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Alessandri G, Fontana F, Mancabelli L, Tarracchini C, Lugli GA, Argentini C, Longhi G, Rizzo SM, Vergna LM, Anzalone R, Viappiani A, Turroni F, Ossiprandi MC, Milani C, Ventura M. Species-level characterization of saliva and dental plaque microbiota reveals putative bacterial and functional biomarkers of periodontal diseases in dogs. FEMS Microbiol Ecol 2024; 100:fiae082. [PMID: 38782729 PMCID: PMC11165276 DOI: 10.1093/femsec/fiae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/08/2024] [Accepted: 05/22/2024] [Indexed: 05/25/2024] Open
Abstract
Periodontal diseases are among the most common bacterial-related pathologies affecting the oral cavity of dogs. Nevertheless, the canine oral ecosystem and its correlations with oral disease development are still far from being fully characterized. In this study, the species-level taxonomic composition of saliva and dental plaque microbiota of 30 healthy dogs was investigated through a shallow shotgun metagenomics approach. The obtained data allowed not only to define the most abundant and prevalent bacterial species of the oral microbiota in healthy dogs, including members of the genera Corynebacterium and Porphyromonas, but also to identify the presence of distinct compositional motifs in the two oral microniches as well as taxonomical differences between dental plaques collected from anterior and posterior teeth. Subsequently, the salivary and dental plaque microbiota of 18 dogs affected by chronic gingival inflammation and 18 dogs with periodontitis were compared to those obtained from the healthy dogs. This analysis allowed the identification of bacterial and metabolic biomarkers correlated with a specific clinical status, including members of the genera Porphyromonas and Fusobacterium as microbial biomarkers of a healthy and diseased oral status, respectively, and genes predicted to encode for metabolites with anti-inflammatory properties as metabolic biomarkers of a healthy status.
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Affiliation(s)
- Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
- Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Leonardo Mancabelli
- Department of Medicine and Surgery, University of Parma, Via Volturno 39, 43125 Parma, Italy
- Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
- Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Sonia Mirjam Rizzo
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Laura Maria Vergna
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | | | | | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
- Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Maria Cristina Ossiprandi
- Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
- Department of Veterinary Medical Science, University of Parma, Via Del Taglio 10, 43126 Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
- Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
- Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
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Liversidge BD, Gomez DE, Dodd SAS, MacNicol JL, Adolphe JL, Blois SL, Verbrugghe A. Comparison of the fecal microbiota of adult healthy dogs fed a plant-based (vegan) or an animal-based diet. Front Microbiol 2024; 15:1367493. [PMID: 38694809 PMCID: PMC11061427 DOI: 10.3389/fmicb.2024.1367493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/02/2024] [Indexed: 05/04/2024] Open
Abstract
Purpose Pet guardians are increasingly seeking vegan dog foods. However, research on the impact of these diets on gastrointestinal (GI) physiology and health is limited. In humans, vegan diets modify the GI microbiota, increasing beneficial digestive microorganisms. This study aimed to examine the canine fecal microbiota in response to a vegan diet compared to an animal-based diet. Methods Sixty-one client-owned healthy adult dogs completed a randomized, double-blinded longitudinal study. Dogs were randomly assigned into two groups that were fed either a commercial extruded animal-based diet (MEAT, n = 30) or an experimental extruded vegan diet (PLANT, n = 31) for 12 weeks. Fecal collections occurred at the start of the experimental period and after 3 months of exclusively feeding either diet. Bacterial DNA was extracted from the feces, and the V4 region of the 16S rRNA gene was amplified using PCR and sequenced on Illumina MiSeq. Beta-diversity was measured using Jaccard and Bray-Curtis distances, and the PERMANOVA was used to assess for differences in fecal microbiota within and between groups. Alpha-diversity indices for richness, evenness, and diversity, as well as relative abundance, were calculated and compared between groups. Results Beta-diversity differences occurred between diet groups at exit time-point with differences on Bray-Curtis distances at the family and genus levels (p = 0.007 and p = 0.001, respectively), and for the Jaccard distance at the family and genus level (p = 0.006 and p = 0.011, respectively). Significant differences in alpha-diversity occurred when comparing the PLANT to the MEAT group at the exit time-point with the PLANT group having a lower evenness (p = 0.012), but no significant differences in richness (p = 0.188), or diversity (p = 0.06). At exit-timepoint, compared to the MEAT group, the relative abundance of Fusobacterium, Bacteroides, and Campylobacter was lower in the PLANT group. The relative abundance of Fusobacterium decreased over time in the PLANT group, while no change was observed in the MEAT group. Conclusion These results indicate that vegan diets may change the canine gut microbiota. Future studies are warranted to confirm our results and determine long-term effects of vegan diets on the canine gut microbiome.
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Affiliation(s)
- Brooklynn D. Liversidge
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Diego E. Gomez
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Sarah A. S. Dodd
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Jennifer L. MacNicol
- Department of Animal Biosciences, Ontario Agricultural College, University of Guelph, Guelph, ON, Canada
| | - Jennifer L. Adolphe
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
- Petcurean Pet Nutrition, Chilliwack, BC, Canada
| | - Shauna L. Blois
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Adronie Verbrugghe
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
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Phimister FD, Anderson RC, Thomas DG, Farquhar MJ, Maclean P, Jauregui R, Young W, Butowski CF, Bermingham EN. Using meta-analysis to understand the impacts of dietary protein and fat content on the composition of fecal microbiota of domestic dogs (Canis lupus familiaris): A pilot study. Microbiologyopen 2024; 13:e1404. [PMID: 38515236 PMCID: PMC10958101 DOI: 10.1002/mbo3.1404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 02/07/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024] Open
Abstract
The interplay between diet and fecal microbiota composition is garnering increased interest across various host species, including domestic dogs. While the influence of dietary macronutrients and their associated microbial communities have been extensively reviewed, these reviews are descriptive and do not account for differences in microbial community analysis, nor do they standardize macronutrient content across studies. To address this, a meta-analysis was performed to assess the impact of dietary crude protein ("protein") and dietary crude fat ("fat") on the fecal microbiota composition in healthy dogs. Sixteen publications met the eligibility criteria for the meta-analysis, yielding a final data set of 314 dogs. Diets were classed as low, moderate, high, or supra in terms of protein or fat content. Sequence data from each publication were retrieved from public databases and reanalyzed using consistent bioinformatic pipelines. Analysis of community diversity indices and unsupervised clustering of the data with principal coordinate analysis revealed a small effect size and complete overlap between protein and fat levels at the overall community level. Supervised clustering through random forest analysis and partial least squares-discriminant analysis indicated alterations in the fecal microbiota composition at a more individual taxonomic level, corresponding to the levels of protein or fat. The Prevotellaceae Ga6A1 group and Enterococcus were associated with increasing levels of protein, while Allobaculum and Clostridium sensu stricto 13 were associated with increasing levels of fat. Interestingly, the random forest analyses revealed that Sharpea, despite its low relative abundance in the dog's fecal microbiome, was primarily responsible for the separation of the microbiome for both protein and fat. Future research should focus on validating and understanding the functional roles of these relatively low-abundant genera.
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Affiliation(s)
- Francis D. Phimister
- AgResearch LtdManawatu‐WhanganuiNew Zealand
- School of Agricultural and EnvironmentMassey UniversityManawatu‐WhanganuiNew Zealand
| | | | - David G. Thomas
- School of Agricultural and EnvironmentMassey UniversityManawatu‐WhanganuiNew Zealand
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Podar NA, Carrell AA, Cassidy KA, Klingeman DM, Yang Z, Stahler EA, Smith DW, Stahler DR, Podar M. From wolves to humans: oral microbiome resistance to transfer across mammalian hosts. mBio 2024; 15:e0334223. [PMID: 38299854 PMCID: PMC10936156 DOI: 10.1128/mbio.03342-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 02/02/2024] Open
Abstract
The mammalian mouth is colonized by complex microbial communities, adapted to specific niches, and in homeostasis with the host. Individual microbes interact metabolically and rely primarily on nutrients provided by the host, with which they have potentially co-evolved along the mammalian lineages. The oral environment is similar across mammals, but the diversity, specificity, and evolution of community structure in related or interacting mammals are little understood. Here, we compared the oral microbiomes of dogs with those of wild wolves and humans. In dogs, we found an increased microbial diversity relative to wolves, possibly related to the transition to omnivorous nutrition following domestication. This includes a larger diversity of Patescibacteria than previously reported in any other oral microbiota. The oral microbes are most distinct at bacterial species or strain levels, with few if any shared between humans and canids, while the close evolutionary relationship between wolves and dogs is reflected by numerous shared taxa. More taxa are shared at higher taxonomic levels including with humans, supporting their more ancestral common mammalian colonization followed by diversification. Phylogenies of selected oral bacterial lineages do not support stable human-dog microbial transfers but suggest diversification along mammalian lineages (apes and canids). Therefore, despite millennia of cohabitation and close interaction, the host and its native community controls and limits the assimilation of new microbes, even if closely related. Higher resolution metagenomic and microbial physiological studies, covering a larger mammalian diversity, should help understand how oral communities assemble, adapt, and interact with their hosts.IMPORTANCENumerous types of microbes colonize the mouth after birth and play important roles in maintaining oral health. When the microbiota-host homeostasis is perturbed, proliferation of some bacteria leads to diseases such as caries and periodontitis. Unlike the gut microbiome, the diversity of oral microbes across the mammalian evolutionary space is not understood. Our study compared the oral microbiomes of wild wolves, dogs, and apes (humans, chimpanzees, and bonobos), with the aim of identifying if microbes have been potentially exchanged between humans and dogs as a result of domestication and cohabitation. We found little if any evidence for such exchanges. The significance of our research is in finding that the oral microbiota and/or the host limit the acquisition of exogenous microbes, which is important in the context of natural exclusion of potential novel pathogens. We provide a framework for expanded higher-resolution studies across domestic and wild animals to understand resistance/resilience.
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Affiliation(s)
- Nicholas A. Podar
- School of Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Alyssa A. Carrell
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Kira A. Cassidy
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Dawn M. Klingeman
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Zamin Yang
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Erin A. Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Douglas W. Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Daniel R. Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Mircea Podar
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Wang D, Russel WA, Macdonald KM, De Leon VM, Ay A, Belanger KD. Analysis of the gut microbiome in sled dogs reveals glucosamine- and activity-related effects on gut microbial composition. Front Vet Sci 2024; 11:1272711. [PMID: 38384960 PMCID: PMC10879321 DOI: 10.3389/fvets.2024.1272711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/16/2024] [Indexed: 02/23/2024] Open
Abstract
The composition of the microbiome influences many aspects of physiology and health, and can be altered by environmental factors, including diet and activity. Glucosamine is a dietary supplement often administered to address arthritic symptoms in humans, dogs, and other mammals. To investigate how gut microbial composition varies with glucosamine supplementation, we performed 16S rRNA sequence analysis of fecal samples from 24 Alaskan and Inuit huskies and used mixed effects models to investigate associations with activity, age, and additional factors. Glucosamine ingestion, age, activity, sex, and diet were correlated with differences in alpha-diversity, with diversity decreasing in dogs consuming glucosamine. Beta-diversity analysis revealed clustering of dogs based on glucosamine supplementation status. Glucosamine supplementation and exercise-related activity were associated with greater inter-individual pairwise distances. At the family level, Lactobacillaceae and Anaerovoracaceae relative abundances were lower in supplemented dogs when activity was accounted for. At the genus level, Eubacterium [brachy], Sellimonus, Parvibacter, and an unclassified genus belonging to the same family as Parvibacter (Eggerthellaceae) all were lower in supplemented dogs, but only significantly so post-activity. Our findings suggest that glucosamine supplementation alters microbiome composition in sled dogs, particularly in the context of exercise-related activity.
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Affiliation(s)
- Dong Wang
- Department of Computer Science, Colgate University, Hamilton, NY, United States
- Department of Mathematics, Colgate University, Hamilton, NY, United States
| | - William A. Russel
- Department of Biology, Colgate University, Hamilton, NY, United States
| | | | | | - Ahmet Ay
- Department of Mathematics, Colgate University, Hamilton, NY, United States
- Department of Biology, Colgate University, Hamilton, NY, United States
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Sacoor C, Marugg JD, Lima NR, Empadinhas N, Montezinho L. Gut-Brain Axis Impact on Canine Anxiety Disorders: New Challenges for Behavioral Veterinary Medicine. Vet Med Int 2024; 2024:2856759. [PMID: 38292207 PMCID: PMC10827376 DOI: 10.1155/2024/2856759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 08/28/2023] [Accepted: 10/25/2023] [Indexed: 02/01/2024] Open
Abstract
Anxiety disorders in dogs are ever-growing and represent an important concern in the veterinary behavior field. These disorders are often disregarded in veterinary clinical practice, negatively impacting the animal's and owner's quality of life. Moreover, these anxiety disorders can potentially result in the abandonment or euthanasia of dogs. Growing evidence shows that the gut microbiota is a central player in the gut-brain axis. A variety of microorganisms inhabit the intestines of dogs, which are essential in maintaining intestinal homeostasis. These microbes can impact mental health through several mechanisms, including metabolic, neural, endocrine, and immune-mediated pathways. The disruption of a balanced composition of resident commensal communities, or dysbiosis, is implicated in several pathological conditions, including mental disorders such as anxiety. Studies carried out in rodent models and humans demonstrate that the intestinal microbiota can influence mental health through these mechanisms, including anxiety disorders. Furthermore, novel therapeutic strategies using prebiotics and probiotics have been shown to ameliorate anxiety-related symptoms. However, regarding the canine veterinary behavior field, there is still a lack of insightful research on this topic. In this review, we explore the few but relevant studies performed on canine anxiety disorders. We agree that innovative bacterial therapeutical approaches for canine anxiety disorders will become a promising field of investigation and certainly pave the way for new approaches to these behavioral conditions.
