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Tang X, Yang Q, Hu S, Guo K, Li Y, Wu Z. Comparative transcriptome reveals importance of export apparatus subunit (ascR) in type III secretion system and its roles on biological properties, gene expression profiles, virulence and colonization of Aeromonas veronii. Int J Biol Macromol 2024; 274:133270. [PMID: 38906357 DOI: 10.1016/j.ijbiomac.2024.133270] [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: 04/30/2024] [Revised: 06/14/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
Aeromonas veronii, an opportunistic pathogen, is known to cause serious infections across various species. In our previous study, we discovered that A. veronii GL2 exhibited a virulence up to ten times greater than that of FO1. To ascertain the factors contributing to the disparity in virulence between the two strains, we conducted a comparative transcriptome analysis. This analysis reveals a significant upregulation (P < 0.05) of the ascR gene in GL2 compared with FO1. Additionally, six differentially expressed genes (DEGs) were identified within the "Bacterial secretion system" pathway (map03070), with ascR being an essential component of type III secretion system (T3SS). AscR, considered as SctR family export apparatus subunit within the T3SS, has ambiguous roles in the biological properties, gene expression profiles, virulence and colonization of A. veronii. Therefore, we constructed a mutant strain (ΔascR) by homologous recombination. Comparative analysis with the wide-type GL2 reveals no significant differences in terms of colony morphology, growth curve, hemolytic activity and protease activity. However, significant reductions (P < 0.01) were observed in the abilities of biofilm formation and swimming mobility. No remarkable difference was noted in the lengths of flagella. The LD50 value of ΔascR was to be 5.15 times higher than that of GL2. Interestingly, the mRNA expression of ascC, ascD, ascJ and ascI genes in the T3SS, and mshB, mshE, mshK and mshP genes in the MSHA type pili were significantly upregulated (P < 0.05) in ΔascR, potentially due to transcriptional compensation. Further analysis of enzymatic biomarkers revealed that ΔascR might not destruct the recognition of innate immune response in host remarkably, but the colonization levels of A.veronii were significantly suppressed (P < 0.01) in ΔascR group. In conclusion, the ascR gene may be a key determinant in regulating the virulence of A. veronii, and the destruction of the T3SS caused by ascR deficiency results in these notable changes.
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Affiliation(s)
- Xiaoqi Tang
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing 400715, China
| | - Qinglin Yang
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing 400715, China
| | - Shaoyu Hu
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing 400715, China
| | - Kefan Guo
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing 400715, China
| | - Yanhong Li
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing 400715, China
| | - Zhengli Wu
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing 400715, China.
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Domin H, Zimmermann J, Taubenheim J, Fuentes Reyes G, Saueressig L, Prasse D, Höppner M, Schmitz RA, Hentschel U, Kaleta C, Fraune S. Sequential host-bacteria and bacteria-bacteria interactions determine the microbiome establishment of Nematostella vectensis. MICROBIOME 2023; 11:257. [PMID: 37978412 PMCID: PMC10656924 DOI: 10.1186/s40168-023-01701-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 10/17/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND The microbiota of multicellular organisms undergoes considerable changes during host ontogeny but the general mechanisms that control community assembly and succession are poorly understood. Here, we use bacterial recolonization experiments in Nematostella vectensis as a model to understand general mechanisms determining bacterial establishment and succession. We compared the dynamic establishment of the microbiome on the germfree host and on inert silicone tubes. RESULTS Following the dynamic reconstruction of microbial communities on both substrates, we show that the initial colonization events are strongly influenced by the host but not by the silicone tube, while the subsequent bacteria-bacteria interactions are the main driver of bacterial succession. Interestingly, the recolonization pattern on adult hosts resembles the ontogenetic colonization succession. This process occurs independently of the bacterial composition of the inoculum and can be followed at the level of individual bacteria. To identify potential metabolic traits associated with initial colonization success and potential metabolic interactions among bacteria associated with bacterial succession, we reconstructed the metabolic networks of bacterial colonizers based on their genomes. These analyses revealed that bacterial metabolic capabilities reflect the recolonization pattern, and the degradation of chitin might be a selection factor during early recolonization of the animal. Concurrently, transcriptomic analyses revealed that Nematostella possesses two chitin synthase genes, one of which is upregulated during early recolonization. CONCLUSIONS Our results show that early recolonization events are strongly controlled by the host while subsequent colonization depends on metabolic bacteria-bacteria interactions largely independent of host ontogeny. Video Abstract.
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Affiliation(s)
- H Domin
- Institute for Zoology and Organismic Interactions, Heinrich-Heine-University Düsseldorf, Düsseldorf, 40225, Germany
| | - J Zimmermann
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, 24105, Germany
| | - J Taubenheim
- Institute for Zoology and Organismic Interactions, Heinrich-Heine-University Düsseldorf, Düsseldorf, 40225, Germany
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, 24105, Germany
| | - G Fuentes Reyes
- Institute for Zoology and Organismic Interactions, Heinrich-Heine-University Düsseldorf, Düsseldorf, 40225, Germany
| | - L Saueressig
- Institute for Zoology and Organismic Interactions, Heinrich-Heine-University Düsseldorf, Düsseldorf, 40225, Germany
| | - D Prasse
- Institute for General Microbiology, Christian-Albrechts-University Kiel, Kiel, 24105, Germany
| | - M Höppner
- Institute for Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, 24105, Germany
| | - R A Schmitz
- Institute for General Microbiology, Christian-Albrechts-University Kiel, Kiel, 24105, Germany
| | - U Hentschel
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany
- Christian-Albrechts-University Kiel, Kiel, 24105, Germany
| | - C Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, 24105, Germany
| | - S Fraune
- Institute for Zoology and Organismic Interactions, Heinrich-Heine-University Düsseldorf, Düsseldorf, 40225, Germany.
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Goffredi SK, Appy RG, Hildreth R, deRogatis J. Marine vampires: Persistent, internal associations between bacteria and blood-feeding marine annelids and crustaceans. Front Microbiol 2023; 13:1113237. [PMID: 36713196 PMCID: PMC9876621 DOI: 10.3389/fmicb.2022.1113237] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 12/21/2022] [Indexed: 01/13/2023] Open
Abstract
Persistent bacterial presence is believed to play an important role in host adaptation to specific niches that would otherwise be unavailable, including the exclusive consumption of blood by invertebrate parasites. Nearly all blood-feeding animals examined so far host internal bacterial symbionts that aid in some essential aspect of their nutrition. Obligate blood-feeding (OBF) invertebrates exist in the oceans, yet symbiotic associations between them and beneficial bacteria have not yet been explored. This study describes the microbiome of 6 phylogenetically-diverse species of marine obligate blood-feeders, including leeches (both fish and elasmobranch specialists; e.g., Pterobdella, Ostreobdella, and Branchellion), isopods (e.g., Elthusa and Nerocila), and a copepod (e.g., Lernanthropus). Amplicon sequencing analysis revealed the blood-feeding invertebrate microbiomes to be low in diversity, compared to host fish skin surfaces, seawater, and non-blood-feeding relatives, and dominated by only a few bacterial genera, including Vibrio (100% prevalence and comprising 39%-81% of the average total recovered 16S rRNA gene sequences per OBF taxa). Vibrio cells were localized to the digestive lumen in and among the blood meal for all taxa examined via fluorescence microscopy. For Elthusa and Branchellion, Vibrio cells also appeared intracellularly within possible hemocytes, suggesting an interaction with the immune system. Additionally, Vibrio cultivated from four of the obligate blood-feeding marine taxa matched the dominant amplicons recovered, and all but one was able to effectively lyse vertebrate blood cells. Bacteria from 2 additional phyla and 3 families were also regularly recovered, albeit in much lower abundances, including members of the Oceanospirillaceae, Flavobacteriacea, Porticoccaceae, and unidentified members of the gamma-and betaproteobacteria, depending on the invertebrate host. For the leech Pterobdella, the Oceanospirillaceae were also detected in the esophageal diverticula. For two crustacean taxa, Elthusa and Lernanthropus, the microbial communities associated with brooded eggs were very similar to the adults, indicating possible direct transmission. Virtually nothing is known about the influence of internal bacteria on the success of marine blood-feeders, but this evidence suggests their regular presence in marine parasites from several prominent groups.
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Affiliation(s)
- Shana K. Goffredi
- Department of Biology, Occidental College, Los Angeles, CA, United States
| | - Ralph G. Appy
- Cabrillo Marine Aquarium, San Pedro, CA, United States
| | - Rebecca Hildreth
- Department of Biology, Occidental College, Los Angeles, CA, United States
| | - Julia deRogatis
- Department of Biology, Occidental College, Los Angeles, CA, United States
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Ganesan R, Wierz JC, Kaltenpoth M, Flórez LV. How It All Begins: Bacterial Factors Mediating the Colonization of Invertebrate Hosts by Beneficial Symbionts. Microbiol Mol Biol Rev 2022; 86:e0012621. [PMID: 36301103 PMCID: PMC9769632 DOI: 10.1128/mmbr.00126-21] [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: 01/01/2023] Open
Abstract
Beneficial associations with bacteria are widespread across animals, spanning a range of symbiont localizations, transmission routes, and functions. While some of these associations have evolved into obligate relationships with permanent symbiont localization within the host, the majority require colonization of every host generation from the environment or via maternal provisions. Across the broad diversity of host species and tissue types that beneficial bacteria can colonize, there are some highly specialized strategies for establishment yet also some common patterns in the molecular basis of colonization. This review focuses on the mechanisms underlying the early stage of beneficial bacterium-invertebrate associations, from initial contact to the establishment of the symbionts in a specific location of the host's body. We first reflect on general selective pressures that can drive the transition from a free-living to a host-associated lifestyle in bacteria. We then cover bacterial molecular factors for colonization in symbioses from both model and nonmodel invertebrate systems where these have been studied, including terrestrial and aquatic host taxa. Finally, we discuss how interactions between multiple colonizing bacteria and priority effects can influence colonization. Taking the bacterial perspective, we emphasize the importance of developing new experimentally tractable systems to derive general insights into the ecological factors and molecular adaptations underlying the origin and establishment of beneficial symbioses in animals.
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Affiliation(s)
- Ramya Ganesan
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Jürgen C. Wierz
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Martin Kaltenpoth
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Laura V. Flórez
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Plant and Environmental Sciences, Section for Organismal Biology, University of Copenhagen, Copenhagen, Denmark
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Talagrand-Reboul E, Colston SM, Graf J, Lamy B, Jumas-Bilak E. Comparative and Evolutionary Genomics of Isolates Provide Insight into the Pathoadaptation of Aeromonas. Genome Biol Evol 2021; 12:535-552. [PMID: 32196086 PMCID: PMC7250499 DOI: 10.1093/gbe/evaa055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2020] [Indexed: 02/06/2023] Open
Abstract
Aeromonads are ubiquitous aquatic bacteria that cause opportunistic infections in humans, but their pathogenesis remains poorly understood. A pathogenomic approach was undertaken to provide insights into the emergence and evolution of pathogenic traits in aeromonads. The genomes of 64 Aeromonas strains representative of the whole genus were analyzed to study the distribution, phylogeny, and synteny of the flanking sequences of 13 virulence-associated genes. The reconstructed evolutionary histories varied markedly depending on the gene analyzed and ranged from vertical evolution, which followed the core genome evolution (alt and colAh), to complex evolution, involving gene loss by insertion sequence-driven gene disruption, horizontal gene transfer, and paraphyly with some virulence genes associated with a phylogroup (aer, ser, and type 3 secretion system components) or no phylogroup (type 3 secretion system effectors, Ast, ExoA, and RtxA toxins). The general pathogenomic overview of aeromonads showed great complexity with diverse evolution modes and gene organization and uneven distribution of virulence genes in the genus; the results provided insights into aeromonad pathoadaptation or the ability of members of this group to emerge as pathogens. Finally, these findings suggest that aeromonad virulence-associated genes should be examined at the population level and that studies performed on type or model strains at the species level cannot be generalized to the whole species.
