scholarly journals Comparative Genomics of Bacillus species and its Relevance in Industrial Microbiology

2013 ◽  
Vol 6 ◽  
pp. GEI.S12732 ◽  
Author(s):  
Archana Sharma ◽  
T. Satyanarayana
Keyword(s):  
Comparative Genomics ◽  
Molecular Biology ◽  
Genome Sequencing ◽  
High Throughput Sequencing ◽  
Bacterial Species ◽  
Bacillus Species ◽  
Genome Sequences ◽  
Wide Range ◽  
Sequencing Platforms ◽  
Analytical Tools

With the advent of high throughput sequencing platforms and relevant analytical tools, the rate of microbial genome sequencing has accelerated which has in turn led to better understanding of microbial molecular biology and genetics. The complete genome sequences of important industrial organisms provide opportunities for human health, industry, and the environment. Bacillus species are the dominant workhorses in industrial fermentations. Today, genome sequences of several Bacillus species are available, and comparative genomics of this genus helps in understanding their physiology, biochemistry, and genetics. The genomes of these bacterial species are the sources of many industrially important enzymes and antibiotics and, therefore, provide an opportunity to tailor enzymes with desired properties to suit a wide range of applications. A comparative account of strengths and weaknesses of the different sequencing platforms are also highlighted in the review.

scholarly journals Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing

mSphere ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Bhavna Hora ◽  
Naila Gulzar ◽  
Yue Chen ◽  
Konstantinos Karagiannis ◽  
Fangping Cai ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Vaccine Development ◽  
Consensus Sequence ◽  
Cost Effective ◽  
Recombination Analysis ◽  
Genome Sequences ◽  
Single Genome ◽  
Hiv 1

ABSTRACT High-throughput sequencing (HTS) has been widely used to characterize HIV-1 genome sequences. There are no algorithms currently that can directly determine genotype and quasispecies population using short HTS reads generated from long genome sequences without additional software. To establish a robust subpopulation, subtype, and recombination analysis workflow, we amplified the HIV-1 3′-half genome from plasma samples of 65 HIV-1-infected individuals and sequenced the entire amplicon (∼4,500 bp) by HTS. With direct analysis of raw reads using HIVE-hexahedron, we showed that 48% of samples harbored 2 to 13 subpopulations. We identified various subtypes (17 A1s, 4 Bs, 27 Cs, 6 CRF02_AGs, and 11 unique recombinant forms) and defined recombinant breakpoints of 10 recombinants. These results were validated with viral genome sequences generated by single genome sequencing (SGS) or the analysis of consensus sequence of the HTS reads. The HIVE-hexahedron workflow is more sensitive and accurate than just evaluating the consensus sequence and also more cost-effective than SGS. IMPORTANCE The highly recombinogenic nature of human immunodeficiency virus type 1 (HIV-1) leads to recombination and emergence of quasispecies. It is important to reliably identify subpopulations to understand the complexity of a viral population for drug resistance surveillance and vaccine development. High-throughput sequencing (HTS) provides improved resolution over Sanger sequencing for the analysis of heterogeneous viral subpopulations. However, current methods of analysis of HTS reads are unable to fully address accurate population reconstruction. Hence, there is a dire need for a more sensitive, accurate, user-friendly, and cost-effective method to analyze viral quasispecies. For this purpose, we have improved the HIVE-hexahedron algorithm that we previously developed with in silico short sequences to analyze raw HTS short reads. The significance of this study is that our standalone algorithm enables a streamlined analysis of quasispecies, subtype, and recombination patterns from long HIV-1 genome regions without the need of additional sequence analysis tools. Distinct viral populations and recombination patterns identified by HIVE-hexahedron are further validated by comparison with sequences obtained by single genome sequencing (SGS).

scholarly journals Identification of Novel Viruses in Amblyomma americanum , Dermacentor variabilis , and Ixodes scapularis Ticks

mSphere ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Rafal Tokarz ◽  
Stephen Sameroff ◽  
Teresa Tagliafierro ◽  
Komal Jain ◽  
Simon H. Williams ◽  
...  
Keyword(s):  
New York ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Ixodes Scapularis ◽  
The United States ◽  
Dermacentor Variabilis ◽  
Amblyomma Americanum ◽  
Animal Pathogens ◽  
Wide Range ◽  
Sequencing Platforms