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Affiliation(s)
- Carina Sacoor
- Vasco da Gama Research Center (CIVG), Vasco da Gama University School (EUVG), 3020–210 Coimbra, Portugal
- Department of Veterinary Sciences, School of Agrarian and Veterinary Sciences (ECAV), University of Trás-os-Montes e Alto Douro (UTAD), 5000–801 Vila Real, Portugal
| | - John D. Marugg
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004–504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004–504 Coimbra, Portugal
| | - Nuno R. Lima
- Department of Veterinary Sciences, School of Agrarian and Veterinary Sciences (ECAV), University of Trás-os-Montes e Alto Douro (UTAD), 5000–801 Vila Real, Portugal
- Animal and Veterinary Research Centre (CECAV), UTAD, and Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 5000–801 Vila Real, Portugal
- Innovation in Health and Well-Being Research Unit (iHealth4Well-Being), Polytechnic Health Institute of North (IPSN-CESPU), 4585-116 Gandra, Portugal
| | - Nuno Empadinhas
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004–504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004–504 Coimbra, Portugal
| | - Liliana Montezinho
- Vasco da Gama Research Center (CIVG), Vasco da Gama University School (EUVG), 3020–210 Coimbra, Portugal
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004–504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004–504 Coimbra, Portugal
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Alessandri G, Sangalli E, Facchi M, Fontana F, Mancabelli L, Donofrio G, Ventura M. Metataxonomic analysis of milk microbiota in the bovine subclinical mastitis. FEMS Microbiol Ecol 2023; 99:fiad136. [PMID: 37880979 DOI: 10.1093/femsec/fiad136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/04/2023] [Accepted: 10/23/2023] [Indexed: 10/27/2023] Open
Abstract
Subclinical mastitis is one of the most widespread diseases affecting dairy herds with detrimental effects on animal health, milk productivity, and quality. Despite its multifactorial nature, the presence of pathogenic bacteria is regarded one of the main drivers of subclinical mastitis, causing a disruption of the homeostasis of the bovine milk microbial community. However, bovine milk microbiota alterations associated with subclinical mastitis still represents a largely unexplored research area. Therefore, the species-level milk microbiota of a total of 75 milk samples, collected from both healthy and subclinical mastitis-affected cows from two different stables, was deeply profiled through an ITS, rather than a traditional, and less informative, 16S rRNA gene microbial profiling. Surprisingly, the present pilot study not only revealed that subclinical mastitis is characterized by a reduced biodiversity of the bovine milk microbiota, but also that this disease does not induce standard alterations of the milk microbial community across stables. In addition, a flow cytometry-based total bacterial cell enumeration highlighted that subclinical mastitis is accompanied by a significant increment in the number of milk microbial cells. Furthermore, the combination of the metagenomic and flow cytometry approaches allowed to identify different potential microbial marker strictly correlated with subclinical mastitis across stables.
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Affiliation(s)
- Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Elena Sangalli
- Department of Medical-Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - Mario Facchi
- DVM Bovine Practitioner "Bergamo Veterinari" Group, 24124 Bergamo, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
- GenProbio srl, Via Nazario Sauro 3, 43121 Parma, Italy
| | - Leonardo Mancabelli
- Department of Medicine and Surgery, University of Parma, Via Volturno 39, 43125 Parma, Italy
- Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Gaetano Donofrio
- Department of Medical-Veterinary Science, University of Parma, Strada del Taglio 10, 43126 Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
- Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
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Garrigues Q, Apper E, Rodiles A, Rovere N, Chastant S, Mila H. Composition and evolution of the gut microbiota of growing puppies is impacted by their birth weight. Sci Rep 2023; 13:14717. [PMID: 37679393 PMCID: PMC10484951 DOI: 10.1038/s41598-023-41422-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 08/26/2023] [Indexed: 09/09/2023] Open
Abstract
Low birth weight puppies present an increased risk of neonatal mortality, morbidity, and some long-term health issues. Yet it has not been investigated if those alterations could be linked to the gut microbiota composition and evolution. 57 puppies were weighed at birth and rectal swabs were performed at 5 time points from birth to 28 days of age. Puppies were grouped into three groups based on their birth weight: low birth weight (LBW), normal birth weight (NBW) and high birth weight (HBW). 16S rRNA gene sequencing was used to highlight differences in the fecal microbiota. During the first three weeks, the relative abundance of facultative anaerobic bacteria such as E. coli, C. perfringens and Tyzzerella was higher in LBW feces, but they catch back with the other groups afterwards. HBW puppies showed higher abundances of Faecalibacterium and Bacteroides during the neonatal period, suggesting an earlier maturation of their microbiota. The results of this study suggest that birth weight impact the initial establishment of the gut microbiota in puppies. Innovative strategies would be desired to deal with altered gut microbiota in low birth weight puppies aiming to improve their survival and long term health.
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Affiliation(s)
- Quentin Garrigues
- NeoCare, Reproduction, ENVT, Université de Toulouse, 23 Chemin des Capelles, BP 87614, 31 076, Toulouse Cedex 3, France.
| | | | | | - Nicoletta Rovere
- Department of Health, Animal Science and Food Safety, VESPA, University of Veterinary, 20134, Milan, Italy
| | - Sylvie Chastant
- NeoCare, Reproduction, ENVT, Université de Toulouse, 23 Chemin des Capelles, BP 87614, 31 076, Toulouse Cedex 3, France
| | - Hanna Mila
- NeoCare, Reproduction, ENVT, Université de Toulouse, 23 Chemin des Capelles, BP 87614, 31 076, Toulouse Cedex 3, France
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Stege PB, Hordijk J, Sandholt AKS, Zomer AL, Viveen MC, Rogers MRC, Salomons M, Wagenaar JA, Mughini-Gras L, Willems RJL, Paganelli FL. Gut Colonization by ESBL-Producing Escherichia coli in Dogs Is Associated with a Distinct Microbiome and Resistome Composition. Microbiol Spectr 2023; 11:e0006323. [PMID: 37404183 PMCID: PMC10434115 DOI: 10.1128/spectrum.00063-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
The gut microbiome of humans and animals acts as a reservoir of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC). Dogs are known for having a high prevalence of ESBL-EC in their gut microbiota, although their ESBL-EC carrier status often shifts over time. We hypothesized that the gut microbiome composition of dogs is implicated in ESBL-EC colonization status. Therefore, we assessed whether ESBL-EC carriage in dogs is associated with changes in the gut microbiome and resistome. Fecal samples were collected longitudinally from 57 companion dogs in the Netherlands every 2 weeks for a total of 6 weeks (n = 4 samples/dog). Carriage of ESBL-EC was determined through selective culturing and PCR and in line with previous studies, we observed a high prevalence of ESBL-EC carriage in dogs. Using 16s rRNA gene profiling we found significant associations between detected ESBL-EC carriage and an increased abundance of Clostridium sensu stricto 1, Enterococcus, Lactococcus, and the shared genera of Escherichia-Shigella in the dog microbiome. A resistome capture sequencing approach (ResCap) furthermore, revealed associations between detected ESBL-EC carriage and the increased abundance of the antimicrobial resistance genes: cmlA, dfrA, dhfR, floR, and sul3. In summary, our study showed that ESBL-EC carriage is associated with a distinct microbiome and resistome composition. IMPORTANCE The gut microbiome of humans and animals is an important source of multidrug resistant pathogens, including beta-lactamase-producing Escherichia coli (ESBL-EC). In this study, we assessed if the carriage of ESBL-EC in dogs was associated with changes in gut composition of bacteria and antimicrobial resistant genes (ARGs). Therefore, stool samples from 57 dogs were collected every 2 weeks for a total of 6 weeks. Sixty eight percent of the dogs carried ESBL-EC during at least one of the time points analyzed. By investigating the gut microbiome and resistome composition, we observed specific changes at time points when dogs were colonized with ESBL-EC compared to time points whenESBL-EC were not detected. In conclusion, our study highlights the importance to study the microbial diversity in companion animals, as gut colonization of particular antimicrobial resistant bacteria might be an indication of a changed microbial composition that is associated with the selection of particular ARGs.
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Affiliation(s)
- Paul B. Stege
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Joost Hordijk
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Arnar K. S. Sandholt
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Aldert L. Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from an One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Marco C. Viveen
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Malbert R. C. Rogers
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Moniek Salomons
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from an One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Lapo Mughini-Gras
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Rob J. L. Willems
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Fernanda L. Paganelli
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
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10
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Lapid R, Motro Y, Craddock H, Khalfin B, King R, Bar-Gal GK, Moran-Gilad J. Fecal microbiota of the synanthropic golden jackal (Canis aureus). Anim Microbiome 2023; 5:37. [PMID: 37542305 PMCID: PMC10403885 DOI: 10.1186/s42523-023-00259-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
The golden jackal (Canis aureus), is a medium canid carnivore widespread throughout the Mediterranean region and expanding into Europe. This species thrives near human settlements and is implicated in zoonoses such as rabies. This study explores for the first time, the golden jackal fecal microbiota. We analyzed 111 fecal samples of wild golden jackals using 16S rRNA amplicon sequencing the connection of the microbiome to animal characteristics, burden of pathogens and geographic and climate characteristics. We further compared the fecal microbiota of the golden jackal to the black-backed jackal and domestic dog. We found that the golden jackal fecal microbiota is dominated by the phyla Bacteroidota, Fusobacteriota and Firmicutes. The golden jackal fecal microbiota was associated with different variables, including geographic region, age-class, exposure to rabies oral vaccine, fecal parasites and toxoplasmosis. A remarkable variation in the relative abundance of different taxa was also found associated with different variables, such as age-class. Linear discriminant analysis effect size (LEfSe) analysis found abundance of specific taxons in each region, Megasphaera genus in group 1, Megamonas genus in group 2 and Bacteroides coprocola species in group 3. We also found a different composition between the fecal microbiota of the golden jackal, blacked-backed jackal and the domestic dog. Furthermore, LEfSe analysis found abundance of Fusobacterium and Bacteroides genera in the golden jackal, Clostridia class in blacked-backed jackal and Megamonas genus in domestic dog. The golden jackal fecal microbiota is influenced by multiple factors including host traits and pathogen burden. The characterization of the microbiota of this thriving species may aid in mapping its spread and proximity to human settlements. Moreover, understanding the jackal microbiota could inform the study of potential animal and human health risks and inform control measures.
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Affiliation(s)
- Roi Lapid
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O.B. 12, 7610001, Rehovot, Israel
| | - Yair Motro
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Hillary Craddock
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Boris Khalfin
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Roni King
- Science and Conservation Division, Israel Nature and Parks Authority, 3 Am Ve'Olamo St., 95463, Jerusalem, Israel
| | - Gila Kahila Bar-Gal
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O.B. 12, 7610001, Rehovot, Israel
| | - Jacob Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel.
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11
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St-Pierre B, Perez Palencia JY, Samuel RS. Impact of Early Weaning on Development of the Swine Gut Microbiome. Microorganisms 2023; 11:1753. [PMID: 37512925 PMCID: PMC10385335 DOI: 10.3390/microorganisms11071753] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Considering that pigs are naturally weaned between 12 and 18 weeks of age, the common practice in the modern swine industry of weaning as early as between two and four weeks of age increases challenges during this transition period. Indeed, young pigs with an immature gut are suddenly separated from the sow, switched from milk to a diet consisting of only solid ingredients, and subjected to a new social hierarchy from mixing multiple litters. From the perspective of host gut development, weaning under these conditions causes a regression in histological structure as well as in digestive and barrier functions. While the gut is the main center of immunity in mature animals, the underdeveloped gut of early weaned pigs has yet to contribute to this function until seven weeks of age. The gut microbiota or microbiome, an essential contributor to the health and nutrition of their animal host, undergoes dramatic alterations during this transition, and this descriptive review aims to present a microbial ecology-based perspective on these events. Indeed, as gut microbial communities are dependent on cross-feeding relationships, the change in substrate availability triggers a cascade of succession events until a stable composition is reached. During this process, the gut microbiota is unstable and prone to dysbiosis, which can devolve into a diseased state. One potential strategy to accelerate maturation of the gut microbiome would be to identify microbial species that are critical to mature swine gut microbiomes, and develop strategies to facilitate their establishment in early post-weaning microbial communities.
