scholarly journals Genome-based taxonomic classification

Genome ◽  
2019 ◽  
Vol 62 (2) ◽  
pp. 45-52 ◽  
Author(s):  
Bobby Paul ◽  
Gunjan Dixit ◽  
Thokur Sreepathy Murali ◽  
Kapaettu Satyamoorthy
Keyword(s):  
Genome Assembly ◽  
Bacterial Species ◽  
Sequence Information ◽  
Bacterial Identification ◽  
Biochemical Tests ◽  
Separate Species ◽  
Genome Database ◽  
Bacterial Populations ◽  
A Genome ◽  
Metadata Analysis

Bacterial populations are routinely characterized based on microscopic examination, colony formation, and biochemical tests. However, in the recent past, bacterial identification, classification, and nomenclature have been strongly influenced by genome sequence information. Advances in bioinformatics and growth in genome databases has placed genome-based metadata analysis in the hands of researchers who will require taxonomic experience to resolve intricacies. To achieve this, different tools are now available to quantitatively measure genome relatedness within members of the same species, and genome-wide average nucleotide identity (gANI) is one such reliable tool to measure genome similarity. A genome assembly with a gANI score of <95% at the intraspecies level is generally considered indicative of a separate species. In this study, we have analysed 300 whole-genome sequences belonging to 26 different bacterial species available in the NCBI Genome database and calculated their similarity at the intraspecies level based on gANI score. At the intraspecies level, nine bacterial species showed less than 90% gANI and more than 10% of unaligned regions. We suggest the appropriate use of available bioinformatics resources after genome assembly to arrive at the proper bacterial identification, classification, and nomenclature to avoid erroneous species assignments and disparity due to diversity at the intraspecies level.

scholarly journals A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona

2019 ◽  
Vol 11 (11) ◽  
pp. 3144-3157 ◽  
Author(s):  
Yutaka Satou ◽  
Ryohei Nakamura ◽  
Deli Yu ◽  
Reiko Yoshida ◽  
Mayuko Hamada ◽  
...  
Keyword(s):  
Genome Size ◽  
Inbred Line ◽  
Genome Assembly ◽  
Ciona Intestinalis ◽  
Type A ◽  
Chromosomal Evolution ◽  
Sequence Information ◽  
A Genome ◽  
Biological Studies ◽  
Wide Range

Abstract Since its initial publication in 2002, the genome of Ciona intestinalis type A (Ciona robusta), the first genome sequence of an invertebrate chordate, has provided a valuable resource for a wide range of biological studies, including developmental biology, evolutionary biology, and neuroscience. The genome assembly was updated in 2008, and it included 68% of the sequence information in 14 pairs of chromosomes. However, a more contiguous genome is required for analyses of higher order genomic structure and of chromosomal evolution. Here, we provide a new genome assembly for an inbred line of this animal, constructed with short and long sequencing reads and Hi-C data. In this latest assembly, over 95% of the 123 Mb of sequence data was included in the chromosomes. Short sequencing reads predicted a genome size of 114–120 Mb; therefore, it is likely that the current assembly contains almost the entire genome, although this estimate of genome size was smaller than previous estimates. Remapping of the Hi-C data onto the new assembly revealed a large inversion in the genome of the inbred line. Moreover, a comparison of this genome assembly with that of Ciona savignyi, a different species in the same genus, revealed many chromosomal inversions between these two Ciona species, suggesting that such inversions have occurred frequently and have contributed to chromosomal evolution of Ciona species. Thus, the present assembly greatly improves an essential resource for genome-wide studies of ascidians.

Functional Properties of Plasmids as Related to Enumeration of Bacteria Important to the Food Microbiologist

1978 ◽  
Vol 41 (1) ◽  
pp. 44-47 ◽  
Author(s):  
CLIFFORD HOWELL ◽  
WILLIAM J. MARTIN
Keyword(s):  
Bacterial Species ◽  
Animal Husbandry ◽  
Selective Advantage ◽  
Detailed Knowledge ◽  
Biochemical Tests ◽  
Pathogenic Potential ◽  
Bacterial Populations ◽  
Phenotypic Characters ◽  
Resistance To Antibiotics ◽  
The Family

