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Agunwah IM, Ogueke CC, Nwosu JN, Anyogu A. Microbiological evaluation of the indigenous fermented condiment okpeye available at various retail markets in the south-eastern region of Nigeria. Heliyon 2024; 10:e25493. [PMID: 38356605 PMCID: PMC10865259 DOI: 10.1016/j.heliyon.2024.e25493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
In Africa, indigenous fermented condiments contribute to food security as a low-cost source of protein. Okpeye is an indigenous fermented condiment produced from Prosopis africana seeds. The reliance on spontaneous fermentation processes and unhygienic practices during production often results in the contamination of the final product with microbial hazards. A microbiological evaluation of 18 commercial samples of okpeye purchased from six markets in two cities in southeastern Nigeria was conducted. Fifty-nine (59) bacteria were isolated and identified at the species level by phenotyping and sequencing the 16S rRNA, gyrB and rpoB genes. Bacillus (47.4 %) and Staphylococcus (42.3 %) were the predominant bacterial genera in okpeye. Overall, B. amyloliquefaciens and S. simulans were the most frequently occurring bacteria and were present in all samples. In addition, B. cereus was isolated in samples obtained from all markets. Other bacterial species included B. velezensis, Oceanobacillus caeni, S. cohnii, Escherichia fergusonni and Vagacoccus lutrae. The B. cereus isolates (10) were screened for the presence of 8 enterotoxin genes (hblA, hblC, hblD, nheA, nheB, nheC, cytK, entFM) and one emetic gene (cesB). The non-haemolytic enterotoxin (nheABC) and haemolytic enterotoxin (hblABD) complexes were present in 70 % and 50 % of B. cereus respectively. The positive rate of cytK and entFM genes was 70 %, while the cesB gene was 30 %. Antibiotic susceptibility assessment showed that most of the isolates were susceptible to gentamicin, tetracycline, streptomycin, and erythromycin but resistant to ciprofloxacin and vancomycin. These findings highlight the need for further controls to reduce contamination with potential pathogenic bacteria in indigenous fermented condiments such as okpeye. There is also a need to educate producers regarding hygienic practices to safeguard public health and food security.
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Affiliation(s)
- Ijeoma M. Agunwah
- Department of Food Science and Technology, Federal University of Technology, Owerri, Imo State, Nigeria
| | - Chika C. Ogueke
- Department of Food Science and Technology, Federal University of Technology, Owerri, Imo State, Nigeria
| | - Justina N. Nwosu
- Department of Food Science and Technology, Federal University of Technology, Owerri, Imo State, Nigeria
| | - Amarachukwu Anyogu
- Food Safety and Security, School of Biomedical Sciences, University of West London, St Mary's Road, Ealing, W5 5RF, London, UK
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Ngom SI, Maski S, Rached B, Chouati T, Oliveira Correia L, Juste C, Meylheuc T, Henrissat B, El Fahime E, Amar M, Béra-Maillet C. Exploring the hemicellulolytic properties and safety of Bacillus paralicheniformis as stepping stone in the use of new fibrolytic beneficial microbes. Sci Rep 2023; 13:22785. [PMID: 38129471 PMCID: PMC10740013 DOI: 10.1038/s41598-023-49724-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Bacillus strains from the Moroccan Coordinated Collections of Microorganisms (CCMM) were characterised and tested for fibrolytic function and safety properties that would be beneficial for maintaining intestinal homeostasis, and recommend beneficial microbes in the field of health promotion research. Forty strains were investigated for their fibrolytic activities towards complex purified polysaccharides and natural fibres representative of dietary fibres (DFs) entering the colon for digestion. We demonstrated hemicellulolytic activities for nine strains of Bacillus aerius, re-identified as Bacillus paralicheniformis and Bacillus licheniformis, using xylan, xyloglucan or lichenan as purified polysaccharides, and orange, apple and carrot natural fibres, with strain- and substrate-dependent production of glycoside hydrolases (GHs). Our combined methods, based on enzymatic assays, secretome, and genome analyses, highlighted the hemicellulolytic activities of B. paralicheniformis and the secretion of specific glycoside hydrolases, in particular xylanases, compared to B. licheniformis. Genomic features of these strains revealed a complete set of GH genes dedicated to the degradation of various polysaccharides from DFs, including cellulose, hemicellulose and pectin, which may confer on the strains the ability to digest a variety of DFs. Preliminary experiments on the safety and immunomodulatory properties of B. paralicheniformis fibrolytic strains were evaluated in light of applications as beneficial microbes' candidates for health improvement. B. paralicheniformis CCMM B969 was therefore proposed as a new fibrolytic beneficial microbe candidate.
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Affiliation(s)
- Serigne Inssa Ngom
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Soufiane Maski
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Département de Biologie, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
| | - Bahia Rached
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Laboratoire de Chimie-Physique et Biotechnologies des Biomolécules et Matériaux/Equipe Microbiologie Biomolécules et Biotechnologies, Faculté des Sciences et Techniques, Mohammedia, Morocco
| | - Taha Chouati
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Biologie médicale, Pathologie humaine et Expérimentale et Environnement, Faculté de Médecine et de pharmacie de Rabat, Rabat, Morocco
| | - Lydie Oliveira Correia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, PAPPSO, 78350, Jouy-en-Josas, France
| | - Catherine Juste
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Thierry Meylheuc
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, MIMA2, 78350, Jouy en Josas, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, 13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Elmostafa El Fahime
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Biologie médicale, Pathologie humaine et Expérimentale et Environnement, Faculté de Médecine et de pharmacie de Rabat, Rabat, Morocco
| | - Mohamed Amar
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
| | - Christel Béra-Maillet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco.
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Cheng Y, Zhang J, Ren W, Zhang L, Xu X. Response of a new rumen-derived Bacillus licheniformis to different carbon sources. Front Microbiol 2023; 14:1238767. [PMID: 38029181 PMCID: PMC10646532 DOI: 10.3389/fmicb.2023.1238767] [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: 06/12/2023] [Accepted: 09/22/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Bacillus licheniformis (B. licheniformis) is a microorganism with a wide range of probiotic properties and applications. Isolation and identification of novel strains is a major aspect of microbial research. Besides, different carbon sources have varying effects on B. licheniformis in regulating the microenvironment, and these mechanisms need to be investigated further. Methods In this study, we isolated and identified a new strain of B. licheniformis from bovine rumen fluid and named it B. licheniformis NXU98. The strain was treated with two distinct carbon sources-microcrystalline cellulose (MC) and cellobiose (CB). A combination of transcriptome and proteome analyses was used to investigate different carbon source effects. Results The results showed that B. licheniformis NXU98 ABC transporter proteins, antibiotic synthesis, flagellar assembly, cellulase-related pathways, and proteins were significantly upregulated in the MC treatment compared to the CB treatment, and lactate metabolism was inhibited. In addition, we used MC as a distinct carbon source to enhance the antibacterial ability of B. licheniformis NXU98, to improve its disease resistance, and to regulate the rumen microenvironment. Discussion Our research provides a potential new probiotic for feed research and a theoretical basis for investigating the mechanisms by which bacteria respond to different carbon sources.
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Affiliation(s)
| | | | | | - Lili Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Xiaofeng Xu
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
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Asif M, Li-Qun Z, Zeng Q, Atiq M, Ahmad K, Tariq A, Al-Ansari N, Blom J, Fenske L, Alodaini HA, Hatamleh AA. Comprehensive genomic analysis of Bacillus paralicheniformis strain BP9, pan-genomic and genetic basis of biocontrol mechanism. Comput Struct Biotechnol J 2023; 21:4647-4662. [PMID: 37841331 PMCID: PMC10568305 DOI: 10.1016/j.csbj.2023.09.043] [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: 08/26/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
Many Bacillus species are essential antibacterial agents, but their antibiosis potential still needs to be elucidated to its full extent. Here, we isolated a soil bacterium, BP9, which has significant antibiosis activity against fungal and bacterial pathogens. BP9 improved the growth of wheat seedlings via active colonization and demonstrated effective biofilm and swarming activity. BP9 sequenced genome contains 4282 genes with a mean G-C content of 45.94% of the whole genome. A single copy concatenated 802 core genes of 28 genomes, and their calculated average nucleotide identity (ANI) discriminated the strain BP9 from Bacillus licheniformis and classified it as Bacillus paralicheniformis. Furthermore, a comparative pan-genome analysis of 40 B. paralicheniformis strains suggested that the genetic repertoire of BP9 belongs to open-type genome species. A comparative analysis of a pan-genome dataset using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Gene groups (COG) revealed the diversity of secondary metabolic pathways, where BP9 distinguishes itself by exhibiting a greater prevalence of loci associated with the metabolism and transportation of organic and inorganic substances, carbohydrate and amino acid for effective inhabitation in diverse environments. The primary secondary metabolites and their genes involved in synthesizing bacillibactin, fencing, bacitracin, and lantibiotics were identified as acquired through a recent Horizontal gene transfer (HGT) event, which contributes to a significant part of the strain`s antimicrobial potential. Finally, we report some genes essential for plant-host interaction identified in BP9, which reduce spore germination and virulence of multiple fungal and bacterial species. The effective colonization, diverse predicted metabolic pathways and secondary metabolites (antibiotics) suggest testing the suitability of strain BP9 as a potential bio-preparation in agricultural fields.
