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Merker Breyer G, De Carli S, Rocha Jacques Da Silva ME, Dias ME, Muterle Varela AP, Bertoni Mann M, Frazzon J, Quoos Mayer F, Góes Neto A, Maboni Siqueira F. Alternative amplicon-PCR protocol for maximizing bacterial and fungal sequencing in low-biomass samples. Anal Biochem 2024; 687:115449. [PMID: 38145697 DOI: 10.1016/j.ab.2023.115449] [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: 08/23/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 12/27/2023]
Abstract
Determining bacterial and fungal communities from low-biomass samples remains a challenge for high-throughput sequencing. Due to the low microbial load and host contamination, some sites, including the female upper reproductive tract and the lower respiratory tract, were even considered sterile until recent years. Despite efforts to improve sampling and DNA isolation protocols, some samples provide insufficient microbial DNA input for library preparation and sequencing. Herein, we propose an alternative amplicon-PCR protocol to be used in bacterial and fungal sequencing in low-biomass samples, targeting 16S-rDNA and the internal transcribed spacer region (ITS), respectively. Similar to a nested-PCR, we performed two sequential PCR reactions to maximise the target amplicon. We compared metagenomic results from the original Illumina protocol (Protocol 1 - P1) and the alternative one (Protocol 2 - P2), using a mock community and clinical samples with different microbial loads. Our findings showed no significant differences in data generated by P1 and P2, indicating that the second amplification round does not bias the microbiota diversity rates. Thus, the alternative protocol can be applied for low-biomass samples when the original protocol results in spurious output, preventing library preparation and sequencing.
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Affiliation(s)
- Gabriela Merker Breyer
- Laboratório de Bacteriologia Veterinária (LaBacVet), Universidade Federal do Rio Grande do Sul, Departamento de Patologia Veterinária, Porto Alegre, Brazil; Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Silvia De Carli
- Laboratório de Bacteriologia Veterinária (LaBacVet), Universidade Federal do Rio Grande do Sul, Departamento de Patologia Veterinária, Porto Alegre, Brazil; Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Maria Eduarda Rocha Jacques Da Silva
- Laboratório de Bacteriologia Veterinária (LaBacVet), Universidade Federal do Rio Grande do Sul, Departamento de Patologia Veterinária, Porto Alegre, Brazil
| | - Maria Eduarda Dias
- Laboratório de Bacteriologia Veterinária (LaBacVet), Universidade Federal do Rio Grande do Sul, Departamento de Patologia Veterinária, Porto Alegre, Brazil
| | - Ana Paula Muterle Varela
- Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Michele Bertoni Mann
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jeverson Frazzon
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Laboratório de Bioquímica e Biologia Molecular de Microrganismos, Departamento de Ciência de Alimentos, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor, Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, Brazil
| | - Aristóteles Góes Neto
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Franciele Maboni Siqueira
- Laboratório de Bacteriologia Veterinária (LaBacVet), Universidade Federal do Rio Grande do Sul, Departamento de Patologia Veterinária, Porto Alegre, Brazil; Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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Montserrat-Malagarriga M, Castillejos L, Salas-Mani A, Torre C, Martín-Orúe SM. The Impact of Fiber Source on Digestive Function, Fecal Microbiota, and Immune Response in Adult Dogs. Animals (Basel) 2024; 14:196. [PMID: 38254365 PMCID: PMC10812474 DOI: 10.3390/ani14020196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
This study evaluated the impact of different fiber sources on intestinal function, fecal microbiota, and overall health in dogs. Twelve dogs were used in a crossover design, involving three periods of 6 weeks and three diets: a low-fiber diet (CTR), a cereal-fiber and beet-pulp-supplemented diet (BRA), and a fruit-fiber-supplemented diet (FRU). Each period included a digestibility trial and fecal and blood sampling in the last week. Short-chain fatty acids (SCFAs) and microbiota taxonomy (16S rRNA Illumina-MiSeq) and functionality (Shotgun-NovaSeq 6000) were determined in the feces. General biochemistry, complete blood cells, and lymphocyte subsets were also analyzed. The fiber-supplemented diets showed lower digestibility without significant changes in the fecal consistency. The BRA diet showed higher total SCFA concentrations (p = 0.056), with increases in alpha diversity and particular beneficial genera, such as Lachnospira, Bifidobacterium, and Faecalibacterium. The BRA microbiota was also associated with an overabundance of genes related to carbohydrate and amino acid metabolism. The FRU diet had a distinct impact on the microbiota composition and functionality, leading to higher levels of CD8 lymphocytes. These findings emphasize the importance of selecting the right fiber source when formulating dog diets, as it can have a differential impact on gut microbiota and animal health.