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Affiliation(s)
- Benoit St-Pierre
- Department of Animal Science, South Dakota State University, Animal Science Complex, Box 2170, Brookings, SD 57007, USA
| | - Jorge Yair Perez Palencia
- Department of Animal Science, South Dakota State University, Animal Science Complex, Box 2170, Brookings, SD 57007, USA
| | - Ryan S Samuel
- Department of Animal Science, South Dakota State University, Animal Science Complex, Box 2170, Brookings, SD 57007, USA
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12
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Fan C, Xue H, Xu J, Wang S, Wu M, Chen L, Xu L. Host-Specific Differences in Gut Microbiota Between Cricetulus barabensis and Phodopus sungorus. Curr Microbiol 2023; 80:149. [PMID: 36971869 DOI: 10.1007/s00284-023-03274-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 03/17/2023] [Indexed: 03/29/2023]
Abstract
Gut microbiota plays an important role in the health of the host and is usually associated with the physiological processes of animals. Both host-specific factors and environmental factors are involved in the shaping of the gut microbial community, and it is necessary to identify the host-dominated differences in gut microbiota among animal species to better explain how they affect the choice of life history strategies in hosts. Here, striped hamsters Cricetulus barabensis and Djungarian hamsters Phodopus sungorus were housed under the same controlled conditions, and fecal samples were collected to compare gut microbiota. A higher Shannon index was observed in striped hamsters than in Djungarian hamsters. Linear discriminant analysis of effect size showed enrichment of the family Lachnospiraceae and genera Muribaculum and Oscillibacter in striped hamsters, with the enrichment of family Erysipelotrichaceae and genus Turicibacter in Djungarian hamsters. Among the top 10 amplicon sequence variants (ASVs), eight showed significantly different relative abundance between the two hamster species. The positive correlations and average degree in the co-occurrence network of striped hamsters were less than those of Djungarian hamsters, showing different complexity of synergistic effects among the gut bacteria. The gut microbial community of striped hamsters had a higher R2 value than that of Djungarian hamsters when fitted with a neutral community model. These differences have a degree of consistency with the variation in the lifestyles of the two hamster species. The study provides insights into the understanding of gut microbiota and its connections with rodent hosts.
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Affiliation(s)
- Chao Fan
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China.
| | - Huiliang Xue
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Jinhui Xu
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Shuo Wang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Ming Wu
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Lei Chen
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Laixiang Xu
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
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13
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Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium. NPJ Biofilms Microbiomes 2022; 8:88. [PMID: 36316342 PMCID: PMC9622858 DOI: 10.1038/s41522-022-00349-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
In vitro gut cultivation models provide host-uncoupled, fast, and cost-efficient solutions to investigate the effects of intrinsic and extrinsic factors impacting on both composition and functionality of the intestinal microbial ecosystem. However, to ensure the maintenance and survival of gut microbial players and preserve their functions, these systems require close monitoring of several variables, including oxygen concentration, pH, and temperature, as well as the use of a culture medium satisfying the microbial nutritional requirements. In this context, in order to identify the macro- and micro-nutrients necessary for in vitro cultivation of the infant gut microbiota, a meta-analysis based on 1669 publicly available shotgun metagenomic samples corresponding to fecal samples of healthy, full-term infants aged from a few days to three years was performed to define the predominant species characterizing the “infant-like” gut microbial ecosystem. A subsequent comparison of growth performances was made using infant fecal samples that contained the most abundant bacterial taxa of the infant gut microbiota, when cultivated on 18 different culture media. This growth analysis was performed by means of flow cytometry-based bacterial cell enumeration and shallow shotgun sequencing, which allowed the formulation of an optimized growth medium, i.e., Infant Gut Super Medium (IGSM), which maintains and sustains the infant gut microbial biodiversity under in vitro growth conditions. Furthermore, this formulation was used to evaluate the in vitro effect of two drugs commonly used in pediatrics, i.e., acetaminophen and simethicone, on the taxonomic composition of the infant gut microbiota.
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14
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The Resemblance between Bacterial Gut Colonization in Pigs and Humans. Microorganisms 2022; 10:microorganisms10091831. [PMID: 36144433 PMCID: PMC9500663 DOI: 10.3390/microorganisms10091831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/02/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
Thorough understanding of the initial colonization process of human intestines is important to optimize the prevention of microbiota-associated diseases, and also to further improve the current microbial therapies. In recent years, therefore, colonization of the human gut has gained renewed interest. However, due to a lack of standardization of life events that might influence this early colonization process in humans, many generally accepted insights are based on deduction and assumption. In our review, we compare knowledge on colonization in humans with research in piglets, because the intestinal tract of pigs is remarkably similar to that of humans and the early-life events are more standardized. We assess potential similarities and challenge some concepts that have been widely accepted in human microbiota research. Bacterial colonization of the human gut is characterized by successive waves in a progressive process, to a complex gut microbiota community. After re-analyzing available data from piglets, we found that the bacterial colonization process is very similar in terms of the wave sequence and functionality of each wave. Moreover, based on the piglet data, we found that, in addition to external factors such as suckling and nutrition, the bacterial community itself appears to have a major influence on the colonization success of additional bacteria in the intestine. Thus, the colonization process in piglets might rely, at least in part, on niche dependency, an ecological principle to be considered in the intestinal colonization process in humans.
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15
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Phenotypic correlates of the working dog microbiome. NPJ Biofilms Microbiomes 2022; 8:66. [PMID: 35995802 PMCID: PMC9395329 DOI: 10.1038/s41522-022-00329-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
Dogs have a key role in law enforcement and military work, and research with the goal of improving working dog performance is ongoing. While there have been intriguing studies from lab animal models showing a potential connection between the gut microbiome and behavior or mental health there is a dearth of studies investigating the microbiome-behavior relationship in working dogs. The overall objective of this study was to characterize the microbiota of working dogs and to determine if the composition of the microbiota is associated with behavioral and performance outcomes. Freshly passed stools from each working canine (Total n = 134) were collected and subject to shotgun metagenomic sequencing using Illumina technology. Behavior, performance, and demographic metadata were collected. Descriptive statistics and prediction models of behavioral/phenotypic outcomes using gradient boosting classification based on Xgboost were used to study associations between the microbiome and outcomes. Regarding machine learning methodology, only microbiome features were used for training and predictors were estimated in cross-validation. Microbiome markers were statistically associated with motivation, aggression, cowardice/hesitation, sociability, obedience to one trainer vs many, and body condition score (BCS). When prediction models were developed based on machine learning, moderate predictive power was observed for motivation, sociability, and gastrointestinal issues. Findings from this study suggest potential gut microbiome markers of performance and could potentially advance care for working canines.
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16
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Meazzi S, Lauzi S, Martini V, Ferriani R, Peri M, Zanzani SA, Giordano A. Gut Microbiota and Lymphocyte Subsets in Canine Leishmaniasis. Front Vet Sci 2022; 9:868967. [PMID: 35909678 PMCID: PMC9326463 DOI: 10.3389/fvets.2022.868967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/16/2022] [Indexed: 11/19/2022] Open
Abstract
Gut microbiota seems to interact with immune system. Canine leishmaniasis pathogenesis and severity of disease lean on the host immunity, but there is no information in literature about gut microbiota in infected animals. Thus, this study aims to compare the microbiota composition and leukocyte subset of healthy dogs with those of asymptomatic dogs exposed to Leishmania spp. and dogs with clinical leishmaniasis. Thirty-nine dogs were enrolled and grouped into three groups: healthy, exposed asymptomatic and infected symptomatic for Leishmania spp. Flow cytometry on whole blood evaluated the prevalence of CD4, CD5, CD8, CD11b, CD14, and CD21 positive cells. Gut microbiota was investigated using a next generation sequencing (NGS) technique. Firmicutes resulted significantly more abundant in the healthy dogs compared with the other two groups. Conversely, Proteobacteria were more abundant in symptomatic dogs. Even in rarest phyla comparison some significant differences were found, as well as in comparison at classes, order, family and genus levels. The symptomatic group had lower concentration of all the lymphocyte classes (CD5, CD21, CD4, CD8) compared to the other groups. A lower abundance of Firmicutes is reported in literature in diseased animals compared to the healthy ones and this is in agreement with the results of this study. Increased Proteobacteria in sick animals could suggest a dysbiosis status, even without distinct gastrointestinal signs. The leukocyte classes results indicate a decreased Th1 response in symptomatic dogs. Studies also investigating the cytokine response could deepen the knowledge on the pathogenesis of canine leishmaniasis.
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Affiliation(s)
- Sara Meazzi
- Department of Veterinary Medicine and Animal Sciences, University of Milan, Lodi, Italy
| | - Stefania Lauzi
- Department of Veterinary Medicine and Animal Sciences, University of Milan, Lodi, Italy
- *Correspondence: Stefania Lauzi
| | - Valeria Martini
- Department of Veterinary Medicine and Animal Sciences, University of Milan, Lodi, Italy
| | | | - Margherita Peri
- Department of Veterinary Medicine and Animal Sciences, University of Milan, Lodi, Italy
| | | | - Alessia Giordano
- Department of Veterinary Medicine and Animal Sciences, University of Milan, Lodi, Italy
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17
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Morelli G, Patuzzi I, Losasso C, Ricci A, Contiero B, Andrighetto I, Ricci R. Characterization of intestinal microbiota in normal weight and overweight Border Collie and Labrador Retriever dogs. Sci Rep 2022; 12:9199. [PMID: 35655089 PMCID: PMC9163050 DOI: 10.1038/s41598-022-13270-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/12/2022] [Indexed: 11/08/2022] Open
Abstract
Obesity in dogs is an emerging issue that affects canine health and well-being. Its development is ascribed to several factors, including genetic predisposition and dietary management, and recent evidence suggests that intestinal microbiota may be involved as well. Previous works have shown obesity to be linked to significant changes in gut microbiota composition in humans and mice, but only limited information is available on the role played by canine gut microbiota. The aim of this exploratory study was to investigate whether composition of canine faecal microbiota may be influenced by overweight condition and breed. All the enrolled companion dogs were young adults, intact, healthy, and fed commercial extruded pet food; none had received antibiotics, probiotics or immunosuppressant drugs in the previous six months. Labrador Retriever (LR) and Border Collie (BC) were chosen as reference breeds and Body Condition Score (BCS) on a 9-point scale as reference method for evaluating body fat. The faecal microbial communities of 15 lean (BCS 4-5/9; 7 LRs and 8 BCs) and 14 overweight (BCS > 5/9; 8 LRs and 6 BCs) family dogs were analysed using 16S rRNA gene sequencing. Moreover, for each dog, the daily intake of energy (kcal/d) and dietary macronutrients (g/d) were calculated according to an accurate feeding history collection. Firmicutes and Bacteroidetes resulted the predominant phyla (51.5 ± 10.0% and 33.4 ± 8.5%, respectively) in all dogs. Bioinformatic and statistical analysis revealed that no bacterial taxon differed significantly based on body condition, except for genus Allisonella (p < 0.05); BC gut microbiota was richer (p < 0.05) in bacteria belonging to phyla Actinobacteria (family Coriobacteriaceae in particular) and Firmicutes (Allobaculum and Roseburia genera). No remarkable differences were recorded either for diversity indices (i.e., alpha diversity, p > 0.10) or for divergence within the sample set (i.e., beta diversity, p > 0.05). PERMANOVA tests performed on single factors demonstrated the tendency of dietary protein to influence the recruited dogs' microbiota beta-diversity at amplicon sequence variant level (p = 0.08). In conclusion, the faecal microbiota of dogs involved in this exploratory study showed no major variations based on body condition. However, our findings suggested that certain bacterial taxa previously acknowledged in obesity-related studies may be detected in dissimilar amounts depending on canine breed.
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Affiliation(s)
- Giada Morelli
- Department of Animal Medicine, Production and Health, University of Padua, 35020, Legnaro, PD, Italy.
| | - Ilaria Patuzzi
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, 35020, Legnaro, PD, Italy
- Research and Development Division, EuBiome S.R.L., 35129, Padua, Italy
| | - Carmen Losasso
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, 35020, Legnaro, PD, Italy
| | - Antonia Ricci
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, 35020, Legnaro, PD, Italy
| | - Barbara Contiero
- Department of Animal Medicine, Production and Health, University of Padua, 35020, Legnaro, PD, Italy
| | - Igino Andrighetto
- Department of Animal Medicine, Production and Health, University of Padua, 35020, Legnaro, PD, Italy
| | - Rebecca Ricci
- Department of Animal Medicine, Production and Health, University of Padua, 35020, Legnaro, PD, Italy
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18
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Zhao R, Hao J, Yang J, Tong C, Xie L, Xiao D, Zeng Z, Xiong W. The co-occurrence of antibiotic resistance genes between dogs and their owners in families. IMETA 2022; 1:e21. [PMID: 38868570 PMCID: PMC10989978 DOI: 10.1002/imt2.21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/18/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2024]
Abstract
The intimate relationship between humans and companion animals causes a unique and critical aspect of antimicrobial resistance in humans. However, a comprehensive analysis of antimicrobial resistance between companion animals and their owners is lacking. Here, we chose 13 owned dogs and 16 owners as well as 22 kennel dogs to analyze the effect of an intimate relationship between owned dogs and owners on their gut microbiome, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) and study the correlation of antimicrobial resistance between dogs and their owners in families by metagenomics. Dog gut microbiota had a higher abundance and diversity of ARGs while owners had a higher diversity of taxonomy. In the owned dog gut microbial community, ARG and MGE compositions were significantly more similar to the owner's gut microbiota than those of others. From the perspective of families, there was a strong correlation between macrolide resistance genes between dogs and their owners. In conclusion, our study demonstrated the correlation of ARGs between dogs and their owners at a community-wide level. These findings can alarm the use of antibiotics in companion animals, which implies the potential to harbor antimicrobial resistance and threaten public health.
