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Oles RE, Terrazas MC, Loomis LR, Neal MJ, Paulchakrabarti M, Zuffa S, Hsu CY, Vasquez Ayala A, Lee MH, Tribelhorn C, Belda-Ferre P, Bryant M, Zemlin J, Young J, Dulai P, Sandborn WJ, Sivagnanam M, Raffatellu M, Pride D, Dorrestein PC, Zengler K, Choudhury B, Knight R, Chu H. Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599758. [PMID: 38948766 PMCID: PMC11213024 DOI: 10.1101/2024.06.19.599758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Bacteroides fragilis is a prominent member of the human gut microbiota, playing crucial roles in maintaining gut homeostasis and host health. Although it primarily functions as a beneficial commensal, B. fragilis can become pathogenic. To determine the genetic basis of its duality, we conducted a comparative genomic analysis of 813 B. fragilis strains, representing both commensal and pathogenic origins. Our findings reveal that pathogenic strains emerge across diverse phylogenetic lineages, due in part to rapid gene exchange and the adaptability of the accessory genome. We identified 16 phylogenetic groups, differentiated by genes associated with capsule composition, interspecies competition, and host interactions. A microbial genome-wide association study identified 44 genes linked to extra-intestinal survival and pathogenicity. These findings reveal how genomic diversity within commensal species can lead to the emergence of pathogenic traits, broadening our understanding of microbial evolution in the gut.
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Affiliation(s)
- Renee E. Oles
- Department of Pathology, University of California, San Diego, La Jolla, CA
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | | | - Luke R. Loomis
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | - Maxwell J. Neal
- Department of Bioengineering, University of California, San Diego, La Jolla, CA
| | | | - Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA
| | - Chia-Yun Hsu
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | | | - Michael H. Lee
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Caitlin Tribelhorn
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Pedro Belda-Ferre
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - MacKenzie Bryant
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA
| | - Jocelyn Young
- Division of Gastroenterology, Hepatology and Nutrition, University of California, San Diego and Rady Children’s Hospital, San Diego, CA
| | - Parambir Dulai
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA
- Division of Gastroenterology, Northwestern University, Chicago, Illinois
| | - William J. Sandborn
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
| | - Mamata Sivagnanam
- Division of Gastroenterology, Hepatology and Nutrition, University of California, San Diego and Rady Children’s Hospital, San Diego, CA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, La Jolla, CA
| | - David Pride
- Department of Pathology, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Center for Innovative Phage Applications and Therapeutics (IPATH), University of California, San Diego, La Jolla, CA
- Center of Advanced Laboratory Medicine (CALM), University of California, San Diego, La Jolla, CA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA
| | - Karsten Zengler
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Program in Materials Science and Engineering, University of California, San Diego, La Jolla, CA
| | - Biswa Choudhury
- GlycoAnalytics Core, University of California San Diego, San Diego, CA
| | - Rob Knight
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA
- Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, La Jolla, CA
