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Skopkó BE, Homoki JR, Fazekas MÉ, Paholcsek M, Fauszt P, Dávid P, Stündl L, Molnár PB, Forgács IN, Váradi J, Bágyi KÁ, Remenyik J. Changes in the Composition of Unstimulated and Stimulated Saliva Due to Chewing Sour Cherry Gum and a Toothbrush Change. Cells 2024; 13:251. [PMID: 38334643 PMCID: PMC10854574 DOI: 10.3390/cells13030251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/17/2023] [Accepted: 11/29/2023] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Our previous studies demonstrated that sour cherry anthocyanins (AC) reduce the salivary count of Streptococcus mutans and inhibit salivary amylase activity within 30 minutes after chewing AC gum. AC gum and changing toothbrushes after scaling reduced the Gram-negative species in the unstimulated salivary microbiota. The present study examined the effect of AC gums on salivary factors, including changes in microbiome. METHODS The study was conducted over three weeks with two groups; young adults (18-30) and adults (30-45). Ten participants changed their toothbrushes, while the other 10 participants did not change after the control period. After scaling, all participants received three doses of AC gum daily. The salivary mRNA and protein levels of cytokines, mucins, melatonin, and the microbiota of unstimulated and stimulated saliva were determined by polymerase chain reaction, enzyme-linked immunosorbent assay, and 16S rRNA gene sequencing. RESULTS Significantly higher levels of tumor necrosis factor α (TNFα), interleukin-1β (IL-1β), mucin5B (MUC5B), mucin7 (MUC7), and melatonin were detected in stimulated saliva. Correlation analysis of these factors with the microbiota showed positive correlations with the genera Lachnospiraceae, Eikenella, Saccharibacteria_(TM7), Streptococcus, Prevotella, and Haemophilus. CONCLUSIONS AC chewing gum has a beneficial effect on the composition of the oral microbiome, and toothbrush replacement leads to changes in the levels of salivary pro-inflammatory cytokines.
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Affiliation(s)
- Boglárka Emese Skopkó
- Department of Dentoalveolar Surgery, Faculty of Dentistry, University of Debrecen, 4032 Debrecen, Hungary;
| | - Judit Rita Homoki
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary (M.É.F.); (M.P.); (P.D.); (L.S.); (P.B.M.); (I.N.F.)
| | - Mónika Éva Fazekas
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary (M.É.F.); (M.P.); (P.D.); (L.S.); (P.B.M.); (I.N.F.)
| | - Melinda Paholcsek
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary (M.É.F.); (M.P.); (P.D.); (L.S.); (P.B.M.); (I.N.F.)
| | - Péter Fauszt
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary (M.É.F.); (M.P.); (P.D.); (L.S.); (P.B.M.); (I.N.F.)
| | - Péter Dávid
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary (M.É.F.); (M.P.); (P.D.); (L.S.); (P.B.M.); (I.N.F.)
| | - László Stündl
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary (M.É.F.); (M.P.); (P.D.); (L.S.); (P.B.M.); (I.N.F.)
| | - Piroska Bíróné Molnár
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary (M.É.F.); (M.P.); (P.D.); (L.S.); (P.B.M.); (I.N.F.)
| | - Ildikó Noémi Forgács
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary (M.É.F.); (M.P.); (P.D.); (L.S.); (P.B.M.); (I.N.F.)
| | - Judit Váradi
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary;
| | - Kinga Ágnes Bágyi
- Department of Operative Dentistry and Endodontics, Faculty of Dentistry, University of Debrecen, 4032 Debrecen, Hungary;
| | - Judit Remenyik
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary (M.É.F.); (M.P.); (P.D.); (L.S.); (P.B.M.); (I.N.F.)
