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Han H, Lee HJ, Kim KS, Chung J, Na HS. Comparison of the performance of MiSeq and NovaSeq in oral microbiome study. J Oral Microbiol 2024; 16:2344293. [PMID: 38645704 PMCID: PMC11028001 DOI: 10.1080/20002297.2024.2344293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/05/2024] [Accepted: 04/15/2024] [Indexed: 04/23/2024] Open
Abstract
Objective Next generation sequencing is commonly used to characterize the microbiome structure. MiSeq is most commonly used to analyze the microbiome due to its relatively long read length. Illumina also introduced the 250 × 2 chip for NovaSeq. The purpose of this study was to compare the performance of MiSeq and NovaSeq in the context of oral microbiome study. Methods Total read count, read quality score, relative bacterial abundance, community diversity, and correlation between two platforms were analyzed. Phylogenetic trees were analyzed for Streptococcus and periodontopathogens. Results NovaSeq produced significantly more read counts and assigned more operational taxonomic units (OTUs) compared to MiSeq. Community diversity was similar between MiSeq and NovaSeq. NovaSeq were able to detect more unique OTUs compared to MiSeq. When phylogenetic trees were constructed for Streptococcus and periodontopathogens, both platforms detected OTUs for most of the clades. Conclusion Taken together, while both MiSeq and NovaSeq platforms effectively characterize the oral microbiome, NovaSeq outperformed MiSeq in terms of read counts and detection of unique OTUs, highlighting its potential as a valuable tool for large scale oral microbiome studies.
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Affiliation(s)
- Hyejung Han
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, South Korea
| | - Hyo-Jung Lee
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam-si, South Korea
| | - Keun-Suh Kim
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam-si, South Korea
| | - Jin Chung
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, South Korea
| | - Hee Sam Na
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, South Korea
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Kumar V, Ameen F, Verma P. Unraveling the shift in bacterial communities profile grown in sediments co-contaminated with chlorolignin waste of pulp-paper mill by metagenomics approach. Front Microbiol 2024; 15:1350164. [PMID: 38529176 PMCID: PMC10961449 DOI: 10.3389/fmicb.2024.1350164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/21/2024] [Indexed: 03/27/2024] Open
Abstract
Pulp-paper mills (PPMs) are known for consistently generating a wide variety of pollutants, that are often unidentified and highly resistant to environmental degradation. The current study aims to investigate the changes in the indigenous bacterial communities profile grown in the sediment co-contaminated with organic and inorganic pollutants discharged from the PPMs. The two sediment samples, designated PPS-1 and PPS-2, were collected from two different sites. Physico-chemical characterization of PPS-1 and PPS-2 revealed the presence of heavy metals (mg kg-1) like Cu (0.009-0.01), Ni (0.005-0.002), Mn (0.078-0.056), Cr (0.015-0.009), Pb (0.008-0.006), Zn (0.225-0.086), Fe (2.124-0.764), Al (3.477-22.277), and Ti (99.792-45.012) along with high content of chlorophenol, and lignin. The comparative analysis of organic pollutants in sediment samples using gas chromatography-mass spectrometry (GC-MS) revealed the presence of major highly refractory compounds, such as stigmasterol, β-sitosterol, hexadecanoic acid, octadecanoic acid; 2,4-di-tert-butylphenol; heptacosane; dimethyl phthalate; hexachlorobenzene; 1-decanol,2-hexyl; furane 2,5-dimethyl, etc in sediment samples which are reported as a potential toxic compounds. Simultaneously, high-throughput sequencing targeting the V3-V4 hypervariable region of the 16S rRNA genes, resulted in the identification of 1,249 and 1,345 operational taxonomic units (OTUs) derived from a total of 115,665 and 119,386 sequences read, in PPS-1 and PPS-2, respectively. Analysis of rarefaction curves indicated a diversity in OTU abundance between PPS-1 (1,249 OTUs) and PPS-2 (1,345 OTUs). Furthermore, taxonomic assignment of metagenomics sequence data showed that Proteobacteria (55.40%; 56.30%), Bacteoidetes (11.30%; 12.20%), and Planctomycetes (5.40%; 4.70%) were the most abundant phyla; Alphproteobacteria (20.50%; 23.50%), Betaproteobacteria (16.00%; 12.30%), and Gammaproteobacteria were the most recorded classes in PPS-1 and PPS-2, respectively. At the genus level, Thiobacillus (7.60%; 4.50%) was the most abundant genera grown in sediment samples. The results indicate significant differences in both the diversity and relative abundance of taxa in the bacterial communities associated with PPS-2 when compared to PPS-1. This study unveils key insights into contaminant characteristics and shifts in bacterial communities within contaminated environments. It highlights the potential for developing efficient bioremediation techniques to restore ecological balance in pulp-paper mill waste-polluted areas, stressing the importance of identifying a significant percentage of unclassified genera and species to explore novel genes.
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Affiliation(s)
- Vineet Kumar
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Pradeep Verma
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
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3
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Pillai CA, Thirunavukkarasu N, Gonzalez-Escalona N, Melka D, Curry P, Binet R, Tallent S, Brown E, Sharma S. Closed genome sequence of Clostridium botulinum type B1 strain isolated from an infant botulism case in the United States. Microbiol Resour Announc 2024; 13:e0085423. [PMID: 38179913 PMCID: PMC10868279 DOI: 10.1128/mra.00854-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
We present the closed genome sequence of the Clostridium botulinum BT-22100019 strain isolated from the stool specimen of an infant diagnosed with botulism. With 4.33-Mb genome size and 28.0% G + C content, the bont/B1 gene encoded for botulinum neurotoxin serotype B was found on a 262 kb plasmid arranged in a ha+ orfx - cluster.
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Affiliation(s)
- Christine A. Pillai
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Nagarajan Thirunavukkarasu
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Narjol Gonzalez-Escalona
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - David Melka
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Phillip Curry
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Rachel Binet
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Sandra Tallent
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Eric Brown
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Shashi Sharma
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
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4
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He Z, Naganuma T, Melville HIAS. Bacteriomic Profiles of Rock-Dwelling Lichens from the Venezuelan Guiana Shield and the South African Highveld Plateau. Microorganisms 2024; 12:290. [PMID: 38399694 PMCID: PMC10892498 DOI: 10.3390/microorganisms12020290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Lichens are not only fungal-algal symbiotic associations but also matrices for association with bacteria, and the bacterial diversity linked to lichens has been receiving more attention in studies. This study compares the diversity and possible metabolism of lichen-associated bacteria from saxicolous foliose and fruticose taxa Alectoria, Canoparmelia, Crocodia, Menegazzia, Usnea, and Xanthoparmelia from the Venezuelan Guiana Shield and the South African Highveld Plateau. We used DNA extractions from the lichen thalli to amplify the eukaryotic 18S rRNA gene (rDNA) and the V3-V4 region of the bacterial 16S rDNA, of which amplicons were then Sanger- and MiSeq-sequenced, respectively. The V3-V4 sequences of the associated bacteria were grouped into operational taxonomic units (OTUs) ascribed to twelve bacterial phyla previously found in the rock tripe Umbilicaria lichens. The bacterial OTUs emphasized the uniqueness of each region, while, at the species and higher ranks, the regional microbiomes were shown to be somewhat similar. Nevertheless, regional biomarker OTUs were screened to predict relevant metabolic pathways, which implicated different regional metabolic features.
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Affiliation(s)
- Zichen He
- Graduate School of Integrated Science for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-hiroshima 739-8528, Japan
| | - Takeshi Naganuma
- Graduate School of Integrated Science for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-hiroshima 739-8528, Japan
| | - Haemish I. A. S. Melville
- Department of Environmental Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Florida, 0-41 Calabash Building, Unisa Science Campus, cnr Pioneer Avenue and Christiaan de Wet Road, Florida 1710, Gauteng, South Africa;
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5
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Wu Q, Kinoti WM, Habili N, Tyerman SD, Rinaldo A, Constable FE. Genetic Diversity of Grapevine Virus A in Three Australian Vineyards Using Amplicon High Throughput Sequencing (Amplicon-HTS). Viruses 2023; 16:42. [PMID: 38257742 PMCID: PMC10819895 DOI: 10.3390/v16010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Shiraz disease (SD) is one of the most destructive viral diseases of grapevines in Australia and is known to cause significant economic loss to local growers. Grapevine virus A (GVA) was reported to be the key pathogen associated with this disease. This study aimed to better understand the diversity of GVA variants both within and between individual SD and grapevine leafroll disease (LRD) affected grapevines located at vineyards in South Australia. Amplicon high throughput sequencing (Amplicon-HTS) combined with median-joining networks (MJNs) was used to analyze the variability in specific gene regions of GVA variants. Several GVAII variant groups contain samples from both vineyards studied, suggesting that these GVAII variants were from a common origin. Variant groups analyzed by MJNs using the overall data set denote that there may be a possible relationship between variant groups of GVA and the geographical location of the grapevines.
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Affiliation(s)
- Qi Wu
- School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia (S.D.T.)
- Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove crn Paratoo Road, Urrbrae, SA 5064, Australia
| | - Wycliff M. Kinoti
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
| | - Nuredin Habili
- School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia (S.D.T.)
- Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove crn Paratoo Road, Urrbrae, SA 5064, Australia
| | - Stephen D. Tyerman
- School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia (S.D.T.)
| | - Amy Rinaldo
- Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove crn Paratoo Road, Urrbrae, SA 5064, Australia
| | - Fiona E. Constable
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia
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6
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Qin Y, Wu L, Zhang Q, Wen C, Van Nostrand JD, Ning D, Raskin L, Pinto A, Zhou J. Effects of error, chimera, bias, and GC content on the accuracy of amplicon sequencing. mSystems 2023; 8:e0102523. [PMID: 38038441 PMCID: PMC10734440 DOI: 10.1128/msystems.01025-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE Amplicon sequencing of targeted genes is the predominant approach to estimate the membership and structure of microbial communities. However, accurate reconstruction of community composition is difficult due to sequencing errors, and other methodological biases and effective approaches to overcome these challenges are essential. Using a mock community of 33 phylogenetically diverse strains, this study evaluated the effect of GC content on sequencing results and tested different approaches to improve overall sequencing accuracy while characterizing the pros and cons of popular amplicon sequence data processing approaches. The sequencing results from this study can serve as a benchmarking data set for future algorithmic improvements. Furthermore, the new insights on sequencing error, chimera formation, and GC bias from this study will help enhance the quality of amplicon sequencing studies and support the development of new data analysis approaches.
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Affiliation(s)
- Yujia Qin
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Liyou Wu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Qiuting Zhang
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Chongqin Wen
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- Fisheries College, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Joy D. Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Daliang Ning
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Ameet Pinto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma, USA
- School of Computer Science, University of Oklahoma, Norman, Oklahoma, USA
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7
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Khalaf EM, Shrestha A, Reid M, McFadyen BJ, Raizada MN. Conservation and diversity of the pollen microbiome of Pan-American maize using PacBio and MiSeq. Front Microbiol 2023; 14:1276241. [PMID: 38179444 PMCID: PMC10764481 DOI: 10.3389/fmicb.2023.1276241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/21/2023] [Indexed: 01/06/2024] Open
Abstract
Pollen is a vector for diversification, fitness-selection, and transmission of plant genetic material. The extent to which the pollen microbiome may contribute to host diversification is largely unknown, because pollen microbiome diversity within a plant species has not been reported, and studies have been limited to conventional short-read 16S rRNA gene sequencing (e.g., V4-MiSeq) which suffers from poor taxonomic resolution. Here we report the pollen microbiomes of 16 primitive and traditional accessions of maize (corn) selected by indigenous peoples across the Americas, along with the modern U.S. inbred B73. The maize pollen microbiome has not previously been reported. The pollen microbiomes were identified using full-length (FL) 16S rRNA gene PacBio SMRT sequencing compared to V4-MiSeq. The Pan-American maize pollen microbiome encompasses 765 taxa spanning 39 genera and 46 species, including known plant growth promoters, insect-obligates, plant pathogens, nitrogen-fixers and biocontrol agents. Eleven genera and 13 species composed the core microbiome. Of 765 taxa, 63% belonged to only four genera: 28% were Pantoea, 15% were Lactococcus, 11% were Pseudomonas, and 10% were Erwinia. Interestingly, of the 215 Pantoea taxa, 180 belonged to a single species, P. ananatis. Surprisingly, the diversity within P. ananatis ranged nearly 10-fold amongst the maize accessions analyzed (those with ≥3 replicates), despite being grown in a common field. The highest diversity within P. ananatis occurred in accessions that originated near the center of diversity of domesticated maize, with reduced diversity associated with the north-south migration of maize. This sub-species diversity was revealed by FL-PacBio but missed by V4-MiSeq. V4-MiSeq also mis-identified some dominant genera captured by FL-PacBio. The study, though limited to a single season and common field, provides initial evidence that pollen microbiomes reflect evolutionary and migratory relationships of their host plants.