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Affiliation(s)
- Emilie Talagrand-Reboul
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, University of Montpellier, France.,Laboratoire de Bactériologie, Hôpitaux universitaires de Strasbourg, France
| | - Sophie M Colston
- US Naval Research Laboratory, National Academy of Sciences, National Research Council, Washington, District of Columbia
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut
| | - Brigitte Lamy
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, University of Montpellier, France.,Département de Bactériologie, CHU de Nice and Université Côte d'Azur, INSERM, C3M, Nice, France
| | - Estelle Jumas-Bilak
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, University of Montpellier, France.,Département d'Hygiène Hospitalière, CHRU de Montpellier, France
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Macrobdella decora: Old World Leech Gut Microbial Community Structure Conserved in a New World Leech. Appl Environ Microbiol 2021; 87:AEM.02082-20. [PMID: 33674439 DOI: 10.1128/aem.02082-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/18/2021] [Indexed: 01/04/2023] Open
Abstract
Leeches are found in terrestrial, aquatic, and marine habitats on all continents. Sanguivorous leeches have been used in medicine for millennia. Modern scientific uses include studies of neurons, anticoagulants, and gut microbial symbioses. Hirudo verbana, the European medicinal leech, maintains a gut community dominated by two bacterial symbionts, Aeromonas veronii and Mucinivorans hirudinis, which sometimes account for as much as 97% of the total crop microbiota. The highly simplified gut anatomy and microbiome of H. verbana make it an excellent model organism for studying gut microbial dynamics. The North American medicinal leech, Macrobdella decora, is a hirudinid leech native to Canada and the northern United States. In this study, we show that M. decora symbiont communities are very similar to those in H. verbana. We performed an extensive study using field-caught M. decora and purchased H. verbana from two suppliers. Deep sequencing of the V4 region of the 16S rRNA gene allowed us to determine that the core microbiome of M. decora consists of Bacteroides, Aeromonas, Proteocatella, and Butyricicoccus. The analysis revealed that the compositions of the gut microbiomes of the two leech species were significantly different at all taxonomic levels. The R 2 value was highest at the genus and amplicon sequence variant (ASV) levels and much lower at the phylum, class, and order levels. The gut and bladder microbial communities were distinct. We propose that M. decora is an alternative to H. verbana for studies of wild-caught animals and provide evidence for the conservation of digestive-tract and bladder symbionts in annelid models.IMPORTANCE Building evidence implicates the gut microbiome in critical animal functions such as regulating digestion, nutrition, immune regulation, and development. Simplified, phylogenetically diverse models for hypothesis testing are necessary because of the difficulty of assigning causative relationships in complex gut microbiomes. Previous research used Hirudo verbana as a tractable animal model of digestive-tract symbioses. Our data show that Macrobdella decora may work just as well without the drawback of being an endangered organism and with the added advantage of easy access to field-caught specimens. The similarity of the microbial community structures of species from two different continents reveals the highly conserved nature of the microbial symbionts in sanguivorous leeches.
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Yang B, Chen C, Sun Y, Cao L, Zhang D, Sun W, Zhang L, Wang G, Shan X, Kang Y, Qian A. Comparative genomic analysis of different virulence strains reveals reasons for the increased virulence of Aeromonas veronii. JOURNAL OF FISH DISEASES 2021; 44:11-24. [PMID: 33137224 DOI: 10.1111/jfd.13262] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Aeromonas veronii is an important zoonotic and aquatic agent. More and more cases have shown that it has caused huge economic losses in the aquaculture industry in addition to threatening human health. But the reasons for the increasing virulence of A. veronii are still unclear. In order to further understand the reasons for the increased virulence of A. veronii, we conducted a comparative analysis of the genomes of A. veronii with different virulence. The analysis revealed that there are multiple virulence factors, such as those related to fimbriae, flagella, toxins, iron ion uptake systems and type II, type III and type VI secretion systems in the virulent strain TH0426 genome. And comparative analysis showed that there were two complete type III secretion systems (API1 and API2), of which the API2 and iron ion transport system were unique to the TH0426 strain. In addition, TH0426 strain also has unique functional gene clusters, which may play important roles in terms of resisting infection, adapting to different environments and genetic evolution. These particular virulence factors and gene clusters may be the important reasons for the increased virulence. These insights will provide a reference for the study of the pathogenesis of A. veronii.
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Affiliation(s)
- Bintong Yang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
- College of Life Science, Changchun Sci-Tech University, Changchun, China
| | - Chong Chen
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yufeng Sun
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Linan Cao
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Dongxing Zhang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Wuwen Sun
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Lei Zhang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Guiqin Wang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xiaofeng Shan
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yuanhuan Kang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Aidong Qian
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
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Smyrli M, Triga A, Dourala N, Varvarigos P, Pavlidis M, Quoc VH, Katharios P. Comparative Study on A Novel Pathogen of European Seabass. Diversity of Aeromonas veronii in the Aegean Sea. Microorganisms 2019; 7:microorganisms7110504. [PMID: 31671797 PMCID: PMC6921072 DOI: 10.3390/microorganisms7110504] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/16/2019] [Accepted: 10/25/2019] [Indexed: 01/01/2023] Open
Abstract
Aeromonas veronii is an emerging pathogen causing severe pathology and mortalities in European seabass aquaculture in the Aegean Sea, Mediterranean. More than 50 strains of the pathogen were characterized biochemically and genetically in order to study the epidemiology of the disease, as well as the phylogeny and virulence of the bacterium. Based on the phenotypic characteristics, the isolates form three groups consisting of: (a) the West Aegean Sea, non-motile, non-pigment-producing strains, (b) the West Aegean Sea, motile, and pigment-producing strains and (c) the East Aegean Sea motile strains that produce minute amounts of pigment. All strains were highly similar at the genomic level; however, the pattern of West/East geographic origin was reflected in biochemical properties, in general genomic level comparison and in the putative virulent factors studied. Type VI secretion system was not detected in the western strains. The outer membrane protein (OMP) profile which contains proteins that are putative antigenic factors, was very similar between strains from the different areas. Although most of the OMPs were detected in all strains with great sequence similarity, diversification according to geographic origin was evident in known antigenic factors such as the maltoporin LamB. A systematic comparative analysis of the strains is presented and discussed in view of the emergence of A. veronii as a significant pathogen for the Mediterranean aquaculture.
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Affiliation(s)
- Maria Smyrli
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece.
- Department of Biology, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Adriana Triga
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece.
- Department of Biology, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Nancy Dourala
- Fish Pathology Department, Selonda Aquaculture, 15125 Athens, Greece.
| | | | - Michael Pavlidis
- Department of Biology, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Viet Ha Quoc
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece.
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece.
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Tekedar HC, Kumru S, Blom J, Perkins AD, Griffin MJ, Abdelhamed H, Karsi A, Lawrence ML. Comparative genomics of Aeromonas veronii: Identification of a pathotype impacting aquaculture globally. PLoS One 2019; 14:e0221018. [PMID: 31465454 PMCID: PMC6715197 DOI: 10.1371/journal.pone.0221018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 07/29/2019] [Indexed: 12/30/2022] Open
Abstract
Aeromonas veronii is a gram-negative species abundant in aquatic environments that causes disease in humans as well as terrestrial and aquatic animals. In the current study, 41 publicly available A. veronii genomes were compared to investigate distribution of putative virulence genes, global dissemination of pathotypes, and potential mechanisms of virulence. The complete genome of A. veronii strain ML09-123 from an outbreak of motile aeromonas septicemia in farm-raised catfish in the southeastern United States was included. Dissemination of A. veronii strain types was discovered in dispersed geographical locations. Isolate ML09-123 is highly similar to Chinese isolate TH0426, suggesting the two strains have a common origin and may represent a pathotype impacting aquaculture in both countries. Virulence of strain ML09-123 in catfish in a dose-dependent manner was confirmed experimentally. Subsystem category disposition showed the majority of genomes exhibit similar distribution of genomic elements. The type I secretion system (T1SS), type II secretion system (T2SS), type 4 pilus (T4P), and flagellum core elements are conserved in all A. veronii genomes, whereas the type III secretion system (T3SS), type V secretion system (T5SS), type VI secretion system (T6SS), and tight adherence (TAD) system demonstrate variable dispersal. Distribution of mobile elements is dependent on host and geographic origin, suggesting this species has undergone considerable genetic exchange. The data presented here lends insight into the genomic variation of A. veronii and identifies a pathotype impacting aquaculture globally.
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Affiliation(s)
- Hasan C. Tekedar
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Salih Kumru
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Jochen Blom
- Bioinformatics & Systems Biology, Justus-Liebig-University Giessen, Giessen, Hesse, Germany
| | - Andy D. Perkins
- Department of Computer Science and Engineering, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Matt J. Griffin
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
- Thad Cochran National Warmwater Aquaculture Center, Stoneville, Mississippi State, United States of America
| | - Hossam Abdelhamed
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Attila Karsi
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Mark L. Lawrence
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
- * E-mail:
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Espadinha D, Sobral RG, Mendes CI, Méric G, Sheppard SK, Carriço JA, de Lencastre H, Miragaia M. Distinct Phenotypic and Genomic Signatures Underlie Contrasting Pathogenic Potential of Staphylococcus epidermidis Clonal Lineages. Front Microbiol 2019; 10:1971. [PMID: 31507574 PMCID: PMC6719527 DOI: 10.3389/fmicb.2019.01971] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/12/2019] [Indexed: 12/31/2022] Open
Abstract
Background: Staphylococcus epidermidis is a common skin commensal that has emerged as a pathogen in hospitals, mainly related to medical devices-associated infections. Noteworthy, infection rates by S. epidermidis have the tendency to rise steeply in next decades together with medical devices use and immunocompromized population growth. Staphylococcus epidermidis population structure includes two major clonal lineages (A/C and B) that present contrasting pathogenic potentials. To address this distinction and explore the basis of increased pathogenicity of A/C lineage, we performed a detailed comparative analysis using phylogenetic and integrated pangenome-wide-association study (panGWAS) approaches and compared the lineages's phenotypes in in vitro conditions mimicking carriage and infection. Results: Each S. epidermidis lineage had distinct phenotypic signatures in skin and infection conditions and differed in genomic content. Combination of phenotypic and genotypic data revealed that both lineages were well adapted to skin environmental cues. However, they appear to occupy different skin niches, perform distinct biological functions in the skin and use different mechanisms to complete the same function: lineage B strains showed evidence of specialization to survival in microaerobic and lipid rich environment, characteristic of hair follicle and sebaceous glands; lineage A/C strains showed evidence for adaption to diverse osmotic and pH conditions, potentially allowing them to occupy a broader and more superficial skin niche. In infection conditions, A/C strains had an advantage, having the potential to bind blood-associated host matrix proteins, form biofilms at blood pH, resist antibiotics and macrophage acidity and to produce proteases. These features were observed to be rare in the lineage B strains. PanGWAS analysis produced a catalog of putative S. epidermidis virulence factors and identified an epidemiological molecular marker for the more pathogenic lineage. Conclusion: The prevalence of A/C lineage in infection is probably related to a higher metabolic and genomic versatility that allows rapid adaptation during transition from a commensal to a pathogenic lifestyle. The putative virulence and phenotypic factors associated to A/C lineage constitute a reliable framework for future studies on S. epidermidis pathogenesis and the finding of an epidemiological marker for the more pathogenic lineage is an asset for the management of S. epidermidis infections.
