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Xu B, Huang X, Qin H, Lei Y, Zhao S, Liu S, Liu G, Zhao J. Evaluating the Safety of Bacillus cereus GW-01 Obtained from Sheep Rumen Chyme. Microorganisms 2024; 12:1457. [PMID: 39065225 PMCID: PMC11278751 DOI: 10.3390/microorganisms12071457] [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: 06/08/2024] [Revised: 06/26/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Bacillus cereus is responsible for 1.4-12% food poisoning outbreaks worldwide. The safety concerns associated with the applications of B. cereus in health and medicine have been controversial due to its dual role as a pathogen for foodborne diseases and a probiotic in humans and animals. In this study, the pathogenicity of B. cereus GW-01 was assessed by comparative genomic, and transcriptome analysis. Phylogenetic analysis based on a single-copy gene showed clustering of the strain GW-01, and 54 B. cereus strains from the NCBI were classified into six major groups (I-VI), which were then associated with the source region and sequence types (STs). Transcriptome results indicated that the expression of most genes related with toxins secretion in GW-01 was downregulated compared to that in the lag phase. Overall, these findings suggest that GW-01 is not directly associated with pathogenic Bacillus cereus and highlight an insightful strategy for assessing the safety of novel B. cereus strains.
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Affiliation(s)
- Bowen Xu
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Ministry of Education, Sichuan Normal University, Chengdu 610101, China; (B.X.); (X.H.); (H.Q.); (Y.L.); (S.Z.); (S.L.); (G.L.)
- College of Life Science, Sichuan Normal University, Chengdu 610101, China
| | - Xinyi Huang
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Ministry of Education, Sichuan Normal University, Chengdu 610101, China; (B.X.); (X.H.); (H.Q.); (Y.L.); (S.Z.); (S.L.); (G.L.)
- College of Life Science, Sichuan Normal University, Chengdu 610101, China
| | - Haixiong Qin
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Ministry of Education, Sichuan Normal University, Chengdu 610101, China; (B.X.); (X.H.); (H.Q.); (Y.L.); (S.Z.); (S.L.); (G.L.)
- College of Life Science, Sichuan Normal University, Chengdu 610101, China
| | - Ying Lei
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Ministry of Education, Sichuan Normal University, Chengdu 610101, China; (B.X.); (X.H.); (H.Q.); (Y.L.); (S.Z.); (S.L.); (G.L.)
| | - Sijia Zhao
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Ministry of Education, Sichuan Normal University, Chengdu 610101, China; (B.X.); (X.H.); (H.Q.); (Y.L.); (S.Z.); (S.L.); (G.L.)
- College of Life Science, Sichuan Normal University, Chengdu 610101, China
| | - Shan Liu
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Ministry of Education, Sichuan Normal University, Chengdu 610101, China; (B.X.); (X.H.); (H.Q.); (Y.L.); (S.Z.); (S.L.); (G.L.)
- College of Life Science, Sichuan Normal University, Chengdu 610101, China
| | - Gang Liu
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Ministry of Education, Sichuan Normal University, Chengdu 610101, China; (B.X.); (X.H.); (H.Q.); (Y.L.); (S.Z.); (S.L.); (G.L.)
- College of Life Science, Sichuan Normal University, Chengdu 610101, China
| | - Jiayuan Zhao
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Ministry of Education, Sichuan Normal University, Chengdu 610101, China; (B.X.); (X.H.); (H.Q.); (Y.L.); (S.Z.); (S.L.); (G.L.)
- College of Life Science, Sichuan Normal University, Chengdu 610101, China
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Muyshondt B, Wuyts K, Van Mensel A, Smets W, Lebeer S, Aleixo C, Alós Ortí M, Casanelles-Abella J, Chiron F, Giacomo P, Laanisto L, Moretti M, Niinemets Ü, Pinho P, Tryjanowski P, Woszczyło P, Samson R. Phyllosphere bacterial communities in urban green areas throughout Europe relate to urban intensity. FEMS Microbiol Ecol 2022; 98:6695091. [PMID: 36085374 DOI: 10.1093/femsec/fiac106] [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: 04/25/2022] [Revised: 08/25/2022] [Accepted: 09/07/2022] [Indexed: 12/14/2022] Open
Abstract
The phyllosphere harbours a diverse and specific bacterial community, which influences plant health and ecosystem functioning. In this study, we investigated the impact of urban green areas connectivity and size on the composition and diversity of phyllosphere bacterial communities. Hereto, we evaluated the diversity and composition of phyllosphere bacterial communities of 233 Platanus x acerifolia and Acer pseudoplatanus trees in 77 urban green areas throughout 6 European cities. The community composition and diversity significantly differed between cities but only to a limited extent between tree species. We could show that urban intensity correlated significantly with the community composition of phyllosphere bacteria. In particular, a significant correlation was found between the relative abundances for 29 out of the 50 most abundant families and the urban intensity: the abundances of classic phyllosphere families, such as Acetobacteraceae, Planctomycetes, and Beijerinkiaceae, decreased with urban intensity (i.e. more abundant in areas with more green, lower air pollution, and lower temperature), while those related to human activities, such as Enterobacteriaceae and Bacillaceae, increased with urban intensity. The results of this study suggest that phyllosphere bacterial communities in European cities are associated with urban intensity and that effect is mediated by several combined stress factors.
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Affiliation(s)
- Babette Muyshondt
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
| | - Karen Wuyts
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
| | - Anskje Van Mensel
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
| | - Wenke Smets
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
| | - Sarah Lebeer
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
| | - Cristiana Aleixo
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, 3810-135, Lisbon, Portugal
| | - Marta Alós Ortí
- Chair of Biodiversity and Nature Tourism, Estonian University of Life Sciences, 51005, Tartu, Estonia
| | - Joan Casanelles-Abella
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland.,Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zurich, CH-8092, Zurich, Switzerland
| | - François Chiron
- CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, 91405 Orsay, France
| | - Puglielli Giacomo
- Chair of Biodiversity and Nature Tourism, Estonian University of Life Sciences, 51005, Tartu, Estonia
| | - Lauri Laanisto
- Chair of Biodiversity and Nature Tourism, Estonian University of Life Sciences, 51005, Tartu, Estonia
| | - Marco Moretti
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland
| | - Ülo Niinemets
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, 51006, Tartu, Estonia
| | - Pedro Pinho
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, 3810-135, Lisbon, Portugal
| | - Piotr Tryjanowski
- Department of Zoology, Poznan University of Life Sciences, 60-637, Poland
| | - Patrycja Woszczyło
- Department of Zoology, Poznan University of Life Sciences, 60-637, Poland
| | - Roeland Samson
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
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Pan-Genome Portrait of Bacillus mycoides Provides Insights into the Species Ecology and Evolution. Microbiol Spectr 2021; 9:e0031121. [PMID: 34287030 PMCID: PMC8552610 DOI: 10.1128/spectrum.00311-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Bacillus mycoides is poorly known despite its frequent occurrence in a wide variety of environments. To provide direct insight into its ecology and evolutionary history, a comparative investigation of the species pan-genome and the functional gene categorization of 35 isolates obtained from soil samples from northeastern Poland was performed. The pan-genome of these isolates is composed of 20,175 genes and is characterized by a strong predominance of adaptive genes (∼83%), a significant amount of plasmid genes (∼37%), and a great contribution of prophages and insertion sequences. The pan-genome structure and phylodynamic studies had suggested a wide genomic diversity among the isolates, but no correlation between lineages and the bacillus origin was found. Nevertheless, the two B. mycoides populations, one from Białowieża National Park, the last European natural primeval forest with soil classified as organic, and the second from mineral soil samples taken in a farm in Jasienówka, a place with strong anthropogenic pressure, differ significantly in the frequency of genes encoding proteins enabling bacillus adaptation to specific stress conditions and production of a set of compounds, thus facilitating their colonization of various ecological niches. Furthermore, differences in the prevalence of essential stress sigma factors might be an important trail of this process. Due to these numerous adaptive genes, B. mycoides is able to quickly adapt to changing environmental conditions. IMPORTANCE This research allows deeper understanding of the genetic organization of natural bacterial populations, specifically, Bacillus mycoides, a psychrotrophic member of the Bacillus cereus group that is widely distributed worldwide, especially in areas with continental cold climates. These thorough analyses made it possible to describe, for the first time, the B. mycoides pan-genome, phylogenetic relationship within this species, and the mechanisms behind the species ecology and evolutionary history. Our study indicates a set of functional properties and adaptive genes, in particular, those encoding sigma factors, associated with B. mycoides acclimatization to specific ecological niches and changing environmental conditions.
