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Methylocaldum marinum strain:S8

ABSTRACT: Transcriptome analysis of Methylocaldum marinum S8

PROVIDER: PRJDB10788 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR255674_1.fastq.gz	Fastqsanger.gz
	DRR255674_2.fastq.gz	Fastqsanger.gz
	DRR255675_1.fastq.gz	Fastqsanger.gz
	DRR255675_2.fastq.gz	Fastqsanger.gz

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Methylocaldum marinum

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Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8.

Project description:Non-methanotrophic bacteria such as methylotrophs often coexist with methane-oxidizing bacteria (methanotrophs) by cross-feeding on methane-derived carbon. Methanol has long been considered a major compound that mediates cross-feeding of methane-derived carbon. Despite the potential importance of cross-feeding in the global carbon cycle, only a few studies have actually explored metabolic responses of a bacteria when cross-feeding on a methanotroph. Recently, we isolated a novel facultative methylotroph, Methyloceanibacter caenitepidi Gela4, which grows syntrophically with the methanotroph, Methylocaldum marinum S8. To assess the potential metabolic pathways in M. caenitepidi Gela4 co-cultured with M. marinum S8, we conducted genomic analyses of the two strains, as well as RNA-Seq and chemical analyses of M. caenitepidi Gela4, both in pure culture with methanol and in co-culture with methanotrophs. Genes involved in the serine pathway were downregulated in M. caenitepidi Gela4 under co-culture conditions, and methanol was below the detection limit (< 310 nM) in both pure culture of M. marinum S8 and co-culture. In contrast, genes involved in the tricarboxylic acid cycle, as well as acetyl-CoA synthetase, were upregulated in M. caenitepidi Gela4 under co-culture conditions. Notably, a pure culture of M. marinum S8 produced acetate (< 16 μM) during growth. These results suggested that an organic compound other than methanol, possibly acetate, might be the major carbon source for M. caenitepidi Gela4 cross-fed by M. marinum S8. Co-culture of M. caenitepidi Gela4 and M. marinum S8 may represent a model system to further study methanol-independent cross-feeding from methanotrophs to non-methanotrophic bacteria.

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Correction: Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8.

Project description:[This corrects the article DOI: 10.1371/journal.pone.0213535.].

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Streptomyces sp. S8 strain:S8

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Transcriptome Profiles of Mycobacterium marinum sRNA B11-Deleted and -Completed Strains

Project description:Understanding the regulatory roles of small RNAs (sRNAs) in Mycobacterium marinum is crucial for elucidating its pathogenesis. Here, we present transcriptome profiles of M. marinum strains with deletions and completions of sRNA B11. Through RNA sequencing analysis, we identified significant alterations in gene expression patterns between the B11-deleted and completed strains.

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Characterization of the immune response to Mycobacterium marinum infection in zebrafish [mutant 463]

Project description:Mycobacterium marinum infection in zebrafish (Danio rerio) has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole-genome level transcriptome analysis. In addition, we carried out a medium-scale forward genetic screen to identify genes underlying defense mechanisms against M. marinum infection in zebrafish. Our aim was to gain more information about the genetic mechanisms important in the immune defense against human tuberculosis. In this screen, we identified a mutant zebrafish line with impaired resistance to a low-dose M. marinum infection. In this line, the transcriptome analysis at 14 days post infection revealed decreased expression of a gene homologous to human UNC119 which has been shown to have a role in T cell activation.

2019-10-16 | GSE118350 | GEO

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