Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota

ABSTRACT Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease. Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, M. schaedleri reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species in vivo, which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, M. schaedleri harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The M. schaedleri genome has been shaped by extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria, indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem. IMPORTANCE Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease.

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Modulating Pathogenesis with Mobile-CRISPRi

Journal of Bacteriology ◽

10.1128/jb.00304-19 ◽

2019 ◽

Vol 201 (22) ◽

Cited By ~ 7

Author(s):

Jiuxin Qu ◽

Neha K. Prasad ◽

Michelle A. Yu ◽

Shuyan Chen ◽

Amy Lyden ◽

...

Keyword(s):

Gene Expression ◽

Pathogenic Bacteria ◽

Bacterial Species ◽

Effector Proteins ◽

Infection Model ◽

Secretion Systems ◽

Bacterial Genomes ◽

Gene Encoding ◽

Content Type ◽

Animal Infection

ABSTRACT Conditionally essential (CE) genes are required by pathogenic bacteria to establish and maintain infections. CE genes encode virulence factors, such as secretion systems and effector proteins, as well as biosynthetic enzymes that produce metabolites not found in the host environment. Due to their outsized importance in pathogenesis, CE gene products are attractive targets for the next generation of antimicrobials. However, the precise manipulation of CE gene expression in the context of infection is technically challenging, limiting our ability to understand the roles of CE genes in pathogenesis and accordingly design effective inhibitors. We previously developed a suite of CRISPR interference-based gene knockdown tools that are transferred by conjugation and stably integrate into bacterial genomes that we call Mobile-CRISPRi. Here, we show the efficacy of Mobile-CRISPRi in controlling CE gene expression in an animal infection model. We optimize Mobile-CRISPRi in Pseudomonas aeruginosa for use in a murine model of pneumonia by tuning the expression of CRISPRi components to avoid nonspecific toxicity. As a proof of principle, we demonstrate that knock down of a CE gene encoding the type III secretion system (T3SS) activator ExsA blocks effector protein secretion in culture and attenuates virulence in mice. We anticipate that Mobile-CRISPRi will be a valuable tool to probe the function of CE genes across many bacterial species and pathogenesis models. IMPORTANCE Antibiotic resistance is a growing threat to global health. To optimize the use of our existing antibiotics and identify new targets for future inhibitors, understanding the fundamental drivers of bacterial growth in the context of the host immune response is paramount. Historically, these genetic drivers have been difficult to manipulate precisely, as they are requisite for pathogen survival. Here, we provide the first application of Mobile-CRISPRi to study conditionally essential virulence genes in mouse models of lung infection through partial gene perturbation. We envision the use of Mobile-CRISPRi in future pathogenesis models and antibiotic target discovery efforts.

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A Novel Legionella Genomic Island Encodes a Copper-Responsive Regulatory System and a Single Icm/Dot Effector Protein Transcriptionally Activated by Copper

mBio ◽

10.1128/mbio.03232-19 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Marika Linsky ◽

Yevgeniya Vitkin ◽

Gil Segal

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Legionella Pneumophila ◽

Genomic Island ◽

Regulatory System ◽

Secretion System ◽

Effector Proteins ◽

Host Cells ◽

Effector Protein ◽

Content Type

ABSTRACT The intracellular pathogen Legionella pneumophila utilizes the Icm/Dot type IV secretion system to translocate >300 effector proteins into host cells during infection. The regulation of some of these effector-encoding genes was previously shown to be coordinated by several global regulators, including three two-component systems (TCSs) found in all the Legionella species examined. Here, we describe the first Legionella genomic island encoding a single Icm/Dot effector and a dedicated TCS, which regulates its expression. This genomic island, which we named Lci, undergoes horizontal gene transfer in the Legionella genus, and the TCS encoded from this island (LciRS) is homologous to TCSs that control the expression of various metal resistance systems found in other bacteria. We found that the L. pneumophila sensor histidine kinase LciS is specifically activated by copper via a unique, small periplasmic sensing domain. Upon activation by LciS, the response regulator LciR directly binds to a conserved regulatory element and activates the expression of the adjacently located lciE effector-encoding gene. Thus, LciR represents the first local regulator of effectors identified in L. pneumophila. Moreover, we found that the expression of the lciRS operon is repressed by the Fis1 and Fis3 regulators, leading to Fis-mediated effects on copper induction of LciE and silencing of the expression of this genomic island in the absence of copper. This island represents a novel type of effector regulation in Legionella, shedding new light on the ways by which the Legionella pathogenesis system evolves its effector repertoire and expands its activating signals. IMPORTANCE Legionella pneumophila is an intracellular human pathogen that utilizes amoebae as its environmental host. The adaptation of L. pneumophila to the intracellular environment requires coordination of expression of its multicomponent pathogenesis system, which is composed of a secretion system and effector proteins. However, the regulatory factors controlling the expression of this pathogenesis system are only partially uncovered. Here, we discovered a novel regulatory system that is activated by copper and controls the expression of a single effector protein. The genes encoding both the regulatory system and the effector protein are located on a genomic island that undergoes horizontal gene transfer within the Legionella genus. This regulator-effector genomic island represents the first reported case of local regulation of effectors in Legionella. The discovery of this regulatory mechanism is an important step forward in the understanding of how the regulatory network of effectors functions and evolves in the Legionella genus.