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2
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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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3
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Zakaria ND, Hamzah HH, Salih IL, Balakrishnan V, Abdul Razak K. A Review of Detection Methods for Vancomycin-Resistant Enterococci (VRE) Genes: From Conventional Approaches to Potentially Electrochemical DNA Biosensors. BIOSENSORS 2023; 13:294. [PMID: 36832060 PMCID: PMC9954664 DOI: 10.3390/bios13020294] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/24/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Vancomycin-resistant Enterococci (VRE) genes are bacteria strains generated from Gram-positive bacteria and resistant to one of the glycopeptides antibiotics, commonly, vancomycin. VRE genes have been identified worldwide and exhibit considerable phenotypic and genotypic variations. There are six identified phenotypes of vancomycin-resistant genes: VanA, VanB, VanC, VanD, VanE, and VanG. The VanA and VanB strains are often found in the clinical laboratory because they are very resistant to vancomycin. VanA bacteria can pose significant issues for hospitalized patients due to their ability to spread to other Gram-positive infections, which changes their genetic material to increase their resistance to the antibiotics used during treatment. This review summarizes the established methods for detecting VRE strains utilizing traditional, immunoassay, and molecular approaches and then focuses on potential electrochemical DNA biosensors to be developed. However, from the literature search, no information was reported on developing electrochemical biosensors for detecting VRE genes; only the electrochemical detection of vancomycin-susceptible bacteria was reported. Thus, strategies to create robust, selective, and miniaturized electrochemical DNA biosensor platforms to detect VRE genes are also discussed.
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Affiliation(s)
- Nor Dyana Zakaria
- Nanobiotechnology Research and Innovation (NanoBRI), Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
| | - Hairul Hisham Hamzah
- School of Chemical Sciences, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
| | - Ibrahim Luqman Salih
- School of Chemical Sciences, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
| | - Venugopal Balakrishnan
- Nanobiotechnology Research and Innovation (NanoBRI), Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
| | - Khairunisak Abdul Razak
- Nanobiotechnology Research and Innovation (NanoBRI), Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
- School of Materials and Mineral Resources Engineering, Universiti Sains Malaysia, Nibong Tebal 14300, Penang, Malaysia
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4
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Skopkó B, Paholcsek M, Szilágyi-Rácz A, Fauszt P, Dávid P, Stündl L, Váradi J, Kovács R, Bágyi K, Remenyik J. High-Throughput Sequencing Analysis of the Changes in the Salivary Microbiota of Hungarian Young and Adult Subpopulation by an Anthocyanin Chewing Gum and Toothbrush Change. Dent J (Basel) 2023; 11:dj11020044. [PMID: 36826189 PMCID: PMC9954944 DOI: 10.3390/dj11020044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/23/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
The sour cherry contains anthocyanins, which have bactericide action against some oral bacteria (Klebsiella pneumoniae, Pseudomonas aeruginosa). Sour cherry also has antibiofilm action against Streptococcus mutans, Candida albicans, and Fusobacterium nucleatum. Our earlier research proved that chewing sour cherry anthocyanin gum significantly reduces the amount of human salivary alpha-amylase and Streptococcus mutans levels. The microbiota of a toothbrush affects oral health and regular toothbrush change is recommended. A total of 20 healthy participants were selected for the study. We analysed saliva samples with 16S rRNA sequencing to investigate the effect of 2 weeks (daily three times, after main meals) of chewing sour cherry anthocyanin gum-supplemented by toothbrush change in half of our case-control study cohort-after scaling on human oral microbiota. A more stable and diverse microbiome could be observed after scaling by the anthocyanin gum. Significant differences between groups (NBR: not toothbrush changing; BR: toothbrush changing) were evaluated by log2 proportion analysis of the most abundant family and genera. The analysis showed that lower level of some Gram-negative anaerobic (Prevotella melaninogenica, Porphyromonas pasteri, Fusobacterium nucleatum subsp. vincentii) and Gram-positive (Rothia mucilaginosa) bacteria could be observed in the case group (BR), accompanied by build-up of health-associated Streptococcal network connections.