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Affiliation(s)
- Diana Espadinha
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Rita G. Sobral
- Laboratory of Molecular Microbiology of Bacterial Pathogens, UCIBIO/REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Costa de Caparica, Portugal
| | - Catarina Inês Mendes
- Molecular Microbiology and Infection Unit, Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisbon, Portugal
| | - Guillaume Méric
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Samuel K. Sheppard
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- MRC CLIMB Consortium, Bath, United Kingdom
| | - João A. Carriço
- Molecular Microbiology and Infection Unit, Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisbon, Portugal
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, United States
| | - Maria Miragaia
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Rangel LT, Marden J, Colston S, Setubal JC, Graf J, Gogarten JP. Identification and characterization of putative Aeromonas spp. T3SS effectors. PLoS One 2019; 14:e0214035. [PMID: 31163020 PMCID: PMC6548356 DOI: 10.1371/journal.pone.0214035] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 05/21/2019] [Indexed: 11/23/2022] Open
Abstract
The genetic determinants of bacterial pathogenicity are highly variable between species and strains. However, a factor that is commonly associated with virulent Gram-negative bacteria, including many Aeromonas spp., is the type 3 secretion system (T3SS), which is used to inject effector proteins into target eukaryotic cells. In this study, we developed a bioinformatics pipeline to identify T3SS effector proteins, applied this approach to the genomes of 105 Aeromonas strains isolated from environmental, mutualistic, or pathogenic contexts and evaluated the cytotoxicity of the identified effectors through their heterologous expression in yeast. The developed pipeline uses a two-step approach, where candidate Aeromonas gene families are initially selected using Hidden Markov Model (HMM) profile searches against the Virulence Factors DataBase (VFDB), followed by strict comparisons against positive and negative control datasets, greatly reducing the number of false positives. This approach identified 21 Aeromonas T3SS likely effector families, of which 8 represent known or characterized effectors, while the remaining 13 have not previously been described in Aeromonas. We experimentally validated our in silico findings by assessing the cytotoxicity of representative effectors in Saccharomyces cerevisiae BY4741, with 15 out of 21 assayed proteins eliciting a cytotoxic effect in yeast. The results of this study demonstrate the utility of our approach, combining a novel in silico search method with in vivo experimental validation, and will be useful in future research aimed at identifying and authenticating bacterial effector proteins from other genera.
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Affiliation(s)
- Luiz Thiberio Rangel
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
- Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brasil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | - Jeremiah Marden
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Sophie Colston
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - João Carlos Setubal
- Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brasil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, United States of America
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, United States of America
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12
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Yuan H, Huang L, Wang M, Jia R, Chen S, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Liu Y, Zhang L, Yu Y, You Y, Chen X, Zhu D, Cheng A. Role of the gldK gene in the virulence of Riemerella anatipestifer. Poult Sci 2019; 98:2414-2421. [DOI: 10.3382/ps/pez028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/10/2019] [Indexed: 01/09/2023] Open
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13
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Shi W, Li M, Wei G, Tian R, Li C, Wang B, Lin R, Shi C, Chi X, Zhou B, Gao Z. The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome. MICROBIOME 2019; 7:14. [PMID: 30709420 PMCID: PMC6359780 DOI: 10.1186/s40168-019-0629-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 01/17/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interactions between CS and the soil microbiome. In this study, four soil-root system compartments (geocaulosphere soil (GS), rhizosphere soil (RS), root-zone soil (ZS), and furrow soil (FS)) were analyzed for potato plants with naturally high (H) and low (L) scab severity levels. We aimed to determine the composition and putative function of the soil microbiome associated with potato CS. RESULTS The copy numbers of the scab phytotoxin biosynthetic gene txtAB and the bacterial 16S rRNA gene as well as the diversity and composition of each of the four soil-root system compartments were examined; GS was the only compartment that exhibited significant differences between the H and L groups. Compared to the H group, the L group exhibited a lower txtAB gene copy number, lower bacterial 16S copy number, higher diversity, higher co-occurrence network complexity, and higher community function similarity within the GS microbiome. The community composition and function of the GS samples were further revealed by shotgun metagenomic sequencing. Variovorax, Stenotrophomonas, and Agrobacterium were the most abundant genera that were significantly and positively correlated with the scab severity level, estimated absolute abundance (EAA) of pathogenic Streptomyces, and txtAB gene copy number. In contrast, Geobacillus, Curtobacterium, and unclassified Geodermatophilaceae were significantly negatively correlated with these three parameters. Compared to the function profiles in the L group, several genes involved in "ABC transporters," the "bacterial secretion system," "quorum sensing (QS)," "nitrogen metabolism," and some metabolism by cytochrome P450 were enriched in the H group. In contrast, some antibiotic biosynthesis pathways were enriched in the L group. Based on the differences in community composition and function, a simple model was proposed to explain the putative relationships between the soil microbiome and CS occurrence. CONCLUSIONS The GS microbiome was closely associated with CS severity in the soil-root system, and the occurrence of CS was accompanied by changes in community composition and function. The differential functions provide new clues to elucidate the mechanism underlying the interaction between CS occurrence and the soil microbiome, and varying community compositions provide novel insights into CS occurrence.
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Affiliation(s)
- Wencong Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Mingcong Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Guangshan Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, 361005, China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Sun Yat-Sen University, Guangzhou, 510275, China
| | - Renmao Tian
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, USA
| | - Cuiping Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Bing Wang
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, 271018, China
| | - Rongshan Lin
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, 271018, China
| | - Chunyu Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiuli Chi
- Plant Protection Station, Jiaozhou Agricultural Bureau, Qingdao, 266300, China
| | - Bo Zhou
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, 271018, China.
| | - Zheng Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China.
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, USA.
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14
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Talagrand-Reboul E, Latif-Eugenín F, Beaz-Hidalgo R, Colston S, Figueras MJ, Graf J, Jumas-Bilak E, Lamy B. Genome-driven evaluation and redesign of PCR tools for improving the detection of virulence-associated genes in aeromonads. PLoS One 2018; 13:e0201428. [PMID: 30110345 PMCID: PMC6093642 DOI: 10.1371/journal.pone.0201428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/16/2018] [Indexed: 12/16/2022] Open
Abstract
Many virulence factors have been described for opportunistic pathogens within the genus Aeromonas. Polymerase Chain Reactions (PCRs) are commonly used in population studies of aeromonads to detect virulence-associated genes in order to better understand the epidemiology and emergence of Aeromonas from the environment to host, but their performances have never been thoroughly evaluated. We aimed to determine diagnostic sensitivity and specificity of PCR assays for the detection of virulence-associated genes in a collection of Aeromonas isolates representative for the genetic diversity in the genus. Thirty-nine Aeromonas strains belonging to 27 recognized species were screened by published PCR assays for virulence-associated genes (act, aerA, aexT, alt, ascFG, ascV, ast, lafA, lip, ser, stx1, stx2A). In parallel, homologues of the 12 putative virulence genes were searched from the genomes of the 39 strains. Of the 12 published PCR assays for virulence factors, the comparison of PCR results and genome analysis estimated diagnostic sensitivities ranging from 34% to 100% and diagnostic specificities ranged from 71% to 100% depending upon the gene. To improve the detection of virulence-associated genes in aeromonads, we have designed new primer pairs for aerA/act, ser, lafA, ascFG and ascV, which showed excellent diagnostic sensitivity and specificity. Altogether, the analysis of high quality genomic data, which are more and more easy to obtain, provides significant improvements in the genetic detection of virulence factors in bacterial strains.
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Affiliation(s)
- Emilie Talagrand-Reboul
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de Montpellier, Montpellier, France
- Laboratoire de Bactériologie, Hôpitaux universitaires de Strasbourg, Strasbourg, France
- * E-mail: (BL); (ETR)
| | - Fadua Latif-Eugenín
- Unidad de Microbiología, Departamento de Ciencias Médicas Básicas, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i Virgili, Reus, Spain
| | - Roxana Beaz-Hidalgo
- Unidad de Microbiología, Departamento de Ciencias Médicas Básicas, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i Virgili, Reus, Spain
| | - Sophie Colston
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Maria-Jose Figueras
- Unidad de Microbiología, Departamento de Ciencias Médicas Básicas, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i Virgili, Reus, Spain
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Estelle Jumas-Bilak
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de Montpellier, Montpellier, France
- Département d’Hygiène Hospitalière, CHRU de Montpellier, Montpellier, France
| | - Brigitte Lamy
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de Montpellier, Montpellier, France
- Département de Bactériologie, CHU de Nice, Nice, France
- * E-mail: (BL); (ETR)
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15
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Draft Genome Sequence of Aeromonas lusitana sp. nov. Strain DSM 24905 T, Isolated from a Hot Spring in Vila-Real, Portugal. GENOME ANNOUNCEMENTS 2018; 6:6/15/e00226-18. [PMID: 29650570 PMCID: PMC5897795 DOI: 10.1128/genomea.00226-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Aeromonas lusitana sp. nov. is an isolate derived from a study aimed at characterizing Aeromonas spp. from water sources used for recreation and agricultural purposes and assessing the implications these organisms have for human and animal health. We present here the 4.52-Mbp draft genome sequence of this novel species.
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16
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Draft Genome Sequence of Aeromonas cavernicola sp. nov. DSM 24474 T, Isolated from a Cavern Brook in the Moravia Region of the Czech Republic. GENOME ANNOUNCEMENTS 2018; 6:6/15/e00227-18. [PMID: 29650571 PMCID: PMC5897817 DOI: 10.1128/genomea.00227-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Species of the Aeromonas genus can be found in numerous environmental milieus, including various water sources, and some species cause disease in animals. We present here the draft genome sequence for Aeromonas cavernicola DSM 24474T, a novel species isolated from a freshwater brook within a cavern in the Czech Republic.
