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Genomic analysis of a novel strain of Bacillus nealsonii, isolated from Surti buffalo rumen  [PDF]
Neelam M. Nathani, Srinivas M. Duggirala, Vaibhav D. Bhatt, Jay KaPatel, Chaitanya G. Joshi
Advances in Bioscience and Biotechnology (ABB) , 2014, DOI: 10.4236/abb.2014.53030
Abstract:

Aim: Whole genome sequencing and functional annotation of Bacillus nealsonii strain AAU1, an amylolytic anaerobic spore forming isolate from ruminal contents of buffalo. Methods and Results: Morphologically, the strain was observed as slender Grampositive rods, occurring in pairs. Optimal growth was observed at 40°C (range: 30°C to 45°C) and pH 6.5 (range: 5.5 to 7.5) when cultivated in Hungate’s medium supplemented with starch. The microorganism showed extracellular constitutive amylolytic activity, proving to be capable of utilizing glucose, maltose, mannose, trehalose, dextrin and starch under anaerobic conditions. Sequence analysis revealed a GC content of 35.1 mol%. Comparison of housekeeping gene sequences for RNA polymerase subunit B (rpoB) and gyrase A (gyrA) identified sequence similarity within the Bacillus genus, confirmed by 16S rRNA gene sequence similarity which identified Bacillus nealsonii DSM 15077 as the closest publically available relative. Chemotaxonomic analysis provided conflicting results with straight-chain saturated C16: 0/C16:0 aldehyde, C16:0 DMA, C14:0 and monounsaturated 16:1w7c and 16:1w9c the major fatty acids in contrast to those reported for

Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species
Michael W Rey, Preethi Ramaiya, Beth A Nelson, Shari D Brody-Karpin, Elizabeth J Zaretsky, Maria Tang, Alfredo de Leon, Henry Xiang, Veronica Gusti, Ib Groth Clausen, Peter B Olsen, Michael D Rasmussen, Jens T Andersen, Per L J?rgensen, Thomas S Larsen, Alexei Sorokin, Alexander Bolotin, Alla Lapidus, Nathalie Galleron, S Dusko Ehrlich, Randy M Berka
Genome Biology , 2004, DOI: 10.1186/gb-2004-5-10-r77
Abstract: We determined the complete nucleotide sequence of the B. licheniformis ATCC 14580 genome which comprises a circular chromosome of 4,222,336 base-pairs (bp) containing 4,208 predicted protein-coding genes with an average size of 873 bp, seven rRNA operons, and 72 tRNA genes. The B. licheniformis chromosome contains large regions that are colinear with the genomes of B. subtilis and Bacillus halodurans, and approximately 80% of the predicted B. licheniformis coding sequences have B. subtilis orthologs.Despite the unmistakable organizational similarities between the B. licheniformis and B. subtilis genomes, there are notable differences in the numbers and locations of prophages, transposable elements and a number of extracellular enzymes and secondary metabolic pathway operons that distinguish these species. Differences include a region of more than 80 kilobases (kb) that comprises a cluster of polyketide synthase genes and a second operon of 38 kb encoding plipastatin synthase enzymes that are absent in the B. licheniformis genome. The availability of a completed genome sequence for B. licheniformis should facilitate the design and construction of improved industrial strains and allow for comparative genomics and evolutionary studies within this group of Bacillaceae.Bacillus licheniformis is a Gram-positive, spore-forming bacterium widely distributed as a saprophytic organism in the environment. This species is a close relative of Bacillus subtilis, an organism that is second only to Escherichia coli in the level of detail at which it has been studied. Unlike most other bacilli, which are predominantly aerobic, B. licheniformis is a facultative anaerobe, which may allow it to grow in additional ecological niches. Certain B. licheniformis isolates are capable of denitrification; the relevance of this characteristic to environmental denitrification may be small, however, as the species generally persists in soil as endospores [1].There are numerous commercial and agricu