ABSTRACT Ticks carry a wide range of known human and animal pathogens and are postulated to carry others with the potential to cause disease. Here we report a discovery effort wherein unbiased high-throughput sequencing was used to characterize the virome of 2,021 ticks, including Ixodes scapularis ( n = 1,138), Amblyomma americanum ( n = 720), and Dermacentor variabilis ( n = 163), collected in New York, Connecticut, and Virginia in 2015 and 2016. We identified 33 viruses, including 24 putative novel viral species. The most frequently detected viruses were phylogenetically related to members of the Bunyaviridae and Rhabdoviridae families, as well as the recently proposed Chuviridae . Our work expands our understanding of tick viromes and underscores the high viral diversity that is present in ticks. IMPORTANCE The incidence of tick-borne disease is increasing, driven by rapid geographical expansion of ticks and the discovery of new tick-associated pathogens. The examination of the tick microbiome is essential in order to understand the relationship between microbes and their tick hosts and to facilitate the identification of new tick-borne pathogens. Genomic analyses using unbiased high-throughput sequencing platforms have proven valuable for investigations of tick bacterial diversity, but the examination of tick viromes has historically not been well explored. By performing a comprehensive virome analysis of the three primary tick species associated with human disease in the United States, we gained substantial insight into tick virome diversity and can begin to assess a potential role of these viruses in the tick life cycle.

scholarly journals The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life

2021 ◽  
Vol 6 ◽  
pp. 254
Author(s):  
Victoria McKenna ◽  
John M. Archibald ◽  
Roxanne Beinart ◽  
Michael N. Dawson ◽  
Ute Hentschel ◽  
...  
Keyword(s):  
Large Scale ◽  
High Throughput Sequencing ◽  
Eukaryotic Cell ◽  
Genome Sequences ◽  
Wide Range ◽  
Microbial Symbionts ◽  
Symbiotic Organisms ◽  
High Quality Genome ◽  
Reference Genomes ◽  
Environmental Importance

We present the Aquatic Symbiosis Genomics Project, a global collaboration to generate high quality genome sequences for a wide range of eukaryotes and their microbial symbionts. Launched under the Symbiosis in Aquatic Systems Initiative of the Gordon and Betty Moore Foundation, the ASG Project brings together researchers from across the globe who hope to use these reference genomes to augment and extend their analyses of the dynamics, mechanisms and environmental importance of symbiosis. Applying large-scale, high-throughput sequencing and assembly technologies, the ASG collaboration will assemble and annotate the genomes of 500 symbiotic organisms – both the “hosts” and the microbial symbionts with which they associate. These data will be released openly to benefit all who work on symbiosis, from conservation geneticists to those interested in the origin of the eukaryotic cell.

The emergence of inter-clade hybrid SARS-CoV-2 lineages revealed by 2D nucleotide variation mapping

2020 ◽  
Author(s):  
Hai-Long Wang
Keyword(s):  
Big Data ◽  
Genome Sequencing ◽  
High Throughput ◽  
Mayo Clinic ◽  
High Throughput Sequencing ◽  
Genetic Recombination ◽  
Whole Genome ◽  
Nucleotide Variation ◽  
Genome Sequences ◽  
New Era

ABSTRACTI performed whole-genome sequencing on SARS-CoV-2 collected from COVID-19 samples at Mayo Clinic Rochester in mid-April, 2020, generated 85 consensus genome sequences and compared them to other genome sequences collected worldwide. I proposed a novel illustrating method using a 2D map to display populations of co-occurring nucleotide variants for intra- and inter-viral clades. This method is highly advantageous for the new era of “big-data” when high-throughput sequencing is becoming readily available. Using this method, I revealed the emergence of inter-clade hybrid SARS-CoV-2 lineages that are potentially caused by homologous genetic recombination.

scholarly journals Complete Genome Sequences of 12 Species of Stable Defined Moderately Diverse Mouse Microbiota 2: TABLE 1 

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Yasuhiro Uchimura ◽  
Madeleine Wyss ◽  
Sandrine Brugiroux ◽  
Julien P. Limenitakis ◽  
Bärbel Stecher ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Bacterial Species ◽  
Whole Genome ◽  
Genome Sequences ◽  
Pacbio Sequencing ◽  
Sequencing Platform ◽  
Germ Free

