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Maltz-Matyschsyk M, Melchiorre CK, Knecht DA, Lynes MA. Bacterial metallothionein, PmtA, a novel stress protein found on the bacterial surface of Pseudomonas aeruginosa and involved in management of oxidative stress and phagocytosis. mSphere 2024; 9:e0021024. [PMID: 38712943 DOI: 10.1128/msphere.00210-24] [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: 03/14/2024] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
Metallothioneins (MTs) are small cysteine-rich proteins that play important roles in homeostasis and protection against heavy metal toxicity and oxidative stress. The opportunistic pathogen, Pseudomonas aeruginosa, expresses a bacterial MT known as PmtA. Utilizing genetically modified P. aeruginosa PAO1 strains (a human clinical wound isolate), we show that inducing pmtA increases levels of pyocyanin and biofilm compared to other PAO1 isogenic strains, supporting previous results that pmtA is important for pyocyanin and biofilm production. We also show that overexpression of pmtA in vitro provides protection for cells exposed to oxidants, which is a characteristic of inflammation, indicating a role for PmtA as an antioxidant in inflammation. We found that a pmtA clean deletion mutant is phagocytized faster than other PAO1 isogenic strains in THP-1 human macrophage cells, indicating that PmtA provides protection from the phagocytic attack. Interestingly, we observed that monoclonal anti-PmtA antibody binds to PmtA, which is accessible on the surface of PAO1 strains using both flow cytometry and enzyme-linked immunosorbent assay techniques. Finally, we investigated intracellular persistence of these PAO1 strains within THP-1 macrophages cells and found that the phagocytic endurance of PAO1 strains is affected by pmtA expression. These data show for the first time that a bacterial MT (pmtA) can play a role in the phagocytic process and can be found on the outer surface of PAO1. Our results suggest that PmtA plays a role both in protection from oxidative stress and in the resistance to the host's innate immune response, identifying PmtA as a potential therapeutic target in P. aeruginosa infection. IMPORTANCE The pathogen Pseudomonas aeruginosa is a highly problematic multidrug-resistant (MDR) pathogen with complex virulence networks. MDR P. aeruginosa infections have been associated with increased clinical visits, very poor healthcare outcomes, and these infections are ranked as critical on priority lists of both the Centers for Disease Control and Prevention and the World Health Organization. Known P. aeruginosa virulence factors have been extensively studied and are implicated in counteracting host defenses, causing direct damage to the host tissues, and increased microbial competitiveness. Targeting virulence factors has emerged as a new line of defense in the battle against MDR P. aeruginosa strains. Bacterial metallothionein is a newly recognized virulence factor that enables evasion of the host immune response. The studies described here identify mechanisms in which bacterial metallothionein (PmtA) plays a part in P. aeruginosa pathogenicity and identifies PmtA as a potential therapeutic target.
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Affiliation(s)
| | - Clare K Melchiorre
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - David A Knecht
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Michael A Lynes
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
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Zheng S, Tang X, Yang Q, Zhou X, Li Y, Wu Z. Aeromonas veronii tolC modulates its virulence and the immune response of freshwater pearl mussels, Hyriopsis cumingii. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 153:105137. [PMID: 38224762 DOI: 10.1016/j.dci.2024.105137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 01/17/2024]
Abstract
Aeromonas veronii is an opportunistic pathogen that causes diseases in aquatic animals, but its key virulence factors remain unclear. We screened the gene tolC with significantly different expression levels in the two isolates, A. veronii GL2 (higher virulence) and A. veronii FO1 (lower virulence). Therefore, we constructed mutant strain ΔtolC and analyzed its immunological properties. ΔtolC exhibited the reduced ability of biofilms formation, inhibited envelope stress response mediated by several antibiotics except cefuroxime, implying the ability to evade host immunity might be restrained. Challenge tests showed that the LD50 of ΔtolC was 10.89-fold than that of GL2. Enzymatic activities of ΔtolC group were significantly lower and peak time was delayed to 12 h, as demonstrated by qRT-PCR results. Histopathological examination displayed that the degree of tissue damage in ΔtolC group was alleviated. The results show that tolC is an important virulence factor of A. veronii, which provides references for live-attenuated vaccine.
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Affiliation(s)
- Sichun Zheng
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), and Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing, 400715, China
| | - Xiaoqi Tang
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), and 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), and Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing, 400715, China
| | - Xicheng Zhou
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), and 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), and 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), and Research Center for Aquatic Biodiversity Conservation in the Upper Reaches of Yangtze River, Southwest University, Chongqing, 400715, China.
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Maire J, Philip GK, Livingston J, Judd LM, Blackall LL, van Oppen MJH. Functional potential and evolutionary response to long-term heat selection of bacterial associates of coral photosymbionts. mSystems 2023; 8:e0086023. [PMID: 37909753 PMCID: PMC10746172 DOI: 10.1128/msystems.00860-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Symbiotic microorganisms are crucial for the survival of corals and their resistance to coral bleaching in the face of climate change. However, the impact of microbe-microbe interactions on coral functioning is mostly unknown but could be essential factors for coral adaption to future climates. Here, we investigated interactions between cultured dinoflagellates of the Symbiodiniaceae family, essential photosymbionts of corals, and associated bacteria. By assessing the genomic potential of 49 bacteria, we found that they are likely beneficial for Symbiodiniaceae, through the production of B vitamins and antioxidants. Additionally, bacterial genes involved in host-symbiont interactions, such as secretion systems, accumulated mutations following long-term exposure to heat, suggesting symbiotic interactions may change under climate change. This highlights the importance of microbe-microbe interactions in coral functioning.