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Affiliation(s)
- Muhammad Asif
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhang Li-Qun
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qingchao Zeng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Muhammad Atiq
- Department of Plant Pathology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Khalil Ahmad
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Aqil Tariq
- Department of Wildlife, Fisheries, and Aquaculture, College of Forest Resources, Mississippi State, University, MS 39762-9690, USA
| | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen 35392, Germany
| | - Linda Fenske
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen 35392, Germany
| | - Hissah Abdulrahman Alodaini
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Zhang Y, Lv X, Cao W, Zhang H, Shi L, Bai W, Ye L. Survey of Colistin Resistance in Commensal Bacteria from Penaeus vannamei Farms in China. Foods 2023; 12:foods12112143. [PMID: 37297388 DOI: 10.3390/foods12112143] [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: 04/20/2023] [Revised: 05/17/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023] Open
Abstract
Aquatic environments are important reservoirs for drug resistance. Aquatic foods may act as carriers to lead antibiotic-resistant commensal bacteria into the human gastrointestinal system, then contacting gut microbiota and spreading antibiotic resistance. Here, several shrimp farms were investigated to identify colistin resistance among commensal bacteria of aquaculture. A total of 884 (41.6%) colistin-resistant isolates were identified among 2126 strains. Electroporation demonstrated that colistin-resistant fragments were present in some commensal bacteria that could be transferred to other bacteria. Most of the resistant bacteria were Bacillus spp., with 69.3% of the Bacillus species exhibiting multiple drug resistance. Bacillus licheniformis was prevalent, with 58 strains identified that comprised six sequence types (ST) based on multilocus sequence typing. Whole-genome sequencing and comparisons with previous B. licheniformis genomes revealed a high degree of genomic similarity among isolates from different regions. Thus, this species is widely distributed, and this study provides new insights into global antibiotic-resistant characteristics of B. licheniformis. Sequence analyses further revealed some of these strains are even pathogenic and virulent, suggesting the antibiotic resistance and hazards of commensal bacteria in aquaculture should be considered. Considering the "One Health" perspective, improved monitoring of aquatic food is needed to prevent the spread of drug-resistant commensal bacteria from food-associated bacteria to humans.
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Affiliation(s)
- Yilin Zhang
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Xinrui Lv
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Weiwei Cao
- School of Food Science and Biology, Guangdong Polytechnic of Science and Trade, Guangzhou 510640, China
| | - Huang Zhang
- Guangzhou Double Helix Gene Technology Co., Ltd., Guangzhou International Bio Island Co., Ltd., Guangzhou 510320, China
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
- Shandong Yuwang Ecological Food Industry Co., Ltd., Yucheng 251200, China
| | - Weibin Bai
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Lei Ye
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
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Sakthivel K, Manigundan K, Sharma SK, Singh R, Das MM, Devi V, Gautam RK, Nakkeeran S, Kumar A. Diversity of Antimicrobial Peptide Genes in Bacillus from the Andaman and Nicobar Islands: Untapped Island Microbial Diversity for Disease Management in Crop Plants. Curr Microbiol 2022; 80:45. [PMID: 36538096 DOI: 10.1007/s00284-022-03086-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 10/09/2022] [Indexed: 12/29/2022]
Abstract
Taxonomic and functional characterization of a total of 90 bacterial isolates representing bulk and rhizosphere soils of diverse niches of Andaman and Nicobar Islands, India were carried out. Twelve bacterial isolates were found promising for the biological suppression of agriculturally important fungal and bacterial plant pathogens such as Ralstonia solanacearum, Xanthomonas oryzae pv. oryzae, and Colletotrichum gloeosporioides. The 16S rRNA gene sequence analysis revealed their identity as belonging to Bacillus subtilis, Bacillus amyloliquefaciens, and Lysinibacillus sphaericus. The isolates were positive for plant growth promotion (PGP) traits including siderophore production, and nutrient solubilization especially phosphorous, zinc, and potassium. Interestingly, the PCR test confirmed the presence of 62 antimicrobial peptides (AMP) biosynthesis genes specific to the genus Bacillus. Whilst all tested species of Bacillus harboured the bacD biosynthesis gene, the B. subtilis (Ba_Abi), and B. amyloliquefaciens (Ba_Abi) harboured the maximum AMP biosynthesis genes analysed in the study. Upon in planta evaluation, the biocontrol potential of the bacterial isolates against leaf spot disease of chilli was observed. The study culminated in the isolation and identification of diverse Bacillus species for exploitation as bioinoculants for plant health management programmes.
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Affiliation(s)
- Krishnan Sakthivel
- Division of Field Crop Improvement and Protection, ICAR- Central Islands Agricultural Research Institute, Port Blair, Andaman & Nicobar Islands, 744 101, India
| | - Kaari Manigundan
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, India
| | - Sushil Kumar Sharma
- ICAR - National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, Uttar Pradesh, 275 003, India
| | - Reena Singh
- Division of Field Crop Improvement and Protection, ICAR- Central Islands Agricultural Research Institute, Port Blair, Andaman & Nicobar Islands, 744 101, India
| | - Manisha Mohan Das
- Division of Field Crop Improvement and Protection, ICAR- Central Islands Agricultural Research Institute, Port Blair, Andaman & Nicobar Islands, 744 101, India
| | - Varsha Devi
- Division of Field Crop Improvement and Protection, ICAR- Central Islands Agricultural Research Institute, Port Blair, Andaman & Nicobar Islands, 744 101, India
| | - Raj Kumar Gautam
- Division of Field Crop Improvement and Protection, ICAR- Central Islands Agricultural Research Institute, Port Blair, Andaman & Nicobar Islands, 744 101, India
| | - Sevugapperumal Nakkeeran
- Center for Plant Molecular Biology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641 003, India
| | - Aundy Kumar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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7
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Sanchez-Vizuete P, Dergham Y, Bridier A, Deschamps J, Dervyn E, Hamze K, Aymerich S, Le Coq D, Briandet R. The coordinated population redistribution between Bacillus subtilis submerged biofilm and liquid-air pellicle. Biofilm 2022; 4:100065. [PMID: 35024609 PMCID: PMC8732777 DOI: 10.1016/j.bioflm.2021.100065] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 12/15/2022] Open
Abstract
Bacillus subtilis is a widely used bacterial model to decipher biofilm formation, genetic determinants and their regulation. For several years, studies were conducted on colonies or pellicles formed at the interface with air, but more recent works showed that non-domesticated strains were able to form thick and structured biofilms on submerged surfaces. Taking advantage of time-lapse confocal laser scanning microscopy, we monitored bacterial colonization on the surface and observed an unexpected biphasic submerged biofilm development. Cells adhering to the surface firstly form elongated chains before being suddenly fragmented and released as free motile cells in the medium. This switching coincided with an oxygen depletion in the well which preceded the formation of the pellicle at the liquid-air interface. Residual bacteria still associated with the solid surface at the bottom of the well started to express matrix genes under anaerobic metabolism to build the typical biofilm protruding structures.