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Affiliation(s)
- Eman M. Khalaf
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
- Department of Microbiology and Immunology, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Anuja Shrestha
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Michelle Reid
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | | | - Manish N. Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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Garcia-Pedemonte D, Carcereny A, Gregori J, Quer J, Garcia-Cehic D, Guerrero L, Ceretó-Massagué A, Abid I, Bosch A, Costafreda MI, Pintó RM, Guix S. Comparison of Nanopore and Synthesis-Based Next-Generation Sequencing Platforms for SARS-CoV-2 Variant Monitoring in Wastewater. Int J Mol Sci 2023; 24:17184. [PMID: 38139015 PMCID: PMC10743471 DOI: 10.3390/ijms242417184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Shortly after the beginning of the SARS-CoV-2 pandemic, many countries implemented sewage sentinel systems to monitor the circulation of the virus in the population. A fundamental part of these surveillance programs is the variant tracking through sequencing approaches to monitor and identify new variants or mutations that may be of importance. Two of the main sequencing platforms are Illumina and Oxford Nanopore Technologies. Here, we compare the performance of MiSeq (Illumina) and MinION (Oxford Nanopore Technologies), as well as two different data processing pipelines, to determine the effect they may have on the results. MiSeq showed higher sequencing coverage, lower error rate, and better capacity to detect and accurately estimate variant abundances than MinION R9.4.1 flow cell data. The use of different variant callers (LoFreq and iVar) and approaches to calculate the variant proportions had a remarkable impact on the results generated from wastewater samples. Freyja, coupled with iVar, may be more sensitive and accurate than LoFreq, especially with MinION data, but it comes at the cost of having a higher error rate. The analysis of MinION R10.4.1 flow cell data using Freyja combined with iVar narrows the gap with MiSeq performance in terms of read quality, accuracy, sensitivity, and number of detected mutations. Although MiSeq should still be considered as the standard method for SARS-CoV-2 variant tracking, MinION's versatility and rapid turnaround time may represent a clear advantage during the ongoing pandemic.
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Affiliation(s)
- David Garcia-Pedemonte
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (D.G.-P.); (A.C.); (I.A.); (A.B.); (M.I.C.)
- Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
| | - Albert Carcereny
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (D.G.-P.); (A.C.); (I.A.); (A.B.); (M.I.C.)
- Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
| | - Josep Gregori
- Liver Unit, Liver Diseases—Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Campus, 08035 Barcelona, Spain; (J.G.); (J.Q.); (D.G.-C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Josep Quer
- Liver Unit, Liver Diseases—Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Campus, 08035 Barcelona, Spain; (J.G.); (J.Q.); (D.G.-C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Damir Garcia-Cehic
- Liver Unit, Liver Diseases—Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Campus, 08035 Barcelona, Spain; (J.G.); (J.Q.); (D.G.-C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Laura Guerrero
- Catalan Institute for Water Research (ICRA), 17003 Girona, Spain;
| | - Adrià Ceretó-Massagué
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain;
| | - Islem Abid
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (D.G.-P.); (A.C.); (I.A.); (A.B.); (M.I.C.)
- Center of Excellence in Biotechnology Research, College of Applied Science, King Saud University, Riyadh 11495, Saudi Arabia
| | - Albert Bosch
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (D.G.-P.); (A.C.); (I.A.); (A.B.); (M.I.C.)
- Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
| | - Maria Isabel Costafreda
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (D.G.-P.); (A.C.); (I.A.); (A.B.); (M.I.C.)
- Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
| | - Rosa M. Pintó
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (D.G.-P.); (A.C.); (I.A.); (A.B.); (M.I.C.)
- Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (D.G.-P.); (A.C.); (I.A.); (A.B.); (M.I.C.)
- Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
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Lerat S, Roussin-Léveillée C, Sidibé A, Moffett P, Beaulieu C. Evidence of the Involvement of Nematostoma parasiticum in Herpotrichia Needle Browning of Abies balsamea. Plant Dis 2023; 107:2935-2938. [PMID: 37142965 DOI: 10.1094/pdis-01-23-0075-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Herpotrichia needle browning (HNB) is a disease that affects several species of fir trees in Europe and North America. HNB was first described by Hartig in 1884, who isolated a fungal pathogenic agent identified as responsible for the disease. This fungus was later named Herpotrichia parasitica but is currently named Nematostoma parasiticum. However, the identity of the pathogens causing HNB is regularly questioned and, to date, the true causal agent of this disease has not been definitely established. The present study aimed to identify the fungal populations present in needles of Christmas fir trees (Abies balsamea) and to correlate them with needle health status using robust molecular methods. PCR primers specific to N. parasiticum allowed detection of the presence of this fungus in DNA samples from symptomatic needles. Furthermore, high-throughput sequencing (Illumina MiSeq) clearly showed that N. parasiticum was associated with symptomatic needles. However, high-throughput sequencing results revealed that the presence of other species such as Sydowia polyspora and Rhizoctonia sp. may also correlate with the development of HNB. A diagnostic tool, based on quantitative PCR using a probe, was then developed to detect and quantify N. parasiticum in DNA samples. The efficacy of this molecular approach was validated through the detection of the pathogenic agent in symptomatic needle samples as well as in nonsymptomatic needles collected in trees affected by HNB. In contrast, N. parasiticum could not be found in needles from healthy trees. The present study argues for the importance of N. parasiticum in causing HNB symptoms.
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Affiliation(s)
- Sylvain Lerat
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | | | - Amadou Sidibé
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Peter Moffett
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Carole Beaulieu
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
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10
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Abed RMM, Al-Hinai M, Al-Balushi Y, Haider L, Muthukrishnan T, Rinner U. Degradation of starch-based bioplastic bags in the pelagic and benthic zones of the Gulf of Oman. Mar Pollut Bull 2023; 195:115496. [PMID: 37703633 DOI: 10.1016/j.marpolbul.2023.115496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/21/2023] [Accepted: 09/02/2023] [Indexed: 09/15/2023]
Abstract
The Gulf of Oman is becoming increasingly polluted with plastics, hence bioplastics have been considered 'a substitute', although their biodegradability in marine environments has not been well investigated. Most research has been performed on cellulose-based bioplastics, whereas starch-based bioplastics have proven to be a suitable, but less researched, alternative. This study is the first of its kind designed to investigate the degradability of two different types of starch-based bioplastic bags, available in the market and labeled as "biodegradable", in the pelagic and benthic zones of one of the warmest marine environment in the world. Fourier-Transform Infrared Spectroscopy (FTIR) showed a clear reduction in the presence of OH, CH, and CO in the bioplastic bags after 5 weeks of immersion. Thermo-Gravimetric Analysis (TGA) indicated degradation of glycerol, starch, and polyethylene. The biofouling bacterial communities on bioplastic surfaces showed distinct grouping based on the immersion zone. Candidaatus saccharibacteria, Verrucomicrobiae, Acidimicrobiia and Planctomycetia sequences were only detectable on bioplastics in the pelagic zone, whereas Actinomyces, Pseudomonas, Sphingobium and Acinetobacter related sequences were only found on bioplastics in the benthic layer. We conclude that starch-based bioplastics are more readily degradable in the Gulf of Oman than conventional plastics, hence could serve as a better environmentally friendly alternative.
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Affiliation(s)
- Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University, P. O. Box: 36, PC 123 Al Khoud, Sultanate of Oman.
| | - Mahmood Al-Hinai
- Biology Department, College of Science, Sultan Qaboos University, P. O. Box: 36, PC 123 Al Khoud, Sultanate of Oman
| | - Yasmin Al-Balushi
- Biology Department, College of Science, Sultan Qaboos University, P. O. Box: 36, PC 123 Al Khoud, Sultanate of Oman
| | - Lorenz Haider
- Institute of Applied Chemistry, IMC University of Applied Sciences Krems, Piaristengasse 1, 3500 Krems, Austria
| | - Thirumahal Muthukrishnan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario M5S 3E5, Canada
| | - Uwe Rinner
- Institute of Applied Chemistry, IMC University of Applied Sciences Krems, Piaristengasse 1, 3500 Krems, Austria
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11
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Bauer F, Wolfschlaeger I, Geist J, Fastner J, Schmalz CW, Raeder U. Occurrence, Distribution and Toxins of Benthic Cyanobacteria in German Lakes. Toxics 2023; 11:643. [PMID: 37624149 PMCID: PMC10458227 DOI: 10.3390/toxics11080643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/26/2023]
Abstract
Cyanobacteria are favored by climate change and global warming; however, to date, most research and monitoring programs have focused on planktic cyanobacteria. Benthic cyanobacteria blooms also increase and pose a risk to animal and human health; however, there is limited knowledge of their occurrence, distribution and the toxins involved, especially in relation to their planktic conspecifics. Therefore, we analyzed the benthic and planktic life forms of cyanobacterial communities in 34 lakes in Germany, including a monitoring of cyanotoxins. Community analyses were based on microscopic examination and Illumina sequencing of the 16S rRNA gene. The analyses of cyanotoxins were carried out using LC-MS/MS and ELISA. Observed benthic mats containing cyanobacteria consisted mainly of Nostocales and Oscillatoriales, being present in 35% of the lakes. Anatoxin was the most abundant cyanotoxin in the benthic samples, reaching maximum concentrations of 45,000 µg/L, whereas microcystin was the predominate cyanotoxin in the open-water samples, reaching concentrations of up to 18,000 µg/L. Based on the results, specific lakes at risk of toxic cyanobacteria could be identified. Our findings suggest that monitoring of benthic cyanobacteria and their toxins should receive greater attention, ideally complementing existing open-water sampling programs with little additional effort.
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Affiliation(s)
- Franziska Bauer
- Aquatic Systems Biology Unit, Limnological Research Station Iffeldorf, Technical University of Munich, Hofmark 1–3, 82393 Iffeldorf, Germany (U.R.)
| | - Immanuel Wolfschlaeger
- Aquatic Systems Biology Unit, Limnological Research Station Iffeldorf, Technical University of Munich, Hofmark 1–3, 82393 Iffeldorf, Germany (U.R.)
| | - Juergen Geist
- Aquatic Systems Biology Unit, Limnological Research Station Iffeldorf, Technical University of Munich, Hofmark 1–3, 82393 Iffeldorf, Germany (U.R.)
| | - Jutta Fastner
- German Environment Agency, Schichauweg 58, 12307 Berlin, Germany
| | - Carina Wiena Schmalz
- Aquatic Systems Biology Unit, Limnological Research Station Iffeldorf, Technical University of Munich, Hofmark 1–3, 82393 Iffeldorf, Germany (U.R.)
| | - Uta Raeder
- Aquatic Systems Biology Unit, Limnological Research Station Iffeldorf, Technical University of Munich, Hofmark 1–3, 82393 Iffeldorf, Germany (U.R.)
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12
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Trees E, Poates A, Sabol A, LaFon P, Truong J, Lindsey R. Evaluation of the Illumina iSeq whole genome sequencing system for enteric disease surveillance and outbreak detection. J Microbiol Methods 2023; 211:106784. [PMID: 37451348 DOI: 10.1016/j.mimet.2023.106784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
The Illumina iSeq low-capacity sequencing platform was evaluated for use in foodborne disease surveillance and outbreak detection. The platform produced high quality sequence data comparable to that of the Illumina MiSeq and was cost-effective with fast turn-around time in low sample volume environments.
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Affiliation(s)
- Eija Trees
- Centers for Disease Control and Prevention, 1600 Clifton Road, Mail stop H23-7, Atlanta, GA 30329, USA.
| | - Angela Poates
- Centers for Disease Control and Prevention, 1600 Clifton Road, Mail stop H23-7, Atlanta, GA 30329, USA
| | - Ashley Sabol
- Centers for Disease Control and Prevention, 1600 Clifton Road, Mail stop H23-7, Atlanta, GA 30329, USA
| | - Patricia LaFon
- Centers for Disease Control and Prevention, 1600 Clifton Road, Mail stop H23-7, Atlanta, GA 30329, USA
| | - Jenny Truong
- Centers for Disease Control and Prevention, 1600 Clifton Road, Mail stop H23-7, Atlanta, GA 30329, USA
| | - Rebecca Lindsey
- Centers for Disease Control and Prevention, 1600 Clifton Road, Mail stop H23-7, Atlanta, GA 30329, USA
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13
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Rieder J, Kapopoulou A, Bank C, Adrian-Kalchhauser I. Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems. Environ Microbiome 2023; 18:8. [PMID: 36788626 PMCID: PMC9930364 DOI: 10.1186/s40793-023-00459-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/02/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND Microbial communities in recirculating aquaculture systems (RAS) play a role in system success, nutrient cycling, and water quality. Considering the increasing socio-economic role of fish farming, e.g., regarding food security, an in-depth understanding of aquaculture microbial communities is also relevant from a management perspective, especially regarding the growth, development, and welfare of the farmed animal. However, the current data on the composition of microbial communities within RAS is patchy, which is partly attributable to diverging method choices that render comparative analyses challenging. Therefore, there is a need for accurate, standardized, and user-friendly methods to study microbial communities in aquaculture systems. RESULTS We compared sequencing approach performances (3 types of 16S short amplicon sequencing, PacBio long-read amplicon sequencing, and amplification-free shotgun metagenomics) in the characterization of microbial communities in two commercial RAS fish farms. Results showed that 16S primer choice and amplicon length affect some values (e.g., diversity measures, number of assigned taxa or distinguishing ASVs) but have no impact on spatio-temporal patterns between sample types, farms and time points. This implies that 16S rRNA approaches are adequate for community studies. The long-read amplicons underperformed regarding the quantitative resolution of spatio-temporal patterns but were suited to identify functional services, e.g., nitrification cycling and the detection of pathogens. Finally, shotgun metagenomics extended the picture to fungi, viruses, and bacteriophages, opening avenues for exploring inter-domain interactions. All sequencing datasets agreed on major prokaryotic players, such as Actinobacteriota, Bacteroidota, Nitrospirota, and Proteobacteria. CONCLUSION The different sequencing approaches yielded overlapping and highly complementary results, with each contributing unique data not obtainable with the other approaches. We conclude that a tiered approach constitutes a strategy for obtaining the maximum amount of information on aquaculture microbial communities and can inform basic research on community evolution dynamics. For specific and/or applied questions, single-method approaches are more practical and cost-effective and could lead to better farm management practices.
