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Bloemen B, Gand M, Vanneste K, Marchal K, Roosens NHC, De Keersmaecker SCJ. Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance. Sci Rep 2023; 13:19656. [PMID: 37952062 PMCID: PMC10640560 DOI: 10.1038/s41598-023-46771-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/04/2023] [Indexed: 11/14/2023] Open
Abstract
Rapid, accurate and comprehensive diagnostics are essential for outbreak prevention and pathogen surveillance. Real-time, on-site metagenomics on miniaturized devices, such as Oxford Nanopore Technologies MinION sequencing, could provide a promising approach. However, current sample preparation protocols often require substantial equipment and dedicated laboratories, limiting their use. In this study, we developed a rapid on-site applicable DNA extraction and library preparation approach for nanopore sequencing, using portable devices. The optimized method consists of a portable mechanical lysis approach followed by magnetic bead-based DNA purification and automated sequencing library preparation, and resulted in a throughput comparable to a current optimal, laboratory-based protocol using enzymatic digestion to lyse cells. By using spike-in reference communities, we compared the on-site method with other workflows, and demonstrated reliable taxonomic profiling, despite method-specific biases. We also demonstrated the added value of long-read sequencing by recovering reads containing full-length antimicrobial resistance genes, and attributing them to a host species based on the additional genomic information they contain. Our method may provide a rapid, widely-applicable approach for microbial detection and surveillance in a variety of on-site settings.
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Affiliation(s)
- Bram Bloemen
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsman 14, 1050, Brussels, Belgium
- Department of Information Technology, IDLab, Ghent University, IMEC, 9052, Ghent, Belgium
| | - Mathieu Gand
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsman 14, 1050, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsman 14, 1050, Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsman 14, 1050, Brussels, Belgium
| | - Sigrid C J De Keersmaecker
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsman 14, 1050, Brussels, Belgium.
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A Synbiotic Formulation Comprising Bacillus subtilis DSM 32315 and L-Alanyl-L-Glutamine Improves Intestinal Butyrate Levels and Lipid Metabolism in Healthy Humans. Nutrients 2021; 14:nu14010143. [PMID: 35011015 PMCID: PMC8747176 DOI: 10.3390/nu14010143] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/23/2021] [Accepted: 12/26/2021] [Indexed: 01/04/2023] Open
Abstract
The gut microbiota is a crucial modulator of health effects elicited by food components, with SCFA (short chain fatty acids), especially butyrate, acting as important mediators thereof. We therefore developed a nutritional synbiotic composition targeted at shifting microbiome composition and activity towards butyrate production. An intestinal screening model was applied to identify probiotic Bacillus strains plus various amino acids and peptides with suitable effects on microbial butyrate producers and levels. A pilot study was performed to test if the synbiotic formulation could improve fecal butyrate levels in healthy humans. A combination of Bacillus subtilis DSM (Number of German Collection of Microorganisms and Cell Cultures) 32315 plus L-alanyl-L-glutamine resulted in distinctly increased levels of butyrate and butyrate-producing taxa (Clostridium group XIVa, e.g., Faecalibacterium prausnitzii), both in vitro and in humans. Moreover, circulating lipid parameters (LDL-, and total cholesterol and LDL/HDL cholesterol ratio) were significantly decreased and further metabolic effects such as glucose-modulation were observed. Fasting levels of PYY (Peptide YY) and GLP-1 (Glucagon-like Peptide 1) were significantly reduced. In conclusion, our study indicates that this synbiotic composition may provide an effective and safe tool for stimulation of intestinal butyrate production with effects on e.g., lipid and glucose homeostasis. Further investigations in larger cohorts are warranted to confirm and expand these findings.
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Darwish N, Shao J, Schreier LL, Proszkowiec-Weglarz M. Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca. Sci Rep 2021; 11:11848. [PMID: 34088939 PMCID: PMC8178357 DOI: 10.1038/s41598-021-91387-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/26/2021] [Indexed: 01/12/2023] Open
Abstract
We evaluated the effect of applying different sets of 16S rRNA primers on bacterial composition, diversity, and predicted function in chicken ceca. Cecal contents from Ross 708 birds at 1, 3, and 5 weeks of age were collected for DNA isolation. Eight different primer pairs targeting different variable regions of the 16S rRNA gene were employed. DNA sequences were analyzed using open-source platform QIIME2 and the Greengenes database. PICRUSt2 was used to determine the predicted function of bacterial communities. Changes in bacterial relative abundance due to 16S primers were determined by GLMs. The average PCR amplicon size ranged from 315 bp (V3) to 769 bp (V4–V6). Alpha- and beta-diversity, taxonomic composition, and predicted functions were significantly affected by the primer choice. Beta diversity analysis based on Unweighted UniFrac distance matrix showed separation of microbiota with four different clusters of bacterial communities. Based on the alpha- and beta-diversity and taxonomic composition, variable regions V1–V3(1) and (2), and V3–V4 and V3–V5 were in most consensus. Our data strongly suggest that selection of particular sets of the 16S rRNA primers can impact microbiota analysis and interpretation of results in chicken as was shown previously for humans and other animal species.
