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Tong Q, Liu XN, Hu ZF, Ding JF, Bie J, Wang HB, Zhang JT. Effects of Captivity and Season on the Gut Microbiota of the Brown Frog ( Rana dybowskii). Front Microbiol 2019; 10:1912. [PMID: 31507549 PMCID: PMC6716059 DOI: 10.3389/fmicb.2019.01912] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/05/2019] [Indexed: 12/14/2022] Open
Abstract
The gut microbiota of amphibians is affected by exogenous and endogenous factors. We performed a comprehensive analysis using high-throughput sequencing technology and functional predictions and observed general changes in the gut microbiota of frogs in different growth stages, seasons, and growth environments. There were no significant differences in microbial richness and diversity between juvenile and adult wild frogs, between the summer and autumn groups of captive frogs, or between wild and captive frogs. There were significant differences in the gut microbiota community structure of Rana dybowskii between the summer and autumn groups of captive frogs and between wild and captive R. dybowskii, whereas the differences between juvenile and adult wild frogs were not significant. The dominant gut bacterial phyla in frogs from both captive and wild environments included Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Linear discriminant effect size (LEfSe) analysis showed that Bacteroidetes and Firmicutes were significantly enriched in captive and wild R. dybowskii, respectively linear discriminant analysis (LDA > 4). The core operational taxonomical units (OTUs) that were found in >90% of all frogs tested encompassed 15 core OTUs. The captive frogs exhibited 15 core OTUs in addition to the above overall core microbiota, whereas the wild frogs exhibited 19 core OTUs in addition to the above overall core microbiota. Predictions made using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) suggested that eleven KEGG pathways, such as infectious diseases, immune system diseases, metabolism, metabolism of other amino acids, metabolism of cofactors and vitamins, metabolism of terpenoids and polyketides, neurodegenerative diseases, and transport and catabolism, were enriched in captive frogs. The relative abundance of several red-leg-syndrome-related pathogens increased significantly in captive frogs compared with that in wild frogs. To our knowledge, this is the first study on the effects of individual seasons and captivity on the gut microbiota of frogs.
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Affiliation(s)
- Qing Tong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xiao-Ning Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Zong-Fu Hu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jia-Feng Ding
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jia Bie
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Hong-Bin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jian-Tao Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
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Sandri M, Sgorlon S, Conte G, Serra A, Dal Monego S, Stefanon B. Substitution of a commercial diet with raw meat complemented with vegetable foods containing chickpeas or peas affects faecal microbiome in healthy dogs. ITALIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1080/1828051x.2019.1645624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Misa Sandri
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali,, University of Udine, Udine, Italy
| | - Sandy Sgorlon
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali,, University of Udine, Udine, Italy
| | - Giuseppe Conte
- Dipartimento di Scienze agrarie, Alimentari e Agro-Ambientali, University of Pisa, Pisa, Italy
| | - Andrea Serra
- Dipartimento di Scienze agrarie, Alimentari e Agro-Ambientali, University of Pisa, Pisa, Italy
| | - Simeone Dal Monego
- Cluster in Biomedicine, CBM S.c.r.l, Italy Bioinformatic Services, Trieste, Italy
| | - Bruno Stefanon
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali,, University of Udine, Udine, Italy
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Vierbaum L, Eisenhauer L, Vahjen W, Zentek J. In vitro evaluation of the effects of Yucca schidigera and inulin on the fermentation potential of the faecal microbiota of dogs fed diets with low or high protein concentrations. Arch Anim Nutr 2019; 73:399-413. [PMID: 31137970 DOI: 10.1080/1745039x.2019.1616498] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
This in vitro study aimed to evaluate the effects of Yucca schidigera powder (YSP) and inulin (IN) on protein fermentation metabolites (short-chain fatty acids [SCFA] and branched-chain fatty acids, phenolic and indolic compounds, biogenic amines, ammonia and pH) by using faecal inocula from dogs fed either a low (L) or a high (H) protein diet (crude protein 201 or 377 g/kg as fed). Four treatments for each diet were evaluated in an in vitro batch culture system over 24 h: (1) control with no addition of substrates; (2) 4 g YSP/l; (3) 5 g IN/l; (4) 4 g YSP/l in combination with 5 g IN/l of faecal culture of dogs fed Diet L or H. Several changes in fermentation metabolites were analysed. Samples incubated with the faecal inocula of dogs fed Diet L produced higher concentrations of total SCFA, propionate (p = 0.001), acetate (p ≤ 0.001), d-lactate (p = 0.041) and indole (p = 0.003), whereas pH (p = 0.004) was decreased. Supplementation of IN increased the content of putrescine, d- and l-lactate, total SCFA, acetate, propionate, n-butyrate (p ≤ 0.001) and n-valerate (p = 0.003), while i-valerate, indole and pH (p ≤ 0.001) were reduced. Ammonia was lower (p = 0.013) in samples with faecal inocula from dogs fed Diet H and further reduced by the addition of IN (p ≤ 0.001). Samples with faecal inocula from dogs fed Diet L had a fewer quotient of ammonia and total SCFA (p = 0.040). Supplementation of YSP (p = 0.021), IN (p ≤ 0.001) and YSP in combination with IN (p = 0.047) led to a higher reduction of the quotient of ammonia and total SCFA. In conclusion, dietary protein concentration and the supplementation of IN resulted in a stimulation of fermentation while YSP appeared to have only minor effects.
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Affiliation(s)
| | - Laura Eisenhauer
- b Department of Veterinary Medicine, Institute of Animal Nutrition, Freie Universität Berlin , Berlin , Germany
| | - Wilfried Vahjen
- b Department of Veterinary Medicine, Institute of Animal Nutrition, Freie Universität Berlin , Berlin , Germany
| | - Jürgen Zentek
- b Department of Veterinary Medicine, Institute of Animal Nutrition, Freie Universität Berlin , Berlin , Germany
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Oral Beta-Lactamase Protects the Canine Gut Microbiome from Oral Amoxicillin-Mediated Damage. Microorganisms 2019; 7:microorganisms7050150. [PMID: 31137766 PMCID: PMC6560916 DOI: 10.3390/microorganisms7050150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 05/16/2019] [Accepted: 05/23/2019] [Indexed: 01/30/2023] Open
Abstract
Antibiotics damage the gut microbiome, which can result in overgrowth of pathogenic microorganisms and emergence of antibiotic resistance. Inactivation of antibiotics in the small intestine represents a novel strategy to protect the colonic microbiota. SYN-004 (ribaxamase) is a beta-lactamase formulated for oral delivery intended to degrade intravenously administered beta-lactam antibiotics in the gastrointestinal (GI) tract. The enteric coating of ribaxamase protects the enzyme from stomach acid and mediates pH-dependent release in the upper small intestine, the site of antibiotic biliary excretion. Clinical benefit was established in animal and human studies in which ribaxamase was shown to degrade ceftriaxone in the GI tract, thereby preserving the gut microbiome, significantly reducing Clostridioides difficile disease, and attenuating antibiotic resistance. To expand ribaxamase utility to oral beta-lactams, delayed release formulations of ribaxamase, SYN-007, were engineered to allow enzyme release in the lower small intestine, distal to the site of oral antibiotic absorption. Based on in vitro dissolution profiles, three SYN-007 formulations were selected for evaluation in a canine model of antibiotic-mediated gut dysbiosis. Dogs received amoxicillin (40 mg/kg, PO, TID) +/- SYN-007 (10 mg, PO, TID) for five days. Serum amoxicillin levels were measured after the first and last antibiotic doses and gut microbiomes were evaluated using whole genome shotgun sequence metagenomics analyses of fecal DNA prior to and after antibiotic treatment. Serum amoxicillin levels did not significantly differ +/- SYN-007 after the first dose for all SYN-007 formulations, while only one SYN-007 formulation did not significantly reduce systemic antibiotic concentrations after the last dose. Gut microbiomes of animals receiving amoxicillin alone displayed significant loss of diversity and emergence of antibiotic resistance genes. In contrast, for animals receiving amoxicillin + SYN-007, microbiome diversities were not altered significantly and the presence of antibiotic resistance genes was reduced. These data demonstrate that SYN-007 diminishes amoxicillin-mediated microbiome disruption and mitigates emergence and propagation of antibiotic resistance genes without interfering with antibiotic systemic absorption. Thus, SYN-007 has the potential to protect the gut microbiome by inactivation of beta-lactam antibiotics when administered by both oral and parenteral routes and to reduce emergence of antibiotic-resistant pathogens.
