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Liu Y, Pei T, Du J, Zhu H. Polyphasic Characterization and Genomic Insights into an Aerobic Denitrifying Bacterium, Shewanella zhuhaiensis sp. nov., Isolated from a Tidal Flat Sediment. Microorganisms 2023; 11:2870. [PMID: 38138013 PMCID: PMC10745330 DOI: 10.3390/microorganisms11122870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
A new, facultatively anaerobic, light-yellow, and rod-shaped bacterium designated as 3B26T isolated from Qi'ao Island's tidal flat sediment was identified. Strain 3B26T can hydrolyze gelatin, aesculin, and skim milk. The major cellular fatty acids were identified as iso-C15:0, referred to as summed feature 3, and C16:0; the polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, and phospholipid; and the quinones contained Q-7, Q-8, MK-7, and MMK7. The genomic size of strain 3B26T was 4,682,650 bp, and its genomic DNA G + C content was 54.8%. While a 16S rRNA gene-based phylogenetic analysis confirmed that strain 3B26T belongs to the genus Shewanella, both phylogenomic inference and genomic comparison revealed that strain 3B26T is distinguishable from its relatives, and digital DNA-DNA hybridization (dDDH) values of 24.4-62.6% and average nucleotide identities (ANIs) of 83.5-95.6% between them were below the 70% dDDH and 96% ANI thresholds for bacterial species delineation. Genomic functional analysis demonstrated that strain 3B26T possesses complete gene clusters of eicosapentaenoic acid biosynthesis and denitrification. Based on the evidence above, strain 3B26T is considered to represent a novel species of the genus Shewanella, and the name Shewanella zhuhaiensis sp. nov. (type strain 3B26T = GDMCC 1.2057T = KCTC 82339T) is proposed.
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Affiliation(s)
| | | | | | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (Y.L.); (T.P.); (J.D.)
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Sornchuer P, Saninjuk K, Tingpej P. Whole genome sequence analyses of thermotolerant Bacillus sp. isolates from food. Genomics Inform 2023; 21:e35. [PMID: 37813631 PMCID: PMC10584648 DOI: 10.5808/gi.23030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/10/2023] [Accepted: 07/11/2023] [Indexed: 10/11/2023] Open
Abstract
The Bacillus cereus group, also known as B. cereus sensu lato (B. cereus s.l.), is composed of various Bacillus species, some of which can cause diarrheal or emetic food poisoning. Several emerging highly heat-resistant Bacillus species have been identified, these include B. thermoamylovorans, B. sporothermodurans, and B. cytotoxicus NVH 391-98. Herein, we performed whole genome analysis of two thermotolerant Bacillus sp. isolates, Bacillus sp. B48 and Bacillus sp. B140, from an omelet with acacia leaves and fried rice, respectively. Phylogenomic analysis suggested that Bacillus sp. B48 and Bacillus sp. B140 are closely related to B. cereus and B. thuringiensis, respectively. Whole genome alignment of Bacillus sp. B48, Bacillus sp. B140, mesophilic strain B. cereus ATCC14579, and thermophilic strain B. cytotoxicus NVH 391-98 using the Mauve program revealed the presence of numerous homologous regions including genes responsible for heat shock in the dnaK gene cluster. However, the presence of a DUF4253 domain-containing protein was observed only in the genome of B. cereus ATCC14579 while the intracellular protease PfpI family was present only in the chromosome of B. cytotoxicus NVH 391-98. In addition, prophage Clp protease-like proteins were found in the genomes of both Bacillus sp. B48 and Bacillus sp. B140 but not in the genome of B. cereus ATCC14579. The genomic profiles of Bacillus sp. isolates were identified by using whole genome analysis especially those relating to heat-responsive gene clusters. The findings presented in this study lay the foundations for subsequent studies to reveal further insights into the molecular mechanisms of Bacillus species in terms of heat resistance mechanisms.
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Affiliation(s)
- Phornphan Sornchuer
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Klongluang, Pathum Thani 12120, Thailand
- Thammasat University Research Unit in Nutraceuticals and Food Safety, Faculty of Medicine, Thammasat University, Klongluang, Pathum Thani 12120, Thailand
| | - Kritsakorn Saninjuk
- Porcinotec Co., Ltd., Talat Khwan, Mueang Nonthaburi, Nonthaburi 11000, Thailand
| | - Pholawat Tingpej
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Klongluang, Pathum Thani 12120, Thailand
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Intraspecific Diversity and Pathogenicity of Bacillus thuringiensis Isolates from an Emetic Illness. Toxins (Basel) 2023; 15:toxins15020089. [PMID: 36828404 PMCID: PMC9963800 DOI: 10.3390/toxins15020089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/21/2023] Open
Abstract
This study describes an emetic food-borne intoxication associated with a Bacillus cereus group species and the characterization of the bacterial isolates from the incident in aspects of molecular tying, genetic factors, cytotoxicity, and pathogenic mechanisms relating to emetic illness. Through the polyphasic identification approach, all seven isolates obtained from food and clinical samples were identified as Bacillus thuringiensis. According to multilocus sequence typing (MLST) analysis, intraspecific diversity was found within the B. thuringiensis isolates. Four allelic profiles were found, including two previously known STs (ST8 and ST15) and two new STs (ST2804 and ST2805). All isolates harbored gene fragments located in the cereulide synthetase (ces) gene cluster. The heat-treated culture supernatants of three emetic B. thuringiensis isolates, FC2, FC7, and FC8, caused vacuolation and exhibited toxicity to Caco-2 cells, with CC50 values of 56.57, 72.17, and 79.94 µg/mL, respectively. The flow cytometry with the Annexin V/PI assay revealed both apoptosis and necrosis mechanisms, but necrosis was the prominent mechanism that caused Caco-2 cell destruction by FC2, the most toxic isolate.
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Rajalingam N, Jung J, Seo SM, Jin HS, Kim BE, Jeong MI, Kim D, Ryu JG, Ryu KY, Oh KK. Prevalence, distribution, enterotoxin profiles, antimicrobial resistance, and genetic diversity of Bacillus cereus group isolates from lettuce farms in Korea. Front Microbiol 2022; 13:906040. [PMID: 36081801 PMCID: PMC9445581 DOI: 10.3389/fmicb.2022.906040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/31/2022] [Indexed: 11/28/2022] Open
Abstract
Lettuce wraps are popular in Korean cuisine for their high nutritional value and versatility as healthy additions to multiple dishes. Microbial contamination of lettuce is a major concern, as lettuce is consumed fresh without cooking. Among foodborne pathogens, the spore-forming, facultative anaerobic bacterium, Bacillus cereus is one of the frequently detected pathogen in lettuce in Korea. In this study, we investigated the prevalence and distribution of Bacillus cereus strains in lettuce production farms and further evaluated the enterotoxin gene profiles, antibiotic susceptibility, multidrug resistance pattern, and genetic differences among the B. cereus group isolates. Of the 140 samples isolated from 10 lettuce production farms, 30 samples (21.42%) were positive for B. cereus in which 19 (31.6%) and 10 (23.25%) were from soil and lettuce, respectively. The enterotoxin patterns A (hblCDA, nheABC, entFM, and cytK genes) and B (hblCDA, nheABC, and entFM genes) accounted for 50% and 20% of all the isolates, whereas the emetic gene cesB was not detected in any of the B. cereus group isolates. Antibiotic susceptibility testing of the B. cereus group isolates revealed that all the strains were predominantly resistant to β-lactam antibiotics except imipenem and generally susceptible to most of the non β-lactam antibiotics, including gentamycin, streptomycin, chloramphenicol, and tetracycline. ERIC-PCR and MLST analysis revealed high genetic diversity among the 30 B. cereus group isolates, which belonged to 26 different sequence types (STs) and seven new STs. Moreover, isolates with identical STs exhibited similar patterns of antibiotic resistance and enterotoxin profiles. Results of this study indicate a high prevalence of B. cereus group isolates in lettuce production farms in the Republic of Korea.