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Prophage-Dependent Neighbor Predation Fosters Horizontal Gene Transfer by Natural Transformation

mSphere ◽

10.1128/msphere.00975-20 ◽

2020 ◽

Vol 5 (6) ◽

Author(s):

Roberto C. Molina-Quiroz ◽

Triana N. Dalia ◽

Andrew Camilli ◽

Ankur B. Dalia ◽

Cecilia A. Silva-Valenzuela

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Vibrio Cholerae ◽

Natural Transformation ◽

Bacterial Species ◽

Natural Setting ◽

Secretion Systems ◽

Evolutionary Mechanisms ◽

Content Type ◽

Fitness Advantage

ABSTRACT Natural transformation is a broadly conserved mechanism of horizontal gene transfer (HGT) in bacteria that can shape their evolution through the acquisition of genes that promote virulence, antibiotic resistance, and other traits. Recent work has established that neighbor predation via type VI secretion systems, bacteriocins, and virulent phages plays an important role in promoting HGT. Here, we demonstrate that in chitin estuary microcosms, Vibrio cholerae K139 lysogens exhibit prophage-dependent neighbor predation of nonlysogens to enhance HGT. Through predation of nonlysogens, K139 lysogens also have a fitness advantage under these microcosm conditions. The ecological strategy revealed by our work provides a better understanding of the evolutionary mechanisms used by bacteria to adapt in their natural setting and contributes to our understanding of the selective pressures that may drive prophage maintenance in bacterial genomes. IMPORTANCE Prophages are nearly ubiquitous in bacterial species. These integrated phage elements have previously been implicated in horizontal gene transfer (HGT) largely through their ability to carry out transduction (generalized or specialized). Here, we show that prophage-encoded viral particles promote neighbor predation leading to enhanced HGT by natural transformation in the waterborne pathogen Vibrio cholerae. Our findings contribute to a comprehensive understanding of the dynamic forces involved in prophage maintenance which ultimately drive the evolution of naturally competent bacteria in their natural environment.

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Complete Sequences of Two Plasmids Found in a Brazilian Bacillus thuringiensis Serovar israelensis Strain

Microbiology Resource Announcements ◽

10.1128/mra.00051-19 ◽

2019 ◽

Vol 8 (9) ◽

Author(s):

Fabrício S. Campos ◽

Fernando B. Cerqueira ◽

Gil R. Santos ◽

Eliseu J. G. Pereira ◽

Roberto F. T. Corrêia ◽

...

Keyword(s):

Bacillus Thuringiensis ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Crucial Role ◽

Bacterial Genomes ◽

Content Type ◽

Complete Sequences

Plasmids play a crucial role in the evolution of bacterial genomes by mediating horizontal gene transfer. In this work, we sequenced two plasmids found in a Brazilian Bacillus thuringiensis serovar israelensis strain which showed 100% nucleotide identities with Bacillus thuringiensis serovar kurstaki plasmids.

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Type IV secretion systems: tools of bacterial horizontal gene transfer and virulence

Cellular Microbiology ◽

10.1111/j.1462-5822.2008.01187.x ◽

2008 ◽

Vol 10 (12) ◽

pp. 2377-2386 ◽

Cited By ~ 157

Author(s):

Mario Juhas ◽

Derrick W. Crook ◽

Derek W. Hood

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Type Iv Secretion ◽

Secretion Systems ◽

Type Iv ◽

Type Iv Secretion Systems

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An Evolutionary Link between Natural Transformation and CRISPR Adaptive Immunity

mBio ◽

10.1128/mbio.00309-12 ◽

2012 ◽

Vol 3 (5) ◽

Cited By ~ 52

Author(s):