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Chandra A, Chandra P, Tripathi P. Whole genome sequence insight of two plant growth-promoting bacteria (B. subtilis BS87 and B. megaterium BM89) isolated and characterized from sugarcane rhizosphere depicting better crop yield potentiality. Microbiol Res 2021; 247:126733. [PMID: 33676313 DOI: 10.1016/j.micres.2021.126733] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/13/2022]
Abstract
Since sugarcane is a ratoon crop, genome analysis of plant growth-promoting bacteria that exist in its soil rhizosphere, can provide opportunity to better understand their characteristics and use of such bacteria in turn, may especially improve perennial crop productivity. In the present study, genome of two bacterial strains, one each of B. megaterium (BM89) and B. subtilis (BS87), isolated and reported earlier (Chandra et al., 2018), were sequenced and characterized. Though both strains have demonstrated plant growth promoting properties and enhanced in-vitro plant growth responses, functional annotation and analysis of genes indicated superiority of BS87 as it possessed more plant growth promotion attributable genes over BM89. Apart from some common genes, trehalose metabolism, glycine betaine production, peroxidases, super oxide dismutase, cold shock proteins and phenazine production associated genes were selectively identified in BS87 genome indicating better plant growth performances and survival potential under harsh environmental conditions. Genes for chitinase, d-cysteine desulfhydrase and γ-aminobutyric acid (GABA), as found in BM89, propose its selective utilization in defense and bio-control measures. Concomitant with better settlings' growth, scanning electron micrographs indicated these isolated and characterized bacteria exhibiting healthy colonization within root of sugarcane crop. Kegg pathways' assignment also revealed added pathways namely carbohydrate and amino acid metabolism attached to B. subtilis strain BS87, a preferable candidate for bio-fertilizer and its utilization to promote growth of both plant and ratoon crops of sugarcane usually experiencing harsh environmental conditions.
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Affiliation(s)
- Amaresh Chandra
- ICAR-Indian Institute of Sugarcane Research, Rae Bareli Road, Lucknow, 26002, India.
| | - Priyanka Chandra
- ICAR-Central Soil Salinity Research Institute, Karnal, 132001, India
| | - Pramila Tripathi
- ICAR-Indian Institute of Sugarcane Research, Rae Bareli Road, Lucknow, 26002, India
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5
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Baldwin VM. You Can't B. cereus - A Review of Bacillus cereus Strains That Cause Anthrax-Like Disease. Front Microbiol 2020; 11:1731. [PMID: 32973690 PMCID: PMC7468541 DOI: 10.3389/fmicb.2020.01731] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022] Open
Abstract
Emerging strains of Bacillus cereus, traditionally considered a self-limiting foodborne pathogen, have been associated with anthrax-like disease in mammals, including humans. The strains have emerged by divergent evolution and, as exchange of genetic material in the Bacillus genus occurs naturally, it is possible that further isolates will be identified in the future. The strains vary in their genotypes and phenotypes, combining traits of both B. cereus and B. anthracis species. Cases of anthrax-like disease associated with these strains result in similar symptoms and mortality rates as those caused by B. anthracis. The strains are susceptible to frontline antibiotics used in the treatment of anthrax and existing vaccines provide protection in animal models. The emergence of these strains has reignited the debate surrounding classification of the B. cereus sensu lato group and serves as a reminder that the field of medical microbiology is constantly changing and remains an important and ongoing area of research.
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Guo R, Tian Y, Zhang H, Guo D, Pei X, Wen H, Li P, Mehmood K, Yang K, Chang YF, Liu Z, Duan Z, Yuan F, Liu W, Fazlani SA. Biological characteristics and genetic evolutionary analysis of emerging pathogenic Bacillus cereus isolated from Père David's deer (Elaphurus davidianus). Microb Pathog 2020; 143:104133. [PMID: 32169486 DOI: 10.1016/j.micpath.2020.104133] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/06/2020] [Indexed: 12/15/2022]
Abstract
Bacillus cereus (B. cereus) is widely distributed in the environment. It is one of the most common opportunistic food-borne pathogens associated with food poisoning, not only being majorly reported to cause fatal infections of the gastrointestinal tract, but also responsible for abdominal distress and vomiting. The current study was undertaken to evaluate the biological characteristics and the genetic evolution of B. cereus isolated from infected organs of dead Elaphurus davidianus (E. davidianus). B. cereus was characterized through antibiotic sensitivity tests, mouse lethality assay, whole genome sequencing analysis, and genome annotation. The results revealed that the isolated B. cereus strain was highly resistant to rifampicin, lincomycin, sulfamethoxazole, erythromycin, and ampicillin, with a high pathogenicity phenotype. KEGG annotation revealed that "metabolic pathways" had the largest number of unigenes, followed by "biosynthesis of secondary metabolites" and "biosynthesis of antibiotics". GO analysis resulted in 8039 unigenes categorized. Meanwhile, 54,779 unigenes were annotated and grouped into 23 categories based on COG functional classifications. Moreover, one gene (codY) was found to be related to the host in conformity with the analysis done on PHI-base. Other tests led to the identification of 16 B. cereus virulence factor genes and five resistance types, with potential resistance against bacitracin, penicillin, and fosfomycin. We isolated a highly drug-resistant and pathogenic B. cereus strain from E. davidianus, showing that a variety of antimicrobial drugs should be avoided in clinical treatments. Furthermore, to the best of our knowledge, this is the first study to report whole genome sequencing of a emergence of food-borne B. cereus strain isolated from E. davidianus deer; it will be helpful to extensively investigate the genetic and molecular mechanisms of drug resistance and pathogenesis about B. cereus in both humans and animals.
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Affiliation(s)
- Rui Guo
- Animal Husbandry and Veterinary Institute, Hubei Academy of Agricultural Science, Wuhan, 430064, China; Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture, Wuhan, 430070, China
| | - Yongxiang Tian
- Animal Husbandry and Veterinary Institute, Hubei Academy of Agricultural Science, Wuhan, 430064, China; Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture, Wuhan, 430070, China.
| | - Hui Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY, USA.
| | - Dingzong Guo
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoying Pei
- Animal Husbandry and Veterinary Institute, Hubei Academy of Agricultural Science, Wuhan, 430064, China; Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture, Wuhan, 430070, China
| | - Huajun Wen
- Management Office of Shishou Elk National Nature Reserve, Hubei Province, Shishou, 434400, China
| | - Pengfei Li
- Management Office of Shishou Elk National Nature Reserve, Hubei Province, Shishou, 434400, China
| | - Khalid Mehmood
- University College of Veterinary & Animal Sciences, Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Keli Yang
- Animal Husbandry and Veterinary Institute, Hubei Academy of Agricultural Science, Wuhan, 430064, China; Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture, Wuhan, 430070, China
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY, USA
| | - Zewen Liu
- Animal Husbandry and Veterinary Institute, Hubei Academy of Agricultural Science, Wuhan, 430064, China; Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture, Wuhan, 430070, China
| | - Zhengying Duan
- Animal Husbandry and Veterinary Institute, Hubei Academy of Agricultural Science, Wuhan, 430064, China; Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture, Wuhan, 430070, China
| | - Fangyan Yuan
- Animal Husbandry and Veterinary Institute, Hubei Academy of Agricultural Science, Wuhan, 430064, China; Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture, Wuhan, 430070, China
| | - Wei Liu
- Animal Husbandry and Veterinary Institute, Hubei Academy of Agricultural Science, Wuhan, 430064, China; Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture, Wuhan, 430070, China
| | - Sarfaraz Ali Fazlani
- Lasbela University of Agriculture Water & Marine Sciences, Uthal, Balochistan, Pakistan
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Zhao Y, Chen C, Gu HJ, Zhang J, Sun L. Characterization of the Genome Feature and Toxic Capacity of a Bacillus wiedmannii Isolate From the Hydrothermal Field in Okinawa Trough. Front Cell Infect Microbiol 2019; 9:370. [PMID: 31750261 PMCID: PMC6842932 DOI: 10.3389/fcimb.2019.00370] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 10/10/2019] [Indexed: 11/13/2022] Open
Abstract
The Bacillus cereus group is frequently isolated from soil, plants, food, and other environments. In this study, we report the first isolation and characterization of a B. cereus group member, Bacillus wiedmannii SR52, from the hydrothermal field in the Iheya Ridge of Okinawa Trough. SR52 was isolated from the gills of shrimp Alvinocaris longirostris, an invertebrate species found abundantly in the ecosystems of the hydrothermal vents, and is most closely related to B. wiedmannii FSL W8-0169. SR52 is aerobic, motile, and able to form endospores. SR52 can grow in NaCl concentrations up to 9%. SR52 has a circular chromosome of 5,448,361 bp and a plasmid of 137,592 bp, encoding 5,709 and 189 genes, respectively. The chromosome contains 297 putative virulence genes, including those encoding enterotoxins and hemolysins. Fourteen rRNA operons, 107 tRNAs, and 5 sRNAs are present in the chromosome, and 7 tRNAs are present in the plasmid. SR52 possesses 13 genomic islands (GIs), all on the chromosome. Comparing to FSL W8-0169, SR52 exhibits several streaking features in its genome, notably an exceedingly large number of non-coding RNAs and GIs. In vivo studies showed that following intramuscular injection into fish, SR52 was able to disseminate in tissues and cause mortality; when inoculated into mice, SR52 induced acute mortality and disseminated transiently in tissues. In vitro studies showed that SR52 possessed hemolytic activity, and the extracellular product of SR52 exhibited a strong cytotoxic effect. These results provided the first insight into the cytotoxicity and genomic feature of B. wiedmannii from the deep-sea hydrothermal environment.