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Affiliation(s)
- Nagendran Rajalingam
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Jieun Jung
- Functional Food and Nutrition Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Seung-Mi Seo
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Hyun-Sook Jin
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Bo-Eun Kim
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Myeong-In Jeong
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Dawoon Kim
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Jae-Gee Ryu
- Planning and Coordination Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Kyoung-Yul Ryu
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Kwang Kyo Oh
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
- *Correspondence: Kwang Kyo Oh,
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Yudianingtyas DW, Sumiarto B, Susetya H, Salman M, Djatmikowati TF, Haeriah H, Rahman A, Mangidi R. Identification of the molecular characteristics of Bacillus anthracis (1982-2020) isolates in East Indonesia using multilocus variable-number tandem repeat analysis. Vet World 2022; 15:953-961. [PMID: 35698492 PMCID: PMC9178602 DOI: 10.14202/vetworld.2022.953-961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/09/2022] [Indexed: 11/30/2022] Open
Abstract
Background and Aim: Anthrax is one of the endemic strategic diseases in East Indonesia, particularly in the provinces of South Sulawesi, West Sulawesi, Gorontalo, East Nusa Tenggara, and West Nusa Tenggara. Anthrax is an important disease due to its zoonotic and economic impact on the livestock industry. This study aimed to identify the molecular characteristics of Bacillus anthracis in East Indonesia using multilocus variable-number tandem repeat (VNTR) analysis (MLVA). Materials and Methods: Isolates were obtained from an investigation of anthrax outbreaks in five provinces of East Indonesia from 1982 to 2020. Conventional polymerase chain reaction for B. anthracis was used to identify MLVA-8. Deoxyribonucleic acid sequencing analysis was based on MLVA-8 primers for VNTR identification of the phylogenetic relationship among 24 isolates of B. anthracis obtained from 17 distinct districts/cities in East Indonesia. Tandem Repeats Finder was used for VNTR identification, and Molecular Evolutionary Genetics Analysis X was used to construct phylogenetic analysis. Results: In this study, 24 isolates were classified as genotype or lineage A. There were four subgroups of B. anthracis circulating in East Indonesia based on eight molecular marker loci sequence results. Conclusion: The findings of this study show that MLVA-8 typing might be useful as a subtyping tool for the epidemiological investigation of identical genotypes and low genetic diversity of B. anthracis. No other lineage of B. anthracis was circulating in East Indonesia. Other molecular methods are needed, such as extended MLVA, whole-genome sequencing, and canonical single-nucleotide polymorphism, for a more precise study of B. anthracis genetic diversity.
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Affiliation(s)
- D. W. Yudianingtyas
- Doctoral Study Program, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia; Department of Epidemiology and Veterinary Information, Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, The Republic of Indonesia, Indonesia
| | - B. Sumiarto
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - H. Susetya
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mo Salman
- Department of of Clinical Sciences, Animal Population Health Institute, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, United States of America
| | - T. F. Djatmikowati
- Bacteriology laboratory, Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, Indonesia, The Republic of Indonesia, Indonesia
| | - Haeriah Haeriah
- Bacteriology laboratory, Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, Indonesia, The Republic of Indonesia, Indonesia
| | - Abdul Rahman
- Bacteriology laboratory, Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, Indonesia, The Republic of Indonesia, Indonesia
| | - R. Mangidi
- Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, The Republic of Indonesia, Indonesia
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Di Cesare A, Pinnell LJ, Brambilla D, Elli G, Sabatino R, Sathicq MB, Corno G, O'Donnell C, Turner JW. Bioplastic accumulates antibiotic and metal resistance genes in coastal marine sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 291:118161. [PMID: 34537596 DOI: 10.1016/j.envpol.2021.118161] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/01/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
The oceans are increasingly polluted with plastic debris, and several studies have implicated plastic as a reservoir for antibiotic resistance genes and a potential vector for antibiotic-resistant bacteria. Bioplastic is widely regarded as an environmentally friendly replacement to conventional petroleum-based plastic, but the effects of bioplastic pollution on marine environments remain largely unknown. Here, we present the first evidence that bioplastic accumulates antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in marine sediments. Biofilms fouling ceramic, polyethylene terephthalate (PET), and polyhydroxyalkanoate (PHA) were investigated by shotgun metagenomic sequencing. Four ARG groups were more abundant in PHA: trimethoprim resistance (TMP), multidrug resistance (MDR), macrolide-lincosamide-streptogramin resistance (MLS), and polymyxin resistance (PMR). One MRG group was more abundant in PHA: multimetal resistance (MMR). The relative abundance of ARGs and MRGs were strongly correlated based on a Mantel test between the Bray-Curtis dissimilarity matrices (R = 0.97, p < 0.05) and a Pearson's analysis (R = 0.96, p < 0.05). ARGs were detected in more than 40% of the 57 metagenome-assembled genomes (MAGs) while MRGs were detected in more than 90% of the MAGs. Further investigation (e.g., culturing, genome sequencing, antibiotic susceptibility testing) revealed that PHA biofilms were colonized by hemolytic Bacillus cereus group bacteria that were resistant to beta-lactams, vancomycin, and bacitracin. Taken together, our findings indicate that bioplastic, like conventional petroleum-based plastic, is a reservoir for resistance genes and a potential vector for antibiotic-resistant bacteria in coastal marine sediments.
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Affiliation(s)
- Andrea Di Cesare
- Water Research Institute, National Research Council of Italy (CNR-IRSA), MEG - Molecular Ecology Group, Largo Tonolli 50, 28922, Verbania, Italy
| | - Lee J Pinnell
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, 78412, United States
| | - Diego Brambilla
- Water Research Institute, National Research Council of Italy (CNR-IRSA), MEG - Molecular Ecology Group, Largo Tonolli 50, 28922, Verbania, Italy
| | - Giulia Elli
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
| | - Raffaella Sabatino
- Water Research Institute, National Research Council of Italy (CNR-IRSA), MEG - Molecular Ecology Group, Largo Tonolli 50, 28922, Verbania, Italy
| | - María B Sathicq
- Water Research Institute, National Research Council of Italy (CNR-IRSA), MEG - Molecular Ecology Group, Largo Tonolli 50, 28922, Verbania, Italy
| | - Gianluca Corno
- Water Research Institute, National Research Council of Italy (CNR-IRSA), MEG - Molecular Ecology Group, Largo Tonolli 50, 28922, Verbania, Italy
| | - Colin O'Donnell
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, 78412, United States
| | - Jeffrey W Turner
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, 78412, United States.
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Diale MO, Kayitesi E, Serepa-Dlamini MH. Genome In Silico and In Vitro Analysis of the Probiotic Properties of a Bacterial Endophyte, Bacillus Paranthracis Strain MHSD3. Front Genet 2021; 12:672149. [PMID: 34858466 PMCID: PMC8631869 DOI: 10.3389/fgene.2021.672149] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/11/2021] [Indexed: 01/25/2023] Open
Abstract
Spore-forming Bacillus species are gaining interest in human health recently, due to their ability to withstand the harsh environment of the gastrointestinal tract. The present study explores probiotic features of Bacillus paranthracis strain MHSD3 through genomic analysis and in vitro probiotic assays. The draft genome of strain MHSD3 contained genes associated with tolerance to gastrointestinal stress and adhesion. Cluster genes responsible for the synthesis of antimicrobial non-ribosomal peptide synthetases, bacteriocins, and linear azole-containing peptides were identified. Additionally, strain MHSD3 was able to survive in an acidic environment, had the tolerance to bile salt, and exhibited the capability to tolerate gastric juices. Moreover, the isolate was found to possess strong cell surface traits such as high auto-aggregation and hydrophobicity indices of 79 and 54%, respectively. Gas chromatography-mass spectrometry analysis showed that the strain produced secondary metabolites such as amino acids, phenolic compounds, and organic acid, known to exert health-promoting properties, including the improvement of gastrointestinal tract health.