Plasmids are extrachromosomal elements that behave like auxiliary chromosomes and contain the basic structure of the replicating unit. They were initially recognized by the unusual phenotypic characteristics they confer upon a cell, such as ability to promote genetic transfer by conjugation; resistance to antibiotics and metal ions; production of bacteriocins, toxins, antigens; and other factors. Much of the work on plasmids and plasmid-mediated characteristics has been conducted with various genera and species of the family Enterobacteriaceae. Present data indicate that although plasmid transfer occurs with variable frequency, intergeneric transfer within the family is invariably successful. Although a great deal of investigation has been focused on plasmid-mediated resistance to antibiotics, many workers have determined that a number of plasmids control other phenotypic characters. For example such plasmids appear to mediate production of bacterial products and/or enzymes which may confer a selective ecological advantage to bacteria in their inter-relationships with their hosts and other microorganisms. The isolation of these phenotypically altered microorganisms by food, medical, and public health microbiologists may signify an important ubiquitous phenomenon. There is increasing evidence that selective forces operate in both the laboratory and in nature which should alert the microbiologist that any of the present-day identification schema must be utilized with some caution. To this end technical advances in identification of microorganisms by use of a large battery of biochemical tests has increased the accuracy of identification and measurably reduced the misidentification of atypical bacteria. Availability of such data may assist the microbiologist to establish baseline information essential for development of prospective studies for defining the reservoirs of phenotypically altered microorganisms and their pathogenic potential for the general population. The full importance of plasmid-mediated characteristics in bacterial populations in food products and the role they will play in the future is largely unknown. The origin and selective advantage that strains harboring plasmids in the natural ecology is also unknown. Detailed knowledge of microorganisms maintaining plasmids may be important economically, since the emergence of a number of antibiotic-resistant microorganisms may have contributed a significant role in development of disease among domestic animals because oft he manner in which animal husbandry is practiced in many countries. Extrapolated, one could speculate about an ever-increasing reservoir of similar bacterial species, potentially transmissible to man. Because the factors which control mobilization of plasmids and the important ecological selective advantage conferred upon bacterial populations by plasmids, it is essential that we as microbiologists become cognizant of their existence and to fully understand the mechanisms of perpetuation of plasmid-mediated characteristics.

Marsupial chromosomics: bridging the gap between genomes and chromosomes

2019 ◽  
Vol 31 (7) ◽  
pp. 1189 ◽  
Author(s):  
Janine E. Deakin ◽  
Sally Potter
Keyword(s):  
Dna Sequence ◽  
Genome Assembly ◽  
Genome Architecture ◽  
Sequence Information ◽  
Full Potential ◽  
Tasmanian Devil ◽  
Sequencing Technology ◽  
A Genome ◽  
Devil Facial Tumour Disease ◽  
Chromosome Level

Marsupials have unique features that make them particularly interesting to study, and sequencing of marsupial genomes is helping to understand their evolution. A decade ago, it was a huge feat to sequence the first marsupial genome. Now, the advances in sequencing technology have made the sequencing of many more marsupial genomes possible. However, the DNA sequence is only one component of the structures it is packaged into: chromosomes. Knowing the arrangement of the DNA sequence on each chromosome is essential for a genome assembly to be used to its full potential. The importance of combining sequence information with cytogenetics has previously been demonstrated for rapidly evolving regions of the genome, such as the sex chromosomes, as well as for reconstructing the ancestral marsupial karyotype and understanding the chromosome rearrangements involved in the Tasmanian devil facial tumour disease. Despite the recent advances in sequencing technology assisting in genome assembly, physical anchoring of the sequence to chromosomes is required to achieve a chromosome-level assembly. Once chromosome-level assemblies are achieved for more marsupials, we will be able to investigate changes in the packaging and interactions between chromosomes to gain an understanding of the role genome architecture has played during marsupial evolution.

scholarly journals De novo genome assembly and functional annotation for Fusarium langsethiae

2021 ◽  
Author(s):  
Ya Zuo ◽  
Carol Verheecke-Vaessen ◽  
Corentin Molitor ◽  
Angel Medina ◽  
Naresh Magan ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Animal Health ◽  
Data Availability ◽  
Effective Control ◽  
Local Alignment ◽  
De Novo Genome Assembly ◽  
Genome Database ◽  
A Genome ◽  
Fusarium Langsethiae

