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Kuenne C.,Justus Liebig University | Billion A.,Justus Liebig University | Mraheil M.A.,Justus Liebig University | Strittmatter A.,Applied Genomics | And 5 more authors.
BMC Genomics | Year: 2013

Background: Listeria monocytogenes is an important food-borne pathogen and model organism for host-pathogen interaction, thus representing an invaluable target considering research on the forces governing the evolution of such microbes. The diversity of this species has not been exhaustively explored yet, as previous efforts have focused on analyses of serotypes primarily implicated in human listeriosis. We conducted complete genome sequencing of 11 strains employing 454 GS FLX technology, thereby achieving full coverage of all serotypes including the first complete strains of serotypes 1/2b, 3c, 3b, 4c, 4d, and 4e. These were comparatively analyzed in conjunction with publicly available data and assessed for pathogenicity in the Galleria mellonella insect model.Results: The species pan-genome of L. monocytogenes is highly stable but open, suggesting an ability to adapt to new niches by generating or including new genetic information. The majority of gene-scale differences represented by the accessory genome resulted from nine hyper variable hotspots, a similar number of different prophages, three transposons (Tn916, Tn554, IS3-like), and two mobilizable islands. Only a subset of strains showed CRISPR/Cas bacteriophage resistance systems of different subtypes, suggesting a supplementary function in maintenance of chromosomal stability. Multiple phylogenetic branches of the genus Listeria imply long common histories of strains of each lineage as revealed by a SNP-based core genome tree highlighting the impact of small mutations for the evolution of species L. monocytogenes. Frequent loss or truncation of genes described to be vital for virulence or pathogenicity was confirmed as a recurring pattern, especially for strains belonging to lineages III and II. New candidate genes implicated in virulence function were predicted based on functional domains and phylogenetic distribution. A comparative analysis of small regulatory RNA candidates supports observations of a differential distribution of trans-encoded RNA, hinting at a diverse range of adaptations and regulatory impact.Conclusions: This study determined commonly occurring hyper variable hotspots and mobile elements as primary effectors of quantitative gene-scale evolution of species L. monocytogenes, while gene decay and SNPs seem to represent major factors influencing long-term evolution. The discovery of common and disparately distributed genes considering lineages, serogroups, serotypes and strains of species L. monocytogenes will assist in diagnostic, phylogenetic and functional research, supported by the comparative genomic GECO-LisDB analysis server (http://bioinfo.mikrobio.med.uni-giessen.de/geco2lisdb). © 2013 Kuenne et al.; licensee BioMed Central Ltd.


Achari G.A.,ICAR Research Complex for Goa | Achari G.A.,Goa University | Ramesh R.,ICAR Research Complex for Goa
Letters in Applied Microbiology | Year: 2015

Bacterial wilt pathogen Ralstonia solanacearum causes severe crop loss of eggplant, which is of economic importance in India. 3-hydroxy palmitic acid methyl ester (3OH-PAME) is the main quorum sensing molecule governing the expression of virulence factors in R. solanacearum. Ability of 164 bacterial isolates from the xylem of eggplant (Solanum melongena L.), chilli pepper (Capsicum annuum L.) and wild eggplant (Solanum torvum Sw.) to degrade 3OH-PAME was tested by disc diffusion assay. Enzymatic degradation of 3OH-PAME by five bacteria was confirmed by High-Performance Liquid Chromatography-Mass Spectrometry analysis. 3OH-PAME degrading bacteria were identified as Stenotrophomonas maltophilia, Pseudomonas aeruginosa and Rhodococcus corynebacterioides. 3OH-PAME degrading bacteria reduced the expression of virulence factors (exopolysaccharides and endoglucanase) of R. solanacearum in vitro and reduced wilt incidence in eggplant seedlings under greenhouse conditions. Isolates with quorum quenching activity successfully re-colonized eggplant seedlings. Quorum quenching bacteria produced antagonistic compounds, which may act synergistically with quorum quenching in reducing bacterial wilt in eggplant. Significance and Impact of the Study: This is the first report on endophytic bacteria of class Gammaproteobacteria and phylum Actinobacteria having 3OH-PAME degrading activity. This study demonstrates the potential use of endophytic bacteria as quorum quenching biocontrol agents for management of bacterial wilt in eggplant. Significance and Impact of the Study: This is the first report on endophytic bacteria of class Gammaproteobacteria and phylum Actinobacteria having 3OH-PAME degrading activity. This study demonstrates the potential use of endophytic bacteria as quorum quenching biocontrol agents for management of bacterial wilt in eggplant. © 2015 The Society for Applied Microbiology.