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55
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Butowski CF, Thomas DG, Young W, Cave NJ, McKenzie CM, Rosendale DI, Bermingham EN. Addition of plant dietary fibre to a raw red meat high protein, high fat diet, alters the faecal bacteriome and organic acid profiles of the domestic cat (Felis catus). PLoS One 2019; 14:e0216072. [PMID: 31042730 PMCID: PMC6493751 DOI: 10.1371/journal.pone.0216072] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/12/2019] [Indexed: 02/07/2023] Open
Abstract
Commercial diets high in animal protein and fat are increasingly being developed for pets, however little is understood about the impacts of feeding such diets to domestic cats. The carbohydrate content of these diets is typically low, and dietary fibre is often not included. Dietary fibre is believed to be important in the feline gastrointestinal tract, promoting stool formation and providing a substrate for the hindgut microbiome. Therefore, we aimed to determine the effects of adding plant-based dietary fibre to a high animal protein and fat diet. Twelve domestic short hair cats were fed three complete and balanced diets in a cross-over design for blocks of 21 days: raw meat (Raw), raw meat plus fibre (2%, ‘as is’ inclusion of inulin and cellulose; Raw+Fibre) and a commercially available Kibble diet. A commercially available canned diet was fed for 21 days as a washout phase. Apparent macronutrient digestibility, faecal output, score, pH, organic acid concentrations and bacteriome profiles were determined. Diet significantly affected all faecal parameters measured. The addition of dietary fibre to the raw meat diet was found to reduce apparent macronutrient digestibility, increase faecal output, pH and score. Thirty one bacterial taxa were significantly affected by diet. Prevotella was found to dominate in the Kibble diet, Clostridium and Fusobacterium in the Raw diet, and Prevotella and a group of unclassified Peptostreptococcaceae in the Raw+Fibre diet. Our results show that diets of different macronutrient proportions can strongly influence the faecal microbiome composition and metabolism, as shown by altered organic acid concentrations and faecal pH, in the domestic cat. The addition of 2% of each fibre to the Raw diet shifted faecal parameters closer to those produced by feeding a Kibble diet. These results provide a basis for further research assessing raw red meat diets to domestic cats.
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Affiliation(s)
- Christina F Butowski
- Food & Bio-based Products, AgResearch Grasslands, Palmerston North, New Zealand.,Centre for Feline Nutrition, Massey University, Palmerston North, New Zealand
| | - David G Thomas
- Centre for Feline Nutrition, Massey University, Palmerston North, New Zealand
| | - Wayne Young
- Food & Bio-based Products, AgResearch Grasslands, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand.,High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Nick J Cave
- Centre for Feline Nutrition, Massey University, Palmerston North, New Zealand
| | | | - Douglas I Rosendale
- The New Zealand Institute for Plant & Food Research Ltd., Palmerston North, New Zealand
| | - Emma N Bermingham
- Food & Bio-based Products, AgResearch Grasslands, Palmerston North, New Zealand.,High-Value Nutrition National Science Challenge, Auckland, New Zealand
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56
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Yang X, He F, Zhang Y, Xue J, Li K, Zhang X, Zhu L, Wang Z, Wang H, Yang S. Inulin Ameliorates Alcoholic Liver Disease via Suppressing LPS-TLR4-Mψ
Axis and Modulating Gut Microbiota in Mice. Alcohol Clin Exp Res 2019; 43:411-424. [PMID: 30589437 DOI: 10.1111/acer.13950] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 12/17/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Xiaoli Yang
- Clinical Medical College; Ningxia Medical University; Yinchuan Ningxia China
- Department of Gastroenterology; General Hospital of Ningxia Medical University; Yinchuan Ningxia China
| | - Fang He
- Department of Gastroenterology; General Hospital of Ningxia Medical University; Yinchuan Ningxia China
| | - Yanting Zhang
- Department of Gastroenterology; General Hospital of Ningxia Medical University; Yinchuan Ningxia China
| | - Jing Xue
- Department of Pathogenic Biology and Medical Immunology; School of Basic Medical Sciences; Ningxia Medical University; Yinchuan Ningxia China
| | - Ke Li
- Clinical Medical College; Ningxia Medical University; Yinchuan Ningxia China
| | - Xiaoxia Zhang
- College of Traditional Chinese Medicine; Ningxia Medical University; Yinchuan Ningxia China
| | - Lili Zhu
- Department of Pathogenic Biology and Medical Immunology; School of Basic Medical Sciences; Ningxia Medical University; Yinchuan Ningxia China
| | - Zhen Wang
- Clinical Medical College; Ningxia Medical University; Yinchuan Ningxia China
| | - Hao Wang
- Department of Pathogenic Biology and Medical Immunology; School of Basic Medical Sciences; Ningxia Medical University; Yinchuan Ningxia China
| | - Shaoqi Yang
- Department of Gastroenterology; General Hospital of Ningxia Medical University; Yinchuan Ningxia China
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57
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Bresciani F, Minamoto Y, Suchodolski JS, Galiazzo G, Vecchiato CG, Pinna C, Biagi G, Pietra M. Effect of an extruded animal protein-free diet on fecal microbiota of dogs with food-responsive enteropathy. J Vet Intern Med 2018; 32:1903-1910. [PMID: 30353569 PMCID: PMC6271313 DOI: 10.1111/jvim.15227] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 04/13/2018] [Accepted: 05/03/2018] [Indexed: 12/20/2022] Open
Abstract
Background Dietary interventions are thought to modify gut microbial communities in healthy individuals. In dogs with chronic enteropathies, resolution of dysbiosis, along with remission of clinical signs, is expected with treatment. Hypothesis/Objective To evaluate changes in the fecal microbiota in dogs with food‐responsive chronic enteropathy (FRE) and in healthy control (HC) dogs before and after an elimination dietary trial with an animal protein‐free diet (APFD). Animals Dogs with FRE (n = 10) and HC (n = 14). Methods Dogs were fed the APFD for 60 days. Fecal microbiota was analyzed by Illumina 16S rRNA sequencing and quantitative polymerase chain reaction (PCR). Results A significantly lower bacterial alpha‐diversity was observed in dogs with FRE compared with HC dogs at baseline, and compared with FRE dogs after the trial. Distinct microbial communities were observed in dogs with FRE at baseline compared with HC dogs at baseline and compared with dogs with FRE after the trial. Microbial communities still were different in FRE dogs after the trial compared with HC dogs at baseline. In HC dogs, the fecal microbiota did not show a significant modification after administration of the APFD. Conclusion and Clinical Importance Our results suggest that, in FRE dogs, treatment with the APFD led to a partial recovery of the fecal microbiota by significantly increasing microbiota richness, which was significantly closer to a healthy microbiota after the treatment. In contrast, no changes were detected in the fecal microbiota of HC dogs fed the same APFD.
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Affiliation(s)
- Francesca Bresciani
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Yasushi Minamoto
- Department of Small Animal Clinical Sciences, Gastrointestinal Laboratory, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Texas
| | - Jan S Suchodolski
- Department of Small Animal Clinical Sciences, Gastrointestinal Laboratory, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Texas
| | - Giorgia Galiazzo
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Carla G Vecchiato
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Carlo Pinna
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Giacomo Biagi
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Marco Pietra
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
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Grandi M, Pinna C, Bonaldo A, Stefanelli C, Vecchiato CG, Zaghini G, Biagi G. Effects of dietary supplementation with increasing doses of lactose on faecal bacterial populations and metabolites and apparent total tract digestibility in adult dogs. ITALIAN JOURNAL OF ANIMAL SCIENCE 2018. [DOI: 10.1080/1828051x.2018.1459210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Monica Grandi
- Dipartimento di Scienze Mediche Veterinarie, University of Bologna, Ozzano dell’Emilia (BO), Italy
| | - Carlo Pinna
- Dipartimento di Scienze Mediche Veterinarie, University of Bologna, Ozzano dell’Emilia (BO), Italy
| | - Alessio Bonaldo
- Dipartimento di Scienze Mediche Veterinarie, University of Bologna, Ozzano dell’Emilia (BO), Italy
| | - Claudio Stefanelli
- Dipartimento di Scienze per la Qualità della Vita, University of Bologna, Rimini, Italy
| | - Carla Giuditta Vecchiato
- Dipartimento di Scienze Mediche Veterinarie, University of Bologna, Ozzano dell’Emilia (BO), Italy
| | - Giuliano Zaghini
- Dipartimento di Scienze Mediche Veterinarie, University of Bologna, Ozzano dell’Emilia (BO), Italy
| | - Giacomo Biagi
- Dipartimento di Scienze Mediche Veterinarie, University of Bologna, Ozzano dell’Emilia (BO), Italy
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Schmidt M, Unterer S, Suchodolski JS, Honneffer JB, Guard BC, Lidbury JA, Steiner JM, Fritz J, Kölle P. The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets. PLoS One 2018; 13:e0201279. [PMID: 30110340 PMCID: PMC6093636 DOI: 10.1371/journal.pone.0201279] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 07/12/2018] [Indexed: 01/14/2023] Open
Abstract
INTRODUCTION Feeding a Bones and Raw Food (BARF) diet has become an increasing trend in canine nutrition. Bones and Raw Food diets contain a high amount of animal components like meat, offal, and raw meaty bones, combined with comparatively small amounts of plant ingredients like vegetables and fruits as well as different sorts of oil and supplements. While many studies have focused on transmission of pathogens via contaminated meat and on nutritional imbalances, only few studies have evaluated the effect of BARF diets on the fecal microbiome and metabolome. The aim of the study was to investigate differences in the fecal microbiome and the metabolome between dogs on a BARF diet and dogs on a commercial diet (canned and dry dog food). METHODS Naturally passed fecal samples were obtained from 27 BARF and 19 commercially fed dogs. Differences in crude protein, fat, fiber, and NFE (Nitrogen-Free Extract) between diets were calculated with a scientific nutrient database. The fecal microbiota was analyzed by 16S rRNA gene sequencing and quantitative PCR assays. The fecal metabolome was analyzed in 10 BARF and 9 commercially fed dogs via untargeted metabolomics approach. RESULTS Dogs in the BARF group were fed a significantly higher amount of protein and fat and significantly lower amount of NFE and fiber. There was no significant difference in alpha-diversity measures between diet groups. Analysis of similarity (ANOSIM) revealed a significant difference in beta-diversity (p < 0.01) between both groups. Linear discriminant analysis effect size (LefSe) showed a higher abundance of Lactobacillales, Enterobacteriaceae, Fusobacterium and, Clostridium in the BARF group while conventionally fed dogs had a higher abundance of Clostridiaceae, Erysipelotrichaceae, Ruminococcaceae, and Lachnospiraceae. The qPCR assays revealed significantly higher abundance of Escherichia coli (E. coli) and Clostridium (C.). perfringens and an increased Dysbiosis Index in the BARF group. Principal component analysis (PCA) plots of metabolomics data showed clustering between diet groups. Random forest analysis showed differences in the abundance of various components, including increased 4-hydroxybutryric acid (GBH) and 4-aminobutyric acid (GABA) in the BARF group. Based on univariate statistics, several metabolites were significantly different between diet groups, but lost significance after adjusting for multiple comparison. No differences were found in fecal bile acid concentrations, but the BARF group had a higher fecal concentration of cholesterol in their feces compared to conventionally fed dogs. CONCLUSION Microbial communities and metabolome vary significantly between BARF and commercially fed dogs.