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Affiliation(s)
- Pilar Sanchez-Vizuete
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Yasmine Dergham
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.,Faculty of Science, Lebanese University, 1003, Beirut, Lebanon
| | - Arnaud Bridier
- Fougères Laboratory, Antibiotics, Biocides, Residues and Resistance Unit, Anses, 35300, Fougères, France
| | - Julien Deschamps
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Etienne Dervyn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Kassem Hamze
- Faculty of Science, Lebanese University, 1003, Beirut, Lebanon
| | - Stéphane Aymerich
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Dominique Le Coq
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.,Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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8
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Gaballa A, Cheng RA, Trmcic A, Kovac J, Kent DJ, Martin NH, Wiedmann M. Development of a database and standardized approach for rpoB sequence-based subtyping and identification of aerobic spore-forming Bacillales. J Microbiol Methods 2021; 191:106350. [PMID: 34710512 DOI: 10.1016/j.mimet.2021.106350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 10/20/2022]
Abstract
Aerobic spore-forming Bacillales are a highly diverse and ubiquitous group that includes organisms that cause foodborne illnesses and food spoilage. Classical microbiological and biochemical identification of members of the order Bacillales represents a challenge due to the diversity of organisms in this group as well as the fact that the phenotypic-based taxonomic assignment of some named species in this group is not consistent with their phylogenomic characteristics. DNA-sequencing-based tools, on the other hand, can be fast and cost-effective, and can provide for a more reliable identification and characterization of Bacillales isolates. In comparison to 16S rDNA, rpoB was shown to better discriminate between Bacillales isolates and to allow for improved taxonomic assignment to the species level. However, the lack of a publicly accessible rpoB database, as well as the lack of standardized protocols for rpoB-based typing and strain identification, is a major challenge. Here, we report (i) the curation of a DNA sequence database for rpoB-based subtype classification of Bacillales isolates; (ii) the development of standardized protocols for generating rpoB sequence data, and a scheme for rpoB-based initial taxonomic identification of Bacillales isolates at the species level; and (iii) the integration of the database in a publicly accessible online platform that allows for the analysis of rpoB sequence data from uncharacterized Bacillales isolates. Specifically, we curated a database of DNA sequences for a 632-nt internal variable region within the rpoB gene from representative Bacillales reference type strains and a large number of isolates that we have previously isolated and characterized through multiple projects. As of May 21, 2021, the rpoB database contained more than 8350 rpoB sequences representing 1902 distinct rpoB allelic types that can be classified into 160 different genera. The database also includes 1129 rpoB sequences for representative Bacillales reference type strains as available on May 21, 2021 in the NCBI database. The rpoB database is integrated into the online Food Microbe Tracker platform (www.foodmicrobetracker.com) and can be queried using the integrated BLAST tool to initially subtype and taxonomically identify aerobic and facultative anaerobic spore-formers. While whole-genome sequencing is increasingly used in bacterial taxonomy, the rpoB sequence-based identification scheme described here provides a valuable tool as it allows for rapid and cost-effective initial isolate characterization, which can help to identify and characterize foodborne pathogens and food spoilage bacteria. In addition, the database and primers described here can also be adopted for metagenomics approaches that include rpoB as a target, improving discriminatory power and identification over what can be achieved using 16S rDNA as a target.
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Affiliation(s)
- Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
| | - Rachel A Cheng
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Aljosa Trmcic
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Jasna Kovac
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - David J Kent
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Nicole H Martin
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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Zalma SA, El-Sharoud WM. Diverse thermophilic Bacillus species with multiple biotechnological activities are associated within the Egyptian soil and compost samples. Sci Prog 2021; 104:368504211055277. [PMID: 34816770 PMCID: PMC10461379 DOI: 10.1177/00368504211055277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Thermophilic strains of Bacillus can express enzymes of higher thermal stability, which allows carrying out industrial fermentations under higher temperatures. This lowers the contamination potential, accelerates mixing rates and facilitates the recovery of fermentation end products. The present study was thus designed to isolate and characterize thermophilic Bacillus cultures from soil and compost samples. Forty-two thermophilic Bacillus isolates could be identified employing morphological, physiological and the 16S rRNA gene sequencing analyses. The isolates showed a high degree of biological diversity involving 13 Bacillus species and 1 subspecies but were dominated by Bacillus licheniformis. Phylogenetic analysis of B. licheniformis isolates based on the DNA sequencing of gyrA and rpoB genes presented them in two main genetic groups. Isolates of five thermophilic species including B. licheniformis, Bacillus altitudinis, Bacillus paralicheniformis, Bacillus subtilis and Bacillus thermoamylovorans showed multiple activities to degrade all of cellulose, hemicellulose and lignin. Those multifunctional thermophilic Bacillus isolates can be harnessed in the degradation of plant wastes for the production of biofuels and compost.
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Affiliation(s)
- SA Zalma
- Food Safety and Microbial
Physiology Lab, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - WM El-Sharoud
- Food Safety and Microbial
Physiology Lab, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
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Wolf-Jäckel GA, Strube ML, Schou KK, Schnee C, Agerholm JS, Jensen TK. Bovine Abortions Revisited-Enhancing Abortion Diagnostics by 16S rDNA Amplicon Sequencing and Fluorescence in situ Hybridization. Front Vet Sci 2021; 8:623666. [PMID: 33708810 PMCID: PMC7940352 DOI: 10.3389/fvets.2021.623666] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/21/2021] [Indexed: 11/13/2022] Open
Abstract
Abortion in cattle causes significant economic losses for cattle farmers worldwide. The diversity of abortifacients makes abortion diagnostics a complex and challenging discipline that additionally is restrained by time and economy. Microbial culture has traditionally been an important method for the identification of bacterial and mycotic abortifacients. However, it comes with the inherent bias of favoring the easy-to-culture species, e.g., those that do not require cell culture, pre-enrichment, a variety of selective growth media, or different oxygen levels for in vitro growth. Molecular methods such as polymerase chain reaction (PCR) and next-generation sequencing have been established as alternatives to traditional microbial culturing methods in several diagnostic fields including abortion diagnostics. Fluorescence in situ hybridization (FISH), a bridging microscopy technique that combines molecular accuracy with culture independence, and spatial resolution of the pathogen-lesion relation, is also gaining influence in several diagnostic fields. In this study, real-time quantitative PCR (qPCR), 16S rDNA amplicon sequencing, and FISH were applied separately and in combination in order to (i) identify potentially abortifacient bacteria without the bias of culturability, (ii) increase the diagnostic rate using combined molecular methods, (iii) investigate the presence of the difficult-to-culture zoonotic agents Coxiella burnetii, Chlamydia spp., and Leptospira spp. in bovine abortions in Denmark. Tissues from 162 aborted or stillborn bovine fetuses and placentas submitted for routine diagnostics were screened for pathogenic bacteria using 16S rDNA amplicon sequencing. Lesion association of fungal elements, as well as of selection of bacterial abortifacients, was assessed using specific FISH assays. The presence of Chlamydia spp. and chlamydia-like organisms was assessed using qPCR. The study focused on bacterial and fungal abortifacients, because Danish cattle is free from most viral abortifacients. The 16S rDNA amplicon sequencing-guided FISH approach was suitable for enhancing abortion diagnostics, i.e., the diagnostic rate for cases with tissue lesions (n = 115) was increased from 46 to 53% when compared to routine diagnostic methods. Identification of Bacillus licheniformis, Escherichia coli, and Trueperella pyogenes accounted for the majority of additional cases with an established etiology. No evidence for emerging or epizootic bacterial pathogens was found. The difficult-to-culture abortifacients were either not detected or not identified as abortifacients.
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Affiliation(s)
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Christiane Schnee
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Jena, Germany
| | - Jørgen S Agerholm
- Section for Veterinary Reproduction and Obstetrics, Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Taastrup, Denmark
| | - Tim Kåre Jensen
- National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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11
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Muras A, Romero M, Mayer C, Otero A. Biotechnological applications of Bacillus licheniformis. Crit Rev Biotechnol 2021; 41:609-627. [PMID: 33593221 DOI: 10.1080/07388551.2021.1873239] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacillus licheniformis is a Gram positive spore-forming bacterial species of high biotechnological interest with numerous present and potential uses, including the production of bioactive compounds that are applied in a wide range of fields, such as aquaculture, agriculture, food, biomedicine, and pharmaceutical industries. Its use as an expression vector for the production of enzymes and other bioproducts is also gaining interest due to the availability of novel genetic manipulation tools. Furthermore, besides its widespread use as a probiotic, other biotechnological applications of B. licheniformis strains include: bioflocculation, biomineralization, biofuel production, bioremediation, and anti-biofilm activity. Although authorities have approved the use of B. licheniformis as a feed additive worldwide due to the absence of toxigenic potential, some probiotics containing this bacterium are considered unsafe due to the possible transference of antibiotic resistance genes. The wide variability in biological activities and genetic characteristics of this species makes it necessary to establish an exact protocol for describing the novel strains, in order to evaluate its biotechnological potential.
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Affiliation(s)
- Andrea Muras
- Departmento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Manuel Romero
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Celia Mayer
- Departmento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana Otero
- Departmento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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12
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Lee N, Kim MD, Lim MC. Autoinducer-2 Could Affect Biofilm Formation by Food-Derived Bacillus cereus. Indian J Microbiol 2021; 61:66-73. [PMID: 33505094 DOI: 10.1007/s12088-020-00918-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/11/2020] [Indexed: 12/29/2022] Open
Abstract
Bacillus cereus is a foodborne pathogen and cause a frequent problem due to the biofilms forming in equipment of food production plants. Autoinducer-2 (AI-2) involved in interspecies communication, plays a role in the biofilm formation of B. cereus. In this study, biofilm formation by thirty-nine B. cereus strains isolated from foods produced in Korea was determined. To investigate the effect of AI-2 on biofilm formation by B. cereus SBC27, which had the highest biofilm-forming ability, biofilm densities formed after addition of the AI-2 from Staphylococcus aureus and Escherichia coli were analysed. As a result, it was found that the quorum sensing molecule AI-2 could induce biofilm formation by B. cereus within 24 h, but it may also inhibit biofilm formation when more AI-2 is added after 24 h. Thus, these results improve our understanding of biofilm formation by food-derived B. cereus and provide clues that could help to reduce the impact of biofilms, the biggest problem in food processing environments, which has an impact on public health as well as the economy.