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Affiliation(s)
- Justin Maire
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Gayle K. Philip
- Melbourne Bioinformatics, The University of Melbourne, Parkville, Victoria, Australia
| | - Jadzia Livingston
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Louise M. Judd
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Linda L. Blackall
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Madeleine J. H. van Oppen
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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,*Correspondence: Shana K. Goffredi, ✉
| | - 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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Banse AV, VanBeuge S, Smith TJ, Logan SL, Guillemin K. Secreted Aeromonas GlcNAc binding protein GbpA stimulates epithelial cell proliferation in the zebrafish intestine. Gut Microbes 2023; 15:2183686. [PMID: 36859771 PMCID: PMC9988336 DOI: 10.1080/19490976.2023.2183686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/19/2022] [Accepted: 02/16/2023] [Indexed: 03/03/2023] Open
Abstract
In response to microbiota colonization, the intestinal epithelia of many animals exhibit increased rates of cell proliferation. We used gnotobiotic larval zebrafish to identify a secreted factor from the mutualist Aeromonas veronii that is sufficient to promote intestinal epithelial cell proliferation. This secreted A. veronii protein is a homologue of the Vibrio cholerae GlcNAc binding protein GbpA, which was identified as a chitin-binding colonization factor in mice. GbpA was subsequently shown to be a lytic polysaccharide monooxygenase (LPMO) that can degrade recalcitrant chitin. Our phenotypic characterization of gbpA deficient A. veronii found no alterations in these cells' biogeography in the zebrafish intestine and only a modest competitive disadvantage in chitin-binding and colonization fitness when competed against the wild-type strain. These results argue against the model of GbpA being a secreted adhesin that binds simultaneously to bacterial cells and GlcNAc, and instead suggests that GbpA is part of a bacterial GlcNAc utilization program. We show that the host proliferative response to GbpA occurs in the absence of bacteria upon exposure of germ-free zebrafish to preparations of native GbpA secreted from either A. veronii or V. cholerae or recombinant A. veronii GbpA. Furthermore, domain 1 of A. veronii GbpA, containing the predicted LPMO activity, is sufficient to stimulate intestinal epithelial proliferation. We propose that intestinal epithelial tissues upregulate their rates of renewal in response to secreted bacterial GbpA proteins as an adaptive strategy for coexisting with bacteria that can degrade glycan constituents of the protective intestinal lining.
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Affiliation(s)
- Allison V. Banse
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Stephanie VanBeuge
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - T. Jarrod Smith
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | | | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
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Ulhuq FR, Mariano G. Bacterial pore-forming toxins. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001154. [PMID: 35333704 PMCID: PMC9558359 DOI: 10.1099/mic.0.001154] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/03/2022] [Indexed: 12/11/2022]
Abstract
Pore-forming toxins (PFTs) are widely distributed in both Gram-negative and Gram-positive bacteria. PFTs can act as virulence factors that bacteria utilise in dissemination and host colonisation or, alternatively, they can be employed to compete with rival microbes in polymicrobial niches. PFTs transition from a soluble form to become membrane-embedded by undergoing large conformational changes. Once inserted, they perforate the membrane, causing uncontrolled efflux of ions and/or nutrients and dissipating the protonmotive force (PMF). In some instances, target cells intoxicated by PFTs display additional effects as part of the cellular response to pore formation. Significant progress has been made in the mechanistic description of pore formation for the different PFTs families, but in several cases a complete understanding of pore structure remains lacking. PFTs have evolved recognition mechanisms to bind specific receptors that define their host tropism, although this can be remarkably diverse even within the same family. Here we summarise the salient features of PFTs and highlight where additional research is necessary to fully understand the mechanism of pore formation by members of this diverse group of protein toxins.
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Affiliation(s)
- Fatima R. Ulhuq
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Giuseppina Mariano
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
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Pan-Genome Analysis of Delftia tsuruhatensis Reveals Important Traits Concerning the Genetic Diversity, Pathogenicity, and Biotechnological Properties of the Species. Microbiol Spectr 2022; 10:e0207221. [PMID: 35230132 PMCID: PMC9045143 DOI: 10.1128/spectrum.02072-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Delftia tsuruhatensis strains have long been known to promote plant growth and biological control. Recently, it has become an emerging opportunistic pathogen in humans. However, the genomic characteristics of the genetic diversity, pathogenicity, and biotechnological properties have not yet been comprehensively investigated. Here, a comparative pan-genome analysis was constructed. The open pan-genome with a large and flexible gene repertoire exhibited a high degree of genetic diversity. The purifying selection was the main force to drive pan-genome evolution. Significant differences were observed in the evolutionary relationship, functional enrichment, and degree of selective pressure between the different components of the pan-genome. A high degree of genetic plasticity was characterized by the determinations of diverse mobile genetic elements (MGEs), massive genomic rearrangement, and horizontal genes. Horizontal gene transfer (HGT) plays an important role in the genetic diversity of this bacterium and the formation of genomic traits. Our results revealed the occurrence of diverse virulence-related elements associated with macromolecular secretion systems, virulence factors associated with multiple nosocomial infections, and antimicrobial resistance, indicating the pathogenic potential. Lateral flagellum, T1SS, T2SS, T6SS, Tad pilus, type IV pilus, and a part of virulence-related genes exhibited general properties, whereas polar flagellum, T4SS, a part of virulence-related genes, and resistance genes presented heterogeneous properties. The pan-genome also harbors abundant genetic traits related to secondary metabolism, carbohydrate active enzymes (CAZymes), and phosphate transporter, indicating rhizosphere adaptation, plant growth promotion, and great potential uses in agriculture and biological control. This study provides comprehensive insights into this uncommon species from the genomic perspective. IMPORTANCED. tsuruhatensis is considered a plant growth-promoting rhizobacterium (PGPR), an organic pollutant degradation strain, and an emerging opportunistic pathogen to the human. However, the genetic diversity, the evolutionary dynamics, and the genetic basis of these remarkable traits are still little known. We constructed a pan-genome analysis for D. tsuruhatensis and revealed extensive genetic diversity and genetic plasticity exhibited by open pan-genome, diverse mobile genetic elements (MGEs), genomic rearrangement, and horizontal genes. Our results highlight that horizontal gene transfer (HGT) and purifying selection are important forces in D. tsuruhatensis genetic evolution. The abundant virulence-related elements associated with macromolecular secretion systems, virulence factors, and antimicrobial resistance could contribute to the pathogenicity of this bacterium. Therefore, clinical microbiologists need to be aware of D. tsuruhatensis as an opportunistic pathogen. The genetic profiles of secondary metabolism, carbohydrate active enzymes (CAZymes), and phosphate transporter could provide insight into the genetic armory of potential applications for agriculture and biological control of D. tsuruhatensis in general.
