1
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Mehdizadeh Gohari I, Edwards AN, McBride SM, McClane BA. The impact of orphan histidine kinases and phosphotransfer proteins on the regulation of clostridial sporulation initiation. mBio 2024; 15:e0224823. [PMID: 38477571 DOI: 10.1128/mbio.02248-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024] Open
Abstract
Sporulation is an important feature of the clostridial life cycle, facilitating survival of these bacteria in harsh environments, contributing to disease transmission for pathogenic species, and sharing common early steps that are also involved in regulating industrially important solvent production by some non-pathogenic species. Initial genomics studies suggested that Clostridia lack the classical phosphorelay that phosphorylates Spo0A and initiates sporulation in Bacillus, leading to the hypothesis that sporulation in Clostridia universally begins when Spo0A is phosphorylated by orphan histidine kinases (OHKs). However, components of the classical Bacillus phosphorelay were recently identified in some Clostridia. Similar Bacillus phosphorelay components have not yet been found in the pathogenic Clostridia or the solventogenic Clostridia of industrial importance. For some of those Clostridia lacking a classical phosphorelay, the involvement of OHKs in sporulation initiation has received support from genetic studies demonstrating the involvement of several apparent OHKs in their sporulation. In addition, several clostridial OHKs directly phosphorylate Spo0A in vitro. Interestingly, there is considerable protein domain diversity among the sporulation-associated OHKs in Clostridia. Further adding to the emergent complexity of sporulation initiation in Clostridia, several candidate OHK phosphotransfer proteins that were OHK candidates were shown to function as phosphatases that reduce sporulation in some Clostridia. The mounting evidence indicates that no single pathway explains sporulation initiation in all Clostridia and supports the need for further study to fully understand the unexpected and biologically fascinating mechanistic diversity of this important process among these medically and industrially important bacteria.
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Affiliation(s)
- Iman Mehdizadeh Gohari
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Adrianne N Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Shonna M McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Bruce A McClane
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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2
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Serrano M, Martins D, Henriques AO. Clostridioides difficile Sporulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:273-314. [PMID: 38175480 DOI: 10.1007/978-3-031-42108-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Some members of the Firmicutes phylum, including many members of the human gut microbiota, are able to differentiate a dormant and highly resistant cell type, the endospore (hereinafter spore for simplicity). Spore-formers can colonize virtually any habitat and, because of their resistance to a wide variety of physical and chemical insults, spores can remain viable in the environment for long periods of time. In the anaerobic enteric pathogen Clostridioides difficile the aetiologic agent is the oxygen-resistant spore, while the toxins produced by actively growing cells are the main cause of the disease symptoms. Here, we review the regulatory circuits that govern entry into sporulation. We also cover the role of spores in the infectious cycle of C. difficile in relation to spore structure and function and the main control points along spore morphogenesis.
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Affiliation(s)
- Mónica Serrano
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal.
| | - Diogo Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
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3
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Marathe A, Zarazúa-Osorio B, Srivastava P, Fujita M. The master regulator for entry into sporulation in Bacillus subtilis becomes a mother cell-specific transcription factor for forespore engulfment. Mol Microbiol 2023; 120:439-461. [PMID: 37485800 DOI: 10.1111/mmi.15132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
The Spo0A transcription factor is activated by phosphorylation in starving Bacillus subtilis cells. The activated Spo0A (Spo0A~P) regulates genes controlling entry into sporulation and appears to control mother-cell-specific gene expression after asymmetric division, but the latter remains elusive. Here, we found that Spo0A~P directly binds to three conserved DNA sequences (0A1-3) in the promoter region of the mother cell-specific lytic transglycosylase gene spoIID, which is transcribed by σE -RNA polymerase (RNAP) and negatively controlled by the SpoIIID transcription factor and required for forespore engulfment. Systematic mutagenesis of the 0A boxes revealed that the 0A1 and 0A2 boxes located upstream of the promoter positively control the transcription of spoIID. In contrast, the 0A3 box located downstream of the promoter negatively controls the transcription of spoIID. The mutated SpoIIID binding site located between the -35 and -10 promoter elements causes increased expression of spoIID and reduced sporulation. When the mutations of 0A1, 0A2, and IIID sites are combined, sporulation is restored. Collectively, our data suggest that the mother cell-specific spoIID expression is precisely controlled by the coordination of three factors, Spo0A~P, SpoIIID, and σE -RNAP, for proper sporulation. The conservation of this mechanism across spore-forming species was discussed.
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Affiliation(s)
- Anuradha Marathe
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | | | - Priyanka Srivastava
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
- Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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4
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Măgălie A, Schwartz DA, Lennon JT, Weitz JS. Optimal dormancy strategies in fluctuating environments given delays in phenotypic switching. J Theor Biol 2023; 561:111413. [PMID: 36639023 DOI: 10.1016/j.jtbi.2023.111413] [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: 10/10/2022] [Revised: 01/01/2023] [Accepted: 01/05/2023] [Indexed: 01/12/2023]
Abstract
Organisms have evolved different mechanisms in response to periods of environmental stress, including dormancy - a reversible state of reduced metabolic activity. Transitions to and from dormancy can be random or induced by changes in environmental conditions. Prior theoretical work has shown that stochastic transitioning between active and dormant states at the individual level can maximize fitness at the population level. However, such theories of 'bet-hedging' strategies typically neglect certain physiological features of transitions to dormancy, including time lags to gain protective benefits. Here, we construct and analyze a dynamic model that couples stochastic changes in environmental state with the population dynamics of organisms that can initiate dormancy after an explicit time delay. Stochastic environments are simulated using a multi-state Markov chain through which the mean and variance of environmental residence time can be adjusted. In the absence of time lags (or in the limit of very short lags), we find that bet-hedging strategy transition probabilities scale inversely with the mean environmental residence times, consistent with prior theory. We also find that increasing delays in dormancy decreases optimal transitioning probabilities, an effect that can be influenced by the correlations of environmental noise. When environmental residence times - either good or bad - are uncorrelated, the maximum population level fitness is obtained given low levels of transitioning between active and dormant states. However when environmental residence times are correlated, optimal dormancy initiation and termination probabilities increase insofar as the mean environmental persistent time is longer than the delay to reach dormancy. We also find that bet hedging is no longer advantageous when delays to enter dormancy exceed the mean environmental residence times. Altogether, these results show how physiological limits to dormancy and environmental dynamics shape the evolutionary benefits and even viability of bet hedging strategies at population scales.
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Affiliation(s)
- Andreea Măgălie
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | | | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; School of Physics, Georgia Institute of Technology, Atlanta, GA, USA; Institut de Biologie, École Normale Supérieure, Paris, France.
