scholarly journals Duo: A Signature Based Method to Batch-Analyze Functional Similarities of Proteins

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiao Fei ◽  
Qiuchun Li ◽  
John Elmerdahl Olsen ◽  
Xinan Jiao
Keyword(s):  
Genome Sequence ◽  
Protein Function ◽  
Pathogenic Bacteria ◽  
Bacterial Genome ◽  
Sequencing Data ◽  
Protein Coding ◽  
Virulence Proteins ◽  
Bacterial Genome Sequence ◽  
Associated Proteins

With the rapid advancement of sequencing technology, handling of large sequencing data to analyze for protein coding capacity and functionality of predicted proteins has become an urgent demand. There is a lack of simple and effective tools to functionally annotate large number of unknown proteins in a personalized and customized workflow. To address this, we developed Duo, which batch-analyze functional similarities of predicted proteins. Duo can screen query proteins with specific characteristics based on highly flexible and customizable reference inputs from the user. In the current study, Duo was applied to screen for virulence associated proteins in the genome-sequence of Salmonella Typhimurium. Based on the analysis, recommendation for choice of Seed_database in order to get a reasonable number of predicted proteins for further analysis, and recommendation for preparing a Reference_proteins set for Duo was given. Delta-bitscore analysis was shown to be useful tool to focus the follow-up on predicted proteins. A successful screen for virulence proteins in the bacterial genome-sequence was further performed in a selection of 32 pathogenic bacteria, documenting the ability of Duo to work on a broad collection of bacteria. We anticipate that Duo will be a useful auxiliary tool for personalized and customized protein function research in the future.

scholarly journals A Co-abundant Gene Analysis for Identification of Gut Microbial Strains Associated with Immune Responses to Oral Cholera Vaccine

2021 ◽  
Author(s):  
Fred J. Heller ◽  
Hasan Al Banna ◽  
M. Hasanul Kaisar ◽  
Denise Chac ◽  
Fahima Chowdhury ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Immune Responses ◽  
Bacterial Genome ◽  
Short Chain Fatty Acids ◽  
Metagenomic Sequencing ◽  
Vaccine Adjuvants ◽  
Sequencing Data ◽  
Bacterial Strains ◽  
Vaccine Response ◽  
Protein Coding

Background: Oral cholera vaccines (OCVs) are an important tool for reduction of the worldwide cholera burden, but some individuals who receive an OCV do not develop protective immune responses. The gut microbiota is a potential explanation for these differences. Components of the gut microbiota associated with differences in OCV response have not been identified. Results: We used metagenomic sequencing to identify predicted protein-coding genes in the gut microbiota at the time of OCV administration, and then measured immune responses to vaccination. Vaccine recipients were classified as OCV 'responders' if they developed a post-vaccination increase in memory B cell populations that produce IgA or IgG specific for cholera toxin and the V. cholerae O-specific polysaccharide. We next analyzed microbial genes seen at similar abundances across individual samples and classified these into co-abundant gene groupings (CAGs), and correlated CAGs with OCV responses. Next, to identify specific bacterial strains associated with OCV responses, we mapped CAGs to bacterial genomes and generated a 'priority score' for each strain detected in the study population. This score reflects both the number of CAGs aligning to a specific bacterial genome and the strength of the association between the CAGs and the vaccine response. This strain-level analysis revealed relationships between the gut microbiota and immune response to OCV that were not detected at the genus or species level. Bacterial strains which produce short-chain fatty acids and those with sphingolipid-containing cell membranes were correlated with more robust immune responses to vaccination. Conclusion: Our study demonstrates a method for translating metagenomic sequencing data into strain-specific results associated with a biological outcome. Using this approach, we identified strains for the study of bacterial-derived molecules or metabolites associated with immune responses; such agents might have potential utility as vaccine adjuvants.

scholarly journals Complete and Circularized Bacterial Genome Sequence of Gordonia sp. Strain X0973

2021 ◽  
Vol 10 (9) ◽  
Author(s):  
Christopher A. Gulvik ◽  
Dhwani Batra ◽  
Lori A. Rowe ◽  
Milli Sheth ◽  
Sarah Nobles ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Bacterial Genome ◽  
Illumina Miseq ◽  
Gram Positive ◽  
Coding Sequences ◽  
Content Type ◽  
Weakly Acid ◽  
Circular Genome ◽  
Bacterial Genome Sequence ◽  
Phylogenetic Neighbor

ABSTRACT Gordonia sp. strain X0973 is a Gram-positive, weakly acid-fast, aerobic actinomycete obtained from a human abscess with Gordonia araii NBRC 100433T as its closest phylogenetic neighbor. Here, we report using Illumina MiSeq and PacBio reads to assemble the complete and circular genome sequence of 3.75 Mbp with 3,601 predicted coding sequences.

