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Salt C, Saito EK, O’Flynn C, Allaway D. Stratification of companion animal life stages from electronic medical record diagnosis data. J Gerontol A Biol Sci Med Sci 2022; 78:579-586. [PMID: 36330848 DOI: 10.1093/gerona/glac220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Indexed: 11/06/2022] Open
Abstract
Abstract
Aging is a complex, multifactorial process, where different life stages reflect changes in metabolic processes, immune capacities and genetic/epigenetic repertoires. With accumulating exposure to environmental stresses and deterioration of physiological functions, body systems become more prone to low-grade chronic inflammation and an increasing range of pathologies. We hypothesised that differential susceptibility to diseases across lifespan reflect phased changes in an organism’s physiological capacity that may highlight when interventions may be appropriately used. Furthermore, the number of life stages may vary between species and be impacted by signalment such as breed. We tested this hypothesis using disease diagnoses data from veterinary electronic medical records containing almost two million cats and over four million dogs.
Bi-clustering (on rates of disease diagnoses) and adaptive branch pruning were used to identify age clusters that could be used to define adult life stages. Clustering amongst diagnoses were then interpreted within the context of each defined life stage. The analyses identified five age clusters in cats and four age clusters within each of the four canine breed size categories used.
This study, using population scale data for two species, one with differential size and life expectancies, is the first to our knowledge to use disease diagnosis data to define adult life stages. The life stages presented here are a result of a data-driven approach to age and disease stratification and are intended to support conversations between clinicians and clients about appropriate healthcare recommendations.
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Affiliation(s)
- Carina Salt
- Waltham Petcare Science Institute, Freeby Lane , Waltham on the Wolds, Leicestershire
| | - Emi K Saito
- Mars Petcare, 18101 SE 6th Way, Vancouver , WA, 98683, USA
| | - Ciaran O’Flynn
- Waltham Petcare Science Institute, Freeby Lane , Waltham on the Wolds, Leicestershire
| | - David Allaway
- Waltham Petcare Science Institute, Freeby Lane , Waltham on the Wolds, Leicestershire
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Saraiva LR, Riveros-McKay F, Mezzavilla M, Abou-Moussa EH, Arayata CJ, Makhlouf M, Trimmer C, Ibarra-Soria X, Khan M, Van Gerven L, Jorissen M, Gibbs M, O’Flynn C, McGrane S, Mombaerts P, Marioni JC, Mainland JD, Logan DW. A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans. Sci Adv 2019; 5:eaax0396. [PMID: 31392275 PMCID: PMC6669018 DOI: 10.1126/sciadv.aax0396] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 06/24/2019] [Indexed: 05/07/2023]
Abstract
The mammalian olfactory system displays species-specific adaptations to different ecological niches. To investigate the evolutionary dynamics of olfactory sensory neuron (OSN) subtypes across mammalian evolution, we applied RNA sequencing of whole olfactory mucosa samples from mouse, rat, dog, marmoset, macaque, and human. We find that OSN subtypes, representative of all known mouse chemosensory receptor gene families, are present in all analyzed species. Further, we show that OSN subtypes expressing canonical olfactory receptors are distributed across a large dynamic range and that homologous subtypes can be either highly abundant across all species or species/order specific. Highly abundant mouse and human OSN subtypes detect odorants with similar sensory profiles and sense ecologically relevant odorants, such as mouse semiochemicals or human key food odorants. Together, our results allow for a better understanding of the evolution of mammalian olfaction in mammals and provide insights into the possible functions of highly abundant OSN subtypes.
