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Macher JN, Kayal E, Duijm E, van der Hoorn B, Montano S, Speksnijder A. The mitochondrial genome of Nemalecium lighti (Hydrozoa, Leptothecata). Mitochondrial DNA B Resour 2021; 6:3196-3198. [PMID: 34660901 PMCID: PMC8519520 DOI: 10.1080/23802359.2021.1989335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The hydrozoan species Nemalecium lighti (Hargitt, 1924) is widely distributed in tropical marine waters around the world. Here we report the complete linear mitochondrial genome of N. lighti from Sint Eustatius (Lesser Antilles). The mitochondrial genome with a length of 14,320 bp encodes for 13 protein-coding genes, two tRNA genes, and two rRNA genes. Gene arrangement differs from that found in other species of the same taxonomic order and a phylogenetic analysis shows that based on mitochondrial genes, N. lighti clusters outside of the Leptothecata, rendering the order paraphyletic.
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Affiliation(s)
- Jan-Niklas Macher
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Ehsan Kayal
- Université de Caen Normandie, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Caen, France
| | - Elza Duijm
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Berry van der Hoorn
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands.,Inholland University of Applied Sciences, Delft, The Netherlands
| | - Simone Montano
- University of Milano-Bicocca, Department of Earth and Environmental Sciences (DISAT), Milano, Italy
| | - Arjen Speksnijder
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands.,University of Applied Sciences Leiden, Leiden, The Netherlands
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Gomes SIF, van Bodegom PM, van Agtmaal M, Soudzilovskaia NA, Bestman M, Duijm E, Speksnijder A, van Eekeren N. Microbiota in Dung and Milk Differ Between Organic and Conventional Dairy Farms. Front Microbiol 2020; 11:1746. [PMID: 32849375 PMCID: PMC7399162 DOI: 10.3389/fmicb.2020.01746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 07/03/2020] [Indexed: 12/29/2022] Open
Abstract
Organic farming is increasingly promoted as a means to reduce the environmental impact of artificial fertilizers, pesticides, herbicides, and antibiotics in conventional dairy systems. These factors potentially affect the microbial communities of the production stages (soil, silage, dung, and milk) of the entire farm cycle. However, understanding whether the microbiota representative of different production stages reflects different agricultural practices - such as conventional versus organic farming - is unknown. Furthermore, the translocation of the microbial community across production stages is scarcely studied. We sequenced the microbial communities of soil, silage, dung, and milk samples from organic and conventional dairy farms in the Netherlands. We found that community structure of soil fungi and bacteria significantly differed among soil types, but not between organic versus conventional farming systems. The microbial communities of silage also did not differ among conventional and organic systems. Nevertheless, the dung microbiota of cows and the fungal communities in the milk were significantly structured by agricultural practice. We conclude that, while the production stages of dairy farms seem to be disconnected in terms of microbial transfer, certain practices specific for each agricultural system, such as the content of diet and the use of antibiotics, are potential drivers of shifts in the cow's microbiota, including the milk produced. This may reflect differences in farm animal health and quality of dairy products depending on farming practices.
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Affiliation(s)
- Sofia I F Gomes
- Institute of Environmental Sciences, Leiden University, Leiden, Netherlands
| | | | | | | | | | - Elza Duijm
- Naturalis Biodiversity Center, Leiden, Netherlands
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Leese F, Altermatt F, Bouchez A, Ekrem T, Hering D, Meissner K, Mergen P, Pawlowski J, Piggott J, Rimet F, Steinke D, Taberlet P, Weigand A, Abarenkov K, Beja P, Bervoets L, Björnsdóttir S, Boets P, Boggero A, Bones A, Borja Á, Bruce K, Bursić V, Carlsson J, Čiampor F, Čiamporová-Zatovičová Z, Coissac E, Costa F, Costache M, Creer S, Csabai Z, Deiner K, DelValls Á, Drakare S, Duarte S, Eleršek T, Fazi S, Fišer C, Flot JF, Fonseca V, Fontaneto D, Grabowski M, Graf W, Guðbrandsson J, Hellström M, Hershkovitz Y, Hollingsworth P, Japoshvili B, Jones J, Kahlert M, Kalamujic Stroil B, Kasapidis P, Kelly M, Kelly-Quinn M, Keskin E, Kõljalg U, Ljubešić Z, Maček I, Mächler E, Mahon A, Marečková M, Mejdandzic M, Mircheva G, Montagna M, Moritz C, Mulk V, Naumoski A, Navodaru I, Padisák J, Pálsson S, Panksep K, Penev L, Petrusek A, Pfannkuchen M, Primmer C, Rinkevich B, Rotter A, Schmidt-Kloiber A, Segurado P, Speksnijder A, Stoev P, Strand M, Šulčius S, Sundberg P, Traugott M, Tsigenopoulos