Ramesh R.,ICAR Research Complex for Goa | Phadke G.S.,Goa University
Crop Protection | Year: 2012

Forty eight endophytic bacteria and 101 rhizobacteria were screened for their antibacterial activity against . Ralstonia solanacearum, causal agents of eggplant wilt. Among 22 effective antagonistic isolates, 18 were . Pseudomonas spp. forming three groups based on biochemical characterization. Talc formulation of the antagonistic bacteria and non-formulated 24 h old grown antagonistic bacterial cells was evaluated in the greenhouse condition for the suppression of eggplant wilt. Talc formulation of two species of . Pseudomonas (RBh41 and RBh42) completely suppressed the incidence of wilt up to 36 days of inoculation. Treatment with bacterial cells of . Pseudomonas mallei (RBG4, ET17) and one . Bacillus spp. (RCh6) reduced wilt incidence of 83% compared to control. Talc formulations of seventeen isolates of antagonistic bacteria were prepared and used for treating the nursery and seedlings during transplanting. Biocontrol efficiency of 100% was recorded in . Bacillus sp. (RP7) treatment and 80% was recorded by EB69, RCh6 and RBG4 treatments during 2007-08. During 2008-09, EB69 recorded 100% biocontrol efficiency followed by RP7 (96%), RCh6 (93%). Yield increase of over 80% was recorded in RP6 and EB69 treatments followed by RBG4 treatment. EB69, RBG4 (. Pseudomonas sp.) and reduced wilt over 65% and increased the yield (75%) consistently over the two years and hence these isolates could be considered for developing potential biocontrol agents with plant growth promoting characteristics for management of . R. solanacearum in eggplant. © 2012 Elsevier Ltd.


Vaidya V.M.,Indian Veterinary Research Institute | Malik S.V.S.,Indian Veterinary Research Institute | Bhilegaonkar K.N.,Indian Veterinary Research Institute | Rathore R.S.,Indian Veterinary Research Institute | And 2 more authors.
Comparative Immunology, Microbiology and Infectious Diseases | Year: 2010

The occurrence of Coxiella burnetii in animals with reproductive disorders was studied. A total of 920 samples (genital and faecal swabs, milk, urine and serum) were collected from cows (88), buffaloes (33), sheep (43) and goats (53) with a history of reproductive disorders and screened for C. burnetii by a PCR assay targeting the repetitive transposon-like region of C. burnetii (trans-PCR), real-time PCR, indirect immunofluorescence assay (IFA), enzyme-linked immunosorbent assay (ELISA) and isolation method. The overall prevalence of Q fever in animals with the history of reproductive disorders turned out to be 13.82%. The species-wise prevalence of Q fever among animals was observed to be 12.78% in cattle, 16.66% in buffaloes, 11.04% in sheep and 6.13% in goats. In comparison to IFA, the highest sensitivity (85.18%) was shown by both PCR assays followed by ELISA (74.07%) and isolation method (14.81%) whereas, isolation method was the most specific (100%) followed by both PCR assays (99.47%) and ELISA (98.44%). The high excretion rate of pathogen particularly in milk observed in the study posses a potential public health threat from infected animals. © 2008 Elsevier Ltd.