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Affiliation(s)
- Ruonan Zhao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouGuangdongChina
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
| | - Jie Hao
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouGuangdongChina
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
| | - Jintao Yang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
| | - Cuihong Tong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouGuangdongChina
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
| | - Longfei Xie
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouGuangdongChina
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
| | - Danyu Xiao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouGuangdongChina
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouGuangdongChina
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouGuangdongChina
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouGuangdongChina
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19
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Yarlagadda K, Zachwieja AJ, de Flamingh A, Phungviwatnikul T, Rivera-Colón AG, Roseman C, Shackelford L, Swanson KS, Malhi RS. Geographically diverse canid sampling provides novel insights into pre-industrial microbiomes. Proc Biol Sci 2022; 289:20220052. [PMID: 35506233 PMCID: PMC9065982 DOI: 10.1098/rspb.2022.0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Canine microbiome studies are often limited in the geographic and temporal scope of samples studied. This results in a paucity of data on the canine microbiome around the world, especially in contexts where dogs may not be pets or human associated. Here, we present the shotgun sequences of fecal microbiomes of pet dogs from South Africa, shelter and stray dogs from India, and stray village dogs in Laos. We additionally performed a dietary experiment with dogs housed in a veterinary medical school, attempting to replicate the diet of the sampled dogs from Laos. We analyse the taxonomic diversity in these populations and identify the underlying functional redundancy of these microbiomes. Our results show that diet alone is not sufficient to recapitulate the higher diversity seen in the microbiome of dogs from Laos. Comparisons to previous studies and ancient dog fecal microbiomes highlight the need for greater population diversity in studies of canine microbiomes, as modern analogues can provide better comparisons to ancient microbiomes. We identify trends in microbial diversity and industrialization in dogs that mirror results of human studies, suggesting future research can make use of these companion animals as substitutes for humans in studying the effects of industrialization on the microbiome.
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Affiliation(s)
- K Yarlagadda
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - A J Zachwieja
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth, Duluth, Minnesota, USA
| | - A de Flamingh
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - T Phungviwatnikul
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - A G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - C Roseman
- School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - L Shackelford
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - K S Swanson
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - R S Malhi
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Department of Evolution, Ecology, and Behavior, University of Illinois Urbana-Champaign, Urbana, IL, USA.,School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
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20
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Domestic Environment and Gut Microbiota: Lessons from Pet Dogs. Microorganisms 2022; 10:microorganisms10050949. [PMID: 35630391 PMCID: PMC9143008 DOI: 10.3390/microorganisms10050949] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/12/2022] Open
Abstract
Accumulating data show the involvement of intestinal microbiota in the development and maintenance of numerous diseases. Many environmental factors influence the composition and function of the gut microbiota. An animal model subjected to the same environmental constraints that will allow better characterization of the microbiota–host dialogue is awaited. The domestic dog has physiological, dietary and pathological characteristics similar to those of humans and shares the domestic environment and lifestyle of its owner. This review exposes how the domestication of dogs has brought them closer to humans based on their intrinsic and extrinsic similarities which were discerned through examining and comparing the current knowledge and data on the intestinal microbiota of humans and canines in the context of several spontaneous pathologies, including inflammatory bowel disease, obesity and diabetes mellitus.
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Kopper JJ, Iennarella-Servantez C, Jergens AE, Sahoo DK, Guillot E, Bourgois-Mochel A, Martinez MN, Allenspach K, Mochel JP. Harnessing the Biology of Canine Intestinal Organoids to Heighten Understanding of Inflammatory Bowel Disease Pathogenesis and Accelerate Drug Discovery: A One Health Approach. FRONTIERS IN TOXICOLOGY 2022; 3:773953. [PMID: 35295115 PMCID: PMC8915821 DOI: 10.3389/ftox.2021.773953] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022] Open
Abstract
In a recent issue of the Lancet, the prevalence of Inflammatory Bowel Disease (IBD) was estimated at 7 million worldwide. Overall, the burden of IBD is rising globally, with direct and indirect healthcare costs ranging between $14.6 and $31.6 billion in the U.S. alone in 2014. There is currently no cure for IBD, and up to 40% of patients do not respond to medical therapy. Although the exact determinants of the disease pathophysiology remain unknown, the prevailing hypothesis involves complex interplay among host genetics, the intestinal microenvironment (primarily bacteria and dietary constituents), and the mucosal immune system. Importantly, multiple chronic diseases leading to high morbidity and mortality in modern western societies, including type II diabetes, IBD and colorectal cancer, have epidemiologically been linked to the consumption of high-calorie, low-fiber, high monosaccharide, and high-fat diets (HFD). More specifically, data from our laboratory and others have shown that repeated consumption of HFD triggers dysbiotic changes of the gut microbiome concomitant with a state of chronic intestinal inflammation and increased intestinal permeability. However, progress in our understanding of the effect of dietary interventions on IBD pathogenesis has been hampered by a lack of relevant animal models. Additionally, current in vitro cell culture systems are unable to emulate the in vivo interplay between the gut microbiome and the intestinal epithelium in a realistic and translatable way. There remains, therefore, a critical need to develop translatable in vitro and in vivo models that faithfully recapitulate human gut-specific physiological functions to facilitate detailed mechanistic studies on the impact of dietary interventions on gut homeostasis. While the study of murine models has been pivotal in advancing genetic and cellular discoveries, these animal systems often lack key clinical signs and temporal pathological changes representative of IBD. Specifically, some limitations of the mouse model are associated with the use of genetic knockouts to induce immune deficiency and disease. This is vastly different from the natural course of IBD developing in immunologically competent hosts, as is the case in humans and dogs. Noteworthily, abundant literature suggests that canine and human IBD share common clinical and molecular features, such that preclinical studies in dogs with naturally occurring IBD present an opportunity to further our understanding on disease pathogenesis and streamline the development of new therapeutic strategies. Using a stepwise approach, in vitro mechanistic studies investigating the contribution of dietary interventions to chronic intestinal inflammation and "gut leakiness" could be performed in intestinal organoids and organoid derived monolayers. The biologic potential of organoids stems from the method's ability to harness hard-wired cellular programming such that the complexity of the disease background can be reflected more accurately. Likewise, the effect of therapeutic drug candidates could be evaluated in organoids prior to longitudinal studies in dog and human patients with IBD. In this review, we will discuss the value (and limitations) of intestinal organoids derived from a spontaneous animal disease model of IBD (i.e., the dog), and how it can heighten understanding of the interplay between dietary interventions, the gut microbiota and intestinal inflammation. We will also review how intestinal organoids could be used to streamline the preclinical development of therapeutic drug candidates for IBD patients and their best four-legged friends.
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Affiliation(s)
- Jamie J Kopper
- Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States.,SMART Translational Medicine, Biomedical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States
| | - Chelsea Iennarella-Servantez
- SMART Pharmacology, Biomedical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States.,SMART Translational Medicine, Biomedical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States
| | - Albert E Jergens
- Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States
| | - Dipak K Sahoo
- Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States.,SMART Translational Medicine, Biomedical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States
| | - Emilie Guillot
- 3D Health Solutions, Inc., ISU Research Park, Ames, IA, United States
| | - Agnes Bourgois-Mochel
- Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States
| | - Marilyn N Martinez
- Office of New Animal Drug Evaluation, Center for Veterinary Medicine, Food and Drug Administration, Rockville, MD, United States
| | - Karin Allenspach
- Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States.,SMART Translational Medicine, Biomedical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States.,3D Health Solutions, Inc., ISU Research Park, Ames, IA, United States
| | - Jonathan P Mochel
- SMART Pharmacology, Biomedical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States.,SMART Translational Medicine, Biomedical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, United States.,3D Health Solutions, Inc., ISU Research Park, Ames, IA, United States
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22
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Disclosing the Genomic Diversity among Members of the Bifidobacterium Genus of Canine and Feline Origin with Respect to Those from Human. Appl Environ Microbiol 2022; 88:e0203821. [PMID: 35285708 DOI: 10.1128/aem.02038-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In recent decades, much scientific attention has been paid to characterizing members of the genus Bifidobacterium due to their well-accepted ability to exert various beneficial effects upon their host. However, despite the well-accepted status of dogs and cats as principal companion animals of humans, the bifidobacterial communities that colonize their gut still represents a rather unexplored research area. To expand and further investigate the bifidobacterial ecosystem inhabiting the canine and feline intestine, strains belonging to this genus were isolated from fecal samples of dogs and cats and subjected to de novo sequencing. The obtained sequencing data, together with publicly available genomes of strains belonging to the same bifidobacterial species of our isolates, and of both human and animal origin, were employed for in-depth comparative genome analyses. These phylogenomic investigations highlighted a different degree of genetic variability between human- or pet-derived bifidobacteria depending on the considered species, with B. pseudocatenulatum strains of pet origin showing higher genetic variability than human-derived strains of the same bifidobacterial species. Furthermore, in silico evaluation of metabolic activities coupled with in vitro growth assays revealed the crucial role of diet in driving the genetic assembly of bifidobacteria as a result of their adaptation to the specific ecological niche they colonize. IMPORTANCE Despite cats and dogs being well recognized as the most intimate companion animals to humans, current knowledge on canine and feline gut microbial consortia is still far from being fully dissected compared to the significant advances achieved for other microbial ecosystems, such as the human gut microbiota. In this context, a combination of in silico genome-based analysis and in vitro carbohydrate growth assay allowed us to further explore the canine and feline bifidobacterial community with respect to that inhabiting the human intestine. Specifically, these data revealed how strains of different bifidobacterial species seem to have evolved a different degree of host-specific adaptation. In detail, genotypic and phenotypic evidence of how diet can be considered the main factor of this host-specific adaptation is provided.
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23
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Thomson P, Santibáñez R, Rodríguez-Salas C, Flores-Yañez C, Garrido D. Differences in the composition and predicted functions of the intestinal microbiome of obese and normal weight adult dogs. PeerJ 2022; 10:e12695. [PMID: 35190784 PMCID: PMC8857902 DOI: 10.7717/peerj.12695] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023] Open
Abstract
Obesity is a multifactorial nutritional disorder highly prevalent in dogs, observed in developed and developing countries. It is estimated that over 40% of the canine population suffers from obesity, which manifests in an increased risk of chronic osteoarticular, metabolic, and cardiovascular diseases. The intestinal microbiome of obese animals shows increases in the abundance of certain members capable of extracting energy from complex polysaccharides. The objective of this study was to compare the composition and predicted function of the intestinal microbiome of Chilean obese and normal weight adult dogs. Twenty clinically healthy dogs were classified according to their body condition score (BCS) as obese (n = 10) or normal weight (n = 10). DNA was extracted from stool samples, followed by next-generation sequencing of the 16S rRNA V3-V4 region and bioinformatics analysis targeting microbiome composition and function. Significant differences were observed between these groups at the phylum level, with anincrease in Firmicutes and a decrease in Bacteroidetes in obese dogs. Microbiome compositions of these animals correlated with their BCS, and obese dogs showed enrichment in pathways related to transport, chemotaxis, and flagellar assembly. These results highlight the differences in the gut microbiome between normal weight and obese dogs and prompt further research to improve animal health by modulating the gut microbiome.
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Affiliation(s)
- Pamela Thomson
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Nacional Andrés Bello., Santiago, Chile
| | - Rodrigo Santibáñez
- Chemical and Bioprocess Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Camila Rodríguez-Salas
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Nacional Andrés Bello., Santiago, Chile
| | | | - Daniel Garrido
- Chemical and Bioprocess Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
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24
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Isidori M, Corbee RJ, Trabalza-Marinucci M. Nonpharmacological Treatment Strategies for the Management of Canine Chronic Inflammatory Enteropathy—A Narrative Review. Vet Sci 2022; 9:vetsci9020037. [PMID: 35202290 PMCID: PMC8878421 DOI: 10.3390/vetsci9020037] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/15/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
Chronic inflammatory enteropathy (CIE) refers to a heterogeneous group of idiopathic diseases of the dog characterised by persistent gastrointestinal (GI) clinical signs. If conventional dietary treatment alone would be unsuccessful, management of CIE is traditionally attained by the use of pharmaceuticals, such as antibiotics and immunosuppressive drugs. While being rather effective, however, these drugs are endowed with side effects, which may impact negatively on the animal’s quality of life. Therefore, novel, safe and effective therapies for CIE are highly sought after. As gut microbiota imbalances are often associated with GI disorders, a compelling rationale exists for the use of nonpharmacological methods of microbial manipulation in CIE, such as faecal microbiota transplantation and administration of pre-, pro-, syn- and postbiotics. In addition to providing direct health benefits to the host via a gentle modulation of the intestinal microbiota composition and function, these treatments may also possess immunomodulatory and epithelial barrier-enhancing actions. Likewise, intestinal barrier integrity, along with mucosal inflammation, are deemed to be two chief therapeutic targets of mesenchymal stem cells and selected vegetable-derived bioactive compounds. Although pioneering studies have revealed encouraging findings regarding the use of novel treatment agents in CIE, a larger body of research is needed to address fully their mode of action, efficacy and safety.
