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Kowalski CH, Lawhorn S, Smith TJ, Corrigan RM, Barber MF. Adaptation to skin mycobiota promotes antibiotic tolerance in Staphylococcus aureus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592489. [PMID: 38952794 PMCID: PMC11216364 DOI: 10.1101/2024.05.03.592489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
The microbiota can promote host health by inhibiting pathogen colonization, yet how host-resident fungi, or the mycobiota, contribute to this process remains unclear. The human skin mycobiota is uniquely stable compared to other body sites and dominated by yeasts of the genus Malassezia . We observe that colonization of human skin by Malassezia sympodialis significantly reduces subsequent colonization by the prominent bacterial pathogen Staphylococcus aureus . M. sympodialis secreted products possess potent bactericidal activity against S. aureus and are sufficient to impair S. aureus skin colonization. This bactericidal activity requires an acidic environment and is exacerbated by free fatty acids, demonstrating a unique synergy with host-derived epidermal defenses. Leveraging experimental evolution to pinpoint mechanisms of S. aureus adaptation in response to the skin mycobiota, we identified multiple mutations in the stringent response regulator Rel that promote survival against M. sympodialis . Similar Rel alleles have been reported in S. aureus clinical isolates, and natural Rel variants are sufficient for tolerance to M. sympodialis antagonism. Partial stringent response activation underlies tolerance to clinical antibiotics, with both laboratory-evolved and natural Rel variants conferring multidrug tolerance. These findings demonstrate the ability of the mycobiota to mediate pathogen colonization resistance, identify new mechanisms of bacterial adaptation in response to fungal antagonism, and reveal the potential for microbiota-driven evolution to shape pathogen antibiotic susceptibility. Highlights - M. sympodialis reduces colonization of human skin by S. aureus - Bactericidal activity of M. sympodialis is exacerbated by features of the skin niche - S. aureus Rel variants are sufficient for tolerance to Malassezia antagonism - Evolved tolerance to yeast antagonism coincides with S. aureus multidrug tolerance.
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Jiang X, Li H, Ma J, Li H, Ma X, Tang Y, Li J, Chi X, Deng Y, Zeng S, Liu Z. Role of Type VI secretion system in pathogenic remodeling of host gut microbiota during Aeromonas veronii infection. THE ISME JOURNAL 2024; 18:wrae053. [PMID: 38531781 PMCID: PMC11014884 DOI: 10.1093/ismejo/wrae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/31/2024] [Accepted: 03/21/2024] [Indexed: 03/28/2024]
Abstract
Intestinal microbial disturbance is a direct cause of host disease. The bacterial Type VI secretion system (T6SS) often plays a crucial role in the fitness of pathogenic bacteria by delivering toxic effectors into target cells. However, its impact on the gut microbiota and host pathogenesis is poorly understood. To address this question, we characterized a new T6SS in the pathogenic Aeromonas veronii C4. First, we validated the secretion function of the core machinery of A. veronii C4 T6SS. Second, we found that the pathogenesis and colonization of A. veronii C4 is largely dependent on its T6SS. The effector secretion activity of A. veronii C4 T6SS not only provides an advantage in competition among bacteria in vitro, but also contributes to occupation of an ecological niche in the nutritionally deficient and anaerobic environment of the host intestine. Metagenomic analysis showed that the T6SS directly inhibits or eliminates symbiotic strains from the intestine, resulting in dysregulated gut microbiome homeostasis. In addition, we identified three unknown effectors, Tse1, Tse2, and Tse3, in the T6SS, which contribute to T6SS-mediated bacterial competition and pathogenesis by impairing targeted cell integrity. Our findings highlight that T6SS can remodel the host gut microbiota by intricate interplay between T6SS-mediated bacterial competition and altered host immune responses, which synergistically promote pathogenesis of A. veronii C4. Therefore, this newly characterized T6SS could represent a general interaction mechanism between the host and pathogen, and may offer a potential therapeutic target for controlling bacterial pathogens.
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Affiliation(s)
- Xiaoli Jiang
- School of Life and Health Sciences, Hainan University, Haikou 570228, China
| | - Hanzeng Li
- School of Life and Health Sciences, Hainan University, Haikou 570228, China
| | - Jiayue Ma
- School of Life and Health Sciences, Hainan University, Haikou 570228, China
| | - Hong Li
- School of Life and Health Sciences, Hainan University, Haikou 570228, China
| | - Xiang Ma
- School of Life and Health Sciences, Hainan University, Haikou 570228, China
| | - Yanqiong Tang
- School of Life and Health Sciences, Hainan University, Haikou 570228, China
| | - Juanjuan Li
- School of Life and Health Sciences, Hainan University, Haikou 570228, China
| | - Xue Chi
- School of Life and Health Sciences, Hainan University, Haikou 570228, China
| | - Yong Deng
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Sheng Zeng
- Susheng Biotech (Hainan) Co., Ltd, Haikou 570228, China
| | - Zhu Liu
- School of Life and Health Sciences, Hainan University, Haikou 570228, China
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Booth SC, Smith WPJ, Foster KR. The evolution of short- and long-range weapons for bacterial competition. Nat Ecol Evol 2023; 7:2080-2091. [PMID: 38036633 PMCID: PMC10697841 DOI: 10.1038/s41559-023-02234-2] [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: 10/13/2022] [Accepted: 09/22/2023] [Indexed: 12/02/2023]
Abstract
Bacteria possess a diverse range of mechanisms for inhibiting competitors, including bacteriocins, tailocins, type VI secretion systems and contact-dependent inhibition (CDI). Why bacteria have evolved such a wide array of weapon systems remains a mystery. Here we develop an agent-based model to compare short-range weapons that require cell-cell contact, with long-range weapons that rely on diffusion. Our model predicts that contact weapons are useful when an attacking strain is outnumbered, facilitating invasion and establishment. By contrast, ranged weapons tend to be effective only when attackers are abundant. We test our predictions with the opportunistic pathogen Pseudomonas aeruginosa, which naturally carries multiple weapons, including CDI and diffusing tailocins. As predicted, short-range CDI can function at low and high frequencies, while long-range tailocins require high frequency and cell density to function effectively. Head-to-head competition experiments with the two weapon types further support our predictions: a tailocin attacker defeats CDI only when it is numerically dominant, but then we find it can be devastating. Finally, we show that the two weapons work well together when one strain employs both. We conclude that short- and long-range weapons serve different functions and allow bacteria to fight both as individuals and as a group.
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Affiliation(s)
- Sean C Booth
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - William P J Smith
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- Division of Evolution, Infection and Genomics, University of Manchester, Manchester, UK
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
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Yitbarek S, Guittar J, Knutie SA, Ogbunugafor CB. Deconstructing taxa x taxa xenvironment interactions in the microbiota: A theoretical examination. iScience 2023; 26:107875. [PMID: 37860776 PMCID: PMC10583047 DOI: 10.1016/j.isci.2023.107875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 03/21/2023] [Accepted: 09/07/2023] [Indexed: 10/21/2023] Open
Abstract
A major objective of microbial ecology is to identify how the composition of microbial taxa shapes host phenotypes. However, most studies focus on pairwise interactions and ignore the potentially significant effects of higher-order microbial interactions.Here, we quantify the effects of higher-order interactions among taxa on host infection risk. We apply our approach to an in silico dataset that is built to resemble a population of insect hosts with gut-associated microbial communities at risk of infection from an intestinal parasite across a breadth of nutrient environmental contexts.We find that the effect of higher-order interactions is considerable and can change appreciably across environmental contexts. Furthermore, we show that higher-order interactions can stabilize community structure thereby reducing host susceptibility to parasite invasion.Our approach illustrates how incorporating the effects of higher-order interactions among gut microbiota across environments can be essential for understanding their effects on host phenotypes.
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Affiliation(s)
- Senay Yitbarek
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - John Guittar
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
- Kellogg Biological Station, Michigan State University, Hickory Corners, MI 49060, USA
| | - Sarah A. Knutie
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - C. Brandon Ogbunugafor
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
- Vermont Complex Systems Center, University of Vermont, Burlington, VT 05405, USA
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5
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Russ D, Fitzpatrick CR, Teixeira PJPL, Dangl JL. Deep discovery informs difficult deployment in plant microbiome science. Cell 2023; 186:4496-4513. [PMID: 37832524 DOI: 10.1016/j.cell.2023.08.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 10/15/2023]
Abstract
Plant-associated microbiota can extend plant immune system function, improve nutrient acquisition and availability, and alleviate abiotic stresses. Thus, naturally beneficial microbial therapeutics are enticing tools to improve plant productivity. The basic definition of plant microbiota across species and ecosystems, combined with the development of reductionist experimental models and the manipulation of plant phenotypes with microbes, has fueled interest in its translation to agriculture. However, the great majority of microbes exhibiting plant-productivity traits in the lab and greenhouse fail in the field. Therapeutic microbes must reach détente, the establishment of uneasy homeostasis, with the plant immune system, invade heterogeneous pre-established plant-associated communities, and persist in a new and potentially remodeled community. Environmental conditions can alter community structure and thus impact the engraftment of therapeutic microbes. We survey recent breakthroughs, challenges, and opportunities in translating beneficial microbes from the lab to the field.
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Affiliation(s)
- Dor Russ
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paulo J P L Teixeira
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Czuppon P, Day T, Débarre F, Blanquart F. A stochastic analysis of the interplay between antibiotic dose, mode of action, and bacterial competition in the evolution of antibiotic resistance. PLoS Comput Biol 2023; 19:e1011364. [PMID: 37578976 PMCID: PMC10449190 DOI: 10.1371/journal.pcbi.1011364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/24/2023] [Accepted: 07/17/2023] [Indexed: 08/16/2023] Open
Abstract
The use of an antibiotic may lead to the emergence and spread of bacterial strains resistant to this antibiotic. Experimental and theoretical studies have investigated the drug dose that minimizes the risk of resistance evolution over the course of treatment of an individual, showing that the optimal dose will either be the highest or the lowest drug concentration possible to administer; however, no analytical results exist that help decide between these two extremes. To address this gap, we develop a stochastic mathematical model of bacterial dynamics under antibiotic treatment. We explore various scenarios of density regulation (bacterial density affects cell birth or death rates), and antibiotic modes of action (biostatic or biocidal). We derive analytical results for the survival probability of the resistant subpopulation until the end of treatment, the size of the resistant subpopulation at the end of treatment, the carriage time of the resistant subpopulation until it is replaced by a sensitive one after treatment, and we verify these results with stochastic simulations. We find that the scenario of density regulation and the drug mode of action are important determinants of the survival of a resistant subpopulation. Resistant cells survive best when bacterial competition reduces cell birth and under biocidal antibiotics. Compared to an analogous deterministic model, the population size reached by the resistant type is larger and carriage time is slightly reduced by stochastic loss of resistant cells. Moreover, we obtain an analytical prediction of the antibiotic concentration that maximizes the survival of resistant cells, which may help to decide which drug dosage (not) to administer. Our results are amenable to experimental tests and help link the within and between host scales in epidemiological models.