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Affiliation(s)
- Milena Schmidt
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Stefan Unterer
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Julia B. Honneffer
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Blake C. Guard
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Jonathan A. Lidbury
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Jörg M. Steiner
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Julia Fritz
- Napfcheck, small animal nutrition consultation, Munich, Germany
| | - Petra Kölle
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
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Effects of prebiotic inulin-type fructans on blood metabolite and hormone concentrations and faecal microbiota and metabolites in overweight dogs. Br J Nutr 2018; 120:711-720. [PMID: 30064535 DOI: 10.1017/s0007114518001952] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Because obesity is associated with many co-morbidities, including diabetes mellitus, this study evaluated the second-meal effect of a commercial prebiotic, inulin-type fructans, and the effects of the prebiotic on faecal microbiota, metabolites and bile acids (BA). Nine overweight beagles were used in a replicated 3×3 Latin square design to test a non-prebiotic control (cellulose) against a low (equivalent to 0·5 % diet) and high dose (equivalent to 1·0 % diet) of prebiotic over 14-d treatments. All dogs were fed the same diet twice daily, with treatments provided orally via gelatin capsules before meals. On days 13 or 14 of each period, fresh faecal samples were collected, dogs were fed at 08.00 hours and then challenged with 1 g/kg body weight of maltodextrin in place of the 16.00 hours meal. Repeated blood samples were analysed for glucose and hormone concentrations to determine postprandial incremental AUC (IAUC) data. Baseline glucose, insulin and active glucagon-like peptide-1 levels were similar between all groups (P>0·10). Glucose and insulin IAUC after glucose challenge appeared lower following the high dose, but did not reach statistical relevance. Prebiotic intervention resulted in an increase in relative abundance of some Firmicutes and a decrease in the relative abundance of some Proteobacteria. Individual and total faecal SCFA were significantly increased (P<0·05) following prebiotic supplementation. Total concentration of excreted faecal BA tended to increase in dogs fed the prebiotic (P=0·06). Our results indicate that higher doses of inulin-type prebiotics may serve as modulators of gut microbiota, metabolites and BA pool in overweight dogs.
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61
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Moon CD, Young W, Maclean PH, Cookson AL, Bermingham EN. Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats. Microbiologyopen 2018; 7:e00677. [PMID: 29911322 PMCID: PMC6182564 DOI: 10.1002/mbo3.677] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/09/2018] [Accepted: 05/21/2018] [Indexed: 12/17/2022] Open
Abstract
Interests in the impact of the gastrointestinal microbiota on health and wellbeing have extended from humans to that of companion animals. While relatively fewer studies to date have examined canine and feline gut microbiomes, analysis of the metagenomic DNA from fecal communities using next‐generation sequencing technologies have provided insights into the microbes that are present, their function, and potential to contribute to overall host nutrition and health. As carnivores, healthy dogs and cats possess fecal microbiomes that reflect the generally higher concentrations of protein and fat in their diets, relative to omnivores and herbivores. The phyla Firmicutes and Bacteroidetes are highly abundant, and Fusobacteria, Actinobacteria, and Proteobacteria also feature prominently. Proteobacteria is the most diverse bacterial phylum and commonly features in the fecal microbiota of healthy dogs and cats, although its reputation is often sullied as its members include a number of well‐known opportunistic pathogens, such as Escherichia coli, Salmonella, and Campylobacter, which may impact the health of the host and its owner. Furthermore, in other host species, high abundances of Proteobacteria have been associated with dysbiosis in hosts with metabolic or inflammatory disorders. In this review, we seek to gain further insight into the prevalence and roles of the Proteobacteria within the gastrointestinal microbiomes of healthy dogs and cats. We draw upon the growing number of metagenomic DNA sequence‐based studies which now allow us take a culture‐independent approach to examine the functions that this more minor, yet important, group contribute to normal microbiome function. The fecal microbiomes of healthy dogs and cats often include Proteobacteria at varying abundances. This phylum can have a sullied reputation as it contains a number of well‐known pathogenic members. We explored the functions of the Proteobacteria in fecal shotgun metagenome datasets from healthy dogs and cats. The Proteobacteria appeared to be enriched for functions that are consistent with a role in helping to maintain the anaerobic environment of the gut for normal microbiome function.
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Affiliation(s)
- Christina D Moon
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Wayne Young
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand.,High-Value Nutrition, National Science Challenge, Auckland, New Zealand
| | - Paul H Maclean
- AgResearch, Lincoln Research Centre, Lincoln, New Zealand
| | - Adrian L Cookson
- AgResearch, Hopkirk Research Institute, Palmerston North, New Zealand
| | - Emma N Bermingham
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand.,High-Value Nutrition, National Science Challenge, Auckland, New Zealand
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Herstad KMV, Moen AEF, Gaby JC, Moe L, Skancke E. Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors. PLoS One 2018; 13:e0198342. [PMID: 29852000 PMCID: PMC5979030 DOI: 10.1371/journal.pone.0198342] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 05/17/2018] [Indexed: 12/17/2022] Open
Abstract
Colorectal epithelial tumors occur spontaneously in dogs, and the pathogenesis seems to parallel that of humans. The development of human colorectal tumorigenesis has been linked to alterations in the composition of the intestinal microbiota. This study characterized the fecal- and mucosa-associated microbiota in dogs with colorectal epithelial tumors (n = 10). The fecal microbiota was characterized by 16S rDNA analysis and compared with that of control dogs (n = 13). We also determined the mucosa-associated microbiota composition in colonic tumor tissue (n = 8) and in adjacent non-tumor tissue (n = 5) by 16S rDNA- and rRNA profiling. The fecal microbial community structure in dogs with tumors was different from that of control samples and was distinguished by oligotypes affiliated with Enterobacteriaceae, Bacteroides, Helicobacter, Porphyromonas, Peptostreptococcus and Streptococcus, and lower abundance of Ruminococcaceae, Slackia, Clostridium XI and Faecalibacterium. The overall community structure and populations of mucosal bacteria were not different based on either the 16S rDNA or the 16S rRNA profile in tumor tissue vs. adjacent non-tumor tissue. However, the proportion of live, potentially active bacteria appeared to be higher in non-tumor tissue compared with tumor tissue and included Slackia, Roseburia, unclass. Ruminococcaeceae, unclass. Lachnospiraceae and Oscillibacter. Colorectal tumors are rarely diagnosed in dogs, but despite this limitation, we were able to show that dogs with colorectal tumors have distinct fecal microbiota profiles. These initial results support the need for future case-control studies that are adequately powered, as well as age-matched and breed-matched, in order to evaluate the influence of bacteria on colorectal cancer etiopathogenesis and to determine whether the bacteria may have potential as biomarkers in clinical settings.
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Affiliation(s)
- Kristin Marie Valand Herstad
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
- * E-mail:
| | - Aina Elisabeth Fossum Moen
- Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog and University of Oslo, Oslo, Norway
| | - John Christian Gaby
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Lars Moe
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - Ellen Skancke
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
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63
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Deb-Choudhury S, Bermingham EN, Young W, Barnett MPG, Knowles SO, Harland D, Clerens S, Dyer JM. The effects of a wool hydrolysate on short-chain fatty acid production and fecal microbial composition in the domestic cat (Felis catus). Food Funct 2018; 9:4107-4121. [DOI: 10.1039/c7fo02004j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Novel animal-derived fibers are of interest for the pet food industry.