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Affiliation(s)
- Marco Isidori
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy;
- Correspondence:
| | - Ronald Jan Corbee
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Yalelaan 108, 3584 CM Utrecht, The Netherlands;
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García-Belenguer S, Grasa L, Valero O, Palacio J, Luño I, Rosado B. Gut Microbiota in Canine Idiopathic Epilepsy: Effects of Disease and Treatment. Animals (Basel) 2021; 11:ani11113121. [PMID: 34827852 PMCID: PMC8614570 DOI: 10.3390/ani11113121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/22/2021] [Accepted: 10/29/2021] [Indexed: 12/22/2022] Open
Abstract
Simple Summary There is evidence that supports the existence of a gut-brain axis system through which bi-directional communication occurs between gut bacteria and the brain. Epilepsy is one of the most common neurological disorders in humans and dogs. The role of microbiota in epilepsy remains unknown but it has been suggested that it is a possible influence of gut bacteria in controlling seizures. The aim of this study was to investigate the changes in gut microbiota from dogs with idiopathic epilepsy and the possible effect of antiepileptic drugs on the modulation of the composition of this microbiota. In comparison with control dogs, drug-naive epileptic individuals showed a significantly reduced abundance of GABA and SCFAs-producing bacteria, as well as bacteria associated with reduced risk for brain disease. Moreover, the use of phenobarbital or imepitoin monotherapy during one month in epileptic dogs did not modify the gut microbiota composition. These results open up the possibility of studying probiotic interventions in epilepsy. Considering the phylogenetic and metabolic similarities in intestinal microbiome between humans and dogs, this study contributes to the understanding of epilepsy both in human and veterinary medicine. Abstract Epilepsy is one of the most common neurological disorders in humans and dogs. The structure and composition of gut microbiome associated to this disorder has not yet been analyzed in depth but there is evidence that suggests a possible influence of gut bacteria in controlling seizures. The aim of this study was to investigate the changes in gut microbiota associated to canine idiopathic epilepsy (IE) and the possible influence of antiepileptic drugs (AEDs) on the modulation of this microbiota. Faecal microbiota composition was analyzed using sequencing of bacterial 16S rRNA gene in a group of healthy controls (n = 12) and a group of epileptic dogs both before (n = 10) and after a 30-day single treatment with phenobarbital or imepitoin (n = 9). Epileptic dogs showed significantly reduced abundance of GABA (Pseudomonadales, Pseudomonadaceae, Pseudomonas and Pseudomona_graminis) and SCFAs-producing bacteria (Peptococcaceae, Ruminococcaceae and Anaerotruncus) as well as bacteria associated with reduced risk for brain disease (Prevotellaceae) than control dogs. The administration of AEDs during 30 days did not modify the gut microbiota composition. These results are expected to contribute to the understanding of canine idiopathic epilepsy and open up the possibility of studying new therapeutic approaches for this disorder, including probiotic intervention to restore gut microbiota in epileptic individuals.
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Affiliation(s)
- Sylvia García-Belenguer
- Departamento de Patología Animal, Facultad de Veterinaria, Universidad de Zaragoza, Miguel Servet, 177, 50013 Zaragoza, Spain; (O.V.); (J.P.); (I.L.); (B.R.)
- Correspondence:
| | - Laura Grasa
- Departamento de Farmacología, Fisiología y Medicina Legal y Forense, Facultad de Veterinaria, Universidad de Zaragoza, Miguel Servet, 177, 50013 Zaragoza, Spain;
- Instituto de Investigación Sanitaria de Aragón (IIS), 50009 Zaragoza, Spain
- Instituto Agroalimentario de Aragón—IA2, Universidad de Zaragoza—CITA, 50009 Zaragoza, Spain
| | - Olga Valero
- Departamento de Patología Animal, Facultad de Veterinaria, Universidad de Zaragoza, Miguel Servet, 177, 50013 Zaragoza, Spain; (O.V.); (J.P.); (I.L.); (B.R.)
| | - Jorge Palacio
- Departamento de Patología Animal, Facultad de Veterinaria, Universidad de Zaragoza, Miguel Servet, 177, 50013 Zaragoza, Spain; (O.V.); (J.P.); (I.L.); (B.R.)
| | - Isabel Luño
- Departamento de Patología Animal, Facultad de Veterinaria, Universidad de Zaragoza, Miguel Servet, 177, 50013 Zaragoza, Spain; (O.V.); (J.P.); (I.L.); (B.R.)
| | - Belén Rosado
- Departamento de Patología Animal, Facultad de Veterinaria, Universidad de Zaragoza, Miguel Servet, 177, 50013 Zaragoza, Spain; (O.V.); (J.P.); (I.L.); (B.R.)
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26
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Xu J, Becker AAMJ, Luo Y, Zhang W, Ge B, Leng C, Wang G, Ding L, Wang J, Fu X, Janssens GPJ. The Fecal Microbiota of Dogs Switching to a Raw Diet Only Partially Converges to That of Wolves. Front Microbiol 2021; 12:701439. [PMID: 34659139 PMCID: PMC8511826 DOI: 10.3389/fmicb.2021.701439] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/20/2021] [Indexed: 11/13/2022] Open
Abstract
The genomic signature of dog domestication reveals adaptation to a starch-rich diet compared with their ancestor wolves. Diet is a key element to shape gut microbial populations in a direct way as well as through coevolution with the host. We investigated the dynamics in the gut microbiota of dogs when shifting from a starch-rich, processed kibble diet to a nature-like raw meat diet, using wolves as a wild reference. Six healthy wolves from a local zoo and six healthy American Staffordshire Terriers were included. Dogs were fed the same commercial kibble diet for at least 3 months before sampling at day 0 (DC), and then switched to a raw meat diet (the same diet as the wolves) for 28 days. Samples from the dogs were collected at day 1 (DR1), week 1 (DR7), 2 (DR14), 3 (DR21), and 4 (DR28). The data showed that the microbial population of dogs switched from kibble diet to raw diet shifts the gut microbiota closer to that of wolves, yet still showing distinct differences. At phylum level, raw meat consumption increased the relative abundance of Fusobacteria and Bacteroidetes at DR1, DR7, DR14, and DR21 (q < 0.05) compared with DC, whereas no differences in these two phyla were observed between DC and DR28. At genus level, Faecalibacterium, Catenibacterium, Allisonella, and Megamonas were significantly lower in dogs consuming the raw diet from the first week onward and in wolves compared with dogs on the kibble diet. Linear discriminant analysis effect size (LEfSe) showed a higher abundance of Stenotrophomonas, Faecalibacterium, Megamonas, and Lactobacillus in dogs fed kibble diet compared with dogs fed raw diet for 28 days and wolves. In addition, wolves had greater unidentified Lachnospiraceae compared with dogs irrespective of the diets. These results suggested that carbohydrate-fermenting bacteria give way to protein fermenters when the diet is shifted from kibble to raw diet. In conclusion, some microbial phyla, families, and genera in dogs showed only temporary change upon dietary shift, whereas some microbial groups moved toward the microbial profile of wolves. These findings open the discussion on the extent of coevolution of the core microbiota of dogs throughout domestication.
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Affiliation(s)
- Jia Xu
- Department of Veterinary Medicine, Faculty of Agriculture, Jinhua Polytechnic, Jinhua, China
| | - Anne A M J Becker
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Yu Luo
- Department of Veterinary Medicine, Faculty of Agriculture, Jinhua Polytechnic, Jinhua, China
| | - Wenfu Zhang
- Department of Veterinary Medicine, Faculty of Agriculture, Jinhua Polytechnic, Jinhua, China
| | - Bingqian Ge
- Department of Veterinary Medicine, Faculty of Agriculture, Jinhua Polytechnic, Jinhua, China
| | - Chunqing Leng
- Department of Veterinary Medicine, Faculty of Agriculture, Jinhua Polytechnic, Jinhua, China
| | - Guyue Wang
- Department of Veterinary Medicine, Faculty of Agriculture, Jinhua Polytechnic, Jinhua, China
| | - Limin Ding
- Department of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianmei Wang
- Department of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | | | - Geert P J Janssens
- Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
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Butowski CF, Moon CD, Thomas DG, Young W, Bermingham EN. The effects of raw-meat diets on the gastrointestinal microbiota of the cat and dog: a review. N Z Vet J 2021; 70:1-9. [PMID: 34463606 DOI: 10.1080/00480169.2021.1975586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The aim of this review is to summarise the available literature on the effects of consuming raw, red meat diets on the gastrointestinal microbiome of the cat and dog. In recent years, feeding raw meat diets to cats and dogs has increased, in part associated with trends in human nutrition for "natural" and "species-appropriate" diets. These diets range from home-prepared unprocessed, nutritionally incomplete diets to complete and balanced diets with sterilisation steps in their manufacturing process. Feeding some formats of raw meat diets has been associated with nutritional inadequacies and zoonotic transfer of pathogens. The feeding of raw meat diets has been shown to alter the gastrointestinal microbiome of the cat and dog, increasing the relative abundances of bacteria associated with protein and fat utilisation, including members of the genera Fusobacterium and Clostridium. While in humans, these genera are more commonly known for members that are associated with disease, they are a diverse group that also contains harmless commensals that are a normal component of the gastrointestinal microbiota. Moreover, members of these genera are known to produce butyrate from protein and amino acid fermentation and contribute to intestinal homeostasis in raw meat-fed dogs and cats. Currently, only a limited number of studies have examined the impacts of raw meat diets on the cat and dog microbiota, with many of these being descriptive. Additional controlled and systems-based studies are required to functionally characterise the roles of key microbial groups in the metabolism of raw meat diets, and determine their impacts on the health and nutrition of the host.
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Affiliation(s)
- C F Butowski
- Smart Foods, AgResearch Limited, Palmerston North, New Zealand
| | - C D Moon
- Resilient Agriculture, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - D G Thomas
- Centre for Feline Nutrition, Massey University, Palmerston North, New Zealand
| | - W Young
- Smart Foods, AgResearch Limited, Palmerston North, New Zealand
| | - E N Bermingham
- Smart Foods, AgResearch Limited, Palmerston North, New Zealand
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28
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Bowerman KL, Knowles SCL, Bradley JE, Baltrūnaitė L, Lynch MDJ, Jones KM, Hugenholtz P. Effects of laboratory domestication on the rodent gut microbiome. ISME COMMUNICATIONS 2021; 1:49. [PMID: 36747007 PMCID: PMC9723573 DOI: 10.1038/s43705-021-00053-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/22/2021] [Accepted: 09/03/2021] [Indexed: 05/01/2023]
Abstract
The domestication of the laboratory mouse has influenced the composition of its native gut microbiome, which is now known to differ from that of its wild ancestor. However, limited exploration of the rodent gut microbiome beyond the model species Mus musculus has made it difficult to interpret microbiome variation in a broader phylogenetic context. Here, we analyse 120 de novo and 469 public metagenomically-sequenced faecal and caecal samples from 16 rodent hosts representing wild, laboratory and captive lifestyles. Distinct gut bacterial communities were observed between rodent host genera, with broadly distributed species originating from the as-yet-uncultured bacterial genera UBA9475 and UBA2821 in the families Oscillospiraceae and Lachnospiraceae, respectively. In laboratory mice, Helicobacteraceae were generally depleted relative to wild mice and specific Muribaculaceae populations were enriched in different laboratory facilities, suggesting facility-specific outgrowths of this historically dominant rodent gut family. Several bacterial families of clinical interest, including Akkermansiaceae, Streptococcaceae and Enterobacteriaceae, were inferred to have gained over half of their representative species in mice within the laboratory environment, being undetected in most wild rodents and suggesting an association between laboratory domestication and pathobiont emergence.
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Affiliation(s)
- Kate L Bowerman
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.
| | | | | | | | | | - Kathryn M Jones
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.
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Pereira AM, Clemente A. Dogs' Microbiome From Tip to Toe. Top Companion Anim Med 2021; 45:100584. [PMID: 34509665 DOI: 10.1016/j.tcam.2021.100584] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 09/01/2021] [Accepted: 09/07/2021] [Indexed: 12/14/2022]
Abstract
Microbiota and microbiome, which refers, respectively, to the microorganisms and conjoint of microorganisms and genes are known to live in symbiosis with hosts, being implicated in health and disease. The advancements and cost reduction associated with high-throughput sequencing techniques have allowed expanding the knowledge of microbial communities in several species, including dogs. Throughout their body, dogs harbor distinct microbial communities according to the location (e.g., skin, ear canal, conjunctiva, respiratory tract, genitourinary tract, gut), which have been a target of study mostly in the last couple of years. Although there might be a core microbiota for different body sites, shared by dogs, it is likely influenced by intrinsic factors such as age, breed, and sex, but also by extrinsic factors such as the environment (e.g., lifestyle, urban vs rural), and diet. It starts to become clear that some medical conditions are mediated by alterations in microbiota namely dysbiosis. Moreover, understanding microbial colonization and function can be used to prevent medical conditions, for instance, modulation of gut microbiota of puppies is more effective to ensure a healthy gut than interventions in adults. This paper gathers current knowledge of dogs' microbial communities, exploring their function, implications in the development of diseases, and potential interactions among communities while providing hints for further research.
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Affiliation(s)
- Ana Margarida Pereira
- University of the Azores, Faculty of Agricultural and Environmental Sciences, Institute of Agricultural and Environmental Research and Technology (IITAA). Rua Capitão João d'Ávila, Azores, Portugal.
| | - Alfonso Clemente
- Department of Physiology and Biochemistry in Animal Nutrition, Estacion Experimental del Zaidin, Spanish National Research Council (CSIC), Granada, Spain
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30
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Age and Giardia intestinalis Infection Impact Canine Gut Microbiota. Microorganisms 2021; 9:microorganisms9091862. [PMID: 34576757 PMCID: PMC8469385 DOI: 10.3390/microorganisms9091862] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/16/2022] Open
Abstract
Giardia intestinalis is a flagellated protozoan responsible for giardiosis (also called giardiasis in humans), the most prevalent and widespread parasitic infection in humans and mammals worldwide. The intestinal microbiota is highly diverse and any alteration in its composition may impact on the health of the host. While studies on the mouse model of giardiosis described the role of the gut microbiota in host susceptibility to infection by the parasite, little is known about the gut microbiota during natural infections in dogs and particularly in puppies. In this study, we monitored naturally G. intestinalis-infected puppies for 3 months and quantified cyst excretion every 2 weeks. All puppies remained subclinically infected during the sampling period as confirmed by fecal examination. In parallel, we performed 16S Illumina sequencing of fecal samples from the different time points to assess the impact of G. intestinalis infection on gut microbiota development of the puppies, as well as gut health markers of immunity such as fecal IgA and calprotectin. Sequencing results revealed that the canine fecal microbiota of Giardia-infected puppies becomes more complex and less diverse with increasing age. In addition, significant differences in the structure of the microbiota were observed between puppies with high and low Giardia cyst excretion. Chronic subclinical G. intestinalis infection appears to be associated with some detrimental structural changes in the gut microbiota. G. intestinalis-associated dysbiosis is characterized by an enrichment of facultative anaerobic, mucus-degrading, pro-inflammatory species and opportunistic pathogens, as well as a reduction of Lactobacillus johnsonii at specific time points. Calprotectin levels increased with age, suggesting the establishment of chronic low-grade inflammation in puppies. Further work is needed to demonstrate whether these alterations in the canine gut microbiota could lead to a dysbiosis-related disease, such as irritable bowel syndrome (IBS) or inflammatory bowel disease (IBD).