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Affiliation(s)
- Boglárka Skopkó
- Department of Dentoalveolar Surgery, Faculty of Dentistry, University of Debrecen, 4032 Debrecen, Hungary
| | - Melinda Paholcsek
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary
| | - Anna Szilágyi-Rácz
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary
| | - Péter Fauszt
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary
| | - Péter Dávid
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary
| | - László Stündl
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary
| | - Judit Váradi
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary
| | - Renátó Kovács
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Kinga Bágyi
- Department of Operative Dentistry and Endodontics, Faculty of Dentistry, University of Debrecen, 4032 Debrecen, Hungary
| | - Judit Remenyik
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: ; Tel.: +36-52-508-444 (ext. 62310)
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Kifaro EG, Kim MJ, Jung S, Jang YH, Moon S, Lee DH, Song CS, Misinzo G, Kim SK. Microparticles as Viral RNA Carriers from Stool for Stable and Sensitive Surveillance. Diagnostics (Basel) 2023; 13:diagnostics13020261. [PMID: 36673071 PMCID: PMC9857651 DOI: 10.3390/diagnostics13020261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/29/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Since its discovery, polymerase chain reaction (PCR) has emerged as an important technology for the diagnosis and identification of infectious diseases. It is a highly sensitive and reliable nucleic acids (NA) detection tool for various sample types. However, stool, which carries the most abundant micro-organisms and physiological byproducts, remains to be the trickiest clinical specimen for molecular detection of pathogens. Herein, we demonstrate the novel application of hydrogel microparticles as carriers of viral RNA from stool samples without prior RNA purification for real-time polymerase chain reaction (qPCR). In each microparticle of primer-incorporated network (PIN) as a self-sufficient reaction compartment, immobilized reverse transcription (RT) primers capture the viral RNA by hybridization and directly initiate RT of RNA to generate a pool of complementary DNA (PIN-cDNA pool). Through a simple operation with a portable thermostat device, a PIN-cDNA pool for influenza A virus (IAV) was obtained in 20 min. The PIN-cDNA pools can be stored at room temperature, or directly used to deliver cDNA templates for qPCR. The viral cDNA templates were freely released in the subsequent qPCR to allow amplification efficiency of over 91%. The assay displayed good linearity, repeatability, and comparable limit of detection (LoD) with a commercialized viral RNA purification kit. As a proof of concept, this technology carries a huge potential for onsite application to improve human and animal infectious disease surveillance activities using stool samples without the need for a laboratory or centrifuge for sample preparation.
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Affiliation(s)
- Emmanuel George Kifaro
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Department of Veterinary Microbiology, Parasitology, and Biotechnology, Sokoine University of Agriculture (SUA), Morogoro P.O. Box 3019, Tanzania
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture (SUA), Morogoro P.O. Box 3297, Tanzania
| | - Mi Jung Kim
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Seungwon Jung
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Yoon-ha Jang
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Sungyeon Moon
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Dong-Hun Lee
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Chang-Seon Song
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Gerald Misinzo
- Department of Veterinary Microbiology, Parasitology, and Biotechnology, Sokoine University of Agriculture (SUA), Morogoro P.O. Box 3019, Tanzania
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture (SUA), Morogoro P.O. Box 3297, Tanzania
| | - Sang Kyung Kim
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Republic of Korea
- Correspondence:
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Lourenco JM, Welch CB. Using microbiome information to understand and improve animal performance. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2077147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Mooney JP, DonVito SM, Lim R, Keith M, Pickles L, Maguire EA, Wagner-Gamble T, Oldfield T, Bermejo Pariente A, Ehimiyien AM, Philbey AA, Bottomley C, Riley EM, Thompson J. Intestinal inflammation and increased intestinal permeability in Plasmodium chabaudi AS infected mice. Wellcome Open Res 2022; 7:134. [PMID: 36408291 PMCID: PMC9647155 DOI: 10.12688/wellcomeopenres.17781.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Gastrointestinal symptoms are commonly associated with acute Plasmodium spp infection. Malaria-associated enteritis may provide an opportunity for enteric pathogens to breach the intestinal mucosa, resulting in life-threatening systemic infections. Methods: To investigate whether intestinal pathology also occurs during infection with a murine model of mild and resolving malaria, C57BL/6J mice were inoculated with recently mosquito-transmitted Plasmodium chabaudi AS. At schizogony, intestinal tissues were collected for quantification and localisation of immune mediators and malaria parasites, by PCR and immunohistochemistry. Inflammatory proteins were measured in plasma and faeces and intestinal permeability was assessed by FITC-dextran translocation after oral administration. Results: Parasitaemia peaked at approx. 1.5% at day 9 and resolved by day 14, with mice experiencing significant and transient anaemia but no weight loss. Plasma IFN-γ, TNF-α and IL10 were significantly elevated during peak infection and quantitative RT-PCR of the intestine revealed a significant increase in transcripts for ifng and cxcl10. Histological analysis revealed parasites within blood vessels of both the submucosa and intestinal villi and evidence of mild crypt hyperplasia. In faeces, concentrations of the inflammatory marker lactoferrin were significantly raised on days 9 and 11 and FITC-dextran was detected in plasma on days 7 to 14. At day 11, plasma FITC-dextran concentration was significantly positively correlated with peripheral parasitemia and faecal lactoferrin concentration. Conclusions: In summary, using a relevant, attenuated model of malaria, we have found that acute infection is associated with intestinal inflammation and increased intestinal permeability. This model can now be used to explore the mechanisms of parasite-induced intestinal inflammation and to assess the impact of increased intestinal permeability on translocation of enteropathogens.