AbstractMotivationFusarium langsethiae is a T-2 and HT-2 mycotoxins producing Fusarium species firstly characterised in 2004. It is commonly isolated from oats in Northern Europe. T-2 and HT-2 mycotoxins exhibit immunological and haemotological effects in animal health mainly through inhibition of protein, RNA and DNA synthesis. The development of a high-quality and comprehensively annotated assembly for this species is therefore essential in providing the molecular understanding and the mechanism of T-2 and HT-2 biosynthesis in F. langsethiae to help develop effective control strategies.ResultsThe F. langsethiae assembly was produced using PacBio long reads, which were then assembled independently using Canu, SMARTdenovo and Flye; producing a genome assembly total length of 59Mb and N50 of 3.51Mb. A total of 19,336 coding genes were identified using RNA-Seq informed ab-initio gene prediction. Finally, predicting genes were annotated using the basic local alignment search tool (BLAST) against the NCBI non-redundant (NR) genome database and protein hits were annotated using InterProScan. Genes with blast hits were functionally annotated with Gene [email protected] availabilityRaw sequence reads and assembled genome can be downloaded from: GenBank under the accession JAFFKB000000000

scholarly journals Chromosome-level genome assembly of a regenerable maize inbred line A188

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guifang Lin ◽  
Cheng He ◽  
Jun Zheng ◽  
Dal-Hoe Koo ◽  
Ha Le ◽  
...  
Keyword(s):  
Inbred Line ◽  
Genome Assembly ◽  
Gene Function ◽  
Maize Inbred Line ◽  
Carotenoid Cleavage Dioxygenase ◽  
Structural Variations ◽  
Embryonic Callus ◽  
Network Analyses ◽  
A Genome ◽  
Chromosome Level

Abstract Background The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. Results Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. Conclusions The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.

scholarly journals Detection of Food Spoilage and Pathogenic Bacteria Based on Ligation Detection Reaction Coupled to Flow-Through Hybridization on Membranes

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
K. Böhme ◽  
P. Cremonesi ◽  
M. Severgnini ◽  
Tomás G. Villa ◽  
I. C. Fernández-No ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Bacterial Species ◽  
Cost Effective ◽  
Rrna Gene ◽  
Bacterial Identification ◽  
Dot Blot ◽  
Culture Collections ◽  
Ligation Detection Reaction ◽  
Flow Through ◽  
Food Safety And Quality

Traditional culturing methods are still commonly applied for bacterial identification in the food control sector, despite being time and labor intensive. Microarray technologies represent an interesting alternative. However, they require higher costs and technical expertise, making them still inappropriate for microbial routine analysis. The present study describes the development of an efficient method for bacterial identification based on flow-through reverse dot-blot (FT-RDB) hybridization on membranes, coupled to the high specific ligation detection reaction (LDR). First, the methodology was optimized by testing different types of ligase enzymes, labeling, and membranes. Furthermore, specific oligonucleotide probes were designed based on the 16S rRNA gene, using the bioinformatic tool Oligonucleotide Retrieving for Molecular Applications (ORMA). Four probes were selected and synthesized, being specific forAeromonasspp.,Pseudomonasspp.,Shewanellaspp., andMorganella morganii, respectively. For the validation of the probes, 16 reference strains from type culture collections were tested by LDR and FT-RDB hybridization using universal arrays spotted onto membranes. In conclusion, the described methodology could be applied for the rapid, accurate, and cost-effective identification of bacterial species, exhibiting special relevance in food safety and quality.

scholarly journals Evaluation of MicroScan Bacterial Identification Panels for Low-Resource Settings

Diagnostics ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 349
Author(s):  
Sien Ombelet ◽  
Alessandra Natale ◽  
Jean-Baptiste Ronat ◽  
Olivier Vandenberg ◽  
Liselotte Hardy ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Ease Of Use ◽  
Bacterial Identification ◽  
Gram Positive ◽  
Gram Negative ◽  
Low Resource Settings ◽  
Low Resource ◽  
Bacillus Spp ◽  
Gram Negative Organisms ◽  
Instructions For Use

