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O’Connell et al. Microbiome Res Rep 2023;2:21 Microbiome Research
DOI: 10.20517/mrr.2023.17
Reports

Original Article Open Access

Identification of novel genera and subcluster
classifications for mycobacteriophages

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Laura M. O’Connell , Colin Buttimer , Francesca Bottacini , Aidan Coffey , Jim M. O’Mahony 1
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Munster Technological University, Cork T12 P928, Ireland.
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APC Microbiome Ireland, Biosciences Research Institute, University College, Cork T12 YT20, Ireland.
Correspondence to: Dr. Laura M. O’Connell, Munster Technological University, Rossa Avenue, Bishopstown, Cork T12
P928, Ireland. E-mail: laura.oconnell2@mycit.ie
How to cite this article: O’Connell LM, Buttimer C, Bottacini F, Coffey A, O’Mahony JM. Identification of novel genera and
subcluster classifications for mycobacteriophages. Microbiome Res Rep 2023;2:21. https://dx.doi.org/10.20517/mrr.2023.17
Received: 19 Mar 2023 First Decision: 15 Apr 2023 Revised: 2 May 2023 Accepted: 24 May 2023 Published: 15 Jun 2023

Academic Editor: Rodolphe Barrangou Copy Editor: Dong-Li Li Production Editor: Dong-Li Li

Abstract
Aim: To identify novel genera amongst mycobacteriophages (MP) and verify a hypothesised correlation between
the taxonomy set by the International Committee on Taxonomy of Viruses (ICTV) and the National Centre for
Biotechnology Information (NCBI) with that of the Actinobacteriophage Database, which may help formalise
subcluster assignment.

Methods: A dataset of 721 MP genomes was analysed using VIRIDIC, a nucleotide alignment-based software that
predicts genus assignments. Potentially novel genera were analysed using Gegenees and VICTOR, respectively.
These genera were then compared to the subclusters assigned by the Actinobacteriophage Database to verify a
hypothesis that one genus can be assigned to one subcluster (i.e., the genus-subcluster hypothesis).

Results: Initially, when comparing the current genus classifications of the 721 MP dataset to the
Actinobacteriophage database subcluster assignments, 83.3% of subclusters supported the genus-subcluster
hypothesis. Following the sequential VIRIDIC, Gegenees and VICTOR analyses, a total of 20 novel genera were
identified based on a ≥ 70% and ~ 50% similarity threshold for VIRIDIC and Gegenees, respectively, and a
monophyletic nature in the VICTOR output. Interestingly, these criteria also appear to support the creation of 13
novel subclusters, which would increase the support for the genus-subcluster hypothesis to 97.6%.

© The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0
International License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, sharing,
adaptation, distribution and reproduction in any medium or format, for any purpose, even commercially, as
long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and
indicate if changes were made.

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