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Tóth AG, Farkas R, Papp M, Kilim O, Yun H, Makrai L, Maróti G, Gyurkovszky M, Krikó E, Solymosi N. Ixodes ricinus tick bacteriome alterations based on a climatically representative survey in Hungary. Microbiol Spectr 2023; 11:e0124323. [PMID: 37966205 PMCID: PMC10715062 DOI: 10.1128/spectrum.01243-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/10/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE Climate-sensitive disease vectors, such as ticks, respond to the environment with changes in their microbiome. These changes can affect the emergence or re-emergence of various vector-borne pathogens, such as the causative agent of Lyme borreliosis (LB) or tick-borne encephalitis. This aspect is particularly emphasized in light of climate change. The climatically representative assessment of microbiome differences in various developmental stages of the most common Central European tick species, Ixodes ricinus, deepens our understanding of the potential climatic factors behind microbial relative abundance and interaction changes. This knowledge can support the development of novel disease vector control strategies.
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Affiliation(s)
- Adrienn Gréta Tóth
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | - Róbert Farkas
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
| | - Márton Papp
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | - Oz Kilim
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Haeun Yun
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | | | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, HUN-REN, Szeged, Hungary
- Faculty of Water Sciences, University of Public Service, Baja, Hungary
| | - Mónika Gyurkovszky
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
| | - Eszter Krikó
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | - Norbert Solymosi
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
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Draft Genome Sequence of Bacillus wiedmannii Biovar thuringiensis ZZQ-138, Isolated from a Saline Lake. Microbiol Resour Announc 2022; 11:e0096421. [PMID: 35142552 PMCID: PMC8830326 DOI: 10.1128/mra.00964-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ecologically sound approaches to control mosquitoes like Anopheles stephensi, which are obligatory vectors for malaria transmission, are urgently needed because of increasing insecticide resistance. Bacteria from Bacillus are important resources. Here, we report the whole-genome sequence of Bacillus wiedmannii biovar thuringiensis ZZQ-138, which was isolated from sediment from a saline lake.
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Park KM, Kim HJ, Choi JY, Koo M. Antimicrobial Effect of Acetic Acid, Sodium Hypochlorite, and Thermal Treatments against Psychrotolerant Bacillus cereus Group Isolated from Lettuce ( Lactuca sativa L.). Foods 2021; 10:foods10092165. [PMID: 34574273 PMCID: PMC8467346 DOI: 10.3390/foods10092165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/01/2021] [Accepted: 09/10/2021] [Indexed: 11/20/2022] Open
Abstract
Various food products distributed throughout the cold chain can present a health risk for consumers due to the presence of psychrotolerant B. cereus group species that possess enterotoxin genes and antibiotic resistance. As these bacteria can grow at the low temperatures used in the food industry, this study evaluated the antimicrobial efficacy of acetic acid, sodium hypochlorite, and thermal treatments for inhibition of psychrotolerant strains and the effect that differences in activation temperature (30 °C and 10 °C) have on their efficacy. The minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and bacterial growth assay of acetic acid and thermal treatment showed an equal or higher antimicrobial efficacy in isolates activated at 10 °C than in those activated at 30 °C. In particular, psychrotolerant strains from the B. cereus group were completely eliminated with 0.25% acetic acid, regardless of the activation temperature. The possibility of tolerance was determined by observing responses in cells activated at 10 and 30 °C when exposed to different concentrations of sodium hypochlorite. Five isolates activated at 10 °C exhibited enhanced survivability in sodium hypochlorite compared to isolates activated at 30 °C, and these isolates were able to grow in sodium hypochlorite at concentrations of 250 ppm or higher. Although a significant difference in antimicrobial efficacy was observed for psychrotolerant B. cereus group strains depending on the activation temperature, acetic acid may be the most effective antimicrobial agent against psychrotolerant B. cereus species isolated from food products distributed in a cold chain.
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Affiliation(s)
- Kyung-Min Park
- Department of Food Analysis Center, Korea Research Institute, Wanju-gun 55365, Jeollabuk-do, Korea; (K.-M.P.); (J.-Y.C.)
| | - Hyun-Jung Kim
- Department of Research Group of Consumer Safety, Korea Research Institute, Wanju-gun 55365, Jeollabuk-do, Korea;
- Food Biotechnology, University of Science and Technology (UST), Yuseong-gu, Daejeon 34113, Korea
| | - Ji-Yoen Choi
- Department of Food Analysis Center, Korea Research Institute, Wanju-gun 55365, Jeollabuk-do, Korea; (K.-M.P.); (J.-Y.C.)
| | - Minseon Koo
- Department of Food Analysis Center, Korea Research Institute, Wanju-gun 55365, Jeollabuk-do, Korea; (K.-M.P.); (J.-Y.C.)
