scholarly journals Characterization of genomic, physiological, and probiotic features of Lactiplantibacillus plantarum DY46 strain isolated from Turkish fermented turnip juice (Shalgam)

2021 ◽  
Author(s):  
Ahmet E. Yetiman ◽  
Abdullah KESKİN ◽  
Busra Nur DARENDELI ◽  
Seyfullah Enes KOTIL ◽  
Fatih ORTAKCI ◽  
...  
Keyword(s):  
Alcoholic Beverage ◽  
Draft Genome ◽  
Gc Content ◽  
Illumina Miseq ◽  
Trna Genes ◽  
Circular Chromosome ◽  
Acid And Bile Tolerance ◽  
Miseq Platform ◽  
Pass Through

Abstract A new Lb. plantarum strain DY46 was isolated from a traditionally fermented non-alcoholic beverage called shalgam from the Southern region of Anatolia following incubation on MRS agar at 30°C for 5 days. DY46 is gram-positive, short rod and catalase-negative. This bacterium fermented 22 of the 49 substrates tested on API CH50 fermentation panels. Whole-genome sequencing was performed using the Illumina Miseq platform to learn more about the metabolic capabilities of DY46. The sequences were assembled into a 3.32 Mb draft genome using PATRIC 3.6.8. consisting of 153 contigs, and preliminary genome annotation was performed using the RAST algorithm. The DY46 genome consists of a single circular chromosome of 3,332,827 bp that is predicted to carry 3219 genes, including 61 tRNA genes, 2 rRNA operons. The genome has a GC content of 44.3% includes 98 predicted pseudogenes, 25 complete or partial transposases and 3 intact prophages. DY46 genome also predicted to carry genes of Plantaricin-E, Plantaricin-F and Plantaricin-K showing the antimicrobial potential of this bacterium which can be linked-to in vitro antagonism tests that DY46 can inhibit Salmonella Typimirium ATCC14028, Klebsiella pneumonie ATCC13883, and Proteus vulgaris ATCC8427. The acid and bile tolerance of DY46 revealed this strain could potentially pass through the stomach and reach into the gut to provide probiotic therapeutic affects on health.

scholarly journals Draft Genome Sequence of Bacillus subtilis subsp. subtilis MD 32, Isolated from the Korean Fermented Food Kimchi

2021 ◽  
Vol 10 (3) ◽  
Author(s):  
Ji-Young Lee ◽  
Gyu-Sung Cho ◽  
Charles M. A. P. Franz ◽  
Dae-Ook Kang
Keyword(s):  
Bacillus Subtilis ◽  
Draft Genome ◽  
Noncoding Rnas ◽  
Gc Content ◽  
Illumina Miseq ◽  
Fermented Food ◽  
Content Type ◽  
Illumina Miseq Platform ◽  
Miseq Platform ◽  
Subtilis Subsp

ABSTRACT Bacillus subtilis subsp. subtilis MD 32 was isolated from kimchi. The strain was sequenced using an Illumina MiSeq platform, and the genome size was 4,238,856 bp with a GC content of 43.41 mol%. The genome encoded 4,396 proteins, with 45 tRNAs, 6 rRNAs, and 5 noncoding RNAs.

scholarly journals Draft Genome Sequence of Ligilactobacillus salivarius TUCO-L2, Isolated from Lama glama Milk

2020 ◽  
Vol 9 (32) ◽  
Author(s):  
Leonardo Albarracin ◽  
Sandra Quilodrán-Vega ◽  
Kohtaro Fukuyama ◽  
Mikado Tomokiyo ◽  
M. Aminul Islam ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Illumina Miseq ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Content Type ◽  
A Genome ◽  
Miseq Platform ◽  
Lama Glama

ABSTRACT Ligilactobacillus salivarius TUCO-L2 was isolated from llama milk in Bio-Bio, Chile, and sequenced with the Illumina MiSeq platform. TUCO-L2 genome sequencing revealed a genome size of 1,600,747 bp with 1,691 protein-coding genes and a GC content of 33%. This draft genome sequence will contribute to a better understanding of the microbiome of llama milk.

scholarly journals A genomic perspective on the potential of termite-associated Cellulosimicrobium cellulans MP1 as producer of plant biomass-acting enzymes and exopolysaccharides

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11839
Author(s):  
Nguyen Thi-Hanh Vu ◽  
Tung Ngoc Quach ◽  
Xuan Thi-Thanh Dao ◽  
Ha Thanh Le ◽  
Chi Phuong Le ◽  
...  
Keyword(s):  
Plant Biomass ◽  
Draft Genome ◽  
Gc Content ◽  
Rrna Genes ◽  
Trna Genes ◽  
Rrna Gene ◽  
Whole Genome ◽  
Potential Candidate ◽  
Circular Chromosome ◽  
Cellulosimicrobium Cellulans