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Affiliation(s)
- Nari Lee
- Research Group of Consumer Safety, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do 55365 Republic of Korea
| | - Myo-Deok Kim
- Research Group of Consumer Safety, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do 55365 Republic of Korea
| | - Min-Cheol Lim
- Research Group of Consumer Safety, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do 55365 Republic of Korea
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13
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Özdemir F, Arslan S. Molecular Characterization and Toxin Profiles of Bacillus spp. Isolated from Retail Fish and Ground Beef. J Food Sci 2019; 84:548-556. [PMID: 30690739 DOI: 10.1111/1750-3841.14445] [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: 06/11/2018] [Revised: 12/11/2018] [Accepted: 12/21/2018] [Indexed: 02/07/2023]
Abstract
Bacillus species are common in the environment due to their spore-forming ability and nutritional versatility and cause food contamination. Bacilli play a significant role in foodborne illnesses and food spoilage. In this study, 52 Bacillus isolates from retail fish and ground beef were identified and differentiated based on 16S rRNA, gyrB, and rpoB gene sequencing. The presence of genes encoding emetic toxin (ces), hemolytic enterotoxin hemolysin BL (hbl), nonhemolytic enterotoxin (nhe) and cytotoxin K (cytK1) was assessed in all Bacillus isolates. The ability of the Bacillus isolates to produce several extracellular enzymes that contribute to pathogenicity and food spoilage was investigated. The 16S rRNA, rpoB, and gyrB gene sequence similarities of the Bacillus isolates tested were 96.1%, 83.2%, and 77.5%, respectively. The gyrB gene demonstrated a higher degree of sequence variation than the 16S rRNA and rpoB genes. The prevalence of Bacillus isolates producing at least two of the genes of the HBL and NHE complexes was 23.1% and 15.4%, respectively. Of the B. cereus isolates, 10 (41.7%) possessed two or more enterotoxin genes. None of the isolates carried the ces and cytK1 genes. All isolates were positive for the production of enzymes such as protease, lipase, gelatinase, and DNase. However, only 92.3% of the tested isolates were positive for amylase. In conclusion, our results revealed that the presence of genes involved in toxin production and enzyme production in meat-originated B. cereus and other Bacillus isolates may cause spoilage of food and pose a health risk for consumers. PRACTICAL APPLICATION: Bacillus species can be found in various foods due to their ubiquitous nature. Bacillus spp., especially B. cereus, are associated with food poisoning and other infections in humans. Toxins and many extracellular enzymes produced by Bacillus spp. are the causative agents of foodborne outbreaks, food spoilage, and low-quality food with significantly reduced edibility. This study highlights the characterization of Bacillus spp. and presence of potentially pathogenic Bacillus species in meats.
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Affiliation(s)
- Fatma Özdemir
- Dept. of Biology, Faculty of Arts and Sciences, Bolu Abant İzzet Baysal Univ., Gölköy, Bolu, 14030, Turkey
| | - Seza Arslan
- Dept. of Biology, Faculty of Arts and Sciences, Bolu Abant İzzet Baysal Univ., Gölköy, Bolu, 14030, Turkey
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14
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Rapid screening of starter cultures for maari based on antifungal properties. Microbiol Res 2018; 207:66-74. [DOI: 10.1016/j.micres.2017.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 08/17/2017] [Accepted: 11/07/2017] [Indexed: 11/20/2022]
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Isolation and Characterization of Thermophilic Bacteria from Jordanian Hot Springs: Bacillus licheniformis and Thermomonas hydrothermalis Isolates as Potential Producers of Thermostable Enzymes. Int J Microbiol 2017; 2017:6943952. [PMID: 29163641 PMCID: PMC5661075 DOI: 10.1155/2017/6943952] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 08/08/2017] [Accepted: 08/24/2017] [Indexed: 01/02/2023] Open
Abstract
The aim of this study was the isolation and characterization of thermophilic bacteria from hot springs in Jordan. Ten isolates were characterized by morphological, microscopic, biochemical, molecular, and physiological characteristics. Sequencing of the 16S rDNA of the isolates followed by BLAST search revealed that nine strains could be identified as Bacillus licheniformis and one isolate as Thermomonas hydrothermalis. This is the first report on the isolation of Thermomonas species from Jordanian hot springs. The isolates showed an ability to produce some thermostable enzymes such as amylase, protease, cellulose, gelatins, and lecithin. Moreover, the UPGMA dendrogram of the enzymatic characteristics of the ten isolates was constructed; results indicated a high phenotypic diversity, which encourages future studies to explore further industrial and environmental applications.
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Zhang J, Wang PC, Fang L, Zhang QA, Yan CS, Chen JY. Isolation and Characterization of Phosphate-Solubilizing Bacteria from Mushroom Residues and their Effect on Tomato Plant Growth Promotion. Pol J Microbiol 2017; 66:57-65. [DOI: 10.5604/17331331.1234993] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phosphorus is a major essential macronutrient for plant growth, and most of the phosphorus in soil remains in insoluble form. Highly efficient phosphate-solubilizing bacteria can be used to increase phosphorus in the plant rhizosphere. In this study, 13 isolates were obtained from waste mushroom residues, which were composed of cotton seed hulls, corn cob, biogas residues, and wood flour. NBRIP solid medium was used for isolation according to the dissolved phosphorus halo. Eight isolates produced indole acetic acid (61.5%), and six isolates produced siderophores (46.2%). Three highest phosphate-dissolving bacterial isolates, namely, M01, M04, and M11, were evaluated for their beneficial effects on the early growth of tomato plants (Solanum lycopersicum L. Wanza 15). Strains M01, M04, and M11 significantly increased the shoot dry weight by 30.5%, 32.6%, and 26.2%, and root dry weight by 27.1%, 33.1%, and 25.6%, respectively. Based on 16S rRNA gene sequence comparisons and phylogenetic positions, strains M01 and M04 belonged to the genus Acinetobacter, and strain M11 belonged to the genus Ochrobactrum. The findings suggest that waste mushroom residues are a potential resource of plant growth-promoting bacteria exhibiting satisfactory phosphate-solubilizing for sustainable agriculture.
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17
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Sun Y, De Vos P, Heylen K. Nitrous oxide emission by the non-denitrifying, nitrate ammonifier Bacillus licheniformis. BMC Genomics 2016; 17:68. [PMID: 26786044 PMCID: PMC4719734 DOI: 10.1186/s12864-016-2382-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/06/2016] [Indexed: 02/08/2023] Open
Abstract
Background Firmicutes have the capacity to remove excess nitrate from the environment via either denitrification, dissimilatory nitrate reduction to ammonium or both. The recent renewed interest in their nitrogen metabolism has revealed many interesting features, the most striking being their wide variety of dissimilatory nitrate reduction pathways. In the present study, nitrous oxide production from Bacillus licheniformis, a ubiquitous Gram-positive, spore-forming species with many industrial applications, is investigated. Results B. licheniformis has long been considered a denitrifier but physiological experiments on three different strains demonstrated that nitrous oxide is not produced from nitrate in stoichiometric amounts, rather ammonium is the most important end-product, produced during fermentation. Significant strain dependency in end-product ratios, attributed to nitrite and ammonium, and medium dependency in nitrous oxide production were also observed. Genome analyses confirmed the lack of a nitrite reductase to nitric oxide, the key enzyme of denitrification. Based on the gene inventory and building on knowledge from other non-denitrifying nitrous oxide emitters, hypothetical pathways for nitrous oxide production, involving NarG, NirB, qNor and Hmp, are proposed. In addition, all publically available genomes of B. licheniformis demonstrated similar gene inventories, with specific duplications of the nar operon, narK and hmp genes as well as NarG phylogeny supporting the evolutionary separation of previously described distinct BALI1 and BALI2 lineages. Conclusions Using physiological and genomic data we have demonstrated that the common soil bacterium B. licheniformis does not denitrify but is capable of fermentative dissimilatory nitrate/nitrite reduction to ammonium (DNRA) with concomitant production of N2O. Considering its ubiquitous nature and non-fastidious growth in the lab, B. licheniformis is a suitable candidate for further exploration of the actual mechanism of N2O production in DNRA bacteria and its relevance in situ. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2382-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yihua Sun
- Department of Biochemistry and Microbiology, Laboratory of Microbiology, (LM-UGent), University of Ghent, K.L. Ledeganckstraat 35, 9000, Gent, Belgium.
| | - Paul De Vos
- Department of Biochemistry and Microbiology, Laboratory of Microbiology, (LM-UGent), University of Ghent, K.L. Ledeganckstraat 35, 9000, Gent, Belgium. .,BCCM/LMG Bacteria Collection, K.L. Ledeganckstraat 35, 9000, Gent, Belgium.
| | - Kim Heylen
- Department of Biochemistry and Microbiology, Laboratory of Microbiology, (LM-UGent), University of Ghent, K.L. Ledeganckstraat 35, 9000, Gent, Belgium.