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Affiliation(s)
- Nadia Darwish
- Agricultural Research Service, NEA, Animal Biosciences and Biotechnology Laboratory, United States Department of Agriculture, 10300 Baltimore Avenue, B-200, Rm. 100B, BARC-East, Beltsville, MD, 20705, USA.,Agricultural Research Service, Northeast Area, Statistic Group, United States Department of Agriculture, Beltsville, MD, 20705, USA
| | - Jonathan Shao
- Agricultural Research Service, Northeast Area, Statistic Group, United States Department of Agriculture, Beltsville, MD, 20705, USA
| | - Lori L Schreier
- Agricultural Research Service, NEA, Animal Biosciences and Biotechnology Laboratory, United States Department of Agriculture, 10300 Baltimore Avenue, B-200, Rm. 100B, BARC-East, Beltsville, MD, 20705, USA
| | - Monika Proszkowiec-Weglarz
- Agricultural Research Service, NEA, Animal Biosciences and Biotechnology Laboratory, United States Department of Agriculture, 10300 Baltimore Avenue, B-200, Rm. 100B, BARC-East, Beltsville, MD, 20705, USA.
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Abundo MEC, Ngunjiri JM, Taylor KJM, Ji H, Ghorbani A, K. C. M, Weber BP, Johnson TJ, Lee CW. Assessment of two DNA extraction kits for profiling poultry respiratory microbiota from multiple sample types. PLoS One 2021; 16:e0241732. [PMID: 33406075 PMCID: PMC7787465 DOI: 10.1371/journal.pone.0241732] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/15/2020] [Indexed: 01/04/2023] Open
Abstract
Characterization of poultry microbiota is becoming increasingly important due to the growing need for microbiome-based interventions to improve poultry health and production performance. However, the lack of standardized protocols for sampling, sample processing, DNA extraction, sequencing, and bioinformatic analysis can hinder data comparison between studies. Here, we investigated how the DNA extraction process affects microbial community compositions and diversity metrics in different chicken respiratory sample types including choanal and tracheal swabs, nasal cavity and tracheal washes, and lower respiratory lavage. We did a side-by-side comparison of the performances of Qiagen DNeasy blood and tissue (BT) and ZymoBIOMICS DNA Miniprep (ZB) kits. In general, samples extracted with the BT kit yielded higher concentrations of total DNA while those extracted with the ZB kit contained higher numbers of bacterial 16S rRNA gene copies per unit volume. Therefore, the samples were normalized to equal amounts of 16S rRNA gene copies prior to sequencing. For each sample type, all predominant bacterial taxa detected in samples extracted with one kit were present in replicate samples extracted with the other kit and did not show significant differences at the class level. However, a few differentially abundant shared taxa were observed at family and genus levels. Furthermore, between-kit differences in alpha and beta diversity metrics at the amplicon sequence variant level were statistically indistinguishable. Therefore, both kits perform similarly in terms of 16S rRNA gene-based poultry microbiome analysis for the sample types analyzed in this study.
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MESH Headings
- Animals
- Chickens/microbiology
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/genetics
- DNA, Ribosomal/isolation & purification
- Microbiota
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/isolation & purification
- Reagent Kits, Diagnostic
- Respiratory System/microbiology
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Affiliation(s)
- Michael E. C. Abundo
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, United States of America
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - John M. Ngunjiri
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, United States of America
| | - Kara J. M. Taylor
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, United States of America
| | - Hana Ji
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, United States of America
| | - Amir Ghorbani
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, United States of America
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Mahesh K. C.
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, United States of America
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Bonnie P. Weber
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, United States of America
- Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, United States of America
| | - Chang-Won Lee
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, United States of America
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
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Engel K, Pankoke H, Jünemann S, Brandl HB, Sauer J, Griffith SC, Kalinowski J, Caspers BA. Family matters: skin microbiome reflects the social group and spatial proximity in wild zebra finches. BMC Ecol 2020; 20:58. [PMID: 33187490 PMCID: PMC7664024 DOI: 10.1186/s12898-020-00326-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 11/02/2020] [Indexed: 01/04/2023] Open
Abstract
Background So far, large numbers of studies investigating the microbiome have focused on gut microbiota and less have addressed the microbiome of the skin. Especially in avian taxa our understanding of the ecology and function of these bacteria remains incomplete. The involvement of skin bacteria in intra-specific communication has recently received attention, and has highlighted the need to understand what information is potentially being encoded in bacterial communities. Using next generation sequencing techniques, we characterised the skin microbiome of wild zebra finches, aiming to understand the impact of sex, age and group composition on skin bacteria communities. For this purpose, we sampled skin swabs from both sexes and two age classes (adults and nestlings) of 12 different zebra finch families and analysed the bacterial communities. Results Using 16S rRNA sequencing we found no effect of age, sex and family on bacterial diversity (alpha diversity). However, when comparing the composition (beta diversity), we found that animals of social groups (families) harbour highly similar bacterial communities on their skin with respect to community composition. Within families, closely related individuals shared significantly more bacterial taxa than non-related animals. In addition, we found that age (adults vs. nestlings) affected bacterial composition. Finally, we found that spatial proximity of nest sites, and therefore individuals, correlated with the skin microbiota similarity. Conclusions Birds harbour very diverse and complex bacterial assemblages on their skin. These bacterial communities are distinguishable and characteristic for intraspecific social groups. Our findings are indicative for a family-specific skin microbiome in wild zebra finches. Genetics and the (social) environment seem to be the influential factors shaping the complex bacterial communities. Bacterial communities associated with the skin have a potential to emit volatiles and therefore these communities may play a role in intraspecific social communication, e.g. via signalling social group membership.
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Affiliation(s)
- Kathrin Engel
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, Germany.
| | - Helga Pankoke
- Evonik Nutrition & Care GmbH, Kantstr. 2, 33790, Halle, Germany
| | - Sebastian Jünemann
- Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany.,Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Hanja B Brandl
- Institute of Zoology, Behavioural Biology, University of Hamburg, Martin-Luther-King Platz 3, 20146, Hamburg, Germany.,Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Jan Sauer
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, Germany
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany
| | - Barbara A Caspers
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, Germany.
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