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A short 220 bp sequence was used to study the taxonomic organization of the bacterial Order Bacillales. The nucleotide sequences of the 3' end of the 16S rDNA and the 16S-23S Internal transcribed spacer (ITS) were determined for 32 Bacillales species and strains. The data for 40 additional Bacillales species and strains were retrieved directly from...
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Figures S18-S19 Phylogenetic tree of 16S rDNA of novel Clostridium spp. and low frequency Clostridium spp. File contains a neighbor - joining analysis performed on the rrs sequences of novel Clostridium sp. (Additional file 4: Table S2) 56 along with 83 representatives of Clostridium sp. known to occur at low frequency (Additional file 4: Table S3)...
Identifying certain species of Dermacentor ticks in Malaysia is challenging as there is no comprehensive work on their systematics and lack of specific taxonomic keys. In this study, we described and characterized D. steini ticks collected from a forest reserve in the vicinity of the Forest Research Institute of Malaysia using integrated phenotypic...
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... This genomic data has already been employed, to a limited extent, to study the phylogeny and taxonomy of a small number of Caryophanaceae/Planococcaceae species in recent years and continues to develop as a promising resource for clarifying the evolutionary history of Caryophanaceae species (Xu et al., 2015;Maayer et al., 2019). In addition, genome sequences are also available for >150 other species belonging to the family Bacillaceae, its closest phylogenetic relative (Ludwig et al., 2009;Yakoubou et al., 2010;Shivaji et al., 2014;Patel and Gupta, 2019). In the present study, we have used genomic information from Caryophanaceae and Bacillaceae species to comprehensively examine the interrelationships among species within these families using phylogenomic and comparative genomic approaches. ...
The family Caryophanaceae/Planococcaceae is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily Bacillaceae, the evolutionary history of this family, containing the potent mosquitocidal species Lysinibacillus sphaericus, remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family Caryophanaceae/Planococcaceae and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available Caryophanaceae/Planococcaceae and representative Bacillaceae species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved Firmicutes proteins. Using the core proteins, pairwise average amino acid identity was also determined. In parallel, comparative analyses on protein sequences from these species have identified 92 unique molecular markers (synapomorphies) consisting of conserved signature indels that are specifically shared by either the entire family Caryophanaceae/Planococcaceae or different monophyletic clades present within this family, enabling their reliable demarcation in molecular terms. Based on multiple lines of investigations, 18 monophyletic clades can be reliably distinguished within the family Caryophanaceae/Planococcaceae based on their phylogenetic affinities and identified molecular signatures. Some of these clades are comprised of species from several polyphyletic genera within this family as well as other families. Based on our results, we are proposing the creation of three novel genera within the family Caryophanaceae/Planococcaceae, namely Metalysinibacillus gen. nov., Metasolibacillus gen. nov., and Metaplanococcus gen. nov., as well as the transfer of 25 misclassified species from the families Caryophanaceae/Planococcaceae and Bacillaceae into these three genera and in Planococcus, Solibacillus, Sporosarcina, and Ureibacillus genera. These amendments establish a coherent taxonomy and evolutionary history for the family Caryophanaceae/Planococcaceae, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family Planococcaceae within the emended family Caryophanaceae.
... Group VI, the acidophilic thermophiles have recently been allocated to the new genus Alicyclobacillus in which thermophily appears to have independently evolved in many lineages. Recent researches, based on a "pan-genomic" approach, support the division of Bacillus into further new genera and revealed unexpected groupings suggesting that the final picture of Bacillus taxonomy is still far from drawn [3,4]. Bacillus species are an important source of insecticides, antibiotics, vitamins and enzymes [5]. ...
World is threaten to energy crisis which has advances research in bioenergy and specifically development of biofuels to replace petroleum products have increased the use of microbial enzyme like cellulases and xylanases as well as amylases for generation of reducing sugars for their conversion into bioethanol. Extensive research has been carried out in this view but alkaline cellulase production and molecular characterization is not studied in detail so far, this study will aid to achieve it. Optimization of fermentation parameters for production of cellulase was evaluated with the help of Response Surface Methodology (RSM) a statistical design, initial pH (9), moisture ratio (1:1) and incubation time (72 h) (run no.4) were found to be ideal parameters for optimum production of cellulase, substrate Jatropha seed cake without any pre-treatment was found to be an ideal source for cellulase production by Bacillus licheniformis under solid state fermentation. Cellulase gene of size 786 bp was isolated later using PCR techniques, confirmed with sequence analysis and ligated to pRSET A vector for the transformation to E. coli DH5α. Positive clones were identified and sequenced to justify the cloning. Sequence of Bacillus licheniformis endo-β-1,4-glucanase (Cel12A) gene showed 100% similarity with endoglucanase gene sequence from Bacillus licheniformis ATCC 14580 genome, shows successful cloning of Cel12A gene into pRSET A vector.
