Estimating amplification efficiency improves multiplex real-time PCR quantification of Bacillus licheniformis and Bacillus subtilis spores in animal feed

Efficacy of Two Probiotic Products Fed Daily to Reduce Clostridium perfringens-Based Adverse Health and Performance Effects in Dairy Calves

Clostridium perfringens is a spore-forming, anaerobic bacterium which produces toxins and exoenzymes that cause disease in calves, especially necro-hemorrhagic enteritis-associated diarrhea often resulting in death. Clostridium infections are currently being treated with antibiotics, but even with the prudent administration of antibiotics, there are significant rates of recurrence. Probiotics, an alternative to antibiotics, are commonly employed to prevent clostridial infections. The objectives of our study were to demonstrate that two commercially available products, when used as daily, direct-fed microbials, are effective in reducing adverse effects of an experimentally induced C. perfringens infection in dairy calves. We conducted a single site efficacy study with masking using a randomized design comprising 10 calves allocated to 3 treatment groups (probiotic 1, probiotic 2, and control). The procedures such as general health scores, body weight, blood samples, and fecal sample collections were done followed by experimental challenge of calves with C. perfringens. Daily feeding of L. animalis LA51 and P. freudenreichii PF24 without or with Bacillus lichenformis CH200 and Bacillus subtilis CH201, before, during and after an oral challenge of C. perfringens significantly reduced the incidence and severity of diarrhea while improving general impression and appearance scores of calves. Most notably, survival of calves in the two probiotic-fed groups was significantly higher than for control calves and further substantiates the potential economic and health benefits of feeding effective probiotics.

Design and validation of a real-time PCR technique for assessing the level of inclusion of fungus- and yeast-based additives in feeds

A reliable method for quantification of non-viable microbe-based nutritional and zootechnical additives introduced into feed is essential in order to ensure regulatory compliance, feed safety and product authenticity in industrial applications. In the present work, we developed a novel real-time quantitative polymerase chain reaction (qPCR) -based analysis protocol for monitoring two microbial additives in feed matrices. To evaluate the applicability of the method, pelleted wheat- and maize-based broiler chicken diets containing a non-viable phytase-producing strain of Aspergillus niger produced in solid state fermentation (150 or 300 g/t) and a non-viable selenium-enriched Saccharomyces cerevisiae (100 or 200 g/t) as model feed ingredients, were manufactured and subjected to analysis. Power analysis of the qPCR results indicated that 2 to 6 replicate feed samples were required to distinguish the product doses applied, which confirms that the microbial DNA was efficiently recovered and that potential PCR inhibitors present in the feed material were successfully removed in DNA extraction. The analysis concept described here was shown to be an accurate and sensitive tool for monitoring the inclusion levels of non-viable, unculturable microbial supplements in animal diets.

Degradation of microplastic seed film-coating fragments in soil

Encapsulating fungicides and/or insecticides in film-coatings applied to agronomic seeds has become a widely accepted method for enhancing seed germination and overall seedling health by protecting against many diseases and early-season insect pests. Despite advancements in seed film-coating technologies, abrasion of the seed coating can occur during handling and mechanical planting operations, resulting in variable amounts of detached fragments entering the soil. The present study investigated the degradation in soil of these plastic-like, small-sized fragments, referred to here as microplastic coating fragments. Degradation of microplastic coating fragments in soil was found to be highly variable. The lowest degradation rate (≤48 days) was observed in fragments detached from seeds coated with a commercial polymer mixture, while fragments from a biodegradable plastic formulation degraded completely within 32 days. When spores of the plant growth-promoting bacterium, Bacillus subtilis, were incorporated into the bioplastic, degradation was even more rapid (≤24 days). The fragment degradation rate was unaffected by incorporating two commonly used neonicotinoid insecticides, imidacloprid or thiacloprid, into either coating formulations, but insecticide dissipation rates in soil were more rapid when added associated with seed coating fragments than when spiked in directly. Half-lives of these two insecticides were reduced by up to 27% in fragments from bioplastic-coated seeds. These results are consistent with variable and not easily predicted soil degradation rates for seed coating fragments, with enhanced dissipation of coating-entrapped pesticides and with a higher degradation rate for biodegradable seed coating incorporating selected microbial strains.