Genome sequence analysis of the temperate bacteriophage TBP2 of the solvent producer Clostridium saccharoperbutylacetonicum N1-4 (HMT, ATCC 27021)

2020 ◽  
Vol 367 (14) ◽  
Author(s):  
Miriam A Schüler ◽  
Benjamin A Stegmann ◽  
Anja Poehlein ◽  
Rolf Daniel ◽  
Peter Dürre
Keyword(s):  
Sequence Analysis ◽  
Genome Sequence ◽  
Pathogenic Bacteria ◽  
Large Scale ◽  
Bacterial Genome ◽  
Abe Fermentation ◽  
Open Reading Frames ◽  
Temperate Bacteriophage ◽  
Acetone Butanol Ethanol ◽  
Solventogenic Clostridia

ABSTRACT The genus Clostridium consists of a diverse group of pathogenic and non-pathogenic bacteria. The non-pathogenic clostridia contain several solventogenic members of industrial importance, such as Clostridium acetobutylicum or C. beijerinckii. In the process of acetone–butanol–ethanol (ABE) fermentation, these strains are used in large scale fermentation plants since almost 100 years. Soon after establishment of the first plants, the fermentation processes suffered from different bacteriophage infections worldwide. A limited set of studies addressing bacteriophages in solventogenic clostridia have been conducted since then. In this study, we present the genome sequence of the temperate bacteriophage TBP2 of the solventogenic strain C. saccharoperbutylacetonicum N1-4 (HMT) that is used for ABE fermentation. The phage genome consists of 38 039 bp and includes 48 open reading frames. Sequence analysis indicates that the genome encloses random parts of the bacterial genome in addition to its own DNA. It represents the first fully sequenced genome of a temperate bacteriophage infecting solventogenic clostridia.

scholarly journals Optical mapping as a routine tool for bacterial genome sequence finishing

BMC Genomics ◽  
2007 ◽  
Vol 8 (1) ◽  
pp. 321 ◽  
Author(s):  
Phil Latreille ◽  
Stacie Norton ◽  
Barry S Goldman ◽  
John Henkhaus ◽  
Nancy Miller ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Optical Mapping ◽  
Bacterial Genome ◽  
Bacterial Genome Sequence

scholarly journals What does a bacterial genome sequence represent? Mis-assignment of MAFF 303099 to the genospecies Mesorhizobium loti

Microbiology ◽  
2002 ◽  
Vol 148 (11) ◽  
pp. 3330-3331 ◽  
Author(s):  
Sarah L. Turner ◽  
Xue-Xian Zhang ◽  
Fu-Di Li ◽  
J. Peter W. Young
Keyword(s):  
Genome Sequence ◽  
Bacterial Genome ◽  
Mesorhizobium Loti ◽  
Bacterial Genome Sequence

Bacterial genome sequence bagged

Science ◽  
1995 ◽  
Vol 269 (5223) ◽  
pp. 468-470 ◽  
Author(s):  
R Nowak
Keyword(s):  
Genome Sequence ◽  
Bacterial Genome ◽  
Bacterial Genome Sequence

scholarly journals Insights into the Human Virome Using CRISPR Spacers from Microbiomes

Viruses ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 479 ◽  
Author(s):  
Claudio Hidalgo-Cantabrana ◽  
Rosemary Sanozky-Dawes ◽  
Rodolphe Barrangou
Keyword(s):  
Pathogenic Bacteria ◽  
Human Microbiome ◽  
Adaptive Immune System ◽  
Metagenomic Data ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Adaptive Immune ◽  
Associated Proteins ◽  
Health And Disease ◽  
Generation Sequencing

Due to recent advances in next-generation sequencing over the past decade, our understanding of the human microbiome and its relationship to health and disease has increased dramatically. Yet, our insights into the human virome, and its interplay with important microbes that impact human health, is relatively limited. Prokaryotic and eukaryotic viruses are present throughout the human body, comprising a large and diverse population which influences several niches and impacts our health at various body sites. The presence of prokaryotic viruses like phages, has been documented at many different body sites, with the human gut being the richest ecological niche. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated proteins constitute the adaptive immune system of bacteria, which prevents attack by invasive nucleic acid. CRISPR-Cas systems function by uptake and integration of foreign genetic element sequences into the CRISPR array, which constitutes a genomic archive of iterative vaccination events. Consequently, CRISPR spacers can be investigated to reconstruct interplay between viruses and bacteria, and metagenomic sequencing data can be exploited to provide insights into host-phage interactions within a niche. Here, we show how the CRISPR spacer content of commensal and pathogenic bacteria can be used to determine the evidence of their phage exposure. This framework opens new opportunities for investigating host-virus dynamics in metagenomic data, and highlights the need to dedicate more efforts for virome sampling and sequencing.

scholarly journals Complete Genome Sequence of Acinetobacter baumannii ATCC 19606T, a Model Strain of Pathogenic Bacteria Causing Nosocomial Infection

2020 ◽  
Vol 9 (20) ◽  
Author(s):  
Taishi Tsubouchi ◽  
Masato Suzuki ◽  
Makoto Niki ◽  
Ken-Ichi Oinuma ◽  
Mamiko Niki ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Genome Sequence ◽  
Pathogenic Bacteria ◽  
Sequence Type ◽  
Sequencing Data ◽  
Beta Lactam ◽  
Genetic Studies ◽  
Content Type ◽  
Long Read ◽  
Model Strain

Acinetobacter baumannii ATCC 19606T, which is often used in genetic studies as a routine model microorganism, belongs to sequence type 52 (ST52), showing beta-lactam resistance. We present the complete 3.996-Mbp genome sequence (1 chromosome plus 2 plasmids), generated by combining long-read (MinION) and short-read (MiniSeq) sequencing data.

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