOP utilization responses.

Label-free electrochemical genosensor based on mesoporous silica thin film.

A novel label-free electrochemical strategy for nucleic acid detection was developed by using gold electrodes coated with mesoporous silica thin films as sensing interface. The biosensing approach relies on the covalent attachment of a capture DNA probe on the surface of the silica nanopores and further hybridization with its complementary target oligonucleotide sequence, causing a diffusion hindering of an Fe(CN)6 (3-/4-) electrochemical probe through the nanochannels of the mesoporous film. This DNA-mesoporous silica thin film-modified electrodes allowed sensitive (91.7 A/M) and rapid (45 min) detection of low nanomolar levels of synthetic target DNA (25 fmol) and were successfully employed to quantify the endogenous content of Escherichia coli 16S ribosomal RNA (rRNA) directly in raw bacterial lysate samples without isolation or purification steps. Moreover, the 1-month stability demonstrated by these biosensing devices enables their advanced preparation and storage, as desired for practical real-life applications. Graphical abstract Mesoporous silica thin films as scaffolds for the development of novel label-free electrochemical genosensors to perform selective, sensitive and rapid detection of target oligonucleotide sequences. Application towards E. coli determination.

Supplementation with Angelica keiskei inhibits expression of inflammatory mediators in the gastric mucosa of Helicobacter pylori-infected mice.

Oxidative stress is involved in the pathogenesis of Helicobacter pylori-associated gastric ulceration and carcinogenesis. The oxidant-sensitive transcription factor, nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB), regulates expression of inflammatory mediators such as interferon γ (IFN-γ), cyclooxygenase 2 (COX-2), and inducible nitric oxide synthase (iNOS). These inflammatory mediators increased in gastric mucosal tissues from patients infected with H pylori. Angelica keiskei (AK), a green leafy vegetable, is rich in carotenoids and flavonoids and shows antioxidant and anti-inflammatory activities. Therefore, we hypothesized that AK may protect the gastric mucosa of H pylori-infected mice against inflammation. We determined lipid peroxide abundance, myeloperoxidase activity, expression levels of inflammatory mediators (IFN-γ, COX-2, and iNOS), NF-κB-DNA binding activity, and histologic changes in gastric mucosal tissues. The antioxidant N-acetylcysteine served as the positive control treatment. Supplementation with AK suppressed increases in lipid peroxide abundance, myeloperoxidase activity, induction of inflammatory mediators (IFN-γ, COX-2, and iNOS), activation of NF-κB, and degradation of nuclear factor of κ light polypeptide gene enhancer in B-cells inhibitor α in gastric mucosal tissue from H pylori-infected mice. Inhibition of H pylori-induced alterations by AK was similar to that by N-acetylcysteine. Taken together, these results suggest that supplementation with AK may prevent H pylori-induced gastric inflammation by inhibiting NF-κB-mediated induction of inflammatory mediators in the gastric mucosa of patients infected with H pylori.

Evaluation of bacterial transmission to the paranasal sinuses through sinus irrigation.

BACKGROUND: Saline nasal irrigation is effective in the treatment of sinonasal disorders, including chronic rhinosinusitis (CRS). Despite bacterial contamination in rinse bottles and reports of infections from contaminated irrigation water, tap water is still used by ∼50% of irrigation users, raising a potential public health concern. This study aimed to determine whether bacteria from the water supply used in sinus irrigations colonizes the paranasal sinuses. METHODS: Samples were taken from the: (1) water used for irrigation, (2) faucet or container the water originated from, (3) rinse bottle, and (4) postoperative ethmoid cavity from 13 subjects with CRS. Microbiota were characterized using quantitative polymerase chain reaction (qPCR) and 16S ribosomal RNA (rRNA) gene sequencing. The Morisita-Horn beta-diversity index (M-H) was used to assess similarity in microbiota between samples, and genomic analysis was performed to assess clonality of cultured bacteria. RESULTS: Of 13 subjects, 6 used distilled water, 6 used tap water, and 1 used well water in this institutional review board (IRB)-approved observational study. Well-water had markedly more bacteria than tap or distilled water. There was a trend toward tap having more bacteria than distilled water. The sinus samples were notably dissimilar to the bottle, faucet, and irrigant (M-H 0.15, 0.09, and 0.18, respectively). There was no difference in postoperative microbiotas between distilled and tap water users. CONCLUSION: The current study suggests that irrigation plays little role in establishing the sinus microbiome. Although rinsing with tap water may never be formally recommended, these data are useful to counsel patients who prefer to do so in non-endemic areas if the municipal water supply is appropriately treated.

The effect of oil spills on the bacterial diversity and catabolic function in coastal sediments: a case study on the Prestige oil spill.