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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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Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides. mSystems 2020; 5:5/5/e00448-20. [PMID: 32934114 PMCID: PMC7498682 DOI: 10.1128/msystems.00448-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements. Plesiomonas shigelloides is an emerging pathogen that has been shown to be involved in gastrointestinal diseases and extraintestinal infections in humans. However, the taxonomic position, evolutionary dynamics, and pathogenesis of P. shigelloides remain unclear. We reported the draft genome sequences of 12 P. shigelloides strains representing different serogroups. We were able to determine a clear distinction between P. shigelloides and other members of Enterobacterales via core genome phylogeny, Neighbor-Net network, and average genome identity analysis. The pan-genome analysis of P. shigelloides revealed extensive genetic diversity and presented large flexible gene repertoires, while the core genome phylogeny exhibited a low level of clonality. The discordance between the core genome phylogeny and the pan-genome phylogeny indicated that flexible accessory genomes account for an important proportion of the evolution of P. shigelloides, which was subsequently characterized by determinations of hundreds of horizontally transferred genes (horizontal genes), massive gene expansions and contractions, and diverse mobile genetic elements (MGEs). The apparently high levels of horizontal gene transfer (HGT) in P. shigelloides were conferred from bacteria with novel properties from other taxa (mainly Vibrionaceae and Aeromonadaceae), which caused the historical taxonomic confusion and shaped the virulence gene pools. Furthermore, P. shigelloides genomes contain many macromolecular secretion system genes, virulence factor genes, and resistance genes, indicating its potential to cause intestinal and invasive infections. Collectively, our work provides insights into the phylogenetic position, evolutionary dynamic, and pathogenesis of P. shigelloides at the genomic level, which could facilitate the observation and research of this important pathogen. IMPORTANCE The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.
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Sass K, Güllert S, Streit WR, Perner M. A hydrogen-oxidizing bacterium enriched from the open ocean resembling a symbiont. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:396-405. [PMID: 32338395 DOI: 10.1111/1758-2229.12847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 03/31/2020] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
A new autotrophic hydrogen-oxidizing Chromatiaceae bacterium, namely bacterium CTD079, was enriched from a water column sample at 1500 m water depth in the southern Pacific Ocean. Based on the phylogeny of 16S rRNA genes, it was closely related to a scaly snail endosymbiont (99.2% DNA sequence identity) whose host so far is only known to colonize hydrothermal vents along the Indian ridge. The average nucleotide identity between the genomes of CTD079 and the snail endosymbiont was 91%. The observed differences likely reflect adaptations to their specific habitats. For example, CTD079 encodes additional enzymes like the formate dehydrogenase increasing the organism's spectrum of energy generation pathways. Other additional physiological features of CTD079 included the increase of viral defence strategies, secretion systems and specific transporters for essential elements. These important genome characteristics suggest an adaptation to life in the open ocean.
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Affiliation(s)
- Katharina Sass
- Molecular Biology of Microbial Consortia, Universität Hamburg, Hamburg, Germany
- Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Simon Güllert
- Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Wolfgang R Streit
- Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Mirjam Perner
- Molecular Biology of Microbial Consortia, Universität Hamburg, Hamburg, Germany
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12
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Lemke S, Vilcinskas A. European Medicinal Leeches-New Roles in Modern Medicine. Biomedicines 2020; 8:biomedicines8050099. [PMID: 32349294 PMCID: PMC7277884 DOI: 10.3390/biomedicines8050099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/18/2020] [Accepted: 04/24/2020] [Indexed: 11/16/2022] Open
Abstract
Before the advent of modern medicine, natural resources were widely used by indigenous populations for the prevention and treatment of diseases. The associated knowledge, collectively described as folk medicine or traditional medicine, was largely based on trial-and-error testing of plant extracts (herbal remedies) and the use of invertebrates, particularly medicinal maggots of the blowfly Lucilia sericata and blood-sucking leeches. The widespread use of traditional medicine in the West declined as scientific advances allowed reproducible testing under controlled conditions and gave rise to the modern fields of biomedical research and pharmacology. However, many drugs are still derived from natural resources, and interest in traditional medicine has been renewed by the ability of researchers to investigate the medical potential of diverse species by high-throughput screening. Likewise, researchers are starting to look again at the benefits of maggot and leech therapy, based on the hypothesis that the use of such animals in traditional medicine is likely to reflect the presence of specific bioactive molecules that can be developed as drug leads. In this review, we consider the modern medical benefits of European medicinal leeches based on the systematic screening of their salivary proteins.
