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Mullinax SR, Darby AM, Gupta A, Chan P, Smith BR, Unckless RL. A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide. eLife 2025; 12:RP90638. [PMID: 40445192 PMCID: PMC12124834 DOI: 10.7554/elife.90638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2025] Open
Abstract
The innate immune system provides hosts with a crucial first line of defense against pathogens. While immune genes are often among the fastest evolving genes in the genome, in Drosophila, antimicrobial peptides (AMPs) are notable exceptions. Instead, AMPs may be under balancing selection, such that over evolutionary timescales, multiple alleles are maintained in populations. In this study, we focus on the Drosophila AMP Diptericin A, which has a segregating amino acid polymorphism associated with differential survival after infection with the Gram-negative bacteria Providencia rettgeri. Diptericin A also helps control opportunistic gut infections by common Drosophila gut microbes, especially those of Lactobacillus plantarum. In addition to genotypic effects on gut immunity, we also see strong sex-specific effects that are most prominent in flies without functional diptericin A. To further characterize differences in microbiomes between different diptericin genotypes, we used 16S metagenomics to look at the microbiome composition. We used both lab-reared and wild-caught flies for our sequencing and looked at overall composition as well as the differential abundance of individual bacterial families. Overall, we find flies that are homozygous for one allele of diptericin A are better equipped to survive a systemic infection from P. rettgeri, but in general have a shorter lifespans after being fed common gut commensals. Our results suggest a possible mechanism for the maintenance of genetic variation of diptericin A through the complex interactions of sex, systemic immunity, and the maintenance of the gut microbiome.
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Affiliation(s)
- Sarah R Mullinax
- Department of Molecular Biosciences, University of KansasLawrenceUnited States
| | - Andrea M Darby
- Department of Entomology, Cornell UniversityIthacaUnited States
| | - Anjali Gupta
- Department of Ecology and Evolutionary Biology, University of KansasLawrenceUnited States
| | - Patrick Chan
- Department of Molecular Biosciences, University of KansasLawrenceUnited States
| | - Brittny R Smith
- Department of Molecular Biosciences, University of KansasLawrenceUnited States
| | - Robert L Unckless
- Department of Molecular Biosciences, University of KansasLawrenceUnited States
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2
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Chmel M, Ježek P, Šafránková R, Ileninová Z, Vlasatá V, Mališová L. Escherichia marmotae: a multidrug-resistant opportunistic human pathogen - first clinical isolation in the Czech Republic. Folia Microbiol (Praha) 2025:10.1007/s12223-025-01267-3. [PMID: 40423922 DOI: 10.1007/s12223-025-01267-3] [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: 06/04/2024] [Accepted: 04/23/2025] [Indexed: 05/28/2025]
Abstract
The genus Escherichia comprises seven species, including Escherichia marmotae, described in 2015 from the feces of healthy Himalayan marmots (Marmota himalayana). This species exhibits atypical biochemical properties, such as negative lactose fermentation and indole production. The pathogenic potential of E. marmotae is demonstrated by its ability to invade epithelial cells and the presence of virulence genes. The first human infections with E. marmotae were recorded in Norway in 2021. This article describes the case of a 64-year-old man undergoing chemotherapy for urinary tract cancer, who was hospitalized with febrile neutropenia. An infection caused by E. marmotae and K. pneumoniae was detected. Laboratory diagnostics revealed a multidrug-resistant strain of E. coli producing KPC-type carbapenemase, subsequently identified as E. marmotae by MALDI-TOF MS (Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry) and confirmed by 16S rRNA sequencing and whole genome sequencing. Biochemical tests indicated similarities to E. coli. Virulence analysis revealed the presence of genes typical of pathogenic strains of E. coli. This case report is the first documented instance of E. marmotae in the Czech Republic and highlights the difficulty of distinguishing this species from E. coli in routine diagnostics. Accurate identification requires advanced methods such as MALDI-TOF and sequencing analysis.
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Affiliation(s)
- Martin Chmel
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, 12108, Prague, Czech Republic.
- Military Health Institute, Military Medical Agency, 16200, Prague, Czech Republic.
| | - Petr Ježek
- Department of Clinical Microbiology and Parasitology, Regional Hospital Příbram, Czechia, Czech Republic
| | - Renata Šafránková
- Czech National Collection of Type Cultures, National Institute of Public Health, Prague, Czech Republic
| | - Zuzana Ileninová
- National Reference Laboratory for E. Coli and Shigella, National Institute of Public Health, Prague, Czech Republic
| | - Valentyna Vlasatá
- Department of Clinical Microbiology and Parasitology, Regional Hospital Příbram, Czechia, Czech Republic
| | - Lucia Mališová
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czech Republic
- Department of Microbiology, 3, Faculty of Medicine, Charles University, University Hospital Kralovske Vinohrady and National Institute of Public Health, Prague, Czech Republic
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3
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Dumjahn L, Wein P, Molloy EM, Scherlach K, Trottmann F, Meisinger PR, Judd LM, Pidot SJ, Stinear TP, Richter I, Hertweck C. Dual-use virulence factors of the opportunistic pathogen Chromobacterium haemolyticum mediate hemolysis and colonization. mBio 2025; 16:e0360524. [PMID: 40178269 PMCID: PMC12077216 DOI: 10.1128/mbio.03605-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Accepted: 03/04/2025] [Indexed: 04/05/2025] Open
Abstract
Chromobacterium haemolyticum is an environmental bacterium that can cause severe and fatal opportunistic infections in humans and animals. Although C. haemolyticum is characterized by its strong β-hemolytic activity, the molecular basis of this phenotype has remained elusive over the more than 15 years since the species was first described. Herein, we report a family of cyclic lipodepsipeptides, the jagaricins, that are responsible for the potent hemolytic activity of C. haemolyticum. Comparative genomics of C. haemolyticum strains revealed a completely conserved gene locus (hml) encoding a nonribosomal peptide synthetase. Metabolic profiling of C. haemolyticum DSM 19808 identified a suite of cyclic lipodepsipeptides as the products, with the three main congeners (jagaricin A-C) being elucidated by a combination of tandem mass spectrometry, chemical derivatization, and nuclear magnetic resonance spectroscopy. Significantly, a C. haemolyticum hml deletion mutant is devoid of hemolytic activity. Moreover, purified jagaricins are hemolytic at low micromolar concentrations in an erythrocyte lysis assay. Further bioassays demonstrated that the cyclic lipodepsipeptides are crucial for the biofilm-forming and swarming behavior of C. haemolyticum. Matrix-assisted laser desorption ionization mass spectrometry imaging showed that primarily jagaricin B and C are involved in these processes in vitro. Our data shed light on the bioactivities of jagaricins, specialized metabolites that likely contribute to both successful niche colonization and the virulence potential of C. haemolyticum.IMPORTANCEDespite the rising incidence of Chromobacterium haemolyticum as a serious opportunistic pathogen, there is limited information on whether the competitive traits that ensure its survival in its freshwater niche also influence host infection. We reveal that C. haemolyticum produces specialized metabolites that not only cause its pronounced hemolytic phenotype but are also crucial for biofilm formation and swarming motility. These results exemplify a case of coincidental evolution, wherein the selective pressures encountered in a primary environmental niche drive the evolution of a trait impacting virulence. This knowledge provides a foundation for the development of antivirulence therapies against the emerging pathogen C. haemolyticum.
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Affiliation(s)
- Leo Dumjahn
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Philipp Wein
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Evelyn M. Molloy
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Felix Trottmann
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Philippe R. Meisinger
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Louise M. Judd
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Ingrid Richter
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
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4
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Cao Y, Song L, Zhu Y, Huang R, Zhang D, Christakos G, Wu J. A comparative analysis of the microbial community structure and functional gene profile between healthy and diseased Gracilaria lemaneiformis. MARINE ENVIRONMENTAL RESEARCH 2025; 209:107167. [PMID: 40306044 DOI: 10.1016/j.marenvres.2025.107167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 01/31/2025] [Accepted: 04/19/2025] [Indexed: 05/02/2025]
Abstract
Marine macroalgae and their associated microbial communities are pivotal in shaping coastal ecosystems and facilitating biogenic elements' biochemical cycles. In this study, we implemented the high-throughput sequencing technology to sequence bacterial 16S rRNA gene to comprehensively analyze the bacterial communities of healthy and diseased macroalgae as well as the surrounding seawaters. The results revealed that Proteobacteria and Bacteroidota were the two main phylum in all samples. Alphaproteobacteria, Gammaproteobacteria and Bacteroidota were the predominant bacterial classes. This observation underscored that the composition of bacterial communities remains comparably consistent at higher taxonomic levels, regardless of variations in their health statuses. The alpha-diversity indices of seawater bacterial communities, epiphytic communities, and endophytic communities showed no significant differences. Epiphytic bacterial communities harbored a greater proportion of colonized bacteria, such as Vibrio and Pseudomonas. While endophytic bacterial communities contained a higher presence of tissue-degrading microbial assemblages, the primary bacterial communities were predominantly affiliated with Rhodobacteraceae and Flavobacteriaceae. Temperature, salinity, nitrate and nitrite concentration were the most significant properties correlated with seawater, epiphytic and endophytic bacterial communities in different health statuses revealed by Canonical correspondence analysis. A PICRUSt analysis demonstrated the metabolic functional prediction. Nitrogen and sulfate reduction genes were mainly concentrated in epiphytic bacterial communities in good health. Endophytic bacterial communities in disease had higher carbon and nitrogen fixation potentials. These results confirmed that bacteria, macroalgae, and environmental properties had an interactive relationship, all related to the momentous ecological benefits of macroalgae.
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Affiliation(s)
- Yawen Cao
- Donghai Laboratory, Zhoushan, 316021, Zhejiang, China; Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Li Song
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Yaojia Zhu
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China.
| | - Runqiu Huang
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Dongdong Zhang
- Donghai Laboratory, Zhoushan, 316021, Zhejiang, China; Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - George Christakos
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Jiaping Wu
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China.
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5
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Kumar M, Devi WM, Choudhury TG, Kamilya D, Monsang SJ, Irungbam S, Saha RK. Unraveling the Bioactivities and Immunomodulatory Potential of Postbiotics Derived from Bacillus subtilis and B. amyloliquefaciens for Aquaculture. Probiotics Antimicrob Proteins 2025:10.1007/s12602-025-10528-z. [PMID: 40186049 DOI: 10.1007/s12602-025-10528-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2025] [Indexed: 04/07/2025]
Abstract
Postbiotics are molecules or soluble factors released as a result of a probiotic's metabolic activity. Their use in enhancing the growth, health, and disease resistance of aquatic animals has gained considerable attention in aquaculture. The present investigation was designed to assess the beneficial effects of postbiotic products derived from two probiotic strains, Bacillus subtilis and B. amyloliquefaciens. Postbiotics from B. subtilis exhibited significantly greater (p < 0.05) antibacterial activity against various pathogenic bacterial strains, more robust antagonistic growth kinetics, stronger anti-virulence potential, enhanced inhibition of biofilm formation, and increased antioxidant activity compared to those from B. amyloliquefaciens. Additionally, B. subtilis postbiotics triggered a significant (p < 0.05) cellular immune response, including higher myeloperoxidase activity, leucocyte proliferation, and production of nitric oxide and superoxide anions, along with a notable upregulation of immune-related gene expression (IL-1β, IL-10, IFN-γ, and TNF-α) in the head kidney leucocytes of Labeo rohita. A challenge test on L. rohita fingerlings confirmed the safety of B. subtilis postbiotics. These findings highlight the anti-pathogenic, immunostimulatory, and disease-resistant properties of B. subtilis postbiotics, suggesting their promising application in aquaculture.
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Affiliation(s)
- Monalisha Kumar
- Department of Aquatic Health and Environment, College of Fisheries, Central Agricultural University (Imphal), Lembucherra, Tripura, 799210, India
| | - Wangkheimayum Malemnganbi Devi
- Department of Aquatic Health and Environment, College of Fisheries, Central Agricultural University (Imphal), Lembucherra, Tripura, 799210, India
| | - Tanmoy Gon Choudhury
- Department of Aquatic Health and Environment, College of Fisheries, Central Agricultural University (Imphal), Lembucherra, Tripura, 799210, India.
| | - Dibyendu Kamilya
- Agricultural and Food Engineering Department, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India.
| | - Shongsir Joy Monsang
- Department of Aquatic Health and Environment, College of Fisheries, Central Agricultural University (Imphal), Lembucherra, Tripura, 799210, India
| | - Surajkumar Irungbam
- Department of Aquatic Health and Environment, College of Fisheries, Central Agricultural University (Imphal), Lembucherra, Tripura, 799210, India
| | - Ratan Kumar Saha
- Department of Aquatic Health and Environment, College of Fisheries, Central Agricultural University (Imphal), Lembucherra, Tripura, 799210, India
- Techno India University, Tripura, Agartala, 799004, Tripura, India
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6
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Silva LM, King KC, Koella JC. Dissecting transmission to understand parasite evolution. PLoS Pathog 2025; 21:e1012964. [PMID: 40132042 PMCID: PMC11936216 DOI: 10.1371/journal.ppat.1012964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2025] Open
Abstract
Parasite transmission is a complex, multi-stage process that significantly impacts host-parasite dynamics. Transmission plays a key role in epidemiology and virulence evolution, where it is expected to trade off with virulence. However, the extent to which classical models on virulence-transmission relationships apply in the real world is unclear. This insight piece proposes a novel framework that breaks transmission into three distinct stages: within-host infectiousness, an intermediate between-host stage (biotic or abiotic), and new host infection. Each stage is influenced by intrinsic and extrinsic factors to the parasite, which together will determine its transmission success. Analyzing the transmission stages separately and how they affect each other might enhance our understanding of which host-, parasite- or environmental-driven factors might shape parasite evolution and inform us about new effectors to act on when designing disease control strategies.