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Affiliation(s)
- Jessica Rieder
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, Institute for Fish and Wildlife Health, University of Bern, Länggasstrasse 122, 3001 Bern, Switzerland
- Division of Theoretical Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Adamandia Kapopoulou
- Division of Theoretical Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Claudia Bank
- Division of Theoretical Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Irene Adrian-Kalchhauser
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, Institute for Fish and Wildlife Health, University of Bern, Länggasstrasse 122, 3001 Bern, Switzerland
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14
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He Y, Zhang Q, Yu X, Zhang S, Guo W. Overview of microbial profiles in human hepatocellular carcinoma and adjacent nontumor tissues. J Transl Med 2023; 21:68. [PMID: 36732743 PMCID: PMC9893660 DOI: 10.1186/s12967-023-03938-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Intratumoral microbial communities have been recently discovered to exist in a variety of cancers and have been found to be intricately involved in tumour progression. Therefore, investigating the profiles and functions of intratumoral microbial distribution in hepatocellular carcinoma (HCC) is imperative. METHODS To verify the presence of microorganisms in HCC, we performed fluorescence in situ hybridization (FISH) using HCC tissues and conducted MiSeq using 99 HCC and paracancerous tissues to identify the key microorganisms and changes in metabolic pathways affecting HCC progression through a variety of bioinformatics methods. RESULTS Microbial diversity was significantly higher in HCC tissues than in adjacent tissues. The abundances of microorganisms such as Enterobacteriaceae, Fusobacterium and Neisseria were significantly increased in HCC tissues, while the abundances of certain antitumour bacteria such as Pseudomonas were decreased. Processes such as fatty acid and lipid synthesis were significantly enhanced in the microbiota in HCC tissues, which may be a key factor through which intratumoral microbes influence tumour progression. There were considerable differences in the microbes and their functions within tumour tissue collected from patients with different clinical features. CONCLUSION We comprehensively evaluated the intratumoral microbial atlas of HCC tissue and preliminarily explored the mechanism of the effects of the microbial community involving changes in lipid metabolism and effects on HCC progression, which lays the foundation for further research in this field.
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Affiliation(s)
- Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China. .,Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China. .,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China. .,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China.
| | - Qiyao Zhang
- grid.412633.10000 0004 1799 0733Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.412633.10000 0004 1799 0733Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.256922.80000 0000 9139 560XOpen and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052 China
| | - Xiao Yu
- grid.412633.10000 0004 1799 0733Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.412633.10000 0004 1799 0733Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.256922.80000 0000 9139 560XOpen and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052 China
| | - Shuijun Zhang
- grid.412633.10000 0004 1799 0733Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.412633.10000 0004 1799 0733Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.256922.80000 0000 9139 560XOpen and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052 China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China. .,Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China. .,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China. .,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China.
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15
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Giorgio M, Niccolò BGM, Benedetta T, Luisa M, Leonardo BF, Gregory B, Pietro B, Alberto A, Domizia D, Emidio A. Fungal and Bacterial Diversity in the Tuber magnatum Ecosystem and Microbiome. Microb Ecol 2023; 85:508-521. [PMID: 35237850 DOI: 10.1007/s00248-021-01950-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Fungi belonging to the genus Tuber produce edible ascocarps known as truffles. Tuber magnatum Picco may be the most appreciated truffle species given its peculiar aroma. While its life cycle is not yet fully elucidated, some studies demonstrated an active role of microorganisms. The main goal of this study was to determine how the T. magnatum microbiome varies across space and time. To address this, we characterized microbial communities associated with T. magnatum through high-throughput amplicon sequencing of internal transcribed spacer (ITS) and 16S rDNAs in three productive natural sites in Italy across 2 years. At each site, four truffles were sampled as well as the soil underneath and at 40, 100, and 200 cm from the harvesting points, to assess for microbial variation between substrates, years, and sites. A statistically significant site-related effect on microbial communities was identified, whereas only the prokaryotic community was significantly affected by the distance of soil from the truffle. Significant differences between sampling years were also found, demonstrating a possible relation among rainfall precipitation and Firmicutes and Actinobacteria. Thirty-six bacterial OTUs in truffles and 11 bacterial OTUs in soils beneath truffles were identified as indicator taxa. As shown for other truffle species, the dominance of Bradyrhizobium, Rhizobium, and Ensifer spp. within the truffle fruiting body suggests an evolutionary adaptation of this microorganism to the genus Tuber. The present work offers novel and relevant insights into the microbial ecology of T. magnatum ecosystems and fruiting bodies. The function and role of these bacteria in the truffle microbiome and life cycle are in need of further investigation.
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Affiliation(s)
- Marozzi Giorgio
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Benucci Gian Maria Niccolò
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA.
| | - Turchetti Benedetta
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Massaccesi Luisa
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100, Viterbo, Italy
| | - Baciarelli Falini Leonardo
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Bonito Gregory
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Buzzini Pietro
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Agnelli Alberto
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Donnini Domizia
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Albertini Emidio
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
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16
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Mabwi HA, Lee HJ, Hitayezu E, Mauliasari IR, Pan C, Mwaikono KS, Komba EVG, Lee C, Cha KH. Emodin modulates gut microbial community and triggers intestinal immunity. J Sci Food Agric 2023; 103:1273-1282. [PMID: 36088620 PMCID: PMC10087506 DOI: 10.1002/jsfa.12221] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/31/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The gut microbiota (GM) plays an important role in human health and is being investigated as a possible target for new therapies. Although there are many studies showing that emodin can improve host health, emodin-GM studies are scarce. Here, the effects of emodin on the GM were investigated in vitro and in vivo. RESULTS In vitro single bacteria cultivation showed that emodin stimulated the growth of beneficial bacteria Akkermansia, Clostridium, Roseburia, and Ruminococcus but inhibited major gut enterotypes (Bacteroides and Prevotella). Microbial community analysis from a synthetic gut microbiome model through co-culture indicated the consistent GM change by emodin. Interestingly, emodin stimulated Clostridium and Ruminococcus (which are related to Roseburia and Faecalibacterium) in a mice experiment and induced anti-inflammatory immune cells, which may correlate with its impact on specific gut bacteria. CONCLUSION Emodin (i) showed similar GM changes in monoculture, co-culture, and in an in vivo mice experiment and (ii) simulated regulatory T-cell immune responses in vivo. This suggest that emodin may be used to modulate the GM and improve health. © 2022 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Humphrey A. Mabwi
- Natural Product Informatics Research CenterKorea Institute of Science and TechnologyGangneungSouth Korea
- Department of Microbiology, Parasitology, and Biotechnology, College of Veterinary Medicine and Biomedical SciencesSokoine University of AgricultureMorogoroTanzania
- SACIDS Foundation for One Health, College of Veterinary Medicine and Biomedical SciencesSokoine University of AgricultureMorogoroTanzania
- Division of Bio‐Medical Science and TechnologyKIST School, University of Science and TechnologySeoulSouth Korea
| | - Hee Ju Lee
- Natural Product Informatics Research CenterKorea Institute of Science and TechnologyGangneungSouth Korea
| | - Emmanuel Hitayezu
- Natural Product Informatics Research CenterKorea Institute of Science and TechnologyGangneungSouth Korea
| | - Intan Rizki Mauliasari
- Natural Product Informatics Research CenterKorea Institute of Science and TechnologyGangneungSouth Korea
| | - Cheol‐Ho Pan
- Natural Product Informatics Research CenterKorea Institute of Science and TechnologyGangneungSouth Korea
- Division of Bio‐Medical Science and TechnologyKIST School, University of Science and TechnologySeoulSouth Korea
| | - Kilaza Samson Mwaikono
- Department of Science and Laboratory TechnologyDar es Salaam Institute of TechnologyDar es SalaamTanzania
| | - Erick V. G. Komba
- SACIDS Foundation for One Health, College of Veterinary Medicine and Biomedical SciencesSokoine University of AgricultureMorogoroTanzania
| | - Choong‐Gu Lee
- Natural Product Informatics Research CenterKorea Institute of Science and TechnologyGangneungSouth Korea
- Division of Bio‐Medical Science and TechnologyKIST School, University of Science and TechnologySeoulSouth Korea
| | - Kwang Hyun Cha
- Natural Product Informatics Research CenterKorea Institute of Science and TechnologyGangneungSouth Korea
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17
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Raiyani NM, Singh SP. Microbial community and predictive functionalities associated with the marine sediment of Coastal Gujarat. Environ Sci Pollut Res Int 2023; 30:43245-43266. [PMID: 36650368 DOI: 10.1007/s11356-023-25196-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023]
Abstract
Marine sediments are complex ecosystems where structures and functions constantly change due to natural and anthropogenic influences. In this investigation, a comprehensive and comparative analysis of the bacterial communities and their functional potential of the pristine and polluted marine sediments were carried out using MiSeq. The phylum Proteobacteria was dominant in all study sites. Other phyla were Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Chloroflexi, Nitrospirae, Cyanobacteria, Verrucomicrobia, Tenericutes, and Chlorobi. Interestingly, about 50% of genera belong to the unclassified categories. The key genera were identified as Acinetobacter, Bacillus, Pseudomona, Idiomarina, Thalassospira, and Marinobacter, Halomonas, Planctomyces, Psychrobacter, and Vogesella. PICRUSt analysis revealed that major functions are associated with the metabolism category. Additionally, metabolism related to amino acids, carbohydrates, energy generation, xenobiotics degradation, nitrogen, sulfate, and methane were prominent. Similarly, the predicted metabolisms by COG and KEGG were observed in the microbial communities of the marine sediments. To date, a comprehensive description of the microbial life with metabolic potential in these study sites has not been investigated. This study therefore significantly adds to our understanding of the microbiome and its functional attributes of marine sediments.
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Affiliation(s)
- Nirali M Raiyani
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, 360 005, Gujarat, India
| | - Satya P Singh
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, 360 005, Gujarat, India.
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18
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Butt SL, Kariithi HM, Volkening JD, Taylor TL, Leyson C, Pantin-Jackwood M, Suarez DL, Stanton JB, Afonso CL. Comparable outcomes from long and short read random sequencing of total RNA for detection of pathogens in chicken respiratory samples. Front Vet Sci 2022; 9:1073919. [PMID: 36532355 PMCID: PMC9751482 DOI: 10.3389/fvets.2022.1073919] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/14/2022] [Indexed: 01/10/2024] Open
Abstract
Co-infections of avian species with different RNA viruses and pathogenic bacteria are often misdiagnosed or incompletely characterized using targeted diagnostic methods, which could affect the accurate management of clinical disease. A non-targeted sequencing approach with rapid and precise characterization of pathogens should help respiratory disease management by providing a comprehensive view of the causes of disease. Long-read portable sequencers have significant potential advantages over established short-read sequencers due to portability, speed, and lower cost. The applicability of short reads random sequencing for direct detection of pathogens in clinical poultry samples has been previously demonstrated. Here we demonstrate the feasibility of long read random sequencing approaches to identify disease agents in clinical samples. Experimental oropharyngeal swab samples (n = 12) from chickens infected with infectious bronchitis virus (IBV), avian influenza virus (AIV) and Mycoplasma synoviae (MS) and field-collected clinical oropharyngeal swab samples (n = 11) from Kenyan live bird markets previously testing positive for Newcastle disease virus (NDV) were randomly sequenced on the MinION platform and results validated by comparing to real time PCR and short read random sequencing in the Illumina MiSeq platform. In the swabs from experimental infections, each of three agents in every RT-qPCR-positive sample (Ct range 19-34) was detectable within 1 h on the MinION platform, except for AIV one agent in one sample (Ct = 36.21). Nine of 12 IBV-positive samples were assigned genotypes within 1 h, as were five of 11 AIV-positive samples. MinION relative abundances of the test agent (AIV, IBV and MS) were highly correlated with RT-qPCR Ct values (R range-0.82 to-0.98). In field-collected clinical swab samples, NDV (Ct range 12-37) was detected in all eleven samples within 1 h of MinION sequencing, with 10 of 11 samples accurately genotyped within 1 h. All NDV-positive field samples were found to be co-infected with one or more additional respiratory agents. These results demonstrate that MinION sequencing can provide rapid, and sensitive non-targeted detection and genetic characterization of co-existing respiratory pathogens in clinical samples with similar performance to the Illumina MiSeq.
