scholarly journals Whole Genome Sequence of Sphingobacterium sp. G1-14, a Strain With Effective Paichongding Biodegradation

2019 ◽  
Vol 10 (1) ◽  
pp. 58
Author(s):  
Peng Yin ◽  
Suyu Liu ◽  
Xingke Wu
Keyword(s):  
Mutant Strain ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Original Strain ◽  
Illumina Hiseq ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Sequencing Platform ◽  
Third Generation Sequencing ◽  
Phylogenomic Analyses

In this study, we obtained a Paichongding (RR/SS-IPP) degrading Sphingobacterium sp. G1-14 by UV irradiation of the original strain G1-13. This new mutant strain showed excellent RR/SS-IPP degradation performance, and the degradation of ratio was up to 30 per cent after 7 days. Subsequently, we determined the mutant strain G 1-14 as Sphingobacterium based on the phylogenomic analyses. The circular chromosome of Sphingobacterium sp. G1-14 was presented in this paper by Illumina Hiseq platform combined with a third-generation sequencing platform. 5583 protein-coding sequences of the complete genome sequence were obtained, which is beneficial to deduced genes related to RR/SS-IPP degradation.

scholarly journals Whole-Genome Sequence of Rummeliibacillus stabekisii Strain PP9 Isolated from Antarctic Soil

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Fábio Faria da Mota ◽  
Renata Estebanez Vollú ◽  
Diogo Jurelevicius ◽  
Lucy Seldin
Keyword(s):  
Soil Sample ◽  
Genome Sequence ◽  
Noncoding Rnas ◽  
Whole Genome Sequence ◽  
Trna Genes ◽  
Whole Genome ◽  
Antarctic Soil ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Protein Coding Genes

The whole genome of Rummeliibacillus stabekisii PP9, isolated from a soil sample from Antarctica, consists of a circular chromosome of 3,412,092 bp and a circular plasmid of 8,647 bp, with 3,244 protein-coding genes, 12 copies of the 16S-23S-5S rRNA operon, 101 tRNA genes, and 6 noncoding RNAs (ncRNAs).

scholarly journals Whole-Genome Sequence of Leuconostoc mesenteroides LT-38, a Non-Spore-Forming Gram-Positive Lactic Acid Bacterium

2017 ◽  
Vol 5 (31) ◽  
Author(s):  
Shiro Kato ◽  
Tadao Oikawa
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacterium ◽  
Genome Sequence ◽  
Leuconostoc Mesenteroides ◽  
Whole Genome Sequence ◽  
Gram Positive ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Content Type ◽  
Putative Protein

ABSTRACT The present study reports the complete genome sequence of Leuconostoc mesenteroides strain LT-38, which is a non-spore-forming Gram-positive lactic acid bacterium. The genome is composed of a 2,022,184-bp circular chromosome and contains 2,005 putative protein-coding genes.

scholarly journals The complete genome sequence of a bile-isolated Stenotrophomonas maltophilia ZT1

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Min Zhang ◽  
Lixiang Li ◽  
Hongwei Pan ◽  
Tao Zhou
Keyword(s):  
Genome Sequence ◽  
Stenotrophomonas Maltophilia ◽  
Gc Content ◽  
Genomic Analysis ◽  
Whole Genome Sequence ◽  
Functional Verification ◽  
Comparative Genomic ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Human Bile

Abstract Background Stenotrophomonas maltophilia is one of the most frequently isolated opportunistic pathogens that can cause infections in humans. Many researches concerned the mechanism of antibiotic resistance displayed by S. maltophilia, however, the mechanism of its pathogenesis and its adaptation to special niches, such as bile, remain unclear. Results In this study, the S. maltophilia strain ZT1 was isolated from human bile. Its genome was sequenced and a circular chromosome of 4,391,471 bp was obtained with a GC content of 66.51%. There were 3962 protein-coding sequences, 7 rRNAs and 74 tRNAs in the chromosome. Compared with Virulence Factor Database, we identified more than 500 candidate virulence genes including genes encoding fimbrial assembly protein, enterobactin synthesis pathway proteins, efflux pumps, and the DNA and/or proteins secretion system in the genome of strain ZT1. Additionally, there were at least 22 genes related to bile adaption, including emrAB, acrRAB, galU, rfbC, tolC and mdtABC. Conclusions This is the first study to reveal the whole genome sequence of the ZT1 strain of S. maltophilia isolated from human bile. We identified hundreds virulence factors and 22 bile adaptation-related genes in the genome of the S. maltophilia strain ZT1. Further comparative genomic analysis and functional verification would aid in understanding the pathogenesis and bile adaptation of S. maltophilia.

scholarly journals Whole-Genome Sequence of Mycoplasma bovis Strain Ningxia-1

2018 ◽  
Vol 6 (4) ◽  
Author(s):  
Peng Sun ◽  
Haifeng Luo ◽  
Xin Zhang ◽  
Jingyi Xu ◽  
Yanan Guo ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Single Molecule ◽  
Whole Genome Sequence ◽  
Mycoplasma Bovis ◽  
Sequencing Technology ◽  
Circular Chromosome ◽  
A Genome ◽  
Variable Surface ◽  
Integrative Conjugative Elements ◽  
Single Circular Chromosome