... The position of Lactobacillales within the Bacillales clade is not recovered in the analysis of Ciccarelli et al. (2006); we attribute this topological difference to the fact that we used only 20 of the 31 genes used in that reconstruction. There are phylogenies of Firmicutes with a more complete taxon sampling in which one or a few genes were used, but they are highly incongruent and/or have poor resolution (Wolf et al., 2004; Yakoubou et al., 2010). So the approach for highly resolved, congruent, and true bacterial phylogenies has to be good taxon sampling and a careful selection of genes. ...
The Cuatro Ciénegas Basin (CCB) has been identified as a center of endemism for many life-forms. Nearly half the bacterial species found in the spring systems have their closest relatives in the ocean. This raises the question of whether the high diversity observed today is the product of an adaptive radiation similar to that of the Galapagos Islands or whether the bacterial groups are "survivors" of an ancient sea, which would be of interest for astrobiology. To help answer this question, we focused on Firmicutes from Cuatro Ciénegas (mainly Bacillus and Exiguobacterium). We reconstructed the phylogenetic relationships of Firmicutes with 28 housekeeping genes and dated the resulting tree using geological events as calibration points. Our results show that marine Bacillus diverged from other Bacillus strains 838 Ma, while Bacillus from Cuatro Ciénegas have divergence dates that range from 770 to 202 Ma. The members of Exiguobacterium from the CCB conform to a much younger group that diverged from the Andes strain 60 Ma and from the one in Yellowstone 183 Ma. Therefore, the diversity of Firmicutes in Cuatro Ciénegas is not the product of a recent radiation but the product of the isolation of lineages from an ancient ocean. Hence, Cuatro Ciénegas is not a Galapagos Archipelago for bacteria but is more like an astrobiological "time machine" in which bacterial lineages survived in an oligotrophic environment that may be very similar to that of the Precambrian. Key Words: Firmicutes-Cuatro Ciénegas-Precambrian-Molecular dating-Western Interior Seaway.
... The acidophilic thermophiles (group VI) have recently been allocated to the new genus Alicyclobacillus in which thermophily appears to have independently evolved in many lineages. Recent researches, based on a "pan-genomic" approach, support the division of Bacillus into further new genera and revealed unexpected groupings [5,6] suggesting that the final picture of Bacillus taxonomy is still far to be drawn. ...
The Bacillus genus is a heterogeneous group of Gram-positive, facultative anaerobic, endospore-forming bacteria spread into the environment, even though soil is generally accepted as its natural reservoir. The ability to produce endospores allows Bacillus to withstand extreme environmental conditions as those occurring in food processing. Bacillus spp., particularly B. subtilis, are usually found in foods such as dry cured sausages, cheeses, traditional fermented milks, sourdough, etc. in which they cooperate with other microorganisms during fermentation, releasing amylases, lipases and proteases. One of the main characteristics shared among Bacillus strains is the ability to produce a wide range of antimicrobial compounds active against bacteria and fungi. Even though microbial control exerted by these metabolites was demonstrated in plant environments, few reports focused their attention on how these compounds can interact with food microbiota. One single Bacillus strain is often able to produce several types of molecules stable over a wide range of pH and temperature and partially resistant to enzyme treatments. These substances are usually protein-and peptide-based compounds such as enzymes, bacteriocins and lipopeptides. Thanks to their chemical characteristics and inhibitory spectrum, Bacillus producer strains could be applied during food processing as innovative tools for the control of food pathogens and spoilage microorganisms. In this paper, current and potential applications of Bacillus strains in food environments are discussed, focussing on antimicrobial compounds contributing to improve food safety and quality.
... topology of the neighbor-joining tree was, however, in agreement with phylogenetic trees based on the 16S rRNA [13] and the 16S-23S ITS [15]. In previous studies, we showed that a DNA sequence from 3' end 16S rRNA gene and 5' end 16S-23S ITS could be used as a marker in the reconstruction of phylogenies in the Gram-positive genus Bacillus and closely-related genera [32], the Gram-positive Order Bacillales [33], and the Gram-negative Class γ-proteobacteria [26]. This maker ranged in size from 220 bp to 232 bp. ...
... Owing to its higher rate of nucleotide substitutions, the 67-75 bp from the 5' end of the 16S-23S ITS added resolving power among closely related species from same genus. This marker had proven useful in reconstructing the phylogenies of the genus Bacillus and closely-related genera [32], the Order Bacillales [33] and the Class γ-proteobacteria [26] in accordance with accepted phylogenies inferred from much more comprehensive datasets. This marker presented several advantages over the use of the entire 16S rRNA gene or the 16S-23S ITS or the generation of extensive phenotypic and genotypic data in phylogenetic analyses. ...