Barbuddhe S.B.,ICAR Research Complex for Goa | Malik S.V.S.,Indian Veterinary Research Institute | Kumar J.A.,ICAR Research Complex for Goa | Kalorey D.R.,Maharashtra Animal and Fishery Sciences University | Chakraborty T.,Justus Liebig University
International Journal of Food Microbiology | Year: 2012

Listeria monocytogenes is a foodborne pathogen that can cause serious invasive illness, mainly in certain well-defined high-risk groups, including elderly and immunocompromised patients, pregnant women, newborns and infants. In India, this pathogen has been isolated from humans, animals and foods. The incidence of Listeria is generally comparable to those reported elsewhere in the world. In humans, maternal/neonatal listeriosis is the most common clinical form reported. Among animal populations, spontaneous abortions, subclinical mastitis, meningoencephalitis and endometritis were the commonest forms reported. The disease largely remains undiagnosed and under reported. From reported analyses of a variety of foods for Listeria, milk and milk products, meat and meat products, seafood and vegetables have been reported to be contaminated in India. The legal framework for microbiological safety of foods against microbes including L. monocytogenes is summarised. The epidemiological studies would help in understanding of the sources of infection and persistence and their risk assessment, routes of transmission, clinical forms and allow for better management of the infection. © 2011 Elsevier B.V.


Mohanta K.N.,ICAR Research Complex for Goa | Subramanian S.,ICAR Research Complex for Goa | Korikanthimath V.S.,ICAR Research Complex for Goa
Journal of Aquaculture Research and Development | Year: 2013

Based on the nutrient requirement of blue gourami, Trichogaster trichopterus fingerlings as reported earlier, nine experimental diets with 350 g protein, 80-100 g lipid and 16-17 MJ digestible energy/kg diet were formulated using snail meat (D-1), freshwater fish processing waste (D-2), surimi by-product (D-3), chicken offal (D-4), earthworm (D-5), squid (D-6), mussel (T-7), chicken liver (T-8) and lean prawn (T-9) as major protein source in addition to fish meal and peanut oil cake and fed ad libitum to the fish (3.54 ± 0.02 g) for a period of 45 days. Twenty seven indoor circular fiber-reinforced plastic tanks with 200 L of water were used for rearing the fish. At the end of the experiment it was found that the fish fed squid meal Diet (D-6) had the best results in terms of weight gain, food conversion ratio (FCR), specific growth rate (SGR) and protein efficiency ratio (PER). However, the freshwater fish processing waste (D-2) and surimi by-product (D-3) diets had almost similar (p>0.05) growth and dietary performance as that of squid, mussel, chicken liver and lean prawn meal diets and therefore, both these fish processing waste and surimi by-product could be used as non-conventional protein sources in formulating the nutritionally balanced cost-effective diets for blue gourami. © 2013 Mohanta KN, et al.


Maruthadurai R.,ICAR Research Complex for Goa | Desai A.R.,ICAR Research Complex for Goa | Singh N.P.,ICAR Research Complex for Goa
Phytoparasitica | Year: 2014

The occurrence of ambrosia beetle Euplatypus parallelus (Fabricius) (Coleoptera: Curculioninae: Platypodinae) infestation on cashew (Anacardium occidentale L.) is reported for the first time from Goa, India. Most of the infested trees were either previously attacked by cashew stem and root borer Plocaederus ferrugineus (Coleoptera: Cerambycidae) or were pruned trees. The visible symptoms of attack include appearance of numerous round bore holes on the tree trunk and branches, and extrusion of fibrous dust frass on the tree trunk and in loose piles at the base of the tree. Large numbers of larvae, pupae and adults were observed in the galleries of the affected trees. Adult beetles measure 4.0-4.3 mm in length and are brown in color, having long and slender bodies with yellow hairs. They have a characteristic feature of absence of pores on the pronotum. Male and female insects were identified based on the elytral declivity. © 2013 Springer Science+Business Media Dordrecht.