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Comparative Genomics of Bacteroides fragilis Group Isolates Reveals Species-Dependent Resistance Mechanisms and Validates Clinical Tools for Resistance Prediction. mBio 2022; 13:e0360321. [PMID: 35038926 PMCID: PMC8764542 DOI: 10.1128/mbio.03603-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Bacteroides fragilis group (BFG) are the most frequently recovered anaerobic bacteria from human infections, and resistance to frontline antibiotics is emerging. In the absence of routine antimicrobial susceptibility testing (AST) for BFG in most clinical settings, we assessed the utility of clinical and modern genomics tools to determine BFG species-level identification and resistance patterns. A total of 174 BFG clinical isolates supplemented with 20 archived carbapenem-resistant B. fragilis sensu stricto (BFSS) isolates underwent antimicrobial susceptibility testing, MALDI-ToF mass-spectrometry, and whole-genome sequencing (WGS). Bruker BioTyper and VITEK-MS MALDI-ToF systems demonstrated accurate species-level identifications (91% and 90% agreement, respectively) compared to average nucleotide identity (ANI) analysis of WGS data. Distinct β-lactamase gene profiles were observed between BFSS and non-fragilis Bacteroides species, with significantly higher MICs to piperacillin-tazobactam in B. vulgatus and B. thetaiotaomicron relative to BFSS (P ≤ 0.034). We also uncovered phylogenetic diversity at the genomospecies level between division I and division II BFSS (ANI <0.95) and demonstrate that division II BFSS strains harbor an increased capacity to achieve carbapenem resistance through chromosomal activation of the CfiA carbapenemase. Finally, we report that CfiA detection by the Bruker BioTyper Subtyping Module accurately detected carbapenem resistance in BFSS with positive and negative percent agreement of 94%/90% and 95%/95% compared to ertapenem and meropenem susceptibility, respectively. These comparative analyses indicate that resistance mechanisms are distinct at both the phenotypic and genomic level across species within the BFG and that modern MALDI-ToF identification systems can be used for accurate species-level identification and resistance prediction of the BFG. IMPORTANCE Anaerobic infections present unique challenges in terms of detecting and identifying the etiologic agent and selecting the optimal antimicrobial therapy. Antimicrobial resistance is increasing in anaerobic pathogens, and it is critical to understand the prevalence and mechanisms of resistance to commonly prescribed antimicrobial therapies. This study uses comparative genomics to validate clinical tools for species-level identification and phenotypic resistance prediction in 194 isolates of Bacteroides fragilis group (BFG) bacteria, which represent the most commonly isolated organisms among anaerobic infections. We demonstrate species-specific patterns in antimicrobial resistance and validate new strategies for species-level organism identification and phenotypic resistance prediction in a routine clinical laboratory setting. These findings expand our understanding and management of anaerobic infections and justify further investigations into the molecular basis for species-specific resistance patterns observed within this study.
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Shin DS, Rhee KJ, Eom YB. Effect of Probiotic Clostridium butyricum NCTC 7423 Supernatant on Biofilm Formation and Gene Expression of Bacteroides fragilis. J Microbiol Biotechnol 2020; 30:368-377. [PMID: 32066216 PMCID: PMC9728305 DOI: 10.4014/jmb.2001.01027] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Enterotoxigenic Bacteroides fragilis (ETBF) is the main pathogen causing severe inflammatory diseases and colorectal cancer. Its biofilm plays a key role in the development of colorectal cancer. The objective of this study was to determine the antagonistic effects of cell-free supernatants (CFS) derived from Clostridium butyricum against the growth and biofilm of ETBF. Our data showed that C. butyricum CFS inhibited the growth of B. fragilis in planktonic culture. In addition, C. butyricum CFS exhibited an antibiofilm effect by inhibiting biofilm development, disassembling preformed biofilms and reducing the metabolic activity of cells in biofilms. Using confocal laser scanning microscopy, we found that C. butyricum CFS significantly suppressed the proteins and extracellular nucleic acids among the basic biofilm components. Furthermore, C. butyricum CFS significantly downregulated the expression of virulence- and efflux pump-related genes including ompA and bmeB3 in B. fragilis. Our findings suggest that C. butyricum can be used as biotherapeutic agent by inhibiting the growth and biofilm of ETBF.
