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Xu J, Wang Z, Niu Y, Tang Y, Wang Y, Huang J, Leung ELH. TRP Channels in Cancer: Therapeutic Opportunities and Research Strategies. Pharmacol Res 2024; 209:107412. [PMID: 39303771 DOI: 10.1016/j.phrs.2024.107412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 09/11/2024] [Accepted: 09/11/2024] [Indexed: 09/22/2024]
Abstract
The influence of gut microbiota on transient receptor potential (TRP) channels has been identified as an important element in developing gastrointestinal conditions, yet its involvement in cancer progression is not as thoroughly understood. This review explores the multifaceted roles of TRP channels in oncogenesis and emphasizes their significance in cancer progression and therapeutic outcomes. Critical focus was placed on the influence of traditional medicines, such as traditional Chinese medicine (TCM) related aromatic medicines, on TRP channel functions. Moreover, we explored the interplay between the gut microbiota and TRP channels in cancer signaling, highlighting the therapeutic potential of targeting this axis in cancer treatment. The impact of current therapies on TRP channel function was examined, highlighting the need for a comprehensive understanding of how different modalities affect TRP channels in cancer. Technological advancements, including artificial intelligence (AI) tools and computer-aided drug development (CADD), have been discussed in the context of leveraging TRP channels for innovative cancer therapies. Future directions emphasize the potential applications of TRP channel research in advancing cancer treatment and enhancing patient well-being.
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Affiliation(s)
- Jiahui Xu
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau; MOE Frontiers Science Centre for Precision Oncology, University of Macau, Macau
| | - Ziming Wang
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau; MOE Frontiers Science Centre for Precision Oncology, University of Macau, Macau
| | - Yuqing Niu
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau; MOE Frontiers Science Centre for Precision Oncology, University of Macau, Macau
| | - Yuping Tang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, Shaanxi University of Chinese Medicine, Xianyang 712046, Shaanxi Province, China
| | - Yuwei Wang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, Shaanxi University of Chinese Medicine, Xianyang 712046, Shaanxi Province, China.
| | - Jumin Huang
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau; MOE Frontiers Science Centre for Precision Oncology, University of Macau, Macau.
| | - Elaine Lai-Han Leung
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau; MOE Frontiers Science Centre for Precision Oncology, University of Macau, Macau; State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macau.
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2
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Ozsefil IC, Miraloglu IH, Ozbayram EG, Uzun O, Ince B, Ince O. Is a floodplain forest a valuable source for lignin-degrading anaerobic microbial communities: A metagenomic approach. CHEMOSPHERE 2023; 339:139675. [PMID: 37517669 DOI: 10.1016/j.chemosphere.2023.139675] [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: 01/23/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
Lignin is one of the most substantial obstacles in the evaluation of lignocellulosic compounds. Although there are numerous approaches for the enhancement of lignin digestion in the literature, there has yet to be an optimized system to date. In this study, samples taken from Igneada floodplain forests were enriched anaerobically at 25 °C and 37 °C, with alkali lignin as the sole carbon source. The activity of the anaerobic lignin-degrading microbial consortium was detected more efficiently at 37 °C, where biogas production exceeded 3.5 mLgas/mLmedium. It was observed that the microbial community initially dominated by Proteobacteria (around 60%) changed completely after enrichment and was led by members of the Firmicutes phylum (up to 90%). The dominant species (Sporomusa termitida, Desulfitobacterium hafniense, Citrobacter freundii, Citrobacter portucalensis, Alkalibacter rhizosphaerae, and Gudongella oleilytica) occupying more than 50% in the final enrichment culture were only around 2% in the raw samples. Therefore, this study, one of the few in which enriched environmental samples were sequenced using MinION, demonstrated that longoses are exceptional reservoirs for lignin-digesting anaerobic microorganisms.
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Affiliation(s)
- Ibrahim Cem Ozsefil
- Bogazici University, Institute of Environmental Sciences, Bebek, 34342, Istanbul, Turkey.
| | | | - E Gozde Ozbayram
- Istanbul University, Faculty of Aquatic Sciences, Department of Marine and Freshwater Resources Management, Fatih, 34134, Istanbul, Turkey
| | - Omer Uzun
- Bogazici University, Institute of Environmental Sciences, Bebek, 34342, Istanbul, Turkey
| | - Bahar Ince
- Bogazici University, Institute of Environmental Sciences, Bebek, 34342, Istanbul, Turkey
| | - Orhan Ince
- Department of Environmental Engineering, Faculty of Civil Engineering, Istanbul Technical University, Maslak, 34396, Istanbul, Turkey
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Mesloub Y, Beury D, Vandermeeren F, Caboche S. CuReSim-LoRM: A Tool to Simulate Metabarcoding Long Reads. Int J Mol Sci 2023; 24:14005. [PMID: 37762307 PMCID: PMC10531135 DOI: 10.3390/ijms241814005] [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: 08/07/2023] [Revised: 09/07/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
Metabarcoding DNA sequencing has revolutionized the study of microbial communities. Third-generation sequencing producing long reads had opened up new perspectives. Obtaining the full-length ribosomal RNA gene would permit one to reach a better taxonomic resolution at the species or the strain level. However, Oxford Nanopore Technologies (ONT) sequencing produces reads with high error rates, which introduces biases in analysis. Understanding the biases introduced during the analysis allows one to better interpret the biological results and take care of conclusions drawn from metabarcoding experiments. To benchmark an analysis process, the ground truth, i.e., the real composition of the microbial community, has to be known. In addition to artificial mock communities, simulated data are often used to evaluate the biases and performances of the bioinformatics analysis step. Currently, no specific tool has been developed to simulate metabarcoding long reads, mimic the error rate and the length distribution, and allow one to benchmark the analysis process. Here, we introduce CuReSim-LoRM, for the customized read simulator to generate long reads for metabarcoding. We showed that CuReSim-LoRM is able to produce reads with varying error rates and length distributions by mimicking the real data very well.