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5
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Xiao Y, Wang H, Lan Y, Zhong C, Yan G, Xu Z, Lu G, Chen J, Wei T, Wong WC, Kwan YH, Qian PY. Changes in community structures and functions of the gut microbiomes of deep-sea cold seep mussels during in situ transplantation experiment. Anim Microbiome 2023; 5:17. [PMID: 36906632 PMCID: PMC10008618 DOI: 10.1186/s42523-023-00238-8] [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: 06/01/2022] [Accepted: 02/25/2023] [Indexed: 03/13/2023] Open
Abstract
BACKGROUND Many deep-sea invertebrates largely depend on chemoautotrophic symbionts for energy and nutrition, and some of them have reduced functional digestive tracts. By contrast, deep-sea mussels have a complete digestive system although symbionts in their gills play vital roles in nutrient supply. This digestive system remains functional and can utilise available resources, but the roles and associations among gut microbiomes in these mussels remain unknown. Specifically, how the gut microbiome reacts to environmental change is unclear. RESULTS The meta-pathway analysis showed the nutritional and metabolic roles of the deep-sea mussel gut microbiome. Comparative analyses of the gut microbiomes of original and transplanted mussels subjected to environmental change revealed shifts in bacterial communities. Gammaproteobacteria were enriched, whereas Bacteroidetes were slightly depleted. The functional response for the shifted communities was attributed to the acquisition of carbon sources and adjusting the utilisation of ammonia and sulphide. Self-protection was observed after transplantation. CONCLUSION This study provides the first metagenomic insights into the community structure and function of the gut microbiome in deep-sea chemosymbiotic mussels and their critical mechanisms for adapting to changing environments and meeting of essential nutrient demand.
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Affiliation(s)
- Yao Xiao
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Hao Wang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, People's Republic of China
| | - Yi Lan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Cheng Zhong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Guoyong Yan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Zhimeng Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Guangyuan Lu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China.,Research Center for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 51807, People's Republic of China
| | - Jiawei Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Tong Wei
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Wai Chuen Wong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Yick Hang Kwan
- Department of Biology, HADAL and Nordcee, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China. .,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China.
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6
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Chouayekh H, Farhat-Khemakhem A, Karray F, Boubaker I, Mhiri N, Abdallah MB, Alghamdi OA, Guerbej H. Effects of Dietary Supplementation with Bacillus amyloliquefaciens US573 on Intestinal Morphology and Gut Microbiota of European Sea Bass. Probiotics Antimicrob Proteins 2023; 15:30-43. [PMID: 35933471 DOI: 10.1007/s12602-022-09974-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2022] [Indexed: 01/18/2023]
Abstract
Probiotics or direct-fed microbials (DFM) have proven strong potential for improving aquaculture sustainability. This study aims to evaluate the effects of dietary supplementation with the DFM Bacillus amyloliquefaciens US573 on growth performance, intestinal morphology, and gut microbiota (GM) of European sea bass. For this purpose, healthy fish were divided into two feeding trials in triplicate of 25 fish in each tank. The fish were fed with a control basal diet or a DFM-supplemented diet for 42 days. Results showed that, while no significant effects on growth performance were observed, the length and abundance of villi were higher in the DFM-fed group. The benefic effects of DFM supplementation included also the absence of cysts formation and the increase in number of goblet cells playing essential role in immune response. Through DNA metabarcoding analysis of GM, 5 phyla and 14 major genera were identified. At day 42, the main microbiome changes in response to B. amyloliquefaciens US573 addition included the significant decrease in abundance of Actinobacteria phylum that perfectly correlates with a decrease in Nocardia genus representatives which represent serious threat in marine and freshwater fish. On the contrary, an obvious dominance of Betaproteobacteria associated with the abundance in Variovorax genus members, known for their ability to metabolize numerous substrates, was recorded. Interestingly, Firmicutes, particularly species affiliated to the genus Sporosarcina with recent promising probiotic potential, were identified as the most abundant. These results suggest that B. amyloliquefaciens US573 can be effectively recommended as health-promoting DFM in European sea bass farming.
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Affiliation(s)
- Hichem Chouayekh
- Department of Biological Sciences, College of Science, University of Jeddah, Asfan Road, 21959, P.O. Box 34, Jeddah, Kingdom of Saudi Arabia. .,Laboratory of Microbial Biotechnology, Enzymatic and Biomolecules (LMBEB), Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia.
| | - Ameny Farhat-Khemakhem
- Laboratory of Microbial Biotechnology, Enzymatic and Biomolecules (LMBEB), Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia
| | - Fatma Karray
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia
| | - Insaf Boubaker
- Laboratory of Microbial Biotechnology, Enzymatic and Biomolecules (LMBEB), Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia
| | - Najla Mhiri
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia
| | - Manel Ben Abdallah
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, Road Sidi Mansour 6 km, Sfax, 3018, Tunisia
| | - Othman A Alghamdi
- Department of Biological Sciences, College of Science, University of Jeddah, Asfan Road, 21959, P.O. Box 34, Jeddah, Kingdom of Saudi Arabia
| | - Hamadi Guerbej
- National Institute of Sea Sciences and Technologies, Monastir, Tunisia
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7
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Gonçalves G, Santos RA, Coutinho F, Pedrosa N, Curado M, Machado M, Costas B, Bonneville L, Serrano M, Carvalho AP, Díaz-Rosales P, Oliva-Teles A, Couto A, Serra CR. Oral vaccination of fish against vibriosis using spore-display technology. Front Immunol 2022; 13:1012301. [DOI: 10.3389/fimmu.2022.1012301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Oral vaccines are highly demanded by the aquaculture sector, to allow mass delivery of antigens without using the expensive and labor-intensive injectable vaccines. These later require individual handling of fish, provoking stress-related mortalities.One possible strategy to create injection-free vaccine delivery vehicles is the use of bacterial spores, extremely resistant structures with wide biotechnological applications, including as probiotics, display systems, or adjuvants. Bacterial spores, in particular those of Bacillus subtilis, have been shown to behave as mucosal vaccine adjuvants in mice models. However, such technology has not been extensively explored against fish bacterial disease.In this study, we used a laboratory strain of B. subtilis, for which a variety of genetic manipulation tools are available, to display at its spores surface either a Vibrio antigenic protein, OmpK, or the green fluorescence protein, GFP. When previously vaccinated by immersion with the OmpK- carrying spores, zebrafish survival upon a bacterial challenge with V. anguillarum and V. parahaemolyticus, increased up to 50 - 90% depending on the pathogen targeted. Further, we were able to detect anti-GFP-antibodies in the serum of European seabass juveniles fed diets containing the GFP-carrying spores and anti-V. anguillarum antibodies in the serum of European seabass juveniles fed the OmpK-carrying spores containing diet. More important, seabass survival was increased from 60 to 86% when previously orally vaccinated with in-feed OmpK- carrying spores. Our results indicate that B. subtilis spores can effectively be used as antigen-carriers for oral vaccine delivery in fish.