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Affiliation(s)
- Salman L. Butt
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, United States
| | - Henry M. Kariithi
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, United States
- Biotechnology Research Institute, Kenyan Agricultural and Livestock Research Organization, Nairobi, Kenya
| | | | - Tonya L. Taylor
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, United States
| | - Christina Leyson
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, United States
| | - Mary Pantin-Jackwood
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, United States
| | - David L. Suarez
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, United States
| | - James B. Stanton
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
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Crispell G, Williams K, Zielinski E, Iwami A, Homas Z, Thomas K. Method comparison for Japanese encephalitis virus detection in samples collected from the Indo-Pacific region. Front Public Health 2022; 10:1051754. [PMID: 36504937 PMCID: PMC9730272 DOI: 10.3389/fpubh.2022.1051754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Introduction Japanese encephalitis virus (JEV) is a mosquito-borne viral pathogen, which is becoming a growing public health concern throughout the Indo-Pacific. Five genotypes of JEV have been identified. Current vaccines are based on genotype III and provide a high degree of protection for four of the five known genotypes. Methods RT-PCR, Magpix, Twist Biosciences Comprehensive Viral Research Panel (CVRP), and SISPA methods were used to detect JEV from mosquito samples collected in South Korea during 2021. These methods were compared to determine which method would be most effective for biosurveillance in the Indo-Pacific region. Results Our data showed that RT-PCR, Twist CVRP, and SISPA methods were all able to detect JEV genotype I, however, the proprietary Magpix panel was only able to detect JEV genotype III. Use of minION sequencing for pathogen detection in arthropod samples will require further method development. Conclusion Biosurveillance of vectorborne pathogens remains an area of concern throughout the Indo-Pacific. RT-PCR was the most cost effective method used in the study, but TWIST CVRP allows for the identification of over 3,100 viral genomes. Further research and comparisons will be conducted to ensure optimal methods are used for large scale biosurveillance.
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20
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Salamon D, Zapała B, Krawczyk A, Potasiewicz A, Nikiforuk A, Stój A, Gosiewski T. Comparison of iSeq and MiSeq as the two platforms for 16S rRNA sequencing in the study of the gut of rat microbiome. Appl Microbiol Biotechnol 2022; 106:7671-7681. [PMID: 36322250 PMCID: PMC9628524 DOI: 10.1007/s00253-022-12251-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/16/2022] [Revised: 10/11/2022] [Accepted: 10/15/2022] [Indexed: 11/17/2022]
Abstract
Abstract Amplicon-based next-generation sequencing (NGS) of the 16S ribosomal RNA (16S) regions is a culture-free method used to identify and analyze Procaryota occurring within a given sample. The prokaryotic 16S rRNA gene contains conserved regions and nine variable regions (V1-V9) frequently used for phylogenetic classification of genus or species in diverse microbial populations. This work compares the accuracy and efficacy of two platforms, iSeq and MiSeq from Illumina, used in sequencing 16S rRNA. The most important similarities and differences of 16S microbiome sequencing in 20 fecal rat samples were described. Genetic libraries were prepared according to 16S Metagenomic Sequencing Library Preparation (Illumina) for the V3 and V4 regions of the 16S. The species richness obtained using iSeq technology was lower compared to MiSeq. At the second taxonomy level (L2), the abundance of taxa was comparable for both platforms. At the L7, the taxa abundance was significantly different, and the number of taxa was higher for the MiSeq. The alpha diversity was lower for iSeq than for MiSeq, starting from the order to the species level. The beta diversity estimation revealed statistically significant differences in microbiota diversity starting from the class level to the species level in samples sequenced on two investigated platforms. This work disclosed that the iSeq platform could be used to evaluate the bacterial profile of the samples to characterize the overall profile. The MiSeq System seems to be better for a detailed analysis of the differences in the microbiota composition. Key points • iSeq platform allows to shorten the sequencing time three times compared to the MiSeq. • iSeq can only be used for an initial and quick microbiome assessment. • MiSeq is better for a detailed analysis of the differences in the microbiota composition. Supplementary information The online version contains supplementary material available at 10.1007/s00253-022-12251-z.
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Affiliation(s)
- Dominika Salamon
- grid.5522.00000 0001 2162 9631Department of Molecular Medical Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | - Barbara Zapała
- grid.5522.00000 0001 2162 9631Department of Clinical Biochemistry, Jagiellonian University Medical College, Krakow, Poland
| | - Agnieszka Krawczyk
- grid.5522.00000 0001 2162 9631Department of Molecular Medical Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | - Agnieszka Potasiewicz
- grid.418903.70000 0001 2227 8271Department of Behavioural Neuroscience and Drug Development, Polish Academy of Sciences, Maj Institute of Pharmacology, Krakow, Poland
| | - Agnieszka Nikiforuk
- grid.418903.70000 0001 2227 8271Department of Behavioural Neuroscience and Drug Development, Polish Academy of Sciences, Maj Institute of Pharmacology, Krakow, Poland
| | - Anastazja Stój
- grid.412700.00000 0001 1216 0093Department of Hematology Diagnostics and Genetics, University Hospital, Krakow, Poland
| | - Tomasz Gosiewski
- grid.5522.00000 0001 2162 9631Department of Molecular Medical Microbiology, Jagiellonian University Medical College, Krakow, Poland
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21
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Gosai HB, Panseriya HZ, Patel PG, Patel AC, Shankar A, Varjani S, Dave BP. Exploring bacterial communities through metagenomics during bioremediation of polycyclic aromatic hydrocarbons from contaminated sediments. Sci Total Environ 2022; 842:156794. [PMID: 35738384 DOI: 10.1016/j.scitotenv.2022.156794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
The goal of this study was to evaluate the degradation effectiveness of PAHs degrading bacteria at the mesocosm level, including Stenotrophomonas maltophilia (SC), mixed culture (MC), and enriched native microflora (EC) at the mesocosm level. Maximum degradation was found in the mesocosm MC (26.67 %), followed by SC (25.08 %) and EC (18.25 %) after 60 days. Thus, mixed culture and Stenotrophomonas maltophilia could be a game changer in the PAHs bioremediation at the chronically contaminated sites. MiSeq sequencing has revealed dominancy of γ-Proteobacteria, α-Proteobacteria, β-Proteobacteria at class level and Sphingomonadales, oceanospirillales, Rhodothermales at Order level. Families Alcanivoracaceae, Alteromonadaceae, Nocardiaceae, Rhodospirillaceae and genus Stenotrophomonas, Alcanivorax, Methylophaga, Fluviicola and Rhodoplanes were considerably increased which play key role in the PAHs degradation. Dominant bacterial communities have revealed resilience community to enable potential PAHs degradation process in all the mesocosms. To the best our knowledge this is the first ever attempt in PAHs biodegradation study conducted at the mesocosm level mimicking natural environmental conditions. Consequently, this study could be a benchmark against which future progress studies for the policy makers and stakeholders to design appropriate bioremediation study for the historically PAHs polluted contaminate sites.
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Affiliation(s)
- Haren B Gosai
- Department of Biosciences, School of Sciences, Indrashil University, Rajpur-Kadi, Mehasana, Gujarat, India; Department of Life Sciences, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat, India
| | - Haresh Z Panseriya
- Department of Life Sciences, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat, India; Gujarat Ecology Society, Synergy House, Subhanpura, Vadodara, Gujarat, India
| | - Payal G Patel
- Department of Biosciences, School of Sciences, Indrashil University, Rajpur-Kadi, Mehasana, Gujarat, India
| | - Ajay C Patel
- Department of Biosciences, School of Sciences, Indrashil University, Rajpur-Kadi, Mehasana, Gujarat, India
| | - Alka Shankar
- Department of Plant Molecular Biology, University of Delhi, South Campus, Dhaula Kuan, New Delhi, India
| | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar, Gujarat 382 010, India.
| | - Bharti P Dave
- Department of Biosciences, School of Sciences, Indrashil University, Rajpur-Kadi, Mehasana, Gujarat, India; Department of Life Sciences, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat, India.
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22
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Ahmed L, Al-Najjar Y, Cramer ERA, Thareja G, Suhre K, Chen KC. Development and characterization of microsatellite primers for Triops granarius (Branchiopoda: Notostraca) using MiSeq technology. Mol Biol Rep 2022; 49:10121-10125. [PMID: 36057875 PMCID: PMC9515016 DOI: 10.1007/s11033-022-07804-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/15/2022] [Indexed: 12/03/2022]
Abstract
Background Next-generation sequencing technology has allowed for the rapid development of microsatellites, neutral polymorphic markers that can be used for the analysis of population structure. Methods and Results In this study, we performed whole-genome sequencing using the Illumina MiSeq system and de novo assembly to design microsatellite primers for Triops granarius populations in Qatar. The developed microsatellites are suitable for future studies of genetic structuring among geographically isolated freshwater pools. A total of 23 different primer pairs produced typical microsatellite results, with each pair successfully amplified in up to 40 individuals. Only five of the loci produced a significant departure from Hardy-Weinberg equilibrium. Conclusions Some of the underlying mechanisms regarding the few loci that deviated from HWE may be further investigated to determine the source of deviation. As T. granarius is the most widely distributed species of the family, the development of these molecular markers would be useful for conducting population genetics and biogeographical studies broadly.
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Affiliation(s)
- Lina Ahmed
- Department of Medical Education Education City, Qatar Foundation, Weill Cornell Medicine - Qatar, 24144, Doha, Qatar
| | - Yousef Al-Najjar
- Department of Medical Education Education City, Qatar Foundation, Weill Cornell Medicine - Qatar, 24144, Doha, Qatar
| | - Emily R A Cramer
- Natural History Museum, University of Oslo, Sars Gate 1, 0562, Oslo, Norway
| | - Gaurav Thareja
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar Education City, Qatar Foundation, P.O. Box 24144, Doha, Qatar
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar Education City, Qatar Foundation, P.O. Box 24144, Doha, Qatar
| | - Kuei-Chiu Chen
- Department of Premedical Education, Weill Cornell Medicine-Qatar Education City, Qatar Foundation, P.O. Box 24144, Doha, Qatar.
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23
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Liu H, Zhang B, Li F, Liu L, Li F. Shifts in the intestinal microflora of meat rabbits in response to glucocorticoids. J Sci Food Agric 2022; 102:5422-5428. [PMID: 35338488 DOI: 10.1002/jsfa.11895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/04/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND As major stress hormones, glucocorticoids can directly or indirectly affect the intestinal microflora, although few studies have focused on changes in the composition of the intestinal microflora. In this study, rabbits were randomly divided into two groups: gavage administration with saline, and the same doses of dexamethasone (1 mg kg-1 ). After 7 days, the microbial diversity of the jejunum contents was analysed. RESULTS The gut microflora richness and diversity had no significant difference between the two groups. The proportions of Firmicutes and Bacteroidetes were the most abundant in the jejunum of meat rabbits. Dexamethasone injection led to a change in the structure of the gut microflora composition, and we found that there were six biomarkers with linear discriminant analysis score >4 (Firmicutes, Caproiciproducens, Clostridiales, Clostridia, Psychrobacter, and Psychrobacter faecalis), moreover, the results of this study provide new insight into alleviating the effects of stress on meat rabbits. CONCLUSION It was concluded that glucocorticoids caused changes in the composition of intestinal microflora. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Hongli Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Department of Animal Science and Technology, Shandong Agricultural University, Taian, China
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation, Department of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Bin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Department of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Fan Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Department of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Lei Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Department of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Fuchang Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Department of Animal Science and Technology, Shandong Agricultural University, Taian, China
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24
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Ozbayram EG, Akcaalan R, Isinibilir M, Albay M. Insights into the bacterial community structure of marine mucilage by metabarcoding. Environ Sci Pollut Res Int 2022; 29:53249-53258. [PMID: 35278186 DOI: 10.1007/s11356-022-19626-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/05/2022] [Indexed: 06/14/2023]
Abstract
This prospective study was aimed to explore the bacterial diversity of marine mucilage developed in the Marmara Sea and the North Aegean Sea by metabarcoding. For this purpose, mucilage samples were collected from five different sampling locations, and the bacterial community structure was analyzed by 16S rRNA gene amplicon sequencing. The results highlighted a diverse bacterial community dominated by Proteobacteria and Bacteroidetes species. A negative and significant correlation between pH level and Campylobacterales, Clostridiales, and Vibronales abundances was detected, while a strong positive correlation was determined between total phosphorus (TP) and Campylobacterales. Results revealed that the bacterial community in the mucilage samples was predominated by particle-attached species preferring high-nutrient concentrations. This is the first study evaluating the bacterial diversity in a mucilage outbreak using a metabarcoding approach. Its results may contribute to this growing area of research and provide a database for further studies.