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Affiliation(s)
- Yan Zhao
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chen Chen
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Han-Jie Gu
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Zhang
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
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Activation of the Extracytoplasmic Function σ Factor σ P by β-Lactams in Bacillus thuringiensis Requires the Site-2 Protease RasP. mSphere 2019; 4:4/4/e00511-19. [PMID: 31391284 PMCID: PMC6686233 DOI: 10.1128/msphere.00511-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The discovery of antibiotics to treat bacterial infections has had a dramatic and positive impact on human health. However, shortly after the introduction of a new antibiotic, bacteria often develop resistance. The bacterial cell envelope is essential for cell viability and is the target of many of the most commonly used antibiotics, including β-lactam antibiotics. Resistance to β-lactams is often dependent upon β-lactamases. In B. cereus, B. thuringiensis, and some B. anthracis strains, the expression of some β-lactamases is inducible. This inducible β-lactamase expression is controlled by activation of an alternative σ factor called σP. Here, we show that β-lactam antibiotics induce σP activation by degradation of the anti-σ factor RsiP. Bacteria can utilize alternative σ factors to regulate sets of genes in response to changes in the environment. The largest and most diverse group of alternative σ factors are the extracytoplasmic function (ECF) σ factors. σP is an ECF σ factor found in Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis. Previous work showed that σP is induced by ampicillin, a β-lactam antibiotic, and required for resistance to ampicillin. However, it was not known how activation of σP is controlled or what other antibiotics may activate σP. Here, we report that activation of σP is specific to a subset of β-lactams and that σP is required for resistance to these β-lactams. We demonstrate that activation of σP is controlled by the proteolytic destruction of the anti-σ factor RsiP and that degradation of RsiP requires multiple proteases. Upon exposure to β-lactams, the extracellular domain of RsiP is cleaved by an unknown protease, which we predict cleaves at site-1. Following cleavage by the unknown protease, the N terminus of RsiP is further degraded by the site-2 intramembrane protease RasP. Our data indicate that RasP cleavage of RsiP is not the rate-limiting step in σP activation. This proteolytic cascade leads to activation of σP, which induces resistance to β-lactams likely via increased expression of β-lactamases. IMPORTANCE The discovery of antibiotics to treat bacterial infections has had a dramatic and positive impact on human health. However, shortly after the introduction of a new antibiotic, bacteria often develop resistance. The bacterial cell envelope is essential for cell viability and is the target of many of the most commonly used antibiotics, including β-lactam antibiotics. Resistance to β-lactams is often dependent upon β-lactamases. In B. cereus, B. thuringiensis, and some B. anthracis strains, the expression of some β-lactamases is inducible. This inducible β-lactamase expression is controlled by activation of an alternative σ factor called σP. Here, we show that β-lactam antibiotics induce σP activation by degradation of the anti-σ factor RsiP.
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9
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Gupta S, Fernandes J, Kiron V. Antibiotic-Induced Perturbations Are Manifested in the Dominant Intestinal Bacterial Phyla of Atlantic Salmon. Microorganisms 2019; 7:E233. [PMID: 31382431 PMCID: PMC6723382 DOI: 10.3390/microorganisms7080233] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/26/2019] [Accepted: 07/28/2019] [Indexed: 12/25/2022] Open
Abstract
The intestinal microbiota of certain farmed fish are often exposed to antimicrobial substances, such as antibiotics, that are used to prevent and treat bacterial diseases. Antibiotics that kill or inhibit the growth of harmful microbes can rapidly alter intestinal microbial diversity and composition, with potential effects on the host health. In this study, we have elucidated the impact of two antibiotics, florfenicol and oxolinic acid, by employing a high-throughput 16S rRNA gene amplicon sequencing technique on the distal and mid intestinal microbial communities of Atlantic salmon (Salmo salar). For this, Atlantic salmon were offered diets with or without antibiotics. We then investigated the bacterial communities in the intestinal mucus of the fish. Our results showed that antibiotic exposure shifts the intestinal microbial profile differentially. In addition, the bacterial compositions of the control and antibiotic-fed groups were significantly different. Antibiotic feeding altered the composition and abundance of the dominant bacterial phyla, namely Proteobacteria, Actinobacteria, Firmicutes, Spirochaetes, Bacteroidetes, Tenericutes, and Thermotogae. The bacterial association network analysis also indicated the differential pattern of co-occurrence of bacteria in the three study groups. The results regarding the differences in the structure and association of the intestinal microbiota of Atlantic salmon after florfenicol and oxolinic acid feeding can be employed to attenuate the adverse effects of antibiotic feeding on fish.
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Affiliation(s)
- Shruti Gupta
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Jorge Fernandes
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway.
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10
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Phylogenetics and antibacterial properties of exopolysaccharides from marine bacteria isolated from Mauritius seawater. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01487-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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11
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Mirhaj H, Honari H, Zamani E. Evaluation of immune response to recombinant Bacillus anthracis LFD1-PA4 chimeric protein. IRANIAN JOURNAL OF VETERINARY RESEARCH 2019; 20:112-119. [PMID: 31531033 PMCID: PMC6716276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 12/27/2018] [Accepted: 01/01/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Anthrax is a particularly dangerous infectious disease that affects humans and livestock. Efficacious vaccines that can rapidly induce a long-term immune response are required to prevent anthrax infection in humans. Domains 4 and 1 of the protective antigen (PA) and lethal factor (LF), respectively, have very high antigenic properties. AIMS In this experimental study, the pET28a-lfD1-pa4 expression vector was designed, constructed and transferred into E. coli BL21 (DE3) plysS. METHODS For this purpose, pa4 gene was amplified by polymerase chain reaction (PCR) and cloned in a pGEM T-easy vector. The pGEM-pa4 and pGEM-lfD1 were digested by XbaI and HindIII enzymes. The ligation reaction was performed by ligase T4 enzyme and the gene cassette, lfD1-pa4, was subcloned in pET28a and transferred to E. coli BL21 (DE3) PlysS. Expression and purification of chimeric proteins were confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting techniques. The chimera LFD1-PA4 and mixed LFD1+PA4 proteins were injected four times into mice and antibody production was relativity evaluated by enzyme-linked immunosorbent assay (ELISA) test. RESULTS The results showed that both chimeric and mixed proteins are immunogenic, but LFD1-PA4 has a higher potential to stimulate mice immune system. CONCLUSION LFD1-PA4 chimeric protein induced a higher immune response than LFD1+PA4 mixed protein and elicited antibody responses to LF and edema factor (EF), therefore, it holds promise to be a more effective trivalent vaccine candidate to use in anthrax prevention.
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Affiliation(s)
- H. Mirhaj
- Ph.D. Student in Nano Biotechnology, Department of Biology, Faculty of Basic Science, Imam Hossein University, Tehran, Iran
| | - H. Honari
- Department of Biology, Faculty of Basic Science, Imam Hossein University, Tehran, Iran
| | - E. Zamani
- MSc Student in Cellular and Molecular Biology, Department of Biology, Faculty of Basic Science, Imam Hossein University, Tehran, Iran
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12
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Gargis AS, McLaughlin HP, Conley AB, Lascols C, Michel PA, Gee JE, Marston CK, Kolton CB, Rodriguez-R LM, Hoffmaster AR, Weigel LM, Sue D. Analysis of Whole-Genome Sequences for the Prediction of Penicillin Resistance and β-Lactamase Activity in Bacillus anthracis. mSystems 2018; 3:e00154-18. [PMID: 30574557 PMCID: PMC6290263 DOI: 10.1128/msystems.00154-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/14/2018] [Indexed: 12/01/2022] Open
Abstract
Penicillin (PEN) is a low-cost option for anthrax treatment, but naturally occurring resistance has been reported. β-Lactamase expression (bla1, bla2) in Bacillus anthracis is regulated by a sigma factor (SigP) and its cognate anti-sigma factor (RsiP). Mutations leading to truncation of RsiP were previously described as a basis for PEN resistance. Here, we analyze whole-genome sequencing (WGS) data and compare the chromosomal sigP-bla1 regions from 374 B. anthracis strains to determine the frequency of mutations, identify mutations associated with PEN resistance, and evaluate the usefulness of WGS for predicting PEN resistance. Few (3.5%) strains contained at least 1 of 11 different mutations in sigP, rsiP, or bla1. Nine of these mutations have not been previously associated with PEN resistance. Four strains showed PEN resistance (PEN-R) by conventional broth microdilution, including 1 strain with a novel frameshift in rsiP. One strain that carries the same rsiP frameshift mutation as that found previously in a PEN-R strain showed a PEN-susceptible (PEN-S) phenotype and exhibited decreased bla1 and bla2 transcription. An unexpectedly small colony size, a reduced growth rate, and undetectable β-lactamase activity levels (culture supernatant and cell lysate) were observed in this PEN-S strain. Sequence analysis revealed mutations in genes associated with growth defects that may contribute to this phenotype. While B. anthracis rsiP mutations cannot be exclusively used to predict resistance, four of the five strains with rsiP mutations were PEN-R. Therefore, the B. anthracis sigP-bla1 region is a useful locus for WGS-based PEN resistance prediction, but phenotypic testing remains essential. IMPORTANCE Determination of antimicrobial susceptibility of B. anthracis is essential for the appropriate distribution of antimicrobial agents for postexposure prophylaxis (PEP) and treatment of anthrax. Analysis of WGS data allows for the rapid detection of mutations in antimicrobial resistance (AMR) genes in an isolate, but the presence of a mutation in an AMR gene does not always accurately predict resistance. As mutations in the anti-sigma factor RsiP have been previously associated with high-level penicillin resistance in a limited number of strains, we investigated WGS assemblies from 374 strains to determine the frequency of mutations and performed functional antimicrobial susceptibility testing. Of the five strains that contained mutations in rsiP, only four were PEN-R by functional antimicrobial susceptibility testing. We conclude that while sequence analysis of this region is useful for AMR prediction in B. anthracis, genetic analysis should not be used exclusively and phenotypic susceptibility testing remains essential.