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8
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Ul Haq H, Huang W, Li Y, Zhang T, Ma S, Zhang Y, Song Y, Lin D, Tian B. Genetic and genomic characterization of multidrug resistant Bacillus subtilis M3 isolated from an activated sludge reactor treating wastewater. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-021-01006-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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9
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Nordgaard M, Mortensen RMR, Kirk NK, Gallegos‐Monterrosa R, Kovács ÁT. Deletion of Rap-Phr systems in Bacillus subtilis influences in vitro biofilm formation and plant root colonization. Microbiologyopen 2021; 10:e1212. [PMID: 34180604 PMCID: PMC8236291 DOI: 10.1002/mbo3.1212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/19/2022] Open
Abstract
Natural isolates of the soil-dwelling bacterium Bacillus subtilis form robust biofilms under laboratory conditions and colonize plant roots. B. subtilis biofilm gene expression displays phenotypic heterogeneity that is influenced by a family of Rap-Phr regulatory systems. Most Rap-Phr systems in B. subtilis have been studied independently, in different genetic backgrounds and under distinct conditions, hampering true comparison of the Rap-Phr systems' impact on bacterial cell differentiation. Here, we investigated each of the 12 Rap-Phr systems of B.subtilis NCIB 3610 for their effect on biofilm formation. By studying single ∆rap-phr mutants, we show that despite redundancy between the cell-cell communication systems, deletion of each of the 12 Rap-Phr systems influences matrix gene expression. These Rap-Phr systems therefore enable fine-tuning of the timing and level of matrix production in response to specific conditions. Furthermore, some of the ∆rap-phr mutants demonstrated altered biofilm formation in vitro and colonization of Arabidopsis thaliana roots, but not necessarily similarly in both processes, indicating that the pathways regulating matrix gene expression and other factors important for biofilm formation may be differently regulated under these distinct conditions.
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Affiliation(s)
- Mathilde Nordgaard
- Bacterial Interactions and Evolution GroupDTU BioengineeringTechnical University of DenmarkLyngbyDenmark
| | | | - Nikolaj Kaae Kirk
- Bacterial Interactions and Evolution GroupDTU BioengineeringTechnical University of DenmarkLyngbyDenmark
| | | | - Ákos T. Kovács
- Bacterial Interactions and Evolution GroupDTU BioengineeringTechnical University of DenmarkLyngbyDenmark
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10
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Gallegos-Monterrosa R, Christensen MN, Barchewitz T, Koppenhöfer S, Priyadarshini B, Bálint B, Maróti G, Kempen PJ, Dragoš A, Kovács ÁT. Impact of Rap-Phr system abundance on adaptation of Bacillus subtilis. Commun Biol 2021; 4:468. [PMID: 33850233 PMCID: PMC8044106 DOI: 10.1038/s42003-021-01983-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/12/2021] [Indexed: 02/07/2023] Open
Abstract
Microbes commonly display great genetic plasticity, which has allowed them to colonize all ecological niches on Earth. Bacillus subtilis is a soil-dwelling organism that can be isolated from a wide variety of environments. An interesting characteristic of this bacterium is its ability to form biofilms that display complex heterogeneity: individual, clonal cells develop diverse phenotypes in response to different environmental conditions within the biofilm. Here, we scrutinized the impact that the number and variety of the Rap-Phr family of regulators and cell-cell communication modules of B. subtilis has on genetic adaptation and evolution. We examine how the Rap family of phosphatase regulators impacts sporulation in diverse niches using a library of single and double rap-phr mutants in competition under 4 distinct growth conditions. Using specific DNA barcodes and whole-genome sequencing, population dynamics were followed, revealing the impact of individual Rap phosphatases and arising mutations on the adaptability of B. subtilis.
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Affiliation(s)
- Ramses Gallegos-Monterrosa
- grid.9613.d0000 0001 1939 2794Terrestrial Biofilms Group, Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Mathilde Nordgaard Christensen
- grid.5170.30000 0001 2181 8870Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tino Barchewitz
- grid.9613.d0000 0001 1939 2794Terrestrial Biofilms Group, Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Sonja Koppenhöfer
- grid.9613.d0000 0001 1939 2794Terrestrial Biofilms Group, Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany ,grid.25055.370000 0000 9130 6822Present Address: Department of Biology, Memorial University of Newfoundland, St. John’s, NL Canada
| | - B. Priyadarshini
- grid.5170.30000 0001 2181 8870Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Balázs Bálint
- grid.475919.7Seqomics Biotechnology Ltd., Mórahalom, Hungary
| | - Gergely Maróti
- grid.5018.c0000 0001 2149 4407Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Paul J. Kempen
- grid.5170.30000 0001 2181 8870Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Dragoš
- grid.5170.30000 0001 2181 8870Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ákos T. Kovács
- grid.9613.d0000 0001 1939 2794Terrestrial Biofilms Group, Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany ,grid.5170.30000 0001 2181 8870Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
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11
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Martins D, DiCandia MA, Mendes AL, Wetzel D, McBride SM, Henriques AO, Serrano M. CD25890, a conserved protein that modulates sporulation initiation in Clostridioides difficile. Sci Rep 2021; 11:7887. [PMID: 33846410 PMCID: PMC8041843 DOI: 10.1038/s41598-021-86878-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/17/2021] [Indexed: 12/16/2022] Open
Abstract
Bacteria that reside in the gastrointestinal tract of healthy humans are essential for our health, sustenance and well-being. About 50-60% of those bacteria have the ability to produce resilient spores that are important for the life cycle in the gut and for host-to-host transmission. A genomic signature for sporulation in the human intestine was recently described, which spans both commensals and pathogens such as Clostridioides difficile and contains several genes of unknown function. We report on the characterization of a signature gene, CD25890, which, as we show is involved in the control of sporulation initiation in C. difficile under certain nutritional conditions. Spo0A is the main regulatory protein controlling entry into sporulation and we show that an in-frame deletion of CD25890 results in increased expression of spo0A per cell and increased sporulation. The effect of CD25890 on spo0A is likely indirect and mediated through repression of the sinRR´ operon. Deletion of the CD25890 gene, however, does not alter the expression of the genes coding for the cytotoxins or the genes involved in biofilm formation. Our results suggest that CD25890 acts to modulate sporulation in response to the nutrients present in the environment.
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Affiliation(s)
- Diogo Martins
- Instituto de Tecnologia Química E Biológica António Xavier, Avenida da República, 2780-157, Oeiras, Portugal
| | - Michael A DiCandia
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Aristides L Mendes
- Instituto de Tecnologia Química E Biológica António Xavier, Avenida da República, 2780-157, Oeiras, Portugal
| | - Daniela Wetzel
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Shonna M McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Adriano O Henriques
- Instituto de Tecnologia Química E Biológica António Xavier, Avenida da República, 2780-157, Oeiras, Portugal
| | - Mónica Serrano
- Instituto de Tecnologia Química E Biológica António Xavier, Avenida da República, 2780-157, Oeiras, Portugal.