ABSTRACT A genome sequence of the Mycoplasma bovis Ningxia-1 strain was tested by Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing technology. The strain was isolated from a lesioned calf lung in 2013 in Pengyang, Ningxia, China. The single circular chromosome of 1,033,629 bp shows differences between complete Mycoplasma bovis genome in insertion-like sequences (ISs), integrative conjugative elements (ICEs), lipoproteins (LPs), variable surface lipoproteins (VSPs), pathogenicity islands (PAIs), etc.

scholarly journals Whole-Genome Sequence of Lactobacillus salivarius DJ-sa-01, Isolated from Chicken Small Intestine

2018 ◽  
Vol 7 (14) ◽  
Author(s):  
Dongjun Kim ◽  
Mun-Ju Cho ◽  
Seungchan Cho ◽  
Yongjun Lee ◽  
Sung June Byun ◽  
...  
Keyword(s):  
Small Intestine ◽  
Genome Sequence ◽  
Probiotic Strain ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Lactobacillus Salivarius ◽  
Circular Chromosome ◽  
Content Type ◽  
Single Circular Chromosome

We have identified the whole-genome sequence of Lactobacillus salivarius DJ-sa-01, a potential probiotic strain for poultry, isolated from a chicken small intestine. We used the PacBio and Illumina platforms to obtain the sequence of the entire single circular chromosome.

scholarly journals Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine

2017 ◽  
Author(s):  
Jacoline Gerritsen ◽  
Bastian Hornung ◽  
Bernadette Renckens ◽  
Sacha A.F.T. van Hijum ◽  
Vitor A.P. Martins dos Santos ◽  
...  
Keyword(s):  
Amino Acids ◽  
Small Intestine ◽  
Short Chain Fatty Acids ◽  
Limited Capacity ◽  
Illumina Hiseq ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Mate Pair ◽  
Simple Carbohydrates

Background. The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host. Methods. The genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired end, mate pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) while growing on three different carbohydrate sources and short chain fatty acids were measured via HPLC. Results. Hence, we present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed pinpointing the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides. Discussion. This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available and uncovered potential mechanisms for competition with mucus-degrading microbes.

scholarly journals Complete Genome Sequence of Thiohalobacter sp. Strain COW1, Isolated from Activated Sludge Treating Coke Oven Wastewater

2021 ◽  
Vol 10 (7) ◽  
Author(s):  
Kentaro Miyazaki ◽  
Hikaru Suenaga ◽  
Mamoru Oshiki ◽  
Shuichi Kawano ◽  
Toshikazu Fukushima
Keyword(s):  
Activated Sludge ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Coke Oven ◽  
Rrna Genes ◽  
Trna Genes ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Degrading Bacterium

ABSTRACT A thiocyanate-degrading bacterium, Thiohalobacter sp. strain COW1, was isolated from activated sludge treating coke oven wastewater, and the complete genome sequence was determined. COW1 contained a single circular chromosome (3.23 Mb; G+C content, 63.4%) in which 2,788 protein-coding genes, 39 tRNA genes, and 3 rRNA genes were identified.

scholarly journals Whole-Genome Sequence of SARS-CoV-2 Isolate Siena-1/2020

2020 ◽  
Vol 9 (39) ◽  
Author(s):  
Maria Grazia Cusi ◽  
David Pinzauti ◽  
Claudia Gandolfo ◽  
Gabriele Anichini ◽  
Gianni Pozzi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Severe Acute Respiratory Syndrome ◽  
Genome Sequence ◽  
Amino Acid Change ◽  
Amplicon Sequencing ◽  
Spike Protein ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Nanopore Sequencing ◽  
Protein Coding

ABSTRACT The complete genome sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolate Siena-1/2020 was obtained by Nanopore sequencing, combining the direct RNA sequencing and amplicon sequencing approaches. The isolate belongs to the B1.1 lineage, which is prevalent in Europe, and contains a mutation in the spike protein coding sequence leading to the D614G amino acid change.

scholarly journals Complete Genome Sequence of Bifidobacterium longum Strain Jih1, Isolated from Human Feces

2020 ◽  
Vol 9 (22) ◽  
Author(s):  
Hikaru Inoue ◽  
Sayaka Shibata ◽  
Konosuke Ii ◽  
Joe Inoue ◽  
Shinji Fukuda ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Bifidobacterium Longum ◽  
Human Feces ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes

ABSTRACT We report the complete genome sequence of Bifidobacterium longum strain Jih1, isolated from human feces. The assembled genome comprised one circular chromosome of 2.37 Mb. The chromosome harbors 1,941 protein-coding genes.

scholarly journals Complete Genome Sequence of the Live Attenuated Vaccine StrainBrucella melitensisRev.1

2018 ◽  
Vol 6 (12) ◽  
pp. e00175-18 ◽  
Author(s):  
Mali Salmon-Divon ◽  
Menachem Banai ◽  
Svetlana Bardenstein ◽  
Shlomo E. Blum ◽  
David Kornspan
Keyword(s):  
Genome Sequence ◽  
Brucella Melitensis ◽  
Small Ruminants ◽  
Essential Elements ◽  
Whole Genome Sequence ◽  
Original Strain ◽  
Live Attenuated Vaccine ◽  
Content Type ◽  
Live Attenuated Vaccines ◽  
Control Programs

ABSTRACTLive attenuated vaccines are essential elements in control programs for the prevention of brucellosis. Here, we report the whole-genome sequence of the original ElbergBrucella melitensisRev.1 vaccine strain, passage 101 (1970). Commercial lines of the original strain have been successfully used in small ruminants worldwide.

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