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Affiliation(s)
- Mamonokane Olga Diale
- Department of Biotechnology and Food Technology, University of Johannesburg, Johannesburg, South Africa
| | - Eugenie Kayitesi
- Department of Consumer and Food Science, University of Pretoria, Pretoria, South Africa
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Martelli F, Marrella M, Lazzi C, Neviani E, Bernini V. Microbiological Contamination of Ready-to-Eat Algae and Evaluation of Bacillus cereus Behavior by Microbiological Challenge Test. J Food Prot 2021; 84:1275-1280. [PMID: 33725095 DOI: 10.4315/jfp-20-407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/15/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Consumption of seaweeds (forms of algae), often categorized as a superfood, is becoming popular in western countries. Algae can be marketed fresh, but are usually sold dehydrated to ensure longer shelf life. Their consumption, often as ready-to-eat, opens up possible risks for public health because of foodborne pathogens that can contaminate the raw material during harvesting or manipulation. In this study, 14 ready-to-eat foods based on dehydrated algae, representative of the most consumed species, were considered. The microbial content, with a focus on Listeria monocytogenes and Bacillus cereus, was investigated by plate counts, and B. cereus strains were isolated and identified by 16S rRNA gene sequencing. The microbiological quality was heterogeneous among the samples and, in particular, marine bacteria, Listeria spp., B. cereus, and coliforms were detected. To contribute to related risk assessment, the ability of B. cereus to grow during refrigerated storage was evaluated, to our knowledge for the first time, by a microbiological challenge test on two ready-to-eat foods based on Undaria pinnatifida and Palmaria palmata. Despite this study demonstrating the inability of B. cereus to proliferate in seaweed-based food, its presence in dehydrated foodstuffs cannot rule out replication after rehydration before consumption, making it necessary to elucidate the possible risks for consumers. HIGHLIGHTS
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Affiliation(s)
- Francesco Martelli
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 49/A, Parma 43124, Italy
| | - Martina Marrella
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 49/A, Parma 43124, Italy
| | - Camilla Lazzi
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 49/A, Parma 43124, Italy
| | - Erasmo Neviani
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 49/A, Parma 43124, Italy
| | - Valentina Bernini
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 49/A, Parma 43124, Italy
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Sittmann J, Bae M, Mevers E, Li M, Quinn A, Sriram G, Clardy J, Liu Z. Bacterial diketopiperazines stimulate diatom growth and lipid accumulation. PLANT PHYSIOLOGY 2021; 186:1159-1170. [PMID: 33620482 PMCID: PMC8195512 DOI: 10.1093/plphys/kiab080] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/03/2021] [Indexed: 06/10/2023]
Abstract
Diatoms are photosynthetic microalgae that fix a significant fraction of the world's carbon. Because of their photosynthetic efficiency and high-lipid content, diatoms are priority candidates for biofuel production. Here, we report that sporulating Bacillus thuringiensis and other members of the Bacillus cereus group, when in co-culture with the marine diatom Phaeodactylum tricornutum, significantly increase diatom cell count. Bioassay-guided purification of the mother cell lysate of B. thuringiensis led to the identification of two diketopiperazines (DKPs) that stimulate both P. tricornutum growth and increase its lipid content. These findings may be exploited to enhance P. tricornutum growth and microalgae-based biofuel production. As increasing numbers of DKPs are isolated from marine microbes, the work gives potential clues to bacterial-produced growth factors for marine microalgae.
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Affiliation(s)
- John Sittmann
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Munhyung Bae
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Emily Mevers
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Muzi Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Andrew Quinn
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Ganesh Sriram
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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Fu X, Gong L, Liu Y, Lai Q, Li G, Shao Z. Bacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation. Front Microbiol 2021; 12:571212. [PMID: 34025591 PMCID: PMC8139322 DOI: 10.3389/fmicb.2021.571212] [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: 06/10/2020] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Background Members of the Bacillus pumilus group (abbreviated as the Bp group) are quite diverse and ubiquitous in marine environments, but little is known about correlation with their terrestrial counterparts. In this study, 16 marine strains that we had isolated before were sequenced and comparative genome analyses were performed with a total of 52 Bp group strains. The analyses included 20 marine isolates (which included the 16 new strains) and 32 terrestrial isolates, and their evolutionary relationships, differentiation, and environmental adaptation. Results Phylogenomic analysis revealed that the marine Bp group strains were grouped into three species: B. pumilus, B. altitudinis and B. safensis. All the three share a common ancestor. However, members of B. altitudinis were observed to cluster independently, separating from the other two, thus diverging from the others. Consistent with the universal nature of genes involved in the functioning of the translational machinery, the genes related to translation were enriched in the core genome. Functional genomic analyses revealed that the marine-derived and the terrestrial strains showed differences in certain hypothetical proteins, transcriptional regulators, K+ transporter (TrK) and ABC transporters. However, species differences showed the precedence of environmental adaptation discrepancies. In each species, land specific genes were found with possible functions that likely facilitate survival in diverse terrestrial niches, while marine bacteria were enriched with genes of unknown functions and those related to transcription, phage defense, DNA recombination and repair. Conclusion Our results indicated that the Bp isolates show distinct genomic features even as they share a common core. The marine and land isolates did not evolve independently; the transition between marine and non-marine habitats might have occurred multiple times. The lineage exhibited a priority effect over the niche in driving their dispersal. Certain intra-species niche specific genes could be related to a strains adaptation to its respective marine or terrestrial environment(s). In summary, this report describes the systematic evolution of 52 Bp group strains and will facilitate future studies toward understanding their ecological role and adaptation to marine and/or terrestrial environments.
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Affiliation(s)
- Xiaoteng Fu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Yang Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Guangyu Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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11
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Like Ginting E, Poluan GG, L Wantania L, Mauren Moko E, Warouw V, S Siby M, Wullur S. Screening and Identification of Sponge-Associated Chitinolytic Bacteria by Forming Chitosan from Manado Bay, Indonesia. Pak J Biol Sci 2021; 24:227-234. [PMID: 33683052 DOI: 10.3923/pjbs.2021.227.234] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE Chitosan can be produced through the enzymatic process catalyzed by chitin deacetylase which can be produced by bacteria. The biotransformation of chitin to chitosan by bacteria is interesting because the process is economical and environmentally friendly. This study described the potential of sponge-associated bacterium capability in degrading chitin and forming chitosan. MATERIALS AND METHODS The bacteria were isolated from sponge Cribrochalina sp. at Manado Bay, Indonesia. In the screening of the chitinase activity of bacteria, chitin media was used. Meanwhile, the transformation of chitin to chitosan was tested by using Chitinase Degrading Activity media. Molecular identification of bacteria was based on 16S rRNA gene sequences. RESULTS The results showed that the SS1, SS2, SS3, SS4 and SS5 bacterial isolates could degrade chitin based on chitinolytic indexes. These five bacteria could also form chitosan exhibited through the presence of chitosan in the form of precipitation in the fermented broth of bacteria. SS1 had the highest chitinase activity based on the chitinolytic index identified as Bacillus subtilis (100% identity), hence it is called B. subtilis strain SS1. The partial rRNA gene sequences data were deposited at GenBank under accession number MN999892. CONCLUSION The bacteria strain isolated from Cribrochalina sp. can be utilized in degrading chitin and form chitosan which could be a promising candidate for an economical and eco-friendly process of chitosan.
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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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Gupta RS, Patel S, Saini N, Chen S. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int J Syst Evol Microbiol 2020; 70:5753-5798. [PMID: 33112222 DOI: 10.1099/ijsem.0.004475] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium. The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer 'Bacillus kyonggiensis' to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis) or the Cereus clade (containing B. anthracis and B. cereus). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.