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12
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Examining the Gastrointestinal and Immunomodulatory Effects of the Novel Probiotic Bacillus subtilis DE111. Int J Mol Sci 2021; 22:ijms22052453. [PMID: 33671071 PMCID: PMC7957723 DOI: 10.3390/ijms22052453] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022] Open
Abstract
Probiotics make up a large and growing segment of the commercial market of dietary supplements and are touted as offering a variety of human health benefits. Some of the purported positive impacts of probiotics include, but are not limited to, stabilization of the gut microbiota, prevention of gastrointestinal disorders and modulation of the host immune system. Current research suggests that the immunomodulatory effects of probiotics are strain-specific and vary in mode of action. Here, we examined the immunomodulatory properties of Bacillus subtilis strain DE111 in a healthy human population. In a pilot randomized, double blind, placebo-controlled four-week intervention, we examined peripheral blood mononuclear cells (PBMCs) at basal levels pre- and post-intervention, as well as in response to stimulation with bacterial lipopolysaccharide (LPS). We observed an increase in anti-inflammatory immune cell populations in response to ex vivo LPS stimulation of PBMCs in the DE111 intervention group. Overall perceived gastrointestinal health, microbiota, and circulating and fecal markers of inflammation (Il-6, sIgA) and gut barrier function (plasma zonulin) were largely unaffected by DE111 intervention, although the study may have been underpowered to detect these differences. These pilot data provide information and justification to conduct an appropriately powered clinical study to further examine the immunomodulatory potential of B. subtilis DE111 in human populations.
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13
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Li C, Cheng P, Zheng L, Li Y, Chen Y, Wen S, Yu G. Comparative genomics analysis of two banana Fusarium wilt biocontrol endophytes Bacillus subtilis R31 and TR21 provides insights into their differences on phytobeneficial trait. Genomics 2021; 113:900-909. [PMID: 33592313 DOI: 10.1016/j.ygeno.2021.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/26/2020] [Accepted: 02/08/2021] [Indexed: 01/27/2023]
Abstract
Fusarium wilt of banana is considered one of the most destructive plant diseases. Bacillus subtilis R31 and TR21, isolated from Dendrobium sp. leaves, exhibit different phytobeneficial effects on banana Fusarium wilt bio-controlling. Here, we performed genome sequencing and comparative genomics analysis of R31 and TR21 to enhance our understanding of the different phytobeneficial traits. These results revealed that the strain-specific genes of R31 involved in sporulation, quorum sensing, and antibiotic synthesis allow R31 to present a better capacity of sporulation, rhizosphere adaptation, and quorum sensing than TR21. Selective pressure analysis indicated that the glycosylase and endo-alpha-(1- > 5)-L-arabinanase genes were strong positive selected, which may contribute to the TR21 to colonize well in banana's vascular bundles. Altogether, our findings presented here should advance further agricultural application of R31 and TR21 as two promising resources of plant growth promotion and biological control via genetic engineering.
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Affiliation(s)
- Chunji Li
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China.
| | - Ping Cheng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China.
| | - Li Zheng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China
| | - Yongjian Li
- Zhuhai Modern Agriculture Development Center, Zhuhai 519075, People's Republic of China
| | - Yanhong Chen
- Zhuhai Modern Agriculture Development Center, Zhuhai 519075, People's Republic of China
| | - Shuheng Wen
- Guangdong Geolong Biotechnology Co., Ltd., Zhuhai 519050, People's Republic of China
| | - Guohui Yu
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China.
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14
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Dragoš A, Priyadarshini B, Hasan Z, Strube ML, Kempen PJ, Maróti G, Kaspar C, Bose B, Burton BM, Bischofs IB, Kovács ÁT. Pervasive prophage recombination occurs during evolution of spore-forming Bacilli. ISME JOURNAL 2020; 15:1344-1358. [PMID: 33343000 DOI: 10.1038/s41396-020-00854-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/12/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023]
Abstract
Phages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SPβ prophage of Bacillus subtilis, leading to direct antagonistic interactions within the population. Herein, we reveal that under a sporulation selection regime, SPβ recombines with low copy number phi3Ts phage DNA present within the B. subtilis population. Recombination results in a new prophage occupying a different integration site, as well as the spontaneous release of virulent phage hybrids. Analysis of Bacillus sp. strains suggests that SPβ and phi3T belong to a distinct cluster of unusually large phages inserted into sporulation-related genes that are equipped with a spore-related genetic arsenal. Comparison of Bacillus sp. genomes indicates that similar diversification of SPβ-like phages takes place in nature. Our work is a stepping stone toward empirical studies on phage evolution, and understanding the eco-evolutionary relationships between bacteria and their phages. By capturing the first steps of new phage evolution, we reveal striking relationship between survival strategy of bacteria and evolution of their phages.
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Affiliation(s)
- Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
| | - B Priyadarshini
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Zahraa Hasan
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Paul J Kempen
- Department of Health Technology, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6701, Hungary
| | - Charlotte Kaspar
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | | | - Briana M Burton
- Department of Bacteriology, University of Wisconsin, Madison, WI, 53706, USA
| | - Ilka B Bischofs
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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15
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Barreto HC, Cordeiro TN, Henriques AO, Gordo I. Rampant loss of social traits during domestication of a Bacillus subtilis natural isolate. Sci Rep 2020; 10:18886. [PMID: 33144634 PMCID: PMC7642357 DOI: 10.1038/s41598-020-76017-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/22/2020] [Indexed: 12/16/2022] Open
Abstract
Most model bacteria have been domesticated in laboratory conditions. Yet, the tempo with which a natural isolate diverges from its ancestral phenotype under domestication to a novel laboratory environment is poorly understood. Such knowledge, however is essential to understanding the rate of evolution, the time scale over which a natural isolate can be propagated without loss of its natural adaptive traits, and the reliability of experimental results across labs. Using experimental evolution, phenotypic assays, and whole-genome sequencing, we show that within a week of propagation in a common laboratory environment, a natural isolate of Bacillus subtilis acquires mutations that cause changes in a multitude of traits. A single adaptive mutational step in the gene coding for the transcriptional regulator DegU impairs a DegU-dependent positive autoregulatory loop and leads to loss of robust biofilm architecture, impaired swarming motility, reduced secretion of exoproteases, and to changes in the dynamics of sporulation across environments. Importantly, domestication also resulted in improved survival when the bacteria face pressure from cells of the innate immune system. These results show that degU is a target for mutations during domestication and underscores the importance of performing careful and extremely short-term propagations of natural isolates to conserve the traits encoded in their original genomes.