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Affiliation(s)
- Peter Czuppon
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, UPEC, CNRS, IRD, INRA, Paris, France
- Center for Interdisciplinary Research in Biology, CNRS, Collège de France, PSL Research University, Paris, France
| | - Troy Day
- Department of Mathematics and Statistics, Department of Biology, Queen’s University, Kingston, Canada
| | - Florence Débarre
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, UPEC, CNRS, IRD, INRA, Paris, France
| | - François Blanquart
- Center for Interdisciplinary Research in Biology, CNRS, Collège de France, PSL Research University, Paris, France
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Ding Y, Wang Q, Li D, Li Y, Yao K, Wang T. Differences in the effects of Bordetella pertussis and respiratory syncytial virus infection on the composition of nasopharyngeal flora in neonates. Front Pediatr 2023; 11:1034147. [PMID: 37351319 PMCID: PMC10282602 DOI: 10.3389/fped.2023.1034147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/25/2023] [Indexed: 06/24/2023] Open
Abstract
Introduction Bordetella pertussis and respiratory syncytial virus (RSV) are important pathogens causing cough in neonates. Few studies have investigated the differences in the effects of these two specific infections on respiratory flora. The aim of this study was to explore whether infections with Bordetella pertussis and RSV have different effects on respiratory floral composition in neonates. Methods Nasopharyngeal respiratory flora was assessed by 16S ribosomal RNA amplification and V3-V4 region sequencing. Shannon and Simpson indices were calculated to determine the α diversity and principal coordinate analysis was performed to determine the β diversity. Results In total, 111 hospitalized neonates were divided into the pertussis (n = 29), RSV (n = 57), and control groups (n = 25) according to the pathogens detected. The relative abundance of Bordetella was significantly higher in the pertussis group (median: 19.18%, interquartile range: 72.57%). In contrast, this species was not detected in the other two groups. In the RSV group, the relative abundance of Streptococcus (median: 77.15%, interquartile range: 45.84%) was significantly higher than those in the pertussis and control groups (both P < 0.001). The α diversity of the RSV group was significantly lower than that of the control group (P < 0.001). Moreover, no statistically significant differences in the Shannon and Simpson indices were observed between the pertussis and control groups (P = 0.101 and P = 0.202, respectively). Principal coordinate analysis revealed a large overlap between the pertussis and control groups and a significant distance between the RSV and control groups without any overlap. Discussion Thus, the effects of infections with the two species, B. pertussis and RSV, impacted the diversity of nasopharyngeal flora differently. The principles underlying the difference in the effects of different pathogens on microbial flora require further investigation.
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Affiliation(s)
- Yijun Ding
- Department of Neonatology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Qing Wang
- Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Dongfang Li
- R&D Department, BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
| | - Yue Li
- Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Kaihu Yao
- Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Tianyou Wang
- Department of Hematology and Oncology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
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Prigot-Maurice C, Lheraud B, Guéritault S, Beltran-Bech S, Cordaux R, Peccoud J, Braquart-Varnier C. Investigating Wolbachia symbiont-mediated host protection against a bacterial pathogen using a natural Wolbachia nuclear insert. J Invertebr Pathol 2023; 197:107893. [PMID: 36754115 DOI: 10.1016/j.jip.2023.107893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023]
Abstract
Wolbachia bacterial endosymbionts provide protection against pathogens in various arthropod species but the underlying mechanisms remain misunderstood. By using a natural Wolbachia nuclear insert (f-element) in the isopod Armadillidium vulgare, we explored whether Wolbachia presence is mandatory to observe protection in this species or the presence of its genes is sufficient. We assessed survival of closely related females carrying or lacking the f-element (and lacking Wolbachia) challenged with the bacterial pathogen Salmonella enterica. Despite marginal significant effects, the f-element alone did not appear to confer survival benefits to its host, suggesting that Wolbachia presence in cells is crucial for protection.
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Affiliation(s)
- Cybèle Prigot-Maurice
- Laboratoire Écologie et Biologie des Interactions, équipe Écologie, Évolution, Symbiose. Université de Poitiers UMR CNRS 7267, 3, rue Jacques Fort, TSA 51106, F-86073, POITIERS Cedex 9, France.
| | - Baptiste Lheraud
- Laboratoire Écologie et Biologie des Interactions, équipe Écologie, Évolution, Symbiose. Université de Poitiers UMR CNRS 7267, 3, rue Jacques Fort, TSA 51106, F-86073, POITIERS Cedex 9, France
| | - Samuel Guéritault
- Laboratoire Écologie et Biologie des Interactions, équipe Écologie, Évolution, Symbiose. Université de Poitiers UMR CNRS 7267, 3, rue Jacques Fort, TSA 51106, F-86073, POITIERS Cedex 9, France
| | - Sophie Beltran-Bech
- Laboratoire Écologie et Biologie des Interactions, équipe Écologie, Évolution, Symbiose. Université de Poitiers UMR CNRS 7267, 3, rue Jacques Fort, TSA 51106, F-86073, POITIERS Cedex 9, France
| | - Richard Cordaux
- Laboratoire Écologie et Biologie des Interactions, équipe Écologie, Évolution, Symbiose. Université de Poitiers UMR CNRS 7267, 3, rue Jacques Fort, TSA 51106, F-86073, POITIERS Cedex 9, France
| | - Jean Peccoud
- Laboratoire Écologie et Biologie des Interactions, équipe Écologie, Évolution, Symbiose. Université de Poitiers UMR CNRS 7267, 3, rue Jacques Fort, TSA 51106, F-86073, POITIERS Cedex 9, France
| | - Christine Braquart-Varnier
- Laboratoire Écologie et Biologie des Interactions, équipe Écologie, Évolution, Symbiose. Université de Poitiers UMR CNRS 7267, 3, rue Jacques Fort, TSA 51106, F-86073, POITIERS Cedex 9, France
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Is Plant Microbiota a Driver of Resistance to the Vector-Borne Pathogen Xylella fastidiosa? Pathogens 2022; 11:pathogens11121492. [PMID: 36558826 PMCID: PMC9782604 DOI: 10.3390/pathogens11121492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Xylella fastidiosa is a vector-borne plant vascular bacterial pathogen that causes several economically important diseases, including Pierce's disease (PD) in grapevine and olive quick decline syndrome (OQDS) in olive trees, among others [...].
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Kuhn T, Mamin M, Bindschedler S, Bshary R, Estoppey A, Gonzalez D, Palmieri F, Junier P, Richter XYL. Spatial scales of competition and a growth-motility trade-off interact to determine bacterial coexistence. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211592. [PMID: 36483758 PMCID: PMC9727664 DOI: 10.1098/rsos.211592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
The coexistence of competing species is a long-lasting puzzle in evolutionary ecology research. Despite abundant experimental evidence showing that the opportunity for coexistence decreases as niche overlap increases between species, bacterial species and strains competing for the same resources are commonly found across diverse spatially heterogeneous habitats. We thus hypothesized that the spatial scale of competition may play a key role in determining bacterial coexistence, and interact with other mechanisms that promote coexistence, including a growth-motility trade-off. To test this hypothesis, we let two Pseudomonas putida strains compete at local and regional scales by inoculating them either in a mixed droplet or in separate droplets in the same Petri dish, respectively. We also created conditions that allow the bacterial strains to disperse across abiotic or fungal hyphae networks. We found that competition at the local scale led to competitive exclusion while regional competition promoted coexistence. When competing in the presence of dispersal networks, the growth-motility trade-off promoted coexistence only when the strains were inoculated in separate droplets. Our results provide a mechanism by which existing laboratory data suggesting competitive exclusion at a local scale is reconciled with the widespread coexistence of competing bacterial strains in complex natural environments with dispersal.
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Affiliation(s)
- Thierry Kuhn
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Marine Mamin
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Redouan Bshary
- Laboratory of Eco-Ethology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Diego Gonzalez
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Xiang-Yi Li Richter
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
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11
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Dimas Martins A, ten Bosch Q, Heesterbeek JAP. Exploring the influence of competition on arbovirus invasion risk in communities. PLoS One 2022; 17:e0275687. [PMID: 36223367 PMCID: PMC9555654 DOI: 10.1371/journal.pone.0275687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/22/2022] [Indexed: 11/18/2022] Open
Abstract
Arbovirus outbreaks in communities are affected by how vectors, hosts and non-competent species interact. In this study, we investigate how ecological interactions between species and epidemiological processes influence the invasion potential of a vector-borne disease. We use an eco-epidemiological model to explore the basic reproduction number R0 for a range of interaction strengths in key processes, using West Nile virus infection to parameterize the model. We focus our analysis on intra and interspecific competition between vectors and between hosts, as well as competition with non-competent species. We show that such ecological competition has non-linear effects on R0 and can greatly impact invasion risk. The presence of multiple competing vector species results in lower values for R0 while host competition leads to the highest values of risk of disease invasion. These effects can be understood in terms of how the competitive pressures influence the vector-to-host ratio, which has a positive relationship with R0. We also show numerical examples of how vector feeding preferences become more relevant in high competition conditions between hosts. Under certain conditions, non-competent hosts, which can lead to a dilution effect for the pathogen, can have an amplification effect if they compete strongly with the competent hosts, hence facilitating pathogen invasion in the community.