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Key Words
- classification of Bacillus species
- conserved signature indels
- emendation of genus Bacillus
- genus Bacillus and the family Bacillaceae
- novel Bacillaceae genera Alteribacter, Ectobacillus, Evansella, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Niallia, Priestia, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sutcliffiella and Weizmannia
- phylogenomic and comparative genomic analyses
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Sudip Patel
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Navneet Saini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Shu Chen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
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Liu C, Yu P, Yu S, Wang J, Guo H, Zhang Y, Zhang J, Liao X, Li C, Wu S, Gu Q, Zeng H, Zhang Y, Wei X, Zhang J, Wu Q, Ding Y. Assessment and molecular characterization of Bacillus cereus isolated from edible fungi in China. BMC Microbiol 2020; 20:310. [PMID: 33054711 PMCID: PMC7557095 DOI: 10.1186/s12866-020-01996-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 10/05/2020] [Indexed: 12/17/2022] Open
Abstract
Background Bacillus cereus is a foodborne pathogen commonly found in nature and food and can cause food spoilage and health issues. Although the prevalence of B. cereus in foods has been reported worldwide, the extent of contamination in edible fungi, which has become increasingly popular as traditional or functional food, is largely unknown. Here we investigated the prevalence, toxin genes’ distribution, antibiotic resistance, and genetic diversity of B. cereus isolated from edible fungi in China. Results Six hundred and ninety-nine edible fungi samples were collected across China, with 198 (28.3%) samples found to be contaminated by B. cereus, with an average contamination level of 55.4 most probable number (MPN)/g. Two hundred and forty-seven B. cereus strains were isolated from the contaminated samples. Seven enterotoxin genes and one cereulide synthetase gene were detected. The detection frequencies of all enterotoxin genes were ≥ 80%, whereas the positive rate of the cesB gene in B. cereus was 3%. Most isolates were resistant to penicillins, β-lactam/β-lactamase inhibitor combinations, cephems, and ansamycins, but were susceptible to penems, aminoglycosides, macrolides, ketolide, glycopeptides, quinolones, phenylpropanol, tetracyclines, lincosamides, streptogramins, and nitrofurans. Meanwhile, 99.6% of all isolates displayed multiple antimicrobial resistance to three or more classes of antimicrobials. Using genetic diversity analysis, all isolates were defined in 171 sequence types (STs), of which 83 isolates were assigned to 78 new STs. Conclusions This study provides large-scale insight into the prevalence and potential risk of B. cereus in edible fungi in China. Approximately one-third of the samples were contaminated with B. cereus, and almost all isolates showed multiple antimicrobial resistance. Detection frequencies of all seven enterotoxin genes were equal to or more than 80%. These new findings may indicate a need for proper pre-/post-processing of edible fungi to eliminate B. cereus, thereby preventing the potential risk to public health.
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Affiliation(s)
- Chengcheng Liu
- Guangdong Institute of Microbiology, Guangdong Academy of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Open Laboratory of Applied Microbiology, Xianlie Zhong Road 100#, 58th Building, Guangzhou, 510070, China.,Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Huangpu Ave. 601, Guangzhou, 510632, China
| | - Pengfei Yu
- Guangdong Institute of Microbiology, Guangdong Academy of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Open Laboratory of Applied Microbiology, Xianlie Zhong Road 100#, 58th Building, Guangzhou, 510070, China.,Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Huangpu Ave. 601, Guangzhou, 510632, China
| | - Shubo Yu
- Guangdong Institute of Microbiology, Guangdong Academy of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Open Laboratory of Applied Microbiology, Xianlie Zhong Road 100#, 58th Building, Guangzhou, 510070, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Hui Guo
- Guangdong Institute of Microbiology, Guangdong Academy of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Open Laboratory of Applied Microbiology, Xianlie Zhong Road 100#, 58th Building, Guangzhou, 510070, China.,Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Huangpu Ave. 601, Guangzhou, 510632, China
| | - Ying Zhang
- Guangdong Institute of Microbiology, Guangdong Academy of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Open Laboratory of Applied Microbiology, Xianlie Zhong Road 100#, 58th Building, Guangzhou, 510070, China.,Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Huangpu Ave. 601, Guangzhou, 510632, China
| | - Junhui Zhang
- Guangdong Institute of Microbiology, Guangdong Academy of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Open Laboratory of Applied Microbiology, Xianlie Zhong Road 100#, 58th Building, Guangzhou, 510070, China.,Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Huangpu Ave. 601, Guangzhou, 510632, China
| | - Xiyu Liao
- Guangdong Institute of Microbiology, Guangdong Academy of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Open Laboratory of Applied Microbiology, Xianlie Zhong Road 100#, 58th Building, Guangzhou, 510070, China.,Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Huangpu Ave. 601, Guangzhou, 510632, China
| | - Chun Li
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Huangpu Ave. 601, Guangzhou, 510632, China
| | - Shi Wu
- Guangdong Institute of Microbiology, Guangdong Academy of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Open Laboratory of Applied Microbiology, Xianlie Zhong Road 100#, 58th Building, Guangzhou, 510070, China
| | - Qihui Gu
- Guangdong Institute of Microbiology, Guangdong Academy of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Open Laboratory of Applied Microbiology, Xianlie Zhong Road 100#, 58th Building, Guangzhou, 510070, China
| | - Haiyan Zeng
- Guangdong Institute of Microbiology, Guangdong Academy of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Open Laboratory of Applied Microbiology, Xianlie Zhong Road 100#, 58th Building, Guangzhou, 510070, China
| | - Youxiong Zhang
- Guangdong Institute of Microbiology, Guangdong Academy of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Open Laboratory of Applied Microbiology, Xianlie Zhong Road 100#, 58th Building, Guangzhou, 510070, China
| | - Xianhu Wei
- Guangdong Institute of Microbiology, Guangdong Academy of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Open Laboratory of Applied Microbiology, Xianlie Zhong Road 100#, 58th Building, Guangzhou, 510070, China
| | - Jumei Zhang
- Guangdong Institute of Microbiology, Guangdong Academy of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Open Laboratory of Applied Microbiology, Xianlie Zhong Road 100#, 58th Building, Guangzhou, 510070, China
| | - Qingping Wu
- Guangdong Institute of Microbiology, Guangdong Academy of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Open Laboratory of Applied Microbiology, Xianlie Zhong Road 100#, 58th Building, Guangzhou, 510070, China.
| | - Yu Ding
- Guangdong Institute of Microbiology, Guangdong Academy of Science, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Open Laboratory of Applied Microbiology, Xianlie Zhong Road 100#, 58th Building, Guangzhou, 510070, China. .,Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Huangpu Ave. 601, Guangzhou, 510632, China.
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Rousset L, Alpha-Bazin B, Château A, Armengaud J, Clavel T, Berge O, Duport C. Groundwater promotes emergence of asporogenic mutants of emetic Bacillus cereus. Environ Microbiol 2020; 22:5248-5264. [PMID: 32815215 DOI: 10.1111/1462-2920.15203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 01/15/2023]
Abstract
Bacillus cereus is a ubiquitous endospore-forming bacterium, which mainly affects humans as a food-borne pathogen. Bacillus cereus can contaminate groundwater used to irrigate food crops. Here, we examined the ability of the emetic strain B. cereus F4810/72 to survive abiotic conditions encountered in groundwater. Our results showed that vegetative B. cereus cells rapidly evolved in a mixed population composed of endospores and asporogenic variants bearing spo0A mutations. One asporogenic variant, VAR-F48, was isolated and characterized. VAR-F48 can survive in sterilized groundwater over a long period in a vegetative form and has a competitive advantage compared to its parental strain. Proteomics analysis allowed us to quantify changes to cellular and exoproteins after 24 and 72 h incubation in groundwater, for VAR-F48 compared to its parental strain. The results revealed a significant re-routing of the metabolism in the absence of Spo0A. We concluded that VAR-F48 maximizes its energy use to deal with oligotrophy, and the emergence of spo0A-mutated variants may contribute to the persistence of emetic B. cereus in natural oligotrophic environments.