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Affiliation(s)
- Da-Seul Shin
- Department of Medical Sciences, College of Medical Sciences, Soonchunhyang University, Asan 3538, Republic of Korea
| | - Ki-Jong Rhee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University at Wonju, Wonju 6493, Republic of Korea
| | - Yong-Bin Eom
- Department of Medical Sciences, College of Medical Sciences, Soonchunhyang University, Asan 3538, Republic of Korea,Department of Biomedical Laboratory Science, College of Medical Sciences, Soonchunhyang University, Asan 158, Republic of Korea,Corresponding author Phone: +82-41-530-3039 Fax: +82-41-530-3085 E-mail:
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Antibiofilm and antibacterial activities of repurposing auranofin against Bacteroides fragilis. Arch Microbiol 2019; 202:473-482. [PMID: 31705142 DOI: 10.1007/s00203-019-01764-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/03/2019] [Accepted: 10/31/2019] [Indexed: 01/10/2023]
Abstract
The aim of this study is to evaluate the antibiofilm and antibacterial effects of auranofin against WT-ETBF, rETBF, WT-NTBF and clinically isolated Bacteroides fragilis strains. The minimum inhibitory concentration and biofilm inhibitory concentration of 0.25 μg/ml for auranofin against B. fragilis were determined, and the biofilm eradication concentration was 1 μg/ml. At an auranofin concentration of 0.5 μg/ml, little cellular metabolic activity was found. Confocal laser scanning microcopy results confirmed the inhibition of biofilm by auranofin. The effects of auranofin on the outer membrane protein (ompA) gene and the RND-type efflux pump (bmeB3) gene were investigated using quantitative real-time polymerase chain reaction (qRT-PCR). The qRT-PCR results showed that treatment with auranofin significantly reduced the gene expression compared to controls without auranofin. These data indicate the applicability of auranofin as a repurposed drug due to its inhibitory effect against biofilm formation of B. fragilis. Therefore, our study demonstrates that auranofin, already approved for human use, is a promising drug that has strong antibiofilm and antibacterial activity against B. fragilis.
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Lindholm M, Min Aung K, Nyunt Wai S, Oscarsson J. Role of OmpA1 and OmpA2 in Aggregatibacter actinomycetemcomitans and Aggregatibacter aphrophilus serum resistance. J Oral Microbiol 2018; 11:1536192. [PMID: 30598730 PMCID: PMC6225413 DOI: 10.1080/20002297.2018.1536192] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/03/2018] [Accepted: 10/10/2018] [Indexed: 12/27/2022] Open
Abstract
Aggregatibacter actinomycetemcomitans and Aggregatibacter aphrophilus belong to the HACEK group of fastidious Gram-negative organisms, a recognized cause of infective endocarditis. A. actinomycetemcomitans is also implicated in aggressive forms of periodontitis. We demonstrated that A. aphrophilus strains, as A. actinomycetemcomitans are ubiquitously serum resistant. Both species encode two Outer membrane protein A paralogues, here denoted OmpA1 and OmpA2. As their respective pangenomes contain several OmpA1 and OmpA2 alleles, they represent potential genotypic markers. A naturally competent strain of A. actinomycetemcomitans and A. aphrophilus, respectively were used to elucidate if OmpA1 and OmpA2 contribute to serum resistance. Whereas OmpA1 was critical for survival of A. actinomycetemcomitans D7SS in 50% normal human serum (NHS), serum resistant ompA1 mutants were fortuitously obtained, expressing enhanced levels of OmpA2. Similarly, OmpA1 rather than OmpA2 was a major contributor to serum resistance of A. aphrophilus HK83. Far-Western blot revealed that OmpA1AA, OmpA2AA, and OmpA1AP can bind to C4-binding protein, an inhibitor of classical and mannose-binding lectin (MBL) complement activation. Indeed, ompA1 mutants were susceptible to these pathways, but also to alternative complement activation. This may at least partly reflect a compromised outer membrane integrity but is also consistent with alternative mechanisms involved in OmpA-mediated serum resistance.
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Affiliation(s)
- Mark Lindholm
- Oral Microbiology, Department of Odontology, Umeå University, Umeå, Sweden
| | - Kyaw Min Aung
- Department of Molecular Biology and the Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Sun Nyunt Wai
- Department of Molecular Biology and the Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Jan Oscarsson
- Oral Microbiology, Department of Odontology, Umeå University, Umeå, Sweden
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Yaung SJ, Deng L, Li N, Braff JL, Church GM, Bry L, Wang HH, Gerber GK. Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics. Mol Syst Biol 2016; 11:788. [PMID: 26148351 PMCID: PMC4380924 DOI: 10.15252/msb.20145866] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Elucidating functions of commensal microbial genes in the mammalian gut is challenging because many commensals are recalcitrant to laboratory cultivation and genetic manipulation. We present Temporal FUnctional Metagenomics sequencing (TFUMseq), a platform to functionally mine bacterial genomes for genes that contribute to fitness of commensal bacteria in vivo. Our approach uses metagenomic DNA to construct large‐scale heterologous expression libraries that are tracked over time in vivo by deep sequencing and computational methods. To demonstrate our approach, we built a TFUMseq plasmid library using the gut commensal Bacteroides thetaiotaomicron (Bt) and introduced Escherichia coli carrying this library into germfree mice. Population dynamics of library clones revealed Bt genes conferring significant fitness advantages in E. coli over time, including carbohydrate utilization genes, with a Bt galactokinase central to early colonization, and subsequent dominance by a Bt glycoside hydrolase enabling sucrose metabolism coupled with co‐evolution of the plasmid library and E. coli genome driving increased galactose utilization. Our findings highlight the utility of functional metagenomics for engineering commensal bacteria with improved properties, including expanded colonization capabilities in vivo.