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Affiliation(s)
- Afonso Dimas Martins
- Department of Population Health Sciences, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, The Netherlands,* E-mail:
| | - Quirine ten Bosch
- Quantitative Veterinary Epidemiology, Wageningen University and Research, Wageningen, The Netherlands
| | - J. A. P. Heesterbeek
- Department of Population Health Sciences, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, The Netherlands
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12
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Evolving antibiotic spectrum. Proc Natl Acad Sci U S A 2022; 119:e2214267119. [PMID: 36191212 PMCID: PMC9565054 DOI: 10.1073/pnas.2214267119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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13
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Hashem I, Van Impe JFM. The territorial nature of aggression in biofilms. Front Microbiol 2022; 13:878223. [PMID: 36081784 PMCID: PMC9445555 DOI: 10.3389/fmicb.2022.878223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Microbial conflicts have a particularly aggressive nature. In addition to other chemical, mechanical, and biological weapons in their repertoire, bacteria have evolved bacteriocins, which are narrow-spectrum toxins that kill closely related strains. Bacterial cells are known to frequently use their arsenal while competing against each other for nutrients and space. This stands in contrast with the animal world, where conflicts over resources and mating opportunities are far less lethal, and get commonly resolved via ritualized fighting or “limited war” tactics. Prevalence of aggression in microbial communities is usually explained as due to their limited ability to resolve conflicts via signaling as well as their limited ability to pull out from conflicts due to the sessile nature of their life within biofilms. We use an approach that combines Evolutionary Game Theory (EGT) and Individual-based Modeling (IbM) to investigate the origins of aggression in microbial conflicts. In order to understand how the spatial mode of growth affects the cost of a fight, we compare the growth dynamics emerging from engaging in aggression in a well-mixed system to a spatially structured system. To this end, a mathematical model is constructed for the competition between two bacterial strains where each strain produces a diffusible toxin to which the other strain is sensitive. It is observed that in the biofilm growth mode, starting from a mixed layer of two strains, mutual aggression gives rise to an exceedingly high level of spatial segregation, which in turn reduces the cost of aggression on both strains compared to when the same competition occurs in a well-mixed culture. Another observation is that the transition from a mixed layer to segregated growth is characterized by a switch in the overall growth dynamics. An increased “lag time” is observed in the overall population growth curve that is associated with the earlier stages of growth, when each strain is still experiencing the inhibiting effect of the toxin produced by its competitor. Afterwards, an exponential phase of growth kicks in once the competing strains start segregating from each other. The emerging “lag time” arises from the spiteful interactions between the two strains rather than acclimation of cells' internal physiology. Our analysis highlights the territorial nature of microbial conflicts as the key driver to their elevated levels of aggression as it increases the benefit-to-cost ratio of participating in antagonistic interactions.
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14
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Babar TK, Glare TR, Hampton JG, Hurst MRH, Narciso JO. Isolation, Purification, and Characterisation of a Phage Tail-Like Bacteriocin from the Insect Pathogenic Bacterium Brevibacillus laterosporus. Biomolecules 2022; 12:biom12081154. [PMID: 36009048 PMCID: PMC9406221 DOI: 10.3390/biom12081154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/13/2022] [Accepted: 08/16/2022] [Indexed: 11/23/2022] Open
Abstract
The Gram-positive and spore-forming bacterium Brevibacillus laterosporus (Bl) belongs to the Brevibacillus brevis phylogenetic cluster. Isolates of the species have demonstrated pesticidal potency against a wide range of invertebrate pests and plant diseases. Two New Zealand isolates, Bl 1821L and Bl 1951, are under development as biopesticides for control of diamondback moth and other pests. However, due to the often-restricted growth of these endemic isolates, production can be an issue. Based on the previous work, it was hypothesised that the putative phages might be involved. During investigations of the cause of the disrupted growth, electron micrographs of crude lysate of Bl 1821L showed the presence of phages’ tail-like structures. A soft agar overlay method with PEG 8000 precipitation was used to differentiate between the antagonistic activity of the putative phage and phage tail-like structures (bacteriocins). Assay tests authenticated the absence of putative phage activity. Using the same method, broad-spectrum antibacterial activity of Bl 1821L lysate against several Gram-positive bacteria was found. SDS-PAGE of sucrose density gradient purified and 10 kD MWCO concentrated lysate showed a prominent protein band of ~48 kD, and transmission electron microscopy revealed the presence of polysheath-like structures. N-terminal sequencing of the ~48 kD protein mapped to a gene with weak predicted amino acid homology to a Bacillus PBSX phage-like element xkdK, the translated product of which shared >90% amino acid similarity to the phage tail-sheath protein of another Bl published genome, LMG15441. Bioinformatic analysis also identified an xkdK homolog in the Bl 1951 genome. However, genome comparison of the region around the xkdK gene between Bl 1821L and Bl 1951 found differences including two glycine rich protein encoding genes which contain imperfect repeats (1700 bp) in Bl 1951, while a putative phage region resides in the analogous Bl 1821L region. Although comparative analysis of the genomic organisation of Bl 1821L and Bl 1951 PBSX-like region with the defective phages PBSX, PBSZ, and PBP 180 of Bacillus subtilis isolates 168 and W23, and Bacillus phage PBP180 revealed low amino acids similarity, the genes encode similar functional proteins in similar arrangements, including phage tail-sheath (XkdK), tail (XkdO), holin (XhlB), and N-acetylmuramoyl-l-alanine (XlyA). AMPA analysis identified a bactericidal stretch of 13 amino acids in the ~48 kD sequenced protein of Bl 1821L. Antagonistic activity of the purified ~48 kD phage tail-like protein in the assays differed remarkably from the crude lysate by causing a decrease of 34.2% in the number of viable cells of Bl 1951, 18 h after treatment as compared to the control. Overall, the identified inducible phage tail-like particle is likely to have implications for the in vitro growth of the insect pathogenic isolate Bl 1821L.
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Affiliation(s)
- Tauseef K. Babar
- Bio-Protection Research Centre, Lincoln University, Lincoln 7674, New Zealand
- Department of Entomology, Faculty of Agriculture Sciences & Technology, Bahauddin Zakariya University, Multan 60000, Pakistan
- Correspondence:
| | - Travis R. Glare
- Bio-Protection Research Centre, Lincoln University, Lincoln 7674, New Zealand
| | - John G. Hampton
- Bio-Protection Research Centre, Lincoln University, Lincoln 7674, New Zealand
| | - Mark R. H. Hurst
- Resilient Agriculture, AgResearch, Lincoln Research Centre, Christchurch 8140, New Zealand
| | - Josefina O. Narciso
- Bio-Protection Research Centre, Lincoln University, Lincoln 7674, New Zealand
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15
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Ford S, Moeskjær S, Young P, Santamaría RI, Harrison E. Introducing a Novel, Broad Host Range Temperate Phage Family Infecting Rhizobium leguminosarum and Beyond. Front Microbiol 2021; 12:765271. [PMID: 34858375 PMCID: PMC8631192 DOI: 10.3389/fmicb.2021.765271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/13/2021] [Indexed: 02/01/2023] Open
Abstract
Temperate phages play important roles in bacterial communities but have been largely overlooked, particularly in non-pathogenic bacteria. In rhizobia the presence of temperate phages has the potential to have significant ecological impacts but few examples have been described. Here we characterize a novel group of 5 Rhizobium leguminosarum prophages, capable of sustaining infections across a broad host range within their host genus. Genome comparisons identified further putative prophages infecting multiple Rhizobium species isolated globally, revealing a wider family of 10 temperate phages including one previously described lytic phage, RHEph01, which appears to have lost the ability to form lysogens. Phylogenetic discordance between prophage and host phylogenies suggests a history of active mobilization between Rhizobium lineages. Genome comparisons revealed conservation of gene content and order, with the notable exception of an approximately 5 kb region of hypervariability, containing almost exclusively hypothetical genes. Additionally, several horizontally acquired genes are present across the group, including a putative antirepressor present only in the RHEph01 genome, which may explain its apparent inability to form lysogens. In summary, both phenotypic and genomic comparisons between members of this group of phages reveals a clade of viruses with a long history of mobilization within and between Rhizobium species.
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Affiliation(s)
- Sam Ford
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Sara Moeskjær
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Peter Young
- Department of Biology, University of York, York, United Kingdom
| | - Rosa I Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, México City, Mexico
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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16
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Shirogane Y, Rousseau E, Voznica J, Xiao Y, Su W, Catching A, Whitfield ZJ, Rouzine IM, Bianco S, Andino R. Experimental and mathematical insights on the interactions between poliovirus and a defective interfering genome. PLoS Pathog 2021; 17:e1009277. [PMID: 34570820 PMCID: PMC8496841 DOI: 10.1371/journal.ppat.1009277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 10/07/2021] [Accepted: 07/28/2021] [Indexed: 01/13/2023] Open
Abstract
During replication, RNA viruses accumulate genome alterations, such as mutations and deletions. The interactions between individual variants can determine the fitness of the virus population and, thus, the outcome of infection. To investigate the effects of defective interfering genomes (DI) on wild-type (WT) poliovirus replication, we developed an ordinary differential equation model, which enables exploring the parameter space of the WT and DI competition. We also experimentally examined virus and DI replication kinetics during co-infection, and used these data to infer model parameters. Our model identifies, and our experimental measurements confirm, that the efficiencies of DI genome replication and encapsidation are two most critical parameters determining the outcome of WT replication. However, an equilibrium can be established which enables WT to replicate, albeit to reduced levels.
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Affiliation(s)
- Yuta Shirogane
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Elsa Rousseau
- Department of Industrial and Applied Genomics, AI and Cognitive Software Division, IBM Almaden Research Center, San Jose, California, United States of America
- NSF Center for Cellular Construction, University of California, San Francisco, California, United States of America
| | - Jakub Voznica
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
- ENS Cachan, Université Paris-Saclay, Cachan, France
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Weiheng Su
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China
| | - Adam Catching
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Zachary J. Whitfield
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Igor M. Rouzine
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
- Laboratoire de Biologie Computationnelle et Quantitative, Sorbonne Universite, Institut de Biologie Paris-Seine, Paris, France
| | - Simone Bianco
- Department of Industrial and Applied Genomics, AI and Cognitive Software Division, IBM Almaden Research Center, San Jose, California, United States of America
- NSF Center for Cellular Construction, University of California, San Francisco, California, United States of America
- * E-mail: (SB); (RA)
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
- * E-mail: (SB); (RA)
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17
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Bailey C, Strepparava N, Ros A, Wahli T, Schmidt-Posthaus H, Segner H, Tafalla C. It's a hard knock life for some: Heterogeneity in infection life history of salmonids influences parasite disease outcomes. J Anim Ecol 2021; 90:2573-2593. [PMID: 34165799 PMCID: PMC8597015 DOI: 10.1111/1365-2656.13562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/19/2021] [Indexed: 11/27/2022]
Abstract
Heterogeneity in immunity occurs across numerous disease systems with individuals from the same population having diverse disease outcomes. Proliferative kidney disease (PKD) caused by Tetracapsuloides bryosalmonae, is a persistent parasitic disease negatively impacting both wild and farmed salmonids. Little is known of how PKD is spread or maintained within wild susceptible populations. We investigated an aspect of fish disease that has been largely overlooked, that is, the role of the host phenotypic heterogeneity in disease outcome. We examined how host susceptibility to T. bryosalmonae infection, and the disease PKD, varied across different infection life-history stages and how it differs between naïve, re-infected and persistently infected hosts. We investigated the response to parasite exposure in host phenotypes with (a) different ages and (b) heterogeneous infection life histories. Among (a) the age phenotypes were young-of-the-year (YOY) fish and juvenile 1+ fish (fish older than one) and, for (b) juvenile 1+ infection survivors were either re-exposed or not re- exposed to the parasite and response phenotypes were assigned post-hoc dependant on infection status. In fish not re-exposed this included fish that cleared infection (CI) or had a persistent infection (PI). In fish re-exposed these included fish that were re-infected (RI), or re-exposed and uninfected (RCI). We assessed both parasite-centric (infection prevalence, parasite burden, malacospore transmission) and host-centric parameters (growth rates, disease severity, infection tolerance and the immune response). In (a), YOY fish, parasite success and disease severity were greater and differences in the immune response occurred, demonstrating an ontogenetic decline of susceptibility in older fish. In (b), in PI and RI fish, parasite success and disease severity were comparable. However, expression of several adaptive immunity markers was greater in RI fish, indicating concomitant immunity, as re-exposure did not intensify infection. We demonstrate the relevance of heterogeneity in infection life history on disease outcome and describe several distinctive features of immune ontogeny and protective immunity in this model not previously reported. The relevance of such themes on a population level requires greater research in many aquatic disease systems to generate clearer framework for understanding the spread and maintenance of aquatic pathogens.