DNA sequence conservation between the Bacillus anthracis pXO2 plasmid and genomic sequence from closely related bacteria
James Pannucci, Richard T Okinaka, Erin Williams, Robert Sabin, Lawrence O Ticknor, Cheryl R Kuske
BMC Genomics , 2002, DOI: 10.1186/1471-2164-3-34
Abstract: The two most distantly related isolates examined, B. thuringiensis 33679 and B. thuringiensis AWO6, produced the greatest number of ORF sequences similar to pXO2; 10 detected in 33679 and 16 in AWO6. No more than two of the pXO2 ORFs were detected in any one of the remaining isolates. Dot-blot DNA hybridizations between pXO2 ORF fragments and total genomic DNA from AWO6 were consistent with the PCR assay results for this isolate and also revealed nine additional ORFs shared between these two bacteria. Sequences similar to the B. anthracis cap genes or their regulator, acpA, were not detected among any of the examined isolates.The presence of pXO2 sequences in the other Bacillus isolates did not correlate with genomic relatedness established by AFLP analysis. The presence of pXO2 ORF sequences in other Bacillus species suggests the possibility that certain pXO2 plasmid gene functions may also be present in other closely related bacteria.Bacillus anthracis contains a 96.2 kb plasmid, pXO2, that is required to cause the disease anthrax [1]. Complete sequencing and annotation (GeneMark.hmm) of pXO2 predicted 85 open reading frames (ORFs) [Genbank accession NC_002146]. Little is known about the identity and function of pXO2 ORFs beyond the virulence genes associated with the B. anthracis capsule (dep, capACB, acpA) [2-5]. The goal of this study was to determine if many of the novel pXO2 ORFs were unique to B. anthracis, or were conserved in other closely related Bacillus cereus and Bacillus thuringiensis isolates. Conservation of plasmid sequences can provide clues about the origin of the pXO2 plasmid and about potentially conserved gene functions. Identification of ORFs that are specific to B. anthracis are potentially useful as markers for detection of the pathogen in clinical and forensic applications.B. anthracis is a member of the B. cereus/B. thuringiensis phylogenetic group [6]. The members of this group are nearly indistinguishable by 16S rDNA analysis [7,8]. Pla
Phylogenetic relationships between Bacillus species and related genera inferred from 16s rDNA sequences
Wei Wang, Mi Sun;
Brazilian Journal of Microbiology , 2009, DOI: 10.1590/S1517-83822009000300013
Abstract: neigh-borjoining, maximum-parsimony, minimum-evolution, maximum-likelihood and bayesian trees constructed based on 16s rdna sequences of 181 type strains of bacillus species and related taxa manifested nine phylogenetic groups. the phylogenetic analysis showed that bacillus was not a monophyletic group. b. subtilis was in group 1. group 4, 6 and 8 respectively consisted of thermophiles, halophilic or halotolerant bacilli and alkaliphilic bacilli. group 2, 4 and 8 consisting of bacillus species and related genera demonstrated that the current taxonomic system did not agree well with the 16s rdna evolutionary trees. the position of caryophanaceae and planococcaceae in group 2 suggested that they might be transferred into bacillaceae, and the heterogeneity of group 2 implied that some bacillus species in it might belong to several new genera. group 9 was mainly comprised of the genera (excluding bacillus) of bacillaceae, so some bacillus species in group 9: b. salarius, b. qingdaonensis and b. thermcloacae might not belong to bacillus. four bacillus species, b. schlegelii, b. tusciae, b. edaphicus and b. mucilaginosus were clearly placed outside the nine groups.