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Affiliation(s)
- A. S. Gargis
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - H. P. McLaughlin
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - A. B. Conley
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
| | - C. Lascols
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - P. A. Michel
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J. E. Gee
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - C. K. Marston
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - C. B. Kolton
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - L. M. Rodriguez-R
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - A. R. Hoffmaster
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - L. M. Weigel
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - D. Sue
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Hernández-González IL, Moreno-Hagelsieb G, Olmedo-Álvarez G. Environmentally-driven gene content convergence and the Bacillus phylogeny. BMC Evol Biol 2018; 18:148. [PMID: 30285626 PMCID: PMC6171248 DOI: 10.1186/s12862-018-1261-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 09/13/2018] [Indexed: 01/28/2023] Open
Abstract
Background Members of the Bacillus genus have been isolated from a variety of environments. However, the relationship between potential metabolism and the niche from which bacteria of this genus have been isolated has not been extensively studied. The existence of a monophyletic aquatic Bacillus group, composed of members isolated from both marine and fresh water has been proposed. Here, we present a phylogenetic/phylogenomic analysis to investigate the potential relationship between the environment from which group members have been isolated and their evolutionary origin. We also carried out hierarchical clustering based on functional content to test for potential environmental effects on the genetic content of these bacteria. Results The phylogenetic reconstruction showed that Bacillus strains classified as aquatic have evolutionary origins in different lineages. Although we observed the presence of a clade consisting exclusively of aquatic Bacillus, it is not comprised of the same strains previously reported. In contrast to phylogeny, clustering based on the functional categories of the encoded proteomes resulted in groups more compatible with the environments from which the organisms were isolated. This evidence suggests a detectable environmental influence on bacterial genetic content, despite their different evolutionary origins. Conclusion Our results suggest that aquatic Bacillus species have polyphyletic origins, but exhibit convergence at the gene content level. Electronic supplementary material The online version of this article (10.1186/s12862-018-1261-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ismael L Hernández-González
- Department of Genetic Engineering, CINVESTAV-Irapuato, Km. 9.6 Libramiento Norte, Carr. Irapuato-Leon, Irapuato, 36824, Guanajuato, Mexico
| | - Gabriel Moreno-Hagelsieb
- Department of Biology, Wilfrid Laurier University, 75 University Ave. W., Waterloo, N2L 3C5, Ontario, Canada.
| | - Gabriela Olmedo-Álvarez
- Department of Genetic Engineering, CINVESTAV-Irapuato, Km. 9.6 Libramiento Norte, Carr. Irapuato-Leon, Irapuato, 36824, Guanajuato, Mexico.
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14
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Böttinger B, Semmler F, Zerulla K, Ludt K, Soppa J. Regulated ploidy of Bacillus subtilis and three new isolates of Bacillus and Paenibacillus. FEMS Microbiol Lett 2018; 365:4791518. [PMID: 29315386 DOI: 10.1093/femsle/fnx282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/03/2018] [Indexed: 11/12/2022] Open
Abstract
Bacteria were long assumed to be monoploid, maintaining one copy of a circular chromosome. In recent years it became obvious that the majority of species in several phylogenetic groups of prokaryotes are oligoploid or polyploid. The present study aimed at investigating the ploidy in Gram-positive aerobic endospore-forming bacteria. First, the numbers of origins and termini of the widely used laboratory strain Bacillus subtilis 168 were quantified. The strain was found to be mero-oligoploid in exponential phase (5.9 origins, 1.2 termini) and to down-regulate the number of origins in stationary phase. After inoculation of fresh medium with stationary-phase cells the onset of replication preceded the onset of mass increase. For the analysis of the ploidy in fresh isolates, three strains were isolated from soil, which were found to belong to the genera of Bacillus and Paenibacillus. All three strains were found to be mero-oligoploid in exponential phase and exhibit a growth phase-dependent down-regulation of the ploidy level in stationary phase. Taken together, these results indicate that mero-oligoploidy as well as growth phase-dependent copy number regulation might be widespread in and typical for Bacillus and related genera.
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Affiliation(s)
- Benjamin Böttinger
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Max-von-Laue-Strasse 9, D-60438, Frankfurt, Germany
| | - Florian Semmler
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Max-von-Laue-Strasse 9, D-60438, Frankfurt, Germany
| | - Karolin Zerulla
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Max-von-Laue-Strasse 9, D-60438, Frankfurt, Germany
| | - Katharina Ludt
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Max-von-Laue-Strasse 9, D-60438, Frankfurt, Germany
| | - Jörg Soppa
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Max-von-Laue-Strasse 9, D-60438, Frankfurt, Germany
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15
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Abstract
Bacterial endospores possess multiple integument layers, one of which is the cortex peptidoglycan wall. The cortex is essential for the maintenance of spore core dehydration and dormancy and contains structural modifications that differentiate it from vegetative cell peptidoglycan and determine its fate during spore germination. Following the engulfment stage of sporulation, the cortex is synthesized within the intermembrane space surrounding the forespore. Proteins responsible for cortex synthesis are produced in both the forespore and mother cell compartments. While some of these proteins also contribute to vegetative cell wall synthesis, others are sporulation specific. In order for the bacterial endospore to germinate and resume metabolism, the cortex peptidoglycan must first be degraded through the action of germination-specific lytic enzymes. These enzymes are present, yet inactive, in the dormant spore and recognize the muramic-δ-lactam modification present in the cortex. Germination-specific lytic enzymes across Bacillaceae and Clostridiaceae share this specificity determinant, which ensures that the spore cortex is hydrolyzed while the vegetative cell wall remains unharmed. Bacillus species tend to possess two redundant enzymes, SleB and CwlJ, capable of sufficient cortex degradation, while the clostridia have only one, SleC. Additional enzymes are often present that cannot initiate the cortex degradation process, but which can increase the rate of release of small fragments into the medium. Between the two families, the enzymes also differ in the enzymatic activities they possess and the mechanisms acting to restrict their activation until germination has been initiated.
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Pan T, He H, Wang X, Shen Y, Zhao J, Yan K, Wang X, Liu C, Zhang J, Xiang W. Bacillus solisilvae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:4449-4455. [DOI: 10.1099/ijsem.0.002312] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tong Pan
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, Harbin 150030, PR China
| | - Hairong He
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, Harbin 150030, PR China
| | - Xiaochong Wang
- Shenzhen Institute for Drug Control, ShenZhen 518057, PR China
| | - Yibo Shen
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, Harbin 150030, PR China
| | - Junwei Zhao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, Harbin 150030, PR China
| | - Kai Yan
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, Harbin 150030, PR China
| | - Xiangjing Wang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, Harbin 150030, PR China
| | - Chongxi Liu
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, Harbin 150030, PR China
| | - Ji Zhang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, Harbin 150030, PR China
| | - Wensheng Xiang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, Harbin 150030, PR China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
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17
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Fu Y, Wu Y, Yuan Y, Gao M. Complete Genome Sequence of Bacillus thuringiensis Serovar rongseni Reference Strain SCG04-02, a Strain Toxic to Plutella xylostella. GENOME ANNOUNCEMENTS 2017; 5:e00691-17. [PMID: 28963199 PMCID: PMC5624745 DOI: 10.1128/genomea.00691-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 06/08/2017] [Indexed: 11/21/2022]
Abstract
Bacillus thuringiensis (Bt) is widely used to control agricultural and forestry pests, though there are only a few available complete genome sequences of the Bt reference strain. Here, we report the complete genome sequence of B. thuringiensis serovar rongseni reference strain SCG04-02, which is toxic to Plutella xylostella.