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17
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Liu X, Luo Y, Li Z, Wei G. Functional Analysis of a Putative Type III Secretion System in Stress Adaption by Mesorhizobium alhagi CCNWXJ12-2 T. Front Microbiol 2018. [PMID: 29515545 PMCID: PMC5826200 DOI: 10.3389/fmicb.2018.00263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Mesorhizobium alhagi CCNWXJ12-2T, isolated from root nodules of the desert plant Alhagi sparsifolia, contains two type III secretion systems (T3SSs). T3SSs are specialized machinery with wide distribution in bacteria that inject effector proteins into target cells. Our previous study showed that the expression of M. alhagi T3SS1 is upregulated in high-salt conditions. Here, phylogenetic analysis of T3SS1 using the core protein RhcU suggested that T3SS1 belongs to the α-Rhc II subgroup of the Rhc T3SS family. To elaborate the function of M. alhagi CCNWXJ12-2T T3SS1 in stress adaption, two T3SS1 mutants (ΔrhcQ and ΔMA29250) were constructed and analyzed. β-galactosidase transcriptional fusion assays showed that activity of the promoter of T3SS1 was induced by salts. Mutant ΔrhcQ was more sensitive to NaCl and LiCl than the wild-type, but ΔMA29250 was not. Both mutants were more sensitive to KCl than the wild-type. The intracellular Na+ concentration in ΔrhcQ in high-NaCl conditions (0.4 M) increased by 37% compared to that of the wild-type strain, while the Na+ concentration in ΔMA29250 increased by 13%. The K+ concentration in both mutants increased by 16% compared to the wild-type in high-KCl conditions (0.3 M). Strain ΔrhcQ showed decreased survival compared to the wild-type after treatment with H2O2, while the survival rate of ΔMA29250 was almost the same as that of the wild-type. Antioxidant enzyme activities in ΔrhcQ were lower than those in the wild-type strain, but this was not the case for ΔMA29250. Our data elucidate the beneficial effects of T3SS1 in the adaption of M. alhagi CCNWXJ12-2T to stress.
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Affiliation(s)
- Xiaodong Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, China
| | - Yantao Luo
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, China
| | - Zhefei Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, China
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18
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Francisqueti FV, Nascimento AF, Minatel IO, Dias MC, Luvizotto RDAM, Berchieri-Ronchi C, Ferreira ALA, Corrêa CR. Metabolic syndrome and inflammation in adipose tissue occur at different times in animals submitted to a high-sugar/fat diet. J Nutr Sci 2017; 6:e41. [PMID: 29152245 PMCID: PMC5672321 DOI: 10.1017/jns.2017.42] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 05/23/2017] [Accepted: 06/29/2017] [Indexed: 12/16/2022] Open
Abstract
Obesity is associated with low-grade inflammation, triggered in adipose tissue, which may occur due to an excess of SFA from the diet that can be recognised by Toll-like receptor-4. This condition is involved in the development of components of the metabolic syndrome associated with obesity, especially insulin resistance. The aim of the study was to evaluate the manifestation of the metabolic syndrome and adipose tissue inflammation as a function of the period of time in which rats were submitted to a high-sugar/fat diet (HSF). Male Wistar rats were divided into six groups to receive the control diet (C) or the HSF for 6, 12 or 24 weeks. HSF increased the adiposity index in all HSF groups compared with the C group. HSF was associated with higher plasma TAG, glucose, insulin and leptin levels. Homeostasis model assessment increased in HSF compared with C rats at 24 weeks. Both TNF-α and IL-6 were elevated in the epididymal adipose tissue of HSF rats at 24 weeks compared with HSF at 6 weeks and C at 24 weeks. Only the HSF group at 24 weeks showed increased expression of both Toll-like receptor-4 and NF-κB. More inflammatory cells were found in the HSF group at 24 weeks. We can conclude that the metabolic syndrome occurs independently of the inflammatory response in adipose tissue and that inflammation is associated with hypertrophy of adipocytes, which varies according to duration of exposure to the HSF.
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Affiliation(s)
| | | | - Igor Otávio Minatel
- São Paulo State University, Institute of Bioscience, Botucatu, São Paulo, Brazil
| | - Marcos Correa Dias
- Institute of Health Sciences, Federal University of Mato Grosso (UFMT), Sinop, Mato Grosso, Brazil
| | | | | | - Ana Lúcia A. Ferreira
- São Paulo State University (UNESP), Botucatu Medical School, Botucatu, São Paulo, Brazil
| | - Camila Renata Corrêa
- São Paulo State University (UNESP), Botucatu Medical School, Botucatu, São Paulo, Brazil
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Renoz F, Champagne A, Degand H, Faber AM, Morsomme P, Foray V, Hance T. Toward a better understanding of the mechanisms of symbiosis: a comprehensive proteome map of a nascent insect symbiont. PeerJ 2017; 5:e3291. [PMID: 28503376 PMCID: PMC5426354 DOI: 10.7717/peerj.3291] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/10/2017] [Indexed: 12/18/2022] Open
Abstract
Symbiotic bacteria are common in insects and can affect various aspects of their hosts’ biology. Although the effects of insect symbionts have been clarified for various insect symbiosis models, due to the difficulty of cultivating them in vitro, there is still limited knowledge available on the molecular features that drive symbiosis. Serratia symbiotica is one of the most common symbionts found in aphids. The recent findings of free-living strains that are considered as nascent partners of aphids provide the opportunity to examine the molecular mechanisms that a symbiont can deploy at the early stages of the symbiosis (i.e., symbiotic factors). In this work, a proteomic approach was used to establish a comprehensive proteome map of the free-living S. symbiotica strain CWBI-2.3T. Most of the 720 proteins identified are related to housekeeping or primary metabolism. Of these, 76 were identified as candidate proteins possibly promoting host colonization. Our results provide strong evidence that S. symbiotica CWBI-2.3T is well-armed for invading insect host tissues, and suggest that certain molecular features usually harbored by pathogenic bacteria are no longer present. This comprehensive proteome map provides a series of candidate genes for further studies to understand the molecular cross-talk between insects and symbiotic bacteria.
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Affiliation(s)
- François Renoz
- Biodiversity Reasearch Center, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Antoine Champagne
- Institute of Life Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Hervé Degand
- Institute of Life Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Anne-Marie Faber
- Institute of Life Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Pierre Morsomme
- Institute of Life Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Vincent Foray
- Centre de Recherche de Biochimie Macromoléculaire, Centre National de la Recherche Scientifique, Montpellier, France
| | - Thierry Hance
- Biodiversity Reasearch Center, Université catholique de Louvain, Louvain-la-Neuve, Belgium
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McAnulty SJ, Nyholm SV. The Role of Hemocytes in the Hawaiian Bobtail Squid, Euprymna scolopes: A Model Organism for Studying Beneficial Host-Microbe Interactions. Front Microbiol 2017; 7:2013. [PMID: 28111565 PMCID: PMC5216023 DOI: 10.3389/fmicb.2016.02013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/01/2016] [Indexed: 01/06/2023] Open
Abstract
Most, if not all, animals engage in associations with bacterial symbionts. Understanding the mechanisms by which host immune systems and beneficial bacteria communicate is a fundamental question in the fields of immunology and symbiosis. The Hawaiian bobtail squid (Euprymna scolopes) engages in two known symbioses; a binary relationship with the light organ symbiont Vibrio fischeri, and a bacterial consortium within a specialized organ of the female reproductive system, the accessory nidamental gland (ANG). E. scolopes has a well-developed circulatory system that allows immune cells (hemocytes) to migrate into tissues, including the light organ and ANG. In the association with V. fischeri, hemocytes are thought to have a number of roles in the management of symbiosis, including the recognition of non-symbiotic bacteria and the contribution of chitin as a nutrient source for V. fischeri. Hemocytes are hypothesized to recognize bacteria through interactions between pattern recognition receptors and microbe-associated molecular patterns. Colonization by V. fischeri has been shown to affect the bacteria-binding behavior, gene expression, and proteome of hemocytes, indicating that the symbiont can modulate host immune function. In the ANG, hemocytes have also been observed interacting with the residing bacterial community. As a model host, E. scolopes offers a unique opportunity to study how the innate immune system interacts with both a binary and consortial symbiosis. This mini review will recapitulate what is known about the role of hemocytes in the light organ association and offer future directions for understanding how these immune cells interact with multiple types of symbioses.
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Affiliation(s)
- Sarah J McAnulty
- Department of Molecular and Cell Biology, University of Connecticut, Storrs CT, USA
| | - Spencer V Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs CT, USA
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Marden JN, McClure EA, Beka L, Graf J. Host Matters: Medicinal Leech Digestive-Tract Symbionts and Their Pathogenic Potential. Front Microbiol 2016; 7:1569. [PMID: 27790190 PMCID: PMC5061737 DOI: 10.3389/fmicb.2016.01569] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/20/2016] [Indexed: 12/31/2022] Open
Abstract
Digestive-tract microbiota exert tremendous influence over host health. Host-symbiont model systems are studied to investigate how symbioses are initiated and maintained, as well as to identify host processes affected by resident microbiota. The medicinal leech, Hirudo verbana, is an excellent model to address such questions owing to a microbiome that is consistently dominated by two species, Aeromonas veronii and Mucinivorans hirudinis, both of which are cultivable and have sequenced genomes. This review outlines current knowledge about the dynamics of the H. verbana microbiome. We discuss in depth the factors required for A. veronii colonization and proliferation in the leech crop and summarize the current understanding of interactions between A. veronii and its annelid host. Lastly, we discuss leech usage in modern medicine and highlight how leech-therapy associated infections, often attributable to Aeromonas spp., are of growing clinical concern due in part to an increased prevalence of fluoroquinolone resistant strains.
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Affiliation(s)
- Jeremiah N Marden
- Department of Molecular and Cell Biology, University of Connecticut, Storrs CT, USA
| | - Emily A McClure
- Department of Molecular and Cell Biology, University of Connecticut, Storrs CT, USA
| | - Lidia Beka
- Department of Molecular and Cell Biology, University of Connecticut, Storrs CT, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, StorrsCT, USA; Institute for Systems Genomics, University of Connecticut, StorrsCT, USA
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Abstract
In most animals, digestive tracts harbor the greatest number of bacteria in the animal that contribute to its health: by aiding in the digestion of nutrients, provisioning essential nutrients and protecting against colonization by pathogens. Invertebrates have been used to enhance our understanding of metabolic processes and microbe-host interactions owing to experimental advantages. This review describes how advances in DNA sequencing technologies have dramatically altered how researchers investigate microbe-host interactions, including 16S rRNA gene surveys, metagenome experiments, and metatranscriptome studies. Advantages and challenges of each of these approaches are described herein. Hypotheses generated through omics studies can be directly tested using site-directed mutagenesis, and findings from transposon studies and site-directed experiments are presented. Finally, unique structural aspects of invertebrate digestive tracts that contribute to symbiont specificity are presented. The combination of omics approaches with genetics and microscopy allows researchers to move beyond correlations to identify conserved mechanisms of microbe-host interactions.
