Genome sequence and comparative genomic analysis of a clinically important strain CD11-4 of Janibacter melonis isolated from celiac disease patient

Pseudomonas chlororaphis PCL1606 is a rhizobacterium that has biocontrol activity against many soilborne phytopathogenic fungi. The whole genome sequence of this strain was obtained using the Illumina Hiseq 2000 sequencing platform and was assembled using SOAP denovo software. The resulting 6.66-Mb complete sequence of the PCL1606 genome was further analyzed. A comparative genomic analysis using 10 plant-associated strains within the fluorescent Pseudomonas group, including the complete genome of P. chlororaphis PCL1606, revealed a diverse spectrum of traits involved in multitrophic interactions with plants and microbes as well as biological control. Phylogenetic analysis of these strains using eight housekeeping genes clearly placed strain PCL1606 into the P. chlororaphis group. The genome sequence of P. chlororaphis PCL1606 revealed the presence of sequences that were homologous to biosynthetic genes for the antifungal compounds 2-hexyl, 5-propyl resorcinol (HPR), hydrogen cyanide, and pyrrolnitrin; this is the first report of pyrrolnitrin encoding genes in this P. chlororaphis strain. Single-, double-, and triple-insertional mutants in the biosynthetic genes of each antifungal compound were used to test their roles in the production of these antifungal compounds and in antagonism and biocontrol of two fungal pathogens. The results confirmed the function of HPR in the antagonistic phenotype and in the biocontrol activity of P. chlororaphis PCL1606.

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Draft Genome Sequence of Listeria monocytogenes CIIMS-NV-3, a Strain Isolated from Vaginal Discharge of a Woman from Central India

Microbiology Resource Announcements ◽

10.1128/mra.01553-18 ◽

2019 ◽

Vol 8 (6) ◽

Author(s):

Pooja M. Kishnani ◽

Nitin V. Kurkure ◽

Sukhadeo B. Barbuddhe ◽

Swapnil P. Doijad ◽

Trinad Chakraborty ◽

...

Keyword(s):

Listeria Monocytogenes ◽

Genome Sequence ◽

Draft Genome ◽

Genomic Analysis ◽

Central India ◽

Vaginal Swab ◽

Comparative Genomic Analysis ◽

Draft Genome Sequence ◽

Comparative Genomic ◽

Content Type

We present here the draft genome sequence of Listeria monocytogenes CIIMS-NV-3, a serovar 4b strain isolated from the vaginal swab of a female patient from central India. The availability of this genome may provide useful information on virulence characteristics for comparative genomic analysis.

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Complete Genome Sequence of Weissella hellenica 0916-4-2 and Its Comparative Genomic Analysis

Frontiers in Microbiology ◽

10.3389/fmicb.2019.01619 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 5

Author(s):

Suresh Panthee ◽

Atmika Paudel ◽

Jochen Blom ◽

Hiroshi Hamamoto ◽

Kazuhisa Sekimizu

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic

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Draft Genome Sequence of Vibrio vulnificus 86573B, a Bacterium Isolated from Diseased Tilapia in Taiwan

Microbiology Resource Announcements ◽

10.1128/mra.00813-18 ◽

2018 ◽

Vol 7 (1) ◽

Author(s):

Shu-Ting Cho ◽

Yi-Ming Tsai ◽

Chun-Yao Chen ◽

Chih-Horng Kuo

Keyword(s):

Genome Sequence ◽

Vibrio Vulnificus ◽

Draft Genome ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Draft Genome Sequence ◽

Comparative Genomic ◽

Content Type

Vibrio vulnificus 86573B is a biotype 1 strain isolated from a moribund tilapia collected in Kaohsiung, Taiwan, during an outbreak early in 1997. Here, we report the draft genome sequence of this bacterium to facilitate the investigation of its biology and future comparative genomic analysis.

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Genomic analysis of halophilic bacterium, Lentibacillus sp. CBA3610, derived from human feces

Gut Pathogens ◽

10.1186/s13099-021-00436-2 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Seung Woo Ahn ◽

Se Hee Lee ◽

Hong-Seok Son ◽

Seong Woon Roh ◽

Yoon-E Choi

Keyword(s):

Phylogenetic Analysis ◽

Antibiotic Resistance ◽

Genome Sequence ◽

Dna Sequences ◽

Antibiotic Resistance Gene ◽

Genomic Analysis ◽

Halophilic Bacterium ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Genomic Analyses