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Affiliation(s)
- Sarah Lemke
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany;
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany;
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Department of Bioresources, Ohlebergsweg 12, D-35392 Giessen, Germany
- Correspondence:
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13
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Hegde S, Nilyanimit P, Kozlova E, Anderson ER, Narra HP, Sahni SK, Heinz E, Hughes GL. CRISPR/Cas9-mediated gene deletion of the ompA gene in symbiotic Cedecea neteri impairs biofilm formation and reduces gut colonization of Aedes aegypti mosquitoes. PLoS Negl Trop Dis 2019; 13:e0007883. [PMID: 31790395 PMCID: PMC6907859 DOI: 10.1371/journal.pntd.0007883] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 12/12/2019] [Accepted: 10/26/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Symbiotic bacteria are pervasive in mosquitoes and their presence can influence many host phenotypes that affect vectoral capacity. While it is evident that environmental and host genetic factors contribute in shaping the microbiome of mosquitoes, we have a poor understanding regarding how bacterial genetics affects colonization of the mosquito gut. The CRISPR/Cas9 gene editing system is a powerful tool to alter bacterial genomes facilitating investigations into host-microbe interactions but has yet to be applied to insect symbionts. METHODOLOGY/PRINCIPAL FINDINGS To investigate the role of bacterial genetic factors in mosquito biology and in colonization of mosquitoes we used CRISPR/Cas9 gene editing system to mutate the outer membrane protein A (ompA) gene of a Cedecea neteri symbiont isolated from Aedes mosquitoes. The ompA mutant had an impaired ability to form biofilms and poorly infected Ae. aegypti when reared in a mono-association under gnotobiotic conditions. In adult mosquitoes, the mutant had a significantly reduced infection prevalence compared to the wild type or complement strains, while no differences in prevalence were seen in larvae, suggesting genetic factors are particularly important for adult gut colonization. We also used the CRISPR/Cas9 system to integrate genes (antibiotic resistance and fluorescent markers) into the symbionts genome and demonstrated that these genes were functional in vitro and in vivo. CONCLUSIONS/SIGNIFICANCE Our results shed insights into the role of ompA gene in host-microbe interactions in Ae. aegypti and confirm that CRISPR/Cas9 gene editing can be employed for genetic manipulation of non-model gut microbes. The ability to use this technology for site-specific integration of genes into the symbiont will facilitate the development of paratransgenic control strategies to interfere with arboviral pathogens such Chikungunya, dengue, Zika and Yellow fever viruses transmitted by Aedes mosquitoes.
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Affiliation(s)
- Shivanand Hegde
- Departments of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Pornjarim Nilyanimit
- Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
| | - Elena Kozlova
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Enyia R. Anderson
- Departments of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Hema P. Narra
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Sanjeev K. Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Eva Heinz
- Department of Vector Biology and Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Grant L. Hughes
- Departments of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- * E-mail:
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14
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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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15
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Malek M, Jafarifar F, Roohi Aminjan A, Salehi H, Parsa H. Culture of a new medicinal leech: growth, survival and reproduction of Hirudo orientalis Utevsky and Trontelj, 2005 under laboratory conditions. J NAT HIST 2019. [DOI: 10.1080/00222933.2019.1597200] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Masoumeh Malek
- School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Fatemeh Jafarifar
- School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Atabak Roohi Aminjan
- Department of Biology, Faculty of Science, Bu-Ali Sina University, Hamedan, Iran
| | - Hassan Salehi
- School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Hossein Parsa
- School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
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16
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Rolig AS, Sweeney EG, Kaye LE, DeSantis MD, Perkins A, Banse AV, Hamilton MK, Guillemin K. A bacterial immunomodulatory protein with lipocalin-like domains facilitates host-bacteria mutualism in larval zebrafish. eLife 2018; 7:37172. [PMID: 30398151 PMCID: PMC6219842 DOI: 10.7554/elife.37172] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 10/04/2018] [Indexed: 02/06/2023] Open
Abstract
Stable mutualism between a host and its resident bacteria requires a moderated immune response to control bacterial population size without eliciting excessive inflammation that could harm both partners. Little is known about the specific molecular mechanisms utilized by bacterial mutualists to temper their hosts' responses and protect themselves from aggressive immune attack. Using a gnotobiotic larval zebrafish model, we identified an Aeromonas secreted immunomodulatory protein, AimA. AimA is required during colonization to prevent intestinal inflammation that simultaneously compromises both bacterial and host survival. Administration of exogenous AimA prevents excessive intestinal neutrophil accumulation and protects against septic shock in models of both bacterially and chemically induced intestinal inflammation. We determined the molecular structure of AimA, which revealed two related calycin-like domains with structural similarity to the mammalian immune modulatory protein, lipocalin-2. As a secreted bacterial protein required by both partners for optimal fitness, AimA is an exemplar bacterial mutualism factor.