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Affiliation(s)
- Emine Gozde Ozbayram
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
| | - Reyhan Akcaalan
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey.
| | - Melek Isinibilir
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
| | - Meric Albay
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
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25
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Muthappa DM, Lamba S, Sivasankaran SK, Naithani A, Rogers N, Srikumar S, Macori G, Scannell AGM, Fanning S. 16S rRNA Based Profiling of Bacterial Communities Colonizing Bakery-Production Environments. Foodborne Pathog Dis 2022; 19:485-494. [PMID: 35759425 DOI: 10.1089/fpd.2022.0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Conventional culture-based techniques are largely inadequate in elucidating the microbiota contained in an environment, due to low recovery within a complex bacterial community. This limitation has been mitigated by the use of next-generation sequencing (NGS)-based approaches thereby facilitating the identification and classification of both culturable and uncultivable microorganisms. Amplicon targeted NGS methods, such as 16S ribosomal RNA (16S rRNA) and shotgun metagenomics, are increasingly being applied in various settings such as in food production environments to decipher the microbial consortium therein. Even though multiple food matrices/food production environments have been studied, the low-moisture environment associated with bakery food production remains to be investigated. To address this knowledge gap, in this study, we investigated the microbiome associated with two bakery production sites (designated as A and B) located in Ireland using 16S rRNA-amplicon-based sequencing. Amplicons corresponding to a hypervariable region contained within the 16S rRNA gene were amplified from DNA samples purified from environmental swabs and ingredients collected at both sites at various stages (preparation, production, postproduction, and storage) across the bakery production chain, over three seasons (winter, spring, and summer). These amplicons were sequenced, and data were analyzed using the mothur pipeline and visualized using MicrobiomeAnalyst and a series of R packages. The top seven bacterial phyla identified at both sites were composed of Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Patescibacteria, and Verrucomicrobia. In addition, the phyla Tenericutes (Mycoplasmatota) and Acidobacteria were observed only in samples taken at site B. Different bacterial compositions were identified at each stage of production. These same bacteria were also found to be present in the final processed food suggesting the influence of the environment on the food matrix. This study is the first demonstration of the utility of 16S rRNA amplicon-based sequencing to describe the microbiota associated with bakery processing environments.
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Affiliation(s)
- Dechamma Mundanda Muthappa
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Sakshi Lamba
- Institute of Food and Health, School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | | | - Ankita Naithani
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | | | - Shabarinath Srikumar
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,Department of Food, Nutrition, and Health, College of Food and Agriculture, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Guerrino Macori
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Amalia G M Scannell
- Institute of Food and Health, School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
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26
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Egeter B, Veríssimo J, Lopes-Lima M, Chaves C, Pinto J, Riccardi N, Beja P, Fonseca NA. Speeding up the detection of invasive bivalve species using environmental DNA: a Nanopore and Illumina sequencing comparison. Mol Ecol Resour 2022; 22:2232-2247. [PMID: 35305077 DOI: 10.1111/1755-0998.13610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 02/09/2022] [Accepted: 03/02/2022] [Indexed: 11/30/2022]
Abstract
Traditional detection of aquatic invasive species via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools (msi package) to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves while comparing it with Illumina-based sequencing. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. Samples were extracted, amplified, and sequenced by the two platforms. The mean agreement between sequencing methods was 69% and the difference between methods was non-significant. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples.
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Affiliation(s)
- Bastian Egeter
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,NatureMetrics, Bakeham Lane, Egham, Surrey, TW20 9TY, U.K
| | - Joana Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Manuel Lopes-Lima
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,IUCN SSC Mollusc Specialist Group, c/o 219 Huntingdon Road, Cambridge, CB3 0DL, U.K
| | - Cátia Chaves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Joana Pinto
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | | | - Pedro Beja
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,CIBIO/InBIO, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Nuno A Fonseca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
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27
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McElhoe JA, Wilton PR, Parson W, Holland MM. Exploring statistical weight estimates for mitochondrial DNA matches involving heteroplasmy. Int J Legal Med 2022; 136:671-685. [PMID: 35243529 DOI: 10.1007/s00414-022-02774-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/12/2022] [Indexed: 11/26/2022]
Abstract
Massively parallel sequencing (MPS) of mitochondrial (mt) DNA allows forensic laboratories to report heteroplasmy on a routine basis. Statistical approaches will be needed to determine the relative frequency of observing an mtDNA haplotype when including the presence of a heteroplasmic site. Here, we examined 1301 control region (CR) sequences, collected from individuals in four major population groups (European, African, Asian, and Latino), and covering 24 geographically distributed haplogroups, to assess the rates of point heteroplasmy (PHP) on an individual and nucleotide position (np) basis. With a minor allele frequency (MAF) threshold of 2%, the data was similar across population groups, with an overall PHP rate of 37.7%, and the majority of heteroplasmic individuals (77.3%) having only one site of heteroplasmy. The majority (75.2%) of identified PHPs had an MAF of 2-10%, and were observed at 12.6% of the nps across the CR. Both the broad and phylogenetic testing suggested that in many cases the low number of observations of heteroplasmy at any one np results in a lack of statistical association. The posterior frequency estimates, which skew conservative to a degree depending on the sample size in a given haplogroup, had a mean of 0.152 (SD 0.134) and ranged from 0.031 to 0.83. As expected, posterior frequency estimates decreased in accordance with 1/n as the sample size (n) increased. This provides a proposed conservative statistical framework for assessing haplotype/heteroplasmy matches when applying an MPS technique in forensic cases and will allow for continual refinement as more data is generated, both within the CR and across the mitochondrial genome.
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Affiliation(s)
- Jennifer A McElhoe
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA.
| | - Peter R Wilton
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
- 23andMe Inc, Sunnyvale, CA, 94086, USA
| | - Walther Parson
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstraße 44, 6020, Innsbruck, Austria
| | - Mitchell M Holland
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA
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28
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Ao L, Zhao M, Li X, Sun G. Different Urban Forest Tree Species Affect the Assembly of the Soil Bacterial and Fungal Community. Microb Ecol 2022; 83:447-458. [PMID: 34031701 DOI: 10.1007/s00248-021-01754-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/11/2021] [Indexed: 06/12/2023]
Abstract
The selection of tree species used for the afforestation of urban forests is very important for maintaining the urban ecosystem, while soil microbe is one of the driving factors of material cycling in the urban forest ecosystem and for health of forests. In this study, the characteristics of surface soil bacterial and fungal community structure in four urban forests (primarily composed of Fraxinus mandshurica (Fm), Quercus mongolica (Qm), Pinus sylvestris var. mongolica (Ps), and Pinus tabulaeformis var. Mukdensis (Pt) as the main dominant tree species, respectively) were investigated by high-throughput sequencing. Our results showed that the alpha diversity of the soil microbial community in the Fm urban forest was the highest, while the lowest was in the Ps urban forest. In the bacterial community, Proteobacteria was the most predominant phylum in soils from Fm, Ps, and Pt urban forests. The most relatively abundant phylum of the Qm urban forest soil was Acidobacteria. The relative abundances of the bacterial communities at the genus level in the soil of four urban forests were significantly different. The soil bacterial communities in Ps and Pt urban forests were more similar, and Qm and Fm were also more similar. In the fungal community, Basidiomycota was the most predominant phylum in soils from Qm, Ps, and Pt urban forests. The phylum with the greatest relative abundance in the Fm urban forest soil was Ascomycota. There were differences in the fungal community between Qm, Fm, Ps, and Pt urban forests. Soil microbial community composition was affected by environmental factors: soil bacterial and fungal community compositions were significantly related to soil electrical conductivity (EC), alkali hydrolysable nitrogen (AHN), total nitrogen (TN), and total phosphorus (TP). In conclusion, the soil microbial community structure was related to both forest's tree species and soil properties.
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Affiliation(s)
- Lun Ao
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, 150040, China
| | - Meichun Zhao
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, 150040, China
| | - Xin Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
- School of Forestry, Northeast Forestry University, Harbin, Heilongjiang, 150040, China.
| | - Guangyu Sun
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, 150040, China.
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Nakanishi H, Yoneyama K, Hara M, Takada A, Sakai K, Saito K. Estimating individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq. Int J Legal Med 2022; 136:423-432. [PMID: 35001166 DOI: 10.1007/s00414-021-02763-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/03/2021] [Indexed: 12/30/2022]
Abstract
We tried to estimate individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq. The BAM files produced by MiSeq were viewed using Integrative Genomics Viewer (IGV) to verify mixed bases. By sorting the reads according to base type for each mixed base, partial haplotypes were determined. Then, the BAM files produced by MinKNOW were viewed using IGV. To determine haplotypes with IGV, only mixed bases determined by MiSeq were used as target bases. By sorting the reads according to base type for each target base, each contributor's haplotype was estimated. In mixed samples from two contributors, even a haplotype with a minor contribution of 5% could be distinguished from the haplotype of the major contributor. In mixed samples of three contributors (mixture ratios of 1:1:1 and 4:2:1), each haplotype could also be distinguished. Sequences of C-stretches were determined very inaccurately in the MinION analysis. Although the analysis method was simple, each haplotype was correctly detected in all mixed samples with two or three contributors in various mixture ratios by combining MinION and MiSeq. This should be useful for identifying contributors to mixed samples.
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Affiliation(s)
- Hiroaki Nakanishi
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
| | - Katsumi Yoneyama
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan
| | - Masaaki Hara
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan
| | - Aya Takada
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan
| | - Kentaro Sakai
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
- Tokyo Medical Examiner's Office, Tokyo Metropolitan Government, 4-21-18, Otsuka, Bunkyo-Ku, Tokyo, 112-0012, Japan
| | - Kazuyuki Saito
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
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Sarver J, Schultz E, Apigo A, Gernandt DS, Salas-Lizana R, Oono R. Deep sequencing across multiple host species tests pine-endophyte specificity. Am J Bot 2022; 109:83-98. [PMID: 34695224 DOI: 10.1002/ajb2.1792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Foliar fungal endophytes vary in their distributions across landscapes or plant host taxa, indicative of specialized ecologies and host specific adaptations. Accounts of specialization, however, depend on the taxonomic breadth and geographic range of the host plants included in each study. A broad region-scale study or deep sampling of diverse potential host species still remains relatively rare but is becoming increasingly possible with high-throughput sequencing. METHODS Amplicon sequencing was used to rapidly identify the fungal endophytic community among six pine (Pinus, Pinaceae) species co-occurring across northeastern United States and to test for site and host specialization. We focused on the endophytic genus Lophodermium (Rhytismataceae), whose species members are thought to specialize on different pine species, to test if amplicon sequencing could rapidly verify previously implied or discover new patterns of host specificity. RESULTS While amplicon sequencing could analyze more samples at greater depths and recover greater numbers of unique Lophodermium taxa than when endophyte communities were surveyed with traditional culturing methods, patterns of specialization were not better supported. This may be because amplicon sequencing can indiscriminately capture non-host specific organisms found incidentally from plant tissues or because we have overestimated host-specificity in the past with biased culturing techniques. CONCLUSIONS Amplicon sequencing can quickly identify patterns of host specificity by allowing large-scale surveys but has limitations in quantifying the level of intimacy of these relationships.
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Affiliation(s)
- Jake Sarver
- Department of Ecology, Evolution, and Marine Biology, University of California-Santa Barbara, Santa Barbara, California, 93106, USA
| | - Ella Schultz
- Department of Ecology, Evolution, and Marine Biology, University of California-Santa Barbara, Santa Barbara, California, 93106, USA
| | - Austen Apigo
- Department of Ecology, Evolution, and Marine Biology, University of California-Santa Barbara, Santa Barbara, California, 93106, USA
| | - David S Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Rodolfo Salas-Lizana
- Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Ryoko Oono
- Department of Ecology, Evolution, and Marine Biology, University of California-Santa Barbara, Santa Barbara, California, 93106, USA
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Li W, Luo M, Shi R, Feng D, Yang Z, Chen H, Hu B. Variations in bacterial and archaeal community structure and diversity along the soil profiles of a peatland in Southwest China. Environ Sci Pollut Res Int 2022; 29:2276-2286. [PMID: 34365597 DOI: 10.1007/s11356-021-15774-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
As bacteria and archaea are key components in the ecosystem, information on their dynamics in soil profiles is important for understanding the biogeochemical cycles in peatlands. However, little is known about the vertical distribution patterns of bacteria and archaea in the Bitahai peatland, or about their relationships with soil chemical properties. Here, bacterial and archaeal abundance, diversity, and composition of the Bitahai peatlands at 0-100 cm soil depths were analyzed by sequencing of 16S rRNA genes (Illumina, MiSeq). Soil pH, total C, N, and P concentrations and stoichiometric ratios were also estimated. The results revealed that total C and total N contents, as well as C:P and N:P ratios, significantly increased with increasing peatland soil depths, while total P decreased. The top three dominant phyla were Proteobacteria (39.64%), Acidobacteria (12.93%), and Chloroflexi (12.81%) in bacterial communities, and were Crenarchaeota (58.67%), Thaumarchaeota (14.34%), and Euryarchaeota (10.82%) in archaeal communities in the Bitahai peatland, respectively. The total relative abundance of methanogenic groups and ammonia-oxidizing microorganisms all significantly decreased with soil depth. Both bacterial and archaeal diversities were significantly affected by the soil depth. Soil C, N, and P concentrations and stoichiometric ratios markedly impacted the community structure and diversity in archaea, but not in bacteria. Therefore, these results highlighted that the microbial community structure and diversity depended on soil depth for the Bitahai peatlands, and the factors affecting bacteria and archaea in the Bitahai peatlands were different.