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Affiliation(s)
- Jason P Mooney
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
| | - Sophia M DonVito
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
| | - Rivka Lim
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
| | - Marianne Keith
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Lia Pickles
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
| | - Eleanor A Maguire
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
| | - Tara Wagner-Gamble
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
| | - Thomas Oldfield
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
| | - Ana Bermejo Pariente
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK.,Editorial Team, F1000 Ltd., London, UK
| | - Ajoke M Ehimiyien
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK.,Department of Veterinary Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - Adrian A Philbey
- Easter Bush Pathology, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom., Edinburgh, EH25 9RG, UK
| | - Christian Bottomley
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Eleanor M Riley
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
| | - Joanne Thompson
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
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8
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Mooney JP, DonVito SM, Lim R, Keith M, Pickles L, Maguire EA, Wagner-Gamble T, Oldfield T, Bermejo Pariente A, Ehimiyein AM, Philbey AA, Bottomley C, Riley EM, Thompson J. Intestinal inflammation and increased intestinal permeability in Plasmodium chabaudi AS infected mice. Wellcome Open Res 2022; 7:134. [PMID: 36408291 PMCID: PMC9647155 DOI: 10.12688/wellcomeopenres.17781.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Gastrointestinal symptoms are commonly associated with acute Plasmodium spp infection. Malaria-associated enteritis may provide an opportunity for enteric pathogens to breach the intestinal mucosa, resulting in life-threatening systemic infections. Methods: To investigate whether intestinal pathology also occurs during infection with a murine model of mild and resolving malaria, C57BL/6J mice were inoculated with recently mosquito-transmitted Plasmodium chabaudi AS. At schizogony, intestinal tissues were collected for quantification and localisation of immune mediators and malaria parasites, by PCR and immunohistochemistry. Inflammatory proteins were measured in plasma and faeces and intestinal permeability was assessed by FITC-dextran translocation after oral administration. Results: Parasitaemia peaked at approx. 1.5% at day 9 and resolved by day 14, with mice experiencing significant and transient anaemia but no weight loss. Plasma IFNγ, TNFα and IL10 were significantly elevated during peak infection and quantitative RT-PCR of the intestine revealed a significant increase in transcripts for ifng and cxcl10. Histological analysis revealed parasites within blood vessels of both the submucosa and intestinal villi and evidence of mild crypt hyperplasia. In faeces, concentrations of the inflammatory marker lactoferrin were significantly raised on days 9 and 11 and FITC-dextran was detected in plasma on days 7 to 14. At day 11, plasma FITC-dextran concentration was significantly positively correlated with peripheral parasitemia and faecal lactoferrin concentration. Conclusions: In summary, using a relevant, attenuated model of malaria, we have found that acute infection is associated with intestinal inflammation and increased intestinal permeability. This model can now be used to explore the mechanisms of parasite-induced intestinal inflammation and to assess the impact of increased intestinal permeability on translocation of enteropathogens.