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Affiliation(s)
- Luís M. Silva
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Department of Zoology, University of British Columbia, University Boulevard, Vancouver, British Columbia, Canada
| | - Kayla C. King
- Department of Zoology, University of British Columbia, University Boulevard, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, University of British Columbia, Health Sciences Mall, Vancouver, British Columbia, Canada
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Jacob C. Koella
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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7
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Yang JL, Zhu H, Sadh P, Aumiller K, Guvener ZT, Ludington WB. Commensal acidification of specific gut regions produces a protective priority effect against enteropathogenic bacterial infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.12.637843. [PMID: 39990475 PMCID: PMC11844456 DOI: 10.1101/2025.02.12.637843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
The commensal microbiome has been shown to protect against newly introduced enteric pathogens in multiple host species, a phenomenon known as a priority effect. Multiple mechanisms can contribute to this protective priority effect, including antimicrobial compounds, nutrient competition, and pH changes. In Drosophila melanogaster , Lactiplantibacillus plantarum has been shown to protect against enteric pathogens. However, the strains of L. plantarum studied were derived from laboratory flies or non-fly environments and have been found to be unstable colonizers of the fly gut that mainly reside on the food. To study the priority effect using a naturally occurring microbial relationship, we isolated a wild-fly derived strain of L. plantarum that stably colonizes the fly gut in conjunction with a common enteric pathogen, Serratia marcescens . Flies stably associated with the L. plantarum strain were more resilient to oral Serratia marcescens infection as seen by longer lifespan and lower S. marcescens load in the gut. Through in vitro experiments, we found that L. plantarum inhibits S. marcescens growth due to acidification. We used gut imaging with pH-indicator dyes to show that L. plantarum reduces the gut pH to levels that restrict S. marcescens growth in vivo . In flies colonized with L. plantarum prior to S. marcescens infection, L. plantarum and S. marcescens are spatially segregated in the gut and S. marcescens is less abundant where L. plantarum heavily colonizes, indicating that acidification of specific gut regions is a mechanism of a protective priority effect.
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8
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Zalewska M, Brzozowska P, Rzewuska M, Kawecka-Grochocka E, Urbańska DM, Sakowski T, Bagnicka E. The quality and technological parameters of milk obtained from dairy cows with subclinical mastitis. J Dairy Sci 2025; 108:1285-1300. [PMID: 39521420 DOI: 10.3168/jds.2024-25346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 10/17/2024] [Indexed: 11/16/2024]
Abstract
Mastitis is one of the most common diseases in dairy cattle. It significantly reduces milk quality and yield, thus incurring economic losses for farmers. This study investigates the impact of various bacterial pathogens on the SCC, milk composition, and technological properties of milk samples from 302 clinically healthy Polish Holstein-Friesian cows kept under intensive rearing conditions. Of the 462 milk samples analyzed, 85.06% were contaminated with bacteria. The majority were coagulase-negative staphylococci (52.60%). Escherichia coli, Streptococcus dysgalactiae, and Streptococcus uberis, (Group 4) and Staphylococcus aureus and Streptococcus agalactiae (Group 5), collectively considered major pathogens, were identified in 16.66% of samples; their presence was associated with higher SCC levels. Additionally, contamination with Staph. aureus or Strep. agalactiae had prolonged clotting time, adversely affected curd and whey quality, with curd yield remaining unaltered. Bacterial contamination did not appear to significantly affect the yield of milk or its main components, namely protein, casein, lactose, fat, TS, solid nonfat, free fatty acid, or citric acid. Although pH, freezing point depression (FPD), and acidity also remained unaffected by bacterial contamination, they were significantly influenced by herd-year-season of calving and herd-year-time of sampling interaction effects. The results indicate that the presence of bacteria causing subclinical mastitis negatively influences milk processing potential. However, fixed linear regression indicated that the number of colony-forming units (cfu/mL) only had a significant influence on FPD and clotting time, and as such, the number of bacteria in a sample did not influence milk yield or quality during subclinical chronic mastitis.
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Affiliation(s)
- Magdalena Zalewska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland.
| | - Paulina Brzozowska
- Department of Biotechnology and Nutrigenomics, Institute of Genetics and Animal Biotechnology Polish Academy of Sciences, 05-552 Jastrzębiec, Poland
| | - Magdalena Rzewuska
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences SGGW, 02-787, Warsaw, Poland
| | - Ewelina Kawecka-Grochocka
- Department of Biotechnology and Nutrigenomics, Institute of Genetics and Animal Biotechnology Polish Academy of Sciences, 05-552 Jastrzębiec, Poland
| | - Daria M Urbańska
- Department of Biotechnology and Nutrigenomics, Institute of Genetics and Animal Biotechnology Polish Academy of Sciences, 05-552 Jastrzębiec, Poland
| | - Tomasz Sakowski
- Department of Biotechnology and Nutrigenomics, Institute of Genetics and Animal Biotechnology Polish Academy of Sciences, 05-552 Jastrzębiec, Poland
| | - Emilia Bagnicka
- Department of Biotechnology and Nutrigenomics, Institute of Genetics and Animal Biotechnology Polish Academy of Sciences, 05-552 Jastrzębiec, Poland.
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9
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Li J, Smith CA, Chen J, Bates KA, King KC. Warming During Different Life Stages has Distinct Impacts on Host Resistance Ecology and Evolution. Ecol Lett 2025; 28:e70087. [PMID: 39981937 PMCID: PMC11843851 DOI: 10.1111/ele.70087] [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: 07/17/2024] [Revised: 01/08/2025] [Accepted: 02/01/2025] [Indexed: 02/22/2025]
Abstract
Climate change is increasing extreme heating events and the potential for disease outbreaks. Whether hosts can adapt to infection with rising temperatures is important for forecasting species persistence. We tested whether warming-at different host life stages-affects the ecological and evolutionary dynamics of resistance in Caenorhabditis elegans infected by a wild bacterial pathogen. We competed resistant and susceptible genotypes across 10 passages and tracked the spread of resistance in the population. Infection and prolonged warming strongly selected for the resistant genotype. Warming during host development induced plastic defences against infection, reducing the selective pressure for costly genetic-based resistance. Resistance was lost under ambient temperatures and periodic warming. Selection for resistance was likely weakened at ambient temperatures by the dilution effect, whereby the resistant genotype reduced pathogen transmission. Evolutionary dynamics of resistance depend on the balance among pathogen virulence, costs of genetic-based resistance, the dilution effect and plastic defences induced by temperature stress.
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Affiliation(s)
- Jingdi Li
- Department of BiologyUniversity of OxfordOxfordUK
- Department of ZoologyUniversity of British ColumbiaVancouverCanada
| | | | - Jinlin Chen
- Department of BiologyUniversity of OxfordOxfordUK
| | - Kieran A. Bates
- Blizard Institute, Faculty of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Kayla C. King
- Department of BiologyUniversity of OxfordOxfordUK
- Department of ZoologyUniversity of British ColumbiaVancouverCanada
- Department of Microbiology & ImmunologyUniversity of British ColumbiaVancouverCanada
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10
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Carey CJ, Duggan N, Drabinska J, McClean S. Harnessing hypoxia: bacterial adaptation and chronic infection in cystic fibrosis. FEMS Microbiol Rev 2025; 49:fuaf018. [PMID: 40312783 PMCID: PMC12071387 DOI: 10.1093/femsre/fuaf018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 04/04/2025] [Accepted: 04/29/2025] [Indexed: 05/03/2025] Open
Abstract
The exquisite ability of bacteria to adapt to their environment is essential for their capacity to colonize hostile niches. In the cystic fibrosis (CF) lung, hypoxia is among several environmental stresses that opportunistic pathogens must overcome to persist and chronically colonize. Although the role of hypoxia in the host has been widely reviewed, the impact of hypoxia on bacterial pathogens has not yet been studied extensively. This review considers the bacterial oxygen-sensing mechanisms in three species that effectively colonize the lungs of people with CF, namely Pseudomonas aeruginosa, Burkholderia cepacia complex, and Mycobacterium abscessus and draws parallels between their three proposed oxygen-sensing two-component systems: BfiSR, FixLJ, and DosRS, respectively. Moreover, each species expresses regulons that respond to hypoxia: Anr, Lxa, and DosR, and encode multiple proteins that share similar homologies and function. Many adaptations that these pathogens undergo during chronic infection, including antibiotic resistance, protease expression, or changes in motility, have parallels in the responses of the respective species to hypoxia. It is likely that exposure to hypoxia in their environmental habitats predispose these pathogens to colonization of hypoxic niches, arming them with mechanisms than enable their evasion of the immune system and establish chronic infections. Overcoming hypoxia presents a new target for therapeutic options against chronic lung infections.
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Affiliation(s)
- Ciarán J Carey
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Niamh Duggan
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Joanna Drabinska
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Siobhán McClean
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
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11
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Yabueng N, Sansupa C, Noirungsee N, Kraisitnitikul P, Chansuebsri S, Janta R, Khoomrung S, Disayathanoowat T, Chantara S. Characterization of airborne microbial communities in northern Thailand: Impacts of smoke haze versus non-haze conditions. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2025; 364:125302. [PMID: 39542164 DOI: 10.1016/j.envpol.2024.125302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 11/09/2024] [Accepted: 11/10/2024] [Indexed: 11/17/2024]
Abstract
Data on airborne microorganisms, particularly in Southeast Asia, are more limited compared to chemical data. This study is the first to examine the community and diversity of microorganisms on PM2.5 in an urban area of Northern Thailand during both smoke haze and non-smoke haze periods of 2020. This study evaluated the composition of airborne bacteria and fungi and analyzed their association with the chemical composition of PM2.5 and meteorological variables. Significantly higher concentrations of PM2.5 and more chemical compounds were observed during the smoke haze period compared to the non-smoke haze period. Increased PM2.5 concentrations significantly altered both bacterial and fungal communities. The diversity and richness of airborne bacteria increased, whereas those of fungi decreased. The level of PM2.5 concentration (the carrier), the chemical composition of PM2.5 (the resources for survival), and the local meteorological conditions (relative humidity (RH)) were associated with the differences in bacterial and fungal populations. In addition, air originating from the west of the receptor site, influenced by both terrestrial and marine air mass routes, contributed to higher bacterial diversity and richness during the smoke haze period. In contrast, fungal diversity and richness were greater when the air came from the southwest, following a marine route. However, the primary health concern is pathogens, which were present in both periods (such as Clostridium, Aspergillus, and Cladosporium) and were especially abundant during smoke haze periods. This study highlights those airborne microorganisms, along with the particles and their chemical composition, are important components that can impact health, including that of humans, animals, and the environment.
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Affiliation(s)
- Nuttipon Yabueng
- Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Chakriya Sansupa
- Siriraj Center of Research Excellence in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Metabolomics and Phenomics Center (SiMPC), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Nuttapol Noirungsee
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand; Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Pavidarin Kraisitnitikul
- Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand; Office of Research Administration, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Sarana Chansuebsri
- Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Radshadaporn Janta
- Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand; Office of Research Administration, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Sakda Khoomrung
- Siriraj Center of Research Excellence in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Metabolomics and Phenomics Center (SiMPC), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University Bangkok, 10700, Thailand; Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science Mahidol University, Bangkok, 10400, Thailand; Thailand Metabolomics Society, Thailand
| | - Terd Disayathanoowat
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand; Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200, Thailand; Research Center of Deep Technology in Beekeeping and Bee Products for Sustainable Development Goals (SMART BEE SDGs), Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Somporn Chantara
- Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand; Chemistry Department, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.
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12
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Searle CL, Gutierrez SO, Ciubotariu II, López-Cruz A, Christie MR. Demographic rescue falters when pathogens are present. Ecology 2025; 106:e4495. [PMID: 39648926 DOI: 10.1002/ecy.4495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 07/25/2024] [Accepted: 09/30/2024] [Indexed: 12/10/2024]
Abstract
As natural populations continue to decline globally, direct forms of intervention are increasingly necessary to prevent extinction. One type of intervention, known as demographic rescue, occurs when individuals are added directly to a population to increase abundance and ultimately prevent population extinction. However, the role of infectious disease in demographic rescue remains unknown. To examine the effects of pathogens on demographic rescue, we used a host-pathogen system with the aquatic crustacean Daphnia dentifera as the host and the fungus Metschnikowia bicuspidata as the pathogen. We constructed a randomized 3 × 2 factorial experiment with three rescue treatments (none, low, high) and two pathogen treatments (unexposed, exposed), where the pathogen was introduced via infected individuals during rescue events. We found that adding more individuals to demographically depressed populations increased abundance over the short term; highly supplemented populations initially had 62% more individuals than populations that had no introduced individuals. However, by the end of the experiment, populations that did not have any individuals introduced averaged 640% higher abundance than populations where infected individuals had been added. Thus, the introduction of infected individuals can result in worse demographic outcomes for populations than if no rescue is attempted.
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Affiliation(s)
- Catherine L Searle
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Stephanie O Gutierrez
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Ilinca I Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Alana López-Cruz
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
- Department of Natural Sciences, University of Puerto Rico Aguadilla, Aguadilla, PO, Puerto Rico
- Department of Biology, University of Puerto Rico Rio Piedras, San Juan, PO, Puerto Rico
| | - Mark R Christie
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA
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13
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Entila F, Tsuda K. Taming of the microbial beasts: Plant immunity tethers potentially pathogenic microbiota members. Bioessays 2025; 47:e2400171. [PMID: 39404753 DOI: 10.1002/bies.202400171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 09/22/2024] [Accepted: 09/26/2024] [Indexed: 12/22/2024]
Abstract
Plants are in intimate association with taxonomically structured microbial communities called the plant microbiota. There is growing evidence that the plant microbiota contributes to the holistic performance and general health of plants, especially under unfavorable situations. Despite the attached benefits, surprisingly, the plant microbiota in nature also includes potentially pathogenic strains, signifying that the plant hosts have tight control over these microbes. Despite the conceivable role of plant immunity in regulating its microbiota, we lack a complete understanding of its role in governing the assembly, maintenance, and function of the plant microbiota. Here, we highlight the recent progress on the mechanistic relevance of host immunity in orchestrating plant-microbiota dialogues and discuss the pluses and perils of these microbial assemblies.