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Affiliation(s)
- Christyn Bailey
- Fish Immunology and Pathology Group, Animal Health Research Centre (CISA-INIA), Madrid, Spain
| | - Nicole Strepparava
- Centre for Fish and Wildlife Health, University of Bern, Bern, Switzerland
| | - Albert Ros
- LAZBW, Fischereiforschungsstelle, Langenargen, Germany
| | - Thomas Wahli
- Centre for Fish and Wildlife Health, University of Bern, Bern, Switzerland
| | | | - Helmut Segner
- Centre for Fish and Wildlife Health, University of Bern, Bern, Switzerland
| | - Carolina Tafalla
- Fish Immunology and Pathology Group, Animal Health Research Centre (CISA-INIA), Madrid, Spain
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18
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Thornton CS, Mellett M, Jarand J, Barss L, Field SK, Fisher DA. The respiratory microbiome and nontuberculous mycobacteria: an emerging concern in human health. Eur Respir Rev 2021; 30:30/160/200299. [PMID: 34039671 DOI: 10.1183/16000617.0299-2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/09/2021] [Indexed: 12/24/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) are diverse microbial species encompassing commensals and pathogens with the ability to cause pulmonary disease in both immunocompetent and immunocompromised individuals. In contrast to Mycobacterium tuberculosis, which has seen a reduction in disease rates in developed countries, the incidence and prevalence of NTM disease is increasing. NTM are difficult to treat with standard antimicrobial regimens and may contain both virulence and antibiotic-resistance genes with potential for pathogenicity. With the advent of molecular techniques, it has been elucidated that these organisms do not reside in isolation and are rather part of a complex milieu of microorganisms within the host lung microbiome. Over the last decade, studies have highlighted the impact of the microbiome on host immunity, metabolism and cell-cell communication. This recognition of a broader community raises the possibility that the microbiome may disrupt the balance between infection and disease. Additionally, NTM disease progression and antimicrobial therapy may affect the healthy steady state of the host and function of the microbiome, contributing to further dysbiosis and clinical deterioration. There have been limited studies assessing how NTM may influence the relationship between microbiome and host. In this review, we highlight available studies about NTM and the microbiome, postulate on virulence mechanisms by which these microorganisms communicate and discuss implications for treatment.
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Affiliation(s)
- Christina S Thornton
- Division of Respirology, University of Calgary, Calgary, Canada .,Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Joint first authors
| | - Madeline Mellett
- Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Joint first authors
| | - Julie Jarand
- Division of Respirology, University of Calgary, Calgary, Canada.,Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,TB Services, University of Calgary, Calgary, Canada
| | - Leila Barss
- Division of Respirology, University of Calgary, Calgary, Canada.,Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,TB Services, University of Calgary, Calgary, Canada
| | - Stephen K Field
- Division of Respirology, University of Calgary, Calgary, Canada.,Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,TB Services, University of Calgary, Calgary, Canada
| | - Dina A Fisher
- Division of Respirology, University of Calgary, Calgary, Canada.,Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,TB Services, University of Calgary, Calgary, Canada.,Dept of Community Health Sciences, University of Calgary, Calgary, Canada
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19
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Pedersen RR, Krömker V, Bjarnsholt T, Dahl-Pedersen K, Buhl R, Jørgensen E. Biofilm Research in Bovine Mastitis. Front Vet Sci 2021; 8:656810. [PMID: 34026893 PMCID: PMC8138050 DOI: 10.3389/fvets.2021.656810] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/09/2021] [Indexed: 12/20/2022] Open
Abstract
Bovine mastitis is one of the most important diseases in the dairy industry and has detrimental impact on the economy and welfare of the animals. Further, treatment failure results in increased antibiotic use in the dairy industry, as some of these mastitis cases for unknown reasons are not resolved despite standard antibiotic treatment. Chronic biofilm infections are notoriously known to be difficult to eradicate with antibiotics and biofilm formation could be a possible explanation for mastitis cases that are not resolved by standard treatment. This paper reviews the current literature on biofilm in bovine mastitis research to evaluate the status and methods used in the literature. Focus of the current research has been on isolates from milk samples and investigation of their biofilm forming properties in vitro. However, in vitro observations of biofilm formation are not easily comparable with the in vivo situation inside the udder. Only two papers investigate the location and distribution of bacterial biofilms inside udders of dairy cows with mastitis. Based on the current knowledge, the role of biofilm in bovine mastitis is still unclear and more in vivo investigations are needed to uncover the actual role of biofilm formation in the pathogenesis of bovine mastitis.
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Affiliation(s)
- Regitze Renee Pedersen
- Department of Veterinary Clinical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Volker Krömker
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Department Immunology and Microbiology, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Kirstin Dahl-Pedersen
- Department of Veterinary Clinical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rikke Buhl
- Department of Veterinary Clinical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Elin Jørgensen
- Department Immunology and Microbiology, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
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20
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Abstract
Animals live in symbiosis with numerous microbe species. While some can protect hosts from infection and benefit host health, components of the microbiota or changes to the microbial landscape have the potential to facilitate infections and worsen disease severity. Pathogens and pathobionts can exploit microbiota metabolites, or can take advantage of a depletion in host defences and changing conditions within a host, to cause opportunistic infection. The microbiota might also favour a more virulent evolutionary trajectory for invading pathogens. In this review, we consider the ways in which a host microbiota contributes to infectious disease throughout the host's life and potentially across evolutionary time. We further discuss the implications of these negative outcomes for microbiota manipulation and engineering in disease management.
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Affiliation(s)
- Emily J. Stevens
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kieran A. Bates
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kayla C. King
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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21
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Veschetti L, Sandri A, Patuzzo C, Melotti P, Malerba G, Lleò MM. Mobilome Analysis of Achromobacter spp. Isolates from Chronic and Occasional Lung Infection in Cystic Fibrosis Patients. Microorganisms 2021; 9:microorganisms9010130. [PMID: 33430044 PMCID: PMC7826576 DOI: 10.3390/microorganisms9010130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/23/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022] Open
Abstract
Achromobacter spp. is an opportunistic pathogen that can cause lung infections in patients with cystic fibrosis (CF). Although a variety of mobile genetic elements (MGEs) carrying antimicrobial resistance genes have been identified in clinical isolates, little is known about the contribution of Achromobacter spp. mobilome to its pathogenicity. To provide new insights, we performed bioinformatic analyses of 54 whole genome sequences and investigated the presence of phages, insertion sequences (ISs), and integrative and conjugative elements (ICEs). Most of the detected phages were previously described in other pathogens and carried type II toxin-antitoxin systems as well as other pathogenic genes. Interestingly, the partial sequence of phage Bcep176 was found in all the analyzed Achromobacter xylosoxidans genome sequences, suggesting the integration of this phage in an ancestor strain. A wide variety of IS was also identified either inside of or in proximity to pathogenicity islands. Finally, ICEs carrying pathogenic genes were found to be widespread among our isolates and seemed to be involved in transfer events within the CF lung. These results highlight the contribution of MGEs to the pathogenicity of Achromobacter species, their potential to become antimicrobial targets, and the need for further studies to better elucidate their clinical impact.
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Affiliation(s)
- Laura Veschetti
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (L.V.); (C.P.); (G.M.)
| | - Angela Sandri
- Department of Diagnostics and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy;
| | - Cristina Patuzzo
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (L.V.); (C.P.); (G.M.)
| | - Paola Melotti
- Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Integrata Verona, 37126 Verona, Italy;
| | - Giovanni Malerba
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (L.V.); (C.P.); (G.M.)
| | - Maria M. Lleò
- Department of Diagnostics and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy;
- Correspondence:
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22
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McLaren MR, Callahan BJ. Pathogen resistance may be the principal evolutionary advantage provided by the microbiome. Philos Trans R Soc Lond B Biol Sci 2020. [PMID: 32772671 DOI: 10.1098/rstb.2019.0592rstb20190592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
To survive, plants and animals must continually defend against pathogenic microbes that would invade and disrupt their tissues. Yet they do not attempt to extirpate all microbes. Instead, they tolerate and even encourage the growth of commensal microbes, which compete with pathogens for resources and via direct inhibition. We argue that hosts have evolved to cooperate with commensals in order to enhance the pathogen resistance this competition provides. We briefly describe competition between commensals and pathogens within the host, consider how natural selection might favour hosts that tilt this competition in favour of commensals, and describe examples of extant host traits that may serve this purpose. Finally, we consider ways that this cooperative immunity may have facilitated the adaptive evolution of non-pathogen-related host traits. On the basis of these observations, we argue that pathogen resistance vies with other commensal-provided benefits for being the principal evolutionary advantage provided by the microbiome to host lineages across the tree of life. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Michael R McLaren
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC 27607, USA
| | - Benjamin J Callahan
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC 27607, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
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23
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Martinson JNV, Walk ST. Escherichia coli Residency in the Gut of Healthy Human Adults. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0003-2020. [PMID: 32978935 PMCID: PMC7523338 DOI: 10.1128/ecosalplus.esp-0003-2020] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Indexed: 12/22/2022]
Abstract
Escherichia coli is one of the most well-studied bacterial species, but several significant knowledge gaps remain regarding its ecology and natural history. Specifically, the most important factors influencing its life as a member of the healthy human gut microbiome are either underevaluated or currently unknown. Distinct E. coli population dynamics have been observed over the past century from a handful of temporal studies conducted in healthy human adults. Early studies using serology up to the most recent studies using genotyping and DNA sequencing approaches have all identified long-lived E. coli residents and short-lived transients. This review summarizes these discoveries and other studies that focused on the underlying mechanisms that lead to establishment and maintenance of E. coli residency in healthy human adults. Many fundamental knowledge gaps remain and are highlighted with the hope of facilitating future studies in this exciting research area.