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Affiliation(s)
- Ludivine Rousset
- Avignon Université, INRAE, UMR SQPOV, Avignon, F-84914, France.,INRAE, Pathologie Végétale, Montfavet, F-84140, France
| | - Béatrice Alpha-Bazin
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France
| | - Alice Château
- Avignon Université, INRAE, UMR SQPOV, Avignon, F-84914, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France
| | - Thierry Clavel
- Avignon Université, INRAE, UMR SQPOV, Avignon, F-84914, France
| | - Odile Berge
- INRAE, Pathologie Végétale, Montfavet, F-84140, France
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Adjidé CC, Léké A, Mullié C. Bacillus cereus contamination of pasteurized human milk donations: frequency, origin, seasonal distribution, molecular typing of strains and proposed corrective/preventive actions. J Matern Fetal Neonatal Med 2020; 35:1554-1561. [PMID: 32393084 DOI: 10.1080/14767058.2020.1763295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Objectives: An increase in pasteurized human milk contamination with Bacillus cereus was witnessed in milk donated to the Amiens-Picardie Human Milk Bank over the 2017-2018 period. To better understand the origin of such an increase, this study aimed to describe the frequency of Bacillus cereus contamination in anonymous and personalized human milk donations of Amiens Human Milk Bank in 2018, compare the genetic profiles of Bacillus cereus strains found in pasteurized human milk and set up corrective/preventive actions to reduce Bacillus cereus contamination.Study design: A retrospective cohort study of human milk donated from January to December 2018 was set. Data on the microbiological quality of donated human milk and genetic profiles of Bacillus cereus strains isolated from pasteurized donated human milk and the environment were collected.Results: The overall noncompliance rate related to the microbiological quality in the 1585 batches of analyzed human milk donations was of 27.3%. Post-Holder pasteurization, rejection rates were significantly higher for anonymous donations as compared to personalized ones. Bacillus cereus was the main cause of noncompliance. Bacillus cereus contaminations could not be attributed to a single strain spreading through Amiens human milk bank and Amiens hospital environment as the genetic profiles of the collected strains were different. Corrective actions led to a decrease in the noncompliance rate due to Bacillus cereus (37.7-9.7%) post-Holder pasteurization.Conclusion: Bacillus cereus was the primary cause of rejection for pasteurized human milk donations over the investigated period. These contaminations did not originate from the spread of a single strain. A first round of corrective actions enabled a fair decrease in Bacillus cereus contaminations.
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Affiliation(s)
- Crespin C Adjidé
- Laboratoire Hygiène Risque Biologique & Environnement, Centre Hospitalier Universitaire Amiens-Picardie, Amiens, France
| | - André Léké
- Lactarium-Biberonnerie, Unité des soins intensifs de néonatologie et de médecine néonatale, Centre Hospitalier Universitaire Amiens-Picardie, Amiens, France
| | - Catherine Mullié
- Laboratoire Hygiène Risque Biologique & Environnement, Centre Hospitalier Universitaire Amiens-Picardie, Amiens, France.,Laboratoire AGIR UR UPJV 4294, UFR de Pharmacie, Université de Picardie Jules Verne, Amiens, France
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17
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Isolation and Molecular Level Identification of DNase Producing Halophilic Bacillus cereus Family Isolates from Marine Sediment Sample. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2020. [DOI: 10.22207/jpam.14.1.44] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Abstract
AbstractWe isolated 18 rhizobial strains from root nodules of a leguminous shrub Laburnum anagyroides (common laburnum) grown in Southeast Poland as an exotic plant. With the use of BOX-PCR fingerprinting, the isolates were clustered into 2 main groups and one separate lineage, which was congruent with the ITS-RFLP results. The phylogenetic trees constructed based on 16S rRNA and combined atpD, dnaK, glnA, and recA gene sequence data separated the representative strains into three evolutionary lineages within the Bradyrhizobium jicamae supergroup, with Bradyrhizobium algeriense and Bradyrhizobium valentinum as the closest relatives. The nodA and nifH gene phylogenies proved that the L. anagyroides symbionts carry a symbiotic gene variant known as Clade IV, representing the symbiovar retamae. Phenotypic characteristics of the isolates and reference strains are also reported. Our study of the rhizobia nodulating L. anagyroides growing in Poland complements earlier few findings on the symbiotic associations of this Genisteae species.
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Patel S, Gupta RS. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 2020; 70:406-438. [PMID: 31617837 DOI: 10.1099/ijsem.0.003775] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Bacillus, harbouring 293 species/subspecies, constitutes a phylogenetically incoherent group. In the absence of reliable means for grouping known Bacillus species into distinct clades, restricting the placement of new species into this genus has proven difficult. To clarify the evolutionary relationships among Bacillus species, 352 available genome sequences from the family Bacillaceae were used to perform comprehensive phylogenomic and comparative genomic analyses. Four phylogenetic trees were reconstructed based on multiple datasets of proteins including 1172 core Bacillaceae proteins, 87 proteins conserved within the phylum Firmicutes, GyrA-GyrB-RpoB-RpoC proteins, and UvrD-PolA proteins. All trees exhibited nearly identical branching of Bacillus species and consistently displayed six novel monophyletic clades encompassing 5-23 Bacillus species (denoted as the Simplex, Firmus, Jeotgali, Niacini, Fastidiosus and Alcalophilus clades), interspersed with other Bacillaceae species. Species from these clades also generally grouped together in 16S rRNA gene trees. In parallel, our comparative genomic analyses of Bacillus species led to the identification of 36 molecular markers comprising conserved signature indels in protein sequences that are specifically shared by the species from these six observed clades, thus reliably demarcating these clades based on multiple molecular synapomorphies. Based on the strong evidence from multiple lines of investigations supporting the existence of these six distinct 'Bacillus' clades, we propose the transfer of species from these clades into six novel Bacillaceae genera viz. Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. These results represent an important step towards clarifying the phylogeny/taxonomy of the genus Bacillus.
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Affiliation(s)
- Sudip Patel
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
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20
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Johnson-Mackinnon JC, Crosbie PBB, Karlsbakk E, Marcos-Lopez M, Paley R, Nowak BF, Bridle AR. Multilocus Sequence Typing (MLST) and Random Polymorphic DNA (RAPD) Comparisons of Geographic Isolates of Neoparamoeba perurans, the Causative Agent of Amoebic Gill Disease. Pathogens 2019; 8:pathogens8040244. [PMID: 31752364 PMCID: PMC6963586 DOI: 10.3390/pathogens8040244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 11/07/2019] [Accepted: 11/11/2019] [Indexed: 02/07/2023] Open
Abstract
Neoparamoba perurans, is the aetiological agent of amoebic gill disease (AGD), a disease that affects farmed Atlantic salmon worldwide. Multilocus sequence typing (MLST) and Random Amplified Polymorphic DNA (RAPD) are PCR-based typing methods that allow for the highly reproducible genetic analysis of population structure within microbial species. To the best of our knowledge, this study represents the first use of these typing methods applied to N. perurans with the objective of distinguishing geographical isolates. These analyses were applied to a total of 16 isolates from Australia, Canada, Ireland, Scotland, Norway, and the USA. All the samples from Australia came from farm sites on the island state of Tasmania. Genetic polymorphism among isolates was more evident from the RAPD analysis compared to the MLST that used conserved housekeeping genes. Both techniques consistently identified that isolates of N. perurans from Tasmania, Australia were more similar to each other than to the isolates from other countries. While genetic differences were identified between geographical isolates, a BURST analysis provided no evidence of a founder genotype. This suggests that emerging outbreaks of AGD are not due to rapid translocation of this important salmonid pathogen from the same area.
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Affiliation(s)
- Jessica C. Johnson-Mackinnon
- Institute for Marine and Antarctic Studies, University of Tasmania, Locked Bag 1370 Launceston, Tasmania 7250, Australia; (P.B.B.C.); (A.R.B.)
- Correspondence: (J.C.J.-M.); (B.F.N.)
| | - Philip B. B. Crosbie
- Institute for Marine and Antarctic Studies, University of Tasmania, Locked Bag 1370 Launceston, Tasmania 7250, Australia; (P.B.B.C.); (A.R.B.)
| | - Egil Karlsbakk
- Department of Biology, University of Bergen, N5020 Bergen, Norway;
| | - Mar Marcos-Lopez
- Vet-Aqua International, Unit 7B, Oranmore Business Park, H91 XP3F Galway, Ireland;
| | - Richard Paley
- Centre for Environment Fisheries and Aquaculture Science (Cefas), Weymouth laboratories, The Nothe Barrack Road, Weymouth, Dorset DT4 8UB, UK;
| | - Barbara F. Nowak
- Institute for Marine and Antarctic Studies, University of Tasmania, Locked Bag 1370 Launceston, Tasmania 7250, Australia; (P.B.B.C.); (A.R.B.)