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Affiliation(s)
- Frederickson Entila
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kenichi Tsuda
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
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14
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Shi L, Yang M, Wei G, Wei X, Hong F, Ma J, Wu Z, Zheng Y, Yang M, Chen S, Zhang G, Dong L. Understanding the influence of plant genetic factors on rhizosphere microbiome assembly in Panax notoginseng. Front Microbiol 2024; 15:1479580. [PMID: 39736990 PMCID: PMC11683141 DOI: 10.3389/fmicb.2024.1479580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Accepted: 12/03/2024] [Indexed: 01/01/2025] Open
Abstract
Introduction Functional rhizosphere microbiomes (FRM) are critical for plant health and yield. However, the ecological succession of FRM and their links to plant genetic factors across the life cycle of perennial plants remain poorly understood. Methods This study profiled FRM, including plant-beneficial bacteria (PBB) and fungal plant pathogens (FPP), across different developmental stages of Panax notoginseng. Results The biodiversity of both PBB and FPP were significantly higher in rhizosphere compared with farmland soil, and exhibited different succession patterns with plant growth. The relative abundance of PBB, but not FPP, decreased after plant cultivation. There were significantly negative correlations between FPP and PBB, particularly the biocontrol subgroup (ρ = -0.56, p < 0.001). The antagonistic effects of biocontrol bacteria against fungal pathogens were further validated by in vitro assays. The fitting of neutral community model indicated that the deterministic assembly of PBB, especially the biocontrol subgroup, was the strongest at the 3rd-year root growth stage of P. notoginseng. Plant genes involved in protein export, biosynthesis of alkaloids and amino acids were identified as drivers of the deterministic assembly of biocontrol subcommunity by RNA-Seq analysis. Additionally, a total of 13 transcription factors potentially regulating the expression of these biosynthesis genes were identified through co-expression network. In summary, this study unveils the succession patterns of FRM throughout the life cycle of P. notoginseng and the underlying plant genetic mechanisms, providing valuable insights for developing new plant disease management strategies by manipulating microbes.
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Affiliation(s)
- Liping Shi
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mingming Yang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Guangfei Wei
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiuye Wei
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Fei Hong
- Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd., Zhangzhou, China
| | - Jiaxiang Ma
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhe Wu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuqing Zheng
- Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd., Zhangzhou, China
| | - Miyi Yang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shilin Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Guozhuang Zhang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Linlin Dong
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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15
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Gutiérrez-García K, Aumiller K, Dodge R, Obadia B, Deng A, Agrawal S, Yuan X, Wolff R, Zhu H, Hsia RC, Garud N, Ludington WB. A conserved bacterial genetic basis for commensal-host specificity. Science 2024; 386:1117-1122. [PMID: 39636981 PMCID: PMC11914777 DOI: 10.1126/science.adp7748] [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: 04/10/2024] [Accepted: 10/07/2024] [Indexed: 12/07/2024]
Abstract
Animals selectively acquire specific symbiotic gut bacteria from their environments that aid host fitness. To colonize, a symbiont must locate its niche and sustain growth within the gut. Adhesins are bacterial cell surface proteins that facilitate attachment to host tissues and are often virulence factors for opportunistic pathogens. However, the attachments are often transient and nonspecific, and additional mechanisms are required to sustain infection. In this work, we use live imaging of individual symbiotic bacterial cells colonizing the gut of living Drosophila melanogaster to show that Lactiplantibacillus plantarum specifically recognizes the fruit fly foregut as a distinct physical niche. L. plantarum establishes stably within its niche through host-specific adhesins encoded by genes carried on a colonization island. The adhesin binding domains are conserved throughout the Lactobacillales, and the island also encodes a secretion system widely conserved among commensal and pathogenic bacteria.
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Affiliation(s)
- Karina Gutiérrez-García
- Biosphere Sciences and Engineering Division, Carnegie Institution for Science, Baltimore, MD, USA
| | - Kevin Aumiller
- Biosphere Sciences and Engineering Division, Carnegie Institution for Science, Baltimore, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Ren Dodge
- Biosphere Sciences and Engineering Division, Carnegie Institution for Science, Baltimore, MD, USA
| | - Benjamin Obadia
- Biosphere Sciences and Engineering Division, Carnegie Institution for Science, Baltimore, MD, USA
| | - Ann Deng
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sneha Agrawal
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Xincheng Yuan
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Richard Wolff
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Haolong Zhu
- Biosphere Sciences and Engineering Division, Carnegie Institution for Science, Baltimore, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Ru-Ching Hsia
- Biosphere Sciences and Engineering Division, Carnegie Institution for Science, Baltimore, MD, USA
| | - Nandita Garud
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - William B. Ludington
- Biosphere Sciences and Engineering Division, Carnegie Institution for Science, Baltimore, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
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16
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Hafner L, Gadin E, Huang L, Frouin A, Laporte F, Gaultier C, Vieira A, Maudet C, Varet H, Moura A, Bracq-Dieye H, Tessaud-Rita N, Maury M, Dazas M, Legendre R, Gastineau P, Tsai YH, Coppée JY, Charlier C, Patin E, Chikhi R, Rocha EPC, Leclercq A, Disson O, Aschard H, Lecuit M. Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes. Nat Microbiol 2024; 9:3345-3361. [PMID: 39578578 DOI: 10.1038/s41564-024-01859-8] [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: 03/21/2024] [Accepted: 10/14/2024] [Indexed: 11/24/2024]
Abstract
Microbial pathogenesis is mediated by the expression of virulence genes. However, as microbes with identical virulence gene content can differ in their pathogenic potential, other virulence determinants must be involved. Here, by combining comparative genomics and transcriptomics of a large collection of isolates of the model pathogen Listeria monocytogenes, time-lapse microscopy, in vitro evolution and in vivo experiments, we show that the individual stress responsiveness of L. monocytogenes isolates determines their respective levels of virulence in vivo and reflects their degree of host adaptation. The transcriptional signature that accounts for the heterogeneity in the virulence of L. monocytogenes species is mediated by the stress response regulator SigB and driven by differential stress responsiveness. The tuning of SigB pathway responsiveness is polygenic and influenced by multiple, individually rare gene variations. This study reveals an overarching determinant of microbial virulence, challenging the paradigm of accessory virulence gene content as the major determinant of intraspecies virulence heterogeneity.
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Affiliation(s)
- Lukas Hafner
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Enzo Gadin
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Lei Huang
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Arthur Frouin
- Statistical Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS USR375, Paris, France
| | - Fabien Laporte
- Statistical Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS USR375, Paris, France
| | - Charlotte Gaultier
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Afonso Vieira
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Claire Maudet
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Hugo Varet
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
| | - Alexandra Moura
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
- National Reference Center and WHO Collaborating Center Listeria, Institut Pasteur, Paris, France
| | - Hélène Bracq-Dieye
- National Reference Center and WHO Collaborating Center Listeria, Institut Pasteur, Paris, France
| | - Nathalie Tessaud-Rita
- National Reference Center and WHO Collaborating Center Listeria, Institut Pasteur, Paris, France
| | - Mylène Maury
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
- National Reference Center and WHO Collaborating Center Listeria, Institut Pasteur, Paris, France
| | - Melody Dazas
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Rachel Legendre
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
| | - Pauline Gastineau
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Yu-Huan Tsai
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Jean-Yves Coppée
- Transcriptome et Epigenome Platform, Biomics, Center for Technological Resources and Research, Institut Pasteur, Université Paris Cité, Paris, France
| | - Caroline Charlier
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
- National Reference Center and WHO Collaborating Center Listeria, Institut Pasteur, Paris, France
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, Institut Imagine, APHP, Paris, France
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Rayan Chikhi
- Sequence Bioinformatics Group, Institut Pasteur, Université Paris Cité, Paris, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3525, Paris, France
| | - Alexandre Leclercq
- National Reference Center and WHO Collaborating Center Listeria, Institut Pasteur, Paris, France
| | - Olivier Disson
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France
| | - Hugues Aschard
- Statistical Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS USR375, Paris, France
| | - Marc Lecuit
- Biology of Infection Unit, Institut Pasteur, Université Paris Cité, Inserm U1117, Paris, France.
- National Reference Center and WHO Collaborating Center Listeria, Institut Pasteur, Paris, France.
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, Institut Imagine, APHP, Paris, France.
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17
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Chevillon C, de Thoisy B, Rakestraw AW, Fast KM, Pechal JL, Picq S, Epelboin L, Le Turnier P, Dogbe M, Jordan HR, Sandel MW, Benbow ME, Guégan JF. Ecological and evolutionary perspectives advance understanding of mycobacterial diseases. THE LANCET. MICROBE 2024; 5:100906. [PMID: 39116907 DOI: 10.1016/s2666-5247(24)00138-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 08/10/2024]
Abstract
Predicting the outbreak of infectious diseases and designing appropriate preventive health actions require interdisciplinary research into the processes that drive exposure to and transmission of disease agents. In the case of mycobacterial diseases, the epidemiological understanding of the scientific community hitherto was based on the clinical studies of infections in vertebrates. To evaluate the information gained by comprehensively accounting for the ecological and evolutionary constraints, we conducted literature searches assessing the role of mycobacteria interactions with non-vertebrate species in the origin of their pathogenicity and variations in disease risk. The reviewed literature challenges the current theory of person-to-person transmission for several mycobacterial infections. Furthermore, the findings suggest that diverse non-vertebrate organisms influence virulence, mediate transmission, and contribute to pathogen abundance in relation to vertebrate exposure. We advocate that an ecological and evolutionary framework provides novel insights to support a more comprehensive understanding of the prevention and management of diseases in vertebrates.
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Affiliation(s)
- Christine Chevillon
- MIVEGEC, Université de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Institut National de Recherches pour l'Agriculture, l'Alimentation et l'Environnement, Montpellier, France.
| | - Benoît de Thoisy
- Laboratoire des Interactions Virus Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana, France
| | - Alex W Rakestraw
- Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - Kayla M Fast
- Department of Wildlife, Fisheries, and Aquaculture, Mississippi State University, MS, USA
| | - Jennifer L Pechal
- Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - Sophie Picq
- Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - Loïc Epelboin
- Unité des Maladies Infectieuses et Tropicales, Centre Hospitalier de Cayenne, Cayenne, French Guiana, France; Centre d'Investigation Clinique Antilles-Guyane, Inserm 1424, Centre Hospitalier de Cayenne, Cayenne, French Guiana, France
| | - Paul Le Turnier
- Unité des Maladies Infectieuses et Tropicales, Centre Hospitalier de Cayenne, Cayenne, French Guiana, France; Centre d'Investigation Clinique Antilles-Guyane, Inserm 1424, Centre Hospitalier de Cayenne, Cayenne, French Guiana, France
| | - Magdalene Dogbe
- Department of Biological Sciences, Mississippi State University, MS, USA
| | - Heather R Jordan
- Department of Biological Sciences, Mississippi State University, MS, USA
| | - Michael W Sandel
- Department of Wildlife, Fisheries, and Aquaculture, Mississippi State University, MS, USA; Forest and Wildlife Research Center, Mississippi State University, MS, USA
| | - Mark Eric Benbow
- Department of Entomology, Michigan State University, East Lansing, MI, USA; Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, USA; Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA; Agbioresearch, Michigan State University, East Lansing, MI, USA
| | - Jean-François Guégan
- MIVEGEC, Université de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Institut National de Recherches pour l'Agriculture, l'Alimentation et l'Environnement, Montpellier, France; Epidémiologie des maladies animales et zoonotiques, Université Clermont Auvergne, INRAE, VetAgro Sup, Saint-Genès-Champanelle, France; Epidémiologie des maladies animales et zoonotiques, Université de Lyon, INRAE, VetAgro Sup, Marcy l'Etoile, France
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18
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Dotherow JE, Apenteng B, Hansen A, Aslan A. Private well water stewardship in rural Georgia. PLoS One 2024; 19:e0307281. [PMID: 39298452 PMCID: PMC11412682 DOI: 10.1371/journal.pone.0307281] [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: 08/07/2023] [Accepted: 07/02/2024] [Indexed: 09/21/2024] Open
Abstract
This study sought to identify the psychosocial influences on the practice of well stewardship behaviors (water testing, water treatment, and well maintenance) in rural Georgia, USA. Three interventions (education, the provision of household water treatment systems [HWTS], and both education and HWTS) were evaluated using a four-group, randomized controlled trial. A total of 64 private well owners completed a pretest measuring psychosocial factors and stewardship behaviors before receiving an intervention. Following a 104-day waiting period, participants completed a posttest and interviews were conducted to identify the barriers and facilitators to use (S1 File). Pretest results showed that 34% of well owners have ever tested their water and that only 25% treat their water before consumption. The education-only intervention showed no influence on stewardship behaviors, resulted in no new water tests and had no impact on psychosocial factors. The HWTS-only intervention had no significant effect on testing and treatment behaviors, though it had a significant effect on abilities (R2 = .87, p< 0.05) and self-regulation (R2 = 1.0, p<0.01). The intervention of both education and HWTS had no effect on testing and no significant effect on treatment behaviors, though had a significant effect on abilities (R2 = .84, p<0.05) and self-regulation (R2 = .93, p<0.05). This study identified three barriers to the use of HWTS: beliefs, knowledge, and functionality. Two factors (piece of mind and ease of use) were identified as facilitators to the use of HWTS. The results of this study indicate that providing water treatment systems does not guarantee use and that current educational efforts provided by state and local health departments may be ineffective.
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Affiliation(s)
- J. Edward Dotherow
- Department of Public Health, the University of Texas at Tyler Health Science Center, Tyler, Texas, United States of America
- Institute for Water and Health, Georgia Southern University, Savannah, Georgia, United States of America
| | - Bettye Apenteng
- Department of Health Policy and Community Health, Georgia Southern University, Statesboro, Georgia, United States of America
| | - Andrew Hansen
- Department of Health Policy and Community Health, Georgia Southern University, Statesboro, Georgia, United States of America
| | - Asli Aslan
- Institute for Water and Health, Georgia Southern University, Savannah, Georgia, United States of America
- Department of Biostatistics, Epidemiology and Environmental Health Sciences, Georgia Southern University, Statesboro, Georgia, United States of America
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19
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Piechowicz L, Kosznik-Kwaśnicka K, Jarzembowski T, Daca A, Necel A, Bonawenturczak A, Werbowy O, Stasiłojć M, Pałubicka A. Staphylococcus aureus Co-Infection in COVID-19 Patients: Virulence Genes and Their Influence on Respiratory Epithelial Cells in Light of Risk of Severe Secondary Infection. Int J Mol Sci 2024; 25:10050. [PMID: 39337536 PMCID: PMC11431965 DOI: 10.3390/ijms251810050] [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: 07/31/2024] [Revised: 09/15/2024] [Accepted: 09/16/2024] [Indexed: 09/30/2024] Open
Abstract
Pandemics from viral respiratory tract infections in the 20th and early 21st centuries were associated with high mortality, which was not always caused by a primary viral infection. It has been observed that severe course of infection, complications and mortality were often the result of co-infection with other pathogens, especially Staphylococcus aureus. During the COVID-19 pandemic, it was also noticed that patients infected with S. aureus had a significantly higher mortality rate (61.7%) compared to patients infected with SARS-CoV-2 alone. Our previous studies have shown that S. aureus strains isolated from patients with COVID-19 had a different protein profile than the strains in non-COVID-19 patients. Therefore, this study aims to analyze S. aureus strains isolated from COVID-19 patients in terms of their pathogenicity by analyzing their virulence genes, adhesion, cytotoxicity and penetration to the human pulmonary epithelial cell line A549. We have observed that half of the tested S. aureus strains isolated from patients with COVID-19 had a necrotizing effect on the A549 cells. The strains also showed greater variability in terms of their adhesion to the human cells than their non-COVID-19 counterparts.