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Affiliation(s)
- Luis R. Saraiva
- Sidra Medicine, PO Box 26999, Doha, Qatar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton,, Cambridge CB10 1SD, UK
- Monell Chemical Senses Center, Philadelphia, PA 19104, USA
| | | | | | | | | | | | - Casey Trimmer
- Monell Chemical Senses Center, Philadelphia, PA 19104, USA
| | - Ximena Ibarra-Soria
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mona Khan
- Max Planck Research Unit for Neurogenetics, Max von-Laue-Strasse 4, 60438 Frankfurt, Germany
| | - Laura Van Gerven
- Department of ENT-HNS, UZ Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Mark Jorissen
- Department of ENT-HNS, UZ Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Matthew Gibbs
- Waltham Centre for Pet Nutrition, Leicestershire LE14 4RT, UK
| | - Ciaran O’Flynn
- Waltham Centre for Pet Nutrition, Leicestershire LE14 4RT, UK
| | - Scott McGrane
- Waltham Centre for Pet Nutrition, Leicestershire LE14 4RT, UK
| | - Peter Mombaerts
- Max Planck Research Unit for Neurogenetics, Max von-Laue-Strasse 4, 60438 Frankfurt, Germany
| | - John C. Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton,, Cambridge CB10 1SD, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Joel D. Mainland
- Monell Chemical Senses Center, Philadelphia, PA 19104, USA
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Darren W. Logan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Monell Chemical Senses Center, Philadelphia, PA 19104, USA
- Waltham Centre for Pet Nutrition, Leicestershire LE14 4RT, UK
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Coil DA, Jospin G, Darling AE, Wallis C, Davis IJ, Harris S, Eisen JA, Holcombe LJ, O’Flynn C. Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment. PLoS One 2019; 14:e0214354. [PMID: 31181071 PMCID: PMC6557473 DOI: 10.1371/journal.pone.0214354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/27/2019] [Indexed: 11/18/2022] Open
Abstract
Taxonomy for bacterial isolates is commonly assigned via sequence analysis. However, the most common sequence-based approaches (e.g. 16S rRNA gene-based phylogeny or whole genome comparisons) are still labor intensive and subjective to varying degrees. Here we present a set of 33 bacterial genomes, isolated from the canine oral cavity. Taxonomy of these isolates was first assigned by PCR amplification of the 16S rRNA gene, Sanger sequencing, and taxonomy assignment using BLAST. After genome sequencing, taxonomy was revisited through a manual process using a combination of average nucleotide identity (ANI), concatenated marker gene phylogenies, and 16S rRNA gene phylogenies. This taxonomy was then compared to the automated taxonomic assignment given by the recently proposed Genome Taxonomy Database (GTDB). We found the results of all three methods to be similar (25 out of the 33 had matching genera), but the GTDB approach required fewer subjective decisions, and required far less labor. The primary differences in the non-identical taxonomic assignments involved cases where GTDB has proposed taxonomic revisions.
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Affiliation(s)
- David A. Coil
- Genome Center, University of California, Davis, CA, United States of America
| | - Guillaume Jospin
- Genome Center, University of California, Davis, CA, United States of America
| | - Aaron E. Darling
- The Ithree Institute, University of Technology Sydney, Ultimo NSW, Australia
| | - Corrin Wallis
- The Waltham Centre for Pet Nutrition, Melton Mowbray, Leicestershire, United Kingdom
| | - Ian J. Davis
- The Waltham Centre for Pet Nutrition, Melton Mowbray, Leicestershire, United Kingdom
| | - Stephen Harris
- The Waltham Centre for Pet Nutrition, Melton Mowbray, Leicestershire, United Kingdom
| | - Jonathan A. Eisen
- Genome Center, University of California, Davis, CA, United States of America
- Evolution and Ecology, Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States of America
| | - Lucy J. Holcombe
- The Waltham Centre for Pet Nutrition, Melton Mowbray, Leicestershire, United Kingdom
| | - Ciaran O’Flynn
- The Waltham Centre for Pet Nutrition, Melton Mowbray, Leicestershire, United Kingdom
- * E-mail:
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Deusch O, O’Flynn C, Colyer A, Swanson KS, Allaway D, Morris P. A Longitudinal Study of the Feline Faecal Microbiome Identifies Changes into Early Adulthood Irrespective of Sexual Development. PLoS One 2015; 10:e0144881. [PMID: 26659594 PMCID: PMC4682054 DOI: 10.1371/journal.pone.0144881] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 11/24/2015] [Indexed: 01/16/2023] Open
Abstract