A short phylogenetic marker previously used in the reconstruction of the Class γ-proteobacteria was assessed here at a lower taxa level, species in the genus Xanthomonas. This maker is 224 nucleotides in length. It is a combination of a 157 nucleotide sequence at the 3' end of the 16S rRNA gene and a 67 nucleotide sequence at the 5' end of the 16S-23S ITS sequence. A total of 23 Xanthomonas species were analyzed. Species from the phylogenetically related genera Xylella and Stenotrophomonas were included for com-parison purposes. A bootstrapped neighbor-joining phylogenetic tree was inferred from comparative analyses of the 224 bp nucleotide sequence of all 30 bacterial strains under study. Four major Groups were revealed based on the topology of the neighbor-joining tree, Group I to IV. Group I and II contained the genera Steno-trophomonas and Xylella, respectively. Group III included five Xanthomonas species: X. theicola, X. sacchari, X. albineans, X. transluscens and X. hyacinthi. This group of Xanthomonas species is often referred to as the hyacinthi group. Group IV contained the other 18 Xanthomonas species. The overall topology of the neighbor-joining tree was in agreement with currently accepted phylogenetic. The short phylogenetic marker used here could resolve species from three dif-ferent Xanthomonadacea genera: Stenotro-phomonas, Xylella and Xanthomonas. At the level of the Xanthomonas genus, distant spe-cies could be distinguished, and whereas some closely-related species could be distinguished, others were undistinguishable. Pathovars could not be distinguished. We have met the resolving limit of this marker: pathovars and very closely related species from same genus.
... This marker was a combination of the last 150 bp at the 3' end of the 16S rDNA and the first 70 bp at the 5' end of the 16S- 23S rDNA internal transcribed spacer (ITS). More recently, we assessed the usefulness of the 220 bp marker at a higher taxonomic level, the Order Bacillales [29]. This marker showed several advantages over the use of 16S rDNA sequences or the generation of extensive phenotypic and genotypic data in phylogenetic analyses. ...
... Owing to its higher rate of nucleotide substitutions, the 70 bp at the 5' end of the 16S-23S rDNA (ITS) added discriminating power among closely related species from same genus and closely related genera from same family. Because of its higher percentage of nucleotide sequence divergence than the 16S rDNA, the 220 bp marker could better discriminate among closely related Bacillus [28] and Ba- cillales [29] species. Second, the method was simple, rapid , suited to large screening programs and easily accessible to most laboratories. ...
... This marker was a combination of the last 150 bp at the 3' end of the 16S rDNA and the first 70 bp at the 5' end of the 16S-23S rDNA internal transcribed spacer (ITS). More recently, we assessed the usefulness of the 220 bp marker by extending its analyses at a higher taxonomic level, the Gram-positive Order Bacillales [29]. In parallel, a similar marker was used to infer the phylogeny of the Gram-negative Class γ-pro- teobacteria [33]. ...
A short phylogenetic marker previously used in the reconstruction of the Order Bacillales and the genus Bacillus was assessed here at a lower taxa level: species in the Bacillus cereus group: B. anthracis, B. cereus, B. thuringiensis and B. weihenstephanensis. This maker is 220 bp in length. It is a combination of 150 bp at the 3' end of the 16S rDNA and 70 bp at the 5' end of the 16S-23S ITS sequence. Three additional Bacillus species, B. halodurans, B. licheniformis and B. subtilis, and Clostridium tetani were included for comparison purposes. A total of eight bacte-rial species and 12 strains were analyzed. A boot-strapped neighbor-joining tree was inferred from comparative analyses of all allelic sequences of the bacterial species and strains under study. Based on its topology, four major Groups were revealed at the 90% nucleotide sequence identi-ties, Group I to IV. Group I contains all alleles of the Bacillus cereus group. Group II contains all alleles of B. halodurans. Group III contains all alleles of B. licheniformis and B. subtilis. Group IV contains all alleles of Clostridium tetani. The 220 bp phylogenetic marker used here could resolve different species from different genera. At the genus level, distant species could be dis-tinguished. Very closely-related species, how-ever, were undistinguishable. Species in the B. cereus group, most notably B. cereus, B. anth-racis and B. thuringiensis, could not be distin-guished. After successfully inferring the phylo-genies of the Order Bacillales and the genus Bacillus, we have met the resolving limit of this short phylogenetic marker: B. cereus, B. an-thracis and B. thuringiensis.
... It also created new clusters suggesting the creation of new taxa levels. In a very recent study, we [28] have tested whether or not this marker could reconstruct the phylogeny of the bacterial Grampositive Order of the Bacillales. ...