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Affiliation(s)
| | - Seth T Walk
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717
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24
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McLaren MR, Callahan BJ. Pathogen resistance may be the principal evolutionary advantage provided by the microbiome. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190592. [PMID: 32772671 PMCID: PMC7435163 DOI: 10.1098/rstb.2019.0592] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
To survive, plants and animals must continually defend against pathogenic microbes that would invade and disrupt their tissues. Yet they do not attempt to extirpate all microbes. Instead, they tolerate and even encourage the growth of commensal microbes, which compete with pathogens for resources and via direct inhibition. We argue that hosts have evolved to cooperate with commensals in order to enhance the pathogen resistance this competition provides. We briefly describe competition between commensals and pathogens within the host, consider how natural selection might favour hosts that tilt this competition in favour of commensals, and describe examples of extant host traits that may serve this purpose. Finally, we consider ways that this cooperative immunity may have facilitated the adaptive evolution of non-pathogen-related host traits. On the basis of these observations, we argue that pathogen resistance vies with other commensal-provided benefits for being the principal evolutionary advantage provided by the microbiome to host lineages across the tree of life. This article is part of the theme issue ‘The role of the microbiome in host evolution’.
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Affiliation(s)
- Michael R McLaren
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC 27607, USA
| | - Benjamin J Callahan
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC 27607, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
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25
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Abstract
Bacteria have evolved a wide range of mechanisms to harm and kill their competitors, including chemical, mechanical and biological weapons. Here we review the incredible diversity of bacterial weapon systems, which comprise antibiotics, toxic proteins, mechanical weapons that stab and pierce, viruses, and more. The evolution of bacterial weapons is shaped by many factors, including cell density and nutrient abundance, and how strains are arranged in space. Bacteria also employ a diverse range of combat behaviours, including pre-emptive attacks, suicidal attacks, and reciprocation (tit-for-tat). However, why bacteria carry so many weapons, and why they are so often used, remains poorly understood. By comparison with animals, we argue that the way that bacteria live - often in dense and genetically diverse communities - is likely to be key to their aggression as it encourages them to dig in and fight alongside their clonemates. The intensity of bacterial aggression is such that it can strongly affect communities, via complex coevolutionary and eco-evolutionary dynamics, which influence species over space and time. Bacterial warfare is a fascinating topic for ecology and evolution, as well as one of increasing relevance. Understanding how bacteria win wars is important for the goal of manipulating the human microbiome and other important microbial systems.
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26
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Mosquera S, Stergiopoulos I, Leveau JHJ. Interruption of Aspergillus niger spore germination by the bacterially produced secondary metabolite collimomycin. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:306-313. [PMID: 32162788 DOI: 10.1111/1758-2229.12833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 06/10/2023]
Abstract
Collimonas fungivorans Ter331 (CfTer331) is a soil bacterium that produces collimomycin, a secondary metabolite that inhibits the vegetative growth of fungi. Here we show that CfTer331 can also interfere with fungal spore germination and that collimomycin biosynthesis is required for this activity. More specifically, in co-cultures of Aspergillus niger N402 (AnN402) co-nidiospores with CfTer331, the rate of transition from the isotropic to polarized stage of the germination process was reduced and the relatively few AnN402 conidiospores that completed the germination process were less likely to survive than those that were arrested in the isotropic phase. By contrast, a collimomycin-deficient mutant of CfTer331 had no effect on germination: in its presence, as in the absence or delayed presence of CfTer331, unhindered germination of conidiospores allowed rapid establishment of AnN402 mycelium and the subsequent acidification of the culture medium to the detriment of any bacteria present. However, when challenged early enough with CfTer331, the collimomycin-dependent arrest of the AnN402 germination process enabled CfTer331 to prevent AnN402 from forming mycelia and to gain dominance in the culture. We propose that the collimomycin-dependent arrest of spore germination represents an early intervention strategy used by CfTer331 to mitigate niche construction by fungi in nature.
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Affiliation(s)
- Sandra Mosquera
- Department of Plant Pathology, University of California Davis, One Shields Avenue, Davis, CA, 95616-8751
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California Davis, One Shields Avenue, Davis, CA, 95616-8751
| | - Johan H J Leveau
- Department of Plant Pathology, University of California Davis, One Shields Avenue, Davis, CA, 95616-8751
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27
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The evolution of the type VI secretion system as a disintegration weapon. PLoS Biol 2020; 18:e3000720. [PMID: 32453732 PMCID: PMC7274471 DOI: 10.1371/journal.pbio.3000720] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 06/05/2020] [Accepted: 04/30/2020] [Indexed: 12/22/2022] Open
Abstract
The type VI secretion system (T6SS) is a nanomachine used by many bacteria to drive a toxin-laden needle into other bacterial cells. Although the potential to influence bacterial competition is clear, the fitness impacts of wielding a T6SS are not well understood. Here we present a new agent-based model that enables detailed study of the evolutionary costs and benefits of T6SS weaponry during competition with other bacteria. Our model identifies a key problem with the T6SS. Because of its short range, T6SS activity becomes self-limiting, as dead cells accumulate in its way, forming “corpse barriers” that block further attacks. However, further exploration with the model presented a solution to this problem: if injected toxins can quickly lyse target cells in addition to killing them, the T6SS becomes a much more effective weapon. We tested this prediction with single-cell analysis of combat between T6SS-wielding Acinetobacter baylyi and T6SS-sensitive Escherichia coli. As predicted, delivery of lytic toxins is highly effective, whereas nonlytic toxins leave large patches of E. coli alive. We then analyzed hundreds of bacterial species using published genomic data, which suggest that the great majority of T6SS-wielding species do indeed use lytic toxins, indicative of a general principle underlying weapon evolution. Our work suggests that, in the T6SS, bacteria have evolved a disintegration weapon whose effectiveness often rests upon the ability to break up competitors. Understanding the evolutionary function of bacterial weapons can help in the design of probiotics that can both establish well and eliminate problem species. Bacteria attack each other with poison-tipped spears. This study combines theory and experiments to show that these spears (Type VI Secretion Systems) have evolved to break their targets apart with lytic toxins, as this then clears the way to rapidly stab new victims.
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Matthews AC, Mikonranta L, Raymond B. Shifts along the parasite-mutualist continuum are opposed by fundamental trade-offs. Proc Biol Sci 2020; 286:20190236. [PMID: 30940052 DOI: 10.1098/rspb.2019.0236] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Theory suggests that symbionts can readily evolve more parasitic or mutualistic strategies with respect to hosts. However, many symbionts have stable interactions with hosts that improve nutrient assimilation or confer protection from pathogens. We explored the potential for evolution of increased parasitism or decreased parasitism and mutualism in a natural gut symbiosis between larvae of Plutella xylostella and the microbe Enterobacter cloacae. We focused on interactions with the pathogen, Bacillus thuringiensis: selecting for parasitism in terms of facilitating pathogen infection, or increased mutualism in terms of host protection. Selection for parasitism led to symbionts increasing pathogen-induced mortality but reduced their competitive ability with pathogens and their in vitro growth rates. Symbionts did not evolve to confer protection from pathogens. However, several lineages evolved reduced parasitism, primarily in terms of moderating impacts on host growth, potentially because prudence pays dividends through increased host size. Overall, the evolution of increased parasitism was achievable but was opposed by trade-offs likely to reduce fitness. The evolution of protection may not have occurred because suppressing growth of B. thuringiensis in the gut might provide only weak protection or because evolution towards protective interactions was opposed by the loss of competitive fitness in symbionts.
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Affiliation(s)
- Andrew C Matthews
- 1 School of Biological Science, Royal Holloway University of London , Egham, Surrey TW20 0EX , UK.,2 University of Exeter , Penryn Campus, Penryn, Cornwall TR10 9FE , UK
| | - Lauri Mikonranta
- 2 University of Exeter , Penryn Campus, Penryn, Cornwall TR10 9FE , UK.,3 Department of Biology, University of York , Wentworth Way, York YO10 5DD , UK
| | - Ben Raymond
- 1 School of Biological Science, Royal Holloway University of London , Egham, Surrey TW20 0EX , UK.,2 University of Exeter , Penryn Campus, Penryn, Cornwall TR10 9FE , UK
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29
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Tolmachev IA, Lavrukova OS. [Interaction of various necrobionts during corpse decomposition and application of the microbiological zoological study data for the reconstruction of the conditions of the post-mortem period]. Sud Med Ekspert 2020; 63:61-64. [PMID: 32040091 DOI: 10.17116/sudmed20206301161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Analysis of the scientific literature demonstrated that the study of the dynamic of post-mortem changes is one of the actual problems of the forensic thanatology. The establishment of patterns occurring in the post-mortem period is directly related to the determination of the duration of this period and, accordingly, the post-mortem interval. This is especially difficult in cases where the object of study is in a state of putrefactive changes or in the form of skeletonized remains with a minimal amount of soft tissue. The terms of the post-mortem transformation of the body due to putrefactive processes, the destruction of corpse tissue by insects and vertebral scavengers, its skeletonization and fragmentation are very variable. In this regard, it seems relevant to comprehensively compare the results of traditional methods for studying a corpse and studying the effects of microflora, entomofauna and vertebral scavengers. The data obtained will allow experts to more accurately and objectively reconstruct the conditions of the post-mortem period using forensic-zoological and microbial-entomological criteria.
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Affiliation(s)
- I A Tolmachev
- Department of Forensic Medicine of the S.M. Kirov Military Medical Academy, St. Petersburg, Russia, 194044
| | - O S Lavrukova
- Department of Anatomy, Topographic Anatomy and Operative Surgery, Pathological Anatomy, Forensic Medicine, Petrozavodsk State University, Petrozavodsk, Russia, 185910
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30
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Hernández-Gómez O, Wuerthner V, Hua J. Amphibian Host and Skin Microbiota Response to a Common Agricultural Antimicrobial and Internal Parasite. MICROBIAL ECOLOGY 2020; 79:175-191. [PMID: 31093726 DOI: 10.1007/s00248-019-01351-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/24/2019] [Indexed: 06/09/2023]
Abstract
Holistic approaches that simultaneously characterize responses of both microbial symbionts and their hosts to environmental shifts are imperative to understanding the role of microbiotas on host health. Using the northern leopard frog (Lithobates pipiens) as our model, we investigated the effects of a common trematode (family Echinostomatidae), a common agricultural antimicrobial (Sulfadimethoxine; SDM), and their interaction on amphibian skin microbiota and amphibian health (growth metrics and susceptibility to parasites). In the trematode-exposed individuals, we noted an increase in alpha diversity and a shift in microbial communities. In the SDM-treated individuals, we found a change in the composition of the skin microbiota similar to those induced by the trematode treatment. Groups treated with SDM, echinostomes, or a combination of SDM and echinostomes, had higher relative abundances of OTUs assigned to Flavobacterium and Acinetobacter. Both of these genera have been associated with infectious disease in amphibians and the production of anti-pathogen metabolites. Similar changes in microbial community composition between SDM and trematode exposed individuals may have resulted from stress-related disruption of host immunity. Despite changes in the microbiota, we found no effect of echinostomes and SDM on host health. Given the current disease- and pollution-related threats facing amphibians, our study highlights the need to continue to evaluate the influence of natural and anthropogenic stressors on host-associated microbial communities.