We report here the complete genome sequences of 12 bacterial species of stable defined moderately diverse mouse microbiota 2 (sDMDMm2) used to colonize germ-free mice with defined microbes. Whole-genome sequencing of these species was performed using the PacBio sequencing platform yielding circularized genome sequences of all 12 species.

scholarly journals Genome evolution in trypanosomatid parasites

Parasitology ◽  
2014 ◽  
Vol 142 (S1) ◽  
pp. S40-S56 ◽  
Author(s):  
ANDREW P. JACKSON
Keyword(s):  
Comparative Genomics ◽  
Genome Evolution ◽  
Genome Sequencing ◽  
Molecular Mechanisms ◽  
Genome Sequences ◽  
Parasitic Lifestyle ◽  
Trypanosomatid Parasites ◽  
The Many ◽  
Species Specific ◽  
Fresh Impetus

SUMMARYA decade of genome sequencing has transformed our understanding of how trypanosomatid parasites have evolved and provided fresh impetus to explaining the origins of parasitism in the Kinetoplastida. In this review, I will consider the many ways in which genome sequences have influenced our view of genomic reduction in trypanosomatids; how species-specific genes, and the genomic domains they occupy, have illuminated the innovations in trypanosomatid genomes; and how comparative genomics has exposed the molecular mechanisms responsible for innovation and adaptation to a parasitic lifestyle.

scholarly journals Precise Species Identification and Taxonomy Update for the Genus Kluyvera With Reporting Kluyvera sichuanensis sp. nov.

2020 ◽  
Vol 11 ◽  
Author(s):  
Lina Liu ◽  
Yu Feng ◽  
Li Wei ◽  
Fu Qiao ◽  
Zhiyong Zong
Keyword(s):  
Species Identification ◽  
Genome Sequencing ◽  
Dna Hybridization ◽  
Novel Species ◽  
Bacterial Species ◽  
Genome Sequences ◽  
Bacterial Genomes ◽  
Carbapenem Resistant ◽  
The Family ◽  
Human Infections

Kluyvera is a genus within the family Enterobacteriaceae and can cause various human infections but remains poorly studied. A carbapenem-resistant blaNDM–1-carrying Kluyvera strain 090646T was isolated from a hospital sink in Chengdu, Sichuan province, China. Whole genome sequencing of the strain revealed that it had 28.2 to 42.3% in silico DNA-DNA hybridization (isDDH) scores and 84.15 to 90.10% average nucleotide identity (ANI) values with other Kluyvera species. Both values are well below the ≥ 70.0% isDDH and ≥ 95–96% ANI cutoffs to define bacterial species, suggesting that the strain represents a novel species of the genus Kluyvera, for which the name Kluyvera sichuanensis. nov. is proposed. Type strain of K. sichuanensis is 090646T (=GDMCC 1.1872T =KCTC 82166T). Strain 090646T can be differentiated from other Kluyvera species by its ability to utilize D-sorbitol but not β-galactosidase (ONPG), D-mannose, glycerin, raffinose, nor sucrose. There were 47 genome sequences labeled as Kluyvera in GenBank, which were curated for precise species identification. Only 33 of the 47 genomes were indeed of Kluyvera and four novel Kluyvera genomospecies were identified, highlighting that the species assignation of bacterial genomes in GenBank need to be curated. Genome sequencing for more strains is required to understand the genus Kluyvera.

scholarly journals Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing

mBio ◽  
2014 ◽  
Vol 5 (3) ◽  
Author(s):  
Jason T. Ladner ◽  
Brett Beitzel ◽  
Patrick S. G. Chain ◽  
Matthew G. Davenport ◽  
Eric Donaldson ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Cost Benefit ◽  
Genome Sequences ◽  
Common Component ◽  
Viral Genomes ◽  
Genome Finishing ◽  
Sequencing Technologies ◽  
Trade Offs ◽  
Sequencing Platforms

ABSTRACT Thanks to high-throughput sequencing technologies, genome sequencing has become a common component in nearly all aspects of viral research; thus, we are experiencing an explosion in both the number of available genome sequences and the number of institutions producing such data. However, there are currently no common standards used to convey the quality, and therefore utility, of these various genome sequences. Here, we propose five “standard” categories that encompass all stages of viral genome finishing, and we define them using simple criteria that are agnostic to the technology used for sequencing. We also provide genome finishing recommendations for various downstream applications, keeping in mind the cost-benefit trade-offs associated with different levels of finishing. Our goal is to define a common vocabulary that will allow comparison of genome quality across different research groups, sequencing platforms, and assembly techniques.