Companion animals provide an excellent model for studies of the gut microbiome because potential confounders such as diet and environment can be more readily controlled for than in humans. Additionally, domestic cats and dogs are typically neutered early in life, enabling an investigation into the potential effect of sex hormones on the microbiome. In a longitudinal study to investigate the potential effects of neutering, neutering age and gender on the gut microbiome during growth, the faeces of kittens (16 male, 14 female) were sampled at 18, 30 and 42 weeks of age. DNA was shotgun sequenced on the Illumina platform and sequence reads were annotated for taxonomy and function by comparison to a database of protein coding genes. In a statistical analysis of diversity, taxonomy and functional potential of the microbiomes, age was identified as the only factor with significant associations. No significant effects were detected for gender, neutering, or age when neutered (19 or 31 weeks). At 18 weeks of age the microbiome was dominated by the genera Lactobacillus and Bifidobacterium (35% and 20% average abundance). Structural and functional diversity was significantly increased by week 30 but there was no further significant increase. At 42 weeks of age the most abundant genera were Bacteroides (16%), Prevotella (14%) and Megasphaera (8%). Significant differences in functional potential included an enrichment for genes in energy metabolism (carbon metabolism and oxidative phosphorylation) and depletion in cell motility (flagella and chemotaxis). We conclude that the feline faecal microbiome is predominantly determined by age when diet and environment are controlled for. We suggest this finding may also be informative for studies of the human microbiome, where control over such factors is usually limited.
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Affiliation(s)
- Oliver Deusch
- WALTHAM Centre for Pet Nutrition, Freeby Lane, Waltham-on-the-Wolds, Leicestershire, United Kingdom
- * E-mail:
| | - Ciaran O’Flynn
- WALTHAM Centre for Pet Nutrition, Freeby Lane, Waltham-on-the-Wolds, Leicestershire, United Kingdom
| | - Alison Colyer
- WALTHAM Centre for Pet Nutrition, Freeby Lane, Waltham-on-the-Wolds, Leicestershire, United Kingdom
| | - Kelly S. Swanson
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
- Division of Nutritional Sciences, University of Illinois, Urbana, Illinois, United States of America
- Department of Veterinary Clinical Medicine, University of Illinois, Urbana, Illinois, United States of America
| | - David Allaway
- WALTHAM Centre for Pet Nutrition, Freeby Lane, Waltham-on-the-Wolds, Leicestershire, United Kingdom
| | - Penelope Morris
- WALTHAM Centre for Pet Nutrition, Freeby Lane, Waltham-on-the-Wolds, Leicestershire, United Kingdom
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Harris S, Croft J, O’Flynn C, Deusch O, Colyer A, Allsopp J, Milella L, Davis IJ. A Pyrosequencing Investigation of Differences in the Feline Subgingival Microbiota in Health, Gingivitis and Mild Periodontitis. PLoS One 2015; 10:e0136986. [PMID: 26605793 PMCID: PMC4659563 DOI: 10.1371/journal.pone.0136986] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/11/2015] [Indexed: 12/02/2022] Open
Abstract
Periodontitis is the most frequently diagnosed health problem in cats yet little is known about the bacterial species important for the disease. The objective of this study was to identify bacterial species associated with health, gingivitis or mild periodontitis (<25% attachment loss) in feline plaque. Knowledge of these species is a first step in understanding the potential for improving oral health of cats via dietary interventions that alter the proportions of influential species. Subgingival plaque samples were collected from 92 cats with healthy gingiva, gingivitis or mild periodontitis. Pyrosequencing of the V1-V3 region of the 16S rDNA from these plaque samples generated more than one million reads and identified a total of 267 operational taxonomic units after bioinformatic and statistical analysis. Porphyromonas was the most abundant genus in all gingival health categories, particularly in health along with Moraxella and Fusobacteria. The Peptostreptococcaceae were the most abundant family in gingivitis and mild periodontitis. Logistic regression analysis identified species from various genera that were significantly associated with health, gingivitis or mild periodontitis. The species identified were very similar to those observed in canine plaque in the corresponding health and disease states. Such similarities were not observed between cat and human at the bacterial species level but with disease progression similarities did emerge at the phylum level. This suggests that interventions targeted at human pathogenic species will not be effective for use in cats but there is more potential for commonalities in interventions for cats and dogs.