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Affiliation(s)
- Joerg Graf
- Department of Molecular and Cell Biology, Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269;
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A Tale of Transmission: Aeromonas veronii Activity within Leech-Exuded Mucus. Appl Environ Microbiol 2016; 82:2644-55. [PMID: 26896136 DOI: 10.1128/aem.00185-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 02/16/2016] [Indexed: 11/20/2022] Open
Abstract
Transmission, critical to the establishment and persistence of host-associated microbiotas, also exposes symbionts to new environmental conditions. With horizontal transmission, these different conditions represent major lifestyle shifts. Yet genome-wide analyses of how microbes adjust their transcriptomes toward these dramatic shifts remain understudied. Here, we provide a comprehensive and comparative analysis of the global transcriptional profiles of a symbiont as it shifts between lifestyles during transmission. The gammaproteobacterium Aeromonas veronii is transmitted from the gut of the medicinal leech to other hosts via host mucosal castings, yet A. veronii can also transition from mucosal habitancy to a free-living lifestyle. These three lifestyles are characterized by distinct physiological constraints and consequently lifestyle-specific changes in the expression of stress-response genes. Mucus-bound A. veronii had the greatest expression in terms of both the number of loci and levels of transcription of stress-response mechanisms. However, these bacteria are still capable of proliferating within the mucus, suggesting the availability of nutrients within this environment. We found that A. veronii alters transcription of loci in a synthetic pathway that obtains and incorporates N-acetylglucosamine (NAG; a major component of mucus) into the bacterial cell wall, enabling proliferation. Our results demonstrate that symbionts undergo dramatic local adaptation, demonstrated by widespread transcriptional changes, throughout the process of transmission that allows them to thrive while they encounter new environments which further shape their ecology and evolution.
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Verriere B, Sabatier B, Carbonnelle E, Mainardi JL, Prognon P, Whitaker I, Lantieri L, Hivelin M. Medicinal leech therapy and Aeromonas spp. infection. Eur J Clin Microbiol Infect Dis 2016; 35:1001-6. [PMID: 27039338 DOI: 10.1007/s10096-016-2629-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/16/2016] [Indexed: 01/11/2023]
Abstract
While the use of medicinal leech therapy (MLT) in reconstructive and orthopaedic surgery is widely described, post-operative complications related to leeches remain a major concern. Aeromonas spp. strains are involved in the majority of reported cases. As surgical success rate is directly impacted, an adapted antibiotic prophylaxis should be instituted in order to minimize these complications. We assessed pharmaceutical process, microbiological control and related infections in order to provide data and choose the appropriate antibiotherapy for patients requiring MLT. We report a clinical and microbiological study over a 24-month period. Clinical data were collected from patients' database, and microbiological analysis both on leeches' tank water and crushed leeches were performed to characterize isolated strains and their susceptibility to antibiotics. A total of 595 leeches were used to treat 28 patients (12 in plastic surgery and 16 in orthopaedic surgery), and three documented cases of post-operative infections were reported. Aeromonas spp. isolates yielded from 62 % of analyzed batches (75 % of Aeromonas veronii). Eighteen Aeromonas spp. isolates yielded from 23 water samples and three crushed leeches. Isolates were similar in tank and crushed leeches. Strains were susceptible to fluoroquinolones, sulfamethoxazole/trimethoprim, aminosides, and third-generation cephalosporins but resistant to amoxicillin/clavulanic acid and second-generation cephalosporins. According to collected data, routine tank water microbiological analyses are mandatory in order to identify leeches' batches containing resistant strains and to discard them. In this context, the surgeon is able to select an appropriated antibiotic prophylaxis in order to avoid MLT associated serious post-operative complications.
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Affiliation(s)
- B Verriere
- Pharmacy Department, Georges Pompidou European Hospital, 20 rue Leblanc, 75015, Paris, France.
| | - B Sabatier
- Pharmacy Department, Georges Pompidou European Hospital, 20 rue Leblanc, 75015, Paris, France
| | - E Carbonnelle
- Microbiology Department, Georges Pompidou European Hospital, 20 rue Leblanc, 75015, Paris, France
| | - J L Mainardi
- Microbiology Department, Georges Pompidou European Hospital, 20 rue Leblanc, 75015, Paris, France
| | - P Prognon
- Pharmacy Department, Georges Pompidou European Hospital, 20 rue Leblanc, 75015, Paris, France
| | - I Whitaker
- Reconstructive Surgery and Regenerative Medicine Research Group, Institute of Life Sciences, Swansea University Medical School, Wales, UK
| | - L Lantieri
- Reconstructive Surgery Department, Georges Pompidou European Hospital, 20 rue Leblanc, 75015, Paris, France
| | - M Hivelin
- Reconstructive Surgery Department, Georges Pompidou European Hospital, 20 rue Leblanc, 75015, Paris, France
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Tasiemski A, Massol F, Cuvillier-Hot V, Boidin-Wichlacz C, Roger E, Rodet F, Fournier I, Thomas F, Salzet M. Reciprocal immune benefit based on complementary production of antibiotics by the leech Hirudo verbana and its gut symbiont Aeromonas veronii. Sci Rep 2015; 5:17498. [PMID: 26635240 PMCID: PMC4669451 DOI: 10.1038/srep17498] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 10/30/2015] [Indexed: 02/07/2023] Open
Abstract
The medicinal leech has established a long-term mutualistic association with Aeromonas veronii, a versatile bacterium which can also display free-living waterborne and fish- or human-pathogenic lifestyles. Here, we investigated the role of antibiotics in the dynamics of interaction between the leech and its gut symbiont Aeromonas. By combining biochemical and molecular approaches, we isolated and identified for the first time the antimicrobial peptides (AMPs) produced by the leech digestive tract and by its symbiont Aeromonas. Immunohistochemistry data and PCR analyses evidenced that leech AMP genes are induced in the gut epithelial cells when Aeromonas load is low (starved animals), while repressed when Aeromonas abundance is the highest (post blood feeding). The asynchronous production of AMPs by both partners suggests that these antibiotic substances (i) provide them with reciprocal protection against invasive bacteria and (ii) contribute to the unusual simplicity of the gut microflora of the leech. This immune benefit substantially reinforces the evidence of an evolutionarily stable association between H. verbana and A. veronii. Altogether these data may provide insights into the processes making the association with an Aeromonas species in the digestive tract either deleterious or beneficial.
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Affiliation(s)
- Aurélie Tasiemski
- Univ. Lille, Unité Evolution, Ecologie et Paléontologie (EEP), CNRS UMR 8198, F-59 000 Lille, France
| | - François Massol
- Univ. Lille, Unité Evolution, Ecologie et Paléontologie (EEP), CNRS UMR 8198, F-59 000 Lille, France
| | - Virginie Cuvillier-Hot
- Univ. Lille, Unité Evolution, Ecologie et Paléontologie (EEP), CNRS UMR 8198, F-59 000 Lille, France
| | - Céline Boidin-Wichlacz
- Univ. Lille, Unité Evolution, Ecologie et Paléontologie (EEP), CNRS UMR 8198, F-59 000 Lille, France
| | - Emmanuel Roger
- Univ. Lille, Centre d'infections et d'immunité de Lille, CNRS UMR 8204, INSERM U 1019, F-59 000 Lille, France
| | - Franck Rodet
- Univ. Lille, Unité Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM), INSERM U 1192, F-59 000 Lille, France
| | - Isabelle Fournier
- Univ. Lille, Unité Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM), INSERM U 1192, F-59 000 Lille, France
| | - Frédéric Thomas
- MIVEGEC, UMR IRD/CNRS/UM5290, 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Michel Salzet
- Univ. Lille, Unité Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM), INSERM U 1192, F-59 000 Lille, France
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Maltz M, LeVarge BL, Graf J. Identification of iron and heme utilization genes in Aeromonas and their role in the colonization of the leech digestive tract. Front Microbiol 2015; 6:763. [PMID: 26284048 PMCID: PMC4516982 DOI: 10.3389/fmicb.2015.00763] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 07/13/2015] [Indexed: 01/02/2023] Open
Abstract
It is known that many pathogens produce high-affinity iron uptake systems like siderophores and/or proteins for utilizing iron bound to heme-containing molecules, which facilitate iron-acquisition inside a host. In mutualistic digestive-tract associations, iron uptake systems have not been as well studied. We investigated the importance of two iron utilization systems within the beneficial digestive-tract association Aeromonas veronii and the medicinal leech, Hirudo verbana. Siderophores were detected in A. veronii using chrome azurol S. Using a mini Tn5, a transposon insertion in viuB generated a mutant unable to utilize iron using siderophores. The A. veronii genome was then searched for genes potentially involved in iron utilization bound to heme-containing molecules. A putative outer membrane heme receptor (hgpB) was identified with a transcriptional activator, termed hgpR, downstream. The hgpB gene was interrupted with an antibiotic resistance cassette in both the parent strain and the viuB mutant, yielding an hgpB mutant and a mutant with both iron uptake systems inactivated. In vitro assays indicated that hgpB is involved in utilizing iron bound to heme and that both iron utilization systems are important for A. veronii to grow in blood. In vivo colonization assays revealed that the ability to acquire iron from heme-containing molecules is critical for A. veronii to colonize the leech gut. Since iron and specifically heme utilization is important in this mutualistic relationship and has a potential role in virulence factor of other organisms, genomes from different Aeromonas strains (both clinical and environmental) were queried with iron utilization genes of A. veronii. This analysis revealed that in contrast to the siderophore utilization genes heme utilization genes are widely distributed among aeromonads. The importance of heme utilization in the colonization of the leech further confirms that symbiotic and pathogenic relationships possess similar mechanisms for interacting with animal hosts.
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Affiliation(s)
- Michele Maltz
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Barbara L LeVarge
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
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27
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Xu X, Shen Y, Fu J, Lu L, Li J. Next-generation sequencing identified microRNAs that associate with motile aeromonad septicemia in grass carp. FISH & SHELLFISH IMMUNOLOGY 2015; 45:94-103. [PMID: 25698074 DOI: 10.1016/j.fsi.2015.02.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Revised: 02/04/2015] [Accepted: 02/06/2015] [Indexed: 06/04/2023]
Abstract
MicroRNAs (miRNAs) modulate many biological processes and can be up-or down-regulated in a variety of diseases states, including in bacterial infection. In this study, we characterized miRNAs associated with susceptibility or resistance to motile Aeromonas hydrophila in grass carp (Ctenopharyngodon idella), a commercially important farmed fish species in China. Using Illumina next-generation sequencing, we detected 185 miRNAs in A. hydrophila-susceptible (SGC) and -resistant grass carp (RGC) during immune activation. Twenty-one miRNAs were found to be differentially expressed between SGC and RGC, with 23.8% (5 out 21) exhibiting elevated expression in SGC. Further investigation of a selected five miRNAs indicated differences in the timing and tissue sources of expression. Target genes likely regulated by these miRNAs were identified using computational prediction combined with transcriptome expression data. MiRNA targets of differentially expressed mRNAs included those with functions important for bacterial resistance, such as tlr4 and nfil3-6. In addition, we demonstrated that nfil3-6 and tlr4 genes are direct targets of let-7i and cid-miRn-118. The present study suggested that the multiple miRNAs, displaying diverse kinetics and tissue sources on antibacterial immune processes.
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Affiliation(s)
- Xiaoyan Xu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Yubang Shen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Jianjun Fu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Liqun Lu
- National Pathogen Collection Center for Aquatic Animals, College of Fisheries and Life Science, Shanghai Ocean University, 999 Huchenghuan Road, 201306 Shanghai, PR China
| | - Jiale Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China; E-Institute of Shanghai Universities, Shanghai Ocean University, 999 Huchenghuan Road, 201306 Shanghai, PR China.