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Affiliation(s)
| | | | | | - Ségolène Caboche
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41-UAR 2014-PLBS, F-59000 Lille, France
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4
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Bou Orm E, Sauvagère S, Rocher J, Benezet JC, Bayle S, Siatka C, Bergeret A, Malhautier L. Estimating the bias related to DNA recovery from hemp stems for retting microbial community investigation. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12582-5. [PMID: 37227475 DOI: 10.1007/s00253-023-12582-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023]
Abstract
The industrial hemp plant Cannabis sativa is a source of vegetable fiber for both textiles and biocomposite applications. After harvesting, the plant stems are laid out on the ground and colonized by microorganisms (bacteria and fungi) naturally present in the soil and on the stems. By producing hydrolytic enzymes that degrade the plant wall polymers, the natural cement that binds the fiber bundles together is removed, thus facilitating their dissociation (retting process) which is required for producing high-performant fibers. To investigate temporal dynamics of retting microbial communities (density levels, diversity, and structure), a reliable protocol for extracting genomic DNA from stems is mandatory. However, very little attention has been paid to the methodological aspects of nucleic acid extraction, although they are crucial for the significance of the final result. Three protocols were selected and tested: a commercial kit (FastDNA™ Spin Kit for soil), the Gns-GII procedure, and a custom procedure from the Genosol platform. A comparative analysis was carried out on soil and two different varieties of hemp stem. The efficiency of each method was measured by evaluating both the quantity and quality of the extracted DNA and the abundance and taxonomy of bacterial and fungal populations. The Genosol protocol provides interesting yields in terms of quantity and quality of genomic DNA compared to the other two protocols. However, no major difference was observed in microbial diversity between the two extraction procedures (FastDNA™ SPIN Kit and Genosol protocol). Based on these results, the FastDNA™ SPIN kit or the Genosol procedure seems to be suitable for studying bacterial and fungal communities of the retting process. It should be noted that this work has demonstrated the importance of evaluating biases associated with DNA recovery from hemp stems. KEY POINTS: • Metagenomic DNA was successfully extracted from hemp stem samples using three different protocols. • Further evaluation was performed in terms of DNA yield and purity, abundance level, and microbial community structure. • This work exhibited the crucial importance of DNA recovery bias evaluation.
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Affiliation(s)
- Eliane Bou Orm
- Polymers, Composites and Hybrids (PCH), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Stéphane Sauvagère
- École de l'ADN, Université de Nîmes, 19 Grand Rue BP 81295, 30015, Nîmes cedex 1, France
| | - Janick Rocher
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Jean-Charles Benezet
- Polymers, Composites and Hybrids (PCH), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Sandrine Bayle
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Christian Siatka
- UPR CHROME, Université de Nîmes, Place Gabriel Péri, 30000, Nîmes cedex 1, France
| | - Anne Bergeret
- Polymers, Composites and Hybrids (PCH), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Luc Malhautier
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France.
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Li X, Tseng HT, Hemmings G, Omolehin O, Taylor C, Taylor A, Kong P, Daughtrey M, Gouker F, Hong C. Characterization of Boxwood Shoot Bacterial Communities and Potential Impact from Fungicide Treatments. Microbiol Spectr 2023; 11:e0416322. [PMID: 36853063 PMCID: PMC10100737 DOI: 10.1128/spectrum.04163-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/10/2023] [Indexed: 03/01/2023] Open
Abstract
Phyllosphere bacterial communities play important roles in plant fitness and growth. The objective of this study was to characterize the epiphytic and endophytic bacterial communities of boxwood shoots and determine how they may respond to commonly used fungicides. In early summer and early fall, shoot samples were collected immediately before and 1, 7, and 14 days after three fungicides containing chlorothalonil and/or propiconazole were applied to the canopy. Total genomic DNA from shoot surface washings and surface-sterilized shoot tissues was used as the template for 16S rRNA metabarcoding, and the amplicons were sequenced on a Nanopore MinION sequencer to characterize the epiphytic and endophytic communities. The bacterial communities were phylogenetically more diverse on the boxwood shoot surface than in the internal tissue, although the two communities shared 12.7% of the total 1,649 identified genera. The most abundant epiphytes were Methylobacterium and Pantoea, while Stenotrophomonas and Brevundimonas were the dominant endophytes. Fungicide treatments had strong impacts on epiphytic bacterial community structure and composition. Analysis of compositions of microbiomes with bias correction (ANCOM-BC) and analysis of variance (ANOVA)-like differential expression (ALDEx2) together identified 312 and 1,362 epiphytes changed in abundance due to fungicide treatments in early summer and early fall, respectively, and over 50% of these epiphytes were negatively impacted by fungicide. The two chlorothalonil-based contact fungicides demonstrated more marked effects than the propiconazole-based systemic fungicide. These results are foundational for exploring and utilizing the full potential of the microbiome and fungicide applications and developing a systems approach to boxwood health and production. IMPORTANCE Agrochemicals are important tools for safeguarding plants from invasive pathogens, insects, mites, and weeds. How they may affect the plant microbiome, a critical component of crop health and production, was poorly understood. Here, we used boxwood, an iconic low-maintenance landscape plant, to characterize shoot epiphytic and endophytic bacterial communities and their responses to contact and systemic fungicides. This study expanded our understanding of the above-ground microbiome in ornamental plants and is foundational for utilizing the full benefits of the microbiome in concert with different fungicide chemistries to improve boxwood health. This study also sets an example for a more thorough evaluation of these and other agrochemicals for their effects on boxwood microbiomes during production and offers an expanded systems approach that could be used with other crops for enhanced integrated pest management.