The accident of the Prestige oil tanker in 2002 contaminated approximately 900 km of the coastline along the northern Spanish shore, as well as parts of Portugal and France coast, with a mixture of heavy crude oil consisting of polycyclic aromatic hydrocarbons, alkanes, asphaltenes and resins. The capacity of the autochthonous bacterial communities to respond to the oil spill was assessed indirectly by determining the hydrocarbon profiles of weathered oil samples collected along the shore, as well as through isotope ratios of seawater-dissolved CO2, and directly by analyses of denaturing gradient gel electrophoresis fingerprints and 16S rRNA gene libraries. Overall, the results evidenced biodegradation of crude oil components mediated by natural bacterial communities, with a bias towards lighter and less substituted compounds. The changes observed in the Proteobacteria, the most abundant phylum in marine sediments, were related to the metabolic profiles of the sediment. The presence of crude oil in the supratidal and intertidal zones increased the abundance of Alpha- and Gammaproteobacteria, dominated by the groups Sphingomonadaceae, Rhodobacteraceae and Chromatiales, whilst Gamma- and Deltaproteobacteria were more relevant in subtidal zones. The phylum Actinobacteria, and particularly the genus Rhodococcus, was a key player in the microbial response to the spill, especially in the degradation of the alkane fraction. The addition of inorganic fertilizers enhanced total biodegradation rates, suggesting that, in these environments, nutrients were insufficient to support significant growth after the huge increase in carbon sources, as evidenced in other spills. The presence of bacterial communities able to respond to a massive oil input in this area was consistent with the important history of pollution of the region by crude oil.

Antimicrobial activity of essential oils of Thymus vulgaris and Origanum vulgare on phytopathogenic strains isolated from soybean.

The aim of this work was to study the antimicrobial activity of essential oils obtained from Thymus vulgaris (thyme) and Origanum vulgare (oregano) on phytopathogenic Pseudomonas species isolated from soybean. Strains with characteristics of P. syringae were isolated from leaves of soybean plants with blight symptoms. Ten of these could be identified in Group Ia of LOPAT as P. syringae. Six of these were confirmed as P. syringae using 16S rRNA, indicating the presence of these phytopathogenic bacteria in east and central Argentina. All the phytopathogenic bacteria were re-isolated and identified from the infected plants. MIC values for thyme were 11.5 and 5.7 mg·ml(-1) on P. syringae strains, while oregano showed variability in the inhibitory activity. Both essential oils inhibited all P. syringae strains, with better inhibitory activity than the antibiotic streptomycin. The oils were not bactericidal for all pseudomonads. Both oils contained high carvacrol (29.5% and 19.7%, respectively) and low thymol (1.5%). Natural products obtained from aromatic plants represent potential sources of molecules with biological activity that could be used as new alternatives for the treatment of phytopathogenic bacteria infections.

Reclamation of petrol oil contaminated soil by rhamnolipids producing PGPR strains for growing Withania somnifera a medicinal shrub.

Soil contaminated by hydrocarbons, cannot be used for agricultural intents due to their toxic effect to the plants. Surfactants producing by plant growth promotory rhizobacteria (PGPR) can effectively rig the problem of petroleum hydrocarbon contamination and growth promotion on such contaminated soils. In the present study three Pseudomonas strains isolated from contaminated soil identified by 16S rRNA analysis were ascertained for PGPR as well as biosurfactants property. Biosurfactants produced by the strains were further characterized and essayed for rhamnolipids. Inoculation of the strains in petrol hydrocarbon contaminated soil and its interaction with Withania somnifera in presence of petrol oil hydrocarbons depict that the strains helped in growth promotion of Withania somnifera in petrol oil contaminated soil while rhamnolipids helped in lowering the toxicity of petrol oil. The study was found to be beneficial as the growth and antioxidant activity of Withania sominfera was enhanced. Hence the present study signifies that rhamnolipids producing PGPR strains could be a better measure for reclamation of petrol contaminated sites for growing medicinal plants.

Microbial community and performance of slaughterhouse wastewater treatment filters.

The performance of anaerobic filter bioreactors (AFs) is influenced by the composition of the substrate, support medium, and the microbial species present in the sludge. In this study, the efficiency of a slaughterhouse effluent treatment using three AFs containing different support media was tested, and the microbial diversity was investigated by amplified ribosomal DNA restriction analysis and 16S rRNA gene sequencing. The physicochemical analysis of the AF systems tested suggested their feasibility, with rates of chemical oxygen demand removal of 72±8% in hydraulic retention times of 1 day. Analysis of pH, alkalinity, volatile acidity, total solids, total volatile solids, total Kjeldahl nitrogen, and the microbial community structures indicated high similarity among the three AFs. The composition of prokaryotic communities showed a prevalence of Proteobacteria (27.3%) and Bacteroidetes (18.4%) of the Bacteria domain and Methanomicrobiales (36.4%) and Methanosarcinales (35.3%) of the Archaea domain. Despite the high similarity of the microbial communities among the AFs, the reactor containing pieces of clay brick as a support medium presented the highest richness and diversity of bacterial and archaeal operational taxonomic units.