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Affiliation(s)
| | | | - Wayne Young
- Food & Bio-Based Products
- AgResearch
- New Zealand
- Riddet Institute
- based at Massey University
| | - Matthew P. G. Barnett
- Food & Bio-Based Products
- AgResearch
- New Zealand
- Riddet Institute
- based at Massey University
| | | | | | - Stefan Clerens
- Food & Bio-Based Products
- AgResearch
- New Zealand
- Biomolecular Interaction Centre
- University of Canterbury
| | - Jolon M. Dyer
- Food & Bio-Based Products
- AgResearch
- New Zealand
- Riddet Institute
- based at Massey University
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64
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Barko P, McMichael M, Swanson K, Williams D. The Gastrointestinal Microbiome: A Review. J Vet Intern Med 2018; 32:9-25. [PMID: 29171095 PMCID: PMC5787212 DOI: 10.1111/jvim.14875] [Citation(s) in RCA: 341] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 08/30/2017] [Accepted: 10/12/2017] [Indexed: 12/14/2022] Open
Abstract
The gastrointestinal microbiome is a diverse consortium of bacteria, archaea, fungi, protozoa, and viruses that inhabit the gut of all mammals. Studies in humans and other mammals have implicated the microbiome in a range of physiologic processes that are vital to host health including energy homeostasis, metabolism, gut epithelial health, immunologic activity, and neurobehavioral development. The microbial genome confers metabolic capabilities exceeding those of the host organism alone, making the gut microbiome an active participant in host physiology. Recent advances in DNA sequencing technology and computational biology have revolutionized the field of microbiomics, permitting mechanistic evaluation of the relationships between an animal and its microbial symbionts. Changes in the gastrointestinal microbiome are associated with diseases in humans and animals including inflammatory bowel disease, asthma, obesity, metabolic syndrome, cardiovascular disease, immune-mediated conditions, and neurodevelopmental conditions such as autism spectrum disorder. While there remains a paucity of data regarding the intestinal microbiome in small animals, recent studies have helped to characterize its role in host animal health and associated disease states. This review is intended to familiarize small animal veterinarians with recent advances in the field of microbiomics and to prime them for a future in which diagnostic tests and therapies will incorporate these developments into clinical practice.
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Affiliation(s)
- P.C. Barko
- Veterinary Clinical MedicineUniversity of Illinois at Urbana‐ChampaignUrbanaIL
| | - M.A. McMichael
- Veterinary Clinical MedicineUniversity of Illinois at Urbana‐ChampaignUrbanaIL
| | - K.S. Swanson
- Veterinary Clinical MedicineUniversity of Illinois at Urbana‐ChampaignUrbanaIL
- Department of Animal SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIL
| | - D.A. Williams
- Veterinary Clinical MedicineUniversity of Illinois at Urbana‐ChampaignUrbanaIL
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65
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Harkey MA, Villagran AM, Venkataraman GM, Leisenring WM, Hullar MAJ, Torok-Storb BJ. Associations between gastric dilatation-volvulus in Great Danes and specific alleles of the canine immune-system genes DLA88, DRB1, and TLR5. Am J Vet Res 2017; 78:934-945. [PMID: 28738011 DOI: 10.2460/ajvr.78.8.934] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine whether specific alleles of candidate genes of the major histocompatibility complex (MHC) and innate immune system were associated with gastric dilatation-volvulus (GDV) in Great Danes. ANIMALS 42 healthy Great Danes (control group) and 39 Great Danes with ≥ 1 GDV episode. PROCEDURES Variable regions of the 2 most polymorphic MHC genes (DLA88 and DRB1) were amplified and sequenced from the dogs in each group. Similarly, regions of 3 genes associated with the innate immune system (TLR5, NOD2, and ATG16L1), which have been linked to inflammatory bowel disease, were amplified and sequenced. Alleles were evaluated for associations with GDV, controlling for age and dog family. RESULTS Specific alleles of genes DLA88, DRB1, and TLR5 were significantly associated with GDV. One allele of each gene had an OR > 2 in the unadjusted univariate analyses and retained a hazard ratio > 2 after controlling for temperament, age, and familial association in the multivariate analysis. CONCLUSIONS AND CLINICAL RELEVANCE The 3 GDV-associated alleles identified in this study may serve as diagnostic markers for identification of Great Danes at risk for GDV. Additional research is needed to determine whether other dog breeds have the same genetic associations. These findings also provided a new target for research into the etiology of, and potential treatments for, GDV in dogs.
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66
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Gavazza A, Rossi G, Lubas G, Cerquetella M, Minamoto Y, Suchodolski JS. Faecal microbiota in dogs with multicentric lymphoma. Vet Comp Oncol 2017; 16:E169-E175. [PMID: 29152844 DOI: 10.1111/vco.12367] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/11/2017] [Accepted: 10/10/2017] [Indexed: 12/27/2022]
Abstract
Malignant lymphoma B-cell type is the most common canine haematopoietic malignancy. Changes in intestinal microbiota have been implicated in few types of cancer in humans. The aim of this prospective and case-control study was to determine differences in faecal microbiota between healthy control dogs and dogs with multicentric lymphoma. Twelve dogs affected by multicentric, B-cell, stage III-IV lymphoma, and 21 healthy dogs were enrolled in the study. For each dog, faecal samples were analysed by Illumina sequencing of 16S rRNA genes and quantitative PCR (qPCR) for selected bacterial groups. Alpha diversity was significant lower in lymphoma dogs. Principal coordinate analysis plots showed different microbial clustering (P = .001) and linear discriminant analysis effect size revealed 28 differentially abundant bacterial groups in lymphoma and control dogs. The qPCR analysis showed significant lower abundance of Faecalibacterium spp. (q < .001), Fusobacterium spp. (q = .032), and Turicibacter spp. (q = .043) in dogs with lymphoma compared with control dogs. On the contrary, Streptococcus spp. was significantly higher in dogs with lymphoma (q = .041). The dysbiosis index was significantly higher (P < .0001) in dogs with lymphoma. In conclusion, both sequencing and qPCR analyses provided a global overview of faecal microbial communities and showed significant differences in the microbial communities of dogs presenting with multicentric lymphoma compared with healthy control dogs.
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Affiliation(s)
- A Gavazza
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy.,Department of Veterinary Sciences, University of Pisa, Pisa, Italy
| | - G Rossi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - G Lubas
- Department of Veterinary Sciences, University of Pisa, Pisa, Italy
| | - M Cerquetella
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Y Minamoto
- Gastrointestinal Laboratory, Texas A&M University, College Station, Texas
| | - J S Suchodolski
- Gastrointestinal Laboratory, Texas A&M University, College Station, Texas
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67
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Omori M, Maeda S, Igarashi H, Ohno K, Sakai K, Yonezawa T, Horigome A, Odamaki T, Matsuki N. Fecal microbiome in dogs with inflammatory bowel disease and intestinal lymphoma. J Vet Med Sci 2017; 79:1840-1847. [PMID: 28993566 PMCID: PMC5709562 DOI: 10.1292/jvms.17-0045] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Although alteration of commensal microbiota is associated with chronic gastrointestinal (GI) diseases such as inflammatory bowel disease (IBD) in dogs, the microbiota composition in intestinal lymphoma, an important differential
diagnosis of canine IBD, has not been investigated. The objective of this study was to compare the fecal microbiota in dogs with IBD, dogs with intestinal lymphoma, and healthy dogs. Eight dogs with IBD, eight dogs with intestinal
lymphoma, and fifteen healthy dogs were included in the study. Fecal samples were analyzed by 16S rRNA gene next-generation sequencing. Rarefaction analysis failed to reveal any difference in bacterial diversity among healthy dogs
and diseased dogs. Based on PCoA plots of unweighted UniFrac distances, the bacterial composition in dogs with intestinal lymphoma was different from those observed in dogs with IBD and healthy dogs. When compared with healthy
dogs, intestinal lymphoma subjects showed significant increases in organisms belonging to the Eubacteriaceae family. The proportion of the family Paraprevotellaceae and the genus Porphyromonas was significantly
higher in dogs with IBD compared to healthy dogs. These observations suggest that dysbiosis is associated with intestinal lymphoma as well as IBD in dogs.