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Affiliation(s)
- Lidia Piechowicz
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Gdansk, Debowa 25, 80-204 Gdansk, Poland
| | - Katarzyna Kosznik-Kwaśnicka
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Gdansk, Debowa 25, 80-204 Gdansk, Poland
| | - Tomasz Jarzembowski
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Gdansk, Debowa 25, 80-204 Gdansk, Poland
| | - Agnieszka Daca
- Department of Physiopathology, Medical University of Gdansk, Debinki 7, 80-211 Gdansk, Poland
| | - Agnieszka Necel
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Gdansk, Debowa 25, 80-204 Gdansk, Poland
| | - Ada Bonawenturczak
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Olesia Werbowy
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Małgorzata Stasiłojć
- Department of Cell Biology and Immunology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Debinki 1, 80-211 Gdansk, Poland
| | - Anna Pałubicka
- Specialist Hospital in Koscierzyna Sp. z o.o., Department of Laboratory and Microbiological Diagnostics, Koscierzyna, Alojzego Piechowskiego 36, 83-400 Koscierzyna, Poland
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20
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Rayner E, Lavenir A, Murray GGR, Matusewska M, Tucker AW, Welch JJ, Weinert LA. Variation in bacterial pathotype is consistent with the sit-and-wait hypothesis. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001500. [PMID: 39287974 PMCID: PMC11407517 DOI: 10.1099/mic.0.001500] [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: 05/28/2024] [Accepted: 08/22/2024] [Indexed: 09/19/2024]
Abstract
The sit-and-wait hypothesis predicts that bacteria can become more virulent when they survive and transmit outside of their hosts due to circumventing the costs of host mortality. While this hypothesis is largely supported theoretically and through comparative analysis, experimental validation is limited. Here we test this hypothesis in Streptococcus suis, an opportunistic zoonotic pig pathogen, where a pathogenic ecotype proliferated during the change to intensive pig farming that amplifies opportunities for fomite transmission. We show in an in vitro environmental survival experiment that pathogenic ecotypes survive for longer than commensal ecotypes, despite similar rates of decline. The presence of a polysaccharide capsule has no consistent effect on survival. Our findings suggest that extended survival in the food chain may augment the zoonotic capability of S. suis. Moreover, eliminating the long-term environmental survival of bacteria could be a strategy that will both enhance infection control and curtail the evolution of virulence.
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Affiliation(s)
- Eliza Rayner
- Dept. Veterinary Medicine, Madingley Road, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Amelie Lavenir
- Dept. Veterinary Medicine, Madingley Road, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Gemma G. R. Murray
- Dept. Veterinary Medicine, Madingley Road, University of Cambridge, Cambridge, CB3 0ES, UK
- Dept. Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Marta Matusewska
- Dept. Veterinary Medicine, Madingley Road, University of Cambridge, Cambridge, CB3 0ES, UK
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 2QQ, UK
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1RQ, UK
| | - Alexander W. Tucker
- Dept. Veterinary Medicine, Madingley Road, University of Cambridge, Cambridge, CB3 0ES, UK
| | - John J. Welch
- Dept. Genetics, Downing Street, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Lucy A. Weinert
- Dept. Veterinary Medicine, Madingley Road, University of Cambridge, Cambridge, CB3 0ES, UK
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21
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Hopkins HA, Lopezguerra C, Lau MJ, Raymann K. Making a Pathogen? Evaluating the Impact of Protist Predation on the Evolution of Virulence in Serratia marcescens. Genome Biol Evol 2024; 16:evae149. [PMID: 38961701 PMCID: PMC11332436 DOI: 10.1093/gbe/evae149] [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: 05/20/2024] [Revised: 06/25/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024] Open
Abstract
Opportunistic pathogens are environmental microbes that are generally harmless and only occasionally cause disease. Unlike obligate pathogens, the growth and survival of opportunistic pathogens do not rely on host infection or transmission. Their versatile lifestyles make it challenging to decipher how and why virulence has evolved in opportunistic pathogens. The coincidental evolution hypothesis postulates that virulence results from exaptation or pleiotropy, i.e. traits evolved for adaptation to living in one environment that have a different function in another. In particular, adaptation to avoid or survive protist predation has been suggested to contribute to the evolution of bacterial virulence (the training ground hypothesis). Here, we used experimental evolution to determine how the selective pressure imposed by a protist predator impacts the virulence and fitness of a ubiquitous environmental opportunistic bacterial pathogen that has acquired multidrug resistance: Serratia marcescens. To this aim, we evolved S. marcescens in the presence or absence of generalist protist predator, Tetrahymena thermophila. After 60 d of evolution, we evaluated genotypic and phenotypic changes by comparing evolved S. marcescens with the ancestral strain. Whole-genome shotgun sequencing of the entire evolved populations and individual isolates revealed numerous cases of parallel evolution, many more than statistically expected by chance, in genes associated with virulence. Our phenotypic assays suggested that evolution in the presence of a predator maintained virulence, whereas evolution in the absence of a predator resulted in attenuated virulence. We also found a significant correlation between virulence, biofilm formation, growth, and grazing resistance. Overall, our results provide evidence that bacterial virulence and virulence-related traits are maintained by selective pressures imposed by protist predation.
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Affiliation(s)
- Heather A Hopkins
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Christian Lopezguerra
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Meng-Jia Lau
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Kasie Raymann
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA
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22
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Mullinax SR, Darby AM, Gupta A, Chan P, Smith BR, Unckless RL. A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.18.553899. [PMID: 37662279 PMCID: PMC10473621 DOI: 10.1101/2023.08.18.553899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The innate immune system provides hosts with a crucial first line of defense against pathogens. While immune genes are often among the fastest evolving genes in the genome, in Drosophila , antimicrobial peptides (AMPs) are notable exceptions. Instead, AMPs may be under balancing selection, such that over evolutionary timescales multiple alleles are maintained in populations. In this study, we focus on the Drosophila antimicrobial peptide Diptericin A, which has a segregating amino acid polymorphism associated with differential survival after infection with the Gram-negative bacteria Providencia rettgeri . Diptericin A also helps control opportunistic gut infections by common Drosophila gut microbes, especially those of Lactobacillus plantarum . In addition to genotypic effects on gut immunity, we also see strong sex-specific effects that are most prominent in flies without functional diptericin A . To further characterize differences in microbiomes between different diptericin genotypes, we used 16S metagenomics to look at the microbiome composition. We used both lab reared and wild caught flies for our sequencing and looked at overall composition as well as the differential abundance of individual bacterial families. Overall, we find flies that are homozygous for one allele of diptericin A are better equipped to survive a systemic infection from P. rettgeri , but in general have a shorter lifespans after being fed common gut commensals. Our results suggest a possible mechanism for the maintenance of genetic variation of diptericin A through the complex interactions of sex, systemic immunity, and the maintenance of the gut microbiome.
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23
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Coelho MA, David-Palma M, Shea T, Bowers K, McGinley-Smith S, Mohammad AW, Gnirke A, Yurkov AM, Nowrousian M, Sun S, Cuomo CA, Heitman J. Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis. PLoS Biol 2024; 22:e3002682. [PMID: 38843310 PMCID: PMC11185503 DOI: 10.1371/journal.pbio.3002682] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 06/18/2024] [Accepted: 05/17/2024] [Indexed: 06/19/2024] Open
Abstract
In exploring the evolutionary trajectories of both pathogenesis and karyotype dynamics in fungi, we conducted a large-scale comparative genomic analysis spanning the Cryptococcus genus, encompassing both global human fungal pathogens and nonpathogenic species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species, covering virtually all known diversity within these genera. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at preadaptive pathogenic potential, our analysis found evidence of gene gain (via horizontal gene transfer) and gene loss in pathogenic Cryptococcus species, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the 2 genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5, or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes showed reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Overall, our findings advance our understanding of genetic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.
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Affiliation(s)
- Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Katharine Bowers
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sage McGinley-Smith
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Arman W. Mohammad
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Andrey M. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
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Yalamarty R, Magesh S, John D, Chakladar J, Li WT, Brumund KT, Wang-Rodriguez J, Ongkeko WM. The intratumor microbiome varies by geographical location and anatomical site in head and neck squamous cell carcinoma. Curr Probl Cancer 2024; 50:101100. [PMID: 38820649 DOI: 10.1016/j.currproblcancer.2024.101100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/29/2024] [Accepted: 04/25/2024] [Indexed: 06/02/2024]
Abstract
Head and Neck Squamous Cell Carcinoma (HNSCC) is a highly heterogeneous cancer that is characterized by distinct phenotypes based on anatomical site and etiological agents. Recently, the intratumor microbiome has been implicated in cancer pathogenesis and progression. Although it is well established that the gut microbiome varies with geographical location and is highly influenced by factors such as diet, environment, and genetics, the intratumor microbiome is not very well characterized. In this review, we aim to characterize the HNSCC intratumor microbiome by geographical location and anatomical site. We conducted a review of primary literature from PubMed and assessed studies based on relevancy and recency. To the best of our knowledge, we are the first to comprehensively examine the tumor microenvironment of HNSCC with respect to these two primary factors on a large scale. Our results suggest that there are unique bacterial and fungal biomarkers for HNSCC for each of the following geographical locations: North America, Asia, Europe, Australia, and Africa. We also identified a panel of microbial biomarkers that are unique to two primary HNSCC anatomic sites, as well as microbial biomarkers associated with various etiological agents of HNSCC. Future study of these microbes may improve HNSCC diagnostic and therapeutic modalities by accounting for differences based on geographic regions and anatomical sites.
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Affiliation(s)
- Rishabh Yalamarty
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Shruti Magesh
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Daniel John
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Jaideep Chakladar
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Wei Tse Li
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA; University of California San Francisco School of Medicine, San Francisco, CA 94143, USA
| | - Kevin T Brumund
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; Division of Head and Neck Surgery, Department of Surgery, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Jessica Wang-Rodriguez
- Pathology Service, VA San Diego Healthcare System, San Diego, CA 92161, USA; Department of Pathology, UC San Diego School of Medicine, San Diego, CA 92093, USA
| | - Weg M Ongkeko
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA.
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25
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Onyango LA, Liang J. Manuka honey as a non-antibiotic alternative against Staphylococcus spp. and their small colony variant (SCVs) phenotypes. Front Cell Infect Microbiol 2024; 14:1380289. [PMID: 38868298 PMCID: PMC11168119 DOI: 10.3389/fcimb.2024.1380289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/21/2024] [Indexed: 06/14/2024] Open
Abstract
The antibiotic resistance (ABR) crisis is an urgent global health priority. Staphylococci are among the problematic bacteria contributing to this emergency owing to their recalcitrance to many clinically important antibiotics. Staphylococcal pathogenesis is further complicated by the presence of small colony variants (SCVs), a bacterial subpopulation displaying atypical characteristics including retarded growth, prolific biofilm formation, heightened antibiotic tolerance, and enhanced intracellular persistence. These capabilities severely impede current chemotherapeutics, resulting in chronic infections, poor patient outcomes, and significant economic burden. Tackling ABR requires alternative measures beyond the conventional options that have dominated treatment regimens over the past 8 decades. Non-antibiotic therapies are gaining interest in this arena, including the use of honey, which despite having ancient therapeutic roots has now been reimagined as an alternative treatment beyond just traditional topical use, to include the treatment of an array of difficult-to-treat staphylococcal infections. This literature review focused on Manuka honey (MH) and its efficacy as an anti-staphylococcal treatment. We summarized the studies that have used this product and the technologies employed to study the antibacterial mechanisms that render MH a suitable agent for the management of problematic staphylococcal infections, including those involving staphylococcal SCVs. We also discussed the status of staphylococcal resistance development to MH and other factors that may impact its efficacy as an alternative therapy to help combat ABR.
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Affiliation(s)
- Laura A. Onyango
- Department of Biology, Trinity Western University, Langley, BC, Canada
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26
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Kerro Dego O, Vidlund J. Staphylococcal mastitis in dairy cows. Front Vet Sci 2024; 11:1356259. [PMID: 38863450 PMCID: PMC11165426 DOI: 10.3389/fvets.2024.1356259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/06/2024] [Indexed: 06/13/2024] Open
Abstract
Bovine mastitis is one of the most common diseases of dairy cattle. Even though different infectious microorganisms and mechanical injury can cause mastitis, bacteria are the most common cause of mastitis in dairy cows. Staphylococci, streptococci, and coliforms are the most frequently diagnosed etiological agents of mastitis in dairy cows. Staphylococci that cause mastitis are broadly divided into Staphylococcus aureus and non-aureus staphylococci (NAS). NAS is mainly comprised of coagulase-negative Staphylococcus species (CNS) and some coagulase-positive and coagulase-variable staphylococci. Current staphylococcal mastitis control measures are ineffective, and dependence on antimicrobial drugs is not sustainable because of the low cure rate with antimicrobial treatment and the development of resistance. Non-antimicrobial effective and sustainable control tools are critically needed. This review describes the current status of S. aureus and NAS mastitis in dairy cows and flags areas of knowledge gaps.