Peter Jorth ◽

Marvin Whiteley

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Bacterial Diversity ◽

Natural Transformation ◽

Bacterial Species ◽

Comparative Genomic ◽

Content Type ◽

Immune Systems ◽

Adaptive Immune ◽

Adaptive Immune Systems

ABSTRACTNatural transformation by competent bacteria is a primary means of horizontal gene transfer; however, evidence that competence drives bacterial diversity and evolution has remained elusive. To test this theory, we used a retrospective comparative genomic approach to analyze the evolutionary history ofAggregatibacter actinomycetemcomitans, a bacterial species with both competent and noncompetent sister strains. Through comparative genomic analyses, we reveal that competence is evolutionarily linked to genomic diversity and speciation. Competence loss occurs frequently during evolution and is followed by the loss of clustered regularly interspaced short palindromic repeats (CRISPRs), bacterial adaptive immune systems that protect against parasitic DNA. Relative to noncompetent strains, competent bacteria have larger genomes containing multiple rearrangements. In contrast, noncompetent bacterial genomes are extremely stable but paradoxically susceptible to infective DNA elements, which contribute to noncompetent strain genetic diversity. Moreover, incomplete noncompetent strain CRISPR immune systems are enriched for self-targeting elements, which suggests that the CRISPRs have been co-opted for bacterial gene regulation, similar to eukaryotic microRNAs derived from the antiviral RNA interference pathway.IMPORTANCEThe human microbiome is rich with thousands of diverse bacterial species. One mechanism driving this diversity is horizontal gene transfer by natural transformation, whereby naturally competent bacteria take up environmental DNA and incorporate new genes into their genomes. Competence is theorized to accelerate evolution; however, attempts to test this theory have proved difficult. Through genetic analyses of the human periodontal pathogenAggregatibacter actinomycetemcomitans, we have discovered an evolutionary connection between competence systems promoting gene acquisition and CRISPRs (clustered regularly interspaced short palindromic repeats), adaptive immune systems that protect bacteria against genetic parasites. We show that competentA. actinomycetemcomitansstrains have numerous redundant CRISPR immune systems, while noncompetent bacteria have lost their CRISPR immune systems because of inactivating mutations. Together, the evolutionary data linking the evolution of competence and CRISPRs reveals unique mechanisms promoting genetic heterogeneity and the rise of new bacterial species, providing insight into complex mechanisms underlying bacterial diversity in the human body.

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Acquisition of Beta-Lactamase by Neisseria meningitidis through Possible Horizontal Gene Transfer

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00831-18 ◽

2018 ◽

Vol 62 (9) ◽

Cited By ~ 7

Author(s):

Eva Hong ◽

Ala-Eddine Deghmane ◽

Muhamed-Kheir Taha

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genome Sequencing ◽

Meningococcal Disease ◽

Bacterial Species ◽

Whole Genome ◽

Beta Lactamase ◽

Content Type ◽

Beta Lactamases ◽

Lactamase Gene

ABSTRACT We report the detection in France of a beta-lactamase-producing invasive meningococcal isolate. Whole-genome sequencing of the isolate revealed a ROB-1-type beta-lactamase gene that is frequently encountered in Haemophilus influenzae, suggesting horizontal transfer between isolates of these bacterial species. Beta-lactamases are exceptional in meningococci, with no reports for more than 2 decades. This report is worrying, as the expansion of such isolates may jeopardize the effective treatment against invasive meningococcal disease.

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A Cotransformation Method To Identify a Restriction-Modification Enzyme That Reduces Conjugation Efficiency inCampylobacter jejuni

Applied and Environmental Microbiology ◽

10.1128/aem.02004-18 ◽

2018 ◽

Vol 84 (23) ◽

Author(s):

Ximin Zeng ◽

Zuowei Wu ◽

Qijing Zhang ◽

Jun Lin

Keyword(s):

Comparative Genomics ◽

Heat Shock ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Campylobacter Jejuni ◽