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Affiliation(s)
- Hugo C Barreto
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tiago N Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
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16
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Hernandez-Valdes JA, Zhou L, de Vries MP, Kuipers OP. Impact of spatial proximity on territoriality among human skin bacteria. NPJ Biofilms Microbiomes 2020; 6:30. [PMID: 32764612 PMCID: PMC7413532 DOI: 10.1038/s41522-020-00140-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/14/2020] [Indexed: 12/30/2022] Open
Abstract
Bacteria display social behavior and establish cooperative or competitive interactions in the niches they occupy. The human skin is a densely populated environment where many bacterial species live. Thus, bacterial inhabitants are expected to find a balance in these interactions, which eventually defines their spatial distribution and the composition of our skin microbiota. Unraveling the physiological basis of the interactions between bacterial species in organized environments requires reductionist analyses using functionally relevant species. Here, we study the interaction between two members of our skin microbiota, Bacillus subtilis and Staphylococcus epidermidis. We show that B. subtilis actively responds to the presence of S. epidermidis in its proximity by two strategies: antimicrobial production and development of a subpopulation with migratory response. The initial response of B. subtilis is production of chlorotetain, which degrades the S. epidermidis at the colony level. Next, a subpopulation of B. subtilis motile cells emerges. Remarkably this subpopulation slides towards the remaining S. epidermidis colony and engulfs it. A slow response back from S. epidermidis cells give origin to resistant cells that prevent both attacks from B. subtilis. We hypothesized that this niche conquering and back-down response from B. subtilis and S. epidermidis, respectively, which resembles other conflicts in nature as the ones observed in animals, may play a role in defining the presence of certain bacterial species in the specific microenvironments that these bacteria occupy on our skin.
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Affiliation(s)
- Jhonatan A Hernandez-Valdes
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Lu Zhou
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Marcel P de Vries
- Department of Biomedical Engineering Antonius Deusinglaan 1, University Medical Center Groningen, Groningen University, 9713 AW, Groningen, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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17
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Mutlu A, Kaspar C, Becker N, Bischofs IB. A spore quality-quantity tradeoff favors diverse sporulation strategies in Bacillus subtilis. ISME JOURNAL 2020; 14:2703-2714. [PMID: 32724142 PMCID: PMC7784978 DOI: 10.1038/s41396-020-0721-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 07/05/2020] [Accepted: 07/15/2020] [Indexed: 11/24/2022]
Abstract
Quality–quantity tradeoffs govern the production of propagules across taxa and can explain variability in life-history traits in higher organisms. A quality–quantity tradeoff was recently discovered in spore forming bacteria, but whether it impacts fitness is unclear. Here we show both theoretically and experimentally that the nutrient supply during spore revival determines the fitness advantage associated with different sporulation behaviors in Bacillus subtilis. By tuning sporulation rates we generate spore-yield and spore-quality strategists that compete with each other in a microscopic life-cycle assay. The quality (yield) strategist is favored when spore revival is triggered by poor (rich) nutrients. We also show that natural isolates from the gut and soil employ different life-cycle strategies that result from genomic variations in the number of rap-phr signaling systems. Taken together, our results suggest that a spore quality–quantity tradeoff contributes to the evolutionary adaptation of sporulating bacteria.
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Affiliation(s)
- Alper Mutlu
- Max-Planck-Institute for Terrestrial Microbiology, D-35043, Marburg, Germany.,BioQuant Center of Heidelberg University, D-69120, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), Heidelberg University, D-69120, Heidelberg, Germany
| | - Charlotte Kaspar
- Max-Planck-Institute for Terrestrial Microbiology, D-35043, Marburg, Germany.,BioQuant Center of Heidelberg University, D-69120, Heidelberg, Germany
| | - Nils Becker
- BioQuant Center of Heidelberg University, D-69120, Heidelberg, Germany.,Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
| | - Ilka B Bischofs
- Max-Planck-Institute for Terrestrial Microbiology, D-35043, Marburg, Germany. .,BioQuant Center of Heidelberg University, D-69120, Heidelberg, Germany. .,Center for Molecular Biology (ZMBH), Heidelberg University, D-69120, Heidelberg, Germany.
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18
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Full-repertoire comparison of the microscopic objects composing the human gut microbiome with sequenced and cultured communities. J Microbiol 2020; 58:377-386. [PMID: 32281049 DOI: 10.1007/s12275-020-9365-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 02/11/2020] [Accepted: 02/11/2020] [Indexed: 12/16/2022]
Abstract
The study of the human gut microbiome is essential in microbiology and infectious diseases as specific alterations in the gut microbiome might be associated with various pathologies, such as chronic inflammatory disease, intestinal infection and colorectal cancer. To identify such dysregulations, several strategies are being used to create a repertoire of the microorganisms composing the human gut microbiome. In this study, we used the "microscomics" approach, which consists of creating an ultrastructural repertoire of all the cell-like objects composing stool samples from healthy donors using transmission electron microscopy (TEM). We used TEM to screen ultrathin sections of 8 resin-embedded stool samples. After exploring hundreds of micrographs, we managed to elaborate ultrastructural categories based on morphological criteria or features. This approach explained many inconsistencies observed with other techniques, such as metagenomics and culturomics. We highlighted the value of our culture-independent approach by comparing our microscopic images to those of cultured bacteria and those reported in the literature. This study helped to detect "minimicrobes" Candidate Phyla Radiation (CPR) for the first time in human stool samples. This "microscomics" approach is non-exhaustive but complements already existing approaches and adds important data to the puzzle of the microbiota.
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19
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Serra CR, Almeida EM, Guerreiro I, Santos R, Merrifield DL, Tavares F, Oliva-Teles A, Enes P. Selection of carbohydrate-active probiotics from the gut of carnivorous fish fed plant-based diets. Sci Rep 2019; 9:6384. [PMID: 31011158 PMCID: PMC6476879 DOI: 10.1038/s41598-019-42716-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 03/25/2019] [Indexed: 02/06/2023] Open
Abstract
The gastrointestinal microbiota plays a critical role on host health and metabolism. This is particularly important in teleost nutrition, because fish do not possess some of the necessary enzymes to cope with the dietary challenges of aquaculture production. A main difficulty within fish nutrition is its dependence on fish meal, an unsustainable commodity and a source of organic pollutants. The most obvious sustainable alternatives to fish meal are plant feedstuffs, but their nutritive value is limited by the presence of high levels of non-starch polysaccharides (NSP), which are not metabolized by fish. The composition of fish-gut microbial communities have been demonstrated to adapt when the host is fed different ingredients. Thus, we hypothesized that a selective pressure of plant-based diets on fish gut microbiota, could be a beneficial strategy for an enrichment of bacteria with a secretome able to mobilize dietary NSP. By targeting bacterial sporulating isolates with diverse carbohydrase activities from the gut of European sea bass, we have obtained isolates with high probiotic potential. By inferring the adaptive fitness to the fish gut and the amenability to industrial processing, we identified the best two candidates to become industrially valuable probiotics. This potential was confirmed in vivo, since one of the select isolates lead to a better growth and feed utilization efficiency in fish fed probiotic-supplemented plant-based diets, thus contributing for sustainable and more cost-effective aquaculture practices.