- Food Biotechnology, University of Science and Technology (UST), Yuseong-gu, Daejeon 34113, Korea
- Correspondence: ; Tel.: +82-63-219-9161
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Larvicidal Activities against Aedes aegypti of Supernatant and Pellet Fractions from Cultured Bacillus spp. Isolated from Amazonian Microenvironments. Trop Med Infect Dis 2021; 6:tropicalmed6020104. [PMID: 34204476 PMCID: PMC8293452 DOI: 10.3390/tropicalmed6020104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/30/2021] [Accepted: 06/13/2021] [Indexed: 11/16/2022] Open
Abstract
The Aedes aegypti mosquito is the primary vector of Dengue, Chikungunya and Zika causing major problems for public health, which requires new strategies for its control, like the use of entomopathogenic microorganisms. In this study, bacteria from various Amazonian environments were isolated and tested for their pathogenicity to A. aegypti larvae. Following thermal shock to select sporulated Bacillus spp., 77 bacterial strains were isolated. Molecular identification per 16S RNA sequences revealed that the assembled strains contained several species of the genus Bacillus and one species each of Brevibacillus, Klebsiella, Serratia, Achromobacter and Brevundimonas. Among the isolated Bacillus sp. strains, 19 showed larvicidal activity against A. aegypti. Two strains of Brevibacillus halotolerans also displayed larvicidal activity. For the first time, larvicidal activity against A. aegypti was identified for a strain of Brevibacillus halotolerans. Supernatant and pellet fractions of bacterial cultures were tested separately for larvicidal activities. Eight strains contained isolated fractions resulting in at least 50% mortality when tested at a concentration of 5 mg/mL. Further studies are needed to characterize the active larvicidal metabolites produced by these microorganisms and define their mechanisms of action.
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Carroll LM, Cheng RA, Wiedmann M, Kovac J. Keeping up with the Bacillus cereus group: taxonomy through the genomics era and beyond. Crit Rev Food Sci Nutr 2021; 62:7677-7702. [PMID: 33939559 DOI: 10.1080/10408398.2021.1916735] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Bacillus cereus group, also known as B. cereus sensu lato (s.l.), is a species complex that contains numerous closely related lineages, which vary in their ability to cause illness in humans and animals. The classification of B. cereus s.l. isolates into species-level taxonomic units is thus essential for informing public health and food safety efforts. However, taxonomic classification of these organisms is challenging. Numerous-often conflicting-taxonomic changes to the group have been proposed over the past two decades, making it difficult to remain up to date. In this review, we discuss the major nomenclatural changes that have accumulated in the B. cereus s.l. taxonomic space prior to 2020, particularly in the genomic sequencing era, and outline the resulting problems. We discuss several contemporary taxonomic frameworks as applied to B. cereus s.l., including (i) phenotypic, (ii) genomic, and (iii) hybrid nomenclatural frameworks, and we discuss the advantages and disadvantages of each. We offer suggestions as to how readers can avoid B. cereus s.l. taxonomic ambiguities, regardless of the nomenclatural framework(s) they choose to employ. Finally, we discuss future directions and open problems in the B. cereus s.l. taxonomic realm, including those that cannot be solved by genomic approaches alone.