Selection Marker ◽

Sequencing Analysis ◽

Content Type ◽

Restriction Modification ◽

Modification Enzyme

ABSTRACTConjugation is an important mechanism for horizontal gene transfer inCampylobacter jejuni, the leading cause of human bacterial gastroenteritis in developed countries. However, to date, the factors that significantly influence conjugation efficiency inCampylobacterspp. are still largely unknown. Given that multiple recombinant loci could independently occur within one recipient cell during natural transformation, the genetic materials from a high-frequency conjugation (HFC)C. jejunistrain may be cotransformed with a selection marker into a low-frequency conjugation (LFC) recipient strain, creating new HFC transformants suitable for the identification of conjugation factors using a comparative genomics approach. To test this, an erythromycin resistance selection marker was created in an HFCC. jejunistrain; subsequently, the DNA of this strain was naturally transformed into NCTC 11168, an LFCC. jejunistrain, leading to the isolation of NCTC 11168-derived HFC transformants. Whole-genome sequencing analysis and subsequent site-directed mutagenesis identified Cj1051c, a putative restriction-modification enzyme (akaCjeI) that could drastically reduce the conjugation efficiency of NCTC 11168 (>5,000-fold). Chromosomal complementation of three diverse HFCC. jejunistrains with CjeI also led to a dramatic reduction in conjugation efficiency (∼1,000-fold). The purified recombinant CjeI could effectively digest theEscherichia coli-derived shuttle vector pRY107. The endonuclease activity of CjeI was abolished upon short heat shock treatment at 50°C, which is consistent with our previous observation that heat shock enhanced conjugation efficiency inC. jejuni. Together, in this study, we successfully developed and utilized a unique cotransformation strategy to identify a restriction-modification enzyme that significantly influences conjugation efficiency inC. jejuni.IMPORTANCEConjugation is an important horizontal gene transfer mechanism contributing to the evolution of bacterial pathogenesis and antimicrobial resistance.Campylobacter jejuni, the leading foodborne bacterial organism, displays significant strain diversity due to horizontal gene transfer; however, the molecular components influencing conjugation efficiency inC. jejuniare still largely unknown. In this study, we developed a cotransformation strategy for comparative genomics analysis and successfully identified a restriction-modification enzyme that significantly influences conjugation efficiency inC. jejuni. The new cotransformation strategy developed in this study is also expected to be broadly applied in other naturally competent bacteria for functional comparative genomics research.

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Fortification of tempeh with encapsulated iron improves iron status and gut microbiota composition in iron deficiency anemia condition

Nutrition & Food Science ◽

10.1108/nfs-01-2018-0027 ◽

2018 ◽

Vol 48 (6) ◽

pp. 962-972 ◽

Cited By ~ 1

Author(s):

Rio Jati Kusuma ◽

Aviria Ermamilia

Keyword(s):

Iron Deficiency ◽

Gut Microbiota ◽

Iron Deficiency Anemia ◽

Iron Status ◽

Deficiency Anemia ◽

Microbiota Composition ◽

Iron Fortification ◽

Iron Matrix ◽

Content Type ◽

Gut Microbiota Composition

Purpose Iron deficiency anemia (IDA) is one of the most major micronutrient deficiencies worldwide. Food fortification is one strategy for reducing IDA in the population despite concern regarding the gut pathogenic bacteria overgrowth. The purpose of this study was to evaluate the effect of iron encapsulation in banana peel matrix on iron status and gut microbiota composition in iron deficiency anemia. Design/methodology/approach Anemia was induced in 35 male Sprague Dawley rats of age two weeks by the administration of iron-free diet for two weeks. Rats then randomly divided into control, iron-fortified tempeh (temFe) dose 10 and 20 ppm, iron matrix-fortified tempeh dose 10 and 20 ppm and iron matrix fortified tempeh dose 10 and 20 ppm with probiotic mixture. Blood was drawn at Weeks 2 and 6 for hemoglobin and serum iron analysis. Rats were sacrificed at the end of Week 6, and cecal contents were collected for Lactobacillus, Bifidobacteria and Enterobactericeae analysis. Findings Hemoglobin and serum iron were significantly increased (p < 0.05) in all iron-fortified group with the highest value found in iron matrix dose 20 ppm (10.71 ± 0.15 g/dl and 335.83 ± 2.17 µg/dl, respectively). The cecal Lactobacillus and Bifidobacteria did not differ significantly between groups. Cecal Enterobactericeae was significantly different (p < 0.05) among groups with the lowest level in the temFe-20 (2.65 ± 0.78 log CFU) group. Research limitations/implications The use of commercial inoculum instead of pure Rhizopus oligosporus mold for developing the fortified tempeh may impact the effect of product on cecal gut microbiota composition, as different molds and lactic acid bacteria can grow in tempeh when using commercial inoculum. Social implications In Indonesia, iron fortification is conducted primarily in noodles and flour that limits the impact of iron fortification for reducing IDA in population. Iron fortification in food that was daily consumed by people, that is, tempeh, is potential strategy in reducing IDA in population. Originality/value Tempeh fortification using encapsulated iron improved iron status and gut microbiota composition in iron deficiency anemia.

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