Abstract Background Lentibacillus species are gram variable aerobic bacteria that live primarily in halophilic environments. Previous reports have shown that bacteria belonging to this species are primarily isolated from salty environments or food. We isolated a bacterial strain CBA3610, identified as a novel species of the genus Lentibacillus, from a human fecal sample. In this report, the whole genome sequence of Lentibacillus sp. CBA3610 is presented, and genomic analyses are performed. Results Complete genome sequence of strain CBA3610 was obtained through PacBio RSII and Illumina HiSeq platforms. The size of genome is 4,035,571 bp and genes estimated to be 4714 coding DNA sequences and 64 tRNA and 17 rRNA were identified. The phylogenetic analysis confirmed that it belongs to the genus Lentibacillus. In addition, there were genes related to antibiotic resistance and virulence, and genes predicted as CRISPR and prophage were also identified. Genes related to osmotic stress were found according to the characteristics of halophilic bacterium. Genomic differences from other Lentibacillus species were also confirmed through comparative genomic analysis. Conclusions Strain CBA3610 is predicted to be a novel candidate species of Lentibacillus through phylogenetic analysis and comparative genomic analysis with other species in the same genus. This strain has antibiotic resistance gene and pathogenic genes. In future, the information derived from the results of several genomic analyses of this strain is thought to be helpful in identifying the relationship between halophilic bacteria and human gut microbiota.

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Draft Genome Sequence of an Escherichia coli Sequence Type 155 Strain Isolated from Sewage in Kerala, India

Microbiology Resource Announcements ◽

10.1128/mra.01707-18 ◽

2019 ◽

Vol 8 (27) ◽

Author(s):

Amrita Salim ◽

Pradeesh Babu ◽

Keerthi Mohan ◽

Manju Moorthy ◽

Devika Raj ◽

...

Keyword(s):

Escherichia Coli ◽

Genome Sequence ◽

Draft Genome ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Sequence Type ◽

Draft Genome Sequence ◽

Comparative Genomic ◽

Content Type ◽

E Coli

ABSTRACT We report the draft genome sequence of Escherichia coli ASBT-1, a representative of E. coli sequence type 155 (ST155), obtained from India. Considering the known wide variety of pathogenic and antibiotic resistance potentials, this strain should be of great interest for detailed comparative genomic analysis.

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Genome Sequence of Kocuria polaris Strain CD08_4, an Isolate from the Duodenal Mucosa of a Celiac Disease Patient

Genome Announcements ◽

10.1128/genomea.01158-17 ◽

2017 ◽

Vol 5 (43) ◽

Cited By ~ 3

Author(s):

Atul Munish Chander ◽

Munesh Kumari ◽

Rakesh Kochhar ◽

Devinder Kumar Dhawan ◽

Sanjay Kumar Bhadada ◽

...

Keyword(s):

Oxidative Stress ◽

Celiac Disease ◽

Genome Sequence ◽

Iron Acquisition ◽

Disease Patient ◽

Antibiotic Resistance Genes ◽

Duodenal Mucosa ◽

Celiac Disease Patient ◽

Content Type ◽

Specific Virulence

ABSTRACT We report here the 3.8-Mb genome sequence of Kocuria polaris strain CD08_4, an isolate from the duodenal mucosa of a celiac disease patient. The genome consists of specific virulence determinant genes, antibiotic resistance genes, genes for coping with oxidative stress, and genes responsible for iron acquisition and metabolism, suggestive of its pathogenic attributes.

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Complete genome sequence analysis of a lytic Shigella flexneri vB_SflS-ISF001 bacteriophage

TURKISH JOURNAL OF BIOLOGY ◽

10.3906/biy-1808-97 ◽

2019 ◽

pp. 99-112 ◽

Cited By ~ 1

Author(s):

Khashayar SHAHIN ◽

Majid BOUZARI ◽

Ran WANG

Keyword(s):

Antibiotic Resistance ◽

Genome Sequence ◽

Shigella Flexneri ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Open Reading Frames ◽

Whole Genome Sequence ◽

Comparative Genomic ◽

Shigella Spp ◽

Enteric Infections

Shigellosis is one of the most important acute enteric infections caused by different species of Shigella, such as Shigella flexneri. Despite the use of antibiotic therapy to reduce disease duration, this approach is becoming less effective due to the emergence of antibiotic resistance among Shigella spp. Bacteriophages have been introduced as an alternative for controlling shigellosis. However, the bacteriophages must be without any lysogenic or virulence factors, toxin coding, or antibiotic-resistant genes. In this study, the whole genome sequence of vB_SflS-ISF001, a virulent Siphoviridae bacteriophage specific for Shigella flexneri, was obtained, and a comparative genomic analysis was carried out to identify its properties and safety. vB_SflS-ISF001 genomic DNA was measured at 50,552 bp with 78 deduced open reading frames (ORFs), with 24 ORFs (30.77%) sharing similarities with proteins from the genomes of homologous phages that had been reported earlier. Genetic analysis classifies it under the genus T1virus of the subfamily Tunavirinae. Moreover, comparative genomic analysis revealed no undesirable genes in the genome of vB_SflS-ISF001, such as antibiotic resistance, virulence, lysogeny, or toxin-coding genes. The results of this investigation indicate that vB_SflS-ISF001 is a new species, and confirm its safety for the biocontrol of S. flexneri.

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