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18
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Characterization and Application of Biosurfactant Produced by Bacillus licheniformis R2. Appl Biochem Biotechnol 2015; 177:346-61. [PMID: 26186955 DOI: 10.1007/s12010-015-1746-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 07/06/2015] [Indexed: 10/23/2022]
Abstract
The biosurfactant produced by Bacillus licheniformis R2 was characterized and studied for enhancing the heavy crude oil recovery at 80 °C in coreflood experiments. The strain was found to be nonpathogenic and produced biosurfactant, reducing the surface tension of medium from 70 to 28 mN/m with 1.1 g/l yield. The biosurfactant was quite stable during exposure to elevated temperatures (85 °C for 90 days), high salinity (10 % NaCl), and a wide range of pH (5-12) for 10 days. It was characterized as lipopeptide similar to lichenysin-A, with a critical micelle concentration of about 19.4 mg/l. The efficiency of crude biosurfactant for enhanced oil recovery by core flood studies revealed it to recovering additional 37.1 % oil from Berea sandstone cores at 80 °C. The results are indicative of the potential for the development of lipopeptide biosurfactant-based ex situ microbial enhanced heavy oil recovery from depleting oil fields with extreme temperatures.
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Aanniz T, Ouadghiri M, Melloul M, Swings J, Elfahime E, Ibijbijen J, Ismaili M, Amar M. Thermophilic bacteria in Moroccan hot springs, salt marshes and desert soils. Braz J Microbiol 2015; 46:443-53. [PMID: 26273259 PMCID: PMC4507536 DOI: 10.1590/s1517-838246220140219] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 09/30/2014] [Indexed: 11/22/2022] Open
Abstract
The diversity of thermophilic bacteria was investigated in four hot springs, three salt marshes and 12 desert sites in Morocco. Two hundred and forty (240) thermophilic bacteria were recovered, identified and characterized. All isolates were Gram positive, rod-shaped, spore forming and halotolerant. Based on BOXA1R-PCR and 16S rRNA gene sequencing, the recovered isolates were dominated by the genus Bacillus (97.5%) represented by B. licheniformis (119), B. aerius (44), B. sonorensis (33), B. subtilis (subsp. spizizenii (2) and subsp. inaquosurum (6)), B. amyloliquefaciens (subsp. amyloliquefaciens (4) and subsp. plantarum (4)), B. tequilensis (3), B. pumilus (3) and Bacillus sp. (19). Only six isolates (2.5%) belonged to the genus Aeribacillus represented by A. pallidus (4) and Aeribacillus sp. (2). In this study, B. aerius and B. tequilensis are described for the first time as thermophilic bacteria. Moreover, 71.25%, 50.41% and 5.41% of total strains exhibited high amylolytic, proteolytic or cellulolytic activity respectively.
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Affiliation(s)
- Tarik Aanniz
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Maroc, Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Maroc. ; Faculté des Sciences, Université Moulay Ismail, Meknès, Maroc, Faculté des Sciences, Université Moulay Ismail, Meknès, Maroc
| | - Mouna Ouadghiri
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Maroc, Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Maroc. ; Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Maroc, Collections Coordonnées Marocaines de Microorganismes, Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Maroc
| | - Marouane Melloul
- Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Maroc, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Maroc
| | - Jean Swings
- Laboratory of Microbiology, Gent University, Gent, Belgium, Laboratory of Microbiology, Gent University, Gent, Belgium
| | - Elmostafa Elfahime
- Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Maroc, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Maroc
| | - Jamal Ibijbijen
- Faculté des Sciences, Université Moulay Ismail, Meknès, Maroc, Faculté des Sciences, Université Moulay Ismail, Meknès, Maroc
| | - Mohamed Ismaili
- Faculté des Sciences, Université Moulay Ismail, Meknès, Maroc, Faculté des Sciences, Université Moulay Ismail, Meknès, Maroc
| | - Mohamed Amar
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Maroc, Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Maroc. ; Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Maroc, Collections Coordonnées Marocaines de Microorganismes, Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Maroc
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Anyogu A, Awamaria B, Sutherland J, Ouoba L. Molecular characterisation and antimicrobial activity of bacteria associated with submerged lactic acid cassava fermentation. Food Control 2014. [DOI: 10.1016/j.foodcont.2013.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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21
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Draft genome comparison of representatives of the three dominant genotype groups of dairy Bacillus licheniformis strains. Appl Environ Microbiol 2014; 80:3453-62. [PMID: 24657871 DOI: 10.1128/aem.00065-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The spore-forming bacterium Bacillus licheniformis is a common contaminant of milk and milk products. Strains of this species isolated from dairy products can be differentiated into three major groups, namely, G, F1, and F2, using random amplification of polymorphic DNA (RAPD) analysis; however, little is known about the genomic differences between these groups and the identity of the fragments that make up their RAPD profiles. In this work we obtained high-quality draft genomes of representative strains from each of the three RAPD groups (designated strain G-1, strain F1-1, and strain F2-1) and compared them to each other and to B. licheniformis ATCC 14580 and Bacillus subtilis 168. Whole-genome comparison and multilocus sequence typing revealed that strain G-1 contains significant sequence variability and belongs to a lineage distinct from the group F strains. Strain G-1 was found to contain genes coding for a type I restriction modification system, urease production, and bacitracin synthesis, as well as the 8-kbp plasmid pFL7, and these genes were not present in strains F1-1 and F2-1. In agreement with this, all isolates of group G, but no group F isolates, were found to possess urease activity and antimicrobial activity against Micrococcus. Identification of RAPD band sequences revealed that differences in the RAPD profiles were due to differences in gene lengths, 3' ends of predicted primer binding sites, or gene presence or absence. This work provides a greater understanding of the phylogenetic and phenotypic differences observed within the B. licheniformis species.
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Narh CA, Mosi L, Quaye C, Tay SC, Bonfoh B, de Souza DK. Genotyping Tools for Mycobacterium ulcerans-Drawbacks and Future Prospects. ACTA ACUST UNITED AC 2014; 4:1000149. [PMID: 24900947 PMCID: PMC4040416 DOI: 10.4172/2161-1068.1000149] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Mycobacterium ulcerans infection (Buruli ulcer) is a neglected but treatable skin disease endemic in over 30 countries. M. ulcerans is an environmental mycobacteria with an elusive mode of transmission to humans. Ecological and Molecular epidemiological studies to identify reservoirs and transmission vectors are important for source tracking infections especially during outbreaks and elucidating transmission routes. Research efforts have therefore focused on genotyping strains of the mycobacteria from clinical and environmental samples. This review discusses genotyping tools for differentiating M. ulcerans strains from other environmental and Mycolactone Producing Mycobacteria (MPMs). We highlight tools that have been adapted from related fields and propose ways these could be enhanced to resolve intra-species variation for epidemiological, transmission, evolutionary studies, and detection of emerging drug resistant strains. In the wake of increasing cases of Buruli ulcer, cumulative efforts including improvement in diagnostic methods and fine-tuning of genotyping tools are crucial to complement public health efforts in reducing infections.