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Affiliation(s)
- Wei Li
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, 650091, Kunming, China
- Institute for Ecological Research and Pollution Control of Plateau Lakes, Yunnan University, 650091, Kunming, China
| | - Mingmo Luo
- Institute for Ecological Research and Pollution Control of Plateau Lakes, Yunnan University, 650091, Kunming, China
| | - Rui Shi
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650091, China
| | - Defeng Feng
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, 650224, China.
| | - Zhenan Yang
- College of Life Science, China West Normal University, Nanchong, 637002, China
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Bin Hu
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, 650091, Kunming, China.
- Institute for Ecological Research and Pollution Control of Plateau Lakes, Yunnan University, 650091, Kunming, China.
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Aimone CD, Hoyer JS, Dye AE, Deppong DO, Duffy S, Carbone I, Hanley-Bowdoin L. An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing. J Virol Methods 2021; 300:114405. [PMID: 34896458 DOI: 10.1016/j.jviromet.2021.114405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 08/26/2021] [Accepted: 12/07/2021] [Indexed: 10/19/2022]
Abstract
The ability of begomoviruses to evolve rapidly threatens many crops and underscores the importance of detecting these viruses quickly and to understand their genome diversity. This study presents an improved protocol for the enhanced amplification and enrichment of begomovirus DNA for use in next generation sequencing of the viral genomes. An enhanced rolling circle amplification (RCA) method using EquiPhi29 polymerase was combined with size selection to generate a cost-effective, short-read sequencing method. This improved short-read sequencing produced at least 50 % of the reads mapping to the target viral reference genomes, African cassava mosaic virus and East African cassava mosaic virus. This study provided other insights into common misconceptions about RCA and lessons that could be learned from the sequencing of single-stranded DNA virus genomes. This protocol can be used to examine the viral DNA as it moves from host to vector, thus producing valuable information for viral DNA population studies, and would likely work well with other circular Rep-encoding ssDNA viruses (CRESS) DNA viruses.
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Affiliation(s)
- Catherine D Aimone
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
| | - J Steen Hoyer
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Anna E Dye
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - David O Deppong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Siobain Duffy
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
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Vazquez-Iglesias I, McGreig S, Pufal H, Robinson R, Clover GRG, Fox A, Boonham N, Adams IP. A novel high-throughput sequencing approach reveals the presence of a new virus infecting Rosa: rosa ilarvirus-1 (RIV-1). J Virol Methods 2021; 300:114417. [PMID: 34902457 DOI: 10.1016/j.jviromet.2021.114417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 01/11/2023]
Abstract
Roses are one of the most valuable ornamental flowering shrubs grown worldwide. Despite the widespread of rose viruses and their impact on cultivation, they have not been studied in detail in the United Kingdom (UK) since the 1980's. As part of a survey of rose viruses entering the UK, 35 samples were collected at Heathrow Airport (London, UK) and were tested by RT-qPCR for different common rose viruses. Of the 35 samples tested using RT-qPCR for prunus necrotic ringspot virus (PNRSV; genus Ilarvirus), 10 were positive. Confirmatory testing was performed using RT-PCR with both PNRSV-specific and ilarvirus-generic primers, and diverse results were obtained: One sample was exclusively positive when using the ilarvirus-generic primers, and subsequent sequencing of the RT-PCR product revealed homology to other ilarviruses but not PNRSV. Further work to characterise the virus was performed using high throughput sequencing, both the MinION Flongle and Illumina MiSeq. The sequencing confirmed the presence of a new virus within group 2 of the genus Ilarvirus and we propose the name "rosa ilarvirus-1″ (RIV-1). Here, we describe the identification of a novel virus using the low-cost Flongle flow cell and discuss its potential as a front-line diagnostic tool.
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Affiliation(s)
- Ines Vazquez-Iglesias
- Fera Science Ltd., York Biotech Campus, Sand Hutton, York, YO41 1LZ, United Kingdom; School of Natural and Environmental Sciences, Agriculture Building, King's Road, Newcastle upon Tyne, NE1 7RU, United Kingdom.
| | - Sam McGreig
- Fera Science Ltd., York Biotech Campus, Sand Hutton, York, YO41 1LZ, United Kingdom
| | - Hollie Pufal
- Fera Science Ltd., York Biotech Campus, Sand Hutton, York, YO41 1LZ, United Kingdom
| | - Rebekah Robinson
- The Royal Horticultural Society, Wisley, Woking, Surrey, GU23 6QB, United Kingdom
| | - Gerard R G Clover
- The Royal Horticultural Society, Wisley, Woking, Surrey, GU23 6QB, United Kingdom
| | - Adrian Fox
- Fera Science Ltd., York Biotech Campus, Sand Hutton, York, YO41 1LZ, United Kingdom
| | - Neil Boonham
- School of Natural and Environmental Sciences, Agriculture Building, King's Road, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Ian P Adams
- Fera Science Ltd., York Biotech Campus, Sand Hutton, York, YO41 1LZ, United Kingdom; Institute of Agri Food Research, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
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Ma X, Baeza JA, Richards VP, Agudelo P. First Genomic Resource of the Columbia Lance Nematode Hoplolaimus columbus. Phytopathology 2021; 111:2396-2398. [PMID: 33754806 DOI: 10.1094/phyto-12-20-0536-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The Columbia lance nematode Hoplolaimus columbus has been reported frequently from North America due to its negative impact on agricultural production. In this study, for the first time, we sequenced the whole genome of a female specimen by using whole-genome amplification and Illumina MiSeq. Data were de novo assembled to form scaffolds of 205.75 Mbp consisting of 118,374 contigs. The largest scaffold was 636,881 bp. Benchmarking Universal Single-Copy Orthologs completeness was 66.6% (eukaryotic dataset), and >8,000 unique genes were predicted by GeneMark-ES. In total, 61,855 protein sequences were predicted by AUGUSTUS, and 10,085 of them were annotated by PANNZER2 with at least one function. These data will provide valuable resources for studies focusing on pathogenicity and phylogenomics of plant-parasitic nematodes.
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Affiliation(s)
- Xinyuan Ma
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, U.S.A
| | - J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, U.S.A
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL 34949, U.S.A
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile
| | - Vincent P Richards
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, U.S.A
| | - Paula Agudelo
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, U.S.A
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Plitnick J, Griesemer S, Lasek-Nesselquist E, Singh N, Lamson DM, St George K. Whole-Genome Sequencing of SARS-CoV-2: Assessment of the Ion Torrent AmpliSeq Panel and Comparison with the Illumina MiSeq ARTIC Protocol. J Clin Microbiol 2021; 59:e0064921. [PMID: 34550806 DOI: 10.1128/JCM.00649-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Fast and effective methods are needed for sequencing of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome to track genetic mutations and to identify new and emerging variants during the ongoing pandemic. The objectives were to assess the performance of the SARS-CoV-2 AmpliSeq research panel and S5 plug-in analysis tools for whole-genome sequencing analysis of SARS-CoV-2 and to compare the results with those obtained with the MiSeq-based ARTIC analysis pipeline, using metrics such as depth, coverage, and concordance of single-nucleotide variant (SNV) calls. A total of 191 clinical specimens and a single cultured isolate were extracted and sequenced with AmpliSeq technology and analysis tools. Of the 191 clinical specimens, 83 (with threshold cycle [CT] values of 15.58 to 32.54) were also sequenced using an Illumina MiSeq-based method with the ARTIC analysis pipeline, for direct comparison. A total of 176 of the 191 clinical specimens sequenced on the S5XL system and prepared using the SARS-CoV-2 research panel had nearly complete coverage (>98%) of the viral genome, with an average depth of 5,031×. Similar coverage levels (>98%) were observed for 81/83 primary specimens that were sequenced with both methods tested. The sample with the lowest viral load (CT value of 32.54) achieved 89% coverage using the MiSeq method and failed to sequence with the AmpliSeq method. Consensus sequences produced by each method were identical for 81/82 samples in areas of equal coverage, with a single difference present in one sample. The AmpliSeq approach is as effective as the Illumina-based method using ARTIC v3 amplification for sequencing SARS-CoV-2 directly from patient specimens across a range of viral loads (CT values of 15.56 to 32.54 [median, 22.18]). The AmpliSeq workflow is very easily automated with the Ion Chef and S5 instruments and requires less training and experience with next-generation sequencing sample preparation than the Illumina workflow.
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Miguel MA, Kim SH, Lee SS, Cho YI. Impact of Soil Microbes and Oxygen Availability on Bacterial Community Structure of Decomposing Poultry Carcasses. Animals (Basel) 2021; 11:2937. [PMID: 34679958 PMCID: PMC8532636 DOI: 10.3390/ani11102937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022] Open
Abstract
The impact of soil with an intact microbial community and oxygen availability on moisture content, soil pH, and bacterial communities during decomposition of poultry carcasses was investigated. Poultry carcasses were decomposed in soil with or without a microbial community, under aerobic or anaerobic conditions. The samples collected in each microcosm burial set-up were analyzed by targeted 16S rRNA amplicon sequencing and Amplicon sequence variants (ASV) method. Our results showed that moisture was high in the burial set-ups under anaerobic conditions and pH was high in the burial set-ups under aerobic conditions. Meanwhile, the Chao1 and Shannon index significantly differed between the different burial set-ups and across different time points. In addition, bacterial taxa composition during the early period of decomposition differed from that of the late period. A total of 23 phyla, 901 genera, and 1992 species were identified. Firmicutes was the most dominant phyla in all burial set-ups throughout the decomposition. At day 60, Pseudogracilibacillus was dominant in the burial set-ups under aerobic conditions, while Lentibacillus dominated in the burial set-ups under anaerobic conditions. This study demonstrated that the soil microbial community and availability of oxygen significantly affected the changes in moisture content, pH, and bacterial composition during the decomposition process.
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Affiliation(s)
| | | | | | - Yong-Il Cho
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea; (M.A.M.); (S.-H.K.); (S.-S.L.)
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Bernard RF, Willcox EV, Jackson RT, Brown VA, McCracken GF. Feasting, not fasting: winter diets of cave hibernating bats in the United States. Front Zool 2021; 18:48. [PMID: 34556122 DOI: 10.1186/s12983-021-00434-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/09/2021] [Indexed: 11/29/2022] Open
Abstract
Temperate bat species use extended torpor to conserve energy when ambient temperatures are low and food resources are scarce. Previous research suggests that migratory bat species and species known to roost in thermally unstable locations, such as those that roost in trees, are more likely to remain active during winter. However, hibernating colonies of cave roosting bats in the southeastern United States may also be active and emerge from caves throughout the hibernation period. We report what bats are eating during these bouts of winter activity. We captured 2,044 bats of 10 species that emerged from six hibernacula over the course of 5 winters (October–April 2012/2013, 2013/2014, 2015/2016, 2016/2017, and 2017/2018). Using Next Generation sequencing of DNA from 284 fecal samples, we determined bats consumed at least 14 Orders of insect prey while active. Dietary composition did not vary among bat species; however, we did record variation in the dominant prey items represented in species’ diets. We recorded Lepidoptera in the diet of 72.2% of individual Corynorhinus rafinesquii and 67.4% of individual Lasiurus borealis. Diptera were recorded in 32.4% of Myotis leibii, 37.4% of M. lucifugus, 35.5% of M. sodalis and 68.8% of Perimyotis subflavus. Our study is the first to use molecular genetic techniques to identify the winter diet of North American hibernating bats. The information from this study is integral to managing the landscape around bat hibernacula for insect prey, particularly in areas where hibernating bat populations are threatened by white-nose syndrome.
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Ahmed B, Floc'h JB, Lahrach Z, Hijri M. Phytate and Microbial Suspension Amendments Increased Soybean Growth and Shifted Microbial Community Structure. Microorganisms 2021; 9:1803. [PMID: 34576699 DOI: 10.3390/microorganisms9091803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/10/2021] [Accepted: 08/15/2021] [Indexed: 12/22/2022] Open
Abstract
Phytate represents an organic pool of phosphorus in soil that requires hydrolysis by phytase enzymes produced by microorganisms prior to its bioavailability by plants. We tested the ability of a microbial suspension made from an old growth maple forest's undisturbed soil to mineralize phytate in a greenhouse trial on soybean plants inoculated or non-inoculated with the suspension. MiSeq Amplicon sequencing targeting bacterial 16S rRNA gene and fungal ITS was performed to assess microbial community changes following treatments. Our results showed that soybean nodulation and shoot dry weight biomass increased when phytate was applied to the nutrient-poor substrate mixture. Bacterial and fungal diversities of the root and rhizosphere biotopes were relatively resilient following inoculation by microbial suspension; however, bacterial community structure was significantly influenced. Interestingly, four arbuscular mycorrhizal fungi (AMF) were identified as indicator species, including Glomus sp., Claroideoglomus etunicatum, Funneliformis mosseae and an unidentified AMF taxon. We also observed that an ericoid mycorrhizal taxon Sebacina sp. and three Trichoderma spp. were among indicator species. Non-pathogenic Planctobacteria members highly dominated the bacterial community as core and hub taxa for over 80% of all bacterial datasets in root and rhizosphere biotopes. Overall, our study documented that inoculation with a microbial suspension and phytate amendment improved soybean plant growth.