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High-throughput, signature-tagged mutagenic approach to identify novel virulence factors of Yersinia pestis CO92 in a mouse model of infection. Infect Immun 2015; 83:2065-81. [PMID: 25754198 DOI: 10.1128/iai.02913-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 02/26/2015] [Indexed: 12/18/2022] Open
Abstract
The identification of new virulence factors in Yersinia pestis and understanding their molecular mechanisms during an infection process are necessary in designing a better vaccine or to formulate an appropriate therapeutic intervention. By using a high-throughput, signature-tagged mutagenic approach, we created 5,088 mutants of Y. pestis strain CO92 and screened them in a mouse model of pneumonic plague at a dose equivalent to 5 50% lethal doses (LD50) of wild-type (WT) CO92. From this screen, we obtained 118 clones showing impairment in disseminating to the spleen, based on hybridization of input versus output DNA from mutant pools with 53 unique signature tags. In the subsequent screen, 20/118 mutants exhibited attenuation at 8 LD50 when tested in a mouse model of bubonic plague, with infection by 10/20 of the aforementioned mutants resulting in 40% or higher survival rates at an infectious dose of 40 LD50. Upon sequencing, six of the attenuated mutants were found to carry interruptions in genes encoding hypothetical proteins or proteins with putative functions. Mutants with in-frame deletion mutations of two of the genes identified from the screen, namely, rbsA, which codes for a putative sugar transport system ATP-binding protein, and vasK, a component of the type VI secretion system, were also found to exhibit some attenuation at 11 or 12 LD50 in a mouse model of pneumonic plague. Likewise, among the remaining 18 signature-tagged mutants, 9 were also attenuated (40 to 100%) at 12 LD50 in a pneumonic plague mouse model. Previously, we found that deleting genes encoding Braun lipoprotein (Lpp) and acyltransferase (MsbB), the latter of which modifies lipopolysaccharide function, reduced the virulence of Y. pestis CO92 in mouse models of bubonic and pneumonic plague. Deletion of rbsA and vasK genes from either the Δlpp single or the Δlpp ΔmsbB double mutant augmented the attenuation to provide 90 to 100% survivability to mice in a pneumonic plague model at 20 to 50 LD50. The mice infected with the Δlpp ΔmsbB ΔrbsA triple mutant at 50 LD50 were 90% protected upon subsequent challenge with 12 LD50 of WT CO92, suggesting that this mutant or others carrying combinational deletions of genes identified through our screen could potentially be further tested and developed into a live attenuated plague vaccine(s).
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Draft Genome Sequences of Amoeba-Resistant Aeromonas spp. Isolated from Aquatic Environments. GENOME ANNOUNCEMENTS 2014; 2:2/5/e01115-14. [PMID: 25359918 PMCID: PMC4214994 DOI: 10.1128/genomea.01115-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Amoeba-resistant Aeromonas veronii ARB3 and Aeromonas media ARB13 and ARB20, which may be important intracellular pathogens of eukaryotic hosts, were isolated from pond and river waters. The draft genome sequences indicate that the strains harbor multiple protein secretion systems and toxins that induce disruption of the actin cytoskeleton.
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30
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Galán JE, Lara-Tejero M, Marlovits TC, Wagner S. Bacterial type III secretion systems: specialized nanomachines for protein delivery into target cells. Annu Rev Microbiol 2014; 68:415-38. [PMID: 25002086 DOI: 10.1146/annurev-micro-092412-155725] [Citation(s) in RCA: 367] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
One of the most exciting developments in the field of bacterial pathogenesis in recent years is the discovery that many pathogens utilize complex nanomachines to deliver bacterially encoded effector proteins into target eukaryotic cells. These effector proteins modulate a variety of cellular functions for the pathogen's benefit. One of these protein-delivery machines is the type III secretion system (T3SS). T3SSs are widespread in nature and are encoded not only by bacteria pathogenic to vertebrates or plants but also by bacteria that are symbiotic to plants or insects. A central component of T3SSs is the needle complex, a supramolecular structure that mediates the passage of the secreted proteins across the bacterial envelope. Working in conjunction with several cytoplasmic components, the needle complex engages specific substrates in sequential order, moves them across the bacterial envelope, and ultimately delivers them into eukaryotic cells. The central role of T3SSs in pathogenesis makes them great targets for novel antimicrobial strategies.
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Affiliation(s)
- Jorge E Galán
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536;
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31
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Abstract
Most ecosystems are populated by a large number of diversified microorganisms, which interact with one another and form complex interaction networks. In addition, some of these microorganisms may colonize the surface or internal parts of plants and animals, thereby providing an additional level of interaction complexity. These microbial relations range from intraspecific to interspecific interactions, and from simple short-term interactions to intricate long-term ones. They have played a key role in the formation of plant and animal kingdoms, often resulting in coevolution; they control the size, activity level, and diversity patterns of microbial communities. Therefore, they modulate trophic networks and biogeochemical cycles, regulate ecosystem productivity, and determine the ecology and health of plant and animal partners. A better understanding of these interactions is needed to develop microbe-based ecological engineering strategies for environmental sustainability and conservation, to improve environment-friendly approaches for feed and food production, and to address health challenges posed by infectious diseases. The main types of biotic interactions are presented: interactions between microorganisms, interactions between microorganisms and plants, and interactions between microorganisms and animals.
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Characterization of the digestive tract microbiota of Hirudo orientalis (medicinal leech) and antibiotic resistance profile. Plast Reconstr Surg 2014; 133:408e-418e. [PMID: 24572887 DOI: 10.1097/01.prs.0000438461.06217.bb] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND There are at least three distinct European leech species used medicinally: Hirudo medicinalis, H. orientalis, and H. verbana. Infection caused by leech microbiota is the most widely reported complication. Few studies have reported the culturable and unculturable bacteria and examined the antibiotic resistances in H. orientalis. METHODS Following stratified random sampling from a major worldwide leech supplier, Hirudo orientalis leeches were identified by visual comparison and amplification and sequencing the cox1 locus. Combined culture and culture-independent approaches were used to characterize the microbiota of the midgut, and bacterial gyrB sequences from distinct colonies were used to identify the Aeromonas isolates. Nonculturable studies involved clone libraries of 16S rRNA genes, and Etests were used to investigate antibiotic sensitivities. RESULTS Analysis of 16S rRNA gene clone libraries revealed the presence of several species in the intraluminal fluid of the crop, including a new finding of Morganella morganii, with Rikenella-like (35 percent) and Aeromonas veronii (38 percent) dominant members. The intestinum contained bacteria not previously isolated from the leech: Magnetospirillium species and Roseospira marina. Etests showed all A. veronii isolates were sensitive to ciprofloxacin, with either a complete or intermediate resistance to Augmentin. CONCLUSIONS The authors show diverse microbiota in the leech digestive tract. The pathogenic potential of the additional gut symbionts isolated in this study is yet to be elucidated; however, M. morganii, which is a known human pathogen, is a new finding. In addition to adding to the knowledge base regarding antibiotic sensitivities, this article serves as an update to the reconstructive surgeon regarding leech therapy.
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Maltz MA, Bomar L, Lapierre P, Morrison HG, McClure EA, Sogin ML, Graf J. Metagenomic analysis of the medicinal leech gut microbiota. Front Microbiol 2014; 5:151. [PMID: 24860552 PMCID: PMC4029005 DOI: 10.3389/fmicb.2014.00151] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/21/2014] [Indexed: 12/11/2022] Open
Abstract
There are trillions of microbes found throughout the human body and they exceed the number of eukaryotic cells by 10-fold. Metagenomic studies have revealed that the majority of these microbes are found within the gut, playing an important role in the host's digestion and nutrition. The complexity of the animal digestive tract, unculturable microbes, and the lack of genetic tools for most culturable microbes make it challenging to explore the nature of these microbial interactions within this niche. The medicinal leech, Hirudo verbana, has been shown to be a useful tool in overcoming these challenges, due to the simplicity of the microbiome and the availability of genetic tools for one of the two dominant gut symbionts, Aeromonas veronii. In this study, we utilize 16S rRNA gene pyrosequencing to further explore the microbial composition of the leech digestive tract, confirming the dominance of two taxa, the Rikenella-like bacterium and A. veronii. The deep sequencing approach revealed the presence of additional members of the microbial community that suggests the presence of a moderately complex microbial community with a richness of 36 taxa. The presence of a Proteus strain as a newly identified resident in the leech crop was confirmed using fluorescence in situ hybridization (FISH). The metagenome of this community was also pyrosequenced and the contigs were binned into the following taxonomic groups: Rikenella-like (3.1 MB), Aeromonas (4.5 MB), Proteus (2.9 MB), Clostridium (1.8 MB), Eryspelothrix (0.96 MB), Desulfovibrio (0.14 MB), and Fusobacterium (0.27 MB). Functional analyses on the leech gut symbionts were explored using the metagenomic data and MG-RAST. A comparison of the COG and KEGG categories of the leech gut metagenome to that of other animal digestive-tract microbiomes revealed that the leech digestive tract had a similar metabolic potential to the human digestive tract, supporting the usefulness of this system as a model for studying digestive-tract microbiomes. This study lays the foundation for more detailed metatranscriptomic studies and the investigation of symbiont population dynamics.
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Affiliation(s)
- Michele A Maltz
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Lindsey Bomar
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Pascal Lapierre
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Hilary G Morrison
- Marine Biological Laboratory, The Josephine Bay Paul Center Woods Hole, MA, USA
| | - Emily Ann McClure
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Mitchell L Sogin
- Marine Biological Laboratory, The Josephine Bay Paul Center Woods Hole, MA, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
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Discola KF, Förster A, Boulay F, Simorre JP, Attree I, Dessen A, Job V. Membrane and chaperone recognition by the major translocator protein PopB of the type III secretion system of Pseudomonas aeruginosa. J Biol Chem 2013; 289:3591-601. [PMID: 24297169 DOI: 10.1074/jbc.m113.517920] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The type III secretion system is a widespread apparatus used by pathogenic bacteria to inject effectors directly into the cytoplasm of eukaryotic cells. A key component of this highly conserved system is the translocon, a pore formed in the host membrane that is essential for toxins to bypass this last physical barrier. In Pseudomonas aeruginosa the translocon is composed of PopB and PopD, both of which before secretion are stabilized within the bacterial cytoplasm by a common chaperone, PcrH. In this work we characterize PopB, the major translocator, in both membrane-associated and PcrH-bound forms. By combining sucrose gradient centrifugation experiments, limited proteolysis, one-dimensional NMR, and β-lactamase reporter assays on eukaryotic cells, we show that PopB is stably inserted into bilayers with its flexible N-terminal domain and C-terminal tail exposed to the outside. In addition, we also report the crystal structure of the complex between PcrH and an N-terminal region of PopB (residues 51-59), which reveals that PopB lies within the concave face of PcrH, employing mostly backbone residues for contact. PcrH is thus the first chaperone whose structure has been solved in complex with both type III secretion systems translocators, revealing that both molecules employ the same surface for binding and excluding the possibility of formation of a ternary complex. The characterization of the major type III secretion system translocon component in both membrane-bound and chaperone-bound forms is a key step for the eventual development of antibacterials that block translocon assembly.