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Affiliation(s)
- Laura M Carroll
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Rachel A Cheng
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
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Culex quinquefasciatus carrying Wolbachia is less susceptible to entomopathogenic bacteria. Sci Rep 2021; 11:1094. [PMID: 33441735 PMCID: PMC7806911 DOI: 10.1038/s41598-020-80034-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/16/2020] [Indexed: 01/29/2023] Open
Abstract
In an attempt to evaluate the susceptibility of the mosquito Culex quinquefasciatus to bacterial agents, a population naturally infected with a Wolbachia pipientis wPipSJ native strain was tested against the action of three bacterial mosquitocides, Bacillus thuringiensis subsp. israelensis, Bacillus wiedmannii biovar thuringiensis and Lysinibacillus sphaericus. Tests were carried out on mosquito larvae with and without Wolbachia (controls). Cx. quinquefasciatus naturally infected with the native wPipSJ strain proved to be more resistant to the pathogenic action of the three mosquitocidal bacterial strains. Additionally, wPipSJ was fully characterised using metagenome-assembled genomics, PCR-RFLP (PCR-Restriction Fragment Length Polymorphism) and MLST (MultiLocus Sequence Typing) analyses. This Wolbachia strain wPipSJ belongs to haplotype I, group wPip-III and supergroup B, clustering with other mosquito wPip strains, such as wPip PEL, wPip JHB, wPip Mol, and wAlbB; showing the southernmost distribution in America. The cytoplasmic incompatibility phenotype of this strain was revealed via crosses between wildtype (Wolbachia+) and antibiotic treated mosquito populations. The results of the tests with the bacterial agents suggest that Cx. quinquefasciatus naturally infected with wPipSJ is less susceptible to the pathogenic action of mosquitocidal bacterial strains when compared with the antibiotic-treated mosquito isoline, and is more susceptible to B. thuringiensis subsp. israelensis than to the other two mosquitocidal agents.
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Futo M, Opašić L, Koska S, Čorak N, Široki T, Ravikumar V, Thorsell A, Lenuzzi M, Kifer D, Domazet-Lošo M, Vlahoviček K, Mijakovic I, Domazet-Lošo T. Embryo-Like Features in Developing Bacillus subtilis Biofilms. Mol Biol Evol 2021; 38:31-47. [PMID: 32871001 PMCID: PMC7783165 DOI: 10.1093/molbev/msaa217] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure. For instance, it has been increasingly recognized that multicellular behavior underlies biofilm formation in bacteria. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed toward later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants, and fungi. Given that most cells on Earth reside in the form of biofilms and that biofilms represent the oldest known fossils, we anticipate that the widely adopted vision of the first life as a single-cell and free-living organism needs rethinking.
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Affiliation(s)
- Momir Futo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Luka Opašić
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sara Koska
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Nina Čorak
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Tin Široki
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Vaishnavi Ravikumar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Annika Thorsell
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maša Lenuzzi
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Domagoj Kifer
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Mirjana Domazet-Lošo
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Kristian Vlahoviček
- Bioinformatics Group, Division of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
- School of Biosciences, University of Skövde, Skövde, Sweden
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Catholic University of Croatia, Zagreb, Croatia
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8
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Torres Manno MA, Repizo GD, Magni C, Dunlap CA, Espariz M. The assessment of leading traits in the taxonomy of the Bacillus cereus group. Antonie van Leeuwenhoek 2020; 113:2223-2242. [PMID: 33179199 DOI: 10.1007/s10482-020-01494-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 10/23/2020] [Indexed: 12/18/2022]
Abstract
Bacillus cereus sensu lato strains (B. cereus group) are widely distributed in nature and have received interest for decades due to their importance in insect pest management, food production and their positive and negative repercussions in human health. Consideration of practical uses such as virulence, physiology, morphology, or ill-defined features have been applied to describe and classify species of the group. However, current comparative studies have exposed inconsistencies between evolutionary relatedness and biological significance among genomospecies of the B. cereus group. Here, the combined analyses of core-based phylogeny and all versus all Average Nucleotide Identity values based on 2116 strains were conducted to update the genomospecies circumscriptions within B. cereus group. These analyses suggested the existence of 57 genomospecies, 37 of which are novel, thus indicating that the taxonomic identities of more than 39% of the analyzed strains should be revised or updated. In addition, we found that whole-genome in silico analyses were suitable to differentiate genomospecies such as B. anthracis, B. cereus and B. thuringiensis. The prevalence of toxin and virulence factors coding genes in each of the genomospecies of the B. cereus group was also examined, using phylogeny-aware methods at wide-genome scale. Remarkably, Cry and emetic toxins, commonly assumed to be associated with B. thuringiensis and emetic B. paranthracis, respectively, did not show a positive correlation with those genomospecies. On the other hand, anthrax-like toxin and capsule-biosynthesis coding genes were positively correlated with B. anthracis genomospecies, despite not being present in all strains, and with presumably non-pathogenic genomospecies. Hence, despite these features have been so far considered relevant for industrial or medical classification of related species of the B. cereus group, they were inappropriate for their circumscription. In this study, genomospecies of the group were accurately affiliated and representative strains defined, generating a rational framework that will allow comparative analysis in epidemiological or ecological studies. Based on this classification the role of specific markers such as Type VII secretion system, cytolysin, bacillolysin, and siderophores such as petrobactin were pointed out for further analysis.