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Affiliation(s)
- Xiaoping Li
- Hampton Roads Agriculture Research and Extension Center, Virginia Tech, Virginia Beach, Virginia, USA
| | - Hsien Tzer Tseng
- North Carolina Department of Agriculture and Consumer Services, Plant Industry Division, Raleigh, North Carolina, USA
| | - Ginger Hemmings
- North Carolina Department of Agriculture and Consumer Services, Plant Industry Division, Dobson, North Carolina, USA
| | - Olanike Omolehin
- Hampton Roads Agriculture Research and Extension Center, Virginia Tech, Virginia Beach, Virginia, USA
| | - Chad Taylor
- North Carolina Department of Agriculture and Consumer Services, Plant Industry Division, Boone, North Carolina, USA
| | - Amanda Taylor
- North Carolina University Cooperative Extension, Morganton, North Carolina, USA
| | - Ping Kong
- Hampton Roads Agriculture Research and Extension Center, Virginia Tech, Virginia Beach, Virginia, USA
| | - Margery Daughtrey
- Long Island Horticultural Research and Extension Center, Cornell University, Riverhead, New York, USA
| | - Fred Gouker
- USDA-ARS, U.S. National Arboretum, Floral and Nursery Plants Research Unit, Beltsville, Maryland, USA
| | - Chuanxue Hong
- Hampton Roads Agriculture Research and Extension Center, Virginia Tech, Virginia Beach, Virginia, USA
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Planý M, Sitarčík J, Pavlović J, Budiš J, Koreňová J, Kuchta T, Pangallo D. Evaluation of bacterial consortia associated with dairy fermentation by ribosomal RNA (rrn) operon metabarcoding strategy using MinION device. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2022.102308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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7
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Morales-Rivera MF, Valenzuela-Miranda D, Nuñez-Acuña G, Benavente BP, Gallardo-Escárate C, Valenzuela-Muñoz V. Atlantic Salmon ( Salmo salar) Transfer to Seawater by Gradual Salinity Changes Exhibited an Increase in The Intestinal Microbial Abundance and Richness. Microorganisms 2022; 11:microorganisms11010076. [PMID: 36677368 PMCID: PMC9865641 DOI: 10.3390/microorganisms11010076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
The host's physiological history and environment determine the microbiome structure. In that sense, the strategy used for the salmon transfer to seawater after parr-smolt transformation may influence the Atlantic salmon's intestinal microbiota. Therefore, this study aimed to explore the diversity and abundance of the Atlantic salmon intestinal microbiota and metagenome functional prediction during seawater transfer under three treatments. One group was exposed to gradual salinity change (GSC), the other to salinity shock (SS), and the third was fed with a functional diet (FD) before the seawater (SW) transfer. The microbial profile was assessed through full-16S rRNA gene sequencing using the Nanopore platform. In addition, metagenome functional prediction was performed using PICRUSt2. The results showed an influence of salinity changes on Atlantic salmon gut microbiota richness, diversity, and taxonomic composition. The findings reveal that GSC and the FD increased the Atlantic salmon smolt microbiota diversity, suggesting a positive association between the intestinal microbial community and fish health during seawater transfer. The reported knowledge can be applied to surveil the microbiome in smolt fish production, improving the performance of Atlantic salmon to seawater transfer.
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Affiliation(s)
- María F. Morales-Rivera
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Diego Valenzuela-Miranda
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
- Centro de Biotecnología, Universidad de Concepción, Concepcion 4030000, Chile
| | - Gustavo Nuñez-Acuña
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Bárbara P. Benavente
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
- Centro de Biotecnología, Universidad de Concepción, Concepcion 4030000, Chile
- Correspondence: ; Tel.: +56-41-2204402
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Kerry-Barnard S, Zhou L, Phillips L, Furegato M, Witney AA, Sadiq ST, Oakeshott P. Vaginal microbiota in ethnically diverse young women who did or did not develop pelvic inflammatory disease: community-based prospective study. Sex Transm Infect 2022; 98:503-509. [PMID: 35086915 PMCID: PMC9613871 DOI: 10.1136/sextrans-2021-055260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/26/2021] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES A lactobacilli-dominated vaginal microbiome may protect against pelvic inflammatory disease (PID), but one dominated by Gardnerella species might increase susceptibility. Not all lactobacilli are equally protective. Recent research suggests that D(-) isomer lactic acid producing lactobacilli (Lactobacillus crispatus, Lactobacillus jensenii and Lactobacillus gasseri) may protect against infection with Chlamydia trachomatis, an important cause of PID. Lactobacillus iners , which produces L(+) isomer lactic acid, may be less protective. We investigated the microbiome in stored vaginal samples from participants who did or did not develop PID during the prevention of pelvic infection (POPI) chlamydia screening trial. METHODS Long-read 16S rRNA gene nanopore sequencing was used on baseline vaginal samples (one per participant) from all 37 women who subsequently developed clinically diagnosed PID during 12-month follow-up, and 111 frequency matched controls who did not, matched on four possible risk factors for PID: age <20 versus ≥20, black ethnicity versus other ethnicity, chlamydia positive versus negative at baseline and ≥2 sexual partners in the previous year versus 0-1 partners. RESULTS Samples from 106 women (median age 19 years, 40% black ethnicity, 22% chlamydia positive, 54% reporting multiple partners) were suitable for analysis. Three main taxonomic clusters were identified dominated by L. iners, L. crispatus and Gardnerella vaginalis. There was no association between a more diverse, G. vaginalis dominated microbiome and subsequent PID, although increased Shannon diversity was associated with black ethnicity (p=0.002) and bacterial vaginosis (diagnosed by Gram stain p<0.0001). Women who developed PID had similar relative abundance of protective D(-) isomer lactic acid producing lactobacilli to women without PID, but numbers of PID cases were small. CONCLUSIONS In the first-ever community-based prospective study of PID, there was no clear association between the vaginal microbiome and subsequent development of PID. Future studies using serial samples may identify vaginal microbial communities that may predispose to PID.
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Affiliation(s)
- Sarah Kerry-Barnard
- Population Health Research Institute, St George's, University of London, London, UK
| | - Liqing Zhou
- Applied Diagnostic Research and Evaluation Unit, St George's, University of London, London, UK
| | - Laura Phillips
- Applied Diagnostic Research and Evaluation Unit, St George's, University of London, London, UK
| | - Martina Furegato
- Applied Diagnostic Research and Evaluation Unit, St George's, University of London, London, UK
| | - Adam A Witney
- Institute for Infection and Immunity, St George's, University of London, London, UK
| | - S Tariq Sadiq
- Applied Diagnostic Research and Evaluation Unit, St George's, University of London, London, UK,Clinical Academic group in Infection and Immunity, St George’s University Hospitals NHS Foundation Trust, London, UK
| | - Pippa Oakeshott
- Population Health Research Institute, St George's, University of London, London, UK
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Kim H, Jeon S, Kim J, Seol D, Jo J, Cho S, Kim H. Investigation of memory-enhancing effects of Streptococcus thermophilus EG007 in mice and elucidating molecular and metagenomic characteristics using nanopore sequencing. Sci Rep 2022; 12:13274. [PMID: 35918353 PMCID: PMC9346115 DOI: 10.1038/s41598-022-14837-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/13/2022] [Indexed: 11/15/2022] Open
Abstract
Over the past decades, accumulating evidences have highlighted the gut microbiota as a key player in the brain functioning via microbiota–gut–brain axis, and accordingly, the beneficial role of several probiotic strains in cognitive ability also have been actively investigated. However, the majority of the research have demonstrated the effects against age-related cognitive decline or neurological disease. To this end, we aimed to investigate lactic acid bacteria strains having beneficial effects on the cognitive function of healthy young mice and elucidate underlying characteristics by carrying out nanopore sequencing-based genomics and metagenomics analysis. 8-week consumption of Streptococcus thermophilus EG007 demonstrated marked enhancements in behavior tests assessing short-term spatial and non-spatial learning and memory. It was revealed that EG007 possessed genes encoding various metabolites beneficial for a health condition in many aspects, including gamma-aminobutyric acid producing system, a neurotransmitter associated with mood and stress response. Also, by utilizing 16S–23S rRNA operon as a taxonomic marker, we identified more accurate species-level compositional changes in gut microbiota, which was increase of certain species, previously reported to have associations with mental health or down-regulation of inflammation or infection-related species. Moreover, correlation analysis revealed that the EG007-mediated altered microbiota had a significant correlation with the memory traits.