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Affiliation(s)
- Oudessa Kerro Dego
- Department of Animal Science, University of Tennessee, Knoxville, TN, United States
| | - Jessica Vidlund
- Department of Animal Science, University of Tennessee, Knoxville, TN, United States
- East Tennessee AgResearch and Education Center-Little River Animal and Environmental Unit, University of Tennessee, Walland, TN, United States
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27
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Braglia C, Alberoni D, Garrido PM, Porrini MP, Baffoni L, Scott D, Eguaras MJ, Di Gioia D, Mifsud D. Vairimorpha (Nosema) ceranae can promote Serratia development in honeybee gut: an underrated threat for bees? Front Cell Infect Microbiol 2024; 14:1323157. [PMID: 38808063 PMCID: PMC11131372 DOI: 10.3389/fcimb.2024.1323157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/04/2024] [Indexed: 05/30/2024] Open
Abstract
The genus Serratia harbors opportunistic pathogenic species, among which Serratia marcescens is pathogenic for honeybees although little studied. Recently, virulent strains of S. marcescens colonizing the Varroa destructor mite's mouth were found vectored into the honeybee body, leading to septicemia and death. Serratia also occurs as an opportunistic pathogen in the honeybee's gut with a low absolute abundance. The Serratia population seems controlled by the host immune system, but its presence may represent a hidden threat, ready to arise when honeybees are weakened by biotic and abiotic stressors. To shed light on the Serratia pathogen, this research aims at studying Serratia's development dynamics in the honeybee body and its interactions with the co-occurring fungal pathogen Vairimorpha ceranae. Firstly, the degree of pathogenicity and the ability to permeate the gut epithelial barrier of three Serratia strains, isolated from honeybees and belonging to different species (S. marcescens, Serratia liquefaciens, and Serratia nematodiphila), were assessed by artificial inoculation of newborn honeybees with different Serratia doses (104, 106, and 108 cells/mL). The absolute abundance of Serratia in the gut and in the hemocoel was assessed in qPCR with primers targeting the luxS gene. Moreover, the absolute abundance of Serratia was assessed in the gut of honeybees infected with V. ceranae at different development stages and supplied with beneficial microorganisms and fumagillin. Our results showed that all tested Serratia strains could pass through the gut epithelial barrier and proliferate in the hemocoel, with S. marcescens being the most pathogenic. Moreover, under cage conditions, Serratia better proliferates when a V. ceranae infection is co-occurring, with a positive and significant correlation. Finally, fumagillin and some of the tested beneficial microorganisms could control both Serratia and Vairimorpha development. Our findings suggest a correlation between the two pathogens under laboratory conditions, a co-occurring infection that should be taken into consideration by researches when testing antimicrobial compounds active against V. ceranae, and the related honeybees survival rate. Moreover, our findings suggest a positive control of Serratia by the environmental microorganism Apilactobacillus kunkeei in a in vivo model, confirming the potential of this specie as beneficial bacteria for honeybees.
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Affiliation(s)
- Chiara Braglia
- Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), University of Bologna, Bologna, Italy
| | - Daniele Alberoni
- Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), University of Bologna, Bologna, Italy
| | - Paula Melisa Garrido
- Centro de Investigación en Abejas Sociales (CIAS), Faculty of Exact and Natural Sciences (FCEyN), National University of Mar del Plata (UNMdP), Mar del Plata, Buenos Aires, Argentina
- Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM), National Scientific and Technical Research Council (CONICET), UNMdP, Centro Asoc. Simple Scientific research Commission Buenos Aires Province (CIC PBA), Mar del Plata, Buenos Aires, Argentina
| | - Martin Pablo Porrini
- Centro de Investigación en Abejas Sociales (CIAS), Faculty of Exact and Natural Sciences (FCEyN), National University of Mar del Plata (UNMdP), Mar del Plata, Buenos Aires, Argentina
- Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM), National Scientific and Technical Research Council (CONICET), UNMdP, Centro Asoc. Simple Scientific research Commission Buenos Aires Province (CIC PBA), Mar del Plata, Buenos Aires, Argentina
| | - Loredana Baffoni
- Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), University of Bologna, Bologna, Italy
| | | | - Martin Javier Eguaras
- Centro de Investigación en Abejas Sociales (CIAS), Faculty of Exact and Natural Sciences (FCEyN), National University of Mar del Plata (UNMdP), Mar del Plata, Buenos Aires, Argentina
- Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM), National Scientific and Technical Research Council (CONICET), UNMdP, Centro Asoc. Simple Scientific research Commission Buenos Aires Province (CIC PBA), Mar del Plata, Buenos Aires, Argentina
| | - Diana Di Gioia
- Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), University of Bologna, Bologna, Italy
| | - David Mifsud
- Institute of Earth Systems, L-Universita ta’ Malta, Msida, Malta
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28
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Bosch TCG, Blaser MJ, Ruby E, McFall-Ngai M. A new lexicon in the age of microbiome research. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230060. [PMID: 38497258 PMCID: PMC10945402 DOI: 10.1098/rstb.2023.0060] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/04/2023] [Indexed: 03/19/2024] Open
Abstract
At a rapid pace, biologists are learning the many ways in which resident microbes influence, and sometimes even control, their hosts to shape both health and disease. Understanding the biochemistry behind these interactions promises to reveal completely novel and targeted ways of counteracting disease processes. However, in our protocols and publications, we continue to describe these new results using a language that originated in a completely different context. This language developed when microbial interactions with hosts were perceived to be primarily pathogenic, as threats that had to be vanquished. Biomedicine had one dominating thought: winning this war against microorganisms. Today, we know that beyond their defensive roles, host tissues, especially epithelia, are vital to ensuring association with the normal microbiota, the communities of microbes that persistently live with the host. Thus, we need to adopt a language that better encompasses the newly appreciated importance of host-microbiota associations. We also need a language that frames the onset and progression of pathogenic conditions within the context of the normal microbiota. Such a reimagined lexicon should make it clear, from the very nature of its words, that microorganisms are primarily vital to our health, and only more rarely the cause of disease. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
| | - Martin J. Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Edward Ruby
- California Institute of Technology, Pasadena, CA 91125, USA
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29
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Barnes AJ, Bennett EF, Vezina B, Hudson AW, Hernandez GE, Nutter NA, Bray AS, Nagpal R, Wyres KL, Zafar MA. Ethanolamine metabolism through two genetically distinct loci enables Klebsiella pneumoniae to bypass nutritional competition in the gut. PLoS Pathog 2024; 20:e1012189. [PMID: 38713723 PMCID: PMC11101070 DOI: 10.1371/journal.ppat.1012189] [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: 12/03/2023] [Revised: 05/17/2024] [Accepted: 04/10/2024] [Indexed: 05/09/2024] Open
Abstract
Successful microbial colonization of the gastrointestinal (GI) tract hinges on an organism's ability to overcome the intense competition for nutrients in the gut between the host and the resident gut microbiome. Enteric pathogens can exploit ethanolamine (EA) in the gut to bypass nutrient competition. However, Klebsiella pneumoniae (K. pneumoniae) is an asymptomatic gut colonizer and, unlike well-studied enteric pathogens, harbors two genetically distinct ethanolamine utilization (eut) loci. Our investigation uncovered unique roles for each eut locus depending on EA utilization as a carbon or nitrogen source. Murine gut colonization studies demonstrated the necessity of both eut loci in the presence of intact gut microbiota for robust GI colonization by K. pneumoniae. Additionally, while some Escherichia coli gut isolates could metabolize EA, other commensals were incapable, suggesting that EA metabolism likely provides K. pneumoniae a selective advantage in gut colonization. Molecular and bioinformatic analyses unveiled the conservation of two eut loci among K. pneumoniae and a subset of the related taxa in the K. pneumoniae species complex, with the NtrC-RpoN regulatory cascade playing a pivotal role in regulation. These findings identify EA metabolism as a critical driver of K. pneumoniae niche establishment in the gut and propose microbial metabolism as a potential therapeutic avenue to combat K. pneumoniae infections.
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Affiliation(s)
- Andrew J. Barnes
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Emma F. Bennett
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Ben Vezina
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Andrew W. Hudson
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Giovanna E. Hernandez
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Noah A. Nutter
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Andrew S. Bray
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Ravinder Nagpal
- Department of Health, Nutrition, and Food Science, Florida State University, Tallahassee, Florida, United States of America
| | - Kelly L. Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - M. Ammar Zafar
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
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30
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Makowska-Zawierucha N, Trzebny A, Zawierucha K, Manthapuri V, Bradley JA, Pruden A. Arctic plasmidome analysis reveals distinct relationships among associated antimicrobial resistance genes and virulence genes along anthropogenic gradients. GLOBAL CHANGE BIOLOGY 2024; 30:e17293. [PMID: 38687495 DOI: 10.1111/gcb.17293] [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: 10/15/2023] [Revised: 01/30/2024] [Accepted: 03/30/2024] [Indexed: 05/02/2024]
Abstract
Polar regions are relatively isolated from human activity and thus could offer insight into anthropogenic and ecological drivers of the spread of antibiotic resistance. Plasmids are of particular interest in this context given the central role that they are thought to play in the dissemination of antibiotic resistance genes (ARGs). However, plasmidomes are challenging to profile in environmental samples. The objective of this study was to compare various aspects of the plasmidome associated with glacial ice and adjacent aquatic environments across the high Arctic archipelago of Svalbard, representing a gradient of anthropogenic inputs and specific treated and untreated wastewater outflows to the sea. We accessed plasmidomes by applying enrichment cultures, plasmid isolation and shotgun Illumina sequencing of environmental samples. We examined the abundance and diversity of ARGs and other stress-response genes that might be co/cross-selected or co-transported in these environments, including biocide resistance genes (BRGs), metal resistance genes (MRGs), virulence genes (VGs) and integrons. We found striking differences between glacial ice and aquatic environments in terms of the ARGs carried by plasmids. We found a strong correlation between MRGs and ARGs in plasmids in the wastewaters and fjords. Alternatively, in glacial ice, VGs and BRGs genes were dominant, suggesting that glacial ice may be a repository of pathogenic strains. Moreover, ARGs were not found within the cassettes of integrons carried by the plasmids, which is suggestive of unique adaptive features of the microbial communities to their extreme environment. This study provides insight into the role of plasmids in facilitating bacterial adaptation to Arctic ecosystems as well as in shaping corresponding resistomes. Increasing human activity, warming of Arctic regions and associated increases in the meltwater run-off from glaciers could contribute to the release and spread of plasmid-related genes from Svalbard to the broader pool of ARGs in the Arctic Ocean.
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Affiliation(s)
- Nicoletta Makowska-Zawierucha
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Artur Trzebny
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Krzysztof Zawierucha
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Vineeth Manthapuri
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - James A Bradley
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO, Marseille, France
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
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31
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Raulo A, Bürkner PC, Finerty GE, Dale J, Hanski E, English HM, Lamberth C, Firth JA, Coulson T, Knowles SCL. Social and environmental transmission spread different sets of gut microbes in wild mice. Nat Ecol Evol 2024; 8:972-985. [PMID: 38689017 PMCID: PMC11090834 DOI: 10.1038/s41559-024-02381-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/01/2024] [Indexed: 05/02/2024]
Abstract
Gut microbes shape many aspects of organismal biology, yet how these key bacteria transmit among hosts in natural populations remains poorly understood. Recent work in mammals has emphasized either transmission through social contacts or indirect transmission through environmental contact, but the relative importance of different routes has not been directly assessed. Here we used a novel radio-frequency identification-based tracking system to collect long-term high-resolution data on social relationships, space use and microhabitat in a wild population of mice (Apodemus sylvaticus), while regularly characterizing their gut microbiota with 16S ribosomal RNA profiling. Through probabilistic modelling of the resulting data, we identify positive and statistically distinct signals of social and environmental transmission, captured by social networks and overlap in home ranges, respectively. Strikingly, microorganisms with distinct biological attributes drove these different transmission signals. While the social network effect on microbiota was driven by anaerobic bacteria, the effect of shared space was most influenced by aerotolerant spore-forming bacteria. These findings support the prediction that social contact is important for the transfer of microorganisms with low oxygen tolerance, while those that can tolerate oxygen or form spores may be able to transmit indirectly through the environment. Overall, these results suggest social and environmental transmission routes can spread biologically distinct members of the mammalian gut microbiota.
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Affiliation(s)
- Aura Raulo
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Computing, University of Turku, Turku, Finland.
| | | | - Genevieve E Finerty
- Department of Biology, University of Oxford, Oxford, UK
- Department for the Ecology of Animal Societies, Max Planck Institute of Animal Behaviour, Constance, Germany
- Department of Biology, University of Konstanz, Constance, Germany
| | - Jarrah Dale
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Holly M English
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Curt Lamberth
- Department of Biology, University of Oxford, Oxford, UK
| | - Josh A Firth
- Department of Biology, University of Oxford, Oxford, UK
- School of Biology, University of Leeds, Leeds, UK
| | - Tim Coulson
- Department of Biology, University of Oxford, Oxford, UK
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32
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Islam T, Haque MA, Barai HR, Istiaq A, Kim JJ. Antibiotic Resistance in Plant Pathogenic Bacteria: Recent Data and Environmental Impact of Unchecked Use and the Potential of Biocontrol Agents as an Eco-Friendly Alternative. PLANTS (BASEL, SWITZERLAND) 2024; 13:1135. [PMID: 38674544 PMCID: PMC11054394 DOI: 10.3390/plants13081135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024]
Abstract
The economic impact of phytopathogenic bacteria on agriculture is staggering, costing billions of US dollars globally. Pseudomonas syringae is the top most phytopathogenic bacteria, having more than 60 pathovars, which cause bacteria speck in tomatoes, halo blight in beans, and so on. Although antibiotics or a combination of antibiotics are used to manage infectious diseases in plants, they are employed far less in agriculture compared to human and animal populations. Moreover, the majority of antibiotics used in plants are immediately washed away, leading to environmental damage to ecosystems and food chains. Due to the serious risk of antibiotic resistance (AR) and the potential for environmental contamination with antibiotic residues and resistance genes, the use of unchecked antibiotics against phytopathogenic bacteria is not advisable. Despite the significant concern regarding AR in the world today, there are inadequate and outdated data on the AR of phytopathogenic bacteria. This review presents recent AR data on plant pathogenic bacteria (PPB), along with their environmental impact. In light of these findings, we suggest the use of biocontrol agents as a sustainable, eco-friendly, and effective alternative to controlling phytopathogenic bacteria.