Background Lignocellulose is a renewable and enormous biomass resource, which can be degraded efficiently by a range of cocktails of carbohydrate-active enzymes secreted by termite gut symbiotic bacteria. There is an urgent need to find enzymes with novel characteristics for improving the conversion processes in the production of lignocellulosic-based products. Although various studies dedicated to the genus Cellulosimicrobium as gut symbiont, genetic potential related to plant biomass-acting enzymes and exopolysaccharides production has been fully untapped to date. Methods The cellulolytic bacterial strain MP1 was isolated from termite guts and identified to the species level by phenotypic, phylogenetic, and genomic analysis. To further explore genes related to cellulose and hemicellulose degradation, the draft genome of strain MP1 was obtained by using whole-genome sequencing, assembly, and annotation through the Illumina platform. Lignocellulose degrading enzymes and levan production in the liquid medium were also examined to shed light on bacterial activities. Results Among 65 isolates obtained, the strain MP1 was the most efficient cellulase producer with cellulase activity of 0.65 ± 0.02 IU/ml. The whole genome analysis depicted that strain MP1 consists of a circular chromosome that contained 4,580,223 bp with an average GC content of 73.9%. The genome comprises 23 contigs including 67 rRNA genes, three tRNA genes, a single tmRNA gene, and 4,046 protein-coding sequences. In support of the phenotypic identification, the 16S rRNA gene sequence, average nucleotide identity, and whole-genome-based taxonomic analysis demonstrated that the strain MP1 belongs to the species Cellulosimicrobium cellulans. A total of 30 genes related to the degradation of cellulases and hemicellulases were identified in the C. cellulans MP1 genome. Of note, the presence of sacC1-levB-sacC2-ls operon responsible for levan and levan-type fructooligosaccharides biosynthesis was detected in strain MP1 genome, but not with closely related C. cellulans strains, proving this strain to be a potential candidate for further studies. Endoglucanases, exoglucanases, and xylanase were achieved by using cheaply available agro-residues such as rice bran and sugar cane bagasse. The maximum levan production by C. cellulans MP1 was 14.8 ± 1.2 g/l after 20 h of cultivation in media containing 200 g/l sucrose. To the best of our knowledge, the present study is the first genome-based analysis of a Cellulosimicrobium species which focuses on lignocellulosic enzymes and levan biosynthesis, illustrating that the C. cellulans MP1 has a great potential to be an efficient platform for basic research and industrial exploitation.

scholarly journals Draft Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas pseudoalcaligenes KB-10

2021 ◽  
Vol 10 (20) ◽  
Author(s):  
M. M. A. Khan ◽  
Jin Duan ◽  
Bernard R. Glick ◽  
Patrick M. Finnegan ◽  
Saleh A. Kabli ◽  
...  
Keyword(s):  
Plant Growth ◽  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Circular Chromosome ◽  
Pseudomonas Pseudoalcaligenes ◽  
Content Type ◽  
Plant Growth Promoting ◽  
Growth Promoting

ABSTRACT Pseudomonas pseudoalcaligenes KB-10 can enhance salinity tolerance in coriander plants. We report a draft genome sequence of P. pseudoalcaligenes KB-10, comprising a 5,241,174-bp circular chromosome containing 4,921 genes, with a GC content of 62.97%.

scholarly journals Complete Genome Sequence of the Type Strain Pectobacterium punjabense SS95, Isolated from a Potato Plant with Blackleg Symptoms

2020 ◽  
Vol 9 (32) ◽  
Author(s):  
Sohaib Sarfraz ◽  
Saïd Oulghazi ◽  
Jérémy Cigna ◽  
Shahbaz Talib Sahi ◽  
Kashif Riaz ◽  
...  
Keyword(s):  
Complete Genome ◽  
Type Strain ◽  
Gc Content ◽  
Illumina Miseq ◽  
Blackleg Disease ◽  
Circular Chromosome ◽  
Content Type ◽  
Potato Plants ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

ABSTRACT Pectobacterium punjabense is a newly described species causing blackleg disease in potato plants. Therefore, by the combination of long (Oxford Nanopore Technologies, MinION) and short (Illumina MiSeq) reads, we sequenced the complete genome of P. punjabense SS95T, which contains a circular chromosome of 4.793 Mb with a GC content of 50.7%.

scholarly journals Draft Genome Sequence of Bacillus pacificus KVCMST-8A-12, Isolated from a Marine Sediment Sample from the Kanyakumari Coast, India