- Correspondence: (J.C.J.-M.); (B.F.N.)
| | - Andrew R. Bridle
- Institute for Marine and Antarctic Studies, University of Tasmania, Locked Bag 1370 Launceston, Tasmania 7250, Australia; (P.B.B.C.); (A.R.B.)
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21
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Zhao Y, Chen C, Gu HJ, Zhang J, Sun L. Characterization of the Genome Feature and Toxic Capacity of a Bacillus wiedmannii Isolate From the Hydrothermal Field in Okinawa Trough. Front Cell Infect Microbiol 2019; 9:370. [PMID: 31750261 PMCID: PMC6842932 DOI: 10.3389/fcimb.2019.00370] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 10/10/2019] [Indexed: 11/13/2022] Open
Abstract
The Bacillus cereus group is frequently isolated from soil, plants, food, and other environments. In this study, we report the first isolation and characterization of a B. cereus group member, Bacillus wiedmannii SR52, from the hydrothermal field in the Iheya Ridge of Okinawa Trough. SR52 was isolated from the gills of shrimp Alvinocaris longirostris, an invertebrate species found abundantly in the ecosystems of the hydrothermal vents, and is most closely related to B. wiedmannii FSL W8-0169. SR52 is aerobic, motile, and able to form endospores. SR52 can grow in NaCl concentrations up to 9%. SR52 has a circular chromosome of 5,448,361 bp and a plasmid of 137,592 bp, encoding 5,709 and 189 genes, respectively. The chromosome contains 297 putative virulence genes, including those encoding enterotoxins and hemolysins. Fourteen rRNA operons, 107 tRNAs, and 5 sRNAs are present in the chromosome, and 7 tRNAs are present in the plasmid. SR52 possesses 13 genomic islands (GIs), all on the chromosome. Comparing to FSL W8-0169, SR52 exhibits several streaking features in its genome, notably an exceedingly large number of non-coding RNAs and GIs. In vivo studies showed that following intramuscular injection into fish, SR52 was able to disseminate in tissues and cause mortality; when inoculated into mice, SR52 induced acute mortality and disseminated transiently in tissues. In vitro studies showed that SR52 possessed hemolytic activity, and the extracellular product of SR52 exhibited a strong cytotoxic effect. These results provided the first insight into the cytotoxicity and genomic feature of B. wiedmannii from the deep-sea hydrothermal environment.
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Affiliation(s)
- Yan Zhao
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chen Chen
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Han-Jie Gu
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Zhang
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
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22
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Baek I, Lee K, Goodfellow M, Chun J. Comparative Genomic and Phylogenomic Analyses Clarify Relationships Within and Between Bacillus cereus and Bacillus thuringiensis: Proposal for the Recognition of Two Bacillus thuringiensis Genomovars. Front Microbiol 2019; 10:1978. [PMID: 31507580 PMCID: PMC6716467 DOI: 10.3389/fmicb.2019.01978] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/12/2019] [Indexed: 01/03/2023] Open
Abstract
The present study was designed to clarify the taxonomic status of two species classified as Bacillus cereus sensu lato, namely B. cereus sensu stricto and Bacillus thuringiensis. To this end, nearly 900 whole genome sequences of strains assigned to these taxa were the subject of comparative genomic and phylogenomic analyses. A phylogenomic tree based on core gene sequences showed that the type strains of B. cereus and B. thuringiensis formed a well-supported monophyletic clade that was clearly separated from corresponding clades composed of the remaining validly published species classified as B. cereus sensu lato. However, since average nucleotide identity and digital DNA-DNA hybridization similarities between the two types of Bacillus were slightly higher than the thresholds used to distinguish between closely related species we conclude that B. cereus and B. thuringiensis should continue to be recognized as validly published species. The B. thuringiensis strains were assigned to two genomically distinct groups, we propose that these taxa be recognized as genomovars, that is, as B. thuringiensis gv. thuringiensis and B. thuringiensis gv. cytolyticus. The extensive comparative genomic data clearly show that the distribution of pesticidal genes is irregular as strains identified as B. thuringiensis were assigned to several polyphyletic groups/subclades within the B. cereus-B. thuringiensis clade. Consequently, we recommend that genomic or equivalent molecular systematic features should be used to identify B. thuringiensis strains as the presence of pesticidal genes cannot be used as a diagnostic marker for this species. Comparative taxonomic studies are needed to find phenotypic properties that can be used to distinguish between the B. thuringiensis genomovars and between them and B. cereus.
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Affiliation(s)
- Inwoo Baek
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Kihyun Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jongsik Chun
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
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23
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Zhuang K, Li H, Zhang Z, Wu S, Zhang Y, Fox EM, Man C, Jiang Y. Typing and evaluating heat resistance of Bacillus cereus sensu stricto isolated from the processing environment of powdered infant formula. J Dairy Sci 2019; 102:7781-7793. [PMID: 31255274 DOI: 10.3168/jds.2019-16392] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/13/2019] [Indexed: 12/18/2022]
Abstract
Bacillus cereus sensu lato is one of the most harmful bacterial groups affecting the quality and safety of powdered infant formula (PIF). In this study, samples were collected from the raw materials and processing environments of PIF. A total of 84 isolates were identified as Bacillus cereus sensu stricto (B. cereus s. s.) by 16S rRNA analysis, molecular typing technology, and physiological and biochemical tests. The 84 B. cereus s. s. strains were assigned to panC group II, group III, and group IV. Then, the 7 housekeeping genes glpF, gmk, ilvD, pta, pur, pycA, and tpi were selected for multilocus sequence typing. Results showed that the 84 isolates were clustered into 24 sequence types (ST), and 14 novel ST were detected. Among the 24 ST, ST999 (19/84, 22.62%) and ST1343 (13/84, 15.48%) predominated. The correlation between processing areas and ST showed that the processing environments of the production and packing areas were the most susceptible to contamination by B. cereus s. s. Spores of these ST showed different heat resistance phenotypes evaluated by the analysis of DT (time in minutes of spore decimal reduction at each temperature) and Z values (temperature increase required to reduce the DT value to one-tenth of the original). Spores from group III according to panC gene analysis were the most heat resistant. These findings will help us to better understand B. cereus s. s. contamination and control in PIF processing environments.
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Affiliation(s)
- Kejin Zhuang
- Key Laboratory of Dairy Science, Ministry of Education, Department of Food Science, Northeast Agricultural University, Harbin, 150030, China
| | - Hongfu Li
- Key Laboratory of Dairy Science, Ministry of Education, Department of Food Science, Northeast Agricultural University, Harbin, 150030, China
| | - Ziwei Zhang
- Key Laboratory of Dairy Science, Ministry of Education, Department of Food Science, Northeast Agricultural University, Harbin, 150030, China
| | - Shuang Wu
- Key Laboratory of Dairy Science, Ministry of Education, Department of Food Science, Northeast Agricultural University, Harbin, 150030, China
| | - Yashuo Zhang
- Key Laboratory of Dairy Science, Ministry of Education, Department of Food Science, Northeast Agricultural University, Harbin, 150030, China
| | - Edward M Fox
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom NE 98; CSIRO Agriculture and Food, Werribee, VIC 3030, Australia
| | - Chaoxin Man
- Key Laboratory of Dairy Science, Ministry of Education, Department of Food Science, Northeast Agricultural University, Harbin, 150030, China.
| | - Yujun Jiang
- Key Laboratory of Dairy Science, Ministry of Education, Department of Food Science, Northeast Agricultural University, Harbin, 150030, China.