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Affiliation(s)
- Hyaekang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Soomin Jeon
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jina Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.,eGnome, Inc, Seoul, Republic of Korea
| | - JinChul Jo
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seoae Cho
- eGnome, Inc, Seoul, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea. .,eGnome, Inc, Seoul, Republic of Korea.
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Benítez-Páez A, Hartstra AV, Nieuwdorp M, Sanz Y. Species- and strain-level assessment using rrn long-amplicons suggests donor's influence on gut microbial transference via fecal transplants in metabolic syndrome subjects. Gut Microbes 2022; 14:2078621. [PMID: 35604764 PMCID: PMC9132484 DOI: 10.1080/19490976.2022.2078621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Fecal microbiota transplantation (FMT) is currently used for treating Clostridium difficile infection and explored for other clinical applications in experimental trials. However, the effectiveness of this therapy could vary, and partly depend on the donor's bacterial species engraftment, whose evaluation is challenging because there are no cost-effective strategies for accurately tracking the microbe transference. In this regard, the precise identification of bacterial species inhabiting the human gut is essential to define their role in human health unambiguously. We used Nanopore-based device to sequence bacterial rrn operons (16S-ITS-23S) and to reveal species-level abundance changes in the human gut microbiota of a FMT trial. By assessing the donor and recipient microbiota before and after FMT, we further evaluated whether this molecular approach reveals strain-level genetic variation to demonstrate microbe transfer and engraftment. Strict control over sequencing data quality and major microbiota covariates was critical for accurately estimating the changes in gut microbial species abundance in the recipients after FMT. We detected strain-level variation via single-nucleotide variants (SNVs) at rrn regions in a species-specific manner. We showed that it was possible to explore successfully the donor-bacterial strain (e.g., Parabacteroides merdae) engraftment in recipients of the FMT by assessing the nucleotide frequencies at rrn-associated SNVs. Our findings indicate that the engraftment of donors' microbiota is to some extent correlated with the improvement of metabolic health in recipients and that parameters such as the baseline gut microbiota configuration, sex, and age of donors should be considered to ensure the success of FMT in humans. The study was prospectively registered at the Dutch Trial registry - NTR4488 (https://www.trialregister.nl/trial/4488).
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Affiliation(s)
- Alfonso Benítez-Páez
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna-Valencia, Spain,Host-Microbe Interactions in Metabolic Health Laboratory, Principe Felipe Research Center (CIPF), Valencia, Spain,CONTACT Alfonso Benítez-Páez Host-Microbe Interactions in Metabolic Health Laboratory, Principe Felipe Research Center (CIPF), Valencia, Spain
| | - Annick V. Hartstra
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Yolanda Sanz
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna-Valencia, Spain,Yolanda Sanz Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna-Valencia46980, Spain
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11
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Liu B, Fu R, Wu B, Liu X, Xiang M. Rock-inhabiting fungi: terminology, diversity, evolution and adaptation mechanisms. Mycology 2022; 13:1-31. [PMID: 35186410 PMCID: PMC8856086 DOI: 10.1080/21501203.2021.2002452] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rock-inhabiting fungi (RIF) constitute an ecological group associated with terrestrial rocks. This association is generally restricted to the persistent colonisation of rocks and peculiar morphological features based on melanisation and slow growth, which endow RIF with significance in eukaryotic biology, special status in ecology, and exotic potential in biotechnology. There is a need to achieve a better understanding of the hidden biodiversity, antistress biology, origin and convergent evolution of RIF, which will facilitate cultural relic preservation, exploitation of the biogeochemical cycle of rock elements and biotechnology applications. This review focuses on summarising the current knowledge of rock-inhabiting fungi, with particular reference to terminology, biodiversity and geographic distribution, origin and evolution, and stress adaptation mechanisms. We especially teased out the definition through summing up the terms related to rock-inhabting fungi, and also provided a checklist of rock-inhabiting fungal taxa recorded following updated classification schemes.
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Affiliation(s)
- Bingjie Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Rong Fu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bing Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xingzhong Liu
- Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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12
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Latorre-Pérez A, Gimeno-Valero H, Tanner K, Pascual J, Vilanova C, Porcar M. A Round Trip to the Desert: In situ Nanopore Sequencing Informs Targeted Bioprospecting. Front Microbiol 2021; 12:768240. [PMID: 34966365 PMCID: PMC8710813 DOI: 10.3389/fmicb.2021.768240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/15/2021] [Indexed: 12/26/2022] Open
Abstract
Bioprospecting expeditions are often performed in remote locations, in order to access previously unexplored samples. Nevertheless, the actual potential of those samples is only assessed once scientists are back in the laboratory, where a time-consuming screening must take place. This work evaluates the suitability of using Nanopore sequencing during a journey to the Tabernas Desert (Spain) for forecasting the potential of specific samples in terms of bacterial diversity and prevalence of radiation- and desiccation-resistant taxa, which were the target of the bioprospecting activities. Samples collected during the first day were analyzed through 16S rRNA gene sequencing using a mobile laboratory. Results enabled the identification of locations showing the greatest and the least potential, and a second, informed sampling was performed focusing on those sites. After finishing the expedition, a culture collection of 166 strains belonging to 50 different genera was established. Overall, Nanopore and culturing data correlated well, since samples holding a greater potential at the microbiome level also yielded a more interesting set of microbial isolates, whereas samples showing less biodiversity resulted in a reduced (and redundant) set of culturable bacteria. Thus, we anticipate that portable sequencers hold potential as key, easy-to-use tools for in situ-informed bioprospecting strategies.