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Wolves, dogs and humans in regular contact can mutually impact each other's skin microbiota. Sci Rep 2021; 11:17106. [PMID: 34429455 PMCID: PMC8385068 DOI: 10.1038/s41598-021-96160-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/26/2021] [Indexed: 12/31/2022] Open
Abstract
In contrast to humans and dogs, the skin microbiota of wolves is yet to be described. Here, we investigated the skin microbiota of dogs and wolves kept in outdoor packs at the Wolf Science Center (WSC) via 16S rRNA gene amplicon sequencing. Skin swab samples were also collected from human care takers and their pet dogs. When comparing the three canine groups, representing different degrees of human contact to the care takers and each other, the pet dogs showed the highest level of diversity. Additionally, while human skin was dominated by a few abundant phylotypes, the skin microbiota of the care takers who had particularly close contact with the WSC animals was more similar to the microbiota of dogs and wolves compared to the humans who had less contact with these animals. Our results suggest that domestication may have an impact on the diversity of the skin microbiota, and that the canine skin microbiota can be shared with humans, depending on the level of interaction.
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Phungviwatnikul T, Alexander C, Do S, He F, Suchodolski JS, de Godoy MRC, Swanson KS. Effects of Dietary Macronutrient Profile on Apparent Total Tract Macronutrient Digestibility and Fecal Microbiota, Fermentative Metabolites, and Bile Acids of Female Dogs after Spay Surgery. J Anim Sci 2021; 99:6333593. [PMID: 34333604 DOI: 10.1093/jas/skab225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 07/29/2021] [Indexed: 11/13/2022] Open
Abstract
Obesity and estrogen reduction are known to impact the gut microbiota and gut microbial-derived metabolites in some species, but limited information is available in dogs. The aim of this study was to determine the effects of dietary macronutrient profile on apparent total tract macronutrient digestibility, fecal microbiota, and fecal metabolites of adult female dogs after spay surgery. Twenty-eight adult intact female beagles (age: 3.02 ± 0.71 yr, BW: 10.28 ± 0.77 kg; BCS: 4.98 ± 0.57) were used. After a 5-wk baseline phase (wk 0), 24 dogs were spayed and randomly allotted to one of three experimental diets (n=8/group): 1) control (CO) containing moderate protein and fiber (COSP), 2) high-protein, high-fiber (HPHF), or 3) high-protein, high-fiber plus omega-3 and medium-chain fatty acids (HPHFO). Four dogs were sham-operated and fed CO (COSH). All dogs were fed to maintain BW for 12 wk after spay, then allowed to consume twice that amount for 12 wk. Fecal samples were collected at wk 0, 12, and 24 for digestibility, microbiota, and metabolite analysis. All data were analyzed using repeated measures and linear Mixed Models procedure of SAS 9.4, with results reported as change from baseline. Apparent organic matter and energy digestibilities had greater decreases in HPHF and HPHFO than COSH and COSP. Increases in fecal acetate, total short-chain fatty acids, and secondary bile acids were greater and decreases in primary bile acids were greater in HPHF and HPHFO. Principal coordinates analysis of weighted UniFrac distances revealed that HPHF and HPHFO clustered together and separately from COSH and COSP at wk 12 and 24, with relative abundances of Faecalibacterium, Romboutsia, and Fusobacterium increasing to a greater extent and Catenibacterium, Bifidobacterium, Prevotella 9, Eubacterium, and Megamonas decreasing to a greater extent in HPHF or HPHFO. Our results suggest that high-protein, high-fiber diets alter nutrient and energy digestibilities, fecal metabolite concentrations, and fecal gut microbiota, but spay surgery had minor effects. Future research is needed to investigate how food intake, nutrient profile, and changes in hormone production influence gut microbiota and metabolites of dogs individually and how this knowledge may be used to manage spayed pets.
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Affiliation(s)
| | - Celeste Alexander
- Division of Nutritional Sciences, University of Illinois, Urbana, IL, USA
| | - Sungho Do
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | - Fei He
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | - Jan S Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX, USA
| | - Maria R C de Godoy
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA.,Division of Nutritional Sciences, University of Illinois, Urbana, IL, USA
| | - Kelly S Swanson
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA.,Department of Veterinary Clinical Medicine, University of Illinois, Urbana, IL, USA.,Division of Nutritional Sciences, University of Illinois, Urbana, IL, USA
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Rampelli S, Turroni S, Debandi F, Alberdi A, Schnorr SL, Hofman CA, Taddia A, Helg R, Biagi E, Brigidi P, D'Amico F, Cattani M, Candela M. The gut microbiome buffers dietary adaptation in Bronze Age domesticated dogs. iScience 2021; 24:102816. [PMID: 34377966 PMCID: PMC8327155 DOI: 10.1016/j.isci.2021.102816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/14/2021] [Accepted: 07/01/2021] [Indexed: 02/07/2023] Open
Abstract
In an attempt to explore the role of the gut microbiome during recent canine evolutionary history, we sequenced the metagenome of 13 canine coprolites dated ca. 3,600–3,450 years ago from the Bronze Age archaeological site of Solarolo (Italy), which housed a complex farming community. The microbiome structure of Solarolo dogs revealed continuity with that of modern dogs, but it also shared some features with the wild wolf microbiome, as a kind of transitional state between them. The dietary niche, as also inferred from the microbiome composition, was omnivorous, with evidence of consumption of starchy agricultural foods. Of interest, the Solarolo dog microbiome was particularly enriched in sequences encoding alpha-amylases and complemented a low copy number of the host amylase gene. These findings suggest that Neolithic dogs could have responded to the transition to a starch-rich diet by expanding microbial functionalities devoted to starch catabolism, thus compensating for delayed host response. Ancient DNA of Bronze Age canine coprolites from Solarolo was sequenced Solarolo dogs share gut microbiome features with modern wolves and dogs The gut microbiome of Solarolo dogs shows high number of reads for alpha-amylase Neolithic canine gut microbiome complemented delay in host genome adaptation
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Affiliation(s)
- Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Florencia Debandi
- Department of History and Cultures, University of Bologna, Bologna, Italy
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stephanie L Schnorr
- Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria.,Department of Anthropology, University of Nevada, Las Vegas, NV, USA
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Alberto Taddia
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Riccardo Helg
- Department of History and Cultures, University of Bologna, Bologna, Italy
| | - Elena Biagi
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Federica D'Amico
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.,Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Maurizio Cattani
- Department of History and Cultures, University of Bologna, Bologna, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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Tanprasertsuk J, Shmalberg J, Maughan H, Tate DE, Perry LM, Jha AR, Honaker RW. Heterogeneity of gut microbial responses in healthy household dogs transitioning from an extruded to a mildly cooked diet. PeerJ 2021; 9:e11648. [PMID: 34249503 PMCID: PMC8254476 DOI: 10.7717/peerj.11648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/29/2021] [Indexed: 12/28/2022] Open
Abstract
Background The gut microbiota (GM) is associated with canine health and can be impacted by diet. Dog owners in the U.S. have increasingly shown an interest in feeding their dogs a mildly cooked (MC) diet. However, its impact on canine GM and health remains largely unknown. Methods Healthy household dogs were tracked upon switching from various brands of extruded to MC diets for four weeks. A health assessment was completed and stool samples were collected by each owner before (day 0) and after the diet transition (day 28). Shotgun metagenomic sequencing was performed at both time points to characterize the GM. Results Dogs completed the study by either completing the health assessments (n = 31) or providing stool samples at both time points (n = 28). All owners reported either better or no change in overall health at the end of the study (61% and 39%, respectively), and none reported worse overall health. Defecation frequency was also reported to be lower (58%) or about the same (35%). Principal coordinate (PCo) analysis showed a significant shift (p = 0.004) in the β-diversity of the GM upon diet transition (34.2% and 10.3% explained by the first two axes). The abundances of 70 species increased after the diet change (adjusted p < 0.05), 67% and 24% of which belonged to the Lactobacillales and the Enterobacterales orders respectively. The abundances of 28 species decreased (adjusted p < 0.05), 46%, 18%, and 11% of which belonged to the Clostridiales, Bacillales, and Bacteroidales orders, respectively. Lower Lactobacillales and Enterobacterales, and higher Bacteroidales at baseline were associated with a greater shift along the PCo1 axis. Protein content of the baseline diet was correlated with the shift along the PCo1 axis (ρ = 0.67, p = 0.006). Conclusion Owners reported either improvement or no change in health in dogs transitioning from extruded kibble to MC diets for 4 weeks, but this report of health perception requires further exploration in a controlled trial. Diet change also led to a significant shift in the GM profile of healthy dogs. The magnitude of shift was associated with baseline GM and dietary protein, and warrants further examination of individualized responses and personalized nutrition in companion dogs. These results also support future investigation of the impact of a MC diet on health maintenance given its increasing popularity.
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Affiliation(s)
| | - Justin Shmalberg
- NomNomNow, Inc., Nashville, Tennessee, United States of America.,Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States
| | - Heather Maughan
- NomNomNow, Inc., Nashville, Tennessee, United States of America.,Ronin Institute, Montclair, New Jersey, United States of America
| | - Devon E Tate
- NomNomNow, Inc., Nashville, Tennessee, United States of America
| | - LeeAnn M Perry
- NomNomNow, Inc., Nashville, Tennessee, United States of America
| | - Aashish R Jha
- NomNomNow, Inc., Nashville, Tennessee, United States of America.,Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Ryan W Honaker
- NomNomNow, Inc., Nashville, Tennessee, United States of America
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Hashimoto-Hill S, Alenghat T. Inflammation-Associated Microbiota Composition Across Domestic Animals. Front Genet 2021; 12:649599. [PMID: 34239536 PMCID: PMC8257562 DOI: 10.3389/fgene.2021.649599] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/27/2021] [Indexed: 12/26/2022] Open
Abstract
Domestic animals represent important resources for understanding shared mechanisms underlying complex natural diseases that arise due to both genetic and environmental factors. Intestinal inflammation, particularly inflammatory bowel disease (IBD), is a significant health challenge in humans and domestic animals. While the etiology of IBD is multifactorial, imbalance of symbiotic gut microbiota has been hypothesized to play a central role in disease pathophysiology. Advances in genomic sequencing and analytical pipelines have enabled researchers to decipher the composition of the intestinal microbiota during health and in the context of naturally occurring diseases. This review compiles microbiome genomic data across domestic species and highlights a common occurrence of gut microbiome dysbiosis during idiopathic intestinal inflammation in multiple species, including dogs, cats, horses, cows, and pigs. Current microbiome data obtained from animals with intestinal inflammation are mostly limited to taxonomical analyses in association with broad clinical phenotype. In general, a pathogen or pathosymbiont were not detected. Rather, functional potential of the altered microbiota has been suggested to be one of the key etiologic factors. Among the domestic species studied, canine analyses are currently the most advanced with incorporation of functional profiling of microbiota. Canine IBD parallels features of the disease in humans, thus canines represent a strong natural model for human IBD. While deeper analyses of metagenomic data, coupled with host molecular analyses are needed, comparative studies across domestic species can reveal shared microbial alterations and regulatory mechanisms that will improve our understanding of intestinal inflammation in both animals and humans.
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Affiliation(s)
| | - Theresa Alenghat
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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36
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The microbiota of healthy dogs demonstrates individualized responses to synbiotic supplementation in a randomized controlled trial. Anim Microbiome 2021; 3:36. [PMID: 33971985 PMCID: PMC8111948 DOI: 10.1186/s42523-021-00098-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/20/2021] [Indexed: 12/17/2022] Open
Abstract
Background Probiotics have been demonstrated to ameliorate clinical signs of gastrointestinal diseases in dogs in various studies. However, the effect of probiotics in a healthy population, as well as factors contributing individualized responses, remain largely unknown. This trial examined gut microbiota (GM) and health outcomes in household dogs after synbiotic (SN) supplementation containing probiotics and inulin (a prebiotic). Healthy dogs were randomized to receive SN (50 mg/d inulin and 20 billion total CFU/d of L. reuteri, P. acidilactici, E. faecium, L. acidophilus, B. animalis, L. fermentum, L. rhamnosus) or placebo (PL) for 4 weeks. Owners completed a health survey and collected stool samples for GM profiling (shotgun metagenomic sequencing) at baseline and week 4 in both groups, and at week 6 in the SN group. Results A significant shift (p < 0.001) in β-diversity was observed in the SN (n = 24), but not PL group (n = 19), at week 4 relative to baseline. Forty-five bacterial species, 43 (96%) of which were Lactobacillales, showed an increase in the relative abundances (≥2 fold change, adjusted p < 0.05) in the SN group at week 4. E. coli also decreased at week 4 in the SN group (2.8-fold, adjusted p < 0.01). The altered taxa largely returned to baseline at week 6. The degree of changes in β-diversity was associated with GM at baseline. Specifically, dogs with higher Proteobacteria and lower Lactobacillales responded more robustly to supplementation in terms of the change in β-diversity. Dogs fed SN tended to have lower diarrhea incidence (0% vs 16%, p = 0.08). Conclusions SN supplement had a short-term impact on the gut microbiota in healthy household dogs as characterized by shotgun metagenomic sequencing. Findings warrant further investigation with longer duration and populations at risk of gastrointestinal diseases. The magnitude of response to the supplement was associated with microbial profile at baseline. To our knowledge, this is the first study documenting such association and may provide a basis for personalized nutrition in companion dogs. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00098-0.