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Affiliation(s)
- Charles A Narh
- Parasitology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana ; Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Ivory Coast ; Clinical Microbiology Department, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Ghana
| | - Lydia Mosi
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Ivory Coast ; Biochemistry, Cell and Molecular Biology Department, University of Ghana
| | - Charles Quaye
- Parasitology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana ; Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Ivory Coast
| | - Samuel Ck Tay
- Clinical Microbiology Department, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Ghana
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Ivory Coast
| | - Dziedzom K de Souza
- Parasitology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana
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Dhakal R, Chauhan K, Seale RB, Deeth HC, Pillidge CJ, Powell IB, Craven H, Turner MS. Genotyping of dairy Bacillus licheniformis isolates by high resolution melt analysis of multiple variable number tandem repeat loci. Food Microbiol 2013; 34:344-51. [DOI: 10.1016/j.fm.2013.01.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 01/08/2013] [Accepted: 01/10/2013] [Indexed: 11/25/2022]
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24
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Ahaotu I, Anyogu A, Njoku OH, Odu NN, Sutherland JP, Ouoba LII. Molecular identification and safety of Bacillus species involved in the fermentation of African oil beans (Pentaclethra macrophylla Benth) for production of Ugba. Int J Food Microbiol 2013; 162:95-104. [PMID: 23376783 DOI: 10.1016/j.ijfoodmicro.2013.01.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 12/19/2012] [Accepted: 01/02/2013] [Indexed: 11/29/2022]
Abstract
Molecular identification of Bacillus spp. involved in the fermentation of African oil bean seeds for production of Ugba, as well as ability of the Bacillus spp. isolated to produce toxins, were investigated. Forty-nine bacteria were isolated from Ugba produced in different areas of South Eastern Nigeria and identified by phenotyping and sequencing of 16S rRNA, gyrB and rpoB genes. Genotypic diversities at interspecies and intraspecies level of the isolates were screened by PCR amplification of the 16S-23S rDNA intergenic transcribed spacer (ITS-PCR) and repetitive sequence-based PCR (rep-PCR). The ability of the bacteria to produce toxins was also investigated by detection of genes encoding production of haemolysin BL (HblA, HblC, HblD), non-haemolytic enterotoxin (NheA, NheB, NheC), cytotoxin K (CytK) and emetic toxin (EM1) using PCR with specific primers. Moreover, a Bacillus cereus Enterotoxin Reverse Passive Latex Agglutination test kit (BCET-RPLA) was used to screen ability of the isolates to produce haemolysin in broth and during fermentation of African oil bean seeds. The isolates were characterized as motile, rod-shaped, endospore forming, catalase positive, Gram-positive bacteria. They were identified as Bacillus cereus sensu lato (42), Lysinibacillus xylanilyticus (3), Bacillus clausii (1), Bacillus licheniformis (1), Bacillus subtilis (1), and Bacillus safensis (1). B. cereus was the predominant Bacillus species and was present in all samples studied. Using ITS-PCR, interspecies diversity was observed among isolates, with six clusters representing each of the pre-cited species. Rep-PCR was more discriminatory (eight clusters) and allowed further differentiation at intraspecies level for the B. cereus and L. xylanilyticus isolates with two genotypes for each species. Genes encoding production of non-haemolytic enterotoxin (NheA, NheB, NheC) and cytotoxin K (CytK) genes were detected in all B. cereus isolates, while Hbl genes (HblA, HblC, HblD) were detected in only one isolate. The emetic-specific gene fragment was not detected in any of the isolates studied. None of the toxin genes screened was detected in isolates belonging to other Bacillus species. Using RPLA, haemolysin production was detected in one isolate of B. cereus, which showed positive amplicons for Hbl genes, both during cultivation in broth and during fermentation of oil bean seeds.
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Affiliation(s)
- I Ahaotu
- Department of Food Science, Federal University of Technology, Owerri, Nigeria
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Guo Q, Li S, Lu X, Li B, Stummer B, Dong W, Ma P. phoRsequences as a phylogenetic marker to differentiate the species in theBacillus subtilisgroup. Can J Microbiol 2012; 58:1295-305. [DOI: 10.1139/w2012-106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacillus subtilis and its closely related species are indistinguishable from one another by morphological characteristics and 16S rDNA sequences. In this study, the partial phoR sequence was tested to determine the phylogenetic relationship of species in the B. subtilis group. Degenerate primers were developed according to the relatively conserved nucleotide sequences of phoR and the linked gene phoP in the B. subtilis group. The primers amplified a 1100 bp phoR fragment from strains representative of 6 species in the B. subtilis group. Based on the sequenced fragments, 26 type strains comprising these 6 species were clearly distinguished. At the intraspecies level, the phoR sequence similarities were 90%–100%, but at the interspecies level, the phoR sequence similarities were 32.8%–75%. Compared with the gyrB sequence, the phoR sequences showed a larger divergence especially at the interspecies levels. Therefore, the phoR sequence may be an efficient alternative marker for phylogenetic and taxonomic analysis of species in the B. subtilis group. Twenty-three Bacillus undomesticated isolates were tested for identification and phylogenetic analysis based on the phoR and gyrB sequences. The 23 isolates could be clearly delineated into 4 distinct groups, 10 as B. subtilis, 3 as B. mojavensis, 2 as B. atrophaeus, and 8 as B. amyloliquefaciens.
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Affiliation(s)
- Qinggang Guo
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences; IPM Centre of Hebei Province; Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, P.R. China, Baoding, Hebei 071000, People’s Republic of China, 071000
| | - Shezeng Li
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences; IPM Centre of Hebei Province; Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, P.R. China, Baoding, Hebei 071000, People’s Republic of China, 071000
| | - Xiuyun Lu
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences; IPM Centre of Hebei Province; Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, P.R. China, Baoding, Hebei 071000, People’s Republic of China, 071000
| | - Baoqing Li
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences; IPM Centre of Hebei Province; Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, P.R. China, Baoding, Hebei 071000, People’s Republic of China, 071000
| | - Belinda Stummer
- CSIRO Sustainable Agriculture National Research Flagship/CSIRO Ecosystem Sciences, PMB2, Glen Osmond, SA, 5064, Australia
| | - Weixin Dong
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences; IPM Centre of Hebei Province; Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, P.R. China, Baoding, Hebei 071000, People’s Republic of China, 071000
| | - Ping Ma
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences; IPM Centre of Hebei Province; Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, P.R. China, Baoding, Hebei 071000, People’s Republic of China, 071000
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Madslien EH, Olsen JS, Granum PE, Blatny JM. Genotyping of B. licheniformis based on a novel multi-locus sequence typing (MLST) scheme. BMC Microbiol 2012; 12:230. [PMID: 23051848 PMCID: PMC3492095 DOI: 10.1186/1471-2180-12-230] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 09/14/2012] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Bacillus licheniformis has for many years been used in the industrial production of enzymes, antibiotics and detergents. However, as a producer of dormant heat-resistant endospores B. licheniformis might contaminate semi-preserved foods. The aim of this study was to establish a robust and novel genotyping scheme for B. licheniformis in order to reveal the evolutionary history of 53 strains of this species. Furthermore, the genotyping scheme was also investigated for its use to detect food-contaminating strains. RESULTS A multi-locus sequence typing (MLST) scheme, based on the sequence of six house-keeping genes (adk, ccpA, recF, rpoB, spo0A and sucC) of 53 B. licheniformis strains from different sources was established. The result of the MLST analysis supported previous findings of two different subgroups (lineages) within this species, named "A" and "B" Statistical analysis of the MLST data indicated a higher rate of recombination within group "A". Food isolates were widely dispersed in the MLST tree and could not be distinguished from the other strains. However, the food contaminating strain B. licheniformis NVH1032, represented by a unique sequence type (ST8), was distantly related to all other strains. CONCLUSIONS In this study, a novel and robust genotyping scheme for B. licheniformis was established, separating the species into two subgroups. This scheme could be used for further studies of evolution and population genetics in B. licheniformis.
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Affiliation(s)
- Elisabeth H Madslien
- Forsvarets Forskningsinstitutt FFI, Norwegian Defence Research Establishment, P. O. Box 25, Kjeller, N-2027, Norway
- Department of Food Safety and Infection Biology, Section for Food Safety, Norwegian School of Veterinary Science, P. O. Box 8146 Dep, Oslo, N-0033, Norway
| | - Jaran S Olsen
- Forsvarets Forskningsinstitutt FFI, Norwegian Defence Research Establishment, P. O. Box 25, Kjeller, N-2027, Norway
| | - Per E Granum
- Department of Food Safety and Infection Biology, Section for Food Safety, Norwegian School of Veterinary Science, P. O. Box 8146 Dep, Oslo, N-0033, Norway
| | - Janet M Blatny
- Forsvarets Forskningsinstitutt FFI, Norwegian Defence Research Establishment, P. O. Box 25, Kjeller, N-2027, Norway
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Joshi SJ, Suthar H, Yadav AK, Hingurao K, Nerurkar A. Occurrence of Biosurfactant Producing Bacillus spp. in Diverse Habitats. ISRN BIOTECHNOLOGY 2012; 2013:652340. [PMID: 25969778 PMCID: PMC4403617 DOI: 10.5402/2013/652340] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 06/07/2012] [Indexed: 11/23/2022]
Abstract
Diversity among biosurfactant producing Bacillus spp. from diverse habitats was studied among 77 isolates. Cluster analysis based on phenotypic characteristics using unweighted pair-group method with arithmetic averages (UPGMAs) method was performed. Bacillus isolates possessing high surface tension activity and five reference strains were subjected to amplified 16S rDNA restriction analysis (ARDRA). A correlation between the phenotypic and genotypic characterization of Bacillus spp. is explored. Most of the oil reservoir isolates showing high surface activity clustered with B. licheniformis and B. subtilis, the hot water spring isolates clustered in two ingroups, while the petroleum contaminated soil isolates were randomly distributed in all the three ingroups. Present work revealed that diversity exists in distribution of Bacillus spp. from thermal and hydrocarbon containing habitats where majority of organisms belonged to B. licheniformis and B. subtilis group. Isolate B. licheniformis TT42 produced biosurfactant which reduced the surface tension of water from 72 mNm−1 to 28 mNm−1, and 0.05 mNm−1 interfacial tension against crude oil at 80°C. This isolate clustered with B. subtilis and B. licheniformis group on the basis of ARDRA. These findings increase the possibility of exploiting the Bacillus spp. from different habitats and their possible use in oil recovery.
