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Salamzade R, Tran PQ, Martin C, Manson AL, Gilmore MS, Earl AM, Anantharaman K, Kalan LR. zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.07.544063. [PMID: 37333121 PMCID: PMC10274777 DOI: 10.1101/2023.06.07.544063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic elements (MGEs), such as biosynthetic gene clusters (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts and thousands of genomes. First, fai allows the identification of orthologous instances of a query gene cluster of interest amongst a database of target genomes. Subsequently, zol enables reliable, context-specific inference of ortholog groups for individual protein-encoding genes across gene cluster instances. In addition, zol performs functional annotation and computes a variety of evolutionary statistics for each inferred ortholog group. Importantly, in comparison to tools for visual exploration of homologous relationships between gene clusters, zol can scale to thousands of gene cluster instances and produce detailed reports that are easy to digest. To showcase fai and zol, we apply them for: (i) longitudinal tracking of a virus in metagenomes, (ii) discovering novel population-level genetic insights of two common BGCs in the fungal species Aspergillus flavus, and (iii) uncovering large-scale evolutionary trends of a virulence-associated gene cluster across thousands of genomes from a diverse bacterial genus.
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Affiliation(s)
- Rauf Salamzade
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Patricia Q. Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Freshwater and Marine Science Doctoral Program, University of Wisconsin-Madison, WI, USA
| | - Cody Martin
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Abigail L. Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S. Gilmore
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Ophthalmology, Harvard Medical School and Mass Eye and Ear, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School and Mass Eye and Ear, Boston, Massachusetts, USA
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Lindsay R. Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medicine, Division of Infectious Disease, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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Daza-Prieto B, Raicevic N, Cabal A, Hyden P, Mösenbacher T, Ladstätter J, Richter S, Stöger A, Joao Cardoso M, Chakeri A, Hasenberger P, Stadlbauer S, Mach RL, Martinovic A, Ruppitsch W. Enterococcus montenegrensis sp. nov., isolated from artisanal Montenegrin dry sausage. Int J Syst Evol Microbiol 2024; 74. [PMID: 38240650 DOI: 10.1099/ijsem.0.006206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024] Open
Abstract
A novel, Gram-positive, facultative anaerobe, coccoid and non-motile bacterium, designated as CoE-012-22T was isolated from dried beef sausage (the original name in Montenegro is Govedji Kulen) manufactured in the municipality of Rozaje (Montenegro) in 2021. Cells of this strain were oxidase- and catalase-negative. Growth occurred at 4-50 °C, at pH 5.0-8.0 and with 0-6.5 % (w/v) NaCl in diverse growth media. MALDI-TOF analysis identified the strain as Enterococcus canintestini (log score 2). Phylogenetic analysis of the 16S rRNA gene and whole genome sequences assigned the strain to the genus Enterococcus. The closest relatives were E. canintestini DSM 21207T and E. dispar ATCC 51266T with 16S rRNA gene sequence pairwise similarities of 99.34 and 98.59 %, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between isolate CoE-012-22T and other enterococci species were below the thresholds for species delineation thresholds (95.0 % ANI; 70.0 % dDDH) with maximum identities of 84.13 % (ANIb), 86.43 % (ANIm) and 28.4 % (dDDH) to E. saigonensis JCM 31193T and 70.97 % (ANIb), 88.99 % (ANIm) and 32.4 % (dDDH) to E. malodoratus ATCC 43197T. Two unknown Enterococcus isolates, Enterococcus sp. MJM12 and Enterococcus SMC-9, showed identities of 99.87 and 99.94 % (16S rRNA), 98.57 and 98.65 % (ANIb), 98.93 and 99.02 % (ANIm), and 89.8 and 90.0 % (dDDH) to strain CoE-012-22T and can therefore be regarded as the same species. Based on the characterization results, strain CoE-012-22T was considered to represent a novel species, for which the name Enterococcus montenegrensis sp. nov. is proposed. The type strain is CoE-012-22T (=DSM 115843T=NCIMB 15468T).
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Affiliation(s)
- Beatriz Daza-Prieto
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area of Biochemical Technology, Technical University Vienna, Vienna, Austria
| | - Nadja Raicevic
- FoodHub - Centre of Excellence for Digitalisationof Microbial Food Safety Risk Assessment and Quality Parameters for Accurate Food Authenticity Certification, University of Donja Gorica, Podgorica, Montenegro
| | - Adriana Cabal
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Patrick Hyden
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Tobias Mösenbacher
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Johann Ladstätter
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Susanne Richter
- Institute of Veterinary Disease Control, Austrian Agency for Health and Food Safety, Mödling, Austria
| | - Anna Stöger
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Maria Joao Cardoso
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
- ECDC Fellowship Programme, Public Health Microbiology path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Ali Chakeri
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
- Center for Public Health, Medical University Vienna, Vienna, Austria
| | - Petra Hasenberger
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Silke Stadlbauer
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Robert L Mach
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area of Biochemical Technology, Technical University Vienna, Vienna, Austria
| | - Aleksandra Martinovic
- FoodHub - Centre of Excellence for Digitalisationof Microbial Food Safety Risk Assessment and Quality Parameters for Accurate Food Authenticity Certification, University of Donja Gorica, Podgorica, Montenegro
| | - Werner Ruppitsch
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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