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Yossa N, Bell R, Tallent S, Brown E, Binet R, Hammack T. Genomic characterization of Bacillus cereus sensu stricto 3A ES isolated from eye shadow cosmetic products. BMC Microbiol 2022; 22:240. [PMID: 36199032 PMCID: PMC9533521 DOI: 10.1186/s12866-022-02652-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Bacillus cereus group, also known as B. cereus sensu lato (s.l.) contains ubiquitous spore-forming bacteria found in the environment including strains from the B. cereus sensu stricto (s.s.) species. They occur naturally in a wide range of raw materials and in consumer products. Characterizing isolates that have survived in consumer products allows us to better understand the mechanisms that permit spores to persist and potentially cause illness. Here we characterize the draft genome sequence of B. cereus s. s. 3A-ES, originally isolated from eye shadow and since investigated in several cosmetic studies and compared it to other top ten published complete genome sequences of B. cereus s.l. members. RESULTS The draft genome sequence of B. cereus s.s. 3A ES consisted of an average of 90 contigs comprising approximately 5,335,727 bp and a GC content of 34,988%, and with 5509 predicted coding sequences. Based on the annotation statistics and comparison to other genomes within the same species archived in the Pathosystems Resource Integration Center (PATRIC), this genome "was of good quality. Annotation of B. cereus s.s. 3A ES revealed a variety of subsystem features, virulence factors and antibiotic resistant genes. The phylogenetic analysis of ten B. cereus group members showed B. cereus s.s. 3A-ES to be a closely related homolog of B. cereus s.s. ATCC 14,579, an established reference strain that is not adapted for cosmetic microbiological studies. Survival of 3A-ES in eye shadow could be linked to predicted stress-response genes and strengthened by additional stress-response genes such as VanB-type, VanRB, CAT15/16, BcrA, BcrB, Lsa(B), and recA that are lacking in B. cereus s.s. ATCC 14,579. CONCLUSION Our genomic analysis of B. cereus s.s. 3A-ES revealed genes, which may allow this bacterium to withstand the action of preservatives and inhibitors in cosmetics, as well as virulence factors that could contribute to its pathogenicity. Having a well-characterized strain obtained from eye-shadow may be useful for establishing a reference strain for cosmetics testing.
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Affiliation(s)
- Nadine Yossa
- Office of Regulatory Science, FDA, College Park, MD, 20740, USA.
| | - Rebecca Bell
- Office of Regulatory Science, FDA, College Park, MD, 20740, USA
| | - Sandra Tallent
- Office of Regulatory Science, FDA, College Park, MD, 20740, USA
| | - Eric Brown
- Office of Regulatory Science, FDA, College Park, MD, 20740, USA
| | - Rachel Binet
- Office of Regulatory Science, FDA, College Park, MD, 20740, USA
| | - Thomas Hammack
- Office of Regulatory Science, FDA, College Park, MD, 20740, USA
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Beaton A, Lood C, Cunningham-Oakes E, MacFadyen A, Mullins AJ, Bestawy WE, Botelho J, Chevalier S, Coleman S, Dalzell C, Dolan SK, Faccenda A, Ghequire MGK, Higgins S, Kutschera A, Murray J, Redway M, Salih T, da Silva AC, Smith BA, Smits N, Thomson R, Woodcock S, Welch M, Cornelis P, Lavigne R, van Noort V, Tucker NP. Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies. FEMS Microbiol Lett 2019; 365:4951603. [PMID: 29579234 PMCID: PMC5909648 DOI: 10.1093/femsle/fny069] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/21/2018] [Indexed: 12/29/2022] Open
Abstract
Pseudomonas baetica strain a390T is the type strain of this recently described species and here we present its high-contiguity draft genome. To celebrate the 16th International Conference on Pseudomonas, the genome of P. baetica strain a390T was sequenced using a unique combination of Ion Torrent semiconductor and Oxford Nanopore methods as part of a collaborative community-led project. The use of high-quality Ion Torrent sequences with long Nanopore reads gave rapid, high-contiguity and -quality, 16-contig genome sequence. Whole genome phylogenetic analysis places P. baetica within the P. koreensis clade of the P. fluorescens group. Comparison of the main genomic features of P. baetica with a variety of other Pseudomonas spp. suggests that it is a highly adaptable organism, typical of the genus. This strain was originally isolated from the liver of a diseased wedge sole fish, and genotypic and phenotypic analyses show that it is tolerant to osmotic stress and to oxytetracycline.