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Affiliation(s)
- Sanket J Joshi
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
| | - Harish Suthar
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
| | - Amit Kumar Yadav
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
| | - Krushi Hingurao
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
| | - Anuradha Nerurkar
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
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Leekitcharoenphon P, Lukjancenko O, Friis C, Aarestrup FM, Ussery DW. Genomic variation in Salmonella enterica core genes for epidemiological typing. BMC Genomics 2012; 13:88. [PMID: 22409488 PMCID: PMC3359268 DOI: 10.1186/1471-2164-13-88] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 03/12/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Technological advances in high throughput genome sequencing are making whole genome sequencing (WGS) available as a routine tool for bacterial typing. Standardized procedures for identification of relevant genes and of variation are needed to enable comparison between studies and over time. The core genes--the genes that are conserved in all (or most) members of a genus or species--are potentially good candidates for investigating genomic variation in phylogeny and epidemiology. RESULTS We identify a set of 2,882 core genes clusters based on 73 publicly available Salmonella enterica genomes and evaluate their value as typing targets, comparing whole genome typing and traditional methods such as 16S and MLST. A consensus tree based on variation of core genes gives much better resolution than 16S and MLST; the pan-genome family tree is similar to the consensus tree, but with higher confidence. The core genes can be divided into two categories: a few highly variable genes and a larger set of conserved core genes, with low variance. For the most variable core genes, the variance in amino acid sequences is higher than for the corresponding nucleotide sequences, suggesting that there is a positive selection towards mutations leading to amino acid changes. CONCLUSIONS Genomic variation within the core genome is useful for investigating molecular evolution and providing candidate genes for bacterial genome typing. Identification of genes with different degrees of variation is important especially in trend analysis.
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Banykó J, Vyletělová M. Determining the source ofBacillus cereusandBacillus licheniformisisolated from raw milk, pasteurized milk and yoghurt. Lett Appl Microbiol 2009; 48:318-23. [DOI: 10.1111/j.1472-765x.2008.02526.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Porwal S, Lal S, Cheema S, Kalia VC. Phylogeny in aid of the present and novel microbial lineages: diversity in Bacillus. PLoS One 2009; 4:e4438. [PMID: 19212464 PMCID: PMC2639701 DOI: 10.1371/journal.pone.0004438] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 12/18/2008] [Indexed: 11/18/2022] Open
Abstract
Bacillus represents microbes of high economic, medical and biodefense importance. Bacillus strain identification based on 16S rRNA sequence analyses is invariably limited to species level. Secondly, certain discrepancies exist in the segregation of Bacillus subtilis strains. In the RDP/NCBI databases, out of a total of 2611 individual 16S rDNA sequences belonging to the 175 different species of the genus Bacillus, only 1586 have been identified up to species level. 16S rRNA sequences of Bacillus anthracis (153 strains), B. cereus (211 strains), B. thuringiensis (108 strains), B. subtilis (271 strains), B. licheniformis (131 strains), B. pumilus (83 strains), B. megaterium (47 strains), B. sphaericus (42 strains), B. clausii (39 strains) and B. halodurans (36 strains) were considered for generating species-specific framework and probes as tools for their rapid identification. Phylogenetic segregation of 1121, 16S rDNA sequences of 10 different Bacillus species in to 89 clusters enabled us to develop a phylogenetic frame work of 34 representative sequences. Using this phylogenetic framework, 305 out of 1025, 16S rDNA sequences presently classified as Bacillus sp. could be identified up to species level. This identification was supported by 20 to 30 nucleotides long signature sequences and in silico restriction enzyme analysis specific to the 10 Bacillus species. This integrated approach resulted in identifying around 30% of Bacillus sp. up to species level and revealed that B. subtilis strains can be segregated into two phylogenetically distinct groups, such that one of them may be renamed.
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Affiliation(s)
- Shalini Porwal
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Delhi, India
- Department of Biotechnology, University of Pune, Pune, India
| | - Sadhana Lal
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Delhi, India
| | - Simrita Cheema
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Delhi, India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Delhi, India
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Felici C, Vettori L, Toffanin A, Nuti M. Development of a strain-specific genomic marker for monitoring a Bacillus subtilis biocontrol strain in the rhizosphere of tomato. FEMS Microbiol Ecol 2008; 65:289-98. [PMID: 18462399 DOI: 10.1111/j.1574-6941.2008.00489.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
A strain-specific molecular marker enabling the detection and tracking of the biological control agent Bacillus subtilis 101, when released into the environment, was developed. Random amplified polymorphic DNA (RAPD) technique was used to differentiate this from other B. subtilis strains. A differentially amplified fragment obtained from RAPD profiles was sequenced and characterized as sequence-characterized amplified region (SCAR) marker, and four primer pairs were designed and evaluated for their specificity towards this strain. The sensibility of the selected SCAR primer pair was evaluated by qualitative PCR and Southern blotting, and the detection limit was assessed around 10(2) CFU (g dry wt soil)(-1), thus providing a reliable tool for the traceability of this B. subtilis strain in greenhouse or field trials. A plating assay coupled to PCR with the SCAR primer pair was then used as a detection method in microcosm experiments for monitoring the population of B. subtilis 101 in the rhizosphere of tomato, grown under two different soil conditions, i.e. nonsterile peat-based substrate and sandy-loam agricultural soil, respectively. The data of rhizosphere colonization indicated that the soil conditions significantly affected the rhizosphere establishment of strain 101.
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Affiliation(s)
- Cristiana Felici
- Department of Crop Biology, Microbiology Unit, University of Pisa, Pisa, Italy
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De Jonghe V, Coorevits A, Vandroemme J, Heyrman J, Herman L, De Vos P, Heyndrickx M. Intraspecific genotypic diversity of Bacillus species from raw milk. Int Dairy J 2008. [DOI: 10.1016/j.idairyj.2007.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Pineiro SA, Williams HN, Stine OC. Phylogenetic relationships amongst the saltwater members of the genus Bacteriovorax using rpoB sequences and reclassification of Bacteriovorax stolpii as Bacteriolyticum stolpii gen. nov., comb. nov. Int J Syst Evol Microbiol 2008; 58:1203-9. [DOI: 10.1099/ijs.0.65710-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Microbial diversity and genomics in aid of bioenergy. J Ind Microbiol Biotechnol 2008; 35:403-419. [PMID: 18193465 DOI: 10.1007/s10295-007-0300-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Accepted: 12/14/2007] [Indexed: 12/27/2022]
Abstract
In view of the realization that fossil fuels reserves are limited, various options of generating energy are being explored. Biological methods for producing fuels such as ethanol, diesel, hydrogen (H2), methane, etc. have the potential to provide a sustainable energy system for the society. Biological H2 production appears to be the most promising as it is non-polluting and can be produced from water and biological wastes. The major limiting factors are low yields, lack of industrially robust organisms, and high cost of feed. Actually, H2 yields are lower than theoretically possible yields of 4 mol/mol of glucose because of the associated fermentation products such as lactic acid, propionic acid and ethanol. The efficiency of energy production can be improved by screening microbial diversity and easily fermentable feed materials. Biowastes can serve as feed for H2 production through a set of microbial consortia: (1) hydrolytic bacteria, (2) H2 producers (dark fermentative and photosynthetic). The efficiency of the bioconversion process may be enhanced further by the production of value added chemicals such as polydroxyalkanoate and anaerobic digestion. Discovery of enormous microbial diversity and sequencing of a wide range of organisms may enable us to realize genetic variability, identify organisms with natural ability to acquire and transmit genes. Such organisms can be exploited through genome shuffling for transgenic expression and efficient generation of clean fuel and other diverse biotechnological applications.