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Rashid GMM, Taylor CR, Liu Y, Zhang X, Rea D, Fülöp V, Bugg TDH. Identification of Manganese Superoxide Dismutase from Sphingobacterium sp. T2 as a Novel Bacterial Enzyme for Lignin Oxidation. ACS Chem Biol 2015. [PMID: 26198187 DOI: 10.1021/acschembio.5b00298] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The valorization of aromatic heteropolymer lignin is an important unsolved problem in the development of a biomass-based biorefinery, for which novel high-activity biocatalysts are needed. Sequencing of the genomic DNA of lignin-degrading bacterial strain Sphingobacterium sp. T2 revealed no matches to known lignin-degrading genes. Proteomic matches for two manganese superoxide dismutase proteins were found in partially purified extracellular fractions. Recombinant MnSOD1 and MnSOD2 were both found to show high activity for oxidation of Organosolv and Kraft lignin, and lignin model compounds, generating multiple oxidation products. Structure determination revealed that the products result from aryl-Cα and Cα-Cβ bond oxidative cleavage and O-demethylation. The crystal structure of MnSOD1 was determined to 1.35 Å resolution, revealing a typical MnSOD homodimer harboring a five-coordinate trigonal bipyramidal Mn(II) center ligated by three His, one Asp, and a water/hydroxide in each active site. We propose that the lignin oxidation reactivity of these enzymes is due to the production of a hydroxyl radical, a highly reactive oxidant. This is the first demonstration that MnSOD is a microbial lignin-oxidizing enzyme.
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Affiliation(s)
- Goran M. M. Rashid
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Charles R. Taylor
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Yangqingxue Liu
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Xiaoyang Zhang
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Dean Rea
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Vilmos Fülöp
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Timothy D. H. Bugg
- Department of Chemistry and ‡School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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Rios-Covian D, Sánchez B, Salazar N, Martínez N, Redruello B, Gueimonde M, de Los Reyes-Gavilán CG. Different metabolic features of Bacteroides fragilis growing in the presence of glucose and exopolysaccharides of bifidobacteria. Front Microbiol 2015; 6:825. [PMID: 26347720 PMCID: PMC4539542 DOI: 10.3389/fmicb.2015.00825] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/27/2015] [Indexed: 11/20/2022] Open
Abstract
Bacteroides is among the most abundant microorganism inhabiting the human intestine. They are saccharolytic bacteria able to use dietary or host-derived glycans as energy sources. Some Bacteroides fragilis strains contribute to the maturation of the immune system but it is also an opportunistic pathogen. The intestine is the habitat of most Bifidobacterium species, some of whose strains are considered probiotics. Bifidobacteria can synthesize exopolysaccharides (EPSs), which are complex carbohydrates that may be available in the intestinal environment. We studied the metabolism of B. fragilis when an EPS preparation from bifidobacteria was added to the growth medium compared to its behavior with added glucose. 2D-DIGE coupled with the identification by MALDI-TOF/TOF evidenced proteins that were differentially produced when EPS was added. The results were supported by RT-qPCR gene expression analysis. The intracellular and extracellular pattern of certain amino acids, the redox balance and the α-glucosidase activity were differently affected in EPS with respect to glucose. These results allowed us to hypothesize that three general main events, namely the activation of amino acids catabolism, enhancement of the transketolase reaction from the pentose-phosphate cycle, and activation of the succinate-propionate pathway, promote a shift of bacterial metabolism rendering more reducing power and optimizing the energetic yield in the form of ATP when Bacteroides grow with added EPSs. Our results expand the knowledge about the capacity of B. fragilis for adapting to complex carbohydrates and amino acids present in the intestinal environment.
