Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences

ABSTRACTFor decades, bacterial taxonomy has been based onin vitromolecular biology techniques and comparison of molecular marker sequences to measure the degree of genetic similarity and deduce phylogenetic relatedness of novel bacterial species to reference microbial taxa. Due to the advent of the genomic era, access to complete bacterial genome contents has become easier, thereby presenting the opportunity to precisely investigate the overall genetic diversity of microorganisms. Here, we describe a high-accuracy phylogenomic approach to assess the taxonomy of members of the genusBifidobacteriumand identify apparent misclassifications in current bifidobacterial taxonomy. The developed method was validated by the classification of seven novel taxa belonging to the genusBifidobacteriumby employing their overall genetic content. The results of this study demonstrate the potential of this whole-genome approach to become the gold standard for phylogenomics-based taxonomic classification of bacteria.IMPORTANCENowadays, next-generation sequencing has given access to genome sequences of the currently known bacterial taxa. The public databases constructed by means of these new technologies allowed comparison of genome sequences between microorganisms, providing information to perform genomic, phylogenomic, and evolutionary analyses. In order to avoid misclassifications in the taxonomy of novel bacterial isolates, new (bifido)bacterial taxons should be validated with a phylogenomic assessment like the approach presented here.

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Tandem repeats in complete bacterial genome sequences: sequence and structural analyses for comparative studies

Research in Microbiology ◽

10.1016/s0923-2508(99)00118-7 ◽

1999 ◽

Vol 150 (9-10) ◽

pp. 745-754 ◽

Cited By ~ 13

Author(s):

Edouard Yeramian ◽

Henri Buc

Keyword(s):

Comparative Studies ◽

Tandem Repeats ◽

Bacterial Genome ◽

Genome Sequences ◽

Complete Bacterial Genome

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Marine Network Protocols and Security Risks

Journal of Cybersecurity and Privacy ◽

10.3390/jcp1020013 ◽

2021 ◽

Vol 1 (2) ◽

pp. 239-251

Author(s):

Ky Tran ◽

Sid Keene ◽

Erik Fretheim ◽

Michail Tsikerdekis

Keyword(s):

Network Protocols ◽

Network Protocol ◽

Identification System ◽

Automated Identification ◽

Security Risks ◽

Domain Specific ◽

Protocol Security ◽

Challenges And Opportunities

Marine network protocols are domain-specific network protocols that aim to incorporate particular features within the specialized marine context that devices are implemented in. Devices implemented in such vessels involve critical equipment; however, limited research exists for marine network protocol security. In this paper, we provide an analysis of several marine network protocols used in today’s vessels and provide a classification of attack risks. Several protocols involve known security limitations, such as Automated Identification System (AIS) and National Marine Electronic Association (NMEA) 0183, while newer protocols, such as OneNet provide more security hardiness. We further identify several challenges and opportunities for future implementations of such protocols.

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Whole genome characterization of strains belonging to the Ralstonia solanacearum species complex and in silico analysis of TaqMan assays for detection in this heterogenous species complex

European Journal of Plant Pathology ◽

10.1007/s10658-020-02190-8 ◽

2021 ◽

Author(s):

Viola Kurm ◽

Ilse Houwers ◽

Claudia E. Coipan ◽

Peter Bonants ◽

Cees Waalwijk ◽

...

Keyword(s):

Ralstonia Solanacearum ◽

In Silico ◽

Species Complex ◽

Sequence Data ◽

In Silico Analysis ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequences ◽

Pcr Assays

AbstractIdentification and classification of members of the Ralstonia solanacearum species complex (RSSC) is challenging due to the heterogeneity of this complex. Whole genome sequence data of 225 strains were used to classify strains based on average nucleotide identity (ANI) and multilocus sequence analysis (MLSA). Based on the ANI score (>95%), 191 out of 192(99.5%) RSSC strains could be grouped into the three species R. solanacearum, R. pseudosolanacearum, and R. syzygii, and into the four phylotypes within the RSSC (I,II, III, and IV). R. solanacearum phylotype II could be split in two groups (IIA and IIB), from which IIB clustered in three subgroups (IIBa, IIBb and IIBc). This division by ANI was in accordance with MLSA. The IIB subgroups found by ANI and MLSA also differed in the number of SNPs in the primer and probe sites of various assays. An in-silico analysis of eight TaqMan and 11 conventional PCR assays was performed using the whole genome sequences. Based on this analysis several cases of potential false positives or false negatives can be expected upon the use of these assays for their intended target organisms. Two TaqMan assays and two PCR assays targeting the 16S rDNA sequence should be able to detect all phylotypes of the RSSC. We conclude that the increasing availability of whole genome sequences is not only useful for classification of strains, but also shows potential for selection and evaluation of clade specific nucleic acid-based amplification methods within the RSSC.

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Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community

Microbiology Resource Announcements ◽

10.1128/mra.01396-20 ◽

2021 ◽

Vol 10 (17) ◽

Author(s):

Quentin Lamy-Besnier ◽

Romain Koszul ◽

Laurent Debarbieux ◽

Martial Marbouty

Keyword(s):

Murine Model ◽

Bacterial Genome ◽

Chromosome Conformation Capture ◽

Genome Sequences ◽

Pacbio Sequencing ◽

High Quality ◽

Chromosome Conformation

ABSTRACT The Oligo-Mouse-Microbiota (OMM12) gnotobiotic murine model is an increasingly popular model in microbiota studies. However, following Illumina and PacBio sequencing, the genomes of the 12 strains could not be closed. Here, we used genomic chromosome conformation capture (Hi-C) data to reorganize, close, and improve the quality of these 12 genomes.

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Assessing the Robustness of Complete Bacterial Genome Segmentations

Comparative Genomics - Lecture Notes in Computer Science ◽

10.1007/978-3-642-16181-0_15 ◽

2010 ◽

pp. 173-187 ◽

Cited By ~ 1

Author(s):

Hugo Devillers ◽

Hélène Chiapello ◽

Sophie Schbath ◽

Meriem El Karoui

Keyword(s):

Bacterial Genome ◽

Complete Bacterial Genome

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Identification and Classification of Prokaryotes using whole-genome sequences.

Trends in the systematics of bacteria and fungi ◽

10.1079/9781789244984.0217 ◽

2021 ◽

pp. 217-230

Author(s):

Luis M. Rodriguez-R ◽

Ramon Rosselló-Móra ◽

Konstantinos T. Konstantinidis

Keyword(s):

Species Identification ◽

Special Focus ◽

Whole Genome ◽

Genome Sequences ◽

Future Directions ◽

The Past ◽

Major Genome ◽

Taxonomic Studies

Abstract This book chapter attempts to summarize the major findings from genome-based taxonomic studies in the past two decades, and briefly describe the major genome-based approaches currently available for species identification and classification with special focus on the 'uncultivated majority' and associated limitations, as well as outlines future directions towards a truly genome-based taxonomy for prokaryotes that will equally encompass cultured and uncultivated taxa. Importantly, the need for a system to catalogue uncultivated taxa is very urgent, because the genomes and ecological/functional data that are becoming available are already overwhelming, and alphanumeric identifiers and synonyms are creating confusion of Babylonian dimensions.

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