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Menard J, Bagheri S, Menon S, Yu YT, Goodman LB. Noninvasive sampling of the small intestinal chyme for microbiome, metabolome and antimicrobial resistance genes in dogs, a proof of concept. Anim Microbiome 2023; 5:64. [PMID: 38104116 PMCID: PMC10725013 DOI: 10.1186/s42523-023-00286-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND The gastrointestinal microbiome and metabolome vary greatly throughout the different segments of the gastrointestinal tract, however current knowledge of gastrointestinal microbiome and metabolome in health and disease is limited to fecal samples due to ease of sampling. The engineered Small Intestinal MicroBiome Aspiration (SIMBA™) capsule allows specific sampling of the small intestine in humans. We aimed to determine whether administration of SIMBA™ capsules to healthy beagle dogs could reliably and safely sample the small intestinal microbiome and metabolome when compared to their fecal microbiome and metabolome. RESULTS Eleven beagle dogs were used for the study. Median transit time of capsules was 29.93 h (range: 23.83-77.88). Alpha diversity, as measured by the Simpson diversity, was significantly different (P = 0.048). Shannon diversity was not different (P = 0.114). Beta diversity results showed a significant difference between capsule and fecal samples regarding Bray-Curtis, weighted and unweighted unifrac (P = 0.002) and ANOSIM distance metric s (R = 0.59, P = 0.002). In addition to observing a statistically significant difference in the microbial composition of capsules and feces, distinct variation in the metabolite profiles was seen between the sample types. Heat map analysis showed 16 compounds that were significantly different between the 2 sampling modes (adj-P value ranged between 0.004 and 0.036) with 10 metabolites more abundant in the capsule than in the feces and 6 metabolites more abundant in the feces compared to the capsules. CONCLUSIONS The engineered Small Intestinal MicroBiome Aspiration (SIMBA™) capsule was easy and safe to administer to dogs. Microbiome and metabolome analysis from the capsule samples were significantly different than that of the fecal samples and were like previously published small intestinal microbiome and metabolome composition.
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Affiliation(s)
- Julie Menard
- Department of Veterinary Diagnostic and Clinical Sciences, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.
| | - Sahar Bagheri
- International Microbiome Center, Snyder Institute for Chronic Diseases, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Y Tina Yu
- Baker Institute for Animal Health and Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Laura B Goodman
- Baker Institute for Animal Health and Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
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Li J, Cui Z, Wei M, Almutairi MH, Yan P. Omics analysis of the effect of cold normal saline stress through gastric gavage on LPS induced mice. Front Microbiol 2023; 14:1256748. [PMID: 38163070 PMCID: PMC10755949 DOI: 10.3389/fmicb.2023.1256748] [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: 07/11/2023] [Accepted: 11/13/2023] [Indexed: 01/03/2024] Open
Abstract
Cold stress is a significant environmental stimulus that negatively affects the health, production, and welfare of animals and birds. However, the specific effects of cold stimulation combined with lipopolysaccharide (LPS) on the mouse intestine remain poorly understood. Therefore, we designed this research to explore the effect of cold stimulation + LPS on mice intestine via microbiome and microbiota sequencing. Forty-eight mice were randomly divided into four experimental groups (n = 12): Control (CC), LPS-induced (CL), cold normal saline-induced (MC) and LPS + cold normal saline-induced (ML). Our results showed body weight was similar among different groups of mice. However, the body weight of mice in groups CC and CL were slightly higher compared to those in groups MC and ML. The results of gene expressions reflected that CL and ML exposure caused gut injury and barrier dysfunction, as evident by decreased ZO-1, OCCLUDIN (P < 0.01), and CASPASE-1 (P < 0.01) expression in the intestine of mice. Moreover, we found that cold stress induced oxidative stress in LPS-challenged mice by increasing malondialdehyde (MDA) accumulation and decreasing the antioxidant capacity [glutathione peroxidase (GSH-Px), superoxide dismutase (SOD), total and antioxidant capacity (T-AOC)]. The cold stress promoted inflammatory response by increased IL-1β in mice treated with cold normal saline + LPS. Whereas, microbiome sequencing revealed differential abundance in four phyla and 24 genera among the mouse groups. Metabolism analysis demonstrated the presence of 4,320 metabolites in mice, with 43 up-regulated and 19 down-regulated in CC vs. MC animals, as well as 1,046 up-regulated and 428 down-regulated in ML vs. CL animals. It is Concluded that cold stress enhances intestinal damage by disrupting the balance of gut microbiota and metabolites, while our findings contribute in improving management practices of livestock in during cold seasons.