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Affiliation(s)
- Karen F Discola
- From the Institut de Biologie Structurale, Université Grenoble Alpes, 6 rue Jules Horowitz, 38000 Grenoble, France
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35
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Draft Genome Sequence of Aeromonas veronii Hm21, a Symbiotic Isolate from the Medicinal Leech Digestive Tract. GENOME ANNOUNCEMENTS 2013; 1:1/5/e00800-13. [PMID: 24092791 PMCID: PMC3790095 DOI: 10.1128/genomea.00800-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Aeromonas veronii strain Hm21 was isolated from the digestive tract of the medicinal leech Hirudo verbana and has been used to identify genes that are important for host colonization. This species is also a symbiont in the gut of zebrafish and is a pathogen of mammals and fish. We present here a 4.68-Mbp draft genome sequence for Hm21.
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Engel P, Moran NA. The gut microbiota of insects – diversity in structure and function. FEMS Microbiol Rev 2013; 37:699-735. [DOI: 10.1111/1574-6976.12025] [Citation(s) in RCA: 1300] [Impact Index Per Article: 118.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 05/06/2013] [Accepted: 05/13/2013] [Indexed: 02/07/2023] Open
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Weiss BL, Wang J, Maltz MA, Wu Y, Aksoy S. Trypanosome infection establishment in the tsetse fly gut is influenced by microbiome-regulated host immune barriers. PLoS Pathog 2013; 9:e1003318. [PMID: 23637607 PMCID: PMC3630092 DOI: 10.1371/journal.ppat.1003318] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 03/05/2013] [Indexed: 12/22/2022] Open
Abstract
Tsetse flies (Glossina spp.) vector pathogenic African trypanosomes, which cause sleeping sickness in humans and nagana in domesticated animals. Additionally, tsetse harbors 3 maternally transmitted endosymbiotic bacteria that modulate their host's physiology. Tsetse is highly resistant to infection with trypanosomes, and this phenotype depends on multiple physiological factors at the time of challenge. These factors include host age, density of maternally-derived trypanolytic effector molecules present in the gut, and symbiont status during development. In this study, we investigated the molecular mechanisms that result in tsetse's resistance to trypanosomes. We found that following parasite challenge, young susceptible tsetse present a highly attenuated immune response. In contrast, mature refractory flies express higher levels of genes associated with humoral (attacin and pgrp-lb) and epithelial (inducible nitric oxide synthase and dual oxidase) immunity. Additionally, we discovered that tsetse must harbor its endogenous microbiome during intrauterine larval development in order to present a parasite refractory phenotype during adulthood. Interestingly, mature aposymbiotic flies (Gmm(Apo)) present a strong immune response earlier in the infection process than do WT flies that harbor symbiotic bacteria throughout their entire lifecycle. However, this early response fails to confer significant resistance to trypanosomes. Gmm(Apo) adults present a structurally compromised peritrophic matrix (PM), which lines the fly midgut and serves as a physical barrier that separates luminal contents from immune responsive epithelial cells. We propose that the early immune response we observe in Gmm(Apo) flies following parasite challenge results from the premature exposure of gut epithelia to parasite-derived immunogens in the absence of a robust PM. Thus, tsetse's PM appears to regulate the timing of host immune induction following parasite challenge. Our results document a novel finding, which is the existence of a positive correlation between tsetse's larval microbiome and the integrity of the emerging adult PM gut immune barrier.
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Affiliation(s)
- Brian L Weiss
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America.
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Knowing your friends: invertebrate innate immunity fosters beneficial bacterial symbioses. Nat Rev Microbiol 2012; 10:815-27. [PMID: 23147708 DOI: 10.1038/nrmicro2894] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The innate immune system is present in all animals and is a crucial first line of defence against pathogens. However, animals also harbour large numbers of beneficial microorganisms that can be housed in the digestive tract, in specialized organs or on tissue surfaces. Although invertebrates lack conventional antibody-based immunity, they are capable of eliminating pathogens and, perhaps more importantly, discriminating them from other microorganisms. This Review examines the interactions between the innate immune systems of several model invertebrates and the symbionts of these organisms, and addresses the central question of how these long-lived and specific associations are established and maintained.
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Bomar L, Graf J. Investigation into the physiologies of Aeromonas veronii in vitro and inside the digestive tract of the medicinal leech using RNA-seq. THE BIOLOGICAL BULLETIN 2012; 223:155-166. [PMID: 22983040 PMCID: PMC3732745 DOI: 10.1086/bblv223n1p155] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Host-associated microbial communities are widespread in nature and vital to the health and fitness of the host. Deciphering the physiology of the microbiome in vivo is critical to understanding the molecular basis of the symbiosis. Recently, the development and application of high-throughput sequencing techniques, particularly RNA-seq, for studying microbial communities has enabled researchers to address not only which microbes are present in a given community but also how the community functions. For microbes that can also be cultivated in the laboratory, RNA-seq provides the opportunity to identify genes that are differentially expressed during symbiosis by comparing in vitro to in vivo transcriptomes. In the current study, we used RNA-seq to identify genes expressed by the digestive-tract microbiome of the medicinal leech, Hirudo verbana, and by one of the two dominant symbionts, Aeromonas veronii, in a rich medium. We used a comparative approach to identify genes differentially expressed during symbiosis and gain insight into the symbiont's physiology in vivo. Notable findings include evidence for the symbionts experiencing environmental stress, performing arginine catabolism, and expressing noncoding RNAs that are implicated in stationary phase survival, a state in which A. veronii persists for months within the host.
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Affiliation(s)
| | - Joerg Graf
- To whom correspondence should be addressed.
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Abstract
Gastrointestinal microbiomes play important roles in the health and nutrition of animals and humans. The medicinal leech, Hirudo verbana, serves as a powerful model for the study of microbial symbioses of the gut, due to its naturally limited microbiome compared with other popular models, the ability to cultivate the most abundant microbes, and genetically manipulate one of them, Aeromonas veronii. This review covers the relevance and application of leeches in modern medicine as well as recent discoveries detailing the nature of the gut microbiome. Additionally, the dual life-style of A. veronii allows one to do direct comparisons between colonization factors for beneficial and pathogenic associations, and relevant findings are detailed with respect to their role within the host and pathogenicity to other animals.
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Collins AJ, Schleicher TR, Rader BA, Nyholm SV. Understanding the role of host hemocytes in a squid/vibrio symbiosis using transcriptomics and proteomics. Front Immunol 2012; 3:91. [PMID: 22590467 PMCID: PMC3349304 DOI: 10.3389/fimmu.2012.00091] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 04/08/2012] [Indexed: 11/13/2022] Open
Abstract
The symbiosis between the squid, Euprymna scolopes, and the bacterium, Vibrio fischeri, serves as a model for understanding interactions between beneficial bacteria and animal hosts. The establishment and maintenance of the association is highly specific and depends on the selection of V. fischeri and exclusion of non-symbiotic bacteria from the environment. Current evidence suggests that the host's cellular innate immune system, in the form of macrophage-like hemocytes, helps to mediate host tolerance of V. fischeri. To begin to understand the role of hemocytes in this association, we analyzed these cells by high-throughput 454 transcriptomic and liquid chromatography/tandem mass spectrometry (LC-MS/MS) proteomic analyses. 454 high-throughput sequencing produced 650, 686 reads totaling 279.9 Mb while LC-MS/MS analyses of circulating hemocytes putatively identified 702 unique proteins. Several receptors involved with the recognition of microbial-associated molecular patterns were identified. Among these was a complete open reading frame to a putative peptidoglycan recognition protein (EsPGRP5) with conserved residues for amidase activity. Assembly of the hemocyte transcriptome showed EsPGRP5 had high coverage, suggesting it is among the 5% most abundant transcripts in circulating hemocytes. Other transcripts and proteins identified included members of the conserved NF-κB signaling pathway, putative members of the complement pathway, the carbohydrate binding protein galectin, and cephalotoxin. Quantitative Real-Time PCR of complement-like genes, cephalotoxin, EsPGRP5, and a nitric oxide synthase showed differential expression in circulating hemocytes from adult squid with colonized light organs compared to those isolated from hosts where the symbionts were removed. These data suggest that the presence of the symbiont influences gene expression of the cellular innate immune system of E. scolopes.
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Affiliation(s)
- Andrew J Collins
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
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Aujoulat F, Roger F, Bourdier A, Lotthé A, Lamy B, Marchandin H, Jumas-Bilak E. From environment to man: genome evolution and adaptation of human opportunistic bacterial pathogens. Genes (Basel) 2012; 3:191-232. [PMID: 24704914 PMCID: PMC3899952 DOI: 10.3390/genes3020191] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 02/29/2012] [Accepted: 02/29/2012] [Indexed: 02/07/2023] Open
Abstract
Environment is recognized as a huge reservoir for bacterial species and a source of human pathogens. Some environmental bacteria have an extraordinary range of activities that include promotion of plant growth or disease, breakdown of pollutants, production of original biomolecules, but also multidrug resistance and human pathogenicity. The versatility of bacterial life-style involves adaptation to various niches. Adaptation to both open environment and human specific niches is a major challenge that involves intermediate organisms allowing pre-adaptation to humans. The aim of this review is to analyze genomic features of environmental bacteria in order to explain their adaptation to human beings. The genera Pseudomonas, Aeromonas and Ochrobactrum provide valuable examples of opportunistic behavior associated to particular genomic structure and evolution. Particularly, we performed original genomic comparisons among aeromonads and between the strictly intracellular pathogens Brucella spp. and the mild opportunistic pathogens Ochrobactrum spp. We conclude that the adaptation to human could coincide with a speciation in action revealed by modifications in both genomic and population structures. This adaptation-driven speciation could be a major mechanism for the emergence of true pathogens besides the acquisition of specialized virulence factors.
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Affiliation(s)
- Fabien Aujoulat
- Université Montpellier 1, UMR 5119 (UM2, CNRS, IRD, IFREMER, UM1), équipe Pathogènes et Environnements, Montpellier 34093, France.
| | - Frédéric Roger
- Université Montpellier 1, UMR 5119 (UM2, CNRS, IRD, IFREMER, UM1), équipe Pathogènes et Environnements, Montpellier 34093, France.
| | - Alice Bourdier
- Université Montpellier 1, UMR 5119 (UM2, CNRS, IRD, IFREMER, UM1), équipe Pathogènes et Environnements, Montpellier 34093, France.
| | - Anne Lotthé
- Université Montpellier 1, UMR 5119 (UM2, CNRS, IRD, IFREMER, UM1), équipe Pathogènes et Environnements, Montpellier 34093, France.
| | - Brigitte Lamy
- Université Montpellier 1, UMR 5119 (UM2, CNRS, IRD, IFREMER, UM1), équipe Pathogènes et Environnements, Montpellier 34093, France.
| | - Hélène Marchandin
- Université Montpellier 1, UMR 5119 (UM2, CNRS, IRD, IFREMER, UM1), équipe Pathogènes et Environnements, Montpellier 34093, France.
| | - Estelle Jumas-Bilak
- Université Montpellier 1, UMR 5119 (UM2, CNRS, IRD, IFREMER, UM1), équipe Pathogènes et Environnements, Montpellier 34093, France.