Suppression subtractive hybridisation and real-time PCR for strain-specific quantification of the probiotic Bifidobacterium animalis BAN in broiler feed

To ensure quality management during the production processes of probiotics and for efficacy testing in vivo, accurate tools are needed for the identification and quantification of probiotic strains. In this study, a strain-specific qPCR assay based on Suppression Subtractive Hybridisation (SSH) for identifying unique sequences, was developed to quantify the strain Bifidobacterium animalis BAN in broiler feed. Seventy potential BAN specific sequences were obtained after SSH of the BAN genome, with a pool of closely related strain genomes and subsequent differential screening by dot blot hybridisation. Primers were designed for 30 sequences which showed no match with any sequence database entry, using BLAST and FASTA. Primer specificity was assessed by qPCR using 45 non-target strains and species in a stepwise approach. Primer T39_S2 was the only primer pair without any unspecific binding properties and it showed a PCR efficiency of 80% with a Cq value of 17.32 for 20 ng BAN DNA. Optimised feed-matrix dependent calibration curve for the quantification of BAN was generated, ranging from 6.28 × 10(3)cfu g(-1) to 1.61 × 10(6)cfu g(-1). Limit of detection of the qPCR assay was 2 × 10(1)cfu g(-1) BAN. Applicability of the strain-specific qPCR assay was confirmed in a spiking experiment which added BAN to the feed in two concentrations, 2 × 10(6)cfu g(-1) and 2 × 10(4)cfu g(-1). Results showed BAN mean recovery rates in feed of 1.44 × 10(6) ± 4.39 × 10(5)cfu g(-1) and 1.59 × 10(4) ± 1.69 × 10(4)cfu g(-1), respectively. The presented BAN-specific qPCR assay can be applied in animal feeding trials, in order to control the correct inclusion rates of the probiotic to the feed, and it could further be adapted, to monitor the uptake of the probiotic into the gastrointestinal tract of broiler chickens.

Evidence that the biofungicide Serenade (Bacillus subtilis) suppresses clubroot on canola via antibiosis and induced host resistance

This study investigated how the timing of application of the biofungicide Serenade (Bacillus subtilis QST713) or it components (product filtrate and bacterial cell suspension) influenced infection of canola by Plasmodiophora brassicae under controlled conditions. The biofungicide and its components were applied as a soil drench at 5% concentration (vol/vol or equivalent CFU) to a planting mix infested with P. brassicae at seeding or at transplanting 7 or 14 days after seeding (DAS) to target primary and secondary zoospores of P. brassicae. Quantitative polymerase chain reaction (qPCR) was used to assess root colonization by B. subtilis as well as P. brassicae. The biofungicide was consistently more effective than the individual components in reducing infection by P. brassicae. Two applications were more effective than one, with the biofungicide suppressing infection completely and the individual components reducing clubroot severity by 62 to 83%. The biofungicide also reduced genomic DNA of P. brassicae in canola roots by 26 to 99% at 7 and 14 DAS, and the qPCR results were strongly correlated with root hair infection (%) assessed at the same time (r = 0.84 to 0.95). qPCR was also used to quantify the transcript activity of nine host-defense-related genes in inoculated plants treated with Serenade at 14 DAS for potential induced resistance. Genes encoding the jasmonic acid (BnOPR2), ethylene (BnACO), and phenylpropanoid (BnOPCL and BnCCR) pathways were upregulated by 2.2- to 23-fold in plants treated with the biofungicide relative to control plants. This induced defense response was translocated to the foliage (determined based on the inhibition of infection by Leptosphaeria maculans). It is possible that antibiosis and induced resistance are involved in clubroot suppression by Serenade. Activity against the infection from both primary and secondary zoospores of P. brassicae may be required for maximum efficacy against clubroot.

Design of multiplex PCR for simultaneous detection of rope-forming Bacillus strains in Iranian bread dough

BACKGROUND

The objective of this study was optimisation of multiplex polymerase chain reaction (PCR) by a new primer set for simultaneous detection of ropiness agents as the main bacterial spoilage of Iranian bread. After inoculation of bread dough with activated Bacillus licheniformis (ATCC 9789) and Bacillus subtilis (ATCC 6633), DNA was extracted from the dough and subjected to PCR. Then simplex and multiplex PCR tests were optimised.