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Affiliation(s)
- Marie Omori
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shingo Maeda
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hirotaka Igarashi
- Department of Veterinary Internal Medicine, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Koichi Ohno
- Department of Veterinary Internal Medicine, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kosei Sakai
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohiro Yonezawa
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ayako Horigome
- Food Science and Technology Institute, Morinaga Milk Industry Co., Ltd., 5-1-83 Higashihara, Zama, Kanagawa 252-8583, Japan
| | - Toshitaka Odamaki
- Food Science and Technology Institute, Morinaga Milk Industry Co., Ltd., 5-1-83 Higashihara, Zama, Kanagawa 252-8583, Japan
| | - Naoaki Matsuki
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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68
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Herstad KMV, Gajardo K, Bakke AM, Moe L, Ludvigsen J, Rudi K, Rud I, Sekelja M, Skancke E. A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs. BMC Vet Res 2017; 13:147. [PMID: 28558792 PMCID: PMC5450340 DOI: 10.1186/s12917-017-1073-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 05/23/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Diet has a major influence on the composition of the gut microbiota, whose importance for gut health and overall well-being is increasingly recognized. Knowledge is limited regarding health implications, including effects on the faecal microbiota, of feeding a diet with high content of red meat to dogs, despite some owners' apparent preference to do so. The aim of this study was to evaluate how a diet change from commercial dry food to one with a high content of boiled minced beef and vice versa influenced the faecal microbiota, and short chain fatty acid profile in healthy, adult, client-owned dogs. RESULTS The diet change influenced the faecal microbiota composition and diversity (Shannon diversity index). The most abundant OTUs in samples of dogs fed the dry food and high minced beef were affiliated with the species Faecalibacterium prausnitzii and Clostridia hiranonis respectively. The high minced beef diet apparently also influenced the short chain fatty acid profile, with increased isovaleric acid, as well as an increase in faecal pH. These effects were reversed when the commercial dry food was reintroduced in weeks 6 and 7. CONCLUSIONS Results of this study can aid in the understanding of how diet changes influence the faecal microbiota and metabolite content on a short-term basis. Long-term studies are required to investigate potential implications for canine gut and general health.
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Affiliation(s)
- Kristin M V Herstad
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway.
| | - Karina Gajardo
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NBMU), Oslo, Norway
| | - Anne Marie Bakke
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NBMU), Oslo, Norway
| | - Lars Moe
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - Jane Ludvigsen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Knut Rudi
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ida Rud
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Monika Sekelja
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.,Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ellen Skancke
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
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69
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Garcia-Mazcorro JF, Barcenas-Walls JR, Suchodolski JS, Steiner JM. Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing. PeerJ 2017; 5:e3184. [PMID: 28439463 PMCID: PMC5398277 DOI: 10.7717/peerj.3184] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 03/14/2017] [Indexed: 01/18/2023] Open
Abstract
Prebiotics are selectively fermentable dietary compounds that result in changes in the composition and/or activity of the intestinal microbiota, thus conferring benefits upon host health. In veterinary medicine, commercially available products containing prebiotics have not been well studied with regard to the changes they trigger on the composition of the gut microbiota. This study evaluated the effect of a commercially available nutraceutical containing fructo-oligosaccharides (FOS) and inulin on the fecal microbiota of healthy cats and dogs when administered for 16 days. Fecal samples were collected at two time points before and at two time points during prebiotic administration. Total genomic DNA was obtained from fecal samples and 454-pyrosequencing was used for 16S rRNA gene bacterial profiling. The linear discriminant analysis (LDA) effect size (LEfSe) method was used for detecting bacterial taxa that may respond (i.e., increase or decrease in its relative abundance) to prebiotic administration. Prebiotic administration was associated with a good acceptance and no side effects (e.g., diarrhea) were reported by the owners. A low dose of prebiotics (50 mL total regardless of body weight with the end product containing 0.45% of prebiotics) revealed a lower abundance of Gammaproteobacteria and a higher abundance of Veillonellaceae during prebiotic administration in cats, while Staphylococcaceae showed a higher abundance during prebiotic administration in dogs. These differences were not sufficient to separate bacterial communities as shown by analysis of weighted UniFrac distance metrics. A predictive approach of the fecal bacterial metagenome using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) also did not reveal differences between the period before and during prebiotic administration. A second trial using a higher dose of prebiotics (3.2 mL/kg body weight with the end product containing 3.1% of prebiotics) was tested in dogs and revealed a lower abundance of Dorea (family Clostridiaceae) and a higher abundance of Megamonas and other (unknown) members of Veillonellaceae during prebiotic administration. Again, these changes were not sufficient to separate bacterial communities or predicted metabolic profiles according to treatment. A closer analysis of bacterial communities at all time-points revealed highly individualized patterns of variation. This study shows a high interindividual variation of fecal bacterial communities from pet cats and dogs, that these communities are relatively stable over time, and that some of this variation can be attributable to prebiotic administration, a phenomenon that may be affected by the amount of the prebiotic administered in the formulation. This study also provides insights into the response of gut bacterial communities in pet cats and dogs during administration of commercially available products containing prebiotics. More studies are needed to explore potentially beneficial effects on host health beyond changes in bacterial communities.
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Affiliation(s)
- Jose F Garcia-Mazcorro
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States.,Faculty of Veterinary Medicine, Universidad Autónoma de Nuevo León, General Escobedo, Nuevo Leon, Mexico
| | - Jose R Barcenas-Walls
- Center for Research and Development in Health Sciences (CIDICS), Genomics Unit, Universidad Autónoma de Nuevo León, Monterrey, Nuevo Leon, Mexico
| | - Jan S Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Jörg M Steiner
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States
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70
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Qi X, Xu W, Guo M, Chen S, Liu Y, He X, Huang K. Rice- or pork-based diets with similar calorie and content result in different rat gut microbiota. Int J Food Sci Nutr 2017; 68:829-839. [PMID: 28320221 DOI: 10.1080/09637486.2017.1301889] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Rice is the most important food crop, and pork is the most widely eaten meat in the world. In this study, we compared the gut microbiota of the rats fed with rice or pork mixed diets, which have similar caloric contents. The physiological indices (body weights, hematology, serum chemistry, organ weights and histopathology) of two groups were all within the normal range. Two diets did not induce difference in the diversity of gut bacteria. However, Firmicutes were significantly higher in rice diet group, while Bacteroidetes were enriched in pork diet group. Butyrate and the bacteria enzymes β-glucuronidase, β-glucosidase and nitroreductase in the feces were all drastically higher in pork diet group. This study indicates that different diets with similar calorie and nutritional composition could change the community structure but not the diversity of rat fecal microbiota.
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Affiliation(s)
- Xiaozhe Qi
- a Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , China
| | - Wentao Xu
- a Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , China.,b Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , China
| | - Mingzhang Guo
- b Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , China
| | - Siyuan Chen
- b Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , China
| | - Yifei Liu
- a Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , China
| | - Xiaoyun He
- a Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , China
| | - Kunlun Huang
- a Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , China.,b Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , China
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71
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Bermingham EN, Maclean P, Thomas DG, Cave NJ, Young W. Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs. PeerJ 2017; 5:e3019. [PMID: 28265505 PMCID: PMC5337088 DOI: 10.7717/peerj.3019] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/23/2017] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Much of the recent research in companion animal nutrition has focussed on understanding the role of diet on faecal microbiota composition. To date, diet-induced changes in faecal microbiota observed in humans and rodents have been extrapolated to pets in spite of their very different dietary and metabolic requirements. This lack of direct evidence means that the mechanisms by which microbiota influences health in dogs are poorly understood. We hypothesised that changes in faecal microbiota correlate with physiological parameters including apparent macronutrient digestibility. METHODS Fifteen adult dogs were assigned to two diet groups, exclusively fed either a premium kibbled diet (kibble; K; n = 8) or a raw red meat diet (meat; M; n = 7) for nine weeks. Apparent digestibility of macronutrients (protein, fat, gross energy and dry matter), faecal weight, faecal health scores, faecal VFA concentrations and faecal microbial composition were determined. Datasets were integrated using mixOmics in R. RESULTS Faecal weight and VFA levels were lower and the apparent digestibility of protein and energy were higher in dogs on the meat diet. Diet significantly affected 27 microbial families and 53 genera in the faeces. In particular, the abundances of Bacteriodes, Prevotella, Peptostreptococcus and Faecalibacterium were lower in dogs fed the meat diet, whereas Fusobacterium, Lactobacillus and Clostridium were all more abundant. DISCUSSION Our results show clear associations of specific microbial taxa with diet composition. For example, Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae were highly correlated to parameters such as protein and fat digestibility in the dog. By understanding the relationship between faecal microbiota and physiological parameters we will gain better insights into the effects of diet on the nutrition of our pets.