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Affiliation(s)
- Mariano A Torres Manno
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Santa Fe, Argentina
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR - CONICET), sede FCByF - UNR, Rosario, Santa Fe, Argentina
- Área Estadística y Procesamiento de Datos, Departamento de Matemática y Estadística, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guillermo D Repizo
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Rosario, Argentina
- Laboratorio de Resistencia bacteriana a antimicrobianos, Instituto de Biología Molecular y Celular de Rosario (IBR), sede FCByF - UNR, Rosario, Santa Fe, Argentina
| | - Christian Magni
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Santa Fe, Argentina
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR - CONICET), sede FCByF - UNR, Rosario, Santa Fe, Argentina
| | - Christopher A Dunlap
- United States Department of Agriculture, Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, 1815 North University Street, Peoria, IL, 61604, USA
| | - Martín Espariz
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Santa Fe, Argentina.
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR - CONICET), sede FCByF - UNR, Rosario, Santa Fe, Argentina.
- Área Estadística y Procesamiento de Datos, Departamento de Matemática y Estadística, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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Carroll LM, Cheng RA, Kovac J. No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods. Front Microbiol 2020; 11:580691. [PMID: 33072050 PMCID: PMC7536271 DOI: 10.3389/fmicb.2020.580691] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/25/2020] [Indexed: 12/19/2022] Open
Abstract
The Bacillus cereus group, also known as B. cereus sensu lato (s.l.), is a species complex comprising numerous closely related lineages, which vary in their ability to cause illness in humans and animals. The classification of B. cereus s.l. isolates into species-level taxonomic units is essential for facilitating communication between and among microbiologists, clinicians, public health officials, and industry professionals, but is not always straightforward. A recently proposed genomospecies-subspecies-biovar taxonomic framework aims to provide a standardized nomenclature for this species complex but relies heavily on whole-genome sequencing (WGS). It thus is unclear whether popular, low-cost typing methods (e.g., single- and multi-locus sequence typing) remain congruent with the proposed taxonomy. Here, we characterize 2,231 B. cereus s.l. genomes using a combination of in silico (i) average-nucleotide identity (ANI)-based genomospecies assignment, (ii) ANI-based subspecies assignment, (iii) seven-gene multi-locus sequence typing (MLST), (iv) single-locus panC group assignment, (v) rpoB allelic typing, and (vi) virulence factor detection. We show that sequence types (STs) assigned using MLST can be used for genomospecies assignment, and we provide a comprehensive list of ST/genomospecies associations. For panC group assignment, we show that an adjusted, eight-group framework is largely, albeit not perfectly, congruent with the proposed eight-genomospecies taxonomy, as panC alone may not distinguish (i) B. luti from Group II B. mosaicus and (ii) B. paramycoides from Group VI B. mycoides. We additionally provide a list of loci that capture the topology of the whole-genome B. cereus s.l. phylogeny that may be used in future sequence typing efforts. For researchers with access to WGS, MLST, and/or panC data, we showcase how our recently released software, BTyper3 (https://github.com/lmc297/BTyper3), can be used to assign B. cereus s.l. isolates to taxonomic units within this proposed framework with little-to-no user intervention or domain-specific knowledge of B. cereus s.l. taxonomy. We additionally outline a novel method for assigning B. cereus s.l. genomes to pseudo-gene flow units within proposed genomospecies. The results presented here highlight the backward-compatibility and accessibility of the recently proposed genomospecies-subspecies-biovar taxonomic framework and illustrate that WGS is not a necessity for microbiologists who want to use the proposed nomenclature effectively.