RESULTS

From the results obtained, the optimum PCR conditions for simultaneous detection of the target genes in Bacillus species were an annealing temperature of 59 °C and an MgCl(2) concentration of 2.5 mmol L(-1) . To design primers for these two bacteria, owing to close homology and the existence of similar conserved sequences in their 16S rRNA genes, lpaL and aprE genes (497 and 744 bp target sequences) respectively were chosen. Finally, by sequencing of PCR products, accurate and specific detection of the two desired Bacillus species was confirmed. The results were registered with GenBank under accession numbers HQ877873 and HQ871154.

CONCLUSION

Compared with culture-dependent methods, this procedure offers significantly higher accuracy and speed, which are crucial criteria when it comes to food safety and high volumes of referred samples respectively.

Evaluation of real-time PCR methods for quantification of Acanthamoeba in anthropogenic water and biofilms

AIMS

To assess two real-time PCR methods (the Riviere and Qvarnstrom assays) for environmental Acanthamoeba.

METHODS AND RESULTS

DNA extracted from Acanthamoeba castellanii taken from water and biofilms of cooling towers was analysed by the Riviere and Qvarnstrom assays. To quantify environmental Acanthamoeba, the calibration curves (DNA quantity vs cell number) were constructed with samples spiked with A. castellanii. The calibration curves for both quantitative PCR assays showed low variation (coefficient of variation of C(t) ≤ 5·7%) and high linearity (R(2) ≥ 0·99) over six orders of magnitudes with detection limit of three cells per water sample. DNA quantity determined by Qvarnstrom assay was equivalent between trophozoites and cysts (P=0·49), whereas a significant difference was observed with Riviere assay (P<0·0001). Riviere assay failed to detect Acanthamoeba in 21% (15/71) of the environmental samples which were positively detected by Qvarnstrom assay, while one sample (1·4%) was shown positive by Riviere assay but negative by Qvarnstrom assay. Moreover, Acanthamoeba counts by Qvarnstrom assay were greater than those by Riviere assay (P<0·0001).

CONCLUSIONS

Qvarnstrom assay performs better than Riviere assay for detection and quantification of Acanthamoeba in anthropogenic water and biofilms.

SIGNIFICANCE AND IMPACT OF THE STUDY

Qvarnstrom assay may significantly contribute to a better knowledge about the distribution and abundance of Acanthamoeba in environments.

Quantification of Propionibacterium acidipropionici P169 bacteria in environmental samples by use of strain-specific primers derived by suppressive subtractive hybridization

A quantitative PCR (qPCR) assay targeting a gene identified by suppressive subtractive hybridization (SSH) was developed to detect Propionibacterium acidipropionici P169, with a threshold of 10(4) CFU/U of dairy feed or rumen fluid. The report is the first using a molecular marker generated by SSH to quantify a bacterial strain in environmental samples.

The kappa-opioid receptor is upregulated in the spinal cord and locus ceruleus but downregulated in the dorsal root ganglia of morphine tolerant rats

As a non-selective agonist of opioid receptors, morphine can also act on the kappa-opioid receptor (KOR) when activating the mu-opioid receptor (MOR) and delta-opioid receptor (DOR). Although previous findings indicate that KOR plays an important role in morphine analgesia and antinociceptive tolerance, the reasons for the paradoxical functions of KOR in analgesia and anti-analgesia responses are still unclear. The aim of this study was to explore the role of the KOR in morphine analgesia and antinociceptive tolerance. As such, the changes in KOR expression in different regions of the nervous system in morphine tolerant rats were examined. We were able to attain morphine tolerance in rats via subcutaneous injection of morphine (10 mg/kg) twice daily for 7-consecutive days. Competitive real-time PCR, immunohistochemistry, and Western blot analyses were used to assess KOR expression in related regions of the nervous system, including the thalamus, hypothalamus, hippocampus, locus ceruleus (LC), periaqueductal gray (PAG), lumber-sacral spinal cord, and dorsal root ganglia (DRG). The expression of KOR increased in the locus ceruleus and spinal cord, but was significantly decreased in the DRG of morphine tolerant rats (P<0.05). No other significant changes in KOR expression were observed in the other regions. Consequently, we propose that the locus ceruleus and spinal cord are likely the dominant CNS regions and the DRG is the main peripheral site in which chronic morphine exerts its effect on KOR. Prolonged morphine administration induces inconsistent changes of KOR in the central and peripheral nervous system.