Bacterial identification is challenging in low-resource settings (LRS). We evaluated the MicroScan identification panels (Beckman Coulter, Brea, CA, USA) as part of Médecins Sans Frontières’ Mini-lab Project. The MicroScan Dried Overnight Positive ID Type 3 (PID3) panels for Gram-positive organisms and Dried Overnight Negative ID Type 2 (NID2) panels for Gram-negative organisms were assessed with 367 clinical isolates from LRS. Robustness was studied by inoculating Gram-negative species on the Gram-positive panel and vice versa. The ease of use of the panels and readability of the instructions for use (IFU) were evaluated. Of species represented in the MicroScan database, 94.6% (185/195) of Gram-negative and 85.9% (110/128) of Gram-positive isolates were correctly identified up to species level. Of species not represented in the database (e.g., Streptococcus suis and Bacillus spp.), 53.1% out of 49 isolates were incorrectly identified as non-related bacterial species. Testing of Gram-positive isolates on Gram-negative panels and vice versa (n = 144) resulted in incorrect identifications for 38.2% of tested isolates. The readability level of the IFU was considered too high for LRS. Inoculation of the panels was favorably evaluated, whereas the visual reading of the panels was considered error-prone. In conclusion, the accuracy of the MicroScan identification panels was excellent for Gram-negative species and good for Gram-positive species. Improvements in stability, robustness, and ease of use have been identified to assure adaptation to LRS constraints.

scholarly journals Rapid Detection, Identification, and Enumeration ofEscherichia coli Cells in Municipal Water by Chemiluminescent In Situ Hybridization

2001 ◽  
Vol 67 (1) ◽  
pp. 142-147 ◽  
Author(s):  
Henrik Stender ◽  
Adam J. Broomer ◽  
Kenneth Oliveira ◽  
Heather Perry-O'Keefe ◽  
Jens J. Hyldig-Nielsen ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
16S Rrna ◽  
Sensitivity And Specificity ◽  
Bacterial Species ◽  
Rdna Sequence ◽  
Sequence Information ◽  
Sequence Alignments ◽  
E Coli ◽  
Municipal Water

ABSTRACT A new chemiluminescent in situ hybridization (CISH) method provides simultaneous detection, identification, and enumeration of culturableEscherichia coli cells in 100 ml of municipal water within one working day. Following filtration and 5 h of growth on tryptic soy agar at 35°C, individual microcolonies of E. coliwere detected directly on a 47-mm-diameter membrane filter using soybean peroxidase-labeled peptide nucleic acid (PNA) probes targeting a species-specific sequence in E. coli 16S rRNA. Within each microcolony, hybridized, peroxidase-labeled PNA probe and chemiluminescent substrate generated light which was subsequently captured on film. Thus, each spot of light represented one microcolony of E. coli. Following probe selection based on 16S ribosomal DNA (rDNA) sequence alignments and sample matrix interference, the sensitivity and specificity of the probe Eco16S07C were determined by dot hybridization to RNA of eight bacterial species. Only the rRNA of E. coli and Pseudomonas aeruginosa were detected by Eco16S07C with the latter mismatch hybridization being eliminated by a PNA blocker probe targetingP. aeruginosa 16S rRNA. The sensitivity and specificity for the detection of E. coli by PNA CISH were then determined using 8 E. coli strains and 17 other bacterial species, including closely related species. No bacterial strains other thanE. coli and Shigella spp. were detected, which is in accordance with 16S rDNA sequence information. Furthermore, the enumeration of microcolonies of E. coli represented by spots of light correlated 92 to 95% with visible colonies following overnight incubation. PNA CISH employs traditional membrane filtration and culturing techniques while providing the added sensitivity and specificity of PNA probes in order to yield faster and more definitive results.

scholarly journals Identification and antibiogram study of bacterial species isolated from milk samples of different locations in Bangladesh

2016 ◽  
Vol 1 (3) ◽  
pp. 457-462 ◽  
Author(s):  
Md Nuruzzaman Munsi ◽  
Nathu Ram Sarker ◽  
Razia Khatun ◽  
Mohammed Khorshed Alam
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Pathogenic Bacteria ◽  
Bacterial Species ◽  
Salmonella Typhi ◽  
Diffusion Method ◽  
Biochemical Tests ◽  
Public Health Importance ◽  
Milk Samples ◽  
First Choice