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24
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Yu P, Yu S, Wang J, Guo H, Zhang Y, Liao X, Zhang J, Wu S, Gu Q, Xue L, Zeng H, Pang R, Lei T, Zhang J, Wu Q, Ding Y. Bacillus cereus Isolated From Vegetables in China: Incidence, Genetic Diversity, Virulence Genes, and Antimicrobial Resistance. Front Microbiol 2019; 10:948. [PMID: 31156567 PMCID: PMC6530634 DOI: 10.3389/fmicb.2019.00948] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/15/2019] [Indexed: 12/24/2022] Open
Abstract
Bacillus cereus is a food-borne opportunistic pathogen that can induce diarrheal and emetic symptoms. It is widely distributed in different environments and can be found in various foods, including fresh vegetables. As their popularity grows worldwide, the risk of bacterial contamination in fresh vegetables should be fully evaluated, particularly in vegetables that are consumed raw or processed minimally, which are not commonly sterilized by enough heat treatment. Thereby, it is necessary to perform potential risk evaluation of B. cereus in vegetables. In this study, 294 B. cereus strains were isolated from vegetables in different cities in China to analyze incidence, genetic polymorphism, presence of virulence genes, and antimicrobial resistance. B. cereus was detected in 50% of all the samples, and 21/211 (9.95%) of all the samples had contamination levels of more than 1,100 MPN/g. Virulence gene detection revealed that 95 and 82% of the isolates harbored nheABC and hblACD gene clusters, respectively. Additionally, 87% of the isolates harbored cytK gene, and 3% of the isolates possessed cesB. Most strains were resistant to rifampicin and β-lactam antimicrobials but were sensitive to imipenem, gentamicin, ciprofloxacin, kanamycin, telithromycin, ciprofloxacin, and chloramphenicol. In addition, more than 95.6% of the isolates displayed resistance to three kinds of antibiotics. Based on multilocus sequence typing, all strains were classified into 210 different sequence types (STs), of which 145 isolates were assigned to 137 new STs. The most prevalent ST was ST770, but it included only eight isolates. Taken together, our research provides the first reference for the incidence and characteristics of B. cereus in vegetables collected throughout China, indicating a potential hazard of B. cereus when consuming vegetables without proper handling.
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Affiliation(s)
- Pengfei Yu
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Shubo Yu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Hui Guo
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Ying Zhang
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Xiyu Liao
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Junhui Zhang
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Shi Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Qihui Gu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Liang Xue
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Haiyan Zeng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Rui Pang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Tao Lei
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Jumei Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Yu Ding
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
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25
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Fu S, Ni P, Wang Y, Jin S, Jiang Z, Ye S, Li R. Delineating the origins of the multidrug-resistant pathogens in ornamental fish farms by multilocus sequence typing and identification of a novel multidrug-resistant plasmid. Can J Microbiol 2019; 65:551-562. [PMID: 30965017 DOI: 10.1139/cjm-2019-0097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
To evaluate the overuse of antibiotics and to identify the origin of pathogens in the ornamental fish industry, we conducted a field investigation of three representative fish farms in Liaoning province, China. Drug-resistant pathogens in the fishponds and groundwater were isolated and subtyped by multilocus sequence typing (MLST). In total, 33 pathogenic strains, including Aeromonas veronii and five other pathogens, were isolated from diseased fish and from groundwater. MLST revealed that A. veronii obtained from diseased fish in three fish farms can be subtyped into four sequence types, which were also identified in the corresponding groundwater. All of the isolates obtained from diseased fish showed resistance to at least four antibiotics. Notably, Citrobacter freundii JY-17 exhibited resistance to the majority of the antibiotics and was a carrier of a megaplasmid with 15 drug resistance genes. PCR assays targeting β-lactam, kanamycin, macrolide, phenicol, sulfonamide, and trimethoprim resistance genes in the pathogens from the diseased fish and groundwater were also conducted. The results revealed strong correlations between antibiotic treatment and increased antimicrobial resistance in fish pathogens. The results suggested that groundwater is the origin of the pathogens in ornamental fish. Antibiotic treatment of ornamental fish promoted the emergence of resistant pathogens.
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Affiliation(s)
- Songzhe Fu
- a College of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, P.R. China
| | - Ping Ni
- b College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, P.R. China
| | - Yi Wang
- b College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, P.R. China
| | - Shibo Jin
- b College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, P.R. China
| | - Zhiqiang Jiang
- b College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, P.R. China
| | - Shigen Ye
- b College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, P.R. China
| | - Ruijun Li
- b College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, P.R. China
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26
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Ying C, Chang MJ, Hu CH, Chang YT, Chao WL, Yeh SL, Chang SJ, Hsu JT. The effects of marine farm-scale sequentially integrated multi-trophic aquaculture systems on microbial community composition, prevalence of sulfonamide-resistant bacteria and sulfonamide resistance gene sul1. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 643:681-691. [PMID: 29957433 DOI: 10.1016/j.scitotenv.2018.06.204] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/28/2018] [Accepted: 06/17/2018] [Indexed: 06/08/2023]
Abstract
Aquaculture, one of the most important food production practices worldwide, faces serious challenges of mitigating the detrimental impacts of intensive farming on the environment and increased prevalence of antibiotic resistance. To develop an environment-friendly aquaculture system, a land-based and farm-scale sequentially integrated multi-trophic aquaculture (IMTA) system was established for farming Chanos chanos in southwestern Taiwan. In this system, fishes are cultured in combination with organic extractive shellfish and inorganic extractive seaweed. This study aimed to evaluate the prevalence of sulfonamide-resistant bacteria, microbial community structure, and occurrence of sulfonamide resistance genes in the IMTA and traditional aquaculture systems. Water and sediment samples were collected before raising and after harvesting C. chanos. Our results showed that the occurrence of sulfonamide-resistant phenotypes in the IMTA system was comparable with that in influent seawater, while the traditional system exhibited a high sulfonamide resistance rate. Additionally, the traditional system resulted in a deviation of the bacterial community structure from that of seawater. In the water samples from the IMTA system and influent seawater, Proteobacteria and Bacteroidetes were the two dominant phyla, representing approximately 75% and 15% of the community, respectively. In the traditional system, Actinobacteria, constituting 39% of the community, was the dominant bacterial phylum. Thirty-one sulfonamide-resistant bacterial species were isolated. In conclusion, a sequentially IMTA system showed superior ability to maintain the prevalence of antibiotic resistance and the integrity of the bacterial community structure compared to the traditional farming system, representing a potentially valuable aquaculture system for preserving the sustainability of the marine environment.
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Affiliation(s)
- Chingwen Ying
- Department of Microbiology, Soochow University, Taipei 111, Taiwan.
| | - Man-Jung Chang
- Department of Microbiology, Soochow University, Taipei 111, Taiwan
| | - Chia-Hsin Hu
- Department of Microbiology, Soochow University, Taipei 111, Taiwan
| | - Yi-Tang Chang
- Department of Microbiology, Soochow University, Taipei 111, Taiwan
| | - Wei-Liang Chao
- Department of Microbiology, Soochow University, Taipei 111, Taiwan
| | - Shinn-Lih Yeh
- Mariculture Research Center, Fisheries Research Institute, Council of Agriculture, Tainan 724, Taiwan
| | - Su-Jung Chang
- Mariculture Research Center, Fisheries Research Institute, Council of Agriculture, Tainan 724, Taiwan
| | - Jih-Tay Hsu
- Department of Animal Sciences, National Taiwan University, Taipei 111, Taiwan
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27
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Pérez-Cataluña A, Collado L, Salgado O, Lefiñanco V, Figueras MJ. A Polyphasic and Taxogenomic Evaluation Uncovers Arcobacter cryaerophilus as a Species Complex That Embraces Four Genomovars. Front Microbiol 2018; 9:805. [PMID: 29755434 PMCID: PMC5934430 DOI: 10.3389/fmicb.2018.00805] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 04/10/2018] [Indexed: 12/01/2022] Open
Abstract
The species Arcobacter cryaerophilus is found in many food products of animal origin and is the dominating species in wastewater. In addition, it is associated with cases of farm animal and human infectious diseases,. The species embraces two subgroups i.e., 1A (LMG 24291T = LMG 9904T) and 1B (LMG 10829) that can be differentiated by their 16S rRNA-RFLP pattern. However, some authors, on the basis of the shared intermediate levels of DNA-DNA hybridization, have suggested abandoning the subgroup classification. This contradiction indicates that the taxonomy of this species is not yet resolved. The objective of the present study was to perform a taxonomic evaluation of the diversity of A. cryaerophilus. Genomic information was used along with a Multilocus Phylogenetic Analysis (MLPA) and phenotypic characterization on a group of 52 temporally and geographically dispersed strains, coming from different types of samples and hosts from nine countries. The MLPA analysis showed that those strains formed four clusters (I–IV). Values of Average Nucleotide Identity (ANI) and in silico DNA-DNA Hybridization (isDDH) obtained between 13 genomes representing strains of the four clusters were below the proposed cut-offs of 96 and 70%, respectively, confirming that each of the clusters represented a different genomic species. However, none of the evaluated phenotypic tests enabled their unequivocal differentiation into species. Therefore, the genomic delimited clusters should be considered genomovars of the species A. cryaerophilus. These genomovars could have different clinical importance, since only the cluster I included strains isolated from human specimens. The discovery of at least one stable distinctive phenotypic character would be needed to define each cluster or genomovar as a different species. Until then, we propose naming them “A. cryaerophilus gv. pseudocryaerophilus” (Cluster I = LMG 10229T), “A. cryaerophilus gv. crypticus” (Cluster II = LMG 9065T), “A. cryaerophilus gv. cryaerophilus” (Cluster III = LMG 24291T) and “A. cryaerophilus gv. occultus” (Cluster IV = LMG 29976T).