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Affiliation(s)
- Cláudia R Serra
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.
| | - Eduarda M Almeida
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, Ed. FC4, 4169-007, Porto, Portugal.,CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Inês Guerreiro
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, Ed. FC4, 4169-007, Porto, Portugal
| | - Rafaela Santos
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, Ed. FC4, 4169-007, Porto, Portugal
| | - Daniel L Merrifield
- School of Biomedical and Biological Sciences, Plymouth University, 401 Davy Building, Drake Circus, Plymouth, PL4 8AA, Devon, UK
| | - Fernando Tavares
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, Ed. FC4, 4169-007, Porto, Portugal.,CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Aires Oliva-Teles
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, Ed. FC4, 4169-007, Porto, Portugal
| | - Paula Enes
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
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20
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Brown SP, Blackwell HE, Hammer BK. The State of the Union Is Strong: a Review of ASM's 6th Conference on Cell-Cell Communication in Bacteria. J Bacteriol 2018; 200:e00291-18. [PMID: 29760210 PMCID: PMC6018360 DOI: 10.1128/jb.00291-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 6th American Society for Microbiology Conference on Cell-Cell Communication in Bacteria convened from 16 to 19 October 2017 in Athens, GA. In this minireview, we highlight some of the research presented at that meeting that addresses central questions emerging in the field, including the following questions. How are cell-cell communication circuits designed to generate responses? Where are bacteria communicating? Finally, why are bacteria engaging in such behaviors?
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Affiliation(s)
- Sam P Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Brian K Hammer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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21
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Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota. ISME JOURNAL 2018; 12:2403-2416. [PMID: 29899513 DOI: 10.1038/s41396-018-0192-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/20/2018] [Accepted: 03/27/2018] [Indexed: 12/21/2022]
Abstract
Endospore-formers in the human microbiota are well adapted for host-to-host transmission, and an emerging consensus points to their role in determining health and disease states in the gut. The human gut, more than any other environment, encourages the maintenance of endospore formation, with recent culture-based work suggesting that over 50% of genera in the microbiome carry genes attributed to this trait. However, there has been limited work on the ecological role of endospores and other stress-resistant cellular states in the human gut. In fact, there is no data to indicate whether organisms with the genetic potential to form endospores actually form endospores in situ and how sporulation varies across individuals and over time. Here we applied a culture-independent protocol to enrich for endospores and other stress-resistant cells in human feces to identify variation in these states across people and within an individual over time. We see that cells with resistant states are more likely than those without to be shared among multiple individuals, which suggests that these resistant states are particularly adapted for cross-host dissemination. Furthermore, we use untargeted fecal metabolomics in 24 individuals and within a person over time to show that these organisms respond to shared environmental signals, and in particular, dietary fatty acids, that likely mediate colonization of recently disturbed human guts.
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22
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Mutlu A, Trauth S, Ziesack M, Nagler K, Bergeest JP, Rohr K, Becker N, Höfer T, Bischofs IB. Phenotypic memory in Bacillus subtilis links dormancy entry and exit by a spore quantity-quality tradeoff. Nat Commun 2018; 9:69. [PMID: 29302032 PMCID: PMC5754360 DOI: 10.1038/s41467-017-02477-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 12/04/2017] [Indexed: 12/15/2022] Open
Abstract
Some bacteria, such as Bacillus subtilis, withstand starvation by forming dormant spores that revive when nutrients become available. Although sporulation and spore revival jointly determine survival in fluctuating environments, the relationship between them has been unclear. Here we show that these two processes are linked by a phenotypic “memory” that arises from a carry-over of molecules from the vegetative cell into the spore. By imaging life histories of individual B. subtilis cells using fluorescent reporters, we demonstrate that sporulation timing controls nutrient-induced spore revival. Alanine dehydrogenase contributes to spore memory and controls alanine-induced outgrowth, thereby coupling a spore’s revival capacity to the gene expression and growth history of its progenitors. A theoretical analysis, and experiments with signaling mutants exhibiting altered sporulation timing, support the hypothesis that such an intrinsically generated memory leads to a tradeoff between spore quantity and spore quality, which could drive the emergence of complex microbial traits. Bacillus subtilis withstands starvation by forming dormant spores that revive when nutrients become available. Here, Mutlu et al. show that sporulation timing controls spore revival through a phenotypic ‘memory’ that arises from the carry-over of a metabolic enzyme from the vegetative cell into the spore.
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Affiliation(s)
- Alper Mutlu
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Stephanie Trauth
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Marika Ziesack
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, 69120, Heidelberg, Germany
| | - Katja Nagler
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Jan-Philip Bergeest
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology (IPMB), 69120, Heidelberg, Germany.,Department of Bioinformatics and Functional Genomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Karl Rohr
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology (IPMB), 69120, Heidelberg, Germany.,Department of Bioinformatics and Functional Genomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Nils Becker
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Thomas Höfer
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Ilka B Bischofs
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany. .,Center for Molecular Biology (ZMBH), University of Heidelberg, 69120, Heidelberg, Germany. .,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
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23
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Brito PH, Chevreux B, Serra CR, Schyns G, Henriques AO, Pereira-Leal JB. Genetic Competence Drives Genome Diversity in Bacillus subtilis. Genome Biol Evol 2018; 10:108-124. [PMID: 29272410 PMCID: PMC5765554 DOI: 10.1093/gbe/evx270] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2017] [Indexed: 12/18/2022] Open
Abstract
Prokaryote genomes are the result of a dynamic flux of genes, with increases achieved via horizontal gene transfer and reductions occurring through gene loss. The ecological and selective forces that drive this genomic flexibility vary across species. Bacillus subtilis is a naturally competent bacterium that occupies various environments, including plant-associated, soil, and marine niches, and the gut of both invertebrates and vertebrates. Here, we quantify the genomic diversity of B. subtilis and infer the genome dynamics that explain the high genetic and phenotypic diversity observed. Phylogenomic and comparative genomic analyses of 42 B. subtilis genomes uncover a remarkable genome diversity that translates into a core genome of 1,659 genes and an asymptotic pangenome growth rate of 57 new genes per new genome added. This diversity is due to a large proportion of low-frequency genes that are acquired from closely related species. We find no gene-loss bias among wild isolates, which explains why the cloud genome, 43% of the species pangenome, represents only a small proportion of each genome. We show that B. subtilis can acquire xenologous copies of core genes that propagate laterally among strains within a niche. While not excluding the contributions of other mechanisms, our results strongly suggest a process of gene acquisition that is largely driven by competence, where the long-term maintenance of acquired genes depends on local and global fitness effects. This competence-driven genomic diversity provides B. subtilis with its generalist character, enabling it to occupy a wide range of ecological niches and cycle through them.
