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Ma X, Brinker E, Lea CR, Delmain D, Chamorro ED, Martin DR, Graff EC, Wang X. Evaluation of fecal sample collection methods for feline gut microbiome profiling: fecal loop vs. litter box. Front Microbiol 2024; 15:1337917. [PMID: 38800749 PMCID: PMC11127567 DOI: 10.3389/fmicb.2024.1337917] [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: 11/13/2023] [Accepted: 04/12/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Microbial population structures within fecal samples are vital for disease screening, diagnosis, and gut microbiome research. The two primary methods for collecting feline fecal samples are: (1) using a fecal loop, which retrieves a rectal sample using a small, looped instrument, and (2) using the litter box, which collects stool directly from the litter. Each method has its own advantages and disadvantages and is suitable for different research objectives. Methods and results Whole-genome shotgun metagenomic sequencing were performed on the gut microbiomes of fecal samples collected using these two methods from 10 adult cats housed in the same research facility. We evaluated the influence of collection methods on feline microbiome analysis, particularly their impact on DNA extraction, metagenomic sequencing yield, microbial composition, and diversity in subsequent gut microbiome analyses. Interestingly, fecal sample collection using a fecal loop resulted in a lower yield of microbial DNA compared to the litterbox method (p = 0.004). However, there were no significant differences between the two groups in the proportion of host contamination (p = 0.106), virus contamination (p = 0.232), relative taxonomy abundance of top five phyla (Padj > 0.638), or the number of microbial genes covered (p = 0.770). Furthermore, no significant differences were observed in alpha-diversity, beta-diversity, the number of taxa identified at each taxonomic level, and the relative abundance of taxonomic units. Discussion These two sample collection methods do not affect microbial population structures within fecal samples and collecting fecal samples directly from the litterbox within 6 hours after defecation can be considered a reliable approach for microbiome research.
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Affiliation(s)
- Xiaolei Ma
- School of Life Sciences and Technology, Tongji University, Shanghai, China
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Emily Brinker
- Department of Comparative Pathobiology, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States
| | - Christopher R. Lea
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Diane Delmain
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Erin D. Chamorro
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Douglas R. Martin
- Scott-Ritchey Research Center, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Emily C. Graff
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Scott-Ritchey Research Center, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Scott-Ritchey Research Center, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, United States
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
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Tsekouras N, Meletis E, Kostoulas P, Labronikou G, Athanasakopoulou Z, Christodoulopoulos G, Billinis C, Papatsiros VG. Detection of Enterotoxigenic Escherichia coli and Clostridia in the Aetiology of Neonatal Piglet Diarrhoea: Important Factors for Their Prevention. Life (Basel) 2023; 13:life13051092. [PMID: 37240738 DOI: 10.3390/life13051092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/13/2023] [Accepted: 04/23/2023] [Indexed: 05/28/2023] Open
Abstract
This study aimed to research the involvement of enterotoxigenic E. coli (ETEC) and C. difficile or C. perfringens type C in the aetiology of neonatal piglet diarrhoea in Greece and to identify preventive factors for them. A total of 78 pooled faecal samples were collected randomly from 234 suckling piglets (1-4 days of age) with diarrhoea from 26 pig farms (3 piglets × 3 litters × 26 farms = 234 piglets = 78 faecal pool samples). The collected samples were initially screened for the presence of E. coli and C. difficile or C. perfringens via cultivation on MacConkey and anaerobic blood agar, respectively. Subsequently, the samples were pooled on ELUTE cards. From samples tested, 69.23% of those in the farms were ETEC F4-positive, 30.77% were ETEC F5-positive, 61.54% ETEC were F6-positive, 42.31% were ETEC F4- and E. coli enterotoxin LT-positive, 19.23% were ETEC F5- and LT-positive, 42.31% were ETEC F6- and LT-positive, while LT was found in 57.69% of those in the farms. C. difficile was involved in many cases and identified as an emerging neonatal diarrhoea etiological agent. Specifically, Toxin A of C. difficile was found in 84.62% and Toxin B in 88.46% of those in the farms. Antibiotic administration to sows in combination with probiotics or acidifiers was revealed to reduce the detection of antigens of ETEC and the enterotoxin LT of E. coli.
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Affiliation(s)
- Nikolaos Tsekouras
- Clinic of Medicine, Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece
| | - Eleftherios Meletis
- Faculty of Public and Integrated Health, University of Thessaly, 43100 Karditsa, Greece
| | - Polychronis Kostoulas
- Faculty of Public and Integrated Health, University of Thessaly, 43100 Karditsa, Greece
| | | | - Zoi Athanasakopoulou
- Department of Microbiology and Parasitology, Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece
| | - Georgios Christodoulopoulos
- Department of Animal Science, Agricultural University of Athens, 75 Iera Odos Street, Botanikos, 11855 Athens, Greece
| | - Charalambos Billinis
- Faculty of Public and Integrated Health, University of Thessaly, 43100 Karditsa, Greece
- Department of Microbiology and Parasitology, Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece
| | - Vasileios G Papatsiros
- Clinic of Medicine, Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece
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Stringer OW, Bossé JT, Lacouture S, Gottschalk M, Fodor L, Angen Ø, Velazquez E, Penny P, Lei L, Langford PR, Li Y. Rapid Detection and Typing of Actinobacillus pleuropneumoniae Serovars Directly From Clinical Samples: Combining FTA ® Card Technology With Multiplex PCR. Front Vet Sci 2021; 8:728660. [PMID: 34447805 PMCID: PMC8382971 DOI: 10.3389/fvets.2021.728660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Actinobacillus pleuropneumoniae (APP), the causative agent of porcine pleuropneumonia, is highly contagious and responsible for high morbidity, mortality, and economic losses in the swine industry worldwide, but quick serotyping and diagnosis are still not widely available. In this study, we sought to validate the use of Whatman FTA® cards for collection and processing of A. pleuropneumoniae isolates, or porcine lung tissue samples, for direct use in diagnostic multiplex PCRs. We have optimized the processing of 3-mm discs punched from FTA® cards loaded with cultured A. pleuropneumoniae, or imprinted on lesioned regions of lung tissue, with only three distilled water washes before addition into our APP-multiplex PCR (mPCR) assay for rapid, low-cost identification and serotyping. DNA captured on FTA® cards generated the same diagnostic PCR results as DNA extracted using commercial kits for 85 A. pleuropneumoniae clinical isolate cultures and 22 lung samples. Additionally, bacterial DNA bound to FTA® cards was detectable by PCR after 6 months of storage at 37°C. This study provides simple, efficient, rapid, and practical sample processing for detection and molecular serotyping of A. pleuropneumoniae.
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Affiliation(s)
- Oliver W. Stringer
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Janine T. Bossé
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Sonia Lacouture
- Groupe de Recherche sur les Maladies Infectieuses en Production Animale, Faculty of Veterinary Medicine, University of Montreal, Montreal, QC, Canada
| | - Marcelo Gottschalk
- Groupe de Recherche sur les Maladies Infectieuses en Production Animale, Faculty of Veterinary Medicine, University of Montreal, Montreal, QC, Canada
| | - László Fodor
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Budapest, Hungary
| | - Øystein Angen
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | | | - Paul Penny
- Ceva Animal Health Ltd., Amersham, United Kingdom
| | - Liancheng Lei
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Paul R. Langford
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Yanwen Li
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
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