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Affiliation(s)
- Annah S Rolig
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | | | - Lila E Kaye
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Michael D DeSantis
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Arden Perkins
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Allison V Banse
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | | | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, United States.,Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada
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17
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Endosymbiont genomes yield clues of tubeworm success. ISME JOURNAL 2018; 12:2785-2795. [PMID: 30022157 PMCID: PMC6194059 DOI: 10.1038/s41396-018-0220-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/23/2018] [Accepted: 06/11/2018] [Indexed: 11/17/2022]
Abstract
Forty years after discovery of chemosynthetic symbiosis in the tubeworm Riftia pachyptila, how organisms maintain their unique host–symbiont associations at the cellular level is still largely unknown. Previous studies primarily focus on symbionts associated with host lineages living in hydrothermal vents. To understand physiological adaptations and evolution in these holobiont systems in markedly different habitats, we characterized four novel siboglinid-symbiont genomes spanning deep-sea seep and sedimented environments. Our comparative analyses suggest that all sampled siboglinid chemoautotrophic symbionts, except for frenulate symbionts, can use both rTCA and Calvin cycle for carbon fixation. We hypothesize that over evolutionary time siboglinids have been able to utilize different bacterial lineages allowing greater metabolic flexibility of carbon fixation (e.g., rTCA) enabling tubeworms to thrive in more reducing habitats, such as vents and seeps. Moreover, we show that sulfur metabolism and molecular mechanisms related to initial infection are remarkably conserved across chemoautotrophic symbionts in different habitats. Unexpectedly, we find that the ability to use hydrogen, as an additional energy source, is potentially more widespread than previously recognized. Our comparative genomic results help elucidate potential mechanisms used to allow chemosynthetically dependent holobionts adapt to, and evolve in, different environments.
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18
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Abstract
Dysbiosis, or the imbalance in the structural and/or functional properties of the microbiome, is at the origin of important infectious inflammatory diseases such as inflammatory bowel disease (IBD) and periodontal disease. Periodontitis is a polymicrobial inflammatory disease that affects a large proportion of the world's population and has been associated with a wide variety of systemic health conditions, such as diabetes, cardiovascular and respiratory diseases. Dysbiosis has been identified as a key element in the development of the disease. However, the precise mechanisms and environmental signals that lead to the initiation of dysbiosis in the human microbiome are largely unknown. In a series of previous in vivo studies using metatranscriptomic analysis of periodontitis and its progression we identified several functional signatures that were highly associated with the disease. Among them, potassium ion transport appeared to be key in the process of pathogenesis. To confirm its importance we performed a series of in vitro experiments, in which we demonstrated that potassium levels a increased the virulence of the oral community as a whole and at the same time altering the immune response of gingival epithelium, increasing the production of TNF-α and reducing the expression of IL-6 and the antimicrobial peptide human β-defensin 3 (hBD-3). These results indicate that levels of potassium in the periodontal pocket could be an important element in of dysbiosis in the oral microbiome. They are a starting point for the identification of key environmental signals that modify the behavior of the oral microbiome from a symbiotic community to a dysbiotic one. Homeostasis of the human microbiome plays a key role in maintaining the healthy status of the human body. Changes in composition and function of the human microbiome (dysbiosis) are at the origin of important infectious inflammatory diseases such as inflammatory bowel disease (IBD) and periodontal disease. However, the environmental elements that trigger the development of dysbiotic diseases are largely unknown. In previous studies, using community-wide transcriptome analysis, we identified ion potassium transport as one of the most important functions in the pathogenesis of periodontitis and its progression. Here, we confirm with a series of in vitro experiments that potassium can act as an important signal in the dysbiotic process inducing pathogenesis in the oral microbiome and altering the host response in front of the microbial challenge that could lead to microbial immune subversion. Our study provides new insights into the important role that ion potassium plays a signal in oral dysbiosis during periodontitis.
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Affiliation(s)
- Susan Yost
- The Forsyth Institute, Cambridge, Massachusetts, United States of America
| | - Ana E. Duran-Pinedo
- Department of Oral Biology, University of Florida, Gainesville, Florida, United States of America
| | - Keerthana Krishnan
- The Forsyth Institute, Cambridge, Massachusetts, United States of America
| | - Jorge Frias-Lopez
- Department of Oral Biology, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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19
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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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20
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Abstract
Type II secretion (T2S) is one means by which Gram-negative pathogens secrete proteins into the extracellular milieu and/or host organisms. Based upon recent genome sequencing, it is clear that T2S is largely restricted to the Proteobacteria, occurring in many, but not all, genera in the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria classes. Prominent human and/or animal pathogens that express a T2S system(s) include Acinetobacter baumannii, Burkholderia pseudomallei, Chlamydia trachomatis, Escherichia coli, Klebsiella pneumoniae, Legionella pneumophila, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Vibrio cholerae, and Yersinia enterocolitica T2S-expressing plant pathogens include Dickeya dadantii, Erwinia amylovora, Pectobacterium carotovorum, Ralstonia solanacearum, Xanthomonas campestris, Xanthomonas oryzae, and Xylella fastidiosa T2S also occurs in nonpathogenic bacteria, facilitating symbioses, among other things. The output of a T2S system can range from only one to dozens of secreted proteins, encompassing a diverse array of toxins, degradative enzymes, and other effectors, including novel proteins. Pathogenic processes mediated by T2S include the death of host cells, degradation of tissue, suppression of innate immunity, adherence to host surfaces, biofilm formation, invasion into and growth within host cells, nutrient assimilation, and alterations in host ion flux. The reach of T2S is perhaps best illustrated by those bacteria that clearly use it for both environmental survival and virulence; e.g., L. pneumophila employs T2S for infection of amoebae, growth within lung cells, dampening of cytokines, and tissue destruction. This minireview provides an update on the types of bacteria that have T2S, the kinds of proteins that are secreted via T2S, and how T2S substrates promote infection.