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Affiliation(s)
- Jason P Mooney
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
| | - Sophia M DonVito
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
| | - Rivka Lim
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
| | - Marianne Keith
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Lia Pickles
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
| | - Eleanor A Maguire
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
| | - Tara Wagner-Gamble
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
| | - Thomas Oldfield
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
| | - Ana Bermejo Pariente
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK.,Editorial Team, F1000 Ltd., London, UK
| | - Ajoke M Ehimiyein
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK.,Department of Veterinary Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - Adrian A Philbey
- Easter Bush Pathology, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom., Edinburgh, EH25 9RG, UK
| | - Christian Bottomley
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Eleanor M Riley
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
| | - Joanne Thompson
- Institute of Immunology and Infection Research, University of Ediburgh, Edinburgh, Midlothian, EH93JT, UK
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Maixner F, Mitterer C, Jäger HY, Sarhan MS, Valverde G, Lücker S, Piombino‐Mascali D, Szikossy I, Molnár E, Pálfi G, Pap I, Cipollini G, Zink A. Linear polyacrylamide is highly efficient in precipitating and purifying environmental and ancient DNA. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Frank Maixner
- Institute for Mummy Studies Eurac Research Bolzano Italy
| | | | - Heidi Y. Jäger
- Institute for Mummy Studies Eurac Research Bolzano Italy
| | | | - Guido Valverde
- Institute for Mummy Studies Eurac Research Bolzano Italy
| | - Sebastian Lücker
- Department of Microbiology IWWR Radboud University Nijmegen the Netherlands
| | - Dario Piombino‐Mascali
- Department of Anatomy, Histology and Anthropology Faculty of Medicine Vilnius University Vilnius Lithuania
| | - Ildikó Szikossy
- Department of Anthropology Hungarian Natural History Museum Budapest Hungary
| | - Erika Molnár
- Department of Biological Anthropology University of Szeged Szeged Hungary
| | - György Pálfi
- Department of Biological Anthropology University of Szeged Szeged Hungary
| | - Ildikó Pap
- Department of Anthropology Hungarian Natural History Museum Budapest Hungary
| | | | - Albert Zink
- Institute for Mummy Studies Eurac Research Bolzano Italy
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10
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Bindari YR, Gerber PF. Centennial Review: Factors affecting the chicken gastrointestinal microbial composition and their association with gut health and productive performance. Poult Sci 2021; 101:101612. [PMID: 34872745 PMCID: PMC8713025 DOI: 10.1016/j.psj.2021.101612] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 02/08/2023] Open
Abstract
Maintenance of "gut health" is considered a priority in commercial chicken farms, although a precise definition of what constitutes gut health and how to evaluate it is still lacking. In research settings, monitoring of gut microbiota has gained great attention as shifts in microbial community composition have been associated with gut health and productive performance. However, microbial signatures associated with productivity remain elusive because of the high variability of the microbiota of individual birds resulting in multiple and sometimes contradictory profiles associated with poor or high performance. The high costs associated with the testing and the need for the terminal sampling of a large number of birds for the collection of gut contents also make this tool of limited use in commercial settings. This review highlights the existing literature on the chicken digestive system and associated microbiota; factors affecting the gut microbiota and emergence of the major chicken enteric diseases coccidiosis and necrotic enteritis; methods to evaluate gut health and their association with performance; main issues in investigating chicken microbial populations; and the relationship of microbial profiles and production outcomes. Emphasis is given to emerging noninvasive and easy-to-collect sampling methods that could be used to monitor gut health and microbiological changes in commercial flocks.
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Affiliation(s)
- Yugal Raj Bindari
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Priscilla F Gerber
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia.
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11
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Manzari C, Oranger A, Fosso B, Piancone E, Pesole G, D'Erchia AM. Accurate quantification of bacterial abundance in metagenomic DNAs accounting for variable DNA integrity levels. Microb Genom 2021; 6. [PMID: 32749951 PMCID: PMC7660251 DOI: 10.1099/mgen.0.000417] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The quantification of the total microbial content in metagenomic samples is critical for investigating the interplay between the microbiome and its host, as well as for assessing the accuracy and precision of the relative microbial composition which can be strongly biased in low microbial biomass samples. In the present study, we demonstrate that digital droplet PCR (ddPCR) can provide accurate quantification of the total copy number of the 16S rRNA gene, the gene usually exploited for assessing total bacterial abundance in metagenomic DNA samples. Notably, using DNA templates with different integrity levels, as measured by the DNA integrity number (DIN), we demonstrated that 16S rRNA copy number quantification is strongly affected by DNA quality and determined a precise correlation between quantification underestimation and DNA degradation levels. Therefore, we propose an input DNA mass correction, according to the observed DIN value, which could prevent inaccurate quantification of 16S copy number in degraded metagenomic DNAs. Our results highlight that a preliminary evaluation of the metagenomic DNA integrity should be considered before performing metagenomic analyses of different samples, both for the assessment of the reliability of observed differential abundances in different conditions and to obtain significant functional insights.