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Affiliation(s)
| | | | | | | | | | - Manuel Porcar
- Darwin Bioprospecting Excellence S.L., Paterna, Spain
- Institute for Integrative Systems Biology I2SysBio (University of València-CSIC), Paterna, Spain
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13
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de Siqueira GMV, Pereira-dos-Santos FM, Silva-Rocha R, Guazzaroni ME. Nanopore Sequencing Provides Rapid and Reliable Insight Into Microbial Profiles of Intensive Care Units. Front Public Health 2021; 9:710985. [PMID: 34513786 PMCID: PMC8429932 DOI: 10.3389/fpubh.2021.710985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/30/2021] [Indexed: 11/13/2022] Open
Abstract
Fast and accurate identification of pathogens is an essential task in healthcare settings. Second-generation sequencing platforms such as Illumina have greatly expanded the capacity with which different organisms can be detected in hospital samples, and third-generation nanopore-driven sequencing devices such as Oxford Nanopore's minION have recently emerged as ideal sequencing platforms for routine healthcare surveillance due to their long-read capacity and high portability. Despite its great potential, protocols and analysis pipelines for nanopore sequencing are still being extensively validated. In this work, we assess the ability of nanopore sequencing to provide reliable community profiles based on 16S rRNA sequencing in comparison to traditional Illumina platforms using samples collected from Intensive Care Units of a hospital in Brazil. While our results demonstrate that lower throughputs may be a shortcoming of the method in more complex samples, we show that the use of single-use Flongle flowcells in nanopore sequencing runs can provide insightful information on the community composition in healthcare settings.
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Affiliation(s)
| | - Felipe Marcelo Pereira-dos-Santos
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Ribeirão Preto, Brazil
| | - Rafael Silva-Rocha
- Departamento de Biologia, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto (FFCLRP-USP), Ribeirão Preto, Brazil
| | - María-Eugenia Guazzaroni
- Departamento de Biologia, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto (FFCLRP-USP), Ribeirão Preto, Brazil
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14
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Okazaki Y, Fujinaga S, Salcher MM, Callieri C, Tanaka A, Kohzu A, Oyagi H, Tamaki H, Nakano SI. Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing. MICROBIOME 2021; 9:24. [PMID: 33482922 PMCID: PMC7825169 DOI: 10.1186/s40168-020-00974-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/07/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe. RESULTS Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7-101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion. CONCLUSIONS Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future. Video abstract.
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Affiliation(s)
- Yusuke Okazaki
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga, 520-2113, Japan.
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan.
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
| | - Shohei Fujinaga
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga, 520-2113, Japan
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 37005, České Budějovice, Czech Republic
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Zurich, Switzerland
| | - Cristiana Callieri
- CNR, IRSA Institute of Water Research, Largo Tonolli 50, 28922, Verbania, Italy
| | - Atsushi Tanaka
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Ayato Kohzu
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Hideo Oyagi
- Faculty of Policy Studies, Nanzan University, 18 Yamazato-cho, Showa-ku, Nagoya, Aichi, 466-8673, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan
| | - Shin-Ichi Nakano
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga, 520-2113, Japan
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15
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Urban L, Holzer A, Baronas JJ, Hall MB, Braeuninger-Weimer P, Scherm MJ, Kunz DJ, Perera SN, Martin-Herranz DE, Tipper ET, Salter SJ, Stammnitz MR. Freshwater monitoring by nanopore sequencing. eLife 2021; 10:e61504. [PMID: 33461660 PMCID: PMC7815314 DOI: 10.7554/elife.61504] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/01/2020] [Indexed: 12/15/2022] Open
Abstract
While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices.
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Affiliation(s)
- Lara Urban
- European Bioinformatics Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Andre Holzer
- Department of Plant Sciences, University of CambridgeCambridgeUnited Kingdom
| | - J Jotautas Baronas
- Department of Earth Sciences, University of CambridgeCambridgeUnited Kingdom
| | - Michael B Hall
- European Bioinformatics Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | | | - Michael J Scherm
- Department of Biochemistry, University of CambridgeCambridgeUnited Kingdom
| | - Daniel J Kunz
- Wellcome Sanger Institute, Wellcome Trust Genome CampusHinxtonUnited Kingdom
- Department of Physics, University of CambridgeCambridgeUnited Kingdom
| | - Surangi N Perera
- Department of Physiology, Development & Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | | | - Edward T Tipper
- Department of Earth Sciences, University of CambridgeCambridgeUnited Kingdom
| | - Susannah J Salter
- Department of Veterinary Medicine, University of CambridgeCambridgeUnited Kingdom
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16
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Straub D, Blackwell N, Langarica-Fuentes A, Peltzer A, Nahnsen S, Kleindienst S. Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline. Front Microbiol 2020; 11:550420. [PMID: 33193131 PMCID: PMC7645116 DOI: 10.3389/fmicb.2020.550420] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 10/02/2020] [Indexed: 12/11/2022] Open
Abstract
One of the major methods to identify microbial community composition, to unravel microbial population dynamics, and to explore microbial diversity in environmental samples is high-throughput DNA- or RNA-based 16S rRNA (gene) amplicon sequencing in combination with bioinformatics analyses. However, focusing on environmental samples from contrasting habitats, it was not systematically evaluated (i) which analysis methods provide results that reflect reality most accurately, (ii) how the interpretations of microbial community studies are biased by different analysis methods and (iii) if the most optimal analysis workflow can be implemented in an easy-to-use pipeline. Here, we compared the performance of 16S rRNA (gene) amplicon sequencing analysis tools (i.e., Mothur, QIIME1, QIIME2, and MEGAN) using three mock datasets with known microbial community composition that differed in sequencing quality, species number and abundance distribution (i.e., even or uneven), and phylogenetic diversity (i.e., closely related or well-separated amplicon sequences). Our results showed that QIIME2 outcompeted all other investigated tools in sequence recovery (>10 times fewer false positives), taxonomic assignments (>22% better F-score) and diversity estimates (>5% better assessment), suggesting that this approach is able to reflect the in situ microbial community most accurately. Further analysis of 24 environmental datasets obtained from four contrasting terrestrial and freshwater sites revealed dramatic differences in the resulting microbial community composition for all pipelines at genus level. For instance, at the investigated river water sites Sphaerotilus was only reported when using QIIME1 (8% abundance) and Agitococcus with QIIME1 or QIIME2 (2 or 3% abundance, respectively), but both genera remained undetected when analyzed with Mothur or MEGAN. Since these abundant taxa probably have implications for important biogeochemical cycles (e.g., nitrate and sulfate reduction) at these sites, their detection and semi-quantitative enumeration is crucial for valid interpretations. A high-performance computing conformant workflow was constructed to allow FAIR (Findable, Accessible, Interoperable, and Re-usable) 16S rRNA (gene) amplicon sequence analysis starting from raw sequence files, using the most optimal methods identified in our study. Our presented workflow should be considered for future studies, thereby facilitating the analysis of high-throughput 16S rRNA (gene) sequencing data substantially, while maximizing reliability and confidence in microbial community data analysis.