Cow’s milk containing pathogenic bacteria is an important threat to the consumers. The objectives of the present study were to identify the bacterial agents of public health importance in milk samples (n=35) of different locations and to determine their sensitivity to different antibiotics. The milk samples were collected and transported aseptically and subsequently allowed for culture in bacteriological media, Gram’s staining and biochemical tests for the identification of bacterial species. The bacteria identified were Staphylococcus aureus, Escherichia coli and Salmonella typhi, and their prevalence, in case of vendor milk specimens (n=28), were 96.43%, 53.57% and 35.71% respectively, and of brand milk specimens (n=7), were 42.86 %, 28.57% and 0%, respectively. This suggests that cautionary measures should be taken for quality milk production and consumption. The antibiotic sensitivity test was done by disc diffusion method and the average inhibition zones, in case of Staphylococcus aureus, were 32 mm for oxytetracycline, 26 mm for amoxicillin, 35 mm for ciprofloxacin, 27 mm for cefotaxime, 30 mm for ceftriaxone, 30 mm for azithromycin, and 26 mm for erythromycin; in case of Escherichia coli, were 5 mm for oxytetracycline, 9 mm for amoxicillin, 22 mm for ciprofloxacin, 30 mm for cefotaxime, 31 mm for ceftriaxone, 15 mm for azithromycin, and 0 mm for erythromycin; in case of Salmonella typhi., were 25 mm for oxytetracycline, 24 mm for amoxicillin, 38 mm for ciprofloxacin, 31 mm for cefotaxime, 34 mm for ceftriaxone, 24 mm for azithromycin, and 0 mm for erythromycin. Therefore, ciprofloxacin and ceftriaxone may be the antibiotics of first choice, and cefotaxime and azithromycin may be the second choice among the test antibiotics for the treatment of illness caused by these bacteria.Asian J. Med. Biol. Res. December 2015, 1(3): 457-462

Ice nucleation activity of bacteria isolated from snow compared with organic and inorganic substrates

2008 ◽  
Vol 5 (6) ◽  
pp. 373 ◽  
Author(s):  
Roya Mortazavi ◽  
Christopher T. Hayes ◽  
Parisa A. Ariya
Keyword(s):  
Bacterial Species ◽  
Ice Nucleation ◽  
Detailed Knowledge ◽  
Bacterial Populations ◽  
Inorganic Aerosols ◽  
Ice Nucleators ◽  
Species Population ◽  
Nucleation Activity ◽  
Ice Nucleation Activity ◽  
Snow Samples

Environmental context. Biological ice nucleators have been found to freeze water at very warm temperatures. The potential of bio-aerosols to greatly influence cloud chemistry and microphysics is becoming increasingly apparent, yet detailed knowledge of their actual role in atmospheric processes is lacking. The formation of ice in the atmosphere has significant local, regional and global influence, ranging from precipitation to cloud nucleation and thus climate. Ice nucleation tests on bacteria isolated from snow and laboratory-grown bacteria, in comparison with those of known organic and inorganic aerosols, shed light on this issue. Abstract. Ice nucleation experiments on bacteria isolated from snow as well as grown in the laboratory, in comparison with those of known organic and inorganic aerosols, examined the importance of bio-aerosols on cloud processes. Snow samples were collected from urban and suburban sites in the greater Montreal region in Canada (45°28′N, 73°45′W). Among many snow bacterial isolates, eight types of bacterial species, none belonging to known effective ice nucleators such as Pseudomonas or Erwinia genera, were identified to show an intermediate range of ice nucleation activity (–12.9 ± 1.3°C to –17.5 ± 2.8°C). Comparable results were also obtained for molten snow samples and inorganic suspensions (kaolin and montmorillonite) of buffered water solutions. The presence of organic molecules (oxalic, malonic and succinic acids) had minimal effect (<2°C) on ice nucleation. Considering experimental limitations, and drawing from observation in snow samples of a variety of bacterial populations with variable ice-nucleation ability, a shift in airborne-species population may significantly alter glaciation processes in clouds.

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