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Affiliation(s)
- Yajuan Fu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Huaibeizhen, Huairou, Beijing, China
| | - Yan Wu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yihui Yuan
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Meiying Gao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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18
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Hollensteiner J, Poehlein A, Spröer C, Bunk B, Sheppard AE, Rosentstiel P, Schulenburg H, Liesegang H. Complete Genome sequence of the nematicidal Bacillus thuringiensis MYBT18246. Stand Genomic Sci 2017; 12:48. [PMID: 28852435 PMCID: PMC5569534 DOI: 10.1186/s40793-017-0259-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 08/08/2017] [Indexed: 01/22/2023] Open
Abstract
10.1601/nm.5000 is a rod-shaped facultative anaerobic spore forming bacterium of the genus 10.1601/nm.4857. The defining feature of the species is the ability to produce parasporal crystal inclusion bodies, consisting of δ-endotoxins, encoded by cry-genes. Here we present the complete annotated genome sequence of the nematicidal 10.1601/nm.5000 strain MYBT18246. The genome comprises one 5,867,749 bp chromosome and 11 plasmids which vary in size from 6330 bp to 150,790 bp. The chromosome contains 6092 protein-coding and 150 RNA genes, including 36 rRNA genes. The plasmids encode 997 proteins and 4 t-RNA's. Analysis of the genome revealed a large number of mobile elements involved in genome plasticity including 11 plasmids and 16 chromosomal prophages. Three different nematicidal toxin genes were identified and classified according to the Cry toxin naming committee as cry13Aa2, cry13Ba1, and cry13Ab1. Strikingly, these genes are located on the chromosome in close proximity to three separate prophages. Moreover, four putative toxin genes of different toxin classes were identified on the plasmids p120510 (Vip-like toxin), p120416 (Cry-like toxin) and p109822 (two Bin-like toxins). A comparative genome analysis of 10.1601/nm.5000 MYBT18246 with three closely related 10.1601/nm.5000 strains enabled determination of the pan-genome of 10.1601/nm.5000 MYBT18246, revealing a large number of singletons, mostly represented by phage genes, morons and cryptic genes.
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Affiliation(s)
- Jacqueline Hollensteiner
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anna E. Sheppard
- Present address: Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Philip Rosentstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
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19
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Abstract
BACKGROUND Bacillus cereus sensu lato (s. l.) is an ecologically diverse bacterial group of medical and agricultural significance. In this study, I use publicly available genomes and novel bioinformatic workflows to characterize the B. cereus s. l. pan-genome and perform the largest phylogenetic and population genetic analyses of this group to date in terms of the number of genes and taxa included. With these fundamental data in hand, I identify genes associated with particular phenotypic traits (i.e., "pan-GWAS" analysis), and quantify the degree to which taxa sharing common attributes are phylogenetically clustered. METHODS A rapid k-mer based approach (Mash) was used to create reduced representations of selected Bacillus genomes, and a fast distance-based phylogenetic analysis of this data (FastME) was performed to determine which species should be included in B. cereus s. l. The complete genomes of eight B. cereus s. l. species were annotated de novo with Prokka, and these annotations were used by Roary to produce the B. cereus s. l. pan-genome. Scoary was used to associate gene presence and absence patterns with various phenotypes. The orthologous protein sequence clusters produced by Roary were filtered and used to build HaMStR databases of gene models that were used in turn to construct phylogenetic data matrices. Phylogenetic analyses used RAxML, DendroPy, ClonalFrameML, PAUP*, and SplitsTree. Bayesian model-based population genetic analysis assigned taxa to clusters using hierBAPS. The genealogical sorting index was used to quantify the phylogenetic clustering of taxa sharing common attributes. RESULTS The B. cereus s. l. pan-genome currently consists of ≈60,000 genes, ≈600 of which are "core" (common to at least 99% of taxa sampled). Pan-GWAS analysis revealed genes associated with phenotypes such as isolation source, oxygen requirement, and ability to cause diseases such as anthrax or food poisoning. Extensive phylogenetic analyses using an unprecedented amount of data produced phylogenies that were largely concordant with each other and with previous studies. Phylogenetic support as measured by bootstrap probabilities increased markedly when all suitable pan-genome data was included in phylogenetic analyses, as opposed to when only core genes were used. Bayesian population genetic analysis recommended subdividing the three major clades of B. cereus s. l. into nine clusters. Taxa sharing common traits and species designations exhibited varying degrees of phylogenetic clustering. CONCLUSIONS All phylogenetic analyses recapitulated two previously used classification systems, and taxa were consistently assigned to the same major clade and group. By including accessory genes from the pan-genome in the phylogenetic analyses, I produced an exceptionally well-supported phylogeny of 114 complete B. cereus s. l. genomes. The best-performing methods were used to produce a phylogeny of all 498 publicly available B. cereus s. l. genomes, which was in turn used to compare three different classification systems and to test the monophyly status of various B. cereus s. l. species. The majority of the methodology used in this study is generic and could be leveraged to produce pan-genome estimates and similarly robust phylogenetic hypotheses for other bacterial groups.
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Affiliation(s)
- Adam L Bazinet
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, 21702, MD, USA.
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20
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Evolutionary processes and environmental factors underlying the genetic diversity and lifestyles of Bacillus cereus group bacteria. Res Microbiol 2017; 168:309-318. [DOI: 10.1016/j.resmic.2016.07.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 07/03/2016] [Accepted: 07/05/2016] [Indexed: 11/22/2022]
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21
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Argiroff WA, Zak DR, Lanser CM, Wiley MJ. Microbial Community Functional Potential and Composition Are Shaped by Hydrologic Connectivity in Riverine Floodplain Soils. MICROBIAL ECOLOGY 2017; 73:630-644. [PMID: 27807645 DOI: 10.1007/s00248-016-0883-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/17/2016] [Indexed: 05/12/2023]
Abstract
Riverine floodplains are ecologically and economically valuable ecosystems that are heavily threatened by anthropogenic stressors. Microbial communities in floodplain soils mediate critical biogeochemical processes, yet we understand little about the relationship between these communities and variation in hydrologic connectivity related to land management or topography. Here, we present metagenomic evidence that differences among microbial communities in three floodplain soils correspond to a long-term gradient of hydrologic connectivity. Specifically, all strictly anaerobic taxa and metabolic pathways were positively associated with increased hydrologic connectivity and flooding frequency. In contrast, most aerobic taxa and all strictly aerobic pathways were negatively related to hydrologic connectivity and flooding frequency. Furthermore, the genetic potential to metabolize organic compounds tended to decrease as hydrologic connectivity increased, which may reflect either the observed concomitant decline of soil organic matter or the parallel increase in both anaerobic taxa and pathways. A decline in soil N, accompanied by an increased genetic potential for oligotrophic N acquisition subsystems, suggests that soil nutrients also shape microbial communities in these soils. We conclude that differences among floodplain soil microbial communities can be conceptualized along a gradient of hydrologic connectivity. Additionally, we show that these differences are likely due to connectivity-related variation in flooding frequency, soil organic matter, and soil N. Our findings are particularly relevant to the restoration and management of microbially mediated biogeochemical processes in riverine floodplain wetlands.
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Affiliation(s)
- William A Argiroff
- School of Natural Resources and Environment, University of Michigan, 440 Church St., Ann Arbor, MI, 48109, USA.
| | - Donald R Zak
- School of Natural Resources and Environment, University of Michigan, 440 Church St., Ann Arbor, MI, 48109, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, MI, 48109, USA
| | - Christine M Lanser
- School of Natural Resources and Environment, University of Michigan, 440 Church St., Ann Arbor, MI, 48109, USA
| | - Michael J Wiley
- School of Natural Resources and Environment, University of Michigan, 440 Church St., Ann Arbor, MI, 48109, USA
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Transient Duplication-Dependent Divergence and Horizontal Transfer Underlie the Evolutionary Dynamics of Bacterial Cell-Cell Signaling. PLoS Biol 2016; 14:e2000330. [PMID: 28033323 PMCID: PMC5199041 DOI: 10.1371/journal.pbio.2000330] [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: 06/16/2016] [Accepted: 12/02/2016] [Indexed: 01/01/2023] Open
Abstract
Evolutionary expansion of signaling pathway families often underlies the evolution of regulatory complexity. Expansion requires the acquisition of a novel homologous pathway and the diversification of pathway specificity. Acquisition can occur either vertically, by duplication, or through horizontal transfer, while divergence of specificity is thought to occur through a promiscuous protein intermediate. The way by which these mechanisms shape the evolution of rapidly diverging signaling families is unclear. Here, we examine this question using the highly diversified Rap-Phr cell-cell signaling system, which has undergone massive expansion in the genus Bacillus. To this end, genomic sequence analysis of >300 Bacilli genomes was combined with experimental analysis of the interaction of Rap receptors with Phr autoinducers and downstream targets. Rap-Phr expansion is shown to have occurred independently in multiple Bacillus lineages, with >80 different putative rap-phr alleles evolving in the Bacillius subtilis group alone. The specificity of many rap-phr alleles and the rapid gain and loss of Rap targets are experimentally demonstrated. Strikingly, both horizontal and vertical processes were shown to participate in this expansion, each with a distinct role. Horizontal gene transfer governs the acquisition of already diverged rap-phr alleles, while intralocus duplication and divergence of the phr gene create the promiscuous intermediate required for the divergence of Rap-Phr specificity. Our results suggest a novel role for transient gene duplication and divergence during evolutionary shifts in specificity.