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Affiliation(s)
- Ainsley Beaton
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Cédric Lood
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, bus 2460, Leuven B-3001, Belgium.,Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 20, bus 2460, Leuven B-3001, Belgium
| | - Edward Cunningham-Oakes
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Park Place, Cardiff CF10 3AX, UK
| | - Alison MacFadyen
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, Scotland, UK
| | - Alex J Mullins
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Park Place, Cardiff CF10 3AX, UK
| | - Walid El Bestawy
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - João Botelho
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira no. 228 Porto 4050-313, Portugal
| | - Sylvie Chevalier
- Laboratoire Microbiologie Signaux et Microenvironnement (LMSM), Université de Rouen, 55, rue St Germain, Evreux 27000, France
| | - Shannon Coleman
- Lower Mall Research Station, University of British Columbia, 2259 Lower Mall, Vancouver, BC V6T 1Z4, Canada
| | - Chloe Dalzell
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Stephen K Dolan
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Alberto Faccenda
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Maarten G K Ghequire
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, bus 2460, Leuven B-3001, Belgium
| | - Steven Higgins
- Department of Plant and Microbial Biology, University of Zürich, Zürich 8008, Switzerland
| | - Alexander Kutschera
- Department of Phytopathology, Center of Life and Food Sciences, Technical University of Munich, Weihenstephan D-85354, Germany
| | - Jordan Murray
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Martha Redway
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Talal Salih
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Ana C da Silva
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Brian A Smith
- School of Plant Sciences, The University of Arizona, P.O. Box 210036, Forbes Building, 303 Tucson, Arizona 85721-0036, USA
| | - Nathan Smits
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 20, bus 2460, Leuven B-3001, Belgium
| | - Ryan Thomson
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Stuart Woodcock
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Pierre Cornelis
- Laboratoire Microbiologie Signaux et Microenvironnement (LMSM), Université de Rouen, 55, rue St Germain, Evreux 27000, France
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 20, bus 2460, Leuven B-3001, Belgium
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, bus 2460, Leuven B-3001, Belgium
| | - Nicholas P Tucker
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
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Abstract
The manipulation and engineering of microbiomes could lead to improved human health, environmental sustainability, and agricultural productivity. However, microbiomes have proven difficult to alter in predictable ways, and their emergent properties are poorly understood. The history of biology has demonstrated the power of model systems to understand complex problems such as gene expression or development. Therefore, a defined and genetically tractable model community would be useful to dissect microbiome assembly, maintenance, and processes. We have developed a tractable model rhizosphere microbiome, designated THOR, containing Pseudomonas koreensis, Flavobacterium johnsoniae, and Bacillus cereus, which represent three dominant phyla in the rhizosphere, as well as in soil and the mammalian gut. The model community demonstrates emergent properties, and the members are amenable to genetic dissection. We propose that THOR will be a useful model for investigations of community-level interactions. The quest to manipulate microbiomes has intensified, but many microbial communities have proven to be recalcitrant to sustained change. Developing model communities amenable to genetic dissection will underpin successful strategies for shaping microbiomes by advancing an understanding of community interactions. We developed a model community with representatives from three dominant rhizosphere taxa, the Firmicutes, Proteobacteria, and Bacteroidetes. We chose Bacillus cereus as a model rhizosphere firmicute and characterized 20 other candidates, including “hitchhikers” that coisolated with B. cereus from the rhizosphere. Pairwise analysis produced a hierarchical interstrain-competition network. We chose two hitchhikers, Pseudomonas koreensis from the top tier of the competition network and Flavobacterium johnsoniae from the bottom of the network, to represent the Proteobacteria and Bacteroidetes, respectively. The model community has several emergent properties, induction of dendritic expansion of B. cereus colonies by either of the other members, and production of more robust biofilms by the three members together than individually. Moreover, P. koreensis produces a novel family of alkaloid antibiotics that inhibit growth of F. johnsoniae, and production is inhibited by B. cereus. We designate this community THOR, because the members are the hitchhikers of the rhizosphere. The genetic, genomic, and biochemical tools available for dissection of THOR provide the means to achieve a new level of understanding of microbial community behavior.
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Carro L, Nouioui I. Taxonomy and systematics of plant probiotic bacteria in the genomic era. AIMS Microbiol 2017; 3:383-412. [PMID: 31294168 PMCID: PMC6604993 DOI: 10.3934/microbiol.2017.3.383] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.
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Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
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