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Affiliation(s)
- Patrícia H Brito
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Nova Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Portugal
| | - Bastien Chevreux
- DSM Nutritional Products, Ltd., 60 Westview street, Lexington MA, USA
| | - Cláudia R Serra
- Instituto de Tecnologia Química e Biológica, Oeiras, Portugal
| | - Ghislain Schyns
- DSM Nutritional Products, Ltd., 60 Westview street, Lexington MA, USA
| | | | - José B Pereira-Leal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Ophiomics—Precision Medicine, Lisbon, Portugal
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24
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Ferreira MJ, Mendes AL, de Sá-Nogueira I. The MsmX ATPase plays a crucial role in pectin mobilization by Bacillus subtilis. PLoS One 2017; 12:e0189483. [PMID: 29240795 PMCID: PMC5730181 DOI: 10.1371/journal.pone.0189483] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/27/2017] [Indexed: 12/20/2022] Open
Abstract
Carbohydrates from plant cell walls are often found as heteropolysaccharides intertwined with each other. For competitive advantage against other microorganisms, and ability to fully exploit available carbon and energy sources, Bacillus subtilis possesses a high number of proteins dedicated to the uptake of mono- and oligosaccharides. Here, we characterize transporter complexes, belonging to the ATP-binding cassette (ABC) superfamily, involved in the uptake of oligosaccharides commonly found in pectin. The uptake of these carbohydrates is shown to be MsmX-dependent, assigning a key role in pectin mobilization for MsmX, a multipurpose ATPase serving several distinct ABC-type I sugar importers. Mutagenesis analysis of the transmembrane domains of the AraNPQ MsmX-dependent importer revealed putative residues for MsmX interaction. Interestingly however, although MsmX is shown to be essential for energizing various ABC transporters we found that a second B. subtilis ATPase, YurJ, is able to complement its function when placed in trans at a different locus of the chromosome.
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Affiliation(s)
- Mário J. Ferreira
- UCIBIO, REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Aristides L. Mendes
- UCIBIO, REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Isabel de Sá-Nogueira
- UCIBIO, REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
- * E-mail:
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25
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Maffei VJ, Kim S, Blanchard E, Luo M, Jazwinski SM, Taylor CM, Welsh DA. Biological Aging and the Human Gut Microbiota. J Gerontol A Biol Sci Med Sci 2017; 72:1474-1482. [PMID: 28444190 DOI: 10.1093/gerona/glx042] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/01/2017] [Indexed: 12/26/2022] Open
Abstract
The human gastrointestinal microbiota plays a key homeostatic role in normal functioning of physiologic processes commonly undermined by aging. We used a previously validated 34-item frailty index (FI34) to identify changes in gut microbiota community structure associated with biological age of community-dwelling adults. Stool 16S rRNA cDNA libraries from 85 subjects ranging in age (43-79) and FI34 score (0-0.365) were deep sequenced, denoised, and clustered using DADA2. Subject biological age but not chronological age correlated with a decrease in stool microbial diversity. Specific microbial genera were differentially abundant in the lower, middle, and upper 33rd percentiles of biological age. Using Sparse Inverse Covariance Estimation for Ecological Association and Statistical Inference (SPIEC-EASI) and Weighted Gene Co-Expression Network Analysis (WGCNA), we identified modules of coabundant microbial genera that distinguished biological from chronological aging. A biological age-associated module composed of Eggerthella, Ruminococcus, and Coprobacillus genera was robust to correction for subject age, sex, body mass index, antibiotic usage, and other confounders. Subject FI34 score positively correlated with the abundance of this module, which exhibited a distinct inferred metagenome as predicted by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). We conclude that increasing biological age in community-dwelling adults is associated with gastrointestinal dysbiosis.
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Affiliation(s)
- Vincent J Maffei
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center - New Orleans
| | - Sangkyu Kim
- Tulane Center for Aging, Tulane University Health Sciences Center, New Orleans, Louisiana
| | - Eugene Blanchard
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center - New Orleans
| | - Meng Luo
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center - New Orleans
| | - S Michal Jazwinski
- Tulane Center for Aging, Tulane University Health Sciences Center, New Orleans, Louisiana
| | - Christopher M Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center - New Orleans
| | - David A Welsh
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center - New Orleans.,Department of Internal Medicine, Louisiana State University Health Sciences Center - New Orleans
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26
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Edwards AN, Tamayo R, McBride SM. A novel regulator controls Clostridium difficile sporulation, motility and toxin production. Mol Microbiol 2016; 100:954-71. [PMID: 26915493 DOI: 10.1111/mmi.13361] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2016] [Indexed: 01/09/2023]
Abstract
Clostridium difficile is an anaerobic pathogen that forms spores which promote survival in the environment and transmission to new hosts. The regulatory pathways by which C. difficile initiates spore formation are poorly understood. We identified two factors with limited similarity to the Rap sporulation proteins of other spore-forming bacteria. In this study, we show that disruption of the gene CD3668 reduces sporulation and increases toxin production and motility. This mutant was more virulent and exhibited increased toxin gene expression in the hamster model of infection. Based on these phenotypes, we have renamed this locus rstA, for regulator of sporulation and toxins. Our data demonstrate that RstA is a bifunctional protein that upregulates sporulation through an unidentified pathway and represses motility and toxin production by influencing sigD transcription. Conserved RstA orthologs are present in other pathogenic and industrial Clostridium species and may represent a key regulatory protein controlling clostridial sporulation.
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Affiliation(s)
- Adrianne N Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shonna M McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
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27
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Schultz D. Coordination of cell decisions and promotion of phenotypic diversity in B. subtilis via pulsed behavior of the phosphorelay. Bioessays 2016; 38:440-5. [PMID: 26941227 DOI: 10.1002/bies.201500199] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The phosphorelay of Bacillus subtilis, a kinase cascade that activates master regulator Spo0A ~ P in response to starvation signals, is the core of a large network controlling the cell's decision to differentiate into sporulation and other phenotypes. This article reviews recent advances in understanding the origins and purposes of the complex dynamical behavior of the phosphorelay, which pulses with peaks of activity coordinated with the cell cycle. The transient imbalance in the expression of two critical genes caused by their strategic placement at opposing ends of the chromosome proved to be the key for this pulsed behavior. Feedback control loops in the phosphorelay use these pulses to implement a timer mechanism, which creates several windows of opportunity for phenotypic transitions over multiple generations. This strategy allows the cell to coordinate multiple differentiation programs in a decision process that fosters phenotypic diversity and adapts to current conditions.