2021 ◽  
Vol 10 (50) ◽  
Author(s):  
Asha Santhi ◽  
Venkatesh Subramanian ◽  
Krishnaveni Muthan
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Content Type ◽  
Marine Sediment Sample

A DNase-producing Bacillus pacificus strain was isolated, and the whole-genome sequence is reported in this paper. The draft genome sequence of Bacillus pacificus KVCMST-8A-12 constitutes 2.4 Gbp of raw reads, with a GC content of 35.24%. In total, 5,661 protein-coding genes, 64 tRNA genes, and 4 rRNA genes were predicted.

scholarly journals Draft Genome Sequence of Anoxybacillus sp. Strain UARK-01, a New Thermophilic Lignin-Utilizing Bacterium Isolated from Soil in Arkansas, USA

2017 ◽  
Vol 5 (30) ◽  
Author(s):  
Thamir H. Alkahem Albalawi ◽  
Douglas D. Rhoads ◽  
Ravi D. Barabote
Keyword(s):  
United States ◽  
Genome Sequence ◽  
De Novo ◽  
Draft Genome ◽  
Illumina Miseq ◽  
The United States ◽  
Soil Bacterium ◽  
Lignocellulose Degradation ◽  
Illumina Miseq Platform ◽  
Miseq Platform

ABSTRACT The draft genome of Anoxybacillus sp. strain UARK-01, a novel lignin-utilizing thermophilic soil bacterium, represents the first sequence of an Anoxybacillus isolate from the United States. The genome was sequenced using the Illumina MiSeq platform, de novo assembled using SeqMan NGen, and annotated at NCBI. The genome sequence revealed genes for laccase and lignocellulose degradation enzymes.

scholarly journals Draft Genome Sequence of Heavy Metal-Resistant Soil Bacterium Serratia marcescens S2I7, Which Has the Ability To Degrade Polyaromatic Hydrocarbons

2017 ◽  
Vol 5 (48) ◽  
Author(s):  
Rhitu Kotoky ◽  
L. Paikhomba Singha ◽  
Piyush Pandey
Keyword(s):  
Heavy Metal ◽  
Serratia Marcescens ◽  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Metal Resistance ◽  
Draft Genome Sequence ◽  
Circular Chromosome ◽  
Degrading Bacterium ◽  
Heavy Metal Resistant

ABSTRACT Serratia marcescens S2I7 is a heavy metal-resistant, polyaromatic hydrocarbon-degrading bacterium isolated from petroleum-contaminated sites. The genome contains one circular chromosome (5,241,555 bp; GC content 60.1%) with 4,533 coding sequences. The draft genome sequence includes specific genetic elements for degradation of hydrocarbons and for heavy metal resistance.

scholarly journals Genome Sequence of Brevibacillus brevis HK544, an Antimicrobial Bacterium Isolated from Soil in Daejeon, South Korea

2021 ◽  
Vol 10 (31) ◽  
Author(s):  
Bomin Kim ◽  
Yeong Seok Kim ◽  
Jae Woo Han ◽  
Gyung Ja Choi ◽  
Hun Kim
Keyword(s):  
Antimicrobial Activity ◽  
Phytophthora Infestans ◽  
Genome Sequence ◽  
Plant Pathogens ◽  
Erwinia Amylovora ◽  
Draft Genome ◽  
Gc Content ◽  
Circular Chromosome ◽  
Content Type ◽  
Brevibacillus Brevis

The Brevibacillus brevis HK544 strain, which was isolated from soil, exhibited antimicrobial activity against plant pathogens such as Botrytis cinerea , Phytophthora infestans , and Erwinia amylovora . Here, we report the draft genome sequence of the B. brevis HK544 strain, which consists of one circular chromosome of 6,486,246 bp with a GC content of 47.3%.

scholarly journals Draft Genome Sequence of Neobacillus cucumis Strain T4S4, a Stevioside and Rebaudioside A Hydrolytic Strain Isolated from Tropical Forest Soil

2021 ◽  
Vol 10 (21) ◽  
Author(s):  
T. Asawasriworanan ◽  
P. Harnvoravongchai ◽  
J. Somana ◽  
S. Chankhamhaengdecha ◽  
P. Ounjai
Keyword(s):  
Forest Soil ◽  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Steviol Glycosides ◽  
Rebaudioside A ◽  
Circular Chromosome ◽  
Content Type ◽  
Montane Rain Forest

Neobacillus cucumis T4S4 was isolated from montane rain forest soil in Thailand. This strain possesses the ability to hydrolyze stevioside and rebaudioside A, the two major steviol glycosides found in the stevia plant. The draft genome sequence of T4S4 yielded a circular chromosome of 5,978,437 bases with 38.9% GC content.

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