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Affiliation(s)
- Miquel Montserrat-Malagarriga
- Animal Nutrition and Welfare Service, Department of Animal and Food Science, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain; (M.M.-M.); (S.M.M.-O.)
| | - Lorena Castillejos
- Animal Nutrition and Welfare Service, Department of Animal and Food Science, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain; (M.M.-M.); (S.M.M.-O.)
| | - Anna Salas-Mani
- Affinity Pet Care, Hospitalet de Llobregat, 08902 Barcelona, Spain; (A.S.-M.); (C.T.)
| | - Celina Torre
- Affinity Pet Care, Hospitalet de Llobregat, 08902 Barcelona, Spain; (A.S.-M.); (C.T.)
| | - Susana M. Martín-Orúe
- Animal Nutrition and Welfare Service, Department of Animal and Food Science, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain; (M.M.-M.); (S.M.M.-O.)
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Fernández-Pinteño A, Pilla R, Manteca X, Suchodolski J, Torre C, Salas-Mani A. Age-associated changes in intestinal health biomarkers in dogs. Front Vet Sci 2023; 10:1213287. [PMID: 37680388 PMCID: PMC10481537 DOI: 10.3389/fvets.2023.1213287] [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: 04/27/2023] [Accepted: 07/13/2023] [Indexed: 09/09/2023] Open
Abstract
The gut microbiome is critical for maintaining host health. In healthy humans, the aging process is one of the main factors modulating the changes in the intestinal microbiota. However, little is known about the relationship between gut health, microbiota, and the aging process in dogs. The present study aims to explore the differences in the intestinal microbiota and intestinal health based on fecal biomarkers in a population of dogs of different ages. The study involved 106 dogs of different breeds aged between 0.2 and 15 years categorized as senior (>7 years; n = 40), adult (2-7 years; n = 50), and junior (< 2 years; n = 16). Fecal samples were collected during the same period at the same facilities. The analysis included the following gut health indicators: 16S rRNA gene sequencing to investigate the differences in the fecal microbiota; qPCR to determine the dysbiosis index; fecal short-chain fatty acid concentrations; fecal calprotectin; and immunoglobulin A. Beta diversity analysis revealed a significant difference with a small effect size (p = 0.003; R = 0.087) among age categories based on the unweighted UniFrac metric, but no significance was observed based on the weighted UniFrac metric or Bray-Curtis distances. There were no significant differences in the alpha diversity measures or the fecal dysbiosis index among age categories. Senior dogs had significantly higher relative abundance proportions in phyla Bacteroidota and Pseudomonadota and the genus Faecalibacterium, but not on qPCR analysis. At the family level, Ruminococcaceae, Uncl. Clostridiales.1, Veillonellaceae, Prevotellaceae, Succinivibrionaceae, and Bacteroidaceae abundances were higher in the senior category than in the adult and/or junior categories. Relative proportions, but not concentrations of fecal acetate, were higher in the senior category, while butyrate, isovaleric acid, and valeric acid were lower. The valeric acid concentration was significantly lower in the senior category than in the adult category. Calprotectin and immunoglobulin A levels did not differ significantly across groups. In conclusion, this study observed multiple minor changes in the fecal microbiota composition and the relative amount of short-chain fatty acids in dogs among different age groups, but studies in larger populations representative of all ages are warranted to refine the present results.