C, Turon X, Valentini A, van der Hoorn B, Várbíró G, Vasquez Hadjilyra M, Viguri J, Vitonytė I, Vogler A, Vrålstad T, Wägele W, Wenne R, Winding A, Woodward G, Zegura B, Zimmermann J. DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe. RIO 2016. [DOI: 10.3897/rio.2.e11321] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Matser A, Heijman T, Geskus R, de Vries H, Kretzschmar M, Speksnijder A, Xiridou M, Fennema H, Schim van der Loeff M. Perceived HIV status is a key determinant of unprotected anal intercourse within partnerships of men who have sex with men in Amsterdam. AIDS Behav 2014; 18:2442-56. [PMID: 24920343 DOI: 10.1007/s10461-014-0819-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The practice of unprotected anal intercourse (UAI) involves at least two partners. We examined the associations between insertive or receptive UAI and perceived HIV seroconcordance and partnership type in self-perceived HIV-negative and self-perceived HIV-positive men who have sex with men (MSM). MSM (age ≥ 18 years) were recruited for a cross-sectional survey at the sexually transmitted infections clinic in Amsterdam, the Netherlands, in 2008-2009. Participants completed a questionnaire concerning partnerships in the preceding 6 months. Associations were quantified via multinomial logistic regression models using generalized estimating equations. The outcomes were 'no, or safe anal intercourse', 'insertive UAI', and 'receptive UAI'. We included 5,456 partnerships from 1,890 self-perceived HIV-negative men and 1,861 partnerships from 558 self-perceived HIV-positive men. Within the partnerships, perceived HIV status of the partner was an important determinant of UAI (p < 0.001). Among HIV-negative men, perceived HIV discordance was negatively associated with receptive UAI compared with no or safe UAI (OR 0.57; 95 % CI 0.36-0.92); when the partners were more familiar with each other, the risk of receptive UAI was increased relative to no or safe anal intercourse. Among HIV-positive men, perceived HIV discordance was negatively associated with insertive UAI (OR 0.05; 95 % CI 0.03-0.08). Within partnerships, perceived HIV status of the partner was one of the strongest determinants of UAI among self-perceived HIV-negative and HIV-positive MSM, and discordant serostatus was negatively associated with UAI. The findings suggest that serosorting is one of the main strategies when engaging in UAI.
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Affiliation(s)
- Amy Matser
- Department of Research, Cluster of Infectious Diseases, Public Health Service of Amsterdam, Postbox 2200, 1000 CE, Amsterdam, The Netherlands,
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Dirks A, Brink AATP, Speksnijder A, Dukers-Muijrers NHTM, Wolffs PFG, Hoebe CJPA. P3.259 Similar Chlamydia TrachomatisBacterial Load in Patient Samples from STI-Clinic and Population-Based Screening. Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.0715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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van der Knaap N, Grady BPX, Schim van der Loeff MF, Heijman T, Speksnijder A, Geskus R, Prins M. Drug users in Amsterdam: are they still at risk for HIV? PLoS One 2013; 8:e59125. [PMID: 23527107 PMCID: PMC3601054 DOI: 10.1371/journal.pone.0059125] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 02/11/2013] [Indexed: 11/19/2022] Open
Abstract
Background and Aims To examine whether drug users (DU) in the Amsterdam Cohort Study (ACS) are still at risk for HIV, we studied trends in HIV incidence and injecting and sexual risk behaviour from 1986 to 2011. Methods The ACS is an open, prospective cohort study on HIV. Calendar time trends in HIV incidence were modelled using Poisson regression. Trends in risk behaviour were modelled via generalized estimating equations. In 2010, a screening for STI (chlamydia, gonorrhoea and syphilis) was performed. Determinants of unprotected sex were studied using logistic regression analysis. Results The HIV incidence among 1298 participants of the ACS with a total follow-up of 12,921 person-years (PY) declined from 6.0/100 PY (95% confidence interval [CI] 3.2–11.1) in 1986 to less than 1/100 PY from 1997 onwards. Both injection and sexual risk behaviour declined significantly over time. Out of 197 participants screened for STI in 2010–2011, median age 49 years (IQR 43–59), only 5 (2.5%) were diagnosed with an STI. In multivariable analysis, having a steady partner (aOR 4.1, 95% CI 1.6–10.5) was associated with unprotected sex. HIV-infected participants were less likely to report unprotected sex (aOR 0.07, 95% CI 0.02–0.37). Conclusions HIV incidence and injection risk behaviour declined from 1986 onwards. STI prevalence is low; unprotected sex is associated with steady partners and is less common among HIV-infected participants. These findings indicate a low transmission risk of HIV and STI, which suggests that DU do not play a significant role in the current spread of HIV in Amsterdam.