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Affiliation(s)
- Emma N Bermingham
- AgResearch Ltd., Food Nutrition & Health Team , Palmerston North , New Zealand
| | - Paul Maclean
- AgResearch Ltd., Bioinformatics & Statistics Team , Lincoln , New Zealand
| | - David G Thomas
- Massey University, Institute of Veterinary, Animal & Biomedical Sciences , Palmerston North , New Zealand
| | - Nicholas J Cave
- Massey University, Institute of Veterinary, Animal & Biomedical Sciences , Palmerston North , New Zealand
| | - Wayne Young
- AgResearch Ltd., Food Nutrition & Health Team , Palmerston North , New Zealand
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72
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Sandri M, Dal Monego S, Conte G, Sgorlon S, Stefanon B. Raw meat based diet influences faecal microbiome and end products of fermentation in healthy dogs. BMC Vet Res 2017; 13:65. [PMID: 28245817 PMCID: PMC5331737 DOI: 10.1186/s12917-017-0981-z] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 02/17/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Dietary intervention studies are required to deeper understand the variability of gut microbial ecosystem in healthy dogs under different feeding conditions and to improve diet formulations. The aim of the study was to investigate in dogs the influence of a raw based diet supplemented with vegetable foods on faecal microbiome in comparison with extruded food. METHODS Eight healthy adult Boxer dogs were recruited and randomly divided in two experimental blocks of 4 individuals. Dogs were regularly fed a commercial extruded diet (RD) and starting from the beginning of the trial, one group received the raw based diet (MD) and the other group continued to be fed with the RD diet (CD) for a fortnight. After 14 days, the two groups were inverted, the CD group shifted to the MD and the MD shifted to the CD, for the next 14 days. Faeces were collected at the beginning of the study (T0), after 14 days (T14) before the change of diet and at the end of experimental period (T28) for DNA extraction and analysis of metagenome by sequencing 16SrRNA V3 and V4 regions, short chain fatty acids (SCFA), lactate and faecal score. RESULTS A decreased proportion of Lactobacillus, Paralactobacillus (P < 0.01) and Prevotella (P < 0.05) genera was observed in the MD group while Shannon biodiversity Index significantly increased (3.31 ± 0.15) in comparison to the RD group (2.92 ± 0.31; P < 0.05). The MD diet significantly (P < 0.05) decreased the Faecal Score and increased the lactic acid concentration in the feces in comparison to the RD treatment (P < 0.01). Faecal acetate was negatively correlated with Escherichia/Shigella and Megamonas (P < 0.01), whilst butyrate was positively correlated with Blautia and Peptococcus (P < 0.05). Positive correlations were found between lactate and Megamonas (P < 0.05), Escherichia/Shigella (P < 0.01) and Lactococcus (P < 0.01). CONCLUSION These results suggest that the diet composition modifies faecal microbial composition and end products of fermentation. The administration of MD diet promoted a more balanced growth of bacterial communities and a positive change in the readouts of healthy gut functions in comparison to RD diet.
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Affiliation(s)
- Misa Sandri
- Department of AgroFood, Environmental and Animal Sciences, University of Udine, Via delle Scienze 2908, 33100 Udine, Italy
| | - Simeone Dal Monego
- Cluster in Biomedicine, CBM S.c.r.l., Bioinformatic Services, Area Science Park, I‑34149 Basovizza, Italy
| | - Giuseppe Conte
- Department of Agricultural, Food and Agro-Environmental Sciences, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Sandy Sgorlon
- Department of AgroFood, Environmental and Animal Sciences, University of Udine, Via delle Scienze 2908, 33100 Udine, Italy
| | - Bruno Stefanon
- Department of AgroFood, Environmental and Animal Sciences, University of Udine, Via delle Scienze 2908, 33100 Udine, Italy
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Pre- and post-weaning diet alters the faecal metagenome in the cat with differences in vitamin and carbohydrate metabolism gene abundances. Sci Rep 2016; 6:34668. [PMID: 27876765 PMCID: PMC5120286 DOI: 10.1038/srep34668] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/16/2016] [Indexed: 01/14/2023] Open
Abstract
Dietary format, and its role in pet nutrition, is of interest to pet food manufacturers and pet owners alike. The aim of the present study was to investigate the effects of pre- and post-weaning diets (kibbled or canned) on the composition and function of faecal microbiota in the domestic cat by shotgun metagenomic sequencing and gene taxonomic and functional assignment using MG-RAST. Post-weaning diet had a dramatic effect on community composition; 147 of the 195 bacterial species identified had significantly different mean relative abundances between kittens fed kibbled and canned diets. The kittens fed kibbled diets had relatively higher abundances of Lactobacillus (>100-fold), Bifidobacterium (>100-fold), and Collinsella (>9-fold) than kittens fed canned diets. There were relatively few differences in the predicted microbiome functions associated with the pre-weaning diet. Post-weaning diet affected the abundance of functional gene groups. Genes involved in vitamin biosynthesis, metabolism, and transport, were significantly enriched in the metagenomes of kittens fed the canned diet. The impact of post-weaning diet on the metagenome in terms of vitamin biosynthesis functions suggests that modulation of the microbiome function through diet may be an important avenue for improving the nutrition of companion animals.
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Kasiraj AC, Harmoinen J, Isaiah A, Westermarck E, Steiner JM, Spillmann T, Suchodolski JS. The effects of feeding and withholding food on the canine small intestinal microbiota. FEMS Microbiol Ecol 2016; 92:fiw085. [PMID: 27106050 DOI: 10.1093/femsec/fiw085] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2016] [Indexed: 12/20/2022] Open
Abstract
Prolonged lack of enteral feeding has a negative impact on gut physiology, potentially via microbiota modulation. The aims were to investigate the impact of fasting and post-prandial changes in canine jejunal microbiota. To study post-prandial effects, jejunal brushings were analyzed in 8 healthy fistulated dogs 15 min before feeding (baseline) and hourly for 8 h after feeding. To study effects of withholding food (WF), daily samples were collected for 15 days from 5 dogs. The first 5 days (PRE) dogs were fed regular diet. Food was withheld the next 5 days (days 6-10). For days 11-15 (POST), the original diet was reintroduced. Microbiota was characterized via denaturing gradient gel electrophoresis and 454-pyrosequencing of 16S rRNA genes. In the post-prandial study, no changes in microbiome structure were seen after feeding (ANOSIM, P = 0.28), but Betaproteobacteria (P = 0.04) and Bacteroidales decreased compared to baseline. Species richness decreased by 300 min (P = 0.04). During WF, microbiota structure differed from PRE and POST period (P = 0.001). During WF, species richness did not vary over time (P = 0.69). In conclusion, a prolonged period of food withholding results in altered jejunal microbiota. How these changes affect the microbiota metabolism warrants further studies.
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Affiliation(s)
- Alyssa C Kasiraj
- Department of Small Animal Clinical Sciences, Gastrointestinal Laboratory, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4474, USA
| | - Jaana Harmoinen
- Department of Equine and Small Animal Medicine, Helsinki University, 00014 Helsinki, Finland
| | - Anitah Isaiah
- Department of Small Animal Clinical Sciences, Gastrointestinal Laboratory, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4474, USA
| | - Elias Westermarck
- Department of Equine and Small Animal Medicine, Helsinki University, 00014 Helsinki, Finland
| | - Jörg M Steiner
- Department of Small Animal Clinical Sciences, Gastrointestinal Laboratory, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4474, USA
| | - Thomas Spillmann
- Department of Equine and Small Animal Medicine, Helsinki University, 00014 Helsinki, Finland
| | - Jan S Suchodolski
- Department of Small Animal Clinical Sciences, Gastrointestinal Laboratory, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4474, USA
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75
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Pinna C, Vecchiato CG, Zaghini G, Grandi M, Nannoni E, Stefanelli C, Biagi G. In vitro influence of dietary protein and fructooligosaccharides on metabolism of canine fecal microbiota. BMC Vet Res 2016; 12:53. [PMID: 26970915 PMCID: PMC4788874 DOI: 10.1186/s12917-016-0672-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 03/03/2016] [Indexed: 11/18/2022] Open
Abstract
Background The present in vitro study investigated whether the utilization of fructooligosaccharides (FOS) may influence canine fecal microbial population in presence of diets differing in their protein content and digestibility. Fresh fecal samples were collected from five adult dogs, pooled, and incubated for 24 h with the undigested residue of three diets: 1, Low protein high digestibility diet (LP HD, crude protein (CP) 229 g/kg); 2, High protein high digestibility diet (HP HD, CP 304 g/kg); 3, High protein low digestibility diet (HP LD, CP 303 g/kg) that had been previously subjected to enzymatic digestion. In the in vitro fermentation study, there were six treatments: 1) LP HD; 2) HP HD 3) HP LD; 4) LP HD + FOS; 5) HP HD + FOS; 6) HP LD + FOS. Fructooligosaccharides were added at the final concentration of 1.5 g/L. Samples of fermentation fluid were collected at 6 and 24 h of incubation. Results Values of pH were reduced by FOS at 6 and 24 h (P < 0.001); conversely, low protein digestibility and high dietary protein level resulted in higher pH at both sampling times (P < 0.001). At 24 h, FOS lowered ammonia (−10 %; P < 0.001) and resulted (P < 0.05) in higher concentrations of total volatile fatty acids (VFA) (+43 %), acetic acid (+14 %), propionic acid (+75 %) and n-butyric acid (+372 %). Conversely, at 24 h, low protein digestibility resulted (P < 0.01) in lower concentrations of acetic acid (−26 %), propionic acid (−37 %) and total VFA (−21 %). Putrescine concentrations were increased at 6 and 24 h of fermentation by low protein digestibility (+21 and 22 %, respectively; P < 0.05) and FOS (+18 and 24 %, respectively; P < 0.01). After 24 h of fermentation, high dietary protein level resulted in lower counts of lactobacilli and enterococci (−0.5 and −0.7 log cells/mL, respectively; P < 0.05) whereas low protein digestibility tended to increase counts of C. perfringens (+0.2 log cells/mL; P = 0.07). Conclusions Results from the present study showed that diets rich in protein may exert negative influences on the canine intestinal ecosystem, slightly increasing the presence of ammonia and reducing counts of lactobacilli and enterococci. Moreover, the presence of poorly digestible protein resulted in lower concentrations of VFA. Conversely, administration of FOS may improve metabolism of canine intestinal microbiota, reducing ammonia concentrations and enhancing VFA production.