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Affiliation(s)
- Obed Hernández-Gómez
- Department of Environmental Science, Policy, and Management, University of California-Berkeley, Berkeley, CA, 94720, USA.
| | - Vanessa Wuerthner
- Biological Sciences Department, Binghamton University, Binghamton, NY, 13902, USA
| | - Jessica Hua
- Biological Sciences Department, Binghamton University, Binghamton, NY, 13902, USA
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31
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Makowski M, Silva ÍC, Pais do Amaral C, Gonçalves S, Santos NC. Advances in Lipid and Metal Nanoparticles for Antimicrobial Peptide Delivery. Pharmaceutics 2019; 11:E588. [PMID: 31717337 PMCID: PMC6920925 DOI: 10.3390/pharmaceutics11110588] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial peptides (AMPs) have been described as excellent candidates to overcome antibiotic resistance. Frequently, AMPs exhibit a wide therapeutic window, with low cytotoxicity and broad-spectrum antimicrobial activity against a variety of pathogens. In addition, some AMPs are also able to modulate the immune response, decreasing potential harmful effects such as sepsis. Despite these benefits, only a few formulations have successfully reached clinics. A common flaw in the druggability of AMPs is their poor pharmacokinetics, common to several peptide drugs, as they may be degraded by a myriad of proteases inside the organism. The combination of AMPs with carrier nanoparticles to improve delivery may enhance their half-life, decreasing the dosage and thus, reducing production costs and eventual toxicity. Here, we present the most recent advances in lipid and metal nanodevices for AMP delivery, with a special focus on metal nanoparticles and liposome formulations.
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Affiliation(s)
| | | | | | - Sónia Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal; (M.M.); (Í.C.S.); (C.P.d.A.)
| | - Nuno C. Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal; (M.M.); (Í.C.S.); (C.P.d.A.)
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32
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Liang C, Yao Z, Du S, Hong M, Wang K, Zhang D. Sediment pH, not the bacterial diversity, determines Escherichia coli O157:H7 survival in estuarine sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:1078-1086. [PMID: 31252105 DOI: 10.1016/j.envpol.2019.06.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/11/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Shiga toxin-producing Escherichia coli (E. coli) O157:H7 is recognized as a hazardous microorganism in the environment. Its longer survival might contribute to higher contamination risk. In this study, E. coli O157:H7 survival in estuarine sediments collected from south Hangzhou Bay was investigated. The survival time of E. coli O157:H7 in estuarine sediments increased with the distance to the water-land junction. Sediment pH was the most important factor in regulating E. coli O157:H7 survival in estuarine sediments. In addition, sediment nutrients and texture also played significant roles in the survival of E. coli O157:H7 in the sediments. On the other hand, bacterial diversity as determined by the alpha-diversity index had no significant effect on E. coli O157:H7 survival. However, specific families of bacteria were closely associated with E. coli O157:H7 survival in the sediments. Remarkably, some potential bacterial groups, e.g., the Desulfobacteraceae, Desulfobulbaceae and Desulfarculaceae families, which are mainly involved in the sulfur cycle, showed significant negative correlation with the E. coli O157:H7 survival in the sediments. On the whole, abiotic factors showed greater effects on E. coli O157:H7 survival in the test sediments than the bacterial community. Our findings provide a comprehensive understanding of E. coli O157:H7 survival and regulatory factors in estuarine sediments, establishing foundation for the prevention of pathogen contamination.
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Affiliation(s)
- Chunling Liang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Zhiyuan Yao
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; School of Civil and Environmental Engineering, Ningbo University, Ningbo, 315211, China.
| | - Shicong Du
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Man Hong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Kai Wang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo, 315211, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo, 315211, China.
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33
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Bhattacharya A, Toro Díaz VC, Morran LT, Bashey F. Evolution of increased virulence is associated with decreased spite in the insect-pathogenic bacterium Xenorhabdus nematophila. Biol Lett 2019; 15:20190432. [PMID: 31455168 DOI: 10.1098/rsbl.2019.0432] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Disease virulence may be strongly influenced by social interactions among pathogens, both during the time course of an infection and evolutionarily. Here, we examine how spiteful bacteriocin production in the insect-pathogenic bacterium Xenorhabdus nematophila is evolutionarily linked to its virulence. We expected a negative correlation between virulence and spite owing to their inverse correlations with growth. We examined bacteriocin production and growth across 14 experimentally evolved lineages that show faster host-killing relative to their ancestral population. Consistent with expectations, these more virulent lineages showed reduced bacteriocin production and faster growth relative to the ancestor. Further, bacteriocin production was negatively correlated with growth across the examined lineages. These results strongly support an evolutionary trade-off between virulence and bacteriocin production and lend credence to the view that disease management can be improved by exploiting pathogen social interactions.
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Affiliation(s)
- Amrita Bhattacharya
- Department of Biology, Indiana University Bloomington, 1001 E 3rd Street, Bloomington, IN, USA
| | - Valeria C Toro Díaz
- Department of Biology, Indiana University Bloomington, 1001 E 3rd Street, Bloomington, IN, USA
| | - Levi T Morran
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA, USA
| | - Farrah Bashey
- Department of Biology, Indiana University Bloomington, 1001 E 3rd Street, Bloomington, IN, USA
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34
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Murfin KE, Ginete DR, Bashey F, Goodrich-Blair H. Symbiont-mediated competition: Xenorhabdus bovienii confer an advantage to their nematode host Steinernema affine by killing competitor Steinernema feltiae. Environ Microbiol 2018; 21:10.1111/1462-2920.14278. [PMID: 29799156 PMCID: PMC6252146 DOI: 10.1111/1462-2920.14278] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/08/2018] [Accepted: 05/11/2018] [Indexed: 01/05/2023]
Abstract
Bacterial symbionts can affect several biotic interactions of their hosts, including their competition with other species. Nematodes in the genus Steinernema utilize Xenorhabdus bacterial symbionts for insect host killing and nutritional bioconversion. Here, we establish that the Xenorhabdus bovienii bacterial symbiont (Xb-Sa-78) of Steinernema affine nematodes can impact competition between S. affine and S. feltiae by a novel mechanism, directly attacking its nematode competitor. Through co-injection and natural infection assays we demonstrate the causal role of Xb-Sa-78 in the superiority of S. affine over S. feltiae nematodes during competition. Survival assays revealed that Xb-Sa-78 bacteria kill reproductive life stages of S. feltiae. Microscopy and timed infection assays indicate that Xb-Sa-78 bacteria colonize S. feltiae nematode intestines, which alters morphology of the intestine. These data suggest that Xb-Sa-78 may be an intestinal pathogen of the non-native S. feltiae nematode, although it is a nonharmful colonizer of the native nematode host, S. affine. Screening additional X. bovienii isolates revealed that intestinal infection and killing of S. feltiae is conserved among isolates from nematodes closely related to S. affine, although the underlying killing mechanisms may vary. Together, these data demonstrate that bacterial symbionts can modulate competition between their hosts, and reinforce specificity in mutualistic interactions.
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Affiliation(s)
- Kristen E Murfin
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Daren R Ginete
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Microbiology, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
| | - Farrah Bashey
- Department of Biology, Indiana University, Bloomington, IN, 47405-3700, USA
| | - Heidi Goodrich-Blair
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Microbiology, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
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35
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Wale N, Sim DG, Read AF. A nutrient mediates intraspecific competition between rodent malaria parasites in vivo. Proc Biol Sci 2018; 284:rspb.2017.1067. [PMID: 28747479 PMCID: PMC5543226 DOI: 10.1098/rspb.2017.1067] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 06/21/2017] [Indexed: 12/02/2022] Open
Abstract
Hosts are often infected with multiple strains of a single parasite species. Within-host competition between parasite strains can be intense and has implications for the evolution of traits that impact patient health, such as drug resistance and virulence. Yet the mechanistic basis of within-host competition is poorly understood. Here, we demonstrate that a parasite nutrient, para-aminobenzoic acid (pABA), mediates competition between a drug resistant and drug susceptible strain of the malaria parasite, Plasmodium chabaudi. We further show that increasing pABA supply to hosts infected with the resistant strain worsens disease and changes the relationship between parasite burden and pathology. Our experiments demonstrate that, even when there is profound top-down regulation (immunity), bottom-up regulation of pathogen populations can occur and that its importance may vary during an infection. The identification of resources that can be experimentally controlled opens up the opportunity to manipulate competitive interactions between parasites and hence their evolution.
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Affiliation(s)
- Nina Wale
- Center for Infectious Disease Dynamics and Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Derek G Sim
- Center for Infectious Disease Dynamics and Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew F Read
- Center for Infectious Disease Dynamics and Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.,Department of Entomology, The Pennsylvania State University, University Park, PA 16802, USA
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36
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Ashrafi R, Bruneaux M, Sundberg LR, Pulkkinen K, Ketola T. Application of high resolution melting assay (HRM) to study temperature-dependent intraspecific competition in a pathogenic bacterium. Sci Rep 2017; 7:980. [PMID: 28428555 PMCID: PMC5430548 DOI: 10.1038/s41598-017-01074-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/22/2017] [Indexed: 01/18/2023] Open
Abstract
Studies on species’ responses to climate change have focused largely on the direct effect of abiotic factors and in particular temperature, neglecting the effects of biotic interactions in determining the outcome of climate change projections. Many microbes rely on strong interference competition; hence the fitness of many pathogenic bacteria could be a function of both their growth properties and intraspecific competition. However, due to technical challenges in distinguishing and tracking individual strains, experimental evidence on intraspecific competition has been limited so far. Here, we developed a robust application of the high-resolution melting (HRM) assay to study head-to-head competition between mixed genotype co-cultures of a waterborne bacterial pathogen of fish, Flavobacterium columnare, at two different temperatures. We found that competition outcome in liquid cultures seemed to be well predicted by growth yield of isolated strains, but was mostly inconsistent with interference competition results measured in inhibition tests on solid agar, especially as no growth inhibition between strain pairs was detected at the higher temperature. These results suggest that, for a given temperature, the factors driving competition outcome differ between liquid and solid environments.