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Affiliation(s)
- Nienke van der Knaap
- Cluster of Infectious Diseases, Public Health Service, Amsterdam, The Netherlands
- University of Amsterdam (UvA), Amsterdam, The Netherlands
| | - Bart P. X. Grady
- Cluster of Infectious Diseases, Public Health Service, Amsterdam, The Netherlands
- Center of Infectious diseases and Immunology Amsterdam (CINIMA), Department of Internal Medicine, Academic Medical Center (AMC), Amsterdam, The Netherlands
- * E-mail:
| | - Maarten F. Schim van der Loeff
- Cluster of Infectious Diseases, Public Health Service, Amsterdam, The Netherlands
- Center of Infectious diseases and Immunology Amsterdam (CINIMA), Department of Internal Medicine, Academic Medical Center (AMC), Amsterdam, The Netherlands
| | - Titia Heijman
- Cluster of Infectious Diseases, Public Health Service, Amsterdam, The Netherlands
- Center of Infectious diseases and Immunology Amsterdam (CINIMA), Department of Internal Medicine, Academic Medical Center (AMC), Amsterdam, The Netherlands
| | - Arjen Speksnijder
- Cluster of Infectious Diseases, Public Health Service, Amsterdam, The Netherlands
- Laboratory of Public Health, Public Health Service, Amsterdam, The Netherlands
| | - Ronald Geskus
- Cluster of Infectious Diseases, Public Health Service, Amsterdam, The Netherlands
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center (AMC), Amsterdam, The Netherlands
| | - Maria Prins
- Cluster of Infectious Diseases, Public Health Service, Amsterdam, The Netherlands
- Center of Infectious diseases and Immunology Amsterdam (CINIMA), Department of Internal Medicine, Academic Medical Center (AMC), Amsterdam, The Netherlands
- Department of Internal Medicine, Division of Infectious Diseases, Tropical Medicine and AIDS, Academic Medical Center, Amsterdam, The Netherlands
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Dukers-Muijrers NHTM, Morré SA, Speksnijder A, van der Sande MAB, Hoebe CJPA. Chlamydia trachomatis test-of-cure cannot be based on a single highly sensitive laboratory test taken at least 3 weeks after treatment. PLoS One 2012; 7:e34108. [PMID: 22470526 PMCID: PMC3314698 DOI: 10.1371/journal.pone.0034108] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 02/22/2012] [Indexed: 11/25/2022] Open
Abstract
Current test-of-cure practice in patients with Chlamydia trachomatis (Ct) infection is to confirm cure with a single test taken at least 3 weeks after treatment. Effectiveness of single-time-point testing however lacks a scientific evidence basis and the high sensitivity of laboratory assays nowadays in use for this purpose may compromise the clinical significance of their results. Prospectively following 59 treated Ct infections, administering care as usual, the presence of Ct plasmid DNA and rRNA was systematically assessed by multiple time-sequential measurements, i.e. on 18 samples taken per patient during 8 weeks following treatment with a single dose of 1000 mg Azythromycin. A high proportion (42%) of Ct infections tested positive on at least one of the samples taken after 3 weeks. Patients' test results showed substantial inter-individual and intra-individual variation over time and by type of NAAT used. We demonstrated frequent intermittent positive patterns in Ct test results over time, and strongly argue against current test-of-cure practice.
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Affiliation(s)
- Nicole H T M Dukers-Muijrers
- Department of Sexual Health, Infectious Diseases and Environmental Health, Geleen, South Limburg Public Health Service, South Limburg, The Netherlands.
