Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages

Our study, focused on classroom-based research at the introductory level and using the Phage Genomics course as the model, shows evidence that first-year students doing research learn the process of science as well as how scientists practice science. A preliminary but notable outcome of our work, which is based on a small sample, is the change in student interest in considering different career choices such as graduate education and science in general. This is particularly notable, as previous research has described research internships as clarifying or confirming rather than changing undergraduates’ decisions to pursue graduate education. We hypothesize that our results differ from previous studies of the impact of engaging in research because the students in our study are still in the early stages of their undergraduate careers. Our work builds upon the classroom-based research movement and should be viewed as encouraging to the Vision and Change in Undergraduate Biology Education movement advocated by the American Association for the Advancement of Science, the National Science Foundation, and other undergraduate education stakeholders.

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Dark Matter of the Biosphere: the Amazing World of Bacteriophage Diversity

Journal of Virology ◽

10.1128/jvi.01340-15 ◽

2015 ◽

Vol 89 (16) ◽

pp. 8107-8110 ◽

Cited By ~ 99

Author(s):

Graham F. Hatfull

Keyword(s):

Dark Matter ◽

Evolutionary History ◽

Illegitimate Recombination ◽

Host Strain ◽

Long Period ◽

Bacterial Genomics ◽

Phage Genomics ◽

Biological Entities

Bacteriophages are the most abundant biological entities in the biosphere, and this dynamic and old population is, not surprisingly, highly diverse genetically. Relative to bacterial genomics, phage genomics has advanced slowly, and a higher-resolution picture of the phagosphere is only just emerging. This view reveals substantial diversity even among phages known to infect a common host strain, but the relationships are complex, with mosaic genomic architectures generated by illegitimate recombination over a long period of evolutionary history.

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Phage Genomics

Cell ◽

10.1016/s0092-8674(01)00637-7 ◽

2002 ◽

Vol 108 (1) ◽

pp. 13-16 ◽

Cited By ~ 297

Author(s):

Harald Brüssow ◽

Roger W. Hendrix

Keyword(s):

Phage Genomics

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Marine phage genomics: what have we learned?

Current Opinion in Biotechnology ◽

10.1016/j.copbio.2005.03.007 ◽

2005 ◽

Vol 16 (3) ◽

pp. 299-307 ◽

Cited By ~ 72

Author(s):

John H Paul ◽

Matthew B Sullivan

Keyword(s):

Phage Genomics ◽

Marine Phage

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Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features

Nature Communications ◽

10.1038/s41467-021-21350-w ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 3

Author(s):

Natalya Yutin ◽

Sean Benler ◽

Sergei A. Shmakov ◽

Yuri I. Wolf ◽

Igor Tolstoy ◽

...

Keyword(s):

Genomic Analysis ◽

Comparative Genomic ◽

Human Gut ◽

Genomic Features ◽

Viral Genomes ◽

Founding Member ◽

Phage Dna ◽

Conserved Genes ◽

Phage Genomics ◽

Self Splicing

AbstractCrAssphage is the most abundant human-associated virus and the founding member of a large group of bacteriophages, discovered in animal-associated and environmental metagenomes, that infect bacteria of the phylum Bacteroidetes. We analyze 4907 Circular Metagenome Assembled Genomes (cMAGs) of putative viruses from human gut microbiomes and identify nearly 600 genomes of crAss-like phages that account for nearly 87% of the DNA reads mapped to these cMAGs. Phylogenetic analysis of conserved genes demonstrates the monophyly of crAss-like phages, a putative virus order, and of 5 branches, potential families within that order, two of which have not been identified previously. The phage genomes in one of these families are almost twofold larger than the crAssphage genome (145-192 kilobases), with high density of self-splicing introns and inteins. Many crAss-like phages encode suppressor tRNAs that enable read-through of UGA or UAG stop-codons, mostly, in late phage genes. A distinct feature of the crAss-like phages is the recurrent switch of the phage DNA polymerase type between A and B families. Thus, comparative genomic analysis of the expanded assemblage of crAss-like phages reveals aspects of genome architecture and expression as well as phage biology that were not apparent from the previous work on phage genomics.

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Sequence Analysis of Leuconostoc mesenteroides Bacteriophage Φ1-A4 Isolated from an Industrial Vegetable Fermentation

Applied and Environmental Microbiology ◽

10.1128/aem.02126-09 ◽

2010 ◽

Vol 76 (6) ◽

pp. 1955-1966 ◽

Cited By ~ 33

Author(s):

Z. Lu ◽

E. Altermann ◽

F. Breidt ◽

S. Kozyavkin

Keyword(s):

Large Scale ◽

Leuconostoc Mesenteroides ◽

Phage Genome ◽

Cell Lysis ◽

Amino Acid Sequences ◽

Open Reading Frames ◽

Lytic Phage ◽

Structural Protein ◽

Host Interactions ◽

Phage Genomics

ABSTRACT Vegetable fermentations rely on the proper succession of a variety of lactic acid bacteria (LAB). Leuconostoc mesenteroides initiates fermentation. As fermentation proceeds, L. mesenteroides dies off and other LAB complete the fermentation. Phages infecting L. mesenteroides may significantly influence the die-off of L. mesenteroides. However, no L. mesenteroides phages have been previously genetically characterized. Knowledge of more phage genome sequences may provide new insights into phage genomics, phage evolution, and phage-host interactions. We have determined the complete genome sequence of L. mesenteroides phage Φ1-A4, isolated from an industrial sauerkraut fermentation. The phage possesses a linear, double-stranded DNA genome consisting of 29,508 bp with a G+C content of 36%. Fifty open reading frames (ORFs) were predicted. Putative functions were assigned to 26 ORFs (52%), including 5 ORFs of structural proteins. The phage genome was modularly organized, containing DNA replication, DNA-packaging, head and tail morphogenesis, cell lysis, and DNA regulation/modification modules. In silico analyses showed that Φ1-A4 is a unique lytic phage with a large-scale genome inversion (∼30% of the genome). The genome inversion encompassed the lysis module, part of the structural protein module, and a cos site. The endolysin gene was flanked by two holin genes. The tail morphogenesis module was interspersed with cell lysis genes and other genes with unknown functions. The predicted amino acid sequences of the phage proteins showed little similarity to other phages, but functional analyses showed that Φ1-A4 clusters with several Lactococcus phages. To our knowledge, Φ1-A4 is the first genetically characterized L. mesenteroides phage.

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