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37
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Martinez MN, Mochel JP, Neuhoff S, Pade D. Comparison of Canine and Human Physiological Factors: Understanding Interspecies Differences that Impact Drug Pharmacokinetics. AAPS JOURNAL 2021; 23:59. [PMID: 33907906 DOI: 10.1208/s12248-021-00590-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
This review is a summary of factors affecting the drug pharmacokinetics (PK) of dogs versus humans. Identifying these interspecies differences can facilitate canine-human PK extrapolations while providing mechanistic insights into species-specific drug in vivo behavior. Such a cross-cutting perspective can be particularly useful when developing therapeutics targeting diseases shared between the two species such as cancer, diabetes, cognitive dysfunction, and inflammatory bowel disease. Furthermore, recognizing these differences also supports a reverse PK extrapolations from humans to dogs. To appreciate the canine-human differences that can affect drug absorption, distribution, metabolism, and elimination, this review provides a comparison of the physiology, drug transporter/enzyme location, abundance, activity, and specificity between dogs and humans. Supplemental material provides an in-depth discussion of certain topics, offering additional critical points to consider. Based upon an assessment of available state-of-the-art information, data gaps were identified. The hope is that this manuscript will encourage the research needed to support an understanding of similarities and differences in human versus canine drug PK.
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Affiliation(s)
- Marilyn N Martinez
- Office of New Animal Drug Evaluation, Center for Veterinary Medicine, Food and Drug Administration, Rockville, Maryland, 20855, USA.
| | - Jonathan P Mochel
- SMART Pharmacology, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, 50011, USA
| | - Sibylle Neuhoff
- Certara UK Limited, Simcyp Division, 1 Concourse Way, Sheffield, S1 2BJ, UK
| | - Devendra Pade
- Certara UK Limited, Simcyp Division, 1 Concourse Way, Sheffield, S1 2BJ, UK
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38
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Yang C, Huang W, Sun Y, You L, Jin H, Sun Z. Effect of probiotics on diversity and function of gut microbiota in Moschus berezovskii. Arch Microbiol 2021; 203:3305-3315. [PMID: 33860850 DOI: 10.1007/s00203-021-02315-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 11/29/2022]
Abstract
The forest musk deer, Moschus berezovskii, is a nationally protected species of economic importance in China. However, in captive breeding programmes, they usually die as a result of diarrhoea. In this study, six M. berezovskii were randomly selected and divided into two groups: probiotics group (n = 3) and placebo (control) group (n = 3). The two groups were fed a basal diet that included 2 g probiotics (probiotic group) or 2 g whey powder (placebo group) for 30 days. Faecal samples were collected at day 0, 15 and 30 and evaluated for microbial diversity, species richness and metabolic function. Probiotic intervention significantly improved gut health in M. berezovskii by changing the overall community structure of the gut microbiota. Intake of probiotics reduced the relative abundance of pathogenic bacteria such as Escherichia coli and Citrobacter freundii in the intestinal flora and increased the relative abundance of beneficial Bifidobacterium species and other lactic acid bacteria. At the same time, gut microbiota in the probiotics group were involved in regulating degradation of phenylacetic acid and in dTDP-L-rhamnose synthesis; these processes have the potential to enhance immunity in M. berezovskii. This preliminary study revealed the beneficial effects of probiotics on the gut microbiota of M. berezovskii, which the potential to significantly improve the health, wellbeing and economic value of M. berezovskii.
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Affiliation(s)
- Chengcong Yang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Inner Mongolia Agricultural University, Hohhot, People's Republic of China
| | - Weiqiang Huang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Inner Mongolia Agricultural University, Hohhot, People's Republic of China
| | - Yaru Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Inner Mongolia Agricultural University, Hohhot, People's Republic of China
| | - Lijun You
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Inner Mongolia Agricultural University, Hohhot, People's Republic of China
| | - Hao Jin
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Inner Mongolia Agricultural University, Hohhot, People's Republic of China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Inner Mongolia Agricultural University, Hohhot, People's Republic of China.
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Fu H, Zhang L, Fan C, Liu C, Li W, Li J, Zhao X, Jia S, Zhang Y. Domestication Shapes the Community Structure and Functional Metagenomic Content of the Yak Fecal Microbiota. Front Microbiol 2021; 12:594075. [PMID: 33897627 PMCID: PMC8059439 DOI: 10.3389/fmicb.2021.594075] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 03/05/2021] [Indexed: 01/07/2023] Open
Abstract
Domestication is a key factor of genetic variation; however, the mechanism by which domestication alters gut microbiota is poorly understood. Here, to explore the variation in the structure, function, rapidly evolved genes (REGs), and enzyme profiles of cellulase and hemicellulose in fecal microbiota, we studied the fecal microbiota in wild, half-blood, and domestic yaks based on 16S rDNA sequencing, shotgun-metagenomic sequencing, and the measurement of short-chain-fatty-acids (SCFAs) concentration. Results indicated that wild and half-blood yaks harbored an increased abundance of the phylum Firmicutes and reduced abundance of the genus Akkermansia, which are both associated with efficient energy harvesting. The gut microbial diversity decreased in domestic yaks. The results of the shotgun-metagenomic sequencing showed that the wild yak harbored an increased abundance of microbial pathways that play crucial roles in digestion and growth of the host, whereas the domestic yak harbored an increased abundance of methane-metabolism-related pathways. Wild yaks had enriched amounts of REGs in energy and carbohydrate metabolism pathways, and possessed a significantly increased abundance of cellulases and endohemicellulases in the glycoside hydrolase family compared to domestic yaks. The concentrations of acetic, propionic, n-butyric, i-butyric, n-valeric, and i-valeric acid were highest in wild yaks. Our study displayed the domestic effect on the phenotype of composition, function in gut microbiota, and SCFAs associated with gut microbiota, which had a closely association with the growth performance of the livestock. These findings may enlighten the researchers to construct more links between economic characteristics and gut microbiota, and develop new commercial strains in livestock based on the biotechnology of gut microbiota.
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Affiliation(s)
- Haibo Fu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Chao Fan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chuanfa Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Wenjing Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Jiye Li
- Datong Yak Breeding Farm of Qinghai Province, Datong, China
| | - Xinquan Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
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40
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Comparative genome analyses of Lactobacillus crispatus isolated from different ecological niches reveal an environmental adaptation of this species to the human vaginal environment. Appl Environ Microbiol 2021; 87:AEM.02899-20. [PMID: 33579685 PMCID: PMC8091109 DOI: 10.1128/aem.02899-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Vaginal microbiota is defined as the community of bacteria residing in the human vaginal tract. Recent studies have demonstrated that the vaginal microbiota is dominated by members of the Lactobacillus genus, whose relative abundance and microbial taxa composition are dependent on the healthy status of this human body site. Particularly, among members of this genus, the high prevalence of Lactobacillus crispatus is commonly associated with a healthy vaginal environment. In the current study, we assessed the microbial composition of 94 healthy vaginal microbiome samples through shotgun metagenomics analyses. Based on our results we observed that L. crispatus was the most representative species and correlated negatively with bacteria involved in vaginal infections. Therefore, we isolated fifteen L. crispatus strains from different environments in which this species is abounding, ranging from vaginal swabs of healthy women to chicken fecal samples. The genomes of these strains were decoded and their genetic content was analyzed and correlated with their physiological features. An extensive comparative genomic analysis encompassing all publicly available genome sequences of L. crispatus and combined with those decoded in this study, revealed a genetic adaptation of strains to their ecological niche. In addition, in vitro growth experiments involving all isolated L. crispatus strains together with a synthetic vaginal microbiota reveal how this species is able to modulate the composition of the vaginal microbial consortia at strain level. Overall, our findings suggest that L. crispatus plays an important ecological role in reducing the complexity of the vaginal microbiota by depleting pathogenic bacteria.Importance The vaginal microbiota is defined as the community of bacteria residing in the human vaginal tract. Recent studies have demonstrated that the high prevalence of Lactobacillus crispatus species is commonly associated with a healthy vaginal environment. In the current study, we assessed the microbial composition of 94 public healthy vaginal samples through shotgun metagenomics analyses. Results showed that L. crispatus was the most representative species and correlated negatively with bacteria involved in vaginal infections. Moreover, we isolated and sequenced the genome of new L. crispatus strains from different environments and the comparative genomics analysis revealed a genetic adaptation of strains to their ecological niche. In addition, in-vitro growth experiments display the capability of this species to modulate the composition of the vaginal microbial consortia. Overall, our findings suggest an ecological role exploited by L. crispatus in reducing the complexity of the vaginal microbiota toward a depletion of pathogenic bacteria.
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Reese AT, Chadaideh KS, Diggins CE, Schell LD, Beckel M, Callahan P, Ryan R, Emery Thompson M, Carmody RN. Effects of domestication on the gut microbiota parallel those of human industrialization. eLife 2021; 10:60197. [PMID: 33755015 PMCID: PMC7987347 DOI: 10.7554/elife.60197] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 02/12/2021] [Indexed: 12/21/2022] Open
Abstract
Domesticated animals experienced profound changes in diet, environment, and social interactions that likely shaped their gut microbiota and were potentially analogous to ecological changes experienced by humans during industrialization. Comparing the gut microbiota of wild and domesticated mammals plus chimpanzees and humans, we found a strong signal of domestication in overall gut microbial community composition and similar changes in composition with domestication and industrialization. Reciprocal diet switches within mouse and canid dyads demonstrated the critical role of diet in shaping the domesticated gut microbiota. Notably, we succeeded in recovering wild-like microbiota in domesticated mice through experimental colonization. Although fundamentally different processes, we conclude that domestication and industrialization have impacted the gut microbiota in related ways, likely through shared ecological change. Our findings highlight the utility, and limitations, of domesticated animal models for human research and the importance of studying wild animals and non-industrialized humans for interrogating signals of host-microbial coevolution.
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Affiliation(s)
- Aspen T Reese
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States.,Society of Fellows, Harvard University, Cambridge, MA, United States
| | - Katia S Chadaideh
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Caroline E Diggins
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Laura D Schell
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Mark Beckel
- Wildlife Science Center, Stacy, MN, United States
| | | | - Roberta Ryan
- Wildlife Science Center, Stacy, MN, United States
| | | | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
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42
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Alessandri G, van Sinderen D, Ventura M. The genus bifidobacterium: From genomics to functionality of an important component of the mammalian gut microbiota running title: Bifidobacterial adaptation to and interaction with the host. Comput Struct Biotechnol J 2021; 19:1472-1487. [PMID: 33777340 PMCID: PMC7979991 DOI: 10.1016/j.csbj.2021.03.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 02/07/2023] Open
Abstract
Members of the genus Bifidobacterium are dominant and symbiotic inhabitants of the mammalian gastrointestinal tract. Being vertically transmitted, bifidobacterial host colonization commences immediately after birth and leads to a phase of host infancy during which bifidobacteria are highly prevalent and abundant to then transit to a reduced, yet stable abundance phase during host adulthood. However, in order to reach and stably colonize their elective niche, i.e. the large intestine, bifidobacteria have to cope with a multitude of oxidative, osmotic and bile salt/acid stress challenges that occur along the gastrointestinal tract (GIT). Concurrently, bifidobacteria not only have to compete with the myriad of other gut commensals for nutrient acquisition, but they also require protection against bacterial viruses. In this context, Next-Generation Sequencing (NGS) techniques, allowing large-scale comparative and functional genome analyses have helped to identify the genetic strategies that bifidobacteria have developed in order to colonize, survive and adopt to the highly competitive mammalian gastrointestinal environment. The current review is aimed at providing a comprehensive overview concerning the molecular strategies on which bifidobacteria rely to stably and successfully colonize the mammalian gut.
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Affiliation(s)
- Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, University College Cork, Western Road, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
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43
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Liu Y, Liu B, Liu C, Hu Y, Liu C, Li X, Li X, Zhang X, Irwin DM, Wu Z, Chen Z, Jin Q, Zhang S. Differences in the gut microbiomes of dogs and wolves: roles of antibiotics and starch. BMC Vet Res 2021; 17:112. [PMID: 33676490 PMCID: PMC7937242 DOI: 10.1186/s12917-021-02815-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 02/23/2021] [Indexed: 01/24/2023] Open
Abstract
Background Dogs are domesticated wolves. Change of living environment, such as diet and veterinary care may affect the gut bacterial flora of dogs. The aim of this study was to assess the gut bacterial diversity and function in dogs compared with captive wolves. We surveyed the gut bacterial diversity of 27 domestic dogs, which were fed commercial dog food, and 31 wolves, which were fed uncooked meat, by 16S rRNA sequencing. In addition, we collected fecal samples from 5 dogs and 5 wolves for shotgun metagenomic sequencing to explore changes in the functions of their gut microbiome. Results Differences in the abundance of core bacterial genera were observed between dogs and wolves. Together with shotgun metagenomics, the gut microbiome of dogs was found to be enriched in bacteria resistant to clinical drugs (P < 0.001), while wolves were enriched in bacteria resistant to antibiotics used in livestock (P < 0.001). In addition, a higher abundance of putative α-amylase genes (P < 0.05; P < 0.01) was observed in the dog samples. Conclusions Living environment of dogs and domestic wolves has led to increased numbers of bacteria with antibiotic resistance genes, with exposure to antibiotics through direct and indirect methods. In addition, the living environment of dogs has allowed the adaptation of their microbiota to a starch-rich diet. These observations align with a domestic lifestyle for domestic dogs and captive wolves, which might have consequences for public health.