Circumscribed Morphea and Breast Asymmetry in an Adolescent  [PDF]
António Augusto Fernandes Massa,Armando Manuel Sim?es Baptista,António Manuel Ferreira da Silva Abreu Couceiro,Eduarda Macedo Osório Morais Ferreira
Case Reports in Dermatological Medicine , 2014, DOI: 10.1155/2014/418257
Abstract: Morphea is a rare fibrosing disorder of the skin and underlying tissues. Circumscribed morphea presents with less than three discrete indurated plaques and breasts are commonly affected in women. We report the case of a 12-year-old female with a right infra-areolar, nontender, brownish patch and asymmetry of the right breast with 2 years of evolution. Skin biopsy showing thickening of the dermal collagen bundles confirmed the clinical diagnosis of morphea. After a 3-year follow-up period without progression of disease, reconstructive surgery is scheduled. Plaque morphea can involve all layers of the skin but associated breast deformity is rare. It can mimic benign and malignant breast disorders justifying the benefit for early tissue biopsy. Breast morphea generally has a good prognosis but hyperpigmentation and breast deformity in young girls have been rarely described. An early diagnosis can possibly lead to a therapeutic intervention with a different outcome, as it can be the source of severe psychological and social issues in a delicate period of development such as adolescence. 1. Introduction Morphea is a rare fibrosing disorder of the skin and underlying tissues, with equal prevalence both in adults and children, female predominance, and greater prevalence in caucasians. Circumscribed morphea presents with less than three discrete indurated plaques, predominantly on the trunk, and it can be superficial or deep [1–3]. Breasts are commonly affected in women, uniformly sparing the nipples [4]. 2. Case Presentation We report the case of a 12-year-old female patient who was referred to our outpatient clinic for evaluation of a patch in her right breast with 2 years of evolution. Pruritus and pain were denied. No musculoskeletal, respiratory, gastrointestinal, neurologic, and vascular symptoms were present. Her past medical history was irrelevant except for asthma and there was no family history of autoimmune diseases. At the physical exam, right breast asymmetry was noted, with an infra-areolar patch with 7 by 3?cm, with nontender, brownish, hyperpigmented, and hypopigmented areas (Figure 1). There were no other relevant cutaneous lesions. Figure 1: Right breast asymmetry, infra-areolar patch, with 7?cm, with nontender, brownish, hyperpigmented, and hypopigmented areas. A skin biopsy was performed, showing thickening of the collagen bundles in the dermis with a perivascular lymphohistiocytic infiltrate. No eccrine glands were present (Figure 2). These histologic findings confirmed the clinical diagnosis of morphea. Figure 2: Haematoxylin and
Molecular analysis of endophytic bacteria from the genus Bacillus isolated from tropical maize (Zea mays L.)
Figueiredo, José Edson Fontes;Gomes, Eliane Aparecida;Guimar?es, Claudia Teixeira;Lana, Ubiraci Gomes de Paula;Teixeira, Marta Aparecida;Lima, Guilherme Vitor Corrêa;Bressan, Wellington;
Brazilian Journal of Microbiology , 2009, DOI: 10.1590/S1517-83822009000300014
Abstract: endophytic bacteria play an important role in agriculture by improving plant performance and adaptation against biotic and abiotic stresses. in the present study molecular methods were used for identifying bacillus endophytic bacteria isolated from brazilian sweet corn. sds-page of wholecell protein extract of fortytwo isolates revealed a high number of scrutinable bands. twenty-four isolates were identified in nine different groups of duplicated bacteria and eighteen were identified as unique. some high-accumulated polipeptides with variable length were observed in almost isolates. partial sequencing of 16s ribosomal gene revealed that all isolates are bacillus sp. and among thirteen isolates with similar protein profiles, two were different strains. among the forty-two isolates identified by rdna sequencing, bacillus subitilis and b. pumilus were the most frequenty species (15 and 12 isolates, respectively) followed by b. licheniformes (7 isolates), b. cereus (5 isolates) and b. amiloliquefascens (3 isolates). according to present results, sds-page technique could be used as a fast and cheap first tool for identifying interspecific variation in maize endophytic bacterial collections while rdna sequencing could be applied for analyzing intraspecific variation among isolates with similar protein profile as well as for taxonomic studies.
Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics
Luis Alcaraz, Gabriel Moreno-Hagelsieb, Luis E Eguiarte, Valeria Souza, Luis Herrera-Estrella, Gabriela Olmedo
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-332
Abstract: Our analysis is based upon twenty complete and draft Bacillus genomes, including a newly sequenced Bacillus isolate from an aquatic environment that we report for the first time here. Using a core genome, we were able to determine the phylogeny of known Bacilli, including aquatic strains whose position in the phylogenetic tree could not be unambiguously determined in the past. Using the pan-genome from the sequenced Bacillus, we identified functional differences, such as carbohydrate utilization and genes involved in signal transduction, which distinguished the taxonomic groups. We also assessed the genetic architecture of the defining traits of Bacillus, such as sporulation and competence, and showed that less than one third of the B. subtilis genes are conserved across other Bacilli. Most variation was shown to occur in genes that are needed to respond to environmental cues, suggesting that Bacilli have genetically specialized to allow for the occupation of diverse habitats and niches.The aquatic Bacilli are defined here for the first time as a group through the phylogenetic analysis of 814 genes that comprise the core genome. Our data distinguished between genomic components, especially core vs. pan-genome to provide insight into phylogeny and function that would otherwise be difficult to achieve. A phylogeny may mask the diversity of functions, which we tried to uncover in our approach. The diversity of sporulation and competence genes across the Bacilli was unexpected based on previous studies of the B. subtilis model alone. The challenge of uncovering the novelties and variations among genes of the non-subtilis groups still remains. This task will be best accomplished by directing efforts toward understanding phylogenetic groups with similar ecological niches.Bacillus is one of the best characterized bacterial genera. Since the late 19th century, the long history of Bacilli research has included classical microbiology, biochemistry, and more modern genomic and
Antifungal Activity of Selected Indigenous Pseudomonas and Bacillus from the Soybean Rhizosphere  [PDF]
M. León,P. M. Yaryura,M. S. Montecchia,A. I. Hernández,O. S. Correa,N. L. Pucheu,N. L. Kerber,A. F. García
International Journal of Microbiology , 2009, DOI: 10.1155/2009/572049
Abstract: The purpose of this study was to isolate and select indigenous soil Pseudomonas and Bacillus bacteria capable of developing multiple mechanisms of action related to the biocontrol of phytopathogenic fungi affecting soybean crops. The screening procedure consisted of antagonism tests against a panel of phytopathogenic fungi, taxonomic identification, detection by PCR of several genes related to antifungal activity, in vitro detection of the antifungal products, and root colonization assays. Two isolates, identified and designated as Pseudomonas fluorescens BNM296 and Bacillus amyloliquefaciens BNM340, were selected for further studies. These isolates protected plants against the damping-off caused by Pythium ultimum and were able to increase the seedling emergence rate after inoculation of soybean seeds with each bacterium. Also, the shoot nitrogen content was higher in plants when seeds were inoculated with BNM296. The polyphasic approach of this work allowed us to select two indigenous bacterial strains that promoted the early development of soybean plants.
Characterisation of Bacillus thuringiensis kurstaki strains by toxicity, plasmid profiles and numerical analysis of their cryIA genes
S Kashyap, DV Amla
African Journal of Biotechnology , 2007,
Abstract: In the present comparative study, four Bacillus thuringiensis kurstaki strains (HD1, dipel, HD73, HD1dipel) were characterized by investigating their total plasmid profiling; cryIA genes profiling and toxicity towards local isolates of agricultural insects Helicoverpa armigera and Spodoptera litura. Result showed that LC50 for S. litura were 0.11 g of HD73, 0.027 g of HD1, 0.20 g of dipel and 0.018 g of HD1 dipel, while LC50 for H. armigera insect were 0.04 g of HD73, 0.031 g of HD1, 0.011 g of dipel and 0.008 g of HD1dipel. The native plasmid number and type varied from 4 - 8 among these strains and HindIII restriction showed 0.4 to 8.0 kb size fragments. The numerical classification of the cryIA gene profiles showed two distinct clusters at 48% similarity level. Cluster one of 80% similarity comprises of two strains HD73 and dipel, while cluster two of 65% consisted of HD1 and HD1dipel strains. Southern analysis of restricted plasmid combined with cryIA profile can provide an effective approach for investigation of taxonomic relationship within Bacillus thuringiensis kurstaki strains.
Circumscribed congenital alopecias harbouring dual lesions
Rao Shalinee,Janaki Amutha,Kamakshi D,Srinivasan V
Journal of Cutaneous and Aesthetic Surgery , 2010,
Abstract: Treatment of alopecia is often challenging for the clinician as it includes a spectrum of lesions ranging from congenital to acquired causes. We present three cases of congenital circumscribed alopecia, present since birth, clinically diagnosed as nevus sebaceous. Histopathological examination of the excised tissue showed syringocystadenoma papilliferum with dermatophytosis in one and nevus sebaceous with dermatophytosis in the other two cases. Although complete excision is the treatment of choice for these lesions, an antifungal agent is needed to eradicate the concurrent superficial mycosis. A careful histopathological examination of the lesional skin helps in identifying such unexpected dual lesions that would need further treatment.
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