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21
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Hill JH, Franzosa EA, Huttenhower C, Guillemin K. A conserved bacterial protein induces pancreatic beta cell expansion during zebrafish development. eLife 2016; 5:e20145. [PMID: 27960075 PMCID: PMC5154760 DOI: 10.7554/elife.20145] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/03/2016] [Indexed: 12/13/2022] Open
Abstract
Resident microbes play important roles in the development of the gastrointestinal tract, but their influence on other digestive organs is less well explored. Using the gnotobiotic zebrafish, we discovered that the normal expansion of the pancreatic β cell population during early larval development requires the intestinal microbiota and that specific bacterial members can restore normal β cell numbers. These bacteria share a gene that encodes a previously undescribed protein, named herein BefA (β Cell Expansion Factor A), which is sufficient to induce β cell proliferation in developing zebrafish larvae. Homologs of BefA are present in several human-associated bacterial species, and we show that they have conserved capacity to stimulate β cell proliferation in larval zebrafish. Our findings highlight a role for the microbiota in early pancreatic β cell development and suggest a possible basis for the association between low diversity childhood fecal microbiota and increased diabetes risk.
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Affiliation(s)
| | - Eric A Franzosa
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, United States
- The Broad Institute, Cambridge, United States
| | - Curtis Huttenhower
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, United States
- The Broad Institute, Cambridge, United States
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, United States
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada
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22
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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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23
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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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24
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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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25
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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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Rollat-Farnier PA, Santos-Garcia D, Rao Q, Sagot MF, Silva FJ, Henri H, Zchori-Fein E, Latorre A, Moya A, Barbe V, Liu SS, Wang XW, Vavre F, Mouton L. Two host clades, two bacterial arsenals: evolution through gene losses in facultative endosymbionts. Genome Biol Evol 2015; 7:839-55. [PMID: 25714744 PMCID: PMC5322557 DOI: 10.1093/gbe/evv030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bacterial endosymbiosis is an important evolutionary process in insects, which can harbor both obligate and facultative symbionts. The evolution of these symbionts is driven by evolutionary convergence, and they exhibit among the tiniest genomes in prokaryotes. The large host spectrum of facultative symbionts and the high diversity of strategies they use to infect new hosts probably impact the evolution of their genome and explain why they undergo less severe genomic erosion than obligate symbionts. Candidatus Hamiltonella defensa is suitable for the investigation of the genomic evolution of facultative symbionts because the bacteria are engaged in specific relationships in two clades of insects. In aphids, H. defensa is found in several species with an intermediate prevalence and confers protection against parasitoids. In whiteflies, H. defensa is almost fixed in some species of Bemisia tabaci, which suggests an important role of and a transition toward obligate symbiosis. In this study, comparisons of the genome of H. defensa present in two B. tabaci species (Middle East Asia Minor 1 and Mediterranean) and in the aphid Acyrthosiphon pisum revealed that they belong to two distinct clades and underwent specific gene losses. In aphids, it contains highly virulent factors that could allow protection and horizontal transfers. In whiteflies, the genome lost these factors and seems to have a limited ability to acquire genes. However it contains genes that could be involved in the production of essential nutrients, which is consistent with a primordial role for this symbiont. In conclusion, although both lineages of H. defensa have mutualistic interactions with their hosts, their genomes follow distinct evolutionary trajectories that reflect their phenotype and could have important consequences on their evolvability.
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Affiliation(s)
- Pierre-Antoine Rollat-Farnier
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France BAMBOO Research Team, INRIA Grenoble, Rhône-Alpes, France
| | - Diego Santos-Garcia
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
| | - Qiong Rao
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China School of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Lin'an, Hangzhou, China
| | - Marie-France Sagot
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France BAMBOO Research Team, INRIA Grenoble, Rhône-Alpes, France
| | - Francisco J Silva
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain
| | - Hélène Henri
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France
| | - Einat Zchori-Fein
- Department of Entomology, NeweYa'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain
| | - Valérie Barbe
- CEA/DSV/IG/Genoscope, 2 rue Gaston Cremieux, Evry, France
| | - Shu-Sheng Liu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xiao-Wei Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fabrice Vavre
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France BAMBOO Research Team, INRIA Grenoble, Rhône-Alpes, France
| | - Laurence Mouton
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France
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Yoon SS, Kim EK, Lee WJ. Functional genomic and metagenomic approaches to understanding gut microbiota-animal mutualism. Curr Opin Microbiol 2015; 24:38-46. [PMID: 25625313 DOI: 10.1016/j.mib.2015.01.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/26/2014] [Accepted: 01/10/2015] [Indexed: 12/21/2022]
Abstract
Accumulating data sets of gut microbiome by next-generation sequencing allow us to gain a comprehensive view of the functional diversity of the gut-associated metagenome. However, many microbiome functions are unknown and/or have only been predicted, and may not necessarily reflect the in vivo function within a gut niche. Functional genomic and metagenomic approaches have been successfully applied to broaden the understanding of invertebrate and vertebrate gut microbiome involved in diverse functions, including colonization ability, nutritional processing, antibiotic resistance, microbial physiology and metabolism, and the modulation of the host physiology. In this review, we discuss the recent knowledge obtained from the study of functional genomics and metagenomics of the animal intestine and its potential values for understanding gut microbiota-animal mutualism.
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Affiliation(s)
- Sang Sun Yoon
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 120-752, South Korea
| | - Eun-Kyoung Kim
- School of Biological Science and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 151-742, South Korea; Seoul National University, National Creative Research Initiative Center for Symbiosystem, Seoul 151-742, South Korea
| | - Won-Jae Lee
- School of Biological Science and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 151-742, South Korea; Seoul National University, National Creative Research Initiative Center for Symbiosystem, Seoul 151-742, South Korea.