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Affiliation(s)
- Yuting Liu
- Institute of Pet Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Bo Liu
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chengwu Liu
- Shenyang Police Dog Technical College, Shenyang, China
| | - Yumiao Hu
- Shenyang Forest Zoological Garden, Shenyang, China
| | - Chang Liu
- Changchun Animals and Plants Park, Changchun, China
| | - Xiaoping Li
- Institute of Pet Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xibao Li
- Institute of Pet Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xiaoshuang Zhang
- Institute of Pet Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Zhiqiang Wu
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zeliang Chen
- Institute of Pet Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qi Jin
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuyi Zhang
- Institute of Pet Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.
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44
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Scarsella E, Segato J, Zuccaccia D, Swanson KS, Stefanon B. An application of nuclear magnetic resonance spectroscopy to study faecal canine metabolome. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1925602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Elisa Scarsella
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali, Università di Udine, Udine, Italy
| | - Jacopo Segato
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali, Università di Udine, Udine, Italy
| | - Daniele Zuccaccia
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali, Università di Udine, Udine, Italy
| | - Kelly S. Swanson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bruno Stefanon
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali, Università di Udine, Udine, Italy
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45
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An altered microbiome in urban coyotes mediates relationships between anthropogenic diet and poor health. Sci Rep 2020; 10:22207. [PMID: 33335116 PMCID: PMC7746695 DOI: 10.1038/s41598-020-78891-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022] Open
Abstract
Generalist species able to exploit anthropogenic food sources are becoming increasingly common in urban environments. Coyotes (Canis latrans) are one such urban generalist that now resides in cities across North America, where diseased or unhealthy coyotes are frequently reported in cases of human-wildlife conflict. Coyote health and fitness may be related to habitat use and diet via the gut microbiome, which has far-reaching effects on animal nutrition and physiology. In this study, we used stomach contents, stable isotope analysis, 16S rRNA gene amplicon sequencing, and measures of body condition to identify relationships among habitat use, diet, fecal microbiome composition, and health in urban and rural coyotes. Three distinct relationships emerged: (1) Urban coyotes consumed more anthropogenic food, which was associated with increased microbiome diversity, higher abundances of Streptococcus and Enterococcus, and poorer average body condition. (2) Conversely, rural coyotes harbored microbiomes rich in Fusobacteria, Sutterella, and Anaerobiospirillum, which were associated with protein-rich diets and improved body condition. (3) Diets rich in anthropogenic food were associated with increased abundances of Erysipelotrichiaceae, Lachnospiraceae, and Coriobacteriaceae, which correlated with larger spleens in urban coyotes. Urban coyotes also had an increased prevalence of the zoonotic parasite Echinococcus multilocularis, but there were no detectable connections between parasite infection and microbiome composition. Our results demonstrate how the consumption of carbohydrate-rich anthropogenic food by urban coyotes alters the microbiome to negatively affect body condition, with potential relationships to parasite susceptibility and conflict-prone behavior.
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46
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Bragg M, Freeman EW, Lim HC, Songsasen N, Muletz-Wolz CR. Gut Microbiomes Differ Among Dietary Types and Stool Consistency in the Captive Red Wolf ( Canis rufus). Front Microbiol 2020; 11:590212. [PMID: 33304337 PMCID: PMC7693430 DOI: 10.3389/fmicb.2020.590212] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Captive management of many wildlife species can be challenging, with individuals displaying health disorders that are not generally described in the wild population. Retrospective studies have identified gastrointestinal (GI) diseases, in particular inflammatory bowel disease (IBD), as the second leading cause of captive adult red wolf (Canis rufus) mortality. Recent molecular studies show that imbalanced gut microbial composition is tightly linked to IBD in the domestic dog. The goal of the present study was to address two main questions: (1) how do red wolf gut microbiomes differ between animals with loose stool consistency, indicative of GI issues, and those with normal stool consistency and (2) how does dietary type relate to stool consistency and red wolf gut microbiomes? Fresh fecal samples were collected from 48 captive wolves housed in eight facilities in the United States and from two wild wolves living in Alligator River National Wildlife Refuge, NC, United States. For each individual, the stool consistency was categorized as loose or normal using a standardized protocol and their diet was categorized as either wild, whole meat, a mix of whole meat and kibble or kibble. We characterized gut microbiome structure using 16S rRNA gene amplicon sequencing. We found that red wolves with a loose stool consistency differed in composition than wolves with normal stool consistency, suggesting a link between GI health and microbiome composition. Diet was not related to stool consistency but did significantly impact gut microbiome composition; gut microbiome composition of wolves fed a kibble diet were significantly different than the gut microbiome composition of wolves fed a mixed, whole meat and wild diet. Findings from this study increase the understanding of the interplay between diet and GI health in the red wolf, a critical piece of information needed to maintain a healthy red wolf population ex situ.
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Affiliation(s)
- Morgan Bragg
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, United States
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, United States
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States
| | - Elizabeth W. Freeman
- School of Integrative Studies, George Mason University, Fairfax, VA, United States
| | - Haw Chuan Lim
- Department of Biology, George Mason University, Fairfax, VA, United States
| | - Nucharin Songsasen
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, United States
| | - Carly R. Muletz-Wolz
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States
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47
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Alessandri G, Argentini C, Milani C, Turroni F, Cristina Ossiprandi M, van Sinderen D, Ventura M. Catching a glimpse of the bacterial gut community of companion animals: a canine and feline perspective. Microb Biotechnol 2020; 13:1708-1732. [PMID: 32864871 PMCID: PMC7533323 DOI: 10.1111/1751-7915.13656] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
Dogs and cats have gained a special position in human society by becoming our principal companion animals. In this context, efforts to ensure their health and welfare have increased exponentially, with in recent times a growing interest in assessing the impact of the gut microbiota on canine and feline health. Recent technological advances have generated new tools to not only examine the intestinal microbial composition of dogs and cats, but also to scrutinize the genetic repertoire and associated metabolic functions of this microbial community. The application of high-throughput sequencing techniques to canine and feline faecal samples revealed similarities in their bacterial composition, with Fusobacteria, Firmicutes and Bacteroidetes as the most prevalent and abundant phyla, followed by Proteobacteria and Actinobacteria. Although key bacterial members were consistently present in their gut microbiota, the taxonomic composition and the metabolic repertoire of the intestinal microbial population may be influenced by several factors, including diet, age and anthropogenic aspects, as well as intestinal dysbiosis. The current review aims to provide a comprehensive overview of the multitude of factors which play a role in the modulation of the canine and feline gut microbiota and that of their human owners with whom they share the same environment.
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Affiliation(s)
- Giulia Alessandri
- Department of Veterinary Medical ScienceUniversity of ParmaParmaItaly
| | - Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of ParmaParmaItaly
- Microbiome Research HubUniversity of ParmaParmaItaly
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of ParmaParmaItaly
- Microbiome Research HubUniversity of ParmaParmaItaly
| | - Maria Cristina Ossiprandi
- Department of Veterinary Medical ScienceUniversity of ParmaParmaItaly
- Microbiome Research HubUniversity of ParmaParmaItaly
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience InstituteNational University of IrelandCorkIreland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of ParmaParmaItaly
- Microbiome Research HubUniversity of ParmaParmaItaly
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48
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Mancabelli L, Tarracchini C, Milani C, Lugli GA, Fontana F, Turroni F, van Sinderen D, Ventura M. Multi-population cohort meta-analysis of human intestinal microbiota in early life reveals the existence of infant community state types (ICSTs). Comput Struct Biotechnol J 2020; 18:2480-2493. [PMID: 33005310 PMCID: PMC7516180 DOI: 10.1016/j.csbj.2020.08.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022] Open
Abstract
Appropriate development of the intestinal microbiota during infancy is known to be important for human health. In fact, aberrant alterations of the microbial composition during childhood may cause short- and/or long-term negative health effects. Many factors influence the initial assembly and subsequent progression of the gut microbiota of a neonate, such as feeding type, delivery mode, gestational age, maternal metabolic status and antibiotic exposure. In the current study, the composition of the infant gut core-microbiota was explored, revealing particular variations of this core-microbiota during the first three years as influenced by delivery mode and feeding type. A multi-population cohort meta-analysis was performed by selecting 15 publicly available datasets pertaining to taxonomic profiles of 1035 fecal samples of healthy infants, as obtained by means of a 16S rRNA gene-based profiling approach. Interestingly, this multi-population cohort meta-analysis revealed great microbial complexity and specific taxonomic shifts in children older than six months, suggesting a major impact by the introduction of solid foods which prompts progression of infant gut microbiota towards that typical of adults. The taxonomic data sets employed in this multi-population cohort meta-analysis possess the statistical robustness to allow the identification of infant community state types (ICSTs). Our analysis therefore reveals the existence of specific taxonomic patterns that correspond to particular nutritional and developmental stages of early life, and that had previously been obscured by the high variability typical of such infant gut microbiota.
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Affiliation(s)
- Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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Faecal Microbiota of Dogs Offered a Vegetarian Diet with or without the Supplementation of Feather Meal and either Cornmeal, Rye or Fermented Rye: A Preliminary Study. Microorganisms 2020; 8:microorganisms8091363. [PMID: 32899987 PMCID: PMC7565823 DOI: 10.3390/microorganisms8091363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/01/2020] [Accepted: 09/04/2020] [Indexed: 12/30/2022] Open
Abstract
Anthropomorphism of dogs has affected feeding and the choice of components present in diets for dogs. Conflicting trends are present: raw or vegetarian appear more prevalent. Animal-derived proteins seem to have unfavourable impacts on intestinal microflora by decreasing the presence of Bacteroidetes. This preliminary study evaluates whether effects of diets with animal proteins on intestinal microbiota can be compensated by the addition of certain carbohydrates to dog diet. Eight female beagles were included in a cross-over study and fed a vegetarian diet or the same diet supplemented with feather meal (2.7%) and either 20% of cornmeal, fermented or non-fermented rye (moisture content of the diets about 42%). A 16S rRNA gene amplification was performed within the hypervariable region V4 on faecal samples and sequenced with the Illumina MiSeq platform. The Firmicutes/Bacteroidetes ratio tended to shift to the advantage of Firmicutes when feather meal and cornmeal were added (Firmicutes/Bacteroidetes ratio of 5.12 compared to 2.47 when offered the vegetarian diet) and tended to switch back to the advantage of Bacteroidetes if rye: fermented (2.17) or not (1.03) was added. The addition of rye might have the potential to compensate possible unfavourable effects of diets with animal proteins on intestinal microbiota of dogs.
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50
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Fan C, Zhang L, Fu H, Liu C, Li W, Cheng Q, Zhang H, Jia S, Zhang Y. Enterotypes of the Gut Microbial Community and Their Response to Plant Secondary Compounds in Plateau Pikas. Microorganisms 2020; 8:microorganisms8091311. [PMID: 32872148 PMCID: PMC7563992 DOI: 10.3390/microorganisms8091311] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022] Open
Abstract
Animal gut microbiomes can be clustered into “enterotypes” characterized by an abundance of signature genera. The characteristic determinants, stability, and resilience of these community clusters remain poorly understood. We used plateau pika (Ochotona curzoniae) as a model and identified three enterotypes by 16S rDNA sequencing. Among the top 15 genera, 13 showed significantly different levels of abundance between the enterotypes combined with different microbial functions and distinct fecal short-chain fatty acids. We monitored changes in the microbial community associated with the transfer of plateau pikas from field to laboratory and observed that feeding them a single diet reduced microbial diversity, resulting in a single enterotype with an altered composition of the dominant bacteria. However, microbial diversity, an abundance of some changed dominant genera, and enterotypes were partially restored after adding swainsonine (a plant secondary compound found in the natural diet of plateau pikas) to the feed. These results provide strong evidence that gut microbial diversity and enterotypes are directly related to specific diet, thereby indicating that the formation of different enterotypes can help animals adapt to complex food conditions. Additionally, natural plant secondary compounds can maintain dominant bacteria and inter-individual differences of gut microbiota and promote the resilience of enterotypes in small herbivorous mammals.
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Affiliation(s)
- Chao Fan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (C.F.); (L.Z.); (H.F.); (C.L.); (W.L.); (Q.C.); (H.Z.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (C.F.); (L.Z.); (H.F.); (C.L.); (W.L.); (Q.C.); (H.Z.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Haibo Fu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (C.F.); (L.Z.); (H.F.); (C.L.); (W.L.); (Q.C.); (H.Z.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanfa Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (C.F.); (L.Z.); (H.F.); (C.L.); (W.L.); (Q.C.); (H.Z.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Wenjing Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (C.F.); (L.Z.); (H.F.); (C.L.); (W.L.); (Q.C.); (H.Z.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Qi Cheng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (C.F.); (L.Z.); (H.F.); (C.L.); (W.L.); (Q.C.); (H.Z.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - He Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (C.F.); (L.Z.); (H.F.); (C.L.); (W.L.); (Q.C.); (H.Z.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
- Correspondence: (S.J.); (Y.Z.)
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (C.F.); (L.Z.); (H.F.); (C.L.); (W.L.); (Q.C.); (H.Z.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- Correspondence: (S.J.); (Y.Z.)
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