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Affiliation(s)
- Daniel Straub
- Microbial Ecology, Center for Applied Geoscience, Department of Geosciences, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Nia Blackwell
- Microbial Ecology, Center for Applied Geoscience, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Adrian Langarica-Fuentes
- Microbial Ecology, Center for Applied Geoscience, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Alexander Peltzer
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Sara Kleindienst
- Microbial Ecology, Center for Applied Geoscience, Department of Geosciences, University of Tübingen, Tübingen, Germany
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17
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Sanderson ND, Swann J, Barker L, Kavanagh J, Hoosdally S, Crook D, Street TL, Eyre DW. High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing. Genome Res 2020; 30:1354-1363. [PMID: 32873606 PMCID: PMC7545138 DOI: 10.1101/gr.262865.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/27/2020] [Indexed: 12/14/2022]
Abstract
The rise of antimicrobial-resistant Neisseria gonorrhoeae is a significant public health concern. Against this background, rapid culture-independent diagnostics may allow targeted treatment and prevent onward transmission. We have previously shown metagenomic sequencing of urine samples from men with urethral gonorrhea can recover near-complete N. gonorrhoeae genomes. However, disentangling the N. gonorrhoeae genome from metagenomic samples and robustly identifying antimicrobial resistance determinants from error-prone Nanopore sequencing is a substantial bioinformatics challenge. Here, we show an N. gonorrhoeae diagnostic workflow for analysis of metagenomic sequencing data obtained from clinical samples using R9.4.1 Nanopore sequencing. We compared results from simulated and clinical infections with data from known reference strains and Illumina sequencing of isolates cultured from the same patients. We evaluated three Nanopore variant callers and developed a random forest classifier to filter called SNPs. Clair was the most suitable variant caller after SNP filtering. A minimum depth of 20× reads was required to confidently identify resistant determinants over the entire genome. Our findings show that metagenomic Nanopore sequencing can provide reliable diagnostic information in N. gonorrhoeae infection.
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Affiliation(s)
- Nicholas D Sanderson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Jeremy Swann
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Leanne Barker
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - James Kavanagh
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Sarah Hoosdally
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Derrick Crook
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.,National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | | | - Teresa L Street
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - David W Eyre
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.,National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.,Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
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18
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Ibironke O, McGuinness LR, Lu SE, Wang Y, Hussain S, Weisel CP, Kerkhof LJ. Species-level evaluation of the human respiratory microbiome. Gigascience 2020; 9:giaa038. [PMID: 32298431 PMCID: PMC7162353 DOI: 10.1093/gigascience/giaa038] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 03/06/2020] [Accepted: 03/25/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Changes to human respiratory tract microbiome may contribute significantly to the progression of respiratory diseases. However, there are few studies examining the relative abundance of microbial communities at the species level along the human respiratory tract. FINDINGS Bronchoalveolar lavage, throat swab, mouth rinse, and nasal swab samples were collected from 5 participants. Bacterial ribosomal operons were sequenced using the Oxford Nanopore MinION to determine the relative abundance of bacterial species in 4 compartments along the respiratory tract. More than 1.8 million raw operon reads were obtained from the participants with ∼600,000 rRNA reads passing quality assurance/quality control (70-95% identify; >1,200 bp alignment) by Discontiguous MegaBLAST against the EZ BioCloud 16S rRNA gene database. Nearly 3,600 bacterial species were detected overall (>750 bacterial species within the 5 dominant phyla: Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria. The relative abundance of bacterial species along the respiratory tract indicated that most microbes (95%) were being passively transported from outside into the lung. However, a small percentage (<5%) of bacterial species were at higher abundance within the lavage samples. The most abundant lung-enriched bacterial species were Veillonella dispar and Veillonella atypica while the most abundant mouth-associated bacterial species were Streptococcus infantis and Streptococcus mitis. CONCLUSIONS Most bacteria detected in lower respiratory samples do not seem to colonize the lung. However, >100 bacterial species were found to be enriched in bronchoalveolar lavage samples (compared to mouth/nose) and may play a substantial role in lung health.
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Affiliation(s)
- Olufunmilola Ibironke
- Environmental and Occupational Health Sciences Institute, School of Public Health, Rutgers–the State University of New Jersey, 170 Frelinghuysen Road, Piscataway, NJ, USA 08854, NJ, USA
| | - Lora R McGuinness
- Department of Marine and Coastal Sciences, Rutgers–the State University of New Jersey, 71 Dudley Road, New Brunswick, NJ USA 08901
| | - Shou-En Lu
- Environmental and Occupational Health Sciences Institute, School of Public Health, Rutgers–the State University of New Jersey, 170 Frelinghuysen Road, Piscataway, NJ, USA 08854, NJ, USA
| | - Yaquan Wang
- Environmental and Occupational Health Sciences Institute, School of Public Health, Rutgers–the State University of New Jersey, 170 Frelinghuysen Road, Piscataway, NJ, USA 08854, NJ, USA
| | - Sabiha Hussain
- Department of Pulmonary Medicine, Rutgers University-Robert Wood Johnsonchool, 125 Paterson Street, Suite 5200B New Brunswick, NJ 08901
| | - Clifford P Weisel
- Department of Pulmonary Medicine, Rutgers University-Robert Wood Johnsonchool, 125 Paterson Street, Suite 5200B New Brunswick, NJ 08901
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers–the State University of New Jersey, 71 Dudley Road, New Brunswick, NJ USA 08901
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19
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Nanoliter-scale next-generation sequencing library-mediated high-throughput 16S rRNA microbial community profiling. Biotechniques 2020; 68:204-210. [PMID: 32096668 DOI: 10.2144/btn-2019-0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
An ultra-high-throughput workflow for next-generation sequencing library construction at nanoliter scale for amplicon sequencing, termed Smartchip Nanowell Platform for Target Enrichment, was established using a nanodispenser system and a nanoliter-scale PCR chip. To demonstrate its cost and time advantages over conventional methods for library construction, quality control and pooling for large-scale samples, target amplicon sequencing of the 16S ribosomal RNA gene V3-V4 region widely used for microbial community profiling was chosen for comparison. The finding of no significant difference in microbial community profiling between the two methods strongly supports the conclusion that Smartchip Nanowell Platform for Target Enrichment is a cost-effective method for next-generation sequencing library construction for large-scale samples to conduct amplicon sequencing-based applications.