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Affiliation(s)
- Daniel Schultz
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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28
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Shen A. A Gut Odyssey: The Impact of the Microbiota on Clostridium difficile Spore Formation and Germination. PLoS Pathog 2015; 11:e1005157. [PMID: 26468647 PMCID: PMC4607366 DOI: 10.1371/journal.ppat.1005157] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Aimee Shen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
- * E-mail:
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29
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Luche S, Eymard-Vernain E, Diemer H, Van Dorsselaer A, Rabilloud T, Lelong C. Zinc oxide induces the stringent response and major reorientations in the central metabolism of Bacillus subtilis. J Proteomics 2015. [PMID: 26211718 DOI: 10.1016/j.jprot.2015.07.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Microorganisms, such as bacteria, are one of the first targets of nanoparticles in the environment. In this study, we tested the effect of two nanoparticles, ZnO and TiO2, with the salt ZnSO4 as the control, on the Gram-positive bacterium Bacillus subtilis by 2D gel electrophoresis-based proteomics. Despite a significant effect on viability (LD50), TiO2 NPs had no detectable effect on the proteomic pattern, while ZnO NPs and ZnSO4 significantly modified B. subtilis metabolism. These results allowed us to conclude that the effects of ZnO observed in this work were mainly attributable to Zn dissolution in the culture media. Proteomic analysis highlighted twelve modulated proteins related to central metabolism: MetE and MccB (cysteine metabolism), OdhA, AspB, IolD, AnsB, PdhB and YtsJ (Krebs cycle) and XylA, YqjI, Drm and Tal (pentose phosphate pathway). Biochemical assays, such as free sulfhydryl, CoA-SH and malate dehydrogenase assays corroborated the observed central metabolism reorientation and showed that Zn stress induced oxidative stress, probably as a consequence of thiol chelation stress by Zn ions. The other patterns affected by ZnO and ZnSO4 were the stringent response and the general stress response. Nine proteins involved in or controlled by the stringent response showed a modified expression profile in the presence of ZnO NPs or ZnSO4: YwaC, SigH, YtxH, YtzB, TufA, RplJ, RpsB, PdhB and Mbl. An increase in the ppGpp concentration confirmed the involvement of the stringent response during a Zn stress. All these metabolic reorientations in response to Zn stress were probably the result of complex regulatory mechanisms including at least the stringent response via YwaC.
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Affiliation(s)
- Sylvie Luche
- Pro-MD team, Université Joseph Fourier, CEA Grenoble, iRTSV, Laboratoire de Chimie et Biologie des Métaux, UMR CNRS-CEA-UJF, Grenoble, France
| | - Elise Eymard-Vernain
- Pro-MD team, Université Joseph Fourier, CEA Grenoble, iRTSV, Laboratoire de Chimie et Biologie des Métaux, UMR CNRS-CEA-UJF, Grenoble, France
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, Université de Strasbourg, 25 rue Becquerel, 67087 Strasbourg, France; CNRS, UMR7178, 67087 Strasbourg, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, Université de Strasbourg, 25 rue Becquerel, 67087 Strasbourg, France; CNRS, UMR7178, 67087 Strasbourg, France
| | - Thierry Rabilloud
- Pro-MD team, UMR CNRS 5249, Laboratoire de Chimie et Biologie des Métaux, UMR CNRS-CEA-UJF, Grenoble, France
| | - Cécile Lelong
- Pro-MD team, Université Joseph Fourier, CEA Grenoble, iRTSV, Laboratoire de Chimie et Biologie des Métaux, UMR CNRS-CEA-UJF, Grenoble, France.
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30
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Abstract
The problem of not only how but also why cells divide can be tackled using recent ideas. One idea from the origins of life – Life as independent of its constituents – is that a living entity like a cell is a particular pattern of connectivity between its constituents. This means that if the growing cell were just to get bigger the average connectivity between its constituents per unit mass – its cellular connectivity – would decrease and the cell would lose its identity. The solution is division which restores connectivity. The corollary is that the cell senses decreasing cellular connectivity and uses this information to trigger division. A second idea from phenotypic diversity – Life on the Scales of Equilibria – is that a bacterium must find strategies that allow it to both survive and grow. This means that it has learnt to reconcile the opposing constraints that these strategies impose. The solution is that the cell cycle generates daughter cells with different phenotypes based on sufficiently complex equilibrium (E) and non-equilibrium (NE) cellular compounds and structures appropriate for survival and growth, respectively, alias ‘hyperstructures.’ The corollary is that the cell senses both the quantity of E material and the intensity of use of NE material and then uses this information to trigger the cell cycle. A third idea from artificial intelligence – Competitive Coherence – is that a cell selects the active subset of elements that actively determine its phenotype from a much larger set of available elements. This means that the selection of an active subset of a specific size and composition must be done so as to generate both a coherent cell state, in which the cell’s contents work together harmoniously, and a coherent sequence of cell states, each coherent with respect to itself and to an unpredictable environment. The solution is the use of a range of mechanisms ranging from hyperstructure dynamics to the cell cycle itself.
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Affiliation(s)
- Vic Norris
- Laboratory of Microbiology Signals and Microenvironment, Theoretical Biology Unit, University of Rouen, Mont Saint Aignan France
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The RapP-PhrP quorum-sensing system of Bacillus subtilis strain NCIB3610 affects biofilm formation through multiple targets, due to an atypical signal-insensitive allele of RapP. J Bacteriol 2014; 197:592-602. [PMID: 25422306 DOI: 10.1128/jb.02382-14] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The genome of Bacillus subtilis 168 encodes eight rap-phr quorum-sensing pairs. Rap proteins of all characterized Rap-Phr pairs inhibit the function of one or several important response regulators: ComA, Spo0F, or DegU. This inhibition is relieved upon binding of the peptide encoded by the cognate phr gene. Bacillus subtilis strain NCIB3610, the biofilm-proficient ancestor of strain 168, encodes, in addition, the rapP-phrP pair on the plasmid pBS32. RapP was shown to dephosphorylate Spo0F and to regulate biofilm formation, but unlike other Rap-Phr pairs, RapP does not interact with PhrP. In this work we extend the analysis of the RapP pathway by reexamining its transcriptional regulation, its effect on downstream targets, and its interaction with PhrP. At the transcriptional level, we show that rapP and phrP regulation is similar to that of other rap-phr pairs. We further find that RapP has an Spo0F-independent negative effect on biofilm-related genes, which is mediated by the response regulator ComA. Finally, we find that the insensitivity of RapP to PhrP is due to a substitution of a highly conserved residue in the peptide binding domain of the rapP allele of strain NCIB3610. Reversing this substitution to the consensus amino acid restores the PhrP dependence of RapP activity and eliminates the effects of the rapP-phrP locus on ComA activity and biofilm formation. Taken together, our results suggest that RapP strongly represses biofilm formation through multiple targets and that PhrP does not counteract RapP due to a rare mutation in rapP.
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