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Mölsä M, Kalin-Mänttäri L, Tonteri E, Hemmilä H, Nikkari S. Comparison of four commercial DNA extraction kits for the recovery of Bacillus spp. spore DNA from spiked powder samples. J Microbiol Methods 2016; 128:69-73. [PMID: 27435532 DOI: 10.1016/j.mimet.2016.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/15/2016] [Accepted: 07/15/2016] [Indexed: 11/28/2022]
Abstract
Bacillus spp. include human pathogens such as Bacillus anthracis, the causative agent of anthrax and a biothreat agent. Bacillus spp. form spores that are physically highly resistant and may remain active over sample handling. We tested four commercial DNA extraction kits (QIAamp DNA Mini Kit, RTP Pathogen Kit, ZR Fungal/Bacterial DNA MiniPrep, and genesig Easy DNA/RNA Extraction kit) for sample inactivation and DNA recovery from two powders (icing sugar and potato flour) spiked with Bacillus thuringiensis spores. The DNA was analysed using a B. thuringiensis-specific real-time PCR assay. The detection limit was 3×10(1)CFU of spiked B. thuringiensis spores with the QIAamp DNA Mini, RTP Pathogen, and genesig Easy DNA/RNA Extraction kits, and 3×10(3)CFU with the ZR Fungal/Bacterial DNA MiniPrep kit. The results showed that manual extraction kits are effective and safe for fast and easy DNA extraction from powder samples even in field conditions. Adding a DNA filtration step to the extraction protocol ensures the removal of Bacillus spp. spores from DNA samples without affecting sensitivity.
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Affiliation(s)
- Markos Mölsä
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland.
| | | | - Elina Tonteri
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland
| | - Heidi Hemmilä
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland
| | - Simo Nikkari
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland
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Stepanov VG, Tirumalai MR, Montazari S, Checinska A, Venkateswaran K, Fox GE. Bacillus pumilus SAFR-032 Genome Revisited: Sequence Update and Re-Annotation. PLoS One 2016; 11:e0157331. [PMID: 27351589 PMCID: PMC4924849 DOI: 10.1371/journal.pone.0157331] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/29/2016] [Indexed: 12/12/2022] Open
Abstract
Bacillus pumilus strain SAFR-032 is a non-pathogenic spore-forming bacterium exhibiting an anomalously high persistence in bactericidal environments. In its dormant state, it is capable of withstanding doses of ultraviolet (UV) radiation or hydrogen peroxide, which are lethal for the vast majority of microorganisms. This unusual resistance profile has made SAFR-032 a reference strain for studies of bacterial spore resistance. The complete genome sequence of B. pumilus SAFR-032 was published in 2007 early in the genomics era. Since then, the SAFR-032 strain has frequently been used as a source of genetic/genomic information that was regarded as representative of the entire B. pumilus species group. Recently, our ongoing studies of conservation of gene distribution patterns in the complete genomes of various B. pumilus strains revealed indications of misassembly in the B. pumilus SAFR-032 genome. Synteny-driven local genome resequencing confirmed that the original SAFR-032 sequence contained assembly errors associated with long sequence repeats. The genome sequence was corrected according to the new findings. In addition, a significantly improved annotation is now available. Gene orders were compared and portions of the genome arrangement were found to be similar in a wide spectrum of Bacillus strains.
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Affiliation(s)
- Victor G. Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Saied Montazari
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Aleksandra Checinska
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, United States of America
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, United States of America
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- * E-mail:
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25
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Transcriptome analysis of Bacillus thuringiensis spore life, germination and cell outgrowth in a vegetable-based food model. Food Microbiol 2016; 55:73-85. [DOI: 10.1016/j.fm.2015.11.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 11/03/2015] [Accepted: 11/10/2015] [Indexed: 11/19/2022]
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Abstract
Members of the family Bacillaceae are among the most robust bacteria on Earth, which is mainly due to their ability to form resistant endospores. This trait is believed to be the key factor determining the ecology of these bacteria. However, they also perform fundamental roles in soil ecology (i.e., the cycling of organic matter) and in plant health and growth stimulation (e.g., via suppression of plant pathogens and phosphate solubilization). In this review, we describe the high functional and genetic diversity that is found within the Bacillaceae (a family of low-G+C% Gram-positive spore-forming bacteria), their roles in ecology and in applied sciences related to agriculture. We then pose questions with respect to their ecological behavior, zooming in on the intricate social behavior that is becoming increasingly well characterized for some members of Bacillaceae. Such social behavior, which includes cell-to-cell signaling via quorum sensing or other mechanisms (e.g., the production of extracellular hydrolytic enzymes, toxins, antibiotics and/or surfactants) is a key determinant of their lifestyle and is also believed to drive diversification processes. It is only with a deeper understanding of cell-to-cell interactions that we will be able to understand the ecological and diversification processes of natural populations within the family Bacillaceae. Ultimately, the resulting improvements in understanding will benefit practical efforts to apply representatives of these bacteria in promoting plant growth as well as biological control of plant pathogens.
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27
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Kim JGY, Wilson AC. Loss of σI affects heat-shock response and virulence gene expression in Bacillus anthracis. MICROBIOLOGY-SGM 2016; 162:564-574. [PMID: 26744224 DOI: 10.1099/mic.0.000236] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The pathogenesis of Bacillus anthracis depends on several virulence factors, including the anthrax toxin. Loss of the alternative sigma factor σI results in a coordinate decrease in expression of all three toxin subunits. Our observations suggest that loss of σI alters the activity of the master virulence regulator AtxA, but atxA transcription is unaffected by loss of σI. σI-containing RNA polymerase does not appear to directly transcribe either atxA or the toxin gene pagA. As in Bacillus subtilis, loss of σI in B. anthracis results in increased sensitivity to heat shock and transcription of sigI, encoding σI, is induced by elevated temperature. Encoded immediately downstream of and part of a bicistronic message with sigI is an anti-sigma factor, RsgI, which controls σI activity. Loss of RsgI has no direct effect on virulence gene expression. sigI appears to be expressed from both the σI and σA promoters, and transcription from the σA promoter is likely more significant to virulence regulation. We propose a model in which σI can be induced in response to heat shock, whilst, independently, σI is produced under non-heat-shock, toxin-inducing conditions to indirectly regulate virulence gene expression.
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Affiliation(s)
- Jenny Gi Yae Kim
- Department of Biology, Georgia State University, Atlanta, GA 30302, USA
| | - Adam C Wilson
- Department of Biology, Georgia State University, Atlanta, GA 30302, USA
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Hur JM, Park DH. Making soy sauce from defatted soybean meal without the mejus process by submerged cultivation using thermophilic bacteria. Journal of Food Science and Technology 2015; 52:5030-8. [PMID: 26243923 DOI: 10.1007/s13197-014-1536-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 08/10/2014] [Accepted: 08/25/2014] [Indexed: 11/24/2022]
Abstract
The diversity of thermophilic bacteria was not significantly altered while growing in a defatted soybean meal (DFSM) slurry at 60 °C for 10, 20, and 30 days. Five species of thermophilic bacteria, which belong to the genera Aeribacillus (temperature gradient gel electrophoresis [TGGE] band no. 1), Saccharococcus (TGGE band no. 2), Geobacillus (TGGE band no. 3), Bacillus (TGGE band no. 4), and Anoxybacillus (TGGE band no. 5), were detected in the fermenting DFSM slurry. The cell-free culture fluid obtained from the fermenting DFSM slurry on day 14 hydrolyzed starch and soy protein at 60 °C but not at 30 °C. Soy sauce (test soy sauce) was prepared from the fermented DFSM slurry after a 30 day cultivation at 60 °C and a 60 day ripening at 45 °C. Free amino acid (AA) and organic acid contents in the soy sauce increased in proportion to the fermentation period, whereas ammonium decreased proportionally. Mg and Ca contained in the soy sauce decreased proportionally during fermentation and were lower than those in the non-fermented DFSM extract (control). Spectral absorbance of soy sauce prepared from the fermented DFSM slurry was maximal at 430 nm and increased slightly in proportion to the fermentation period. The aroma and flavor of the test soy sauce were significantly different from those of traditional Korean soy sauce. Conclusively, soy sauce may be prepared directly from the fermented DFSM slurry without meju-preparing process and fermentation period may be a factor for control of soy sauce quality.