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20
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Nygaard AB, Tunsjø HS, Meisal R, Charnock C. A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes. Sci Rep 2020; 10:3209. [PMID: 32081924 PMCID: PMC7035348 DOI: 10.1038/s41598-020-59771-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 01/30/2020] [Indexed: 12/02/2022] Open
Abstract
There is a growing awareness of the importance of indoor microbiomes for human health. Given their complexity, these microbiomes can only be adequately surveyed using high throughput sequencing techniques. Oxford Nanopore’s MinION is the newest third generation sequencing technology on the market. With its many advantages such as portability, user friendliness, simplicity, speed of sequencing and long read length, the technology is now an actual contender to established sequencing platforms. MinION’s main disadvantage is a relatively low read accuracy compared to several other platforms, although this is constantly improving. The present study, which appears to be the first of its kind, provides the results of a preliminary analysis of the microbial communities in indoor environments based on 16S rRNA gene amplicon sequencing, using both the Oxford Nanopore Technologies (ONT) MinIOn and the Illumina MiSeq DNA sequencers. At the level of family and above, there was no significant difference between the microbial compositions as revealed by the two platforms. However, at the genus, and particularly at the species level, the ONT MinION reported greater taxonomic resolution than Illumina MiSeq.
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Affiliation(s)
- Anders B Nygaard
- Faculty of Technology, Art and Design, Department of Civil Engineering and Energy Technology, Oslo Metropolitan University (OsloMet), Oslo, Norway. .,Faculty of Health Sciences, Department of Life Sciences and Health, OsloMet, Oslo, Norway.
| | - Hege S Tunsjø
- Faculty of Health Sciences, Department of Life Sciences and Health, OsloMet, Oslo, Norway
| | | | - Colin Charnock
- Faculty of Health Sciences, Department of Life Sciences and Health, OsloMet, Oslo, Norway
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21
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Gonçalves AT, Collipal-Matamal R, Valenzuela-Muñoz V, Nuñez-Acuña G, Valenzuela-Miranda D, Gallardo-Escárate C. Nanopore sequencing of microbial communities reveals the potential role of sea lice as a reservoir for fish pathogens. Sci Rep 2020; 10:2895. [PMID: 32076035 PMCID: PMC7031262 DOI: 10.1038/s41598-020-59747-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/03/2020] [Indexed: 12/11/2022] Open
Abstract
Caligus rogercresseyi is a copepod ectoparasite with a high prevalence in salmon farms in Chile, causing severe welfare and economic concerns to the sector. Information on the parasite's underpinning mechanisms to support its life strategy is recently being investigated. Due to the critical role of microbiota, this study aimed to characterize the microbiota community associated with C. rogercresseyi from different regions with salmon aquaculture in Chile. Using third-generation sequencing with Nanopore technology (MinION) the full 16S rRNA gene from sea lice obtained from 8 areas distributed over the three main aquaculture regions were sequenced. Microbiota of the parasite is mainly comprised of members of phyla Proteobacteria and Bacteroidetes, and a core microbiota community with 147 taxonomical features was identified, and it was present in sea lice from the three regions. This community accounted for 19% of total identified taxa but more than 70% of the total taxonomical abundance, indicating a strong presence in the parasite. Several taxa with bioactive compound secretory capacity were identified, such as members of genus Pseudoalteromonas and Dokdonia, suggesting a possible role of the lice microbiota during the host infestation processes. Furthermore, the microbiota community was differentially associated with the salmon production, where several potential pathogens such as Vibrio, Tenacibaculum, and Aeromonas in Los Lagos, Aysén, and Magallanes region were identified. Notably, the Chilean salmon industry was initially established in the Los Lagos region but it's currently moving to the south, where different oceanographic conditions coexist with lice populations. The results originated by this study will serve as foundation to investigate putative role of sea lice as vectors for fish pathogens and also as reservoirs for antibiotic-resistant genes.
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Affiliation(s)
- Ana Teresa Gonçalves
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile.,Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile
| | - Rayen Collipal-Matamal
- Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile.,Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile
| | - Gustavo Nuñez-Acuña
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile.,Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile
| | - Diego Valenzuela-Miranda
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile.,Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile
| | - Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research, University of Concepción, Concepción, Chile. .,Laboratory of Biotechnology and Aquatic Genomics, Center of Biotechnology, University of Concepción, Concepción, Chile.
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22
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Pietri JE, Yax JA, Agany DD, Gnimpieba EZ, Sheele JM. Body lice and bed bug co-infestation in an emergency department patient, Ohio, USA. IDCases 2020; 19:e00696. [PMID: 31988849 PMCID: PMC6970161 DOI: 10.1016/j.idcr.2020.e00696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 12/17/2022] Open
Abstract
Body lice and bed bugs are hematophagous insects that parasitize humans. Body lice are established vectors of several bacterial pathogens (e.g. Bartonella quintana, Borrelia recurrentis). Bed bugs are biologically competent vectors of some of the same agents, but their vectorial capacity for these in nature is unclear. In particular, a lack of exposure to louse-borne pathogens in bed bugs in the field could be a factor that limits their contribution to transmission. Here, we describe a case of a patient seen in an urban emergency department who was suffering from infestation with both body lice and bed bugs. Insects were collected from the patient and tested for the presence of louse-borne bacterial pathogens using 16S rRNA gene amplicon sequencing. Although no Bartonella, Borrelia, or Rickettsia were detected, this case provides evidence of ecological overlap between body lice and bed bugs and highlights several potential risk factors for co-infestation. The ecological relationships between bed bugs, body lice, and louse-borne bacteria should be further investigated in the field to determine the frequency of co-infestations and identify possible instances of pathogen infection in bed bugs.
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Affiliation(s)
- Jose E. Pietri
- University of South Dakota, Sanford School of Medicine, Division of Basic Biomedical Sciences, Vermillion, SD, United States
| | - Justin A. Yax
- University Hospitals Cleveland Medical Center, Division of Population Health, Department of Emergency Medicine, Cleveland, OH, United States
| | - Diing D.M. Agany
- University of South Dakota, Biomedical Engineering Program, Sioux Falls, SD, United States
| | - Etienne Z. Gnimpieba
- University of South Dakota, Biomedical Engineering Program, Sioux Falls, SD, United States
| | - Johnathan M. Sheele
- Mayo Clinic, Department of Emergency Medicine, Jacksonville, FL, United States
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23
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Unlinked rRNA genes are widespread among bacteria and archaea. ISME JOURNAL 2019; 14:597-608. [PMID: 31712737 DOI: 10.1038/s41396-019-0552-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/23/2019] [Accepted: 10/29/2019] [Indexed: 02/06/2023]
Abstract
Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in bacteria and archaea. Ribosomal RNA genes are typically organized into a single operon, an arrangement thought to facilitate gene regulation. In reality, some bacteria and archaea do not share this canonical rRNA arrangement-their 16S and 23S rRNA genes are separated across the genome and referred to as "unlinked". This rearrangement has previously been treated as an anomaly or a byproduct of genome degradation in intracellular bacteria. Here, we leverage complete genome and long-read metagenomic data to show that unlinked 16S and 23S rRNA genes are more common than previously thought. Unlinked rRNA genes occur in many phyla, most significantly within Deinococcus-Thermus, Chloroflexi, and Planctomycetes, and occur in differential frequencies across natural environments. We found that up to 41% of rRNA genes in soil were unlinked, in contrast to the human gut, where all sequenced rRNA genes were linked. The frequency of unlinked rRNA genes may reflect meaningful life history traits, as they tend to be associated with a mix of slow-growing free-living species and intracellular species. We speculate that unlinked rRNA genes may confer selective advantages in some environments, though the specific nature of these advantages remains undetermined and worthy of further investigation. More generally, the prevalence of unlinked rRNA genes in poorly-studied taxa serves as a reminder that paradigms derived from model organisms do not necessarily extend to the broader diversity of bacteria and archaea.