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Affiliation(s)
- Jing Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhihao Cui
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ming Wei
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Mikhlid H. Almutairi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Peishi Yan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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Sung CH, Pilla R, Chen CC, Ishii PE, Toresson L, Allenspach-Jorn K, Jergens AE, Summers S, Swanson KS, Volk H, Schmidt T, Stuebing H, Rieder J, Busch K, Werner M, Lisjak A, Gaschen FP, Belchik SE, Tolbert MK, Lidbury JA, Steiner JM, Suchodolski JS. Correlation between Targeted qPCR Assays and Untargeted DNA Shotgun Metagenomic Sequencing for Assessing the Fecal Microbiota in Dogs. Animals (Basel) 2023; 13:2597. [PMID: 37627387 PMCID: PMC10451198 DOI: 10.3390/ani13162597] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
DNA shotgun sequencing is an untargeted approach for identifying changes in relative abundances, while qPCR allows reproducible quantification of specific bacteria. The canine dysbiosis index (DI) assesses the canine fecal microbiota by using a mathematical algorithm based on qPCR results. We evaluated the correlation between qPCR and shotgun sequencing using fecal samples from 296 dogs with different clinical phenotypes. While significant correlations were found between qPCR and sequencing, certain taxa were only detectable by qPCR and not by sequencing. Based on sequencing, less than 2% of bacterial species (17/1190) were consistently present in all healthy dogs (n = 76). Dogs with an abnormal DI had lower alpha-diversity compared to dogs with normal DI. Increases in the DI correctly predicted the gradual shifts in microbiota observed by sequencing: minor changes (R = 0.19, DI < 0 with any targeted taxa outside the reference interval, RI), mild-moderate changes (R = 0.24, 0 < DI < 2), and significant dysbiosis (R = 0.54, 0.73, and 0.91 for DI > 2, DI > 5, and DI > 8, respectively), compared to dogs with a normal DI (DI < 0, all targets within the RI), as higher R-values indicated larger dissimilarities. In conclusion, the qPCR-based DI is an effective indicator of overall microbiota shifts observed by shotgun sequencing in dogs.
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Affiliation(s)
- Chi-Hsuan Sung
- Gastrointestinal Laboratory, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-H.S.)
| | - Rachel Pilla
- Gastrointestinal Laboratory, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-H.S.)
| | - Chih-Chun Chen
- Gastrointestinal Laboratory, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-H.S.)
| | - Patricia Eri Ishii
- Gastrointestinal Laboratory, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-H.S.)
| | - Linda Toresson
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, Helsinki University, 00014 Helsinki, Finland
- Evidensia Specialist Animal Hospital, 25466 Helsingborg, Sweden
| | - Karin Allenspach-Jorn
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Albert E. Jergens
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Stacie Summers
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA
| | - Kelly S. Swanson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Holger Volk
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine, 30545 Hannover, Germany
| | - Teresa Schmidt
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine, 30545 Hannover, Germany
| | - Helene Stuebing
- Clinic of Small Animal Medicine, Ludwig-Maximilians University, 80539 Munich, Germany
| | - Johanna Rieder
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine, 30545 Hannover, Germany
| | - Kathrin Busch
- Clinic of Small Animal Medicine, Ludwig-Maximilians University, 80539 Munich, Germany
| | - Melanie Werner
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, 8057 Zurich, Switzerland
| | - Anja Lisjak
- Small Animal Clinic of Veterinary Faculty Ljubljana, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Frederic P. Gaschen
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Sara E. Belchik
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - M. Katherine Tolbert
- Gastrointestinal Laboratory, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-H.S.)
| | - Jonathan A. Lidbury
- Gastrointestinal Laboratory, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-H.S.)
| | - Joerg M. Steiner
- Gastrointestinal Laboratory, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-H.S.)