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Swiatczak B, Rescigno M, Cohen IR. Systemic features of immune recognition in the gut. Microbes Infect 2011; 13:983-91. [DOI: 10.1016/j.micinf.2011.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 06/23/2011] [Accepted: 06/24/2011] [Indexed: 12/15/2022]
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Silver A, Graf J. Innate and procured immunity inside the digestive tract of the medicinal leech. INVERTEBRATE SURVIVAL JOURNAL : ISJ 2011; 8:173-178. [PMID: 22461860 PMCID: PMC3313596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Especially when combined with unique biological adaptations, invertebrate animals provide important insights into innate immunity because the immune response is not complicated by adaptive immunity that vertebrates evolved. One such example is the digestive tract of the medicinal leech, Hirudo verbana, which is unusual in two aspects, it contains a simple microbial community and it stores large amounts of vertebrate blood for a several months. In this review we will discuss aspects of the innate immunity of the leech and from the ingested blood that we term procured immunity to differentiate it from the immunity encoded by the leech genome.
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Affiliation(s)
- Ac Silver
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
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Bomar L, Maltz M, Colston S, Graf J. Directed culturing of microorganisms using metatranscriptomics. mBio 2011; 2:e00012-11. [PMID: 21467263 PMCID: PMC3069634 DOI: 10.1128/mbio.00012-11] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 03/08/2011] [Indexed: 12/16/2022] Open
Abstract
UNLABELLED The vast majority of bacterial species remain uncultured, and this severely limits the investigation of their physiology, metabolic capabilities, and role in the environment. High-throughput sequencing of RNA transcripts (RNA-seq) allows the investigation of the diverse physiologies from uncultured microorganisms in their natural habitat. Here, we report the use of RNA-seq for characterizing the metatranscriptome of the simple gut microbiome from the medicinal leech Hirudo verbana and for utilizing this information to design a medium for cultivating members of the microbiome. Expression data suggested that a Rikenella-like bacterium, the most abundant but uncultured symbiont, forages on sulfated- and sialated-mucin glycans that are fermented, leading to the secretion of acetate. Histological stains were consistent with the presence of sulfated and sialated mucins along the crop epithelium. The second dominant symbiont, Aeromonas veronii, grows in two different microenvironments and is predicted to utilize either acetate or carbohydrates. Based on the metatranscriptome, a medium containing mucin was designed, which enabled the cultivation of the Rikenella-like bacterium. Metatranscriptomes shed light on microbial metabolism in situ and provide critical clues for directing the culturing of uncultured microorganisms. By choosing a condition under which the desired organism is rapidly proliferating and focusing on highly expressed genes encoding hydrolytic enzymes, binding proteins, and transporters, one can identify an organism's nutritional preferences and design a culture medium. IMPORTANCE The number of prokaryotes on the planet has been estimated to exceed 10(30) cells, and the overwhelming majority of them have evaded cultivation, making it difficult to investigate their ecological, medical, and industrial relevance. The application of transcriptomics based on high-throughput sequencing of RNA transcripts (RNA-seq) to microorganisms in their natural environment can provide investigators with insight into their physiologies under optimal growth conditions. We utilized RNA-seq to learn more about the uncultured and cultured symbionts that comprise the relatively simple digestive-tract microbiome of the medicinal leech. The expression data revealed highly expressed hydrolytic enzymes and transporters that provided critical clues for the design of a culture medium enabling the isolation of the previously uncultured Rikenella-like symbiont. This directed culturing method will greatly aid efforts aimed at understanding uncultured microorganisms, including beneficial symbionts, pathogens, and ecologically relevant microorganisms, by facilitating genome sequencing, physiological characterization, and genetic manipulation of the previously uncultured microbes.
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Affiliation(s)
- Lindsey Bomar
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | | | - Sophie Colston
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
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Sachs JL, Essenberg CJ, Turcotte MM. New paradigms for the evolution of beneficial infections. Trends Ecol Evol 2011; 26:202-9. [PMID: 21371775 DOI: 10.1016/j.tree.2011.01.010] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 01/24/2011] [Accepted: 01/25/2011] [Indexed: 10/18/2022]
Abstract
A longstanding paradigm predicts that microbial parasites and mutualists exhibit disparate evolutionary patterns. Parasites are predicted to promote arms races with hosts, rapid evolution and sexual recombination. By contrast, mutualists have been linked with beneficial coadaptation, evolutionary stasis and asexuality. In this review we discuss the recent surge of molecular data on microbes that are being used to test and reshape these ideas. New analyses reveal that beneficial microbes often share mechanisms of infection and defense with parasites, and can also exhibit rapid evolution and extensive genetic exchange. To explain these patterns, new paradigms must take into account the varied population biology of beneficial microbes, their potential conflicts with hosts, and the mosaic nature of genome evolution that requires locus-based tests to analyze the genetics of host adaptation.
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Affiliation(s)
- Joel L Sachs
- Department of Biology, University of California, Riverside, CA 92521, USA.
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Complex evolutionary history of the Aeromonas veronii group revealed by host interaction and DNA sequence data. PLoS One 2011; 6:e16751. [PMID: 21359176 PMCID: PMC3040217 DOI: 10.1371/journal.pone.0016751] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 01/10/2011] [Indexed: 12/23/2022] Open
Abstract
Aeromonas veronii biovar sobria, Aeromonas veronii biovar veronii, and Aeromonas allosaccharophila are a closely related group of organisms, the Aeromonas veronii Group, that inhabit a wide range of host animals as a symbiont or pathogen. In this study, the ability of various strains to colonize the medicinal leech as a model for beneficial symbiosis and to kill wax worm larvae as a model for virulence was determined. Isolates cultured from the leech out-competed other strains in the leech model, while most strains were virulent in the wax worms. Three housekeeping genes, recA, dnaJ and gyrB, the gene encoding chitinase, chiA, and four loci associated with the type three secretion system, ascV, ascFG, aexT, and aexU were sequenced. The phylogenetic reconstruction failed to produce one consensus tree that was compatible with most of the individual genes. The Approximately Unbiased test and the Genetic Algorithm for Recombination Detection both provided further support for differing evolutionary histories among this group of genes. Two contrasting tests detected recombination within aexU, ascFG, ascV, dnaJ, and gyrB but not in aexT or chiA. Quartet decomposition analysis indicated a complex recent evolutionary history for these strains with a high frequency of horizontal gene transfer between several but not among all strains. In this study we demonstrate that at least for some strains, horizontal gene transfer occurs at a sufficient frequency to blur the signal from vertically inherited genes, despite strains being adapted to distinct niches. Simply increasing the number of genes included in the analysis is unlikely to overcome this challenge in organisms that occupy multiple niches and can exchange DNA between strains specialized to different niches. Instead, the detection of genes critical in the adaptation to specific niches may help to reveal the physiological specialization of these strains.
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Noonin C, Jiravanichpaisal P, Söderhäll I, Merino S, Tomás JM, Söderhäll K. Melanization and pathogenicity in the insect, Tenebrio molitor, and the crustacean, Pacifastacus leniusculus, by Aeromonas hydrophila AH-3. PLoS One 2010; 5:e15728. [PMID: 21206752 PMCID: PMC3012084 DOI: 10.1371/journal.pone.0015728] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 11/22/2010] [Indexed: 12/27/2022] Open
Abstract
Aeromonas hydrophila is the most common Aeromonas species causing infections in human and other animals such as amphibians, reptiles, fish and crustaceans. Pathogenesis of Aeromonas species have been reported to be associated with virulence factors such as lipopolysaccharides (LPS), bacterial toxins, bacterial secretion systems, flagella, and other surface molecules. Several mutant strains of A. hydrophila AH-3 were initially used to study their virulence in two animal species, Pacifastacus leniusculus (crayfish) and Tenebrio molitor larvae (mealworm). The AH-3 strains used in this study have mutations in genes involving the synthesis of flagella, LPS structures, secretion systems, and some other factors, which have been reported to be involved in A. hydrophila pathogenicity. Our study shows that the LPS (O-antigen and external core) is the most determinant A. hydrophila AH-3 virulence factor in both animals. Furthermore, we studied the immune responses of these hosts to infection of virulent or non-virulent strains of A. hydrophila AH-3. The AH-3 wild type (WT) containing the complete LPS core is highly virulent and this bacterium strongly stimulated the prophenoloxidase activating system resulting in melanization in both crayfish and mealworm. In contrast, the ΔwaaE mutant which has LPS without O-antigen and external core was non-virulent and lost ability to stimulate this system and melanization in these two animals. The high phenoloxidase activity found in WT infected crayfish appears to result from a low expression of pacifastin, a prophenoloxidase activating enzyme inhibitor, and this gene expression was not changed in the ΔwaaE mutant infected animal and consequently phenoloxidase activity was not altered as compared to non-infected animals. Therefore we show that the virulence factors of A. hydrophila are the same regardless whether an insect or a crustacean is infected and the O-antigen and external core is essential for activation of the proPO system and as virulence factors for this bacterium.
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Affiliation(s)
- Chadanat Noonin
- Department of Comparative Physiology, Uppsala University, Uppsala, Sweden
| | - Pikul Jiravanichpaisal
- Department of Comparative Physiology, Uppsala University, Uppsala, Sweden
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, Thailand
| | - Irene Söderhäll
- Department of Comparative Physiology, Uppsala University, Uppsala, Sweden
| | - Susana Merino
- Departamento de Microbiología, Facultad de Biología, Universidad de Barcelona, Barcelona, Spain
| | - Juan M. Tomás
- Departamento de Microbiología, Facultad de Biología, Universidad de Barcelona, Barcelona, Spain
| | - Kenneth Söderhäll
- Department of Comparative Physiology, Uppsala University, Uppsala, Sweden
- * E-mail:
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The type II secretion system is essential for erythrocyte lysis and gut colonization by the leech digestive tract symbiont Aeromonas veronii. Appl Environ Microbiol 2010; 77:597-603. [PMID: 21097598 DOI: 10.1128/aem.01621-10] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hemolysin and the type II secretion system (T2SS) have been shown to be important for virulence in many pathogens, but very few studies have shown their importance in beneficial microbes. Here, we investigated the importance of the type II secretion pathway in the beneficial digestive-tract association of Aeromonas veronii and the medicinal leech Hirudo verbana and revealed a critical role for the hemolysis of erythrocytes. A mutant with a miniTn5 insertion in exeM, which is involved in forming the inner membrane platform in the T2SS, was isolated by screening mutants for loss of hemolysis on blood agar plates. A hemolysis assay was used to quantify the mutant's deficiency in lysing sheep erythrocytes and revealed a 99.9% decrease compared to the parent strain. The importance of the T2SS in the colonization of the symbiotic host was assessed. Colonization assays revealed that the T2SS is critical for initial colonization of the leech gut. The defect was tied to the loss of hemolysin production by performing a colonization assay with blood containing lysed erythrocytes. This restored the colonization defect in the mutant. Complementation of the mutant using the promoter region and exeMN revealed that the T2SS is responsible for secreting hemolysin into the extracellular space and that both the T2SS and hemolysin export by the T2SS are critical for initial establishment of A. veronii in the leech gut.
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McCoy AJ, Koizumi Y, Higa N, Suzuki T. Differential Regulation of Caspase-1 Activation via NLRP3/NLRC4 Inflammasomes Mediated by Aerolysin and Type III Secretion System during Aeromonas veronii Infection. THE JOURNAL OF IMMUNOLOGY 2010; 185:7077-84. [DOI: 10.4049/jimmunol.1002165] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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