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Affiliation(s)
- Laura M. Carroll
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rachel A. Cheng
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
| | - Jasna Kovac
- Department of Food Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA, United States
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Carroll LM, Wiedmann M, Kovac J. Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes. mBio 2020; 11:e00034-20. [PMID: 32098810 PMCID: PMC7042689 DOI: 10.1128/mbio.00034-20] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 01/15/2020] [Indexed: 02/07/2023] Open
Abstract
The Bacillus cereus group comprises numerous closely related species, including bioterrorism agent B. anthracis, foodborne pathogen B. cereus, and biopesticide B. thuringiensis Differentiating organisms capable of causing illness or death from those used in industry is essential for risk assessment and outbreak preparedness. However, current species definitions facilitate species-phenotype incongruences, particularly when horizontally acquired genes are responsible for a phenotype. Using all publicly available B. cereus group genomes (n = 2,231), we show that current species definitions lead to overlapping genomospecies clusters, in which 66.2% of genomes belong to multiple genomospecies at a conventional 95 average nucleotide identity (ANI) genomospecies threshold. A genomospecies threshold of ≈92.5 ANI is shown to reflect a natural gap in genome similarity for the B. cereus group, and medoid genomes identified at this threshold are shown to yield resolvable genomospecies clusters with minimal overlap (six of 2,231 genomes assigned to multiple genomospecies; 0.269%). We thus propose a nomenclatural framework for the B. cereus group which accounts for (i) genomospecies using resolvable genomospecies clusters obtained at ≈92.5 ANI, (ii) established lineages of medical importance using a formal collection of subspecies names, and (iii) heterogeneity of clinically and industrially important phenotypes using a formalized and extended collection of biovar terms. We anticipate that the proposed nomenclature will remain interpretable to clinicians, without sacrificing genomic species definitions, which can in turn aid in pathogen surveillance; early detection of emerging, high-risk genotypes; and outbreak preparedness.IMPORTANCE Historical species definitions for many prokaryotes, including pathogens, have relied on phenotypic characteristics that are inconsistent with genome evolution. This scenario forces microbiologists and clinicians to face a tradeoff between taxonomic rigor and clinical interpretability. Using the Bacillus cereus group as a model, a conceptual framework for the taxonomic delineation of prokaryotes which reconciles genomic definitions of species with clinically and industrially relevant phenotypes is presented. The nomenclatural framework outlined here serves as a model for genomics-based bacterial taxonomy that moves beyond arbitrarily set genomospecies thresholds while maintaining congruence with phenotypes and historically important species names.
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Affiliation(s)
- Laura M Carroll
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
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Molecular Signatures Related to the Virulence of Bacillus cereus Sensu Lato, a Leading Cause of Devastating Endophthalmitis. mSystems 2019; 4:4/6/e00745-19. [PMID: 31796569 PMCID: PMC6890933 DOI: 10.1128/msystems.00745-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus endophthalmitis is a devastating eye infection that causes rapid blindness through extracellular tissue-destructive exotoxins. Despite its importance, knowledge of the phylogenetic relationships and population structure of intraocular Bacillus spp. is lacking. In this study, we sequenced the whole genomes of eight Bacillus intraocular pathogens independently isolated from 8/52 patients with posttraumatic Bacillus endophthalmitis infections in the Eye Hospital of Wenzhou Medical University between January 2010 and December 2018. Phylogenetic analysis revealed that the pathogenic intraocular isolates belonged to Bacillus cereus, Bacillus thuringiensis and Bacillus toyonensis To determine the virulence of the ocular isolates, three representative strains were injected into mouse models, and severe endophthalmitis leading to blindness was observed. Through incorporating publicly available genomes for Bacillus spp., we found that the intraocular pathogens could be isolated independently but displayed a similar genetic context. In addition, our data provide genome-wide support for intraocular and gastrointestinal sources of Bacillus spp. belonging to different lineages. Importantly, we identified five molecular signatures of virulence and motility genes associated with intraocular infection, namely, plcA-2, InhA-3, InhA-4, hblA-5, and fliD using pangenome-wide association studies. The characterization of overrepresented genes in the intraocular isolates holds value to predict bacterial evolution and for the design of future intervention strategies in patients with endophthalmitis.IMPORTANCE In this study, we provided a detailed and comprehensive clinicopathological and pathogenic report of Bacillus endophthalmitis over the 8 years of the study period. We first reported the whole-genome sequence of Bacillus spp. causing devastating endophthalmitis and found that Bacillus toyonensis is able to cause endophthalmitis. Finally, we revealed significant endophthalmitis-associated virulence genes involved in hemolysis, immunity inhibition, and pathogenesis. Overall, as more sequencing data sets become available, these data will facilitate comparative research and will reveal the emergence of pathogenic "ocular bacteria."
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