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28
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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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Genomics and host specialization of honey bee and bumble bee gut symbionts. Proc Natl Acad Sci U S A 2014; 111:11509-14. [PMID: 25053814 DOI: 10.1073/pnas.1405838111] [Citation(s) in RCA: 242] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Gilliamella apicola and Snodgrassella alvi are dominant members of the honey bee (Apis spp.) and bumble bee (Bombus spp.) gut microbiota. We generated complete genomes of the type strains G. apicola wkB1(T) and S. alvi wkB2(T) (isolated from Apis), as well as draft genomes for four other strains from Bombus. G. apicola and S. alvi were found to occupy very different metabolic niches: The former is a saccharolytic fermenter, whereas the latter is an oxidizer of carboxylic acids. Together, they may form a syntrophic network for partitioning of metabolic resources. Both species possessed numerous genes [type 6 secretion systems, repeats in toxin (RTX) toxins, RHS proteins, adhesins, and type IV pili] that likely mediate cell-cell interactions and gut colonization. Variation in these genes could account for the host fidelity of strains observed in previous phylogenetic studies. Here, we also show the first experimental evidence, to our knowledge, for this specificity in vivo: Strains of S. alvi were able to colonize their native bee host but not bees of another genus. Consistent with specific, long-term host association, comparative genomic analysis revealed a deep divergence and little or no gene flow between Apis and Bombus gut symbionts. However, within a host type (Apis or Bombus), we detected signs of horizontal gene transfer between G. apicola and S. alvi, demonstrating the importance of the broader gut community in shaping the evolution of any one member. Our results show that host specificity is likely driven by multiple factors, including direct host-microbe interactions, microbe-microbe interactions, and social transmission.
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30
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Signal peptide of cellulase. Appl Microbiol Biotechnol 2014; 98:5329-62. [DOI: 10.1007/s00253-014-5742-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/28/2014] [Accepted: 03/30/2014] [Indexed: 12/24/2022]
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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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Abstract
Aeromonas species are inhabitants of aquatic environments and are able to cause disease in humans and fish among other animals. In aquaculture, they are responsible for the economically important diseases of furunculosis and motile Aeromonas septicaemia (MAS). Whereas gastroenteritis and wound infections are the major human diseases associated with the genus. As they inhabit and survive in diverse environments, aeromonads possess a wide range of colonisation factors. The motile species are able to swim in liquid environments through the action of a single polar flagellum, the flagellin subunits of which are glycosylated; although essential for function the biological role of glycan addition is yet to be determined. Approximately 60% of aeromonads possess a second lateral flagella system that is expressed in viscous environments for swarming over surfaces; both flagellar systems have been shown to be important in the initial colonisation of surfaces. Subsequently, other non-flagellar colonisation factors are employed; these can be both filamentous and non-filamentous. The aeromonads possess a number of fimbrial systems with the bundle-forming MSHA type IV pilus system, having a major role in human cell adherence. Furthermore, a series of outer-membrane proteins have also been implicated in the aeromonad adhesion process. A number of strains are also capable of cell invasion and that maybe linked with the more invasive diseases of bacteraemia or wound infections. These strains employ cell surface factors that allow the colonisation of these niches that protect them from the host's immune system such as S-layers, capsules or particular lipopolysaccharides.
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Affiliation(s)
- Rebecca Lowry
- Department of Infection and Immunity, University of Sheffield, Sheffield, United Kingdom
| | - Sabela Balboa
- Department of Infection and Immunity, University of Sheffield, Sheffield, United Kingdom; Departamento de Microbiología y Parasitología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jennifer L Parker
- Department of Infection and Immunity, University of Sheffield, Sheffield, United Kingdom
| | - Jonathan G Shaw
- Department of Infection and Immunity, University of Sheffield, Sheffield, United Kingdom.
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Aeromonas hydrophila and Aeromonas veronii predominate among potentially pathogenic ciprofloxacin- and tetracycline-resistant aeromonas isolates from Lake Erie. Appl Environ Microbiol 2013; 80:841-8. [PMID: 24242249 DOI: 10.1128/aem.03645-13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Members of the genus Aeromonas are ubiquitous in nature and have increasingly been implicated in numerous diseases of humans and other animal taxa. Although some species of aeromonads are human pathogens, their presence, density, and relative abundance are rarely considered in assessing water quality. The objectives of this study were to identify Aeromonas species within Lake Erie, determine their antibiotic resistance patterns, and assess their potential pathogenicity. Aeromonas strains were isolated from Lake Erie water by use of Aeromonas selective agar with and without tetracycline and ciprofloxacin. All isolates were analyzed for hemolytic ability and cytotoxicity against human epithelial cells and were identified to the species level by using 16S rRNA gene restriction fragment length polymorphisms and phylogenetic analysis based on gyrB gene sequences. A molecular virulence profile was identified for each isolate, using multiplex PCR analysis of six virulence genes. We demonstrated that Aeromonas comprised 16% of all culturable bacteria from Lake Erie. Among 119 Aeromonas isolates, six species were identified, though only two species (Aeromonas hydrophila and A. veronii) predominated among tetracycline- and ciprofloxacin-resistant isolates. Additionally, both of these species demonstrated pathogenic phenotypes in vitro. Virulence gene profiles demonstrated a high prevalence of aerolysin and serine protease genes among A. hydrophila and A. veronii isolates, a genetic profile which corresponded with pathogenic phenotypes. Together, our findings demonstrate increased antibiotic resistance among potentially pathogenic strains of aeromonads, illustrating an emerging potential health concern.
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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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Giltner CL, Bobenchik AM, Uslan DZ, Deville JG, Humphries RM. Ciprofloxacin-resistant Aeromonas hydrophila cellulitis following leech therapy. J Clin Microbiol 2013; 51:1324-6. [PMID: 23363826 PMCID: PMC3666766 DOI: 10.1128/jcm.03217-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 01/19/2013] [Indexed: 11/20/2022] Open
Abstract
We report a case of surgical site infection with ciprofloxacin-resistant Aeromonas hydrophila following leech therapy. Antimicrobial and genetic analyses of leech and patient isolates demonstrated that the resistant isolates originated from the leech gut microbiota. These data suggest that ciprofloxacin monotherapy as a prophylaxis regimen prior to leech therapy may not be effective in preventing infection.