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Affiliation(s)
- Roghaieh Ashrafi
- Department of Biological and Environmental Science (and Nanoscience Center), University of Jyvaskyla, Centre of Excellence in Biological Interactions, P.O. Box 35, FI-40014, Jyvaskyla, Finland.
| | - Matthieu Bruneaux
- Department of Biological and Environmental Science (and Nanoscience Center), University of Jyvaskyla, Centre of Excellence in Biological Interactions, P.O. Box 35, FI-40014, Jyvaskyla, Finland
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science (and Nanoscience Center), University of Jyvaskyla, Centre of Excellence in Biological Interactions, P.O. Box 35, FI-40014, Jyvaskyla, Finland
| | - Katja Pulkkinen
- Department of Biological and Environmental Science, University of Jyvaskyla, P.O. Box 35, FI-40014, Jyvaskyla, Finland
| | - Tarmo Ketola
- Department of Biological and Environmental Science (and Nanoscience Center), University of Jyvaskyla, Centre of Excellence in Biological Interactions, P.O. Box 35, FI-40014, Jyvaskyla, Finland
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37
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Faillace CA, Lorusso NS, Duffy S. Overlooking the smallest matter: viruses impact biological invasions. Ecol Lett 2017; 20:524-538. [PMID: 28176452 DOI: 10.1111/ele.12742] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/28/2016] [Accepted: 01/05/2017] [Indexed: 12/12/2022]
Abstract
Parasites and pathogens have recently received considerable attention for their ability to affect biological invasions, however, researchers have largely overlooked the distinct role of viruses afforded by their unique ability to rapidly mutate and adapt to new hosts. With high mutation and genomic substitution rates, RNA and single-stranded DNA (ssDNA) viruses may be important constituents of invaded ecosystems, and could potentially behave quite differently from other pathogens. We review evidence suggesting that rapidly evolving viruses impact invasion dynamics in three key ways: (1) Rapidly evolving viruses may prevent exotic species from establishing self-sustaining populations. (2) Viruses can cause population collapses of exotic species in the introduced range. (3) Viruses can alter the consequences of biological invasions by causing population collapses and extinctions of native species. The ubiquity and frequent host shifting of viruses make their ability to influence invasion events likely. Eludicating the viral ecology of biological invasions will lead to an improved understanding of the causes and consequences of invasions, particularly as regards establishment success and changes to community structure that cannot be explained by direct interspecific interactions among native and exotic species.
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Affiliation(s)
- Cara A Faillace
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ, 08901, USA
| | - Nicholas S Lorusso
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ, 08901, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ, 08901, USA
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38
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Segura M, Calzas C, Grenier D, Gottschalk M. Initial steps of the pathogenesis of the infection caused by Streptococcus suis: fighting against nonspecific defenses. FEBS Lett 2016; 590:3772-3799. [PMID: 27539145 DOI: 10.1002/1873-3468.12364] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 08/11/2016] [Accepted: 08/16/2016] [Indexed: 12/16/2022]
Abstract
Interactions between a bacterial pathogen and its potentially susceptible host are initiated with the colonization step. During respiratory/oral infection, the pathogens must compete with the normal microflora, resist defense mechanisms of the local mucosal immunity, and finally reach, adhere, and breach the mucosal epithelial cell barrier in order to induce invasive disease. This is the case during infection by the swine and zoonotic pathogen Streptococcus suis, which is able to counteract mucosal barriers to induce severe meningitis and sepsis in swine and in humans. The initial steps of the pathogenesis of S. suis infection has been a neglected area of research, overshadowed by studies on the systemic and central nervous phases of the disease. In this Review article, we provide for the first time, an exclusive focus on S. suis colonization and the potential mechanisms involved in S. suis establishment at the mucosa, as well as the mechanisms regulating mucosal barrier breakdown. The role of mucosal immunity is also addressed. Finally, we demystify the extensive list of putative adhesins and virulence factors reported to be involved in the initial steps of pathogenesis by S. suis.
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Affiliation(s)
- Mariela Segura
- Laboratory of Immunology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Quebec, Canada.,Swine and Poultry Infectious Diseases Research Centre (CRIPA), Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Cynthia Calzas
- Laboratory of Immunology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Quebec, Canada.,Swine and Poultry Infectious Diseases Research Centre (CRIPA), Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada.,Laboratory of Streptococcus suis, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Quebec, Canada
| | - Daniel Grenier
- Swine and Poultry Infectious Diseases Research Centre (CRIPA), Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada.,Groupe de Recherche en Écologie Buccale (GREB), Faculté de Médecine Dentaire, Université Laval, Quebec City, Quebec, Canada
| | - Marcelo Gottschalk
- Swine and Poultry Infectious Diseases Research Centre (CRIPA), Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada.,Laboratory of Streptococcus suis, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Quebec, Canada
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40
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McNally L, Brown SP. Building the microbiome in health and disease: niche construction and social conflict in bacteria. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0298. [PMID: 26150664 PMCID: PMC4528496 DOI: 10.1098/rstb.2014.0298] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Microbes collectively shape their environment in remarkable ways via the products of their metabolism. The diverse environmental impacts of macro-organisms have been collated and reviewed under the banner of ‘niche construction’. Here, we identify and review a series of broad and overlapping classes of bacterial niche construction, ranging from biofilm production to detoxification or release of toxins, enzymes, metabolites and viruses, and review their role in shaping microbiome composition, human health and disease. Some bacterial niche-constructing traits can be seen as extended phenotypes, where individuals actively tailor their environment to their benefit (and potentially to the benefit of others, generating social dilemmas). Other modifications can be viewed as non-adaptive by-products from a producer perspective, yet they may lead to remarkable within-host environmental changes. We illustrate how social evolution and niche construction perspectives offer complementary insights into the dynamics and consequences of these traits across distinct timescales. This review highlights that by understanding the coupled bacterial and biochemical dynamics in human health and disease we can better manage host health.
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Affiliation(s)
- Luke McNally
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sam P Brown
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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41
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Vale PF, McNally L, Doeschl-Wilson A, King KC, Popat R, Domingo-Sananes MR, Allen JE, Soares MP, Kümmerli R. Beyond killing: Can we find new ways to manage infection? EVOLUTION MEDICINE AND PUBLIC HEALTH 2016; 2016:148-57. [PMID: 27016341 PMCID: PMC4834974 DOI: 10.1093/emph/eow012] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 03/14/2016] [Indexed: 01/06/2023]
Abstract
The antibiotic pipeline is running dry and infectious disease remains a major threat to public health. An efficient strategy to stay ahead of rapidly adapting pathogens should include approaches that replace, complement or enhance the effect of both current and novel antimicrobial compounds. In recent years, a number of innovative approaches to manage disease without the aid of traditional antibiotics and without eliminating the pathogens directly have emerged. These include disabling pathogen virulence-factors, increasing host tissue damage control or altering the microbiota to provide colonization resistance, immune resistance or disease tolerance against pathogens. We discuss the therapeutic potential of these approaches and examine their possible consequences for pathogen evolution. To guarantee a longer half-life of these alternatives to directly killing pathogens, and to gain a full understanding of their population-level consequences, we encourage future work to incorporate evolutionary perspectives into the development of these treatments.
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Affiliation(s)
- Pedro F Vale
- Centre for Immunity, Infection and Evolution Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Luke McNally
- Centre for Immunity, Infection and Evolution Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | | | - Kayla C King
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Roman Popat
- Centre for Immunity, Infection and Evolution Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Maria R Domingo-Sananes
- Institute for Genetics and Development of Rennes - CNRS UMR 6290, 2, Avenue Du Pr. Léon Bernard, Rennes 35043, France
| | - Judith E Allen
- Centre for Immunity, Infection and Evolution Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Miguel P Soares
- Instituto Gulbenkian De Ciência, Rua Da Quinta Grande, 6, Oeiras 2780-156, Portugal
| | - Rolf Kümmerli
- Department of Plant and Microbial Biology, University of Zürich, Switzerland
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42
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Lokmer A, Kuenzel S, Baines JF, Wegner KM. The role of tissue-specific microbiota in initial establishment success of Pacific oysters. Environ Microbiol 2016; 18:970-87. [DOI: 10.1111/1462-2920.13163] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 11/27/2015] [Indexed: 12/26/2022]
Affiliation(s)
- Ana Lokmer
- Helmholtz Centre for Polar and Marine Research; Alfred Wegener Institute; Coastal Ecology; Wadden Sea Station Sylt; List Sylt Germany
| | - Sven Kuenzel
- Max Planck Institute for Evolutionary Biology; August-Thienemann-Strasse 2 D-24306 Plön Germany
| | - John F. Baines
- Max Planck Institute for Evolutionary Biology; August-Thienemann-Strasse 2 D-24306 Plön Germany
- Institute for Experimental Medicine; Christian-Albrechts-University of Kiel; Arnold-Heller-Strasse 3 D-24105 Kiel Germany
| | - Karl Mathias Wegner
- Helmholtz Centre for Polar and Marine Research; Alfred Wegener Institute; Coastal Ecology; Wadden Sea Station Sylt; List Sylt Germany
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43
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Nedialkova LP, Sidstedt M, Koeppel MB, Spriewald S, Ring D, Gerlach RG, Bossi L, Stecher B. Temperate phages promote colicin-dependent fitness of Salmonella enterica serovar Typhimurium. Environ Microbiol 2015; 18:1591-603. [PMID: 26439675 DOI: 10.1111/1462-2920.13077] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 12/12/2022]
Abstract
Bacteria employ bacteriocins for interference competition in microbial ecosystems. Colicin Ib (ColIb), a pore-forming bacteriocin, confers a significant fitness benefit to Salmonella enterica serovar Typhimurium (S. Tm) in competition against commensal Escherichia coli in the gut. ColIb is released from S. Tm into the environment, where it kills susceptible competitors. However, colicin-specific release proteins, as they are known for other colicins, have not been identified in case of ColIb. Thus, its release mechanism has remained unclear. In the current study, we have established a new link between ColIb release and lysis activity of temperate, lambdoid phages. By the use of phage-cured S. Tm mutant strains, we show that the presence of temperate phages and their lysis genes is necessary and sufficient for release of active ColIb into the culture supernatant. Furthermore, phage-mediated lysis significantly enhanced S. Tm fitness in competition against a ColIb-susceptible competitor. Finally, transduction with the lambdoid phage 933W rescued the defect of E. coli strain MG1655 with respect to ColIb release. In conclusion, ColIb is released from bacteria in the course of phage lysis. Our data reveal a new mechanism for colicin release and point out a novel function of temperate phages in enhancing colicin-dependent bacterial fitness.