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Affiliation(s)
- Anna Fernández-Pinteño
- Department of Research and Development, Affinity Petcare, L'Hospitalet de Llobregat, Spain
| | - Rachel Pilla
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX, United States
| | - Xavier Manteca
- School of Veterinary Science, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Jan Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX, United States
| | - Celina Torre
- Department of Research and Development, Affinity Petcare, L'Hospitalet de Llobregat, Spain
| | - Anna Salas-Mani
- Department of Research and Development, Affinity Petcare, L'Hospitalet de Llobregat, Spain
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Palmqvist H, Höglund K, Ringmark S, Lundh T, Dicksved J. Effects of whole-grain cereals on fecal microbiota and short-chain fatty acids in dogs: a comparison of rye, oats and wheat. Sci Rep 2023; 13:10920. [PMID: 37407634 DOI: 10.1038/s41598-023-37975-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023] Open
Abstract
Dietary fiber in dog food is reported to promote healthy gut microbiota, but few studies have investigated the effects of whole-grain cereals, which contain a variety of fiber types and other bioactive compounds. The aim of the present study was to compare the effects of diets containing whole-grain rye (RYE), oats (OAT) and wheat (WHE) on fecal microbiota and short-chain fatty acid production. Eighteen dogs were fed three experimental diets, each for four weeks, in a cross-over design. Fecal samples were collected at the end of each diet period. Analysis of 16S rRNA gene amplicons showed that family Lachnospiraceae and genus Bacteroides were the gut microbial groups most affected by diet, with lowest relative abundance following consumption of RYE and a trend for a corresponding increase in genus Prevotella_9. Fecal acetate and propionate concentrations were higher after consumption of RYE compared with OAT. In conclusion, rye had the strongest effect on gut microbiota and short-chain fatty acids, although the implications for dog gut health are not yet elucidated.
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Affiliation(s)
- Hanna Palmqvist
- Department of Animal Nutrition and Management, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Katja Höglund
- Department of Anatomy, Physiology and Biochemistry, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Ringmark
- Department of Anatomy, Physiology and Biochemistry, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Torbjörn Lundh
- Department of Animal Nutrition and Management, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Johan Dicksved
- Department of Animal Nutrition and Management, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Gaillard V, Chastant S, England G, Forman O, German AJ, Suchodolski JS, Villaverde C, Chavatte-Palmer P, Péron F. Environmental risk factors in puppies and kittens for developing chronic disorders in adulthood: A call for research on developmental programming. Front Vet Sci 2022; 9:944821. [PMID: 36619947 PMCID: PMC9816871 DOI: 10.3389/fvets.2022.944821] [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: 05/15/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Many dogs and cats are affected by chronic diseases that significantly impact their health and welfare and relationships with humans. Some of these diseases can be challenging to treat, and a better understanding of early-life risk factors for diseases occurring in adulthood is key to improving preventive veterinary care and husbandry practices. This article reviews early-life risk factors for obesity and chronic enteropathy, and for chronic behavioral problems, which can also be intractable with life-changing consequences. Aspects of early life in puppies and kittens that can impact the risk of adult disorders include maternal nutrition, establishment of the gut microbiome, maternal behavior, weaning, nutrition during growth, growth rate, socialization with conspecifics and humans, rehoming and neutering. Despite evidence in some species that the disorders reviewed here reflect the developmental origins of health and disease (DOHaD), developmental programming has rarely been studied in dogs and cats. Priorities and strategies to increase knowledge of early-life risk factors and DOHaD in dogs and cats are discussed. Critical windows of development are proposed: preconception, gestation, the suckling period, early growth pre-neutering or pre-puberty, and growth post-neutering or post-puberty to adult size, the durations of which depend upon species and breed. Challenges to DOHaD research in these species include a large number of breeds with wide genetic and phenotypic variability, and the existence of many mixed-breed individuals. Moreover, difficulties in conducting prospective lifelong cohort studies are exacerbated by discontinuity in pet husbandry between breeders and subsequent owners, and by the dispersed nature of pet ownership.
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Affiliation(s)
- Virginie Gaillard
- Research and Development Center, Royal Canin, Aimargues, France,*Correspondence: Virginie Gaillard ✉
| | - Sylvie Chastant
- NeoCare, Université de Toulouse, Ecole Nationale Vétérinaire de Toulouse (ENVT), Toulouse, France
| | - Gary England
- School of Veterinary Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Oliver Forman
- Wisdom Panel, Kinship, Waltham-on-the-Wolds, Leicestershire, United Kingdom
| | - Alexander J. German
- Institute of Life Course and Medical Sciences of Small Animal Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX, United States
| | | | - Pascale Chavatte-Palmer
- Université Paris-Saclay, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut National de Recherche Pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Biologie de la Reproduction, Environnement, Epigénétique et Développement (BREED), Jouy-en-Josas, France,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Franck Péron
- Research and Development Center, Royal Canin, Aimargues, France
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