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Li Y, Li L, Yu Y, Hu Q, Li X. Impact of Dietary Protein Content on Soil Bacterial and Fungal Communities in a Rice-Crab Co-culture System. Front Microbiol 2021; 12:696427. [PMID: 34234767 PMCID: PMC8256891 DOI: 10.3389/fmicb.2021.696427] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 04/16/2021] [Accepted: 05/27/2021] [Indexed: 12/13/2022] Open
Abstract
Although co-culture of paddy fields with aquatic animals is lucrative, the ecological impacts of high-protein content entering the agricultural soil via animal pellet feed and feces have not been well studied. Moreover, the effects of dietary protein on soils and soil microbes remain unclear. To elucidate this, we examined soil bacterial and fungal community composition and temporal changes in paddy fields subjected to different protein-content diets via 16S/18S rRNA gene amplicon sequencing analysis with a high-throughput next-generation sequencer. MiSeq sequencing revealed that protein content significantly impacted fungal community structure. High-protein diets reduced bacterial community diversity and relative abundance in both July and October. The phylum-level bacterial taxonomic composition was not affected by diet treatment, while in fungi, a major phylum-level shift was evident. Hierarchically clustered analysis showed that high-protein diets significantly reduced the relative abundance of Brevundimonas in both July and October. Saprotrophic macrofungal diversity was negatively related to dietary protein content. Considering microbial community structure and environmental factors, ca. 15% protein content is appropriate for the rice-crab co-culture system that we studied.
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Affiliation(s)
- Yingdong Li
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Lisong Li
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yilin Yu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qingbiao Hu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xiaodong Li
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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Shar S, Reith F, Ball AS, Shahsavari E. Long-term Impact of Gold and Platinum on Microbial Diversity in Australian Soils. Microb Ecol 2021; 81:977-989. [PMID: 33404821 DOI: 10.1007/s00248-020-01663-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
The effects of platinum (Pt) and gold (Au) and on the soil bacterial community was evaluated in four different Australian soil types (acidic Burn Grounds (BGR), organic matter-rich Fox Lane, high silt/metal Pinpinio (PPN), and alkali Minnipa (MNP) spiked with either Pt or Au at 1, 25, and 100 mg kg-1 using a next-generation sequencing approach (amplicon-based, MiSeq). Soil type and metal concentrations were observed to be key drivers of Pt and Au effects on soil microbial community structure. Different trends were therefore observed in the response of the bacterial community to Pt and Au amendments; however in each soil type, Pt and Au amendment caused a detectable shift in community structure that in most samples was positively correlated with increasing metal concentrations. New dominant groups were only observed in BGR and PPN soils at 100 mg kg-1 (Kazan-3B-28 and Verrucomicrobia groups (BGR, Pt) and Firmicutes and Caldithrix groups (PPN, Pt) and WS2 (BGR, Au). The effects of Pt on soil microbial diversity were largely adverse at 100 mg kg-1 and were pronounced in acidic, basic, and metal/silt-rich soils. However, this effect was concentration-related; Au appeared to be more toxic to soil bacterial communities than Pt at 25 mg kg-1 but Pt was more toxic at 100 mg kg-1. More bacterial groups such as those belonging to Burkholderiales/Burkholderiaceae, Alicyclobacillaceae, Rubrobacteraceae, Cytophagaceae, Oxalobacteraceae were selectively enriched by Pt compared to Au (Sphingomonadaceae and Rhodospirillaceae) amendments irrespective of soil type. The research outcomes have important implications in the management (remediation) of Pt- and Au-contaminated environments.
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Affiliation(s)
- Sahar Shar
- School of Science, RMIT University, PO Box 71, Bundoora, Victoria, 3083, Australia
- Deanship of Scientific Research King Saud University, Riyadh, 11451, Saudi Arabia
| | - Frank Reith
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- CSIRO Land and Water, Environmental Contaminant Mitigation and Technologies, PMB2, Glen Osmond, South Australia, 5064, Australia
| | - Andrew S Ball
- School of Science, RMIT University, PO Box 71, Bundoora, Victoria, 3083, Australia
| | - Esmaeil Shahsavari
- School of Science, RMIT University, PO Box 71, Bundoora, Victoria, 3083, Australia.
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Holt CL, Stephens KM, Walichiewicz P, Fleming KD, Forouzmand E, Wu SF. Human Mitochondrial Control Region and mtGenome: Design and Forensic Validation of NGS Multiplexes, Sequencing and Analytical Software. Genes (Basel) 2021; 12:genes12040599. [PMID: 33921728 PMCID: PMC8073089 DOI: 10.3390/genes12040599] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023] Open
Abstract
Forensic mitochondrial DNA (mtDNA) analysis conducted using next-generation sequencing (NGS), also known as massively parallel sequencing (MPS), as compared to Sanger-type sequencing brings modern advantages, such as deep coverage per base (herein referred to as read depth per base pair (bp)), simultaneous sequencing of multiple samples (libraries) and increased operational efficiencies. This report describes the design and developmental validation, according to forensic quality assurance standards, of end-to-end workflows for two multiplexes, comprised of ForenSeq mtDNA control region and mtDNA whole-genome kits the MiSeq FGxTM instrument and ForenSeq universal analysis software (UAS) 2.0/2.1. Polymerase chain reaction (PCR) enrichment and a tiled amplicon approach target small, overlapping amplicons (60–150 bp and 60–209 bp for the control region and mtGenome, respectively). The system provides convenient access to data files that can be used outside of the UAS if desired. Studies assessed a range of environmental and situational variables, including but not limited to buccal samples, rootless hairs, dental and skeletal remains, concordance of control region typing between the two multiplexes and as compared to orthogonal data, assorted sensitivity studies, two-person DNA mixtures and PCR-based performance testing. Limitations of the system and implementation considerations are discussed. Data indicated that the two mtDNA multiplexes, MiSeq FGx and ForenSeq software, meet or exceed forensic DNA quality assurance (QA) guidelines with robust, reproducible performance on samples of various quantities and qualities.
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Fu'adil Amin MH, Lee SR, Irawan B, Andriyono S, Kim HW. Characterization of the complete mitochondrial genome of the Northern Mud Gudgeon, Ophiocara porocephala (Perciformes: Eleotridae) with phylogenetic implications. Mitochondrial DNA B Resour 2021; 6:953-955. [PMID: 33796696 PMCID: PMC7971195 DOI: 10.1080/23802359.2021.1889415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/25/2022]
Abstract
The first mitochondrial genome of Ophiocara porocephala was determined by the combination of next-generation sequencing (NGS) and Sanger sequencing methods. A complete circular mitogenome of O. porocephala (16,529 bp) consisted of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two non-coding regions, including a control region (D-loop) and a light strand origin of replication (OL). Two start codons (ATG and GTG) and four stop codons (TAG, TAA, TA-, and T-) were used in all the PCGs. Except for ND6 and eight transfer RNAs (tRNAs), all the other genes were encoded in the heavy strand. Based on phylogenetic analysis, O. porocephala formed a clade with three other species in the subfamily Butinae, while the other 10 made a subfamily Eleotrinae clade.
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Affiliation(s)
- Muhammad Hilman Fu'adil Amin
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan, Republic of Korea.,Department of Biology, Faculty of Science and Technology, Advance Tropical Biodiversity, Genomics, and Conservation Research Group, Universitas Airlangga, Surabaya, Indonesia
| | - Soo Rin Lee
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan, Republic of Korea
| | - Bambang Irawan
- Department of Biology, Faculty of Science and Technology, Advance Tropical Biodiversity, Genomics, and Conservation Research Group, Universitas Airlangga, Surabaya, Indonesia
| | - Sapto Andriyono
- Department of Marine, Fisheries and Marine Faculty, Universitas Airlangga C Campus Jl. Mulyorejo Surabaya East Java, Surabaya, Indonesia
| | - Hyun-Woo Kim
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan, Republic of Korea.,Department of Marine, Fisheries and Marine Faculty, Universitas Airlangga C Campus Jl. Mulyorejo Surabaya East Java, Surabaya, Indonesia.,Department of Marine Biology, Pukyong National University, Busan, Republic of Korea
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Ali I, Liu K, Long D, Faisal S, Hilal MG, Ali I, Huang X, Long R. Ramadan Fasting Leads to Shifts in Human Gut Microbiota Structured by Dietary Composition. Front Microbiol 2021; 12:642999. [PMID: 33679680 PMCID: PMC7930080 DOI: 10.3389/fmicb.2021.642999] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 12/17/2020] [Accepted: 02/01/2021] [Indexed: 01/14/2023] Open
Abstract
The structure and diversity of human gut microbiota are directly related to diet, though less is known about the influences of ethnicity and diet-related behaviors, such as fasting (intermittent caloric restriction). In this study, we investigated whether fasting for Ramadan altered the microbiota in Chinese and Pakistani individuals. Using high-throughput 16S rRNA gene sequencing and self-reported dietary intake surveys, we determined that both the microbiota and dietary composition were significantly different with little overlap between ethnic groups. Principal Coordinate Analyses (PCoA) comparison of samples collected from both groups before and after fasting showed partial separation of microbiota related to fasting in the Pakistani group, but not in the Chinese group. Measurement of alpha diversity showed that Ramadan fasting significantly altered the coverage and ACE indices among Chinese subjects, but otherwise incurred no changes among either group. Specifically, Prevotella and Faecalibacterium drove predominance of Bacteroidetes and Firmicutes in the Pakistani group, while Bacteroides (phylum Bacteroidetes) were the most prevalent among Chinese participants both before and after fasting. We observed significant enrichment of some specific taxa and depletion of others in individuals of both populations, suggesting that fasting could affect beta diversity. Notably, Dorea, Klebsiella, and Faecalibacterium were more abundant in the Chinese group after fasting, while Sutterella, Parabacteroides, and Alistipes were significantly enriched after fasting in the Pakistani group. Evaluation of the combined groups showed that genera Coprococcus, Clostridium_XlV, and Lachnospiracea were all significantly decreased after fasting. Analysis of food intake and macronutrient energy sources showed that fat-derived energy was positively associated with Oscillibacter and Prevotella, but negatively associated with Bacteroides. In addition, the consumption of sweets was significantly positively correlated with the prevalence of Akkermansia. Our study indicated that diet was the most significant influence on microbiota, and correlated with ethnic groups, while fasting led to enrichment of specific bacterial taxa in some individuals. Given the dearth of understanding about the impacts of fasting on microbiota, our results provide valuable inroads for future study aimed at novel, personalized, behavior-based treatments targeting specific gut microbes for prevention or treatment of digestive disorders.
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Affiliation(s)
- Ikram Ali
- School of Life Sciences, Lanzhou University, Lanzhou, China.,School of Public Health, Lanzhou University, Lanzhou, China
| | - Ke Liu
- School of Public Health, Lanzhou University, Lanzhou, China.,Henan Provincial Center for Disease Control and Prevention, Zhengzhou, China
| | - Danfeng Long
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Shah Faisal
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mian Gul Hilal
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Izhar Ali
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xiaodan Huang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Ruijun Long
- School of Life Sciences, Lanzhou University, Lanzhou, China
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Parente CET, Brito EMS, Caretta CA, Cervantes-Rodríguez EA, Fábila-Canto AP, Vollú RE, Seldin L, Malm O. Bacterial diversity changes in agricultural soils influenced by poultry litter fertilization. Braz J Microbiol 2021; 52:675-86. [PMID: 33590447 DOI: 10.1007/s42770-021-00437-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 02/02/2021] [Indexed: 01/28/2023] Open
Abstract
Poultry litter is widely applied as agricultural fertilizer and can affect the soil microbiome through nutrient overload and antibiotic contamination. In this study, we assessed changes in soil bacterial diversity using high-throughput sequencing approaches. Four samples in triplicate were studied: soils with short- and long-term fertilization by poultry litter (S1 = 10 months and S2 = 30 years, respectively), a soil inside a poultry shed (S3), and a forest soil used as control (S0). Samples S0, S1, and S2 revealed a relatively high richness, with confirmed operational taxonomic units (OTUs) in the three replicates of each sample ranging from 1243 to 1279, while richness in S3 was about three times lower (466). The most abundant phyla were Proteobacteria, Bacteroidetes, and Actinobacteria. Acidobacteria, Planctomycetes, and Verrucomicrobia were also abundant but highly diminished in S3, while Firmicutes was less abundant in S0. Changes in bacterial communities were very evident at the genera level. The genera Gaiella, Rhodoplanes, Solirubacter, and Sphingomonas were predominant in S0 but strongly decreased in the other soils. Pedobacter and Devosia were the most abundant in S1 and were diminished in S2, while Herbiconiux, Brevundimonas, Proteiniphilum, and Petrimonas were abundant in S2. The most abundant genera in S3 were Deinococcus, Truepera, Rhodanobacter, and Castellaniella. A predictive analysis of the metabolic functions with Tax4Fun2 software suggested the potential presence of enzymes associated with antibiotic resistance as well as with denitrification pathways, indicating that the S3 soil is a potential source of nitrous oxide, a powerful greenhouse gas.