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Affiliation(s)
- Tarequl Islam
- Department of Microbiology, Noakhali Science and Technology University, Sonapur, Noakhali 3814, Bangladesh;
| | - Md Azizul Haque
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea;
| | - Hasi Rani Barai
- School of Mechanical and IT Engineering, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea;
| | - Arif Istiaq
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St Louis, MO 63110-1010, USA
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea;
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33
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Behringer MG, Ho WC, Miller SF, Worthan SB, Cen Z, Stikeleather R, Lynch M. Trade-offs, trade-ups, and high mutational parallelism underlie microbial adaptation during extreme cycles of feast and famine. Curr Biol 2024; 34:1403-1413.e5. [PMID: 38460514 PMCID: PMC11066936 DOI: 10.1016/j.cub.2024.02.040] [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: 10/04/2023] [Revised: 12/12/2023] [Accepted: 02/16/2024] [Indexed: 03/11/2024]
Abstract
Microbes are evolutionarily robust organisms capable of rapid adaptation to complex stress, which enables them to colonize harsh environments. In nature, microbes are regularly challenged by starvation, which is a particularly complex stress because resource limitation often co-occurs with changes in pH, osmolarity, and toxin accumulation created by metabolic waste. Often overlooked are the additional complications introduced by eventual resource replenishment, as successful microbes must withstand rapid environmental shifts before swiftly capitalizing on replenished resources to avoid invasion by competing species. To understand how microbes navigate trade-offs between growth and survival, ultimately adapting to thrive in environments with extreme fluctuations, we experimentally evolved 16 Escherichia coli populations for 900 days in repeated feast/famine conditions with cycles of 100-day starvation before resource replenishment. Using longitudinal population-genomic analysis, we found that evolution in response to extreme feast/famine is characterized by narrow adaptive trajectories with high mutational parallelism and notable mutational order. Genetic reconstructions reveal that early mutations result in trade-offs for biofilm and motility but trade-ups for growth and survival, as these mutations conferred positively correlated advantages during both short-term and long-term culture. Our results demonstrate how microbes can navigate the adaptive landscapes of regularly fluctuating conditions and ultimately follow mutational trajectories that confer benefits across diverse environments.
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Affiliation(s)
- Megan G Behringer
- Department of Biological Sciences, Vanderbilt University, 21st Avenue S, Nashville, TN 37232, USA; Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, 21st Avenue S, Nashville, TN 37232, USA.
| | - Wei-Chin Ho
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA; Department of Biology, University of Texas at Tyler, University Blvd., Tyler, TX 75799, USA.
| | - Samuel F Miller
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA
| | - Sarah B Worthan
- Department of Biological Sciences, Vanderbilt University, 21st Avenue S, Nashville, TN 37232, USA
| | - Zeer Cen
- Department of Biological Sciences, Vanderbilt University, 21st Avenue S, Nashville, TN 37232, USA
| | - Ryan Stikeleather
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA
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34
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Pulkkinen K, Taskinen J. Nutrient enrichment increases virulence in an opportunistic environmental pathogen, with greater effect at low bacterial doses. FEMS Microbiol Ecol 2024; 100:fiae013. [PMID: 38305097 PMCID: PMC10959552 DOI: 10.1093/femsec/fiae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/03/2024] Open
Abstract
Eutrophication of aquatic ecosystems is associated with an increased risk of pathogen infection via increased pathogen growth and host exposure via increased pathogen doses. Here, we studied the effect of nutrients on the virulence of an opportunistic bacterial pathogen of fish, Flavobacterium columnare, in challenge experiments with rainbow trout fingerlings. We hypothesized that removing all nutrients by washing the bacteria would reduce virulence as compared to unwashed bacteria, but adding nutrients to the tank water would increase the virulence of the bacterium. Nutrient addition and increase in bacterial dose increased virulence for both unwashed and washed bacteria. For unwashed bacteria, the addition of nutrients reduced the survival probability of fish challenged with low bacterial doses more than for fish challenged with higher bacterial doses, suggesting activation of bacterial virulence factors. Washing and centrifugation reduced viable bacterial counts, and the addition of washed bacteria alone did not lead to fish mortality. However, a small addition of nutrient medium, 0.05% of the total water volume, added separately to the fish container, restored the virulence of the washed bacteria. Our results show that human-induced eutrophication could trigger epidemics of aquatic pathogens at the limits of their survival and affect their ecology and evolution by altering the dynamics between strains that differ in their growth characteristics.
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Affiliation(s)
- Katja Pulkkinen
- Department of Biological and Environmental Science, P.O. Box 35 (Survontie 9), University of Jyväskylä, Jyväskylä, Finland
| | - Jouni Taskinen
- Department of Biological and Environmental Science, P.O. Box 35 (Survontie 9), University of Jyväskylä, Jyväskylä, Finland
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35
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Alexander AM, Luu JM, Raghuram V, Bottacin G, van Vliet S, Read TD, Goldberg JB. Experimentally evolved Staphylococcus aureus shows increased survival in the presence of Pseudomonas aeruginosa by acquiring mutations in the amino acid transporter, GltT. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001445. [PMID: 38426877 PMCID: PMC10999751 DOI: 10.1099/mic.0.001445] [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: 01/03/2024] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
When cultured together under standard laboratory conditions Pseudomonas aeruginosa has been shown to be an effective inhibitor of Staphylococcus aureus. However, P. aeruginosa and S. aureus are commonly observed in coinfections of individuals with cystic fibrosis (CF) and in chronic wounds. Previous work from our group revealed that S. aureus isolates from CF infections are able to persist in the presence of P. aeruginosa strain PAO1 with a range of tolerances with some isolates being eliminated entirely and others maintaining large populations. In this study, we designed a serial transfer, evolution experiment to identify mutations that allow S. aureus to survive in the presence of P. aeruginosa. Using S. aureus USA300 JE2 as our ancestral strain, populations of S. aureus were repeatedly cocultured with fresh P. aeruginosa PAO1. After eight coculture periods, S. aureus populations that survived better in the presence of PAO1 were observed. We found two independent mutations in the highly conserved S. aureus aspartate transporter, gltT, that were unique to evolved P. aeruginosa-tolerant isolates. Subsequent phenotypic testing demonstrated that gltT mutants have reduced uptake of glutamate and outcompeted wild-type S. aureus when glutamate was absent from chemically defined media. These findings together demonstrate that the presence of P. aeruginosa exerts selective pressure on S. aureus to alter its uptake and metabolism of key amino acids when the two are cultured together.
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Affiliation(s)
- Ashley M. Alexander
- Population Biology, Ecology, and Evolution Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
- Division of Infectious Diseases and Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Justin M. Luu
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, Georgia, USA
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Vishnu Raghuram
- Division of Infectious Diseases and Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, Georgia, USA
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Giulia Bottacin
- Biozentrum, University of Basel, Spitalstrasse 41,4056 Basel, Switzerland
| | - Simon van Vliet
- Biozentrum, University of Basel, Spitalstrasse 41,4056 Basel, Switzerland
- Department of Fundamental Microbiology, University of Lausanne, Quartier Unil-Sorge, 1015 Lausanne, Switzerland
| | - Timothy D. Read
- Division of Infectious Diseases and Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Joanna B. Goldberg
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, Georgia, USA
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36
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Kok CR, Bram Z, Thissen JB, Horseman TS, Fong KSK, Reichert-Scrivner SA, Paguirigan C, O'Connor K, Thompson K, Scheiber AE, Mabery S, Ngauy V, Uyehara CF, Be NA. The military gear microbiome: risk factors surrounding the warfighter. Appl Environ Microbiol 2024; 90:e0117623. [PMID: 38170999 PMCID: PMC10807412 DOI: 10.1128/aem.01176-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/16/2023] [Indexed: 01/05/2024] Open
Abstract
Combat extremity wounds are highly susceptible to contamination from surrounding environmental material. This bioburden could be partially transferred from materials in immediate proximity to the wound, including fragments of the uniform and gear. However, the assessment of the microbial bioburden present on military gear during operational conditions of deployment or training is relatively unexplored. Opportunistic pathogens that can survive on gear represent risk factors for infection following injury, especially following combat blasts, where fibers and other materials are embedded in wounded tissue. We utilized 16S rRNA sequencing to assess the microbiome composition of different military gear types (boot, trouser, coat, and canteen) from two operational environments (training in Hawai'i and deployed in Indonesia) across time (days 0 and 14). We found that microbiome diversity, stability, and composition were dependent on gear type, training location, and sampling timepoint. At day 14, species diversity was significantly higher in Hawai'i samples compared to Indonesia samples for boot, coat, and trouser swabs. In addition, we observed the presence of potential microbial risk factors, as opportunistic pathogenic species, such as Acinetobacter, Pseudomonas, and Staphylococcus, were found to be present in all sample types and in both study sites. These study outcomes will be used to guide the design of antimicrobial materials and uniforms and for infection control efforts following combat blasts and other injuries, thereby improving treatment guidance during military training and deployment.IMPORTANCECombat extremity wounds are vulnerable to contamination from environments of proximity to the warfighter, leading to potential detrimental outcomes such as infection and delayed wound healing. Therefore, microbial surveillance of such environments is necessary to aid the advancement of military safety and preparedness through clinical diagnostics, treatment protocols, and uniform material design.
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Affiliation(s)
- Car Reen Kok
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | | | - James B. Thissen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Timothy S. Horseman
- Tripler Army Medical Center, Honolulu, Hawaii, USA
- School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | | | | | | | | | | | | | - Shalini Mabery
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Viseth Ngauy
- Tripler Army Medical Center, Honolulu, Hawaii, USA
| | | | - Nicholas A. Be
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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37
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Coelho MA, David-Palma M, Shea T, Bowers K, McGinley-Smith S, Mohammad AW, Gnirke A, Yurkov AM, Nowrousian M, Sun S, Cuomo CA, Heitman J. Comparative genomics of Cryptococcus and Kwoniella reveals pathogenesis evolution and contrasting karyotype dynamics via intercentromeric recombination or chromosome fusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.27.573464. [PMID: 38234769 PMCID: PMC10793447 DOI: 10.1101/2023.12.27.573464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
A large-scale comparative genomic analysis was conducted for the global human fungal pathogens within the Cryptococcus genus, compared to non-pathogenic Cryptococcus species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species of both genera, resulting in a dataset encompassing virtually all of their known diversity. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at pre-adaptive pathogenic potential, our analysis found evidence in pathogenic Cryptococcus species of specific examples of gene gain (via horizontal gene transfer) and gene loss, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the two genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5 or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes, underwent chromosome reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Taken together, our findings advance our understanding of genomic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.
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Affiliation(s)
- Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Katharine Bowers
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | | | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andrey M. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
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38
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Hudson J, Egan S. Marine diseases and the Anthropocene: Understanding microbial pathogenesis in a rapidly changing world. Microb Biotechnol 2024; 17:e14397. [PMID: 38217393 PMCID: PMC10832532 DOI: 10.1111/1751-7915.14397] [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: 11/22/2023] [Accepted: 12/20/2023] [Indexed: 01/15/2024] Open
Abstract
Healthy marine ecosystems are paramount for Earth's biodiversity and are key to sustaining the global economy and human health. The effects of anthropogenic activity represent a pervasive threat to the productivity of marine ecosystems, with intensifying environmental stressors such as climate change and pollution driving the occurrence and severity of microbial diseases that can devastate marine ecosystems and jeopardise food security. Despite the potentially catastrophic outcomes of marine diseases, our understanding of host-pathogen interactions remains an understudied aspect of both microbiology and environmental research, especially when compared to the depth of information available for human and agricultural systems. Here, we identify three avenues of research in which we can advance our understanding of marine disease in the context of global change, and make positive steps towards safeguarding marine communities for future generations.
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Affiliation(s)
- Jennifer Hudson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyNew South WalesAustralia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyNew South WalesAustralia
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39
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Godoy M, Coca Y, Suárez R, Montes de Oca M, Bledsoe JW, Burbulis I, Caro D, Pontigo JP, Maracaja-Coutinho V, Arias-Carrasco R, Rodríguez-Córdova L, Sáez-Navarrete C. Salmo salar Skin and Gill Microbiome during Piscirickettsia salmonis Infection. Animals (Basel) 2023; 14:97. [PMID: 38200828 PMCID: PMC10778177 DOI: 10.3390/ani14010097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/13/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Maintaining the high overall health of farmed animals is a central tenant of their well-being and care. Intense animal crowding in aquaculture promotes animal morbidity especially in the absence of straightforward methods for monitoring their health. Here, we used bacterial 16S ribosomal RNA gene sequencing to measure bacterial population dynamics during P. salmonis infection. We observed a complex bacterial community consisting of a previously undescribed core pathobiome. Notably, we detected Aliivibrio wodanis and Tenacibaculum dicentrarchi on the skin ulcers of salmon infected with P. salmonis, while Vibrio spp. were enriched on infected gills. The prevalence of these co-occurring networks indicated that coinfection with other pathogens may enhance P. salmonis pathogenicity.
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Affiliation(s)
- Marcos Godoy
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Lago Panguipulli 1390, Puerto Montt 5480000, Región de Los Lagos, Chile; (M.M.d.O.); (D.C.)