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Harris SR, Clarke IN, Seth-Smith HMB, Solomon AW, Cutcliffe LT, Marsh P, Skilton RJ, Holland MJ, Mabey D, Peeling RW, Lewis DA, Spratt BG, Unemo M, Persson K, Bjartling C, Brunham R, de Vries HJC, Morré SA, Speksnijder A, Bébéar CM, Clerc M, de Barbeyrac B, Parkhill J, Thomson NR. Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing. Nat Genet 2012; 44:413-9, S1. [PMID: 22406642 PMCID: PMC3378690 DOI: 10.1038/ng.2214] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 02/06/2012] [Indexed: 11/16/2022]
Abstract
Chlamydia trachomatis is responsible for both trachoma and sexually transmitted infections causing substantial morbidity and economic cost globally. Despite this, our knowledge of its population and evolutionary genetics is limited. Here we present a detailed whole genome phylogeny from representative strains of both trachoma and lymphogranuloma venereum (LGV) biovars from temporally and geographically diverse sources. Our analysis demonstrates that predicting phylogenetic structure using the ompA gene, traditionally used to classify Chlamydia, is misleading because extensive recombination in this region masks true relationships. We show that in many instances ompA is a chimera that can be exchanged in part or whole, both within and between biovars. We also provide evidence for exchange of, and recombination within, the cryptic plasmid, another important diagnostic target. We have used our phylogenetic framework to show how genetic exchange has manifested itself in ocular, urogenital and LGV C. trachomatis strains, including the epidemic LGV serotype L2b.
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Affiliation(s)
- Simon R Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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van der Helm J, Sabajo L, Morre S, Grunberg A, Speksnijder A, de Vries H. P3-S1.26 Novel Chlamydia trachomatis point of care rapid test shows disappointingly low clinical sensitivity in urogenital Chlamydia infections in Paramaribo, Suriname. Sex Transm Infect 2011. [DOI: 10.1136/sextrans-2011-050108.426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Speksnijder A, Gruteke P, Jonker D, de Vries H, van Dam A. O3-S6.01 Improved diagnostics of bacterial vaginosis with molecular techniques. Br J Vener Dis 2011. [DOI: 10.1136/sextrans-2011-050109.133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Dukers-Muijrers N, Werner M, Brouwers E, Speksnijder A, Spauwen L, Bruisten S, van den Broek I, van der Sande M, Morre S, Hoebe C. O3-S4.04 Time to cure chlamydia: prospective study on detection of anorectal and cervicovaginal chlamydia after directly observed treatment with azithromycin. Br J Vener Dis 2011. [DOI: 10.1136/sextrans-2011-050109.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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van der Helm J, Grunberg A, Speksnijder A, de Vries H, Sabajo L. P1-S1.32 Urogenital Chlamydia trachomatis is a hyperendemic disease in Paramaribo Suriname. Results from a multiethnic society. Br J Vener Dis 2011. [DOI: 10.1136/sextrans-2011-050108.32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Hjort K, Lembke A, Speksnijder A, Smalla K, Jansson JK. Community structure of actively growing bacterial populations in plant pathogen suppressive soil. Microb Ecol 2007; 53:399-413. [PMID: 16944345 DOI: 10.1007/s00248-006-9120-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Accepted: 05/01/2006] [Indexed: 05/11/2023]
Abstract
The bacterial community in soil was screened by using various molecular approaches for bacterial populations that were activated upon addition of different supplements. Plasmodiophora brassicae spores, chitin, sodium acetate, and cabbage plants were added to activate specific bacterial populations as an aid in screening for novel antagonists to plant pathogens. DNA from growing bacteria was specifically extracted from the soil by bromodeoxyuridine immunocapture. The captured DNA was fingerprinted by terminal restriction fragment length polymorphism (T-RFLP). The composition of the dominant bacterial community was also analyzed directly by T-RFLP and by denaturing gradient gel electrophoresis (DGGE). After chitin addition to the soil, some bacterial populations increased dramatically and became dominant both in the total and in the actively growing community. Some of the emerging bands on DGGE gels from chitin-amended soil were sequenced and found to be similar to known chitin-degrading genera such as Oerskovia, Kitasatospora, and Streptomyces species. Some of these sequences could be matched to specific terminal restriction fragments on the T-RFLP output. After addition of Plasmodiophora spores, an increase in specific Pseudomonads could be observed with Pseudomonas-specific primers for DGGE. These results demonstrate the utility of microbiomics, or a combination of molecular approaches, for investigating the composition of complex microbial communities in soil.
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Affiliation(s)
- Karin Hjort
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-750 07, Uppsala, Sweden
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