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Affiliation(s)
- Carmen L. Giltner
- David Geffen School of Medicine, Departments of Pathology and Laboratory Medicine
| | - April M. Bobenchik
- David Geffen School of Medicine, Departments of Pathology and Laboratory Medicine
| | | | - Jaime G. Deville
- Pediatrics, University of California, Los Angeles, California, USA
| | - Romney M. Humphries
- David Geffen School of Medicine, Departments of Pathology and Laboratory Medicine
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Shakir Z, Khan S, Sung K, Khare S, Khan A, Steele R, Nawaz M. Molecular characterization of fluoroquinolone-resistant Aeromonas spp. isolated from imported shrimp. Appl Environ Microbiol 2012; 78:8137-41. [PMID: 22923408 PMCID: PMC3485934 DOI: 10.1128/aem.02081-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 08/17/2012] [Indexed: 11/20/2022] Open
Abstract
Sixty-three nalidixic acid-resistant Aeromonas sp. isolates were obtained from imported shrimp. Phylogenetic analysis of gyrB sequences indicated that 18 were A. enteropelogenes, 26 were A. caviae, and 19 were A. sobria. Double missense mutations in the quinolone resistance-determining region (QRDR) of gyrA at codon 83 (Ser→Val/Ile) and codon 92 (Leu→Met) coupled with a point mutation of parC at codon 80 (Ser→Ile/Phe) conferred high levels of quinolone resistance in the isolates. A majority of A. enteropelogenes and A. caviae strains harbored toxin genes, whereas only a few A. sobria strains harbored these genes. The fluoroquinolone-resistant Aeromonas spp. exhibited higher cytotoxicity than fluoroquinolone-sensitive, virulent Aeromonas spp. to rat epithelial cells.
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Affiliation(s)
| | - Saeed Khan
- Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Kidon Sung
- Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Sangeeta Khare
- Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Ashraf Khan
- Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Roger Steele
- Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Mohamed Nawaz
- Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
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OmpA-mediated biofilm formation is essential for the commensal bacterium Sodalis glossinidius to colonize the tsetse fly gut. Appl Environ Microbiol 2012; 78:7760-8. [PMID: 22941073 DOI: 10.1128/aem.01858-12] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Many bacteria successfully colonize animals by forming protective biofilms. Molecular processes that underlie the formation and function of biofilms in pathogenic bacteria are well characterized. In contrast, the relationship between biofilms and host colonization by symbiotic bacteria is less well understood. Tsetse flies (Glossina spp.) house 3 maternally transmitted symbionts, one of which is a commensal (Sodalis glossinidius) found in several host tissues, including the gut. We determined that Sodalis forms biofilms in the tsetse gut and that this process is influenced by the Sodalis outer membrane protein A (OmpA). Mutant Sodalis strains that do not produce OmpA (Sodalis ΔOmpA mutants) fail to form biofilms in vitro and are unable to colonize the tsetse gut unless endogenous symbiotic bacteria are present. Our data indicate that in the absence of biofilms, Sodalis ΔOmpA mutant cells are exposed to and eliminated by tsetse's innate immune system, suggesting that biofilms help Sodalis evade the host immune system. Tsetse is the sole vector of pathogenic African trypanosomes, which also reside in the fly gut. Acquiring a better understanding of the dynamics that promote Sodalis colonization of the tsetse gut may enhance the development of novel disease control strategies.
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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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Whitaker IS, Oboumarzouk O, Rozen WM, Naderi N, Balasubramanian SP, Azzopardi EA, Kon M. The efficacy of medicinal leeches in plastic and reconstructive surgery: a systematic review of 277 reported clinical cases. Microsurgery 2012; 32:240-50. [PMID: 22407551 DOI: 10.1002/micr.20971] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2011] [Accepted: 09/21/2011] [Indexed: 11/11/2022]
Abstract
BACKGROUND Although there are numerous case reports and small case series describing the experiences of leech therapy in various circumstances, there are relatively few large studies evaluating the effectiveness of leeching to relieve venous congestion. The therapeutic value of leeching is illustrated by these reports but the current literature lacks a cohesive summary of previous experiences. METHODS An electronic search of PubMed, the Cochrane library and the Centre for Reviews and Dissemination between 1966 and 2009 was used to retrieve human studies published in the English language evaluating outcomes following leech therapy. The "success" and "failure" of leech therapy were the primary outcome measures and secondary outcomes included complications, number of leeches used, pharmacological adjuncts and blood transfusion requirements. RESULTS In total, out of 461 articles, 394 articles met the exclusion criteria. The 67 included papers reported on 277 cases of leech use with an age range of 2-81 years and a male to female ratio of almost 2:1. The overall reported "success" rate following leech therapy was 77.98% (216/277). In terms of secondary outcome measures, 49.75% of cases (N = 101) required blood transfusions, 79.05% received antibiotics (N = 166) and 54.29% received concomitant anticoagulant therapy. The overall complication rate was 21.8%. CONCLUSION In the absence of robust randomized controlled trials on which the evidence may be based, this synthesis of current best evidence guides clinicians during the process of consenting patients and using leeches in their practice.
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Affiliation(s)
- Iain S Whitaker
- Department of Burns and Plastic Surgery, Morriston Hospital, Swansea, Wales, UK.
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40
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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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