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Sukser V, Rokić F, Barbarić L, Korolija M. Assessment of Illumina® Human mtDNA Genome assay: workflow evaluation with development of analysis and interpretation guidelines. Int J Legal Med 2021; 135:1161-78. [PMID: 33511452 DOI: 10.1007/s00414-021-02508-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/08/2021] [Indexed: 01/27/2023]
Abstract
Mitochondrial DNA (mtDNA) is a small but significant part of the human genome, whose applicability potential has gradually increased with the advent of massively parallel sequencing (MPS) technology. Knowledge of the particular workflow, equipment, and reagents used, along with extensive usage of negative controls to monitor all preparation steps constitute the prerequisites for confident reporting of results. In this study, we performed an assessment of Illumina® Human mtDNA Genome assay on MiSeq FGx™ instrument. Through analysis of several types of negative controls, as well as mtDNA positive controls, we established thresholds for data analysis and interpretation, consisting of several components: minimum read depth (220 reads), minimum quality score (41), percentage of minor allele sufficient for analysis (3.0%), percentage of minor allele sufficient for interpretation (6.0%), and percentage of major allele sufficient for homoplasmic variant call (97.0%). Based on these criteria, we defined internal guidelines for analysis and interpretation of mtDNA results obtained by MPS. Our study shows that the whole mtDNA assay on MiSeq FGx™ produces repeatable and reproducible results, independent of the analyst, which are also concordant with Sanger-type sequencing results for mtDNA control region, as well as with MPS results produced by NextSeq®. Overall, established thresholds and interpretation guidelines were successfully applied for the sequencing of complete mitochondrial genomes from high-quality samples. The underlying principles and proposed methodology on the definition of internal laboratory guidelines for analysis and interpretation of MPS results may be applicable to similar MPS workflows, e.g. targeting good-quality samples in forensic genetics and molecular diagnostics.
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Muturi EJ, Njoroge TM, Dunlap C, Cáceres CE. Blood meal source and mixed blood-feeding influence gut bacterial community composition in Aedes aegypti. Parasit Vectors 2021; 14:83. [PMID: 33509255 PMCID: PMC7841894 DOI: 10.1186/s13071-021-04579-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/01/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND The guts of blood-sucking insects host a community of bacteria that can shift dramatically in response to biotic and abiotic factors. Identifying the key factors structuring these microbial communities has important ecological and epidemiological implications. METHODS We used the yellow fever mosquito, Aedes aegypti, to investigate the impact of mixed blood meals on gut microbiota of vector mosquitoes. Adult females were experimentally fed on sugar or blood from chicken, rabbit or a mixture of chicken and rabbit blood, and their gut microbiota were characterized using 16S rRNA gene amplification and MiSeq sequencing. RESULTS The gut bacterial communities of mosquitoes fed on the three blood meal treatments clustered separately, suggesting that host species identity and mixed blood-feeding are key determinants of gut bacterial community composition in mosquitoes. Mixed blood meal had a synergistic effect on both operational taxonomic unit (OTU) richness and the Shannon diversity index, suggesting that mixed blood-feeding can offset the nutritional deficit of blood meals from certain host species. The microbial communities observed in this study were distinct from those identified from similarly fed Ae. aegypti from our previous study. CONCLUSIONS These findings demonstrate that vector host-feeding preferences can influence gut microbial composition and diversity, which could potentially impact pathogen acquisition and transmission by the vector. The results also demonstrate that different microenvironmental conditions within the laboratory may play an important role in structuring the microbial communities of independently reared mosquito colonies.
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Affiliation(s)
- Ephantus J Muturi
- Crop Bioprotection Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University St, Peoria, 61604, IL, USA.
| | - Teresia M Njoroge
- Department of Entomology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Christopher Dunlap
- Crop Bioprotection Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University St, Peoria, 61604, IL, USA
| | - Carla E Cáceres
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave, Urbana, 61801, IL, USA
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Nantel-Fortier N, Gauthier M, L'Homme Y, Fravalo P, Brassard J. Treatments of porcine fecal samples affect high-throughput virome sequencing results. J Virol Methods 2020; 289:114045. [PMID: 33333107 DOI: 10.1016/j.jviromet.2020.114045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/17/2022]
Abstract
The porcine enteric microbiota is currently extensively studied, taking advantage of developments in high-throughput sequencing technologies. However, the viral part of the microbiota, the virome, is being lightly explored, and the impact of the pretreatments used before sequencing the viruses is barely considered. In this study, the impacts of filtration, RNase and DNase treatments on virus reads recovery and diversity after sequencing on a MiSeq platform were assessed on fecal samples individually taken at <3, 5, 12 and 20 weeks from two piglets. None of the four pretreatment series affected the virus read averages or influenced diversity, but the samples with the higher proportion of reads corresponding to an entry in the "nt" database were those receiving the least number of pretreatments. The enzymatic pretreatments affected the detection of the single-stranded RNA viruses of Aichivirus C, porcine astrovirus, Sapovirus and posavirus, which is worrisome, as these viruses can be involved in swine diarrhea. If enzymatic pretreatments are used when sequencing using a high-throughput method, it may impact single-stranded RNA virus recovery, but not the overall virome diversity. Therefore, filtrated samples may be the better option, reducing the amount of bacterial genetic material while preserving the virus reads.
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Affiliation(s)
- Nicolas Nantel-Fortier
- Research Chair in Meat Safety, Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Quebec, Canada; Swine and Poultry Infections Disease Research Center (CRIPA-FRQNT), University of Montreal, Canada
| | - Martin Gauthier
- Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, Quebec, Canada
| | - Yvan L'Homme
- Swine and Poultry Infections Disease Research Center (CRIPA-FRQNT), University of Montreal, Canada; CEGEP Garneau, Quebec City, Quebec, Canada
| | - Philippe Fravalo
- Research Chair in Meat Safety, Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Quebec, Canada; Swine and Poultry Infections Disease Research Center (CRIPA-FRQNT), University of Montreal, Canada
| | - Julie Brassard
- Swine and Poultry Infections Disease Research Center (CRIPA-FRQNT), University of Montreal, Canada; Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, Quebec, Canada.
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Truelsen D, Pereira V, Phillips C, Morling N, Børsting C. Evaluation of a custom GeneRead™ massively parallel sequencing assay with 210 ancestry informative SNPs using the Ion S5™ and MiSeq platforms. Forensic Sci Int Genet 2020; 50:102411. [PMID: 33176271 DOI: 10.1016/j.fsigen.2020.102411] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 01/20/2023]
Abstract
A custom GeneRead DNAseq SNP panel with 210 markers was evaluated using the Ion S5 and MiSeq sequencing platforms. Sensitivity, PCR cycle number, and the use of half volume of reagents for target enrichment and library preparation were tested. Furthermore, genotype concordance between results obtained with the different sequencing platforms and with known profiles generated using other sequencing assays was analysed. The GeneRead DNASeq SNP assay gave reproducible results with an input of 200 pg DNA on both platforms. A total of 204 loci were successfully sequenced. Three loci failed completely in the PCR amplification, and three additional loci displayed frequent locus drop-outs due to low read depth or high heterozygote imbalance. Overall, the read depth across the loci was more well-balanced with the MiSeq, while the heterozygote balance was less variable with the Ion S5. Noise levels were low on both platforms (median< 0.2 %). Two simple criteria for genotyping were applied: A minimum threshold of 45 reads and an acceptable heterozygote balance range of 0.3-3.0. Complete concordance between platforms was observed except for three genotypes in one of the poorly performing loci, rs1470637. This locus had relatively low read depths on both platforms, skewed heterozygote balance, and frequent locus drop-outs. There was also full genotype concordance between the results from the GeneRead assay and known profiles generated with the QIAseq and Ion AmpliSeq assays. The few discordant results were either due to locus drop-outs in the poorly performing loci or allele drop-outs in the QIAseq assay. Profiles with a minimum of 179 SNPs were obtained from four challenging case work samples (blood swabs, bone, or blood from a corpse). Overall, the GeneRead DNASeq assay showed considerable potential and could provide a reliable method for SNP genotyping in cases involving identification of individuals, prediction of phenotypic traits, and ancestry inference.
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Affiliation(s)
- Ditte Truelsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Chris Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark; Department of Mathematical Sciences, Aalborg University, DK-9220 Aalborg East, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
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Wei PL, Hung CS, Kao YW, Lin YC, Lee CY, Chang TH, Shia BC, Lin JC. Characterization of Fecal Microbiota with Clinical Specimen Using Long-Read and Short-Read Sequencing Platform. Int J Mol Sci 2020; 21:ijms21197110. [PMID: 32993155 PMCID: PMC7582668 DOI: 10.3390/ijms21197110] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/18/2020] [Accepted: 09/25/2020] [Indexed: 12/22/2022] Open
Abstract
Accurate and rapid identification of microbiotic communities using 16S ribosomal (r)RNA sequencing is a critical task for expanding medical and clinical applications. Next-generation sequencing (NGS) is widely considered a practical approach for direct application to communities without the need for in vitro culturing. In this report, a comparative evaluation of short-read (Illumina) and long-read (Oxford Nanopore Technologies (ONT)) platforms toward 16S rRNA sequencing with the same batch of total genomic DNA extracted from fecal samples is presented. Different 16S gene regions were amplified, bar-coded, and sequenced using the Illumina MiSeq and ONT MinION sequencers and corresponding kits. Mapping of the sequenced amplicon using MinION to the entire 16S rRNA gene was analyzed with the cloud-based EPI2ME algorithm. V3–V4 reads generated using MiSeq were aligned by applying the CLC genomics workbench. More than 90% of sequenced reads generated using distinct sequencers were accurately classified at the genus or species level. The misclassification of sequenced reads at the species level between the two approaches was less substantial as expected. Taken together, the comparative results demonstrate that MinION sequencing platform coupled with the corresponding algorithm could function as a practicable strategy in classifying bacterial community to the species level.
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Affiliation(s)
- Po-Li Wei
- Division of Colorectal Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan;
- Cancer Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan
- Translational Laboratory, Department of Medical Research, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan
- Department of Surgery, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Graduate Institute of Cancer Biology and Drug Discovery, Taipei Medical University, Taipei 110, Taiwan
| | - Ching-Sheng Hung
- PhD Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan;
- Department of Laboratory Medicine, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan
| | - Yi-Wei Kao
- Graduate Institute of Business Administration, College of Management. Fu Jen Catholic University, New Taipei City 242062, Taiwan;
| | - Ying-Chin Lin
- Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan;
- Department of Family Medicine, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan
| | - Cheng-Yang Lee
- Office of Information Technology, Taipei Medical University, Taipei 106, Taiwan;
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei 106, Taiwan;
| | - Ben-Chang Shia
- Graduate Institute of Business Administration, College of Management. Fu Jen Catholic University, New Taipei City 242062, Taiwan;
- Correspondence: (B.-C.S.); (J.-C.L.)
| | - Jung-Chun Lin
- PhD Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan;
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
- Pulmonary Research Center, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan
- Correspondence: (B.-C.S.); (J.-C.L.)
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50
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Gagnon CA, Lalonde C, Provost C. Porcine reproductive and respiratory syndrome virus whole-genome sequencing efficacy with field clinical samples using a poly(A)-tail viral genome purification method. J Vet Diagn Invest 2020; 33:216-226. [PMID: 32856560 DOI: 10.1177/1040638720952411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The genomic surveillance of porcine reproductive and respiratory syndrome virus (PRRSV) is based on sequencing of the ORF5 gene of the virus, which covers only 4% of the entire viral genome. It is expected that PRRSV whole-genome sequencing (WGS) will improve PRRSV genomic data and allow better understanding of clinical discrepancies observed in the field when using ORF5 sequencing. Our main objective was to implement an efficient method for WGS of PRRSV from clinical samples. The viral genome was purified using a poly(A)-tail viral genome purification method and sequenced using Illumina technology. We tested 149 PRRSV-positive samples: 80 sera, 33 lungs, 33 pools of tissues, 2 oral fluids, and 1 processing fluid (i.e., castration liquid). Overall, WGS of 67.1% of PRRSV-positive cases was successful. The viral load, in particular for tissues, had a major impact on the PRRSV WGS success rate. Serum was the most efficient type of sample to conduct PRRSV WGS poly(A)-tail assays, with a success rate of 76.3%, and this result can be explained by improved sequencing reads dispersion matching throughout the entire viral genome. WGS was unsuccessful for all pools of tissue and lung samples with Cq values > 26.5, whereas it could still be successful with sera at Cq ≤ 34.1. Evaluation of results of highly qualified personnel confirmed that laboratory skills could affect PRRSV WGS efficiency. Oral fluid samples seem very promising and merit further investigation because, with only 2 samples of low viral load (Cq = 28.8, 32.8), PRRSV WGS was successful.
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Affiliation(s)
- Carl A Gagnon
- Swine and Poultry Infectious Diseases Research Center and Molecular Diagnostic Laboratory of the Service de diagnostic, Faculté de médecine vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - Christian Lalonde
- Swine and Poultry Infectious Diseases Research Center, Faculté de médecine vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - Chantale Provost
- Swine and Poultry Infectious Diseases Research Center and Molecular Diagnostic Laboratory of the Service de diagnostic, Faculté de médecine vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
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