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Affiliation(s)
- Lubov P Nedialkova
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Maja Sidstedt
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Martin B Koeppel
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany.,German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany
| | - Stefanie Spriewald
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Diana Ring
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany.,German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany
| | - Roman G Gerlach
- Wernigerode Branch, Robert Koch Institute, Project Group 5, Burgstr. 37, 38855, Wernigerode, Germany
| | - Lionello Bossi
- CNRS, Centre de Genetique Moleculaire, Gif-sur-Yvette Cedex, 91198, France
| | - Bärbel Stecher
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany.,German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany
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44
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Bashey F. Within-host competitive interactions as a mechanism for the maintenance of parasite diversity. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140301. [PMID: 26150667 PMCID: PMC4528499 DOI: 10.1098/rstb.2014.0301] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2015] [Indexed: 12/11/2022] Open
Abstract
Variation among parasite strains can affect the progression of disease or the effectiveness of treatment. What maintains parasite diversity? Here I argue that competition among parasites within the host is a major cause of variation among parasites. The competitive environment within the host can vary depending on the parasite genotypes present. For example, parasite strategies that target specific competitors, such as bacteriocins, are dependent on the presence and susceptibility of those competitors for success. Accordingly, which parasite traits are favoured by within-host selection can vary from host to host. Given the fluctuating fitness landscape across hosts, genotype by genotype (G×G) interactions among parasites should be prevalent. Moreover, selection should vary in a frequency-dependent manner, as attacking genotypes select for resistance and genotypes producing public goods select for cheaters. I review competitive coexistence theory with regard to parasites and highlight a few key examples where within-host competition promotes diversity. Finally, I discuss how within-host competition affects host health and our ability to successfully treat infectious diseases.
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Affiliation(s)
- Farrah Bashey
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA
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45
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Affiliation(s)
- Troy Day
- Department of Mathematics and Statistics, Department of Biology, Queen's University Kingston, ON K7L 3N6, Canada
| | - Stephen C Stearns
- Department of Ecology and Evolutionary Biology, Yale University New Haven, CT 06520-8106, USA
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46
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Purcell P, Jary H, Perry A, Perry JD, Stewart CJ, Nelson A, Lanyon C, Smith DL, Cummings SP, De Soyza A. Polymicrobial airway bacterial communities in adult bronchiectasis patients. BMC Microbiol 2014; 14:130. [PMID: 24886473 PMCID: PMC4031157 DOI: 10.1186/1471-2180-14-130] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 05/12/2014] [Indexed: 01/19/2023] Open
Abstract
Background Chronic airway infection contributes to the underlying pathogenesis of non-cystic fibrosis bronchiectasis (NCFBr). In contrast to other chronic airway infections, associated with COPD and CF bronchiectasis, where polymicrobial communities have been implicated in lung damage due to the vicious circle of recurrent bacterial infections and inflammation, there is sparse information on the composition of bacterial communities in NCFBr. Seventy consecutive patients were recruited from an outpatient adult NCFBr clinic. Bacterial communities in sputum samples were analysed by culture and pyrosequencing approaches. Bacterial sequences were analysed using partial least square discrimination analyses to investigate trends in community composition and identify those taxa that contribute most to community variation. Results The lower airway in NCFBr is dominated by three bacterial taxa Pasteurellaceae, Streptococcaceae and Pseudomonadaceae. Moreover, the bacterial community is much more diverse than indicated by culture and contains significant numbers of other genera including anaerobic Prevotellaceae, Veillonellaceae and Actinomycetaceae. We found particular taxa are correlated with different clinical states, 27 taxa were associated with acute exacerbations, whereas 11 taxa correlated with stable clinical states. We were unable to demonstrate a significant effect of antibiotic therapy, gender, or lung function on the diversity of the bacterial community. However, presence of clinically significant culturable taxa; particularly Pseudomonas aeruginosa and Haemophilus influenzae correlated with a significant change in the diversity of the bacterial community in the lung. Conclusions We have demonstrated that acute exacerbations, the frequency of exacerbation and episodes of clinical stability are correlated, in some patients, with a significantly different bacterial community structure, that are associated with a presence of particular taxa in the NCFBr lung. Moreover, there appears to be an inverse relationship between the abundance of P. aeruginosa and that of of H. influenzae within the NCFBr lung bacterial community. This interaction requires further exploration.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Stephen P Cummings
- Department of Applied Sciences, Ellison Building, University of Northumbria, Newcastle upon Tyne NE1 8ST, England.
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47
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Fraile A, Hily JM, Pagán I, Pacios LF, García-Arenal F. Host resistance selects for traits unrelated to resistance-breaking that affect fitness in a plant virus. Mol Biol Evol 2014; 31:928-39. [PMID: 24441034 DOI: 10.1093/molbev/msu045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
The acquisition by parasites of the capacity to infect resistant host genotypes, that is, resistance-breaking, is predicted to be hindered by across-host fitness trade-offs. All analyses of costs of resistance-breaking in plant viruses have focused on within-host multiplication without considering other fitness components, which may limit understanding of virus evolution. We have reported that host range expansion of tobamoviruses on L-gene resistant pepper genotypes was associated with severe within-host multiplication penalties. Here, we analyze whether resistance-breaking costs might affect virus survival in the environment by comparing tobamovirus pathotypes differing in infectivity on L-gene resistance alleles. We predicted particle stability from structural models, analyzed particle stability in vitro, and quantified virus accumulation in different plant organs and virus survival in the soil. Survival in the soil differed among tobamovirus pathotypes and depended on differential stability of virus particles. Structure model analyses showed that amino acid changes in the virus coat protein (CP) responsible for resistance-breaking affected the strength of the axial interactions among CP subunits in the rod-shaped particle, thus determining its stability and survival. Pathotypes ranked differently for particle stability/survival and for within-host accumulation. Resistance-breaking costs in survival add to, or subtract from, costs in multiplication according to pathotype. Hence, differential pathotype survival should be considered along with differential multiplication to understand the evolution of the virus populations. Results also show that plant resistance, in addition to selecting for resistance-breaking and for decreased multiplication, also selects for changes in survival, a trait unrelated to the host-pathogen interaction that may condition host range expansion.
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Affiliation(s)
- Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
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48
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Leggett HC, Brown SP, Reece SE. War and peace: social interactions in infections. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130365. [PMID: 24686936 PMCID: PMC3982666 DOI: 10.1098/rstb.2013.0365] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
One of the most striking facts about parasites and microbial pathogens that has emerged in the fields of social evolution and disease ecology in the past few decades is that these simple organisms have complex social lives, indulging in a variety of cooperative, communicative and coordinated behaviours. These organisms have provided elegant experimental tests of the importance of relatedness, kin discrimination, cooperation and competition, in driving the evolution of social strategies. Here, we briefly review the social behaviours of parasites and microbial pathogens, including their contributions to virulence, and outline how inclusive fitness theory has helped to explain their evolution. We then take a mechanistically inspired ‘bottom-up’ approach, discussing how key aspects of the ways in which parasites and pathogens exploit hosts, namely public goods, mobile elements, phenotypic plasticity, spatial structure and multi-species interactions, contribute to the emergent properties of virulence and transmission. We argue that unravelling the complexities of within-host ecology is interesting in its own right, and also needs to be better incorporated into theoretical evolution studies if social behaviours are to be understood and used to control the spread and severity of infectious diseases.
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Affiliation(s)
- Helen C Leggett
- Department of Zoology, Oxford University, , South Parks Road, Oxford OX1 3PS, UK
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49
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Weyrich LS, Feaga HA, Park J, Muse SJ, Safi CY, Rolin OY, Young SE, Harvill ET. Resident microbiota affect Bordetella pertussis infectious dose and host specificity. J Infect Dis 2013; 209:913-21. [PMID: 24227794 DOI: 10.1093/infdis/jit597] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Before contacting host tissues, invading pathogens directly or indirectly interact with host microbiota, but the effects of such interactions on the initial stages of infection are poorly understood. Bordetella pertussis is highly infectious among humans but requires large doses to colonize rodents, unlike a closely related zoonotic pathogen, Bordetella bronchiseptica, raising important questions about the contributions of bacterial competition to initial colonization and host selection. We observed that <100 colony-forming units (CFU) of B. bronchiseptica efficiently infected mice and displaced culturable host microbiota, whereas 10 000 CFU of B. pertussis were required to colonize murine nasal cavities and did not displace host microorganisms. Bacteria isolated from murine nasal cavities but not those from the human lower respiratory tract limited B. pertussis growth in vitro, indicating that interspecies competition may limit B. pertussis colonization of mice. Further, a broad-spectrum antibiotic treatment delivered before B. pertussis inoculation reduced the infectious dose to <100 CFU, and reintroduction of single Staphylococcus or Klebsiella species was sufficient to inhibit B. pertussis colonization of antibiotic-treated mice. Together, these results reveal that resident microorganisms can prevent B. pertussis colonization and influence host specificity, and they provide rationale for manipulating microbiomes to create more-accurate animal models of infectious diseases.
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50
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Interaction between the microbial community and invading Escherichia coli O157:H7 in soils from vegetable fields. Appl Environ Microbiol 2013; 80:70-6. [PMID: 24123745 DOI: 10.1128/aem.03046-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The survival of Escherichia coli O157:H7 in soils can contaminate vegetables, fruits, drinking water, etc. However, data on the impact of E. coli O157:H7 on soil microbial communities are limited. In this study, we monitored the changes in the indigenous microbial community by using the phospholipid fatty acid (PLFA) method to investigate the interaction of the soil microbial community with E. coli O157:H7 in soils. Simple correlation analysis showed that the survival of E. coli O157:H7 in the test soils was negatively correlated with the ratio of Gram-negative (G(-)) to Gram-positive (G(+)) bacterial PLFAs (G(-)/G(+) ratio). In particular, levels of 14 PLFAs were negatively correlated with the survival time of E. coli O157:H7. The contents of actinomycetous and fungal PLFAs in the test soils declined significantly (P, <0.05) after 25 days of incubation with E. coli O157:H7. The G(-)/G(+) ratio declined slightly, while the ratio of bacterial to fungal PLFAs (B/F ratio) and the ratio of normal saturated PLFAs to monounsaturated PLFAs (S/M ratio) increased, after E. coli O157:H7 inoculation. Principal component analysis results further indicated that invasion by E. coli O157:H7 had some effects on the soil microbial community. Our data revealed that the toxicity of E. coli O157:H7 presents not only in its pathogenicity but also in its effect on soil microecology. Hence, close attention should be paid to the survival of E. coli O157:H7 and its potential for contaminating soils.
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