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Affiliation(s)
- David Rios-Covian
- Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas, Villaviciosa Asturias, Spain
| | - Borja Sánchez
- Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas, Villaviciosa Asturias, Spain
| | - Nuria Salazar
- Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas, Villaviciosa Asturias, Spain
| | - Noelia Martínez
- Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas, Villaviciosa Asturias, Spain
| | - Begoña Redruello
- Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas, Villaviciosa Asturias, Spain
| | - Miguel Gueimonde
- Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas, Villaviciosa Asturias, Spain
| | - Clara G de Los Reyes-Gavilán
- Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas, Villaviciosa Asturias, Spain
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Wilson MM, Anderson DE, Bernstein HD. Analysis of the outer membrane proteome and secretome of Bacteroides fragilis reveals a multiplicity of secretion mechanisms. PLoS One 2015; 10:e0117732. [PMID: 25658944 PMCID: PMC4319957 DOI: 10.1371/journal.pone.0117732] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/31/2014] [Indexed: 01/28/2023] Open
Abstract
Bacteroides fragilis is a widely distributed member of the human gut microbiome and an opportunistic pathogen. Cell surface molecules produced by this organism likely play important roles in colonization, communication with other microbes, and pathogenicity, but the protein composition of the outer membrane (OM) and the mechanisms used to transport polypeptides into the extracellular space are poorly characterized. Here we used LC-MS/MS to analyze the OM proteome and secretome of B. fragilis NCTC 9343 grown under laboratory conditions. Of the 229 OM proteins that we identified, 108 are predicted to be lipoproteins, and 61 are predicted to be TonB-dependent transporters. Based on their proximity to genes encoding TonB-dependent transporters, many of the lipoprotein genes likely encode proteins involved in nutrient or small molecule uptake. Interestingly, protease accessibility and biotinylation experiments indicated that an unusually large fraction of the lipoproteins are cell-surface exposed. We also identified three proteins that are members of a novel family of autotransporters, multiple potential type I protein secretion systems, and proteins that appear to be components of a type VI secretion apparatus. The secretome consisted of lipoproteins and other proteins that might be substrates of the putative type I or type VI secretion systems. Our proteomic studies show that B. fragilis differs considerably from well-studied Gram-negative bacteria such as Escherichia coli in both the spectrum of OM proteins that it produces and the range of secretion strategies that it utilizes.
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Affiliation(s)
- Marlena M. Wilson
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - D. Eric Anderson
- Advanced Mass Spectrometry Facility, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Harris D. Bernstein
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States of America
- * E-mail:
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Veeranagouda Y, Husain F, Tenorio EL, Wexler HM. Identification of genes required for the survival of B. fragilis using massive parallel sequencing of a saturated transposon mutant library. BMC Genomics 2014; 15:429. [PMID: 24899126 PMCID: PMC4072883 DOI: 10.1186/1471-2164-15-429] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/27/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacteroides fragilis is a Gram-negative anaerobe that is normally a human gut commensal; it comprises a small percentage of the gut Bacteroides but is the most frequently isolated Bacteroides from human infections. Identification of the essential genes necessary for the survival of B. fragilis provides novel information which can be exploited for the treatment of bacterial infections. RESULTS Massive parallel sequencing of saturated transposon mutant libraries (two mutant pools of approximately 50,000 mutants each) was used to determine the essential genes for the growth of B. fragilis 638R on nutrient rich medium. Among the 4326 protein coding genes, 550 genes (12.7%) were found to be essential for the survival of B. fragilis 638R. Of the 550 essential genes, only 367 genes were assigned to a Cluster of Orthologous Genes, and about 290 genes had Kyoto Encyclopedia of Genes and Genomes orthologous members. Interestingly, genes with hypothetical functions accounted for 41.3% of essential genes (227 genes), indicating that the functions of a significant percentage of the genes used by B. fragilis 638R are still unknown. Global transcriptome analysis using RNA-Seq indicated that most of the essential genes (92%) are, in fact, transcribed in B. fragilis 638R including most of those coding for hypothetical proteins. Three hundred fifty of the 550 essential genes of B. fragilis 638R are present in Database of Essential Genes. 10.02 and 31% of those are genes included as essential genes for nine species (including Gram-positive pathogenic bacteria). CONCLUSIONS The essential gene data described in this investigation provides a valuable resource to study gene function and pathways involved in B. fragilis survival. Thorough examination of the B. fragilis-specific essential genes and genes that are shared between divergent organisms opens new research avenues that will lead to enhanced understanding of survival strategies used by bacteria in different microniches and under different stress situations.