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Affiliation(s)
- Carlo Pinna
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Carla Giuditta Vecchiato
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Giuliano Zaghini
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Monica Grandi
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Eleonora Nannoni
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Claudio Stefanelli
- Department for Life Quality Studies, University of Bologna, Corso d'Augusto 237, 47921, Rimini, Italy
| | - Giacomo Biagi
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy.
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Pinna C, Biagi G. The Utilisation of Prebiotics and Synbiotics in Dogs. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2014.3107] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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77
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Schmitz S, Suchodolski J. Understanding the canine intestinal microbiota and its modification by pro-, pre- and synbiotics - what is the evidence? Vet Med Sci 2016; 2:71-94. [PMID: 29067182 PMCID: PMC5645859 DOI: 10.1002/vms3.17] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 12/02/2015] [Accepted: 12/13/2015] [Indexed: 12/12/2022] Open
Abstract
Interest in the composition of the intestinal microbiota and possibilities of its therapeutic modifications has soared over the last decade and more detailed knowledge specific to the canine microbiota at different mucosal sites including the gut is available. Probiotics, prebiotics or their combination (synbiotics) are a way of modifying the intestinal microbiota and exert effects on the host immune response. Probiotics are proposed to exert their beneficial effects through various pathways, for example production of antimicrobial peptides, enhancing growth of favourable endogenous microorganisms, competition for epithelial colonisation sites and immune‐modulatory functions. Despite widespread use of pro‐, pre‐ and synbiotics, scientific evidence of their beneficial effects in different conditions of the dog is scarce. Specific effects of different strains, their combination or their potential side‐effects have not been evaluated sufficiently. In some instances, in vitro results have been promising, but could not be transferred consistently into in vivo situations. Specific canine gastrointestinal (GI) diseases or conditions where probiotics would be beneficial, their most appropriate dosage and application have not been assessed extensively. This review summarises the current knowledge of the intestinal microbiome composition in the dog and evaluates the evidence for probiotic use in canine GI diseases to date. It wishes to provide veterinarians with evidence‐based information on when and why these products could be useful in preventing or treating canine GI conditions. It also outlines knowledge about safety and approval of commercial probiotic products, and the potential use of faecal microbial transplantation, as they are related to the topic of probiotic usage.
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Affiliation(s)
- Silke Schmitz
- Department of Internal MedicineSmall Animal HospitalJustus-Liebig UniversityGiessenGermany
| | - Jan Suchodolski
- Gastrointestinal LaboratoryDepartment of Small Animal Clinical SciencesCollege of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexasUSA
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78
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Wei YM, Wang JQ, Liu TT, Kong WW, Chen N, He XQ, Jin Y. Bacterial communities of Beijing surface waters as revealed by 454 pyrosequencing of the 16S rRNA gene. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:12605-12614. [PMID: 25911286 DOI: 10.1007/s11356-015-4534-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/12/2015] [Indexed: 06/04/2023]
Abstract
As a better understanding of Beijing surface water ecosystems can provide clues for environmental management and public health, here, we report a study of the bacterial communities of five Beijing surface waters conducted using 454 pyrosequencing of 16S ribosomal RNA (rRNA) genes. We expected to observe a core bacterial community among the surface waters and differences in bacterial community abundance over the different locations of sampling. In this study, we obtained a total of 60,810 trimmed reads from the five samples after the removal of unqualified reads. Bacterial sequences from the five samples were classified into taxonomic classes using the default settings of the mothur platform. Our results provided insight into the bacterial community composition of surface waters and revealed that there was a core microbial community in the microbial populations of surface samples at different geographic locations, with 13 phyla and 40 genera in common. Our findings also revealed the differences in bacterial communities among five surface water samples obtained at different locations.
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Affiliation(s)
- Yu-Mei Wei
- College of Biological Sciences and Technology, Beijing Forestry University, P. O. Box 162, Qinghua East Rd 35, Haidian District, Beijing, 100083, People's Republic of China
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Šlapeta J, Dowd SE, Alanazi AD, Westman ME, Brown GK. Differences in the faecal microbiome of non-diarrhoeic clinically healthy dogs and cats associated with Giardia duodenalis infection: impact of hookworms and coccidia. Int J Parasitol 2015; 45:585-94. [DOI: 10.1016/j.ijpara.2015.04.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 02/07/2023]
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80
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Grześkowiak Ł, Endo A, Beasley S, Salminen S. Microbiota and probiotics in canine and feline welfare. Anaerobe 2015; 34:14-23. [PMID: 25863311 PMCID: PMC7111060 DOI: 10.1016/j.anaerobe.2015.04.002] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 04/02/2015] [Accepted: 04/05/2015] [Indexed: 12/26/2022]
Abstract
Dogs and cats have been cohabiting with us for thousands of years. They are the major human companions. Today, dogs and cats live in urban areas. Cats and most dogs are on high carbohydrate diets and face similar life-style challenges as the human beings. The health and well-being of companion animals, just as their owners, depends on the gut microbes. Providing a proper care and nutritionally balanced diet to companion animals is recognised as a part of our responsibility to maintain the health and well being of our pet. However, as microbiota differences may facilitate exposure to pathogens and harmful environmental influences, it is prudent to search for novel tools to protect dogs and cats and at the same time the human owners from pathogens. Specific probiotic strains and/or their defined combinations may be useful in the canine and feline nutrition, therapy, and care. Probiotic supplementations have been successful in the prevention and treatment of acute gastroenteritis, treatment of IBD, and prevention of allergy in companion animals. New challenges for probiotic applications include maintenance of obesity and overweight, urogenital tract infections, Helicobacter gastritis and parasitic infections. The probiotics of human origin appear to be among the new promising tools for the maintenance of pets' health. However, the host-derived microorganisms might be the most appropriate probiotic source. Therefore, more controlled trials are needed to characterise new and safe probiotic preparations with an impact on general health and well being as well as health maintenance in dogs and cats.
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Affiliation(s)
| | - Akihito Endo
- Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido, Japan
| | | | - Seppo Salminen
- Functional Foods Forum, Univeristy of Turku, Turku, Finland
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81
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Gut microbiota of humans, dogs and cats: current knowledge and future opportunities and challenges. Br J Nutr 2014; 113 Suppl:S6-17. [PMID: 25414978 DOI: 10.1017/s0007114514002943] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
High-throughput DNA sequencing techniques allow for the identification and characterisation of microbes and their genes (microbiome). Using these new techniques, microbial populations in several niches of the human body, including the oral and nasal cavities, skin, urogenital tract and gastrointestinal tract, have been described recently. Very little data on the microbiome of companion animals exist, and most of the data have been derived from the analysis of the faeces of healthy laboratory animals. High-throughput assays provide opportunities to study the complex and dense populations of the gut microbiota, including bacteria, archaea, fungi, protozoa and viruses. Our laboratory and others have recently described the predominant microbial taxa and genes of healthy dogs and cats and how these respond to dietary interventions. In general, faecal microbial phylogeny (e.g. predominance of Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria) and functional capacity (e.g. major functional groups related to carbohydrate, protein, DNA and vitamin metabolism; virulence factors; and cell wall and capsule) of the canine and feline gut are similar to those of the human gut. Initial sequencing projects have provided a glimpse of the microbial super-organism that exists within the canine and feline gut, but leaves much to be explored and discovered. As DNA provides information only about potential functions, studies that focus on the microbial transcriptome, metabolite profiles, and how microbiome changes affect host physiology and health are clearly required. Future studies must determine how diet composition, antibiotics and other drug therapies, breed and disease affect or are affected by the gut microbiome and how this information may be used to improve diets, identify disease biomarkers and develop targeted disease therapies.