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-H.S.)
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Jugan MC, KuKanich K, Freilich L. Clinical response in dogs with acute hemorrhagic diarrhea syndrome following randomized probiotic treatment or fecal microbiota transplant. Front Vet Sci 2023; 10:1050538. [PMID: 36816181 PMCID: PMC9932283 DOI: 10.3389/fvets.2023.1050538] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023] Open
Abstract
Probiotics and fecal microbiota transplants (FMTs) are two microbiome-targeted therapies that have been investigated for use in gastrointestinal diseases associated with dysbiosis. The aim of this study was to compare the effects of an oral multi-strain probiotic and enema-administered FMTs on clinical signs and serum lipopolysaccharide in dogs with acute hemorrhagic diarrhea syndrome (AHDS). A total of 18 client-owned dogs with a diagnosis of AHDS were enrolled in a randomized, blinded study at the time of hospital admission. The dogs were randomized into two groups: the probiotic group received a daily oral probiotic (200 × 109 CFU/10kg q 24 h) for 14 days and a single sham enema; the FMT group received a single FMT via retention enema (10 mL/kg) and placebo oral capsule for 14 days. All dogs received concurrent standard-of-care therapy, including intravenous fluids and anti-emetics; no dogs received antimicrobials. The fecal score, disease severity scores, and serum lipopolysaccharide were measured on days 0, 3, and 14. Fourteen of eighteen enrolled dogs completed the study (n = 9 probiotics; n = 5 FMT). Lipopolysaccharide decreased on days 3 and 14 from baseline and correlated with fecal and disease severity scores. There was no difference in the duration or severity of clinical signs in dogs with AHDS following an enema-administered FMT compared to probiotic treatment. Further evaluation of serum lipopolysaccharide as a marker of disease severity and recovery is warranted.
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Effects of Canine-Obtained Lactic-Acid Bacteria on the Fecal Microbiota and Inflammatory Markers in Dogs Receiving Non-Steroidal Anti-Inflammatory Treatment. Animals (Basel) 2022; 12:ani12192519. [PMID: 36230259 PMCID: PMC9558503 DOI: 10.3390/ani12192519] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 11/17/2022] Open
Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) may cause enteropathy in dogs and probiotics may be one option to prevent this. The objective of this study was to determine whether the administration of canine-obtained lactic acid bacteria (LAB) has an effect on the frequency of diarrhea, the composition of the fecal microbiota, and/or markers of gastrointestinal inflammation in dogs receiving NSAIDs when compared to dogs given NSAIDs and a placebo. A total of 22 dogs treated with NSAIDs for various clinical indications were enrolled in a seven-day randomized, double-blinded placebo-controlled interventional study. Dogs were randomized to receive either placebo or LAB, a product containing Limosilactobacillus fermentum, Lacticaseibacillus rhamnosus, and Lactiplantibacillus plantarum. Fecal samples were collected on days one and seven. The fecal microbiota was evaluated using the fecal dysbiosis index (DI) and individual bacterial taxa. Fecal calprotectin (CP) and S100A12/Calgranulin C concentrations were used as markers of gastrointestinal inflammation. There was a difference in frequency of diarrhea between groups, with it affecting 4/12 dogs (33%) in the placebo group and 1/10 dogs (10%) in the LAB group, but this difference did not reach statistical significance (p = 0.32). There was a correlation between S100A12 and CP (p < 0.001), and Clostridium perfringens correlated with S100A12 (p < 0.015). Neither treatment significantly affected S100A12 (p = 0.37), CP (p = 0.12), or fecal DI (p = 0.65). This study suggests that LAB is a safe supplement to use for short-term treatment in NSAID-treated dogs, but further studies are needed to determine its potential to prevent NSAID-induced enteropathy in dogs.
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