The phylogeny of γ-proteobacteria was inferred from nucleotide sequence comparisons of a short 232 nucleotide sequence marker. A total of 64 γ-proteobacterial strains from 13 Orders, 22 families, 40 genera and 59 species were analyzed. The short 232 nucleotide sequence marker used here was a combination of a 157 nucleotide sequence at the 3’ end of the 16S rRNA gene and a 75 nucleotide sequence at the 5’ end of the 16S-23S Internal Transcribed Spacer (ITS) sequence. Comparative analyses of the 3’ end of the 16S rRNA gene nucleotide sequence showed that the last 157 bp were conserved among strains from same species and less conserved in more distantly related species. This 157 bp sequence was selected as the first part in the construction of our nucleotide sequence marker. A bootstrapped neighbor-joining tree based on the alignment of this 157 bp was constructed. This 157 bp could distinguish γ-proteobacterial species from different genera from same family. Closely related species could not be distinguished. Next, an alignment of the 16S-23S ITS nucleotide sequences of alleles from same bacterial strain was performed. The first 75 bp at the 5’ end of the 16S-23S ITS was highly conserved at the intra-strain level. It was selected as the second part in the construction of our nucleotide sequence marker. Finally, a bootstrapped neighbor-joining tree based on the alignment of this 232 bp sequence was constructed. Based on the topology of the neighbour-joining tree, four major Groups, Group I to IV, were revealed with several sub-groups and clusters. Our results, based on the 232 bp sequence were, in general, in agreement with the phylogeny of γ-proteobacteria based on the 16S rRNA gene. The use of this 232 bp sequence as a phylogenetic marker presents several advantages over the use of the entire 16S rRNA gene or the generation of extensive phenotypic and genotypic data in phylogenetic analyses. First, this marker is not allele-dependant. Second, this 232 bp marker contains 157 bp from the 3’ end of the 16S rRNA gene and 75 bp from the 5’ end of the 16S-23S ITS. The 157 bp allows discrimination among distantly related species. Owing to its higher rate of nucleotide substitutions, the 75 bp adds discriminating power among closely related species from same genus and closely related genera from same family. Because of its higher percentage of nucleotide sequence divergence than the 16S rRNA gene, the 232 bp marker can better discriminate among closely related γ-proteobacterial species. Third, the method is simple, rapid, suited to large screening programs and easily accessible to most laboratories. Fourth, this marker can also reveal γ-proteobacterial species which may appear misassigned and for which additional characterization appear warranted.
Objective. To determine the incidence of coagulase-positive strains of enterotoxigenic Staphylococcus in doble crema (double cream) cheese samples produced in Pamplona. Materials and methods. Bacterial isolation was performed following the routine method for coagulase positive Staphylococcus provided by the Colombian Technical Standard 4779, by using Baird Parker medium with confirmation of typical colonies by performing the coagulase test. Detection of genes for principal enterotoxins was done by PCR. Results. The prevalence of coagulase positive Staphylococcus in cheese samples was 31%, with 27% of the samples failing to meet the requirements of the NTC 750. In 24.6% of the studied isolates, genes for enterotoxin production were detected. The presence, in the isolated strains, of genes for SEB, SEA and SED was 18.5%, 4.6% and 3.0%, respectively. Conclusions. The significant presence of enterotoxigenic genes found in the isolates obtained from samples of double cream cheese made in Pamplona, suggests an important hazard to the health of consumers.
Full text available at http://revistas.unicordoba.edu.co/revistamvz/mvz-201/v20n1a10.pdf
We report the genome of a Staphylococcus aureus strain (ILRI_Eymole1/1) isolated from a nasal swab of a dromedary camel (Camelus dromedarius) in North Kenya. The complete genome sequence of this strain consists of a circular chromosome of 2,874,302 bp with a GC-content of 32.88 %. In silico annotation predicted 2755 protein-encoding genes and 76 non-coding genes. This isolate belongs to MLST sequence type 30 (ST30). Phylogenetic analysis based on a subset of 283 core genes revealed that it falls within the human clonal complex 30 (CC30) S. aureus isolate cluster but is genetically distinct. About 79 % of the protein encoding genes are part of the CC30 core genome (genes common to all CC30 S. aureus isolates), ~18 % were within the variable genome (shared among multiple but not all isolates) and ~ 3 % were found only in the genome of the camel isolate. Among the 85 isolate-specific genes, 79 were located within putative phages and pathogenicity islands. Protein encoding genes associated with bacterial adhesion, and secretory proteins that are essential components of the type VII secretion system were also identified. The complete genome sequence of S. aureus strain ILRI_Eymole1/1 has been deposited in the European Nucleotide Archive under the accession no LN626917.1.
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