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Vanhoutte T, Huys G, De Brandt E, Fahey GC, Swings J. Molecular monitoring and characterization of the faecal microbiota of healthy dogs during fructan supplementation. FEMS Microbiol Lett 2005; 249:65-71. [PMID: 15979820 DOI: 10.1016/j.femsle.2005.06.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Revised: 05/25/2005] [Accepted: 06/01/2005] [Indexed: 10/25/2022] Open
Abstract
The large intestine of dogs contains a complex microbial ecosystem with predominance of streptococci, bifidobacteria, lactobacilli, Bacteroides and Clostridium. Generally, this predominant microbiota in dogs is relatively stable in time but much less is known about its taxonomic composition. Moreover, almost no studies have been conducted to investigate this stability of the faecal microbial population in dogs upon prebiotic administration. The objective of the present study was to monitor possible changes in faecal microbiota of seven healthy adult dogs related to the administration of two fructans, oligofructose and inulin. For this purpose, population fingerprints generated by denaturing gradient gel electrophoresis (DGGE) analysis of universal V3 16 S rRNA gene PCR amplicons were compared between control (baseline) samples and samples collected after prebiotic feeding. From these DGGE gels, marked changes were observed in the faecal microbiota between subjects and before and after fructan administration. One DGGE band that appeared or intensified after fructan intake was further analyzed. Sequence analysis could attribute this band to a member of the Streptococcus bovis-equinus group. Following cultivation on MRS medium, a set of faecal isolates that most likely represent the stimulated streptococci were allocated to the species Streptococcus lutetiensis by (GTG)(5)-PCR fingerprinting and partial 16 S rRNA and sodA gene sequencing. The data provided in this study demonstrate the ability of fructans to influence the bacterial composition of the gut microbiota in healthy dogs. More work is needed to unravel the relevance of S. lutetiensis or other autochthonous organisms of the dog gut as target groups for prebiotic supplementation.
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Affiliation(s)
- Tom Vanhoutte
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
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Scheldeman P, Pil A, Herman L, De Vos P, Heyndrickx M. Incidence and diversity of potentially highly heat-resistant spores isolated at dairy farms. Appl Environ Microbiol 2005; 71:1480-94. [PMID: 15746351 PMCID: PMC1065131 DOI: 10.1128/aem.71.3.1480-1494.2005] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2004] [Accepted: 10/11/2004] [Indexed: 11/20/2022] Open
Abstract
The presence of highly heat-resistant spores of Bacillus sporothermodurans in ultrahigh-temperature or sterilized consumer milk has emerged as an important item in the dairy industry. Their presence is considered undesirable since they hamper the achievement of commercial sterility requirements. By using a selective 30-min heat treatment at 100 degrees C, 17 Belgian dairy farms were screened to evaluate the presence, sources, and nature of potentially highly heat-resistant spores in raw milk. High numbers of these spores were detected in the filter cloth of the milking equipment and in green crop and fodder samples. About 700 strains were isolated after the selective heating, of which 635 could be screened by fatty acid methyl ester analysis. Representative strains were subjected to amplified ribosomal DNA restriction analysis, 16S rRNA gene sequencing, percent G+C content, and DNA-DNA reassociations for further identification. The strain collection showed a remarkable diversity, with representatives of seven aerobic spore-forming genera. Bacillus licheniformis and Bacillus pallidus were the most predominant species overall. Twenty-three percent of the 603 spore-forming isolates proved to belong to 18 separate novel species. These findings suggest that the selective heating revealed a pool of unknown organisms with a higher heat-resistant character. This study showed that high spore counts can occur at the dairy farm and that feed and milking equipment can act as reservoirs or entry points for potentially highly heat-resistant spores into raw milk. Lowering this spore load by good hygienic measures could probably further reduce the contamination level of raw milk, in this way minimizing the aerobic spore-forming bacteria that could lead to spoilage of milk and dairy products. Assessment and characterization of this particular flora are of great importance to allow the dairy or food industry to adequately deal with newly arising microbiological problems.
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MESH Headings
- Animals
- Bacillus/chemistry
- Bacillus/genetics
- Bacillus/isolation & purification
- Belgium
- Cattle
- Colony Count, Microbial
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- Dairying
- Fatty Acids/analysis
- Female
- Food Microbiology
- Genes, Bacterial
- Hot Temperature
- Milk/microbiology
- Molecular Sequence Data
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Species Specificity
- Spores, Bacterial/chemistry
- Spores, Bacterial/genetics
- Spores, Bacterial/isolation & purification
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Affiliation(s)
- Patsy Scheldeman
- Department of Animal Product Quality, Brusselsesteenweg 370, 9090 Melle, Belgium.
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Rey MW, Ramaiya P, Nelson BA, Brody-Karpin SD, Zaretsky EJ, Tang M, de Leon AL, Xiang H, Gusti V, Clausen IG, Olsen PB, Rasmussen MD, Andersen JT, Jørgensen PL, Larsen TS, Sorokin A, Bolotin A, Lapidus A, Galleron N, Ehrlich SD, Berka RM. Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biol 2004; 5:R77. [PMID: 15461803 PMCID: PMC545597 DOI: 10.1186/gb-2004-5-10-r77] [Citation(s) in RCA: 250] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2004] [Revised: 06/30/2004] [Accepted: 08/03/2004] [Indexed: 12/04/2022] Open
Abstract
The complete sequence of the Bacillus licheniformis ATCC 14580 genome was determined, revealing 4,208 predicted protein-coding genes, 7 rRNA operons and 72 tRNA genes. Background Bacillus licheniformis is a Gram-positive, spore-forming soil bacterium that is used in the biotechnology industry to manufacture enzymes, antibiotics, biochemicals and consumer products. This species is closely related to the well studied model organism Bacillus subtilis, and produces an assortment of extracellular enzymes that may contribute to nutrient cycling in nature. Results We determined the complete nucleotide sequence of the B. licheniformis ATCC 14580 genome which comprises a circular chromosome of 4,222,336 base-pairs (bp) containing 4,208 predicted protein-coding genes with an average size of 873 bp, seven rRNA operons, and 72 tRNA genes. The B. licheniformis chromosome contains large regions that are colinear with the genomes of B. subtilis and Bacillus halodurans, and approximately 80% of the predicted B. licheniformis coding sequences have B. subtilis orthologs. Conclusions Despite the unmistakable organizational similarities between the B. licheniformis and B. subtilis genomes, there are notable differences in the numbers and locations of prophages, transposable elements and a number of extracellular enzymes and secondary metabolic pathway operons that distinguish these species. Differences include a region of more than 80 kilobases (kb) that comprises a cluster of polyketide synthase genes and a second operon of 38 kb encoding plipastatin synthase enzymes that are absent in the B. licheniformis genome. The availability of a completed genome sequence for B. licheniformis should facilitate the design and construction of improved industrial strains and allow for comparative genomics and evolutionary studies within this group of Bacillaceae.
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Affiliation(s)
- Michael W Rey
- Novozymes Biotech Inc, 1445 Drew Ave, Davis, CA 95616, USA
| | | | - Beth A Nelson
- Novozymes Biotech Inc, 1445 Drew Ave, Davis, CA 95616, USA
| | | | | | - Maria Tang
- Novozymes Biotech Inc, 1445 Drew Ave, Davis, CA 95616, USA
| | | | - Henry Xiang
- Novozymes Biotech Inc, 1445 Drew Ave, Davis, CA 95616, USA
| | - Veronica Gusti
- Novozymes Biotech Inc, 1445 Drew Ave, Davis, CA 95616, USA
| | - Ib Groth Clausen
- Novozymes A/S, Bagsværd, DK-2880, Denmark
- AstraZeneca International, Lund SE221 87, Sweden
| | | | | | | | | | | | - Alexei Sorokin
- Institut National de la Recherche Agronomique, Paris Cedex 75007, France
| | - Alexander Bolotin
- Institut National de la Recherche Agronomique, Paris Cedex 75007, France
| | - Alla Lapidus
- Institut National de la Recherche Agronomique, Paris Cedex 75007, France
- Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Nathalie Galleron
- Institut National de la Recherche Agronomique, Paris Cedex 75007, France
| | - S Dusko Ehrlich
- Institut National de la Recherche Agronomique, Paris Cedex 75007, France
| | - Randy M Berka
- Novozymes Biotech Inc, 1445 Drew Ave, Davis, CA 95616, USA
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De Clerck E, Van Mol K, Jannes G, Rossau R, De Vos P. Design of a 5' exonuclease-based real-time PCR assay for simultaneous detection of Bacillus licheniformis, members of the 'B. cereus group' and B. fumarioli in gelatine. Lett Appl Microbiol 2004; 39:109-15. [PMID: 15189297 DOI: 10.1111/j.1472-765x.2004.01550.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS The design of a fast, sensitive and specific detection method for Bacillus licheniformis, members of the 'B. cereus group' and B. fumarioli in gelatine. METHODS AND RESULTS Specific Taqman probes were designed and tested in a real-time PCR setting. A specific fluorescent signal could be obtained for all gelatine isolates attributed to these species in one single real-time PCR reaction. After sample preparation, a gelatine sample spiked with 1 CFU provided enough template DNA for a significant signal. CONCLUSION The potential of a real-time PCR assay for simultaneous detection of B. licheniformis, members of the 'B. cereus group' and B. fumarioli in gelatine is demonstrated. SIGNIFICANCE AND IMPACT OF THE STUDY Implementation of the assay in gelatine producing plants may shorten delivery terms and inform on hazards to public health and suitable remediation procedures.
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Affiliation(s)
- E De Clerck
- Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, Ghent, Belgium.
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