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Affiliation(s)
- Alba Pérez-Cataluña
- Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, Reus, Spain
| | - Luis Collado
- Faculty of Sciences, Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile
| | - Oscar Salgado
- Faculty of Sciences, Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile.,Laboratory of Microbial Ecology of Extreme Systems, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Violeta Lefiñanco
- Faculty of Sciences, Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile
| | - María J Figueras
- Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, Reus, Spain
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28
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Liu H, Kong W, Yang W, Chen G, Liang H, Zhang Y. Multilocus sequence typing and variations in the oprD gene of Pseudomonas aeruginosa isolated from a hospital in China. Infect Drug Resist 2018; 11:45-54. [PMID: 29386908 PMCID: PMC5764299 DOI: 10.2147/idr.s152162] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Objectives To provide information about the genetic relationships and mechanism underlying carbapenem resistance in Pseudomonas aeruginosa clinical isolates of a hospital in China. Materials and methods One hundred and sixty P. aeruginosa strains were isolated from a hospital in China. Susceptibility to 14 antimicrobial agents was determined by antimicrobial susceptibility testing. Multilocus sequence typing was used to characterize the genetic backgrounds of these clinical isolates. Forty-five strains were randomly selected for further evaluation of their carbapenem resistance mechanism. Their oprD gene was compared with the PAO1 sequence. Results Multilocus sequence typing analysis demonstrated that these isolates were highly diverse; 68 sequence types were identified, of which 28 were novel sequence types. Polygenic and eBURST analysis demonstrated genetically similar clones with dissimilar resistance profiles. Among the 45 randomly selected strains associated with carbapenem resistance, 2 were metallo β-lactamase producers; all the 45 strains were not AmpC overproducers. Sequence analysis revealed a high diversity in the oprD sequences among isolates. Strains susceptible to imipenem and meropenem with shortened L7 and L8 loops in oprD were the major strain types observed in this hospital. Conclusion This study indicated that oprD provided the main mechanism for carbapenem resistance. The shortened L7 and L8 loops are responsible for carbapenem susceptibility.
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Affiliation(s)
- Huiqin Liu
- College of Life Sciences, Northwest University, Shaanxi, China
| | - Weina Kong
- College of Life Sciences, Northwest University, Shaanxi, China
| | - Weina Yang
- Department of Clinical Laboratory, The Children's Hospital of Xi'an City, Shaanxi, China
| | - Gukui Chen
- College of Life Sciences, Northwest University, Shaanxi, China
| | - Haihua Liang
- College of Life Sciences, Northwest University, Shaanxi, China
| | - Yani Zhang
- College of Life Sciences, Northwest University, Shaanxi, China
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29
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Liu Y, Lai Q, Shao Z. Genome analysis-based reclassification of Bacillus weihenstephanensis as a later heterotypic synonym of Bacillus mycoides. Int J Syst Evol Microbiol 2018; 68:106-112. [DOI: 10.1099/ijsem.0.002466] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
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Liu Y, Du J, Lai Q, Zeng R, Ye D, Xu J, Shao Z. Proposal of nine novel species of the Bacillus cereus group. Int J Syst Evol Microbiol 2017; 67:2499-2508. [PMID: 28792367 DOI: 10.1099/ijsem.0.001821] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nine novel Gram-stain-positive bacteria were investigated by a polyphasic taxonomic approach. Based on the analysis of 16S rRNA gene sequences, these strains belonged to the Bacillus cereus group, sharing over 97 % similarity with the known species of this group, and less than 95 % similarity with other species of the genus Bacillus. Multilocus sequence typing analysis showed that they formed nine robust and well-separated branches from the known species. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the nine strains were, respectively, below the 70 and 96 % threshold values for species definition, and between each strain and the known type strains of this group were also below the two threshold values. On the basis of the phenotypic and phylogenetic data, along with low dDDH and ANI values among these strains, these bacteria are assigned to the following nine novel species of the B. cereus group: Bacillus paranthracis sp. nov., type strain Mn5T (=MCCC 1A00395T=KCTC 33714T=LMG 28873T); Bacillus pacificus sp. nov., type strain EB422T (=MCCC 1A06182T=KCTC 33858T); Bacillus tropicus sp. nov., type strain N24T (=MCCC 1A01406T=KCTC 33711T=LMG 28874T); Bacillus albus sp. nov., type strain N35-10-2T (=MCCC 1A02146T=KCTC 33710T=LMG 28875T); Bacillus mobilis sp. nov., type strain 0711P9-1T (=MCCC 1A05942T=KCTC 33717T=LMG 28877T); Bacillus luti sp. nov., type strain TD41T (=MCCC 1A00359T=KCTC 33716T=LMG 28872T); Bacillus proteolyticus sp. nov., type strain TD42T (=MCCC 1A00365T=KCTC 33715T=LMG 28870T); Bacillus nitratireducens sp. nov., type strain 4049T (=MCCC 1A00732T=KCTC 33713T=LMG 28871T); and Bacillus paramycoides sp. nov., type strain NH24A2T (=MCCC 1A04098T=KCTC 33709T=LMG 28876T).
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Affiliation(s)
- Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Juan Du
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Runying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Dezan Ye
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Institute of Oceanology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
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Liu Y, Lai Q, Shao Z. A Multilocus Sequence Analysis Scheme for Phylogeny of Thioclava Bacteria and Proposal of Two Novel Species. Front Microbiol 2017; 8:1321. [PMID: 28751885 PMCID: PMC5508018 DOI: 10.3389/fmicb.2017.01321] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/29/2017] [Indexed: 11/13/2022] Open
Abstract
A multilocus sequence analysis (MLSA) was established and performed on the genus Thioclava, including 23 strains isolated from diverse marine environments, with the aim of better differentiation of strains and species within this genus. The study was based on sequences of 16S rRNA gene and five protein-coding housekeeping genes, gyrB, rpoD, dnaK, trpB, and recA. In contrast to 16S rRNA gene-based tree that was unable to separate some species within this genus, each tree based on a single housekeeping gene and MLSA had consistently defined seven clades, corresponding to the five established ones and two novel ones. The digital DNA-DNA hybridization and average nucleotide identity analyses based on genome sequences of the representative strains reconfirmed the validity of the MLSA analysis, and recommended a 97.3% MLSA similarity as the soft species threshold and nine species representing the five known and four putative novel species. Two of the four new species were identified as Thioclava sediminum sp. nov. (type strain TAW-CT134T = MCCC 1A10143T = LMG 29615T) and Thioclava marinus sp. nov. (type strain 11.10-0-13T = MCCC 1A03502T = LMG 29618T) by using a polyphasic taxonomic approach. Taken together, the newly established MLSA in this study first described the variability and phylogeny of the genus Thioclava which contributes to better understanding its ecology and evolution.
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Affiliation(s)
- Yang Liu
- School of Municipal and Environmental Engineering, Harbin Institute of TechnologyHarbin, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian ProvinceXiamen, China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian ProvinceXiamen, China
| | - Zongze Shao
- School of Municipal and Environmental Engineering, Harbin Institute of TechnologyHarbin, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian ProvinceXiamen, China
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