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Affiliation(s)
- Jeong Min Hur
- Department of Chemical and Biological Engineering, Seokyeong University, 124 Seokyeong-Ro, Sungbuk-gu Seoul, 136-704 South Korea
| | - Doo Hyun Park
- Department of Chemical and Biological Engineering, Seokyeong University, 124 Seokyeong-Ro, Sungbuk-gu Seoul, 136-704 South Korea
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29
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van Zyl LJ, Sunda F, Taylor MP, Cowan DA, Trindade MI. Identification and characterization of a novel Geobacillus thermoglucosidasius bacteriophage, GVE3. Arch Virol 2015; 160:2269-82. [PMID: 26123922 DOI: 10.1007/s00705-015-2497-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/12/2015] [Indexed: 11/25/2022]
Abstract
The study of extremophilic phages may reveal new phage families as well as different mechanisms of infection, propagation and lysis to those found in phages from temperate environments. We describe a novel siphovirus, GVE3, which infects the thermophile Geobacillus thermoglucosidasius. The genome size is 141,298 bp (G+C 29.6%), making it the largest Geobacillus spp-infecting phage known. GVE3 appears to be most closely related to the recently described Bacillus anthracis phage vB_BanS_Tsamsa, rather than Geobacillus-infecting phages described thus far. Tetranucleotide usage deviation analysis supports this relationship, showing that the GVE3 genome sequence correlates best with B. anthracis and Bacillus cereus genome sequences, rather than Geobacillus spp genome sequences.
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Affiliation(s)
- Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa,
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30
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Stelder SK, Mahmud SA, Dekker HL, de Koning LJ, Brul S, de Koster CG. Temperature Dependence of the Proteome Profile of the Psychrotolerant Pathogenic Food Spoiler Bacillus weihenstephanensis Type Strain WSBC 10204. J Proteome Res 2015; 14:2169-76. [DOI: 10.1021/pr501307t] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sacha K. Stelder
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Siraje A. Mahmud
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Henk L. Dekker
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Leo J. de Koning
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Stanley Brul
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Chris G. de Koster
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
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31
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Toby IT, Widmer J, Dyer DW. Divergence of protein-coding capacity and regulation in the Bacillus cereus sensu lato group. BMC Bioinformatics 2014; 15 Suppl 11:S8. [PMID: 25350501 PMCID: PMC4251056 DOI: 10.1186/1471-2105-15-s11-s8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The Bacillus cereus sensu lato group contains ubiquitous facultative anaerobic soil-borne Gram-positive spore-forming bacilli. Molecular phylogeny and comparative genome sequencing have suggested that these organisms should be classified as a single species. While clonal in nature, there do not appear to be species-specific clonal lineages, excepting B. anthracis, in spite of the wide array of phenotypes displayed by these organisms. RESULTS We compared the protein-coding content of 201 B. cereus sensu lato genomes to characterize differences and understand the consequences of these differences on biological function. From this larger group we selected a subset consisting of 25 whole genomes for deeper analysis. Cluster analysis of orthologous proteins grouped these genomes into five distinct clades. Each clade could be characterized by unique genes shared among the group, with consequences for the phenotype of each clade. Surprisingly, this population structure recapitulates our recent observations on the divergence of the generalized stress response (SigB) regulons in these organisms. Divergence of the SigB regulon among these organisms is primarily due to the placement of SigB-dependent promoters that bring genes from a common gene pool into/out of the SigB regulon. CONCLUSIONS Collectively, our observations suggest the hypothesis that the evolution of these closely related bacteria is a consequence of two distinct processes. Horizontal gene transfer, gene duplication/divergence and deletion dictate the underlying coding capacity in these genomes. Regulatory divergence overlays this protein coding reservoir and shapes the expression of both the unique and shared coding capacity of these organisms, resulting in phenotypic divergence. Data from other organisms suggests that this is likely a common pattern in prokaryotic evolution.
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Affiliation(s)
- Inimary T Toby
- University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC-1106, Oklahoma City, OK 73104, USA
| | - Jonah Widmer
- University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC-1106, Oklahoma City, OK 73104, USA
| | - David W Dyer
- University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC-1106, Oklahoma City, OK 73104, USA
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Wang C, Sui Z, Leclercq SO, Zhang G, Zhao M, Chen W, Feng J. Functional characterization and phylogenetic analysis of acquired and intrinsic macrolide phosphotransferases in theBacillus cereusgroup. Environ Microbiol 2014; 17:1560-73. [DOI: 10.1111/1462-2920.12578] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/21/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Chao Wang
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Zhihai Sui
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Sébastien Olivier Leclercq
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Gang Zhang
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Meilin Zhao
- School of Food and Biological Engineering; Jiangsu University; Zhenjiang Jiangsu 212013 China
| | - Weiqi Chen
- Department of Environmental and Biological Pharmaceutical; Beijing Industrial Technician College; Beijing 100023 China
| | - Jie Feng
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
- Beijing Key Laboratory of Microbial Drug Resistance and Resistome; Beijing 100101 China
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33
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Jiménez G, Urdiain M, Cifuentes A, López-López A, Blanch AR, Tamames J, Kämpfer P, Kolstø AB, Ramón D, Martínez JF, Codoñer FM, Rosselló-Móra R. Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations. Syst Appl Microbiol 2013; 36:383-91. [DOI: 10.1016/j.syapm.2013.04.008] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/16/2013] [Accepted: 04/18/2013] [Indexed: 11/30/2022]
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Targeted enrichment: maximizing orthologous gene comparisons across deep evolutionary time. PLoS One 2013; 8:e67908. [PMID: 23844125 PMCID: PMC3699465 DOI: 10.1371/journal.pone.0067908] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 05/21/2013] [Indexed: 11/19/2022] Open
Abstract
Estimated phylogenies of evolutionarily diverse taxa will be well supported and more likely to be historically accurate when the analysis contains large amounts of data–many genes sequenced across many taxa. Inferring such phylogenies for non-model organisms is challenging given limited resources for whole-genome sequencing. We take advantage of genomic data from a single species to test the limits of hybridization-based enrichment of hundreds of exons across frog species that diverged up to 250 million years ago. Enrichment success for a given species depends greatly on the divergence time between it and the reference species, and the resulting alignment contains a significant proportion of missing data. However, our alignment generates a well-supported phylogeny of frogs, suggesting that this technique is a practical solution towards resolving relationships across deep evolutionary time.
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Molecular signatures for
Bacillus
species: demarcation of the
Bacillus subtilis
and
Bacillus cereus
clades in molecular terms and proposal to limit the placement of new species into the genus
Bacillus. Int J Syst Evol Microbiol 2013; 63:2712-2726. [DOI: 10.1099/ijs.0.048488-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus
Bacillus
is a phylogenetically incoherent taxon with members of the group lacking a common evolutionary history. Comprising aerobic and anaerobic spore-forming bacteria, no characteristics are known that can distinguish species of this genus from other similar endospore-forming genera. With the availability of complete genomic data from over 30 different species from this group, we have constructed detailed phylogenetic trees to determine the relationships among
Bacillus
and other closely related taxa. Additionally, we have performed comparative genomic analysis for the determination of molecular markers, in the form of conserved signature indels (CSIs), to assist in the understanding of relationships among species of the genus
Bacillus
in molecular terms. Based on the analysis, we report here the identification of 11 and 6 CSIs that clearly differentiate a ‘
Bacillus subtilis
clade’ and a ‘
Bacillus cereus
clade’, respectively, from all other species of the genus
Bacillus
. No molecular markers were identified that supported a larger clade within this genus. The subtilis and the cereus clades were also the largest observed monophyletic groupings among species from the genus
Bacillus
in the phylogenetic trees based on 16S rRNA gene sequences and those based upon concatenated sequences for 20 conserved proteins. Thus, the relationships observed among these groups of species through CSIs are independently well supported by phylogenetic analysis. The molecular markers identified in this study provide a reliable means for the reorganization of the currently polyphyletic genus
Bacillus
into a more evolutionarily consistent set of groups. It is recommended that the genus
Bacillus
sensu stricto should comprise only the monophyletic subtilis clade that is demarcated by the identified CSIs, with
B. subtilis
as its type species. Members of the adjoining cereus clade (referred to as the Cereus clade of bacilli), although they are distinct from the subtilis clade, will also retain the
Bacillus
genus name as they contain several clinically important species, and their transfer into a new genus could have serious consequences. However, all other species that are currently part of the genus
Bacillus
and not part of these two clades should be eventually transferred to other genera. We also propose that all novel species of the genus
Bacillus
must meet minimal requirements, foremost among which is that the branching of the prospective species with the
Bacillus
sensu stricto clade or the Cereus clade of bacilli should be strongly supported by 16S rRNA gene sequence trees or trees based upon concatenated protein sequences. Additionally, the presence of one or more of the CSIs that are specific for these clades may be used to confirm molecularly the placement of the species into these clades. The identified CSIs, in addition to their usefulness for taxonomic and diagnostic purposes, also provide novel probes for genetic and biochemical studies of these bacteria.
