Project Title

Metagenome Assembled Genome of a Novel Phage from the Nunu Microbiome

Academic department under which the project should be listed

CSM - Molecular and Cellular Biology

Faculty Sponsor Name

Tsai-Tien Tseng

Abstract (300 words maximum)

The application of next-generation sequencing (NGS) has provided new opportunities in expanding our understanding towards microbiomes in homemade fermented foods. This study explores microbiomes from a homemade dairy product called nunu, which is a West African fermented dairy beverage sold in open-air markets without a standardized starter culture or pasteurization. Raw reads with NCBI accession number of PRJEB20873 were first subjected to quality control and adapter trimming with cutadapt before assembly with MetaSPAdes to generate metagenome assembled genomes (MAGs). One MAG consisted of 42,861 bp with a G + C content of 55% and 56 predicted open-reading frames (ORFs). Structural and functional annotations revealed shared synteny with phage vB_EcoM_ECOO78 that has been classified as a Jilinvirus. As members of the Myoviridae family, Jilinviruses are known to infect the genera of Escherichia and Enterobacter. Functional annotation with BLAST searches revealed eight ORFs that shared no sequence similarities with genes from other Jilinviruses. Seven ORFs have been annotated to function in nucleotide metabolism and replication. Twelve ORFs have been predicted for functions in morphogenesis, including several tail and capsid proteins. Putative small and large terminase subunits were assigned for ORF55 and ORF56. While other Jilinviruses lack integrases, ORF27 was predicted to function as an integrase with sequence similarity of 87% when compared against Pseudomonas phage PPpW-3. This putative integrase from our current study also shares a sequence similarity of 88% with a tyrosine-type recombinase/integrase from E. coli. ORF42 shares sequence similarity at N-terminus with Dpo42 from phage vB_EcoM_ECOO78, that prevents E. coli biofilm formation. In conclusion, this novel phage appears to represent the fifth member of the Jilinvirus and further our understanding towards the nunu microbiome.

Project Type

Poster

How will this be presented?

Yes, in person

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Metagenome Assembled Genome of a Novel Phage from the Nunu Microbiome

The application of next-generation sequencing (NGS) has provided new opportunities in expanding our understanding towards microbiomes in homemade fermented foods. This study explores microbiomes from a homemade dairy product called nunu, which is a West African fermented dairy beverage sold in open-air markets without a standardized starter culture or pasteurization. Raw reads with NCBI accession number of PRJEB20873 were first subjected to quality control and adapter trimming with cutadapt before assembly with MetaSPAdes to generate metagenome assembled genomes (MAGs). One MAG consisted of 42,861 bp with a G + C content of 55% and 56 predicted open-reading frames (ORFs). Structural and functional annotations revealed shared synteny with phage vB_EcoM_ECOO78 that has been classified as a Jilinvirus. As members of the Myoviridae family, Jilinviruses are known to infect the genera of Escherichia and Enterobacter. Functional annotation with BLAST searches revealed eight ORFs that shared no sequence similarities with genes from other Jilinviruses. Seven ORFs have been annotated to function in nucleotide metabolism and replication. Twelve ORFs have been predicted for functions in morphogenesis, including several tail and capsid proteins. Putative small and large terminase subunits were assigned for ORF55 and ORF56. While other Jilinviruses lack integrases, ORF27 was predicted to function as an integrase with sequence similarity of 87% when compared against Pseudomonas phage PPpW-3. This putative integrase from our current study also shares a sequence similarity of 88% with a tyrosine-type recombinase/integrase from E. coli. ORF42 shares sequence similarity at N-terminus with Dpo42 from phage vB_EcoM_ECOO78, that prevents E. coli biofilm formation. In conclusion, this novel phage appears to represent the fifth member of the Jilinvirus and further our understanding towards the nunu microbiome.

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