Premkrishnan B.V.,Kerala University | Arunachalam V.,ICAR Research Complex for Goa
Comparative and Functional Genomics | Year: 2012

RAPD is a simple dominant marker system widely used in biology. Effectiveness of RAPD can be improved by selecting and redesigning primers whose priming sites occur in target sequence(s) of gene or organism at optimum distance. We developed software that uses sequences of random decamer primers and nucleotide sequence(s) as two input files. It locates the priming sites in input sequences and generates output files listing frequency and distance between priming sites. When the priming sites of a single primer occur more than once in a sequence with a distance of 200 to 2000bp, the software also designs pairs of iSCAR primers. An input of 387 RAPD primers and 42,432 expressed sequences of oil palm are used as test. Wet-lab PCR results from a publication that used the same set of primers were compared with software output on priming sites. In the test sequences of oil palm covering 1.4% of genome, we found that at least 60% the primers chosen using software are sure of giving PCR amplification. We designed 641 iSCAR primers suitable for amplification of oil palm DNA. The software successfully predicted 92% (67 out of 73) of published polymorphic RAPD primers in oil palm. © 2012 Balakrishnan Vasanthakumari Premkrishnan and Vadivel Arunachalam.


Mohanta K.N.,ICAR Research Complex for Goa | Subramanian S.,ICAR Research Complex for Goa | Korikanthimath V.S.,ICAR Research Complex for Goa
Journal of Animal Physiology and Animal Nutrition | Year: 2013

Nine semi-purified diets were prepared with three levels each of protein (300, 350 and 400g/kg) and lipid (60, 80 and 100g/kg) and fed ad libitum to Trichogaster trichopterus fingerlings (0.61±0.03g) in triplicate groups (10fish/replicate) for 90days to determine optimum dietary protein and lipid levels. Twenty-seven flow-through fibre-reinforced plastic tanks (200l capacity each with 100l of water) were used for rearing the fish. The dietary protein, lipid and their interactions had significant effects (p<0.05) on weight gain, feed conversion ratio, specific growth rate, nutrient retention and digestibility, but not on hepato- and viscerosomatic indexes (p>0.05). Dietary protein and the interaction of protein with lipid had significant effect (p<0.05) on whole-body dry matter, lipid and energy contents, but not on protein and ash contents (p>0.05). But, the dietary lipid had significant (p<0.05) effect on whole-body dry matter, protein, lipid and energy contents except the ash contents (p>0.05). For each level of dietary protein, the increase in dietary lipid resulted significant increase (p<0.05) in whole-body lipid contents without affecting the protein and ash contents (p>0.05). Based on better growth and dietary performances, the optimum dietary protein and lipid levels of blue gourami fingerling are 350 and 80g/kg diet respectively. © 2011 Blackwell Verlag GmbH.


Maruthadurai R.,ICAR Research Complex for Goa | Singh N.P.,ICAR Research Complex for Goa
Phytoparasitica | Year: 2014

The solenopsis mealybug Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae) has emerged as an aggressive pest on a wide range of host plants in many countries. Mealybug demes were found on young tender leaves, twigs, inflorescence panicles and fruit peduncles of cashew Anacardium occidentale L. (Family: Anacardiaceae). Drying and curling of inflorescences, tender leaves and twigs were observed due to sucking of sap or saliva injection by nymphs and adults of mealybugs. The mealybugs were identified as Phenacoccus solenopsis Tinsley. The peak infestation of 20.73 mealybugs/ 5 cm twig was recorded in the months of April and May during 2012. The endoparasitoid Aenasius bambawalei Hayat (Hymenoptera: Encyrtidae) was also recorded from mummies of P. solenopsis. This is the first report of P. solenopsis infestation on cashew, which may emerge as a sporadic pest of A. occidentale in India. © 2014, Springer Science+Business Media Dordrecht.

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