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24
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Loit K, Adamson K, Bahram M, Puusepp R, Anslan S, Kiiker R, Drenkhan R, Tedersoo L. Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens. Appl Environ Microbiol 2019; 85:e01368-19. [PMID: 31444199 PMCID: PMC6803294 DOI: 10.1128/aem.01368-19] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/18/2019] [Indexed: 02/06/2023] Open
Abstract
Culture-based molecular identification methods have revolutionized detection of pathogens, yet these methods are slow and may yield inconclusive results from environmental materials. The second-generation sequencing tools have much-improved precision and sensitivity of detection, but these analyses are costly and may take several days to months. Of the third-generation sequencing techniques, the portable MinION device (Oxford Nanopore Technologies) has received much attention because of its small size and possibility of rapid analysis at reasonable cost. Here, we compare the relative performances of two third-generation sequencing instruments, MinION and Sequel (Pacific Biosciences), in identification and diagnostics of fungal and oomycete pathogens from conifer (Pinaceae) needles and potato (Solanum tuberosum) leaves and tubers. We demonstrate that the Sequel instrument is efficient for metabarcoding of complex samples, whereas MinION is not suited for this purpose due to a high error rate and multiple biases. However, we find that MinION can be utilized for rapid and accurate identification of dominant pathogenic organisms and other associated organisms from plant tissues following both amplicon-based and PCR-free metagenomics approaches. Using the metagenomics approach with shortened DNA extraction and incubation times, we performed the entire MinION workflow, from sample preparation through DNA extraction, sequencing, bioinformatics, and interpretation, in 2.5 h. We advocate the use of MinION for rapid diagnostics of pathogens and potentially other organisms, but care needs to be taken to control or account for multiple potential technical biases.IMPORTANCE Microbial pathogens cause enormous losses to agriculture and forestry, but current combined culturing- and molecular identification-based detection methods are too slow for rapid identification and application of countermeasures. Here, we develop new and rapid protocols for Oxford Nanopore MinION-based third-generation diagnostics of plant pathogens that greatly improve the speed of diagnostics. However, due to high error rate and technical biases in MinION, the Pacific BioSciences Sequel platform is more useful for in-depth amplicon-based biodiversity monitoring (metabarcoding) from complex environmental samples.
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Affiliation(s)
- Kaire Loit
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Kalev Adamson
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Rasmus Puusepp
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sten Anslan
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Riinu Kiiker
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Rein Drenkhan
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Natural History Museum, University of Tartu, Tartu, Estonia
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25
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Peker N, Garcia-Croes S, Dijkhuizen B, Wiersma HH, van Zanten E, Wisselink G, Friedrich AW, Kooistra-Smid M, Sinha B, Rossen JWA, Couto N. A Comparison of Three Different Bioinformatics Analyses of the 16S-23S rRNA Encoding Region for Bacterial Identification. Front Microbiol 2019; 10:620. [PMID: 31040829 PMCID: PMC6476902 DOI: 10.3389/fmicb.2019.00620] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/12/2019] [Indexed: 11/25/2022] Open
Abstract
Rapid and reliable identification of bacterial pathogens directly from patient samples is required for optimizing antimicrobial therapy. Although Sanger sequencing of the 16S ribosomal RNA (rRNA) gene is used as a molecular method, species identification and discrimination is not always achievable for bacteria as their 16S rRNA genes have sometimes high sequence homology. Recently, next generation sequencing (NGS) of the 16S–23S rRNA encoding region has been proposed for reliable identification of pathogens directly from patient samples. However, data analysis is laborious and time-consuming and a database for the complete 16S–23S rRNA encoding region is not available. Therefore, a better, faster, and stronger approach is needed for NGS data analysis of the 16S–23S rRNA encoding region. We compared speed and diagnostic accuracy of different data analysis approaches: de novo assembly followed by Basic Local Alignment Search Tool (BLAST), operational taxonomic unit (OTU) clustering, or mapping using an in-house developed 16S–23S rRNA encoding region database for the identification of bacterial species. De novo assembly followed by BLAST using the in-house database was superior to the other methods, resulting in the shortest turnaround time (2 h and 5 min), approximately 2 h less than OTU clustering and 4.5 h less than mapping, and a sensitivity of 80%. Mapping was the slowest and most laborious data analysis approach with a sensitivity of 60%, whereas OTU clustering was the least laborious approach with 70% sensitivity. Although the in-house database requires more sequence entries to improve the sensitivity, the combination of de novo assembly and BLAST currently appears to be the optimal approach for data analysis.
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Affiliation(s)
- Nilay Peker
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Sharron Garcia-Croes
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Brigitte Dijkhuizen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Henry H Wiersma
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Evert van Zanten
- Department of Medical Microbiology, Certe, Groningen, Netherlands
| | - Guido Wisselink
- Department of Medical Microbiology, Certe, Groningen, Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Mirjam Kooistra-Smid
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,Department of Medical Microbiology, Certe, Groningen, Netherlands
| | - Bhanu Sinha
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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Abstract
After nearly two decades of subsidized and energy crop-oriented development, agricultural biogas production in Germany is standing at a crossroads. Fundamental challenges need to be met. In this article we sketch a vision of a future agricultural biogas plant that is an integral part of the circular bioeconomy and works mainly on the base of residues. It is flexible with regard to feedstocks, digester operation, microbial communities and biogas output. It is modular in design and its operation is knowledge-based, information-driven and largely automated. It will be competitive with fossil energies and other renewable energies, profitable for farmers and plant operators and favorable for the national economy. In this paper we discuss the required contribution of research to achieve these aims.
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