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Culligan EP, Sleator RD, Marchesi JR, Hill C. Functional environmental screening of a metagenomic library identifies stlA; a unique salt tolerance locus from the human gut microbiome. PLoS One 2013; 8:e82985. [PMID: 24349412 PMCID: PMC3861447 DOI: 10.1371/journal.pone.0082985] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/29/2013] [Indexed: 12/27/2022] Open
Abstract
Functional environmental screening of metagenomic libraries is a powerful means to identify and assign function to novel genes and their encoded proteins without any prior sequence knowledge. In the current study we describe the identification and subsequent analysis of a salt-tolerant clone from a human gut metagenomic library. Following transposon mutagenesis we identified an unknown gene (stlA, for “salt tolerance locus A”) with no current known homologues in the databases. Subsequent cloning and expression in Escherichia coli MKH13 revealed that stlA confers a salt tolerance phenotype in its surrogate host. Furthermore, a detailed in silico analysis was also conducted to gain additional information on the properties of the encoded StlA protein. The stlA gene is rare when searched against human metagenome datasets such as MetaHit and the Human Microbiome Project and represents a novel and unique salt tolerance determinant which appears to be found exclusively in the human gut environment.
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Affiliation(s)
- Eamonn P. Culligan
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Roy D. Sleator
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
- * E-mail: (RS); (JM); (CH)
| | - Julian R. Marchesi
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
- Department of Hepatology and Gastroenterology, Imperial College London, London, United Kingdom
- * E-mail: (RS); (JM); (CH)
| | - Colin Hill
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- * E-mail: (RS); (JM); (CH)
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Wu Z, Kan FWK, She YM, Walker VK. Biofilm, ice recrystallization inhibition and freeze-thaw protection in an epiphyte community. APPL BIOCHEM MICRO+ 2012. [DOI: 10.1134/s0003683812040138] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Abe T, Murakami Y, Nagano K, Hasegawa Y, Moriguchi K, Ohno N, Shimozato K, Yoshimura F. OmpA-like protein influences cell shape and adhesive activity of Tannerella forsythia. Mol Oral Microbiol 2011; 26:374-87. [PMID: 22053965 DOI: 10.1111/j.2041-1014.2011.00625.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Tannerella forsythia, a gram-negative fusiform rod, is implicated in several types of oral anaerobic infections. Most gram-negative bacteria have OmpA-like proteins that are homologous to the OmpA protein in Escherichia coli. We identified an OmpA-like protein in T. forsythia encoded by the tf1331 gene as one of the major proteins by mass spectrometric analysis. Two-dimensional, diagonal electrophoresis showed that the OmpA-like protein formed a dimeric or trimeric structure via intermolecular disulfide bonds. A biotin labeling experiment revealed that a portion of the protein was exposed on the cell surface, even though T. forsythia possesses an S-layer at the outermost cell surface. Using a tf1331-deletion mutant, we showed that the OmpA-like protein affected cell morphology. The length of the mutant cell was reduced almost by half. Cell swelling was observed in more than 40% of the mutant cells. Moreover, the mutant exhibited decreased adhesion to fibronectin, retarded autoaggregation, and reduced cell surface hydrophobicity. These results suggest that the OmpA-like protein in T. forsythia plays an important role in cellular integrity and adhesive function.
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Affiliation(s)
- T Abe
- Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
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