- Laboratorio de Biotecnología, Facultad de Ciencias de la Naturaleza, Escuela de Medicina Veterinaria, Universidad San Sebastián, Sede Patagonia, Lago Panguipulli 1390, Puerto Montt 5480000, Región de Los Lagos, Chile
| | - Yoandy Coca
- Doctorado en Ciencias de la Ingeniería, Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago 7820436, Macul, Chile;
| | - Rudy Suárez
- Programa de Magíster en Acuicultura, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo 1780000, Elqui, Chile;
| | - Marco Montes de Oca
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Lago Panguipulli 1390, Puerto Montt 5480000, Región de Los Lagos, Chile; (M.M.d.O.); (D.C.)
| | - Jacob W. Bledsoe
- Department of Animal, Veterinary, and Food Sciences, Aquaculture Research Institute, University of Idaho, Hagerman, ID 83332, USA;
| | - Ian Burbulis
- Facultad de Medicina y Ciencia, Centro de Investigación Biomédica, Universidad San Sebastián, Sede Patagonia, Lago Panguipulli 1390, Puerto Montt 5480000, Región de Los Lagos, Chile;
| | - Diego Caro
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Lago Panguipulli 1390, Puerto Montt 5480000, Región de Los Lagos, Chile; (M.M.d.O.); (D.C.)
| | - Juan Pablo Pontigo
- Laboratorio Institucional, Facultad de Ciencias de la Naturaleza, Escuela de Medicina Veterinaria, Universidad San Sebastián, Sede Patagonia, Lago Panguipulli 1390, Puerto Montt 5480000, Región de Los Lagos, Chile;
| | - Vinicius Maracaja-Coutinho
- Unidad de Genómica Avanzada, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 7820436, Macul, Chile;
- Centro de Modelamiento Molecular, Biofísica y Bioinformática (CM2B2), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 7820436, Macul, Chile
- Beagle Bioinformatics, Santiago 7820436, Macul, Chile
| | - Raúl Arias-Carrasco
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago 7820436, Macul, Chile;
| | | | - César Sáez-Navarrete
- Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Macul, Chile;
- Centro de Investigación en Nanotecnología y Materiales Avanzados (CIEN-UC), Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Macul, Chile
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40
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Mikucki A, Kahler CM. Microevolution and Its Impact on Hypervirulence, Antimicrobial Resistance, and Vaccine Escape in Neisseria meningitidis. Microorganisms 2023; 11:3005. [PMID: 38138149 PMCID: PMC10745880 DOI: 10.3390/microorganisms11123005] [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: 11/06/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Neisseria meningitidis is commensal of the human pharynx and occasionally invades the host, causing the life-threatening illness invasive meningococcal disease. The meningococcus is a highly diverse and adaptable organism thanks to natural competence, a propensity for recombination, and a highly repetitive genome. These mechanisms together result in a high level of antigenic variation to invade diverse human hosts and evade their innate and adaptive immune responses. This review explores the ways in which this diversity contributes to the evolutionary history and population structure of the meningococcus, with a particular focus on microevolution. It examines studies on meningococcal microevolution in the context of within-host evolution and persistent carriage; microevolution in the context of meningococcal outbreaks and epidemics; and the potential of microevolution to contribute to antimicrobial resistance and vaccine escape. A persistent theme is the idea that the process of microevolution contributes to the development of new hyperinvasive meningococcal variants. As such, microevolution in this species has significant potential to drive future public health threats in the form of hypervirulent, antibiotic-resistant, vaccine-escape variants. The implications of this on current vaccination strategies are explored.
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Affiliation(s)
- August Mikucki
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
| | - Charlene M. Kahler
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
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Abu-Rub LI, Johar ARA, Al Mana H, Abdelrahman HA, Althani AA, Qotba H, Yassine HM, Eltai NO. Bacterial indoor air contaminations in hospitals in MENA region: a systematic review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2023; 33:1218-1232. [PMID: 35658652 DOI: 10.1080/09603123.2022.2083087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Poor indoor air quality in healthcare settings has been tied with the increase in hospital-acquired infections. Thus, this systematic review was conducted to assess the levels and compositions of bacteria in indoor hospital air in the Middle East and North Africa (MENA) region. We examined results provided by different search engines published between 2000 and 2021. Our data showed that most studies were conducted in Iran (80.9%) with a bacterial concentration mean of 172.9 CFU/m3. Comparing sensitive and non-sensitive areas of hospitals, no significant difference was detected in the mean bacterial concentration. The most investigated sensitive hospital areas were operating rooms and intensive care units with mean indoor bacterial concentrations of 180.3 CFU/m3 and 204.6 CFU/m3, respectively. Staphylococcaceae, Enterobacteriaceae, Pseudomonadaceae, and Bacillaceae were commonly identified bacterial families. In conclusion, the mean concentrations of the airborne bacteria were within the acceptable limit compared to WHO standards (300 CFU/m3) for the air in areas occupied by immunosuppressed people.
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Affiliation(s)
| | - Al-Reem A Johar
- Research and Development Department, Barzan Holdings, Doha, Qatar
| | - Hassan Al Mana
- Biomedical Research Center, Qatar University, Doha, Qatar
| | | | | | - Hamda Qotba
- Clinical Research Department, Primary Health Care Corporation, Clinical Research Primary Healthcare Center, Doha, Qatar
| | - Hadi M Yassine
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Nahla O Eltai
- Biomedical Research Center, Qatar University, Doha, Qatar
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Lin D, Hong J, Sanogo B, Du S, Xiang S, Hui JHL, Ding T, Wu Z, Sun X. Core gut microbes Cloacibacterium and Aeromonas associated with different gastropod species could be persistently transmitted across multiple generations. MICROBIOME 2023; 11:267. [PMID: 38017581 PMCID: PMC10685545 DOI: 10.1186/s40168-023-01700-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 10/17/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Studies on the gut microbiota of animals have largely focused on vertebrates. The transmission modes of commensal intestinal bacteria in mammals have been well studied. However, in gastropods, the relationship between gut microbiota and hosts is still poorly understood. To gain a better understanding of the composition of gut microbes and their transmission routes in gastropods, a large-scale and long-term experiment on the dynamics and transmission modes of gut microbiota was conducted on freshwater snails. RESULTS We analyzed 244 microbial samples from the digestive tracts of freshwater gastropods and identified Proteobacteria and Bacteroidetes as dominant gut microbes. Aeromonas, Cloacibacterium, and Cetobacterium were identified as core microbes in the guts, accounting for over 50% of the total sequences. Furthermore, both core bacteria Aeromonas and Cloacibacterium, were shared among 7 gastropod species and played an important role in determining the gut microbial community types of both wild and cultured gastropods. Analysis of the gut microbiota at the population level, including wild gastropods and their offspring, indicated that a proportion of gut microbes could be consistently vertically transmitted inheritance, while the majority of the gut microbes resulted from horizontal transmission. Comparing cultured snails to their wild counterparts, we observed an increasing trend in the proportion of shared microbes and a decreasing trend in the number of unique microbes among wild gastropods and their offspring reared in a cultured environment. Core gut microbes, Aeromonas and Cloacibacterium, remained persistent and dispersed from wild snails to their offspring across multiple generations. Interestingly, under cultured environments, the gut microbiota in wild gastropods could only be maintained for up to 2 generations before converging with that of cultured snails. The difference observed in gut bacterial metabolism functions was associated with this transition. Our study also demonstrated that the gut microbial compositions in gastropods are influenced by developmental stages and revealed the presence of Aeromonas and Cloacibacterium throughout the life cycle in gastropods. Based on the dynamics of core gut microbes, it may be possible to predict the health status of gastropods during their adaptation to new environments. Additionally, gut microbial metabolic functions were found to be associated with the adaptive evolution of gastropods from wild to cultured environments. CONCLUSIONS Our findings provide novel insights into the dynamic processes of gut microbiota colonization in gastropod mollusks and unveil the modes of microbial transmission within their guts. Video Abstract.
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Affiliation(s)
- Datao Lin
- Department of Parasitology, Key Laboratory of Tropical Disease Control (Ministry of Education), Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Provincial Engineering Technology Research Center for Diseases-vectors Control and Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Sun Yat-Sen University, Guangzhou, China.
| | - Jinni Hong
- Department of Traditional Chinese Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Benjamin Sanogo
- Department of Parasitology, Key Laboratory of Tropical Disease Control (Ministry of Education), Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Laboratory of Parasitology, Institut National de Recherche en Sante Publique, Bamako, Mali
| | - Shuling Du
- Department of Parasitology, Key Laboratory of Tropical Disease Control (Ministry of Education), Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Provincial Engineering Technology Research Center for Diseases-vectors Control and Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Sun Yat-Sen University, Guangzhou, China
| | - Suoyu Xiang
- Department of Parasitology, Key Laboratory of Tropical Disease Control (Ministry of Education), Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Provincial Engineering Technology Research Center for Diseases-vectors Control and Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Sun Yat-Sen University, Guangzhou, China
| | - Jerome Ho-Lam Hui
- State Key Laboratory of Agrobiotechnology, School of Life Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Tao Ding
- Department of Parasitology, Key Laboratory of Tropical Disease Control (Ministry of Education), Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Provincial Engineering Technology Research Center for Diseases-vectors Control and Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Sun Yat-Sen University, Guangzhou, China.
| | - Zhongdao Wu
- Department of Parasitology, Key Laboratory of Tropical Disease Control (Ministry of Education), Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Provincial Engineering Technology Research Center for Diseases-vectors Control and Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Sun Yat-Sen University, Guangzhou, China.
| | - Xi Sun
- Department of Parasitology, Key Laboratory of Tropical Disease Control (Ministry of Education), Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Provincial Engineering Technology Research Center for Diseases-vectors Control and Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Sun Yat-Sen University, Guangzhou, China.
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Ekdahl LI, Salcedo JA, Dungan MM, Mason DV, Myagmarsuren D, Murphy HA. Selection on plastic adherence leads to hyper-multicellular strains and incidental virulence in the budding yeast. eLife 2023; 12:e81056. [PMID: 37916911 PMCID: PMC10764007 DOI: 10.7554/elife.81056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/01/2023] [Indexed: 11/03/2023] Open
Abstract
Many disease-causing microbes are not obligate pathogens; rather, they are environmental microbes taking advantage of an ecological opportunity. The existence of microbes whose life cycle does not require a host and are not normally pathogenic, yet are well-suited to host exploitation, is an evolutionary puzzle. One hypothesis posits that selection in the environment may favor traits that incidentally lead to pathogenicity and virulence, or serve as pre-adaptations for survival in a host. An example of such a trait is surface adherence. To experimentally test the idea of 'accidental virulence', replicate populations of Saccharomyces cerevisiae were evolved to attach to a plastic bead for hundreds of generations. Along with plastic adherence, two multicellular phenotypes- biofilm formation and flor formation- increased; another phenotype, pseudohyphal growth, responded to the nutrient limitation. Thus, experimental selection led to the evolution of highly-adherent, hyper-multicellular strains. Wax moth larvae injected with evolved hyper-multicellular strains were significantly more likely to die than those injected with evolved non-multicellular strains. Hence, selection on plastic adherence incidentally led to the evolution of enhanced multicellularity and increased virulence. Our results support the idea that selection for a trait beneficial in the open environment can inadvertently generate opportunistic, 'accidental' pathogens.
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Affiliation(s)
- Luke I Ekdahl
- Department of Biology, College of William and MaryWilliamsburgUnited States
| | - Juliana A Salcedo
- Department of Biology, College of William and MaryWilliamsburgUnited States
| | - Matthew M Dungan
- Department of Biology, College of William and MaryWilliamsburgUnited States
| | - Despina V Mason
- Department of Biology, College of William and MaryWilliamsburgUnited States
| | | | - Helen A Murphy
- Department of Biology, College of William and MaryWilliamsburgUnited States
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Sauters TJC, Roth C, Murray D, Sun S, Floyd Averette A, Onyishi CU, May RC, Heitman J, Magwene PM. Amoeba predation of Cryptococcus: A quantitative and population genomic evaluation of the accidental pathogen hypothesis. PLoS Pathog 2023; 19:e1011763. [PMID: 37956179 PMCID: PMC10681322 DOI: 10.1371/journal.ppat.1011763] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 11/27/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
The "Amoeboid Predator-Fungal Animal Virulence Hypothesis" posits that interactions with environmental phagocytes shape the evolution of virulence traits in fungal pathogens. In this hypothesis, selection to avoid predation by amoeba inadvertently selects for traits that contribute to fungal escape from phagocytic immune cells. Here, we investigate this hypothesis in the human fungal pathogens Cryptococcus neoformans and Cryptococcus deneoformans. Applying quantitative trait locus (QTL) mapping and comparative genomics, we discovered a cross-species QTL region that is responsible for variation in resistance to amoeba predation. In C. neoformans, this same QTL was found to have pleiotropic effects on melanization, an established virulence factor. Through fine mapping and population genomic comparisons, we identified the gene encoding the transcription factor Bzp4 that underlies this pleiotropic QTL and we show that decreased expression of this gene reduces melanization and increases susceptibility to amoeba predation. Despite the joint effects of BZP4 on amoeba resistance and melanin production, we find no relationship between BZP4 genotype and escape from macrophages or virulence in murine models of disease. Our findings provide new perspectives on how microbial ecology shapes the genetic architecture of fungal virulence, and suggests the need for more nuanced models for the evolution of pathogenesis that account for the complexities of both microbe-microbe and microbe-host interactions.
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Affiliation(s)
- Thomas J. C. Sauters
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
| | - Cullen Roth
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
| | - Debra Murray
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Anna Floyd Averette
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Chinaemerem U. Onyishi
- School of Biosciences, College of Life and Environmental Sciences, The University of Birmingham, Birmingham, United Kingdom
| | - Robin C. May
- School of Biosciences, College of Life and Environmental Sciences, The University of Birmingham, Birmingham, United Kingdom
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Paul M. Magwene
- Department of Biology, Duke University, Durham, North Carolina, United States of America
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Wynne KJ, Zolotarskaya O, Jarrell R, Wang C, Amin Y, Brunson K. Facile Modification of Medical-Grade Silicone for Antimicrobial Effectiveness and Biocompatibility: A Potential Therapeutic Strategy against Bacterial Biofilms. ACS APPLIED MATERIALS & INTERFACES 2023; 15:46626-46638. [PMID: 37782835 PMCID: PMC10969938 DOI: 10.1021/acsami.3c08734] [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] [Indexed: 10/04/2023]
Abstract
A one-step modification of biomedical silicone tubing with N,N-dimethyltetradecylamine, C14, results in a composition designated WinGard-1 (WG-1, 1.1 wt % C14). A surface-active silicon-amine phase (SAP) is proposed to account for increased wettability and increased surface charge. To understand the mechanism of antimicrobial effectiveness, several procedures were employed to detect whether C14 leaching occurred. An immersion-growth (IG) test was developed that required knowing the bacterial Minimum Inhibitory Concentrations (MICs) and Minimum Biocidal Concentrations (MBCs). The C14 MIC and MBC for Gm- uropathogenic E. coli (UPEC), commonly associated with catheter-associated urinary tract infections (CAUTI), were 10 and 20 μg/mL, respectively. After prior immersion of WG-1 silicone segments in a growth medium from 1 to 28 d, the IG test for the medium showed normal growth for UPEC over 24 h, indicating that the concentration of C14 must be less than the MIC, 10 μg/mL. GC-MS and studies of the medium inside and outside a dialysis bag containing WG-1 silicone segments supported de minimis leaching. Consequently, a 5 log UPEC reduction (99.999% kill) in 24 h using the shake flask test (ASTM E2149) cannot be due to leaching and is ascribed to contact kill. Interestingly, although the MBC was greater than 100 μg/mL for Pseudomonas aeruginosa, WG-1 silicone affected an 80% reduction via a 24 h shake flask test. For other bacteria and Candida albicans, greater than 99.9% shake flask kill may be understood by proposing increased wettability and concentration of charge illustrated in the TOC. De minimis leaching places WG-1 silicone at an advantage over conventional anti-infectives that rely on leaching of an antibiotic or heavy metals such as silver. The facile process for preparation of WG-1 silicone combined with biocidal effectiveness comprises progress toward the goals of device designation from the FDA for WG-1 and clearance.