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82
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Faecal microbiota of domestic cats fed raw whole chicks v. an extruded chicken-based diet. J Nutr Sci 2014; 3:e22. [PMID: 26101591 PMCID: PMC4473156 DOI: 10.1017/jns.2014.21] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 01/24/2014] [Accepted: 01/30/2014] [Indexed: 12/03/2022] Open
Abstract
Extruded cat foods differ greatly in macronutrient distribution compared with wild-type diets (i.e. small mammals, reptiles, birds and insects). Based on the literature, this variability likely impacts faecal microbial populations. A completely randomised design was utilised to test the impacts of two dietary treatments on faecal microbial populations: (1) chicken-based extruded diet (EXT; n 3 cats) and (2) raw 1–3-d-old chicks (CHI; n 5 cats). Cats were adapted to diets for 10 d. Bacterial DNA was isolated from faecal samples and amplicons of the 16S rRNA V4–V6 region were generated and analysed by 454 pyrosequencing. Faeces of cats fed CHI had greater (P < 0·05) proportions of the following bacterial genera: unidentified Lachnospiraceae (15 v. 5 %), Peptococcus (9 v. 3 %) and Pseudobutyrivibrio (4 v. 1 %). Faeces of cats fed EXT had greater (P < 0·05) proportions of Faecalibacterium (1·0 v. 0·2 %) and Succinivibrio (1·2 v. < 0·1 %). Five genera, including Lactobacillus and Bifidobacterium, were present in a majority of samples (two to three out of three) from cats fed EXT, but were not detected in the samples (zero of five) for cats fed CHI. These shifts in faecal bacterial populations compared with feeding a whole-prey diet may impact the functional capacities of the microbiota and its interaction with the host. Further research is warranted to determine the impacts of these shifts on long-term health of domestic cats.
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83
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Effect of oral administration of metronidazole or prednisolone on fecal microbiota in dogs. PLoS One 2014; 9:e107909. [PMID: 25229475 PMCID: PMC4168260 DOI: 10.1371/journal.pone.0107909] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/18/2014] [Indexed: 12/16/2022] Open
Abstract
Gastrointestinal microbiota have been implicated in the pathogenesis of various gastrointestinal disorders in dogs, including acute diarrhea and chronic enteropathy. Metronidazole and prednisolone are commonly prescribed for the treatment of these diseases; however, their effects on gastrointestinal microbiota have not been investigated. The objective of this study was to evaluate the effects of these drugs on the gastrointestinal microbiota of dogs. Metronidazole was administered twice daily at 12.5 mg/kg to a group of five healthy dogs, and prednisolone at 1.0 mg/kg daily to a second group of five healthy dogs for 14 days. Fecal samples were collected before and after administration (day 0 and 14), and 14 and 28 days after cessation (day 28 and 42). DNA was extracted, and the bacterial diversity and composition of each sample were determined based on 16S ribosomal RNA (rRNA) gene sequences using next-generation sequencing (Illumina MiSeq). In the group administered metronidazole, bacterial diversity indices significantly decreased at day 14, and recovered after the cessation. Principal coordinates analysis and hierarchical dendrogram construction based on unweighted and weighted UniFrac distance matrices revealed that bacterial composition was also significantly altered by metronidazole at day 14 compared with the other time points. The proportions of Bacteroidaceae, Clostridiaceae, Fusobacteriaceae, Lachnospiraceae, Ruminococcaceae, Turicibacteraceae, and Veillonellaceae decreased, while Bifidobacteriaceae, Enterobacteriaceae, Enterococcaceae, and Streptococcaceae increased at day 14 and returned to their initial proportions by day 42. Conversely, no effect of prednisolone was observed on either the bacterial diversity or composition. Reducing pathogenic bacteria such as Fusobacteria and increasing beneficial bacteria such as Bifidobacterium through the administration of metronidazole may be beneficial for promoting gastrointestinal health; however, further investigations into the effects on diseased dogs are needed.
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84
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Kerr KR, Forster G, Dowd SE, Ryan EP, Swanson KS. Effects of dietary cooked navy bean on the fecal microbiome of healthy companion dogs. PLoS One 2013; 8:e74998. [PMID: 24040374 PMCID: PMC3770567 DOI: 10.1371/journal.pone.0074998] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 08/08/2013] [Indexed: 01/14/2023] Open
Abstract
Background Cooked bean powders are a promising novel protein and fiber source for dogs, which have demonstrated potential to alter microbial composition and function for chronic disease control and prevention. This study aimed to determine the impact of cooked navy bean powder fed as a staple food ingredient on the fecal microbiome of healthy adult pet dogs. Methodology/Principal Findings Fecal samples from healthy dogs prior to dietary control and after 4 wk of dietary treatment with macro- and micronutrient matched diets containing either 0 or 25% cooked navy beans (n = 11 and n = 10, respectively) were analyzed by 454-pyrosequencing of the 16S rRNA gene. There were few differences between dogs fed the control and navy bean diets after 4 wk of treatment. These data indicate that there were no major effects of navy bean inclusion on microbial populations. However, significant differences due to dietary intervention onto both research diets were observed (i.e., microbial populations at baseline versus 4 wk of intervention with 0 or 25% navy bean diets). After 4 wk of dietary intervention on either control or navy bean diet, the Phylum Firmicutes was increased and the Phyla Actinobacteria and Fusobacteria were decreased compared to baseline. Conclusions No negative alterations of microbial populations occurred following cooked navy bean intake in dogs, indicating that bean powders may be a viable protein and fiber source for commercial pet foods. The highly variable microbial populations observed in these healthy adult pet dogs at baseline is one potential reason for the difficulty to detect alterations in microbial populations following dietary changes. Given the potential physiological benefits of bean intake in humans and dogs, further evaluation of the impacts of cooked navy bean intake on fecal microbial populations with higher power or more sensitive methods are warranted.
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Affiliation(s)
- Katherine R. Kerr
- Division of Nutritional Sciences and Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Genevieve Forster
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Scot E. Dowd
- MR DNA (Molecular Research LP), Shallowater, Texas, United States of America
| | - Elizabeth P. Ryan
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Kelly S. Swanson
- Division of Nutritional Sciences and Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
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85
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Kerr KR, Beloshapka AN, Swanson KS. 2011 and 2012 Early Careers Achievement Awards: use of genomic biology to study companion animal intestinal microbiota. J Anim Sci 2013; 91:2504-11. [PMID: 23482581 DOI: 10.2527/jas.2012-6225] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although dogs and cats are quite different than many livestock species in that they have evolved by eating diets high in fat and protein and low in carbohydrates, the gastrointestinal microbiota still play a key role in the gut and overall host health of these species. Early experiments in this field used culture-based techniques to evaluate the effects of dietary ingredients, such as fibers and prebiotics, on microbiota and indices of gut health (e.g., fecal scores, pH, fermentative end products). Such studies, however, were limited in scope and lacked precision as it pertained to the microbiota. The DNA-based techniques that have become available over the past decade have greatly upgraded research capabilities and have provided a more encompassing view of the canine and feline gastrointestinal microbiomes. High-throughput sequencing techniques that are much cheaper and faster than Sanger sequencing have been a key development in this progress. Sequence data not only allow for the identification of all microbial taxa but also provide information regarding functional capacity when a shotgun sequencing approach is used. The few canine and feline studies that have used 454 pyrosequencing have identified the predominant microbial taxa and metabolic functions present in healthy populations, differences between healthy and diseased dog and cat populations, and the effects of diet (e.g., dietary fibers, prebiotics, protein to carbohydrate ratio) on gastrointestinal microbiota. Although these studies have provided a foundation from which to work, more research is needed to increase our general understanding of the gastro-intestinal microbiome, how it impacts host health, how its composition and activity may be altered by age, genetic, or environmental factors, and test whether specific pathogens or disease signatures can be identified and used in diagnosis and/or treatment of disease.
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Affiliation(s)
- K R Kerr
- Division of Nutritional Sciences, University of Illinois, Urbana 61801, USA
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86
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Bermingham EN, Young W, Kittelmann S, Kerr KR, Swanson KS, Roy NC, Thomas DG. Dietary format alters fecal bacterial populations in the domestic cat (Felis catus). Microbiologyopen 2013; 2:173-81. [PMID: 23297252 PMCID: PMC3584222 DOI: 10.1002/mbo3.60] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 11/01/2012] [Accepted: 11/12/2012] [Indexed: 12/18/2022] Open
Abstract
The effects of short-term (5-week) exposure to wet or dry diets on fecal bacterial populations in the cat were investigated. Sixteen mixed-sex, neutered, domestic short-haired cats (mean age = 6 years; mean bodyweight = 3.4 kg) were randomly allocated to wet or dry diets in a crossover design. Fecal bacterial DNA was isolated and bacterial 16S rRNA gene amplicons generated and analyzed by 454 Titanium pyrosequencing. Cats fed dry diets had higher abundances (P < 0.05) of Actinobacteria (16.5% vs. 0.1%) and lower abundances of Fusobacteria (0.3% vs. 23.1%) and Proteobacteria (0.4% vs. 1.1%) compared with cats fed the wet diet. Of the 46 genera identified, 30 were affected (P < 0.05) by diet, with higher abundances of Lactobacillus (31.8% vs. 0.1%), Megasphaera (23.0% vs. 0.0%), and Olsenella (16.4% vs. 0.0%), and lower abundances of Bacteroides (0.6% vs. 5.7%) and Blautia (0.3% vs. 2.3%) in cats fed the dry diet compared with cats fed the wet diet. These results demonstrate that short-term dietary exposure to diet leads to large shifts in fecal bacterial populations that have the potential to affect the ability of the cat to process macronutrients in the diet.
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Affiliation(s)
- Emma N Bermingham
- Food Nutrition & Health, Food & Bio-based Products Group, AgResearch Grasslands, Palmerston North, 4442, New Zealand.
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