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Santini T, Turchi L, Ceccarelli G, Di Franco C, Beccari E. Transcriptional analysis of ftsZ within the dcw cluster in Bacillus mycoides. BMC Microbiol 2013; 13:27. [PMID: 23384289 PMCID: PMC3762067 DOI: 10.1186/1471-2180-13-27] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 01/31/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In Bacillus mycoides, as well as in other members of the B. cereus group, the tubulin-like protein of the division septum FtsZ is encoded by the distal gene of the cluster division and cell wall (dcw). Along the cluster the genes coding for structural proteins of the division apparatus are intermingled with those coding for enzymes of peptidoglycan biosynthesis, raising the possibility that genes with this different function might be coexpressed. Transcription of ftsZ in two model bacteria had been reported to differ: in B. subtilis, the ftsZ gene was found transcribed as a bigenic mRNA in the AZ operon; in E. coli, the transcripts of ftsZ were monogenic, expressed by specific promoters. Here we analyzed the size and the initiation sites of RNAs transcribed from ftsZ and from other cluster genes in two B. mycoides strains, DX and SIN, characterized by colonies of different chirality and density, to explore the correlation of the different morphotypes with transcription of the dcw genes. RESULTS In both strains, during vegetative growth, the ftsZ-specific RNAs were composed mainly of ftsZ, ftsA-ftsZ and ftsQ-ftsA-ftsZ transcripts. A low number of RNA molecules included the sequences of the upstream murG and murB genes, which are involved in peptidoglycan synthesis. No cotranscription was detected between ftsZ and the downstream genes of the SpoIIG cluster. The monogenic ftsZ RNA was found in both strains, with the main initiation site located inside the ftsA coding sequence. To confirm the promoter property of the site, a B. mycoides construct carrying the ftsA region in front of the shortened ftsZ gene was inserted into the AmyE locus of B. subtilis 168. The promoter site in the ftsA region was recognized in the heterologous cellular context and expressed as in B. mycoides. CONCLUSIONS The DX and SIN strains of B. mycoides display very similar RNA transcription specificity. The ftsZ messenger RNA can be found either as an independent transcript or expressed together with ftsA and ftsQ and, in low amounts, with genes that are specific to peptidoglycan biosynthesis.
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Affiliation(s)
- Tiziana Santini
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Rome 00185, Italy
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38
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Scott E, Dyer DW. Divergence of the SigB regulon and pathogenesis of the Bacillus cereus sensu lato group. BMC Genomics 2012; 13:564. [PMID: 23088190 PMCID: PMC3485630 DOI: 10.1186/1471-2164-13-564] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 10/10/2012] [Indexed: 12/31/2022] Open
Abstract
Background The Bacillus cereus sensu lato group currently includes seven species (B. cereus, B. anthracis, B. mycoides, B. pseudomycoides, B. thuringiensis, B. weihenstephanensis and B. cytotoxicus) that recent phylogenetic and phylogenomic analyses suggest are likely a single species, despite their varied phenotypes. Although horizontal gene transfer and insertion-deletion events are clearly important for promoting divergence among these genomes, recent studies have demonstrated that a major basis for phenotypic diversity in these organisms may be differential regulation of the highly similar gene content shared by these organisms. To explore this hypothesis, we used an in silico approach to evaluate the relationship of pathogenic potential and the divergence of the SigB-dependent general stress response within the B. cereus sensu lato group, since SigB has been demonstrated to support pathogenesis in Bacillus, Listeria and Staphylococcus species. Results During the divergence of these organisms from a common “SigB-less” ancestor, the placement of SigB promoters at varied locations in the B. cereus sensu lato genomes predict alternative structures for the SigB regulon in different organisms. Predicted promoter changes suggesting differential transcriptional control of a common gene pool predominate over evidence of indels or horizontal gene transfer for explaining SigB regulon divergence. Conclusions Four lineages of the SigB regulon have arisen that encompass different gene contents and suggest different strategies for supporting pathogenesis. This is consistent with the hypothesis that divergence within the B. cereus sensu lato group rests in part on alternative strategies for regulation of a common gene pool.
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Affiliation(s)
- Edgar Scott
- Department of Microbiology and Immunology, Oklahoma University Health Sciences Center, Oklahoma City, 73117, USA
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Antolinos V, Fernández PS, Ros-Chumillas M, Periago PM, Weiss J. Development of a High-Resolution Melting–Based Approach for Efficient Differentiation AmongBacillus cereusGroup Isolates. Foodborne Pathog Dis 2012; 9:777-85. [DOI: 10.1089/fpd.2012.1148] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Vera Antolinos
- Departamento Ingeniería Alimentos y del Equipamiento Agrícola, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, Cartagena, Spain
- Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Pablo S. Fernández
- Departamento Ingeniería Alimentos y del Equipamiento Agrícola, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, Cartagena, Spain
- Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - María Ros-Chumillas
- Departamento Ingeniería Alimentos y del Equipamiento Agrícola, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, Cartagena, Spain
- Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Paula M. Periago
- Departamento Ingeniería Alimentos y del Equipamiento Agrícola, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, Cartagena, Spain
- Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Julia Weiss
- Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Cartagena, Spain
- Departamento de Ciencia y Tecnología Agraria, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, Cartagena, Spain
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Mukhopadhyay J, Braig HR, Rowton ED, Ghosh K. Naturally occurring culturable aerobic gut flora of adult Phlebotomus papatasi, vector of Leishmania major in the Old World. PLoS One 2012; 7:e35748. [PMID: 22629302 PMCID: PMC3358311 DOI: 10.1371/journal.pone.0035748] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 03/23/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Cutaneous leishmaniasis is a neglected, vector-borne parasitic disease and is responsible for persistent, often disfiguring lesions and other associated complications. Leishmania, causing zoonotic cutaneous leishmaniasis (ZCL) in the Old World are mainly transmitted by the predominant sand fly vector, Phlebotomus papatasi. To date, there is no efficient control measure or vaccine available for this widespread insect-borne infectious disease. METHODOLOGY/PRINCIPAL FINDINGS A survey was carried out to study the abundance of different natural gut flora in P. papatasi, with the long-term goal of generating a paratransgenic sand fly that can potentially block the development of Leishmania in the sand fly gut, thereby preventing transmission of leishmania in endemic disease foci. Sand flies, in particular, P. papatasi were captured from different habitats of various parts of the world. Gut microbes were cultured and identified using 16S ribosomal DNA analysis and a phylogenetic tree was constructed. We found variation in the species and abundance of gut flora in flies collected from different habitats. However, a few Gram-positive, nonpathogenic bacteria including Bacillus flexus and B. pumilus were common in most of the sites examined. CONCLUSION/SIGNIFICANCE Our results indicate that there is a wide range of variation of aerobic gut flora inhabiting sand fly guts, which possibly reflect the ecological condition of the habitat where the fly breeds. Also, some species of bacteria (B. pumilus, and B. flexus) were found from most of the habitats. Important from an applied perspective of dissemination, our results support a link between oviposition induction and adult gut flora.
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Affiliation(s)
- Jaba Mukhopadhyay
- Division of Entomology, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Henk R. Braig
- School of Biological Sciences, Bangor University, Bangor, Wales, United Kingdom
| | - Edgar D. Rowton
- Division of Entomology, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Kashinath Ghosh
- Division of Entomology, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
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Iron regulates expression of Bacillus cereus hemolysin II via global regulator Fur. J Bacteriol 2012; 194:3327-35. [PMID: 22522892 DOI: 10.1128/jb.00199-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The capacity of pathogens to respond to environmental signals, such as iron concentration, is key to bacterial survival and establishment of a successful infection. Bacillus cereus is a widely distributed bacterium with distinct pathogenic properties. Hemolysin II (HlyII) is one of its pore-forming cytotoxins and has been shown to be involved in bacterial pathogenicity in a number of cell and animal models. Unlike many other B. cereus pathogenicity factors, HlyII is not regulated by pleiotropic transcriptional regulator PlcR but is controlled by its own regulator, HlyIIR. Using a combination of in vivo and in vitro techniques, we show that hlyII expression is also negatively regulated by iron by the global regulator Fur via direct interaction with the hlyII promoter. DNase I footprinting and in vitro transcription experiments indicate that Fur prevents RNA polymerase binding to the hlyII promoter. HlyII expression profiles demonstrate that both HlyIIR and Fur regulate HlyII expression in a concerted fashion, with the effect of Fur being maximal in the early stages of bacterial growth. In sum, these results show that Fur serves as a transcriptional repressor for hlyII expression.
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