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Affiliation(s)
- Kenneth J. Wynne
- WynnVision LLC, Virginia Bio+Tech Park, Suite 57, 800 East Leigh
Street, Richmond, VA 23219-1551
| | - Olga Zolotarskaya
- WynnVision LLC, Virginia Bio+Tech Park, Suite 57, 800 East Leigh
Street, Richmond, VA 23219-1551
| | - Rebecca Jarrell
- WynnVision LLC, Virginia Bio+Tech Park, Suite 57, 800 East Leigh
Street, Richmond, VA 23219-1551
| | - Chenyu Wang
- WynnVision LLC, Virginia Bio+Tech Park, Suite 57, 800 East Leigh
Street, Richmond, VA 23219-1551
| | - Youssef Amin
- WynnVision LLC, Virginia Bio+Tech Park, Suite 57, 800 East Leigh
Street, Richmond, VA 23219-1551
| | - Kennard Brunson
- WynnVision LLC, Virginia Bio+Tech Park, Suite 57, 800 East Leigh
Street, Richmond, VA 23219-1551
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Zhou X, Kang X, Chen J, Song Y, Jia C, Teng L, Tang Y, Jiang Z, Peng X, Tao X, Xu Y, Huang L, Xu X, Xu Y, Zhang T, Yu S, Gong J, Wang S, Liu Y, Zhu G, Kehrenberg C, Weill FX, Barrow P, Li Y, Zhao G, Yue M. Genome degradation promotes Salmonella pathoadaptation by remodeling fimbriae-mediated proinflammatory response. Natl Sci Rev 2023; 10:nwad228. [PMID: 37965675 PMCID: PMC10642762 DOI: 10.1093/nsr/nwad228] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/07/2023] [Accepted: 08/08/2023] [Indexed: 11/16/2023] Open
Abstract
Understanding changes in pathogen behavior (e.g. increased virulence, a shift in transmission channel) is critical for the public health management of emerging infectious diseases. Genome degradation via gene depletion or inactivation is recognized as a pathoadaptive feature of the pathogen evolving with the host. However, little is known about the exact role of genome degradation in affecting pathogenic behavior, and the underlying molecular detail has yet to be examined. Using large-scale global avian-restricted Salmonella genomes spanning more than a century, we projected the genetic diversity of Salmonella Pullorum (bvSP) by showing increasingly antimicrobial-resistant ST92 prevalent in Chinese flocks. The phylogenomic analysis identified three lineages in bvSP, with an enhancement of virulence in the two recently emerged lineages (L2/L3), as evidenced in chicken and embryo infection assays. Notably, the ancestor L1 lineage resembles the Salmonella serovars with higher metabolic flexibilities and more robust environmental tolerance, indicating stepwise evolutionary trajectories towards avian-restricted lineages. Pan-genome analysis pinpointed fimbrial degradation from a virulent lineage. The later engineered fim-deletion mutant, and all other five fimbrial systems, revealed behavior switching that restricted horizontal fecal-oral transmission but boosted virulence in chicks. By depleting fimbrial appendages, bvSP established persistent replication with less proinflammation in chick macrophages and adopted vertical transovarial transmission, accompanied by ever-increasing intensification in the poultry industry. Together, we uncovered a previously unseen paradigm for remodeling bacterial surface appendages that supplements virulence-enhanced evolution with increased vertical transmission.
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Affiliation(s)
- Xiao Zhou
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
- Ningbo Academy of Agricultural Sciences, Ningbo 315040, China
| | - Xiamei Kang
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Jiaqi Chen
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Yan Song
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Chenghao Jia
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Lin Teng
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Yanting Tang
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Zhijie Jiang
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Xianqi Peng
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Xiaoxi Tao
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Yiwei Xu
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Linlin Huang
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Xuebin Xu
- Department of Microbiology Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
| | - Yaohui Xu
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450053, China
| | - Tengfei Zhang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Shenye Yu
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China
| | - Shaohui Wang
- Department of Animal Public Health, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Yuqing Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Corinna Kehrenberg
- Institute for Veterinary Food Science, Faculty of Veterinary Medicine, Justus-Liebig University Giessen, Giessen 35392, Germany
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des bactéries pathogènes entériques, Paris 75724, France
| | - Paul Barrow
- School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, UK
| | - Yan Li
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Guoping Zhao
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Min Yue
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China
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Umanets A, Surono IS, Venema K. I am better than I look: genome based safety assessment of the probiotic Lactiplantibacillus plantarum IS-10506. BMC Genomics 2023; 24:518. [PMID: 37667166 PMCID: PMC10478331 DOI: 10.1186/s12864-023-09495-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/30/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Safety of probiotic strains that are used in human and animal trials is a prerequisite. Genome based safety assessment of probiotics has gained popularity due its cost efficiency and speed, and even became a part of national regulation on foods containing probiotics in Indonesia. However, reliability of the safety assessment based only on a full genome sequence is not clear. Here, for the first time, we sequenced, assembled, and analysed the genome of the probiotic strain Lactiplantibacillus plantarum IS-10506, that was isolated from dadih, a traditional fermented buffalo milk. The strain has already been used as a probiotic for more than a decade, and in several clinical trials proven to be completely safe. METHODS The genome of the probiotic strain L. plantarum IS-10506 was sequenced using Nanopore sequencing technology, assembled, annotated and screened for potential harmful (PH) and beneficial genomic features. The presence of the PH features was assessed from general annotation, as well as with the use of specialised tools. In addition, PH regions in the genome were compared to all other probiotic and non-probiotic L. plantarum strains available in the NCBI RefSeq database. RESULTS For the first time, a high-quality complete genome of L. plantarum IS-10506 was obtained, and an extensive search for PH and a beneficial signature was performed. We discovered a number of PH features within the genome of L. plantarum IS-10506 based on the general annotation, including various antibiotic resistant genes (AMR); however, with a few exceptions, bioinformatics tools specifically developed for AMR detection did not confirm their presence. We further demonstrated the presence of the detected PH genes across multiple L. plantarum strains, including probiotics, and overall high genetic similarities between strains. CONCLUSION The genome of L. plantarum IS-10506 is predicted to have several PH features. However, the strain has been utilized as a probiotic for over a decade in several clinical trials without any adverse effects, even in immunocompromised children with HIV infection and undernourished children. This implies the presence of PH feature signatures within the probiotic genome does not necessarily indicate their manifestation during administration. Importantly, specialized tools for the search of PH features were found more robust and should be preferred over manual searches in a general annotation.
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Affiliation(s)
- Alexander Umanets
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands
- Chair Group Youth Food and Health, Faculty of Science and Engineering, Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands
| | - Ingrid S Surono
- Food Technology Department, Faculty of Engineering, Bina Nusantara University, Jakarta, 11480, Indonesia
| | - Koen Venema
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands.
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Cao Y, Bai Y, Li H, Ma B, Zhang W. Preparation and evaluation of recombinant pyolysin, fimbriae E and HtaA based protein vaccines against Trueperella pyogenes. Vet Microbiol 2023; 284:109810. [PMID: 37307768 DOI: 10.1016/j.vetmic.2023.109810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/14/2023]
Abstract
Trueperella pyogenes (T. pyogenes) could cause zoonotic disease in various mammals, resulting in significant economic losses. Due to the lack of effective vaccine and the emergence of bacterial resistance, there is a big need for new and improved vaccines. In this study, the non-hemolytic pyolysin mutant (PLOW497F), fimbriae E (FimE) and a truncated cell wall protein (HtaA-2) were selected to generate single or multivalent protein vaccines and their efficacies against lethal T. pyogenes challenge were evaluated in a mouse model. The results showed that the levels of specific antibody were significantly higher than the PBS control group after the booster vaccination. Compared to PBS treated mice, vaccinated mice had upregulated expressions of the inflammatory cytokine genes after the first vaccination. There was a downward trend thereafter, but return to the similar or even higher levels after challenge. Furthermore, co-immunization with rFimE or rHtaA-2 could significantly enhance the anti-hemolysis antibodies induced by rPLOW497F. The supplement of rHtaA-2 induced higher agglutinating antibodies compared with single administration with rPLOW497F or rFimE. Apart from these, the pathological lesions of lung were alleviated in rHtaA-2, rPLOW497F or their combinations immunized mice. Notably, immunization with rPLOW497F, rHtaA-2, combinations of rPLOW497F and rHtaA-2 or rHtaA-2 and rFimE completely protected mice from challenge, whereas the PBS immunized mice could not survive past 1 day post challenge. Thus, PLOW497F and HtaA-2 might be useful in developing efficient vaccines to prevent T. pyogenes infection.
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Affiliation(s)
- Yongsheng Cao
- Laboratory of Veterinary Immunology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Changjiang Street NO.600, Harbin, China; Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, China.
| | - Yunlu Bai
- Laboratory of Veterinary Immunology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Changjiang Street NO.600, Harbin, China; Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, China
| | - Hanqing Li
- Laboratory of Veterinary Immunology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Changjiang Street NO.600, Harbin, China; Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, China
| | - Bo Ma
- Laboratory of Veterinary Immunology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Changjiang Street NO.600, Harbin, China; Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, China
| | - Wenlong Zhang
- Laboratory of Veterinary Immunology, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Changjiang Street NO.600, Harbin, China; Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, China.
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Miner KR, Hollis JR, Miller CE, Uckert K, Douglas TA, Cardarelli E, Mackelprang R. Earth to Mars: A Protocol for Characterizing Permafrost in the Context of Climate Change as an Analog for Extraplanetary Exploration. ASTROBIOLOGY 2023; 23:1006-1018. [PMID: 37566539 PMCID: PMC10510695 DOI: 10.1089/ast.2022.0155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 07/02/2023] [Indexed: 08/13/2023]
Abstract
Abstract Permafrost is important from an exobiology and climate change perspective. It serves as an analog for extraplanetary exploration, and it threatens to emit globally significant amounts of greenhouse gases as it thaws due to climate change. Viable microbes survive in Earth's permafrost, slowly metabolizing and transforming organic matter through geologic time. Ancient permafrost microbial communities represent a crucial resource for gaining novel insights into survival strategies adopted by extremotolerant organisms in extraplanetary analogs. We present a proof-of-concept study on ∼22 Kya permafrost to determine the potential for coupling Raman and fluorescence biosignature detection technology from the NASA Mars Perseverance rover with microbial community characterization in frozen soils, which could be expanded to other Earth and off-Earth locations. Besides the well-known utility for biosignature detection and identification, our results indicate that spectral mapping of permafrost could be used to rapidly characterize organic carbon characteristics. Coupled with microbial community analyses, this method has the potential to enhance our understanding of carbon degradation and emissions in thawing permafrost. Further, spectroscopy can be accomplished in situ to mitigate sample transport challenges and in assessing and prioritizing frozen soils for further investigation. This method has broad-range applicability to understanding microbial communities and their associations with biosignatures and soil carbon and mineralogic characteristics relevant to climate science and astrobiology.
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Affiliation(s)
- Kimberley R. Miner
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | - Charles E. Miller
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Kyle Uckert
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | - Emily Cardarelli
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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50
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Schols R, Vanoverberghe I, Huyse T, Decaestecker E. Host-bacteriome transplants of the schistosome snail host Biomphalaria glabrata reflect species-specific associations. FEMS Microbiol Ecol 2023; 99:fiad101. [PMID: 37632232 PMCID: PMC10481996 DOI: 10.1093/femsec/fiad101] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/09/2023] [Accepted: 08/23/2023] [Indexed: 08/27/2023] Open
Abstract
Microbial symbionts can affect host phenotypes and, thereby, ecosystem functioning. The microbiome is increasingly being recognized as an important player in the tripartite interaction between parasitic flatworms, snail intermediate hosts, and the snail microbiome. In order to better understand these interactions, transplant experiments are needed, which rely on the development of a reliable and reproducible protocol to obtain microbiome-disturbed snails. Here, we report on the first successful snail bacteriome transplants, which indicate that Biomphalaria glabrata can accrue novel bacterial assemblies depending on the available environmental bacteria obtained from donor snails. Moreover, the phylogenetic relatedness of the donor host significantly affected recipients' survival probability, corroborating the phylosymbiosis pattern in freshwater snails. The transplant technique described here, complemented by field-based studies, could facilitate future research endeavors to investigate the role of specific bacteria or bacterial communities in parasitic flatworm resistance of B. glabrata and might ultimately pave the way for microbiome-mediated control of snail-borne diseases.
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Affiliation(s)
- Ruben Schols
- Department of Biology, Royal Museum for Central Africa, 3080 Tervuren, Belgium
- Laboratory of Aquatic Biology, KU Leuven, Campus Kortrijk, 8500 Kortrijk, Belgium
| | - Isabel Vanoverberghe
- Laboratory of Aquatic Biology, KU Leuven, Campus Kortrijk, 8500 Kortrijk, Belgium
| | - Tine Huyse
- Department of Biology, Royal Museum for Central Africa, 3080 Tervuren, Belgium
| | - Ellen Decaestecker
- Laboratory of Aquatic Biology, KU Leuven, Campus Kortrijk, 8500 Kortrijk, Belgium
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