scholarly journals Staphylococcus sciuri C2865 from a distinct subspecies cluster as reservoir of the novel transferable trimethoprim resistance gene, dfrE, and adaptation driving mobile elements

2020 ◽  
Author(s):  
Elena Gómez-Sanz ◽  
Jose Manuel Haro-Moreno ◽  
Slade O. Jensen ◽  
Juan José Roda-García ◽  
Mario López-Pérez
Keyword(s):  
Comparative Genomics ◽  
Whole Genome Sequencing ◽  
Resistance Gene ◽  
Genome Sequencing ◽  
Bacterial Species ◽  
Multidrug Resistant ◽  
Ecological Niches ◽  
Whole Genome ◽  
Genome Plasticity ◽  
Host Tropism

AbstractFour methicillin-resistant Staphylococcus sciuri (MRSS) strains isolated from stranded dogs showed trimethoprim (TMP) resistance, while all staphylococcal TMP resistant dihydrofolate reductase genes (dfr) were negative. An in-depth whole-genome-sequencing approach on strain C2865 was followed for resistome and mobilome profiling, and for comparative genomics with S. sciuri group available genomes. Lack of species host tropism was observed, with MRSS C2865 placed at a separate sub-branch within S. sciuri species, close to the average nucleotide identity to be considered a different species (95-96%). S. sciuri proved a pronounced accessory genome (73% of genes), while MRSS C2865 distinctively harboured the highest total gene number and highest number of unique genes, with 75% associated to the recognised mobilome. A novel multidrug resistance mosaic plasmid (pUR2865-34) with several adaptive, mobilization (oriT mimic) and segregational stability (Type Ib par system) traits and two small single resistance plasmids were identified. Plasmid pUR2865-34 enclosed a novel staphylococcal TMP resistance gene, named dfrE, which shared highest identity with dfr of soil-related Paenibacillus anaericanus (68%). DfrE conferred high-level TMP resistance in S. aureus and Escherichia coli. Database searches revealed that dfrE was formerly denoted (dfr_like) in an Exiguobacterium spp. from a fish-farm sediment and that was present but unnoticed in several staphylococcal and onemacrococcal genomes with different epidemiological backgrounds. Novel chromosomal site-specific mobile islands with resourceful traits were identified, including a multidrug-resistant SCCmec cassette lacking cassette chromosome recombinase (Ccr) genes, a staphylococcal pathogenicity island of the SaPI4 family, and three unrelated siphoviridae prophages, two of which enclosed recombinases with the conserved Ccr-motif. We reveal a novel staphylococcal TMP resistance dfrE gene already present in diverse bacterial backgrounds. We confirm the ubiquity, high genome plasticity and low host tropism of S. sciuri highlighting its role as a resourceful reservoir for evolutionary novel features contributing to its extraordinary versatility and adaptability.Author summaryStaphylococcus spp. are ubiquitous bacteria present in diverse ecological niches, including humans, animals and the environment. They are clinically relevant opportunistic pathogens and are notorious for their ability to acquire antimicrobial resistance (AMR) and virulence properties, resulting in a significant impact for Public Health. Mobile genetic elements (MGEs) play a central role in this adaptation process and are a means to transfer genetic information across bacterial species. Staphylococcus sciuri represents one of the most ancestral species in the genus and has been suggested a reservoir for AMR genes. Here, following a refined whole genome sequencing approach we determined the entire genome of an animal and environment-associated multidrug resistant (MDR) S. sciuri strain uncovering a novel acquired staphylococcal TMP resistance gene already spread among different bacterial species from different epidemiological backgrounds. We also reveal several additional MGEs, including a novel MDR mobilizable plasmid that encloses several adaptive and stabilization features, and novel mobilizable chromosomal islands with resourceful traits, including three unrelated prophages. Together with comparative genomics, we confirm the ubiquity, high intraspecies heterogenicity, genome plasticity and low host tropism of this species, highlighting its role as resourceful reservoir for evolutionary novel features contributing to its extraordinary versatility and adaptability.

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