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Affiliation(s)
- Stephen Harris
- The WALTHAM Centre for Pet Nutrition, Mars Petcare UK, Leicestershire, United Kingdom
| | - Julie Croft
- The WALTHAM Centre for Pet Nutrition, Mars Petcare UK, Leicestershire, United Kingdom
| | - Ciaran O’Flynn
- The WALTHAM Centre for Pet Nutrition, Mars Petcare UK, Leicestershire, United Kingdom
| | - Oliver Deusch
- The WALTHAM Centre for Pet Nutrition, Mars Petcare UK, Leicestershire, United Kingdom
| | - Alison Colyer
- The WALTHAM Centre for Pet Nutrition, Mars Petcare UK, Leicestershire, United Kingdom
| | - Judi Allsopp
- The WALTHAM Centre for Pet Nutrition, Mars Petcare UK, Leicestershire, United Kingdom
| | - Lisa Milella
- The Veterinary Dental Surgery, Surrey, United Kingdom
| | - Ian J. Davis
- The WALTHAM Centre for Pet Nutrition, Mars Petcare UK, Leicestershire, United Kingdom
- * E-mail:
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Holcombe LJ, Patel N, Colyer A, Deusch O, O’Flynn C, Harris S. Early canine plaque biofilms: characterization of key bacterial interactions involved in initial colonization of enamel. PLoS One 2014; 9:e113744. [PMID: 25463050 PMCID: PMC4252054 DOI: 10.1371/journal.pone.0113744] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 10/29/2014] [Indexed: 11/18/2022] Open
Abstract
Periodontal disease (PD) is a significant problem in dogs affecting between 44% and 63.6% of the population. The main etiological agent for PD is plaque, a microbial biofilm that colonizes teeth and causes inflammation of the gingiva. Understanding how this biofilm initiates on the tooth surface is of central importance in developing interventions against PD. Although the stages of plaque development on human teeth have been well characterized little is known about how canine plaque develops. Recent studies of the canine oral microbiome have revealed distinct differences between the canine and human oral environments and the bacterial communities they support, particularly with respect to healthy plaque. These differences mean knowledge about the nature of plaque formation in humans may not be directly translatable to dogs. The aim of this study was to identify the bacterial species important in the early stages of canine plaque formation in vivo and then use isolates of these species in a laboratory biofilm model to develop an understanding of the sequential processes which take place during the initial colonization of enamel. Supra-gingival plaque samples were collected from 12 dogs at 24 and 48 hour time points following a full mouth descale and polish. Pyrosequencing of the 16S rDNA identified 134 operational taxonomic units after statistical analysis. The species with the highest relative abundance were Bergeyella zoohelcum, Neisseria shayeganii and a Moraxella species. Streptococcal species, which tend to dominate early human plaque biofilms, had very low relative abundance. In vitro testing of biofilm formation identified five primary colonizer species, three of which belonged to the genus Neisseria. Using these pioneer bacteria as a starting point, viable two and three species communities were developed. Combining in vivo and in vitro data has led us to construct novel models of how the early canine plaque biofilm develops.
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Affiliation(s)
- Lucy J. Holcombe
- The WALTHAM Centre for Pet Nutrition, Leicestershire, United Kingdom
- * E-mail:
| | - Niran Patel
- The WALTHAM Centre for Pet Nutrition, Leicestershire, United Kingdom
| | - Alison Colyer
- The WALTHAM Centre for Pet Nutrition, Leicestershire, United Kingdom
| | - Oliver Deusch
- The WALTHAM Centre for Pet Nutrition, Leicestershire, United Kingdom
| | - Ciaran O’Flynn
- The WALTHAM Centre for Pet Nutrition, Leicestershire, United Kingdom
| | - Stephen Harris
- The WALTHAM Centre for Pet Nutrition, Leicestershire, United Kingdom
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Deusch O, O’Flynn C, Colyer A, Morris P, Allaway D, Jones PG, Swanson KS. Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens. PLoS One 2014; 9:e101021. [PMID: 25010839 PMCID: PMC4091873 DOI: 10.1371/journal.pone.0101021] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 06/02/