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Affiliation(s)
- Caterina Manzari
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/D-O, 70126 Bari, Italy
| | - Annarita Oranger
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/D-O, 70126 Bari, Italy
| | - Bruno Fosso
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/D-O, 70126 Bari, Italy
| | - Elisabetta Piancone
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/D-O, 70126 Bari, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/D-O, 70126 Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Via Orabona 4, 70126 Bari, Italy
| | - Anna Maria D'Erchia
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/D-O, 70126 Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Via Orabona 4, 70126 Bari, Italy
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12
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Martínez Arbas S, Busi SB, Queirós P, de Nies L, Herold M, May P, Wilmes P, Muller EEL, Narayanasamy S. Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies. Front Genet 2021; 12:666244. [PMID: 34194470 PMCID: PMC8236828 DOI: 10.3389/fgene.2021.666244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/30/2021] [Indexed: 12/21/2022] Open
Abstract
In recent years, multi-omic studies have enabled resolving community structure and interrogating community function of microbial communities. Simultaneous generation of metagenomic, metatranscriptomic, metaproteomic, and (meta) metabolomic data is more feasible than ever before, thus enabling in-depth assessment of community structure, function, and phenotype, thus resulting in a multitude of multi-omic microbiome datasets and the development of innovative methods to integrate and interrogate those multi-omic datasets. Specifically, the application of reference-independent approaches provides opportunities in identifying novel organisms and functions. At present, most of these large-scale multi-omic datasets stem from spatial sampling (e.g., water/soil microbiomes at several depths, microbiomes in/on different parts of the human anatomy) or case-control studies (e.g., cohorts of human microbiomes). We believe that longitudinal multi-omic microbiome datasets are the logical next step in microbiome studies due to their characteristic advantages in providing a better understanding of community dynamics, including: observation of trends, inference of causality, and ultimately, prediction of community behavior. Furthermore, the acquisition of complementary host-derived omics, environmental measurements, and suitable metadata will further enhance the aforementioned advantages of longitudinal data, which will serve as the basis to resolve drivers of community structure and function to understand the biotic and abiotic factors governing communities and specific populations. Carefully setup future experiments hold great potential to further unveil ecological mechanisms to evolution, microbe-microbe interactions, or microbe-host interactions. In this article, we discuss the challenges, emerging strategies, and best-practices applicable to longitudinal microbiome studies ranging from sampling, biomolecular extraction, systematic multi-omic measurements, reference-independent data integration, modeling, and validation.
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Affiliation(s)
- Susana Martínez Arbas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Susheel Bhanu Busi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Pedro Queirós
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laura de Nies
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Malte Herold
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Emilie E. L. Muller
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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13
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Guo L, He J, Zhang J, Zhang X, Zhang D, Zhou L, Yuan Y, Fu S, Qiu Y, Ye C, Liu Y, Wu Z, Hu CAA. Baicalin-Aluminum Modulates the Broiler Gut Microbiome. DNA Cell Biol 2021; 40:881-894. [PMID: 33945308 DOI: 10.1089/dna.2021.0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Baicalin-aluminum regulates the gut microbiome of piglets with diarrhea. However, whether it affects poultry gut microbiome composition and function remains unknown. In this study, we used metagenomic sequencing to explore the effects of baicalin-aluminum on gut microbiome changes in poultry when compared with animals administered colistin sulfate. Our data showed that important gut microbiome components consisted of Ruminococcaceae, Subdoligranulum, Bifidobacterium, Bifidobacterium pseudolongum, and Pseudoflavonifractor when broilers were administered baicalin-aluminum compared with colistin. At the species level, Lactobacillus salivarius, Bacteroides uniformis, Oscillibacter unclassified, Bacteroides fragilis, Ruminococcus torques, and Subdoligranulum unclassified abundance were significantly upregulated upon baicalin-aluminum treatment when compared with colistin administration. In addition, Gene Ontology (GO) enrichment analysis indicated that functional differentially expressed genes, which were in the top 30 GO enrichment terms, were associated with metabolic processes, catalytic activity, and cellular processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that ABC transporters, oxidative phosphorylation, and phosphotransferase systems were the dominant signaling pathways in the baicalin-aluminum group when compared with the colistin group. Taken together, our data indicated that baicalin-aluminum modified broiler gut microbiome composition. These observations enhance our physiological insights of baicalin-aluminum-mediated functions in the broiler microbiome and potentially provide a novel therapy to manage both animal and human health.
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Affiliation(s)
- Ling Guo
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Jing He
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Jiacheng Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Xiaofang Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Dan Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Linglu Zhou
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Yuzhen Yuan
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Shulin Fu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Yinsheng Qiu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Chun Ye
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Yu Liu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Zhongyuan Wu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, P.R. China
| | - Chien-An Andy Hu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, P.R. China.,Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
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14
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Pascoal F, Costa R, Magalhães C. The microbial rare biosphere: current concepts, methods and ecological principles. FEMS Microbiol Ecol 2021; 97:5974270. [PMID: 33175111 DOI: 10.1093/femsec/fiaa227] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/06/2020] [Indexed: 01/04/2023] Open
Abstract
Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.
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Affiliation(s)
- Francisco Pascoal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Rodrigo Costa
- Department of Bioengineering, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais 1049-001, Lisbon, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.,U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, CA 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, CA 94720 Berkeley, USA
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,School of Science, University of Waikato, Gate 1, Knighton Road 3240, Hamilton, New Zealand.,Ocean Frontier Institute, Dalhousie University, Steele Ocean Sciences Building, Dalhousie University 1355 Oxford St., B3H4R2 Halifax, NS, Canada
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15
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Wegl G, Grabner N, Köstelbauer A, Klose V, Ghanbari M. Toward Best Practice in Livestock Microbiota Research: A Comprehensive Comparison of Sample Storage and DNA Extraction Strategies. Front Microbiol 2021; 12:627539. [PMID: 33708184 PMCID: PMC7940207 DOI: 10.3389/fmicb.2021.627539] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/01/2021] [Indexed: 11/24/2022] Open
Abstract
Understanding the roles of microorganisms in the animal gastrointestinal microenvironment is highly important for the development of effective strategies to manage and manipulate these microbial communities. In order to guide future animal gut microbiota research projects and standardization efforts, we have conducted a systematic comparison of 10 currently used sample preservation and DNA extraction approaches for pig and chicken microbiota samples and quantified their effects on bacterial DNA yield, quality, integrity, and on the resulting sequence-based bacterial composition estimates. The results showed how key stages of conducting a microbiota study, including the sample storage and DNA extraction, can substantially affect DNA recovery from the microbial community, and therefore, biological interpretation in a matrix-dependent manner. Our results highlight the fact that the influence of storage and extraction methods on the resulting microbial community structure differed by sample type, even within the same species. As the effects of these technical steps are potentially large compared with the real biological variability to be explained, standardization is crucial for accelerating progress in the area of livestock microbiota research. This study provided a framework to assist future animal gut microbiota research projects and standardization efforts.
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16
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Abstract
Effects of nutraceuticals on the intestinal microbiota are receiving increased attention; however, there are few studies investigating their effects on broiler meat production. The aim of this study was to implement feeding strategies and carry out a comprehensive trial examining the interplay between natural biologically active compounds such as carotenoids, anthocyanins, fermentable oligosaccharides, and synbiotics and the gastrointestinal tract microbiota. Our feeding program was applied to an intensive production system with a flock of 1,080 Ross 308 broilers. Aging induced significant changes through the feeding experiment. Nutraceuticals were shown to modulate broiler intestinal diversity and differentially enriched Lactobacillus, Enterococcus, Campylobacter, and Streptococcus in the core microbiome during the different stages of broiler rearing. Additionally, they did not remarkably affect animal growth performance; nevertheless, a positive correlation was found between body weight and Corynebacteriales and Pseudomonadales. Furthermore, a diet high in carotenoid, fermentable oligosaccharide, and anthocyanin contents affected the number of beneficial genera such as Faecalibacterium, Lactobacillus, Blautia, and Ruminococcus. With this comprehensive trial, we revealed that nutraceuticals induced modulations in broiler gastrointestinal tract microbiota. We believe that plant-derived immunostimulants, recycled from plant food waste products, can supplement antibiotic-free broiler meat production. IMPORTANCE In this trial, nutraceuticals were manufactured from waste products of food industry processing of Hungarian red sweet pepper and sour cherry and incorporated into the diet of poultry to investigate their effects on broilers’ growth and the broiler gastrointestinal tract microbiota. To avoid the generation of food waste products, we believe that this approach can be developed into a sustainable, green approach that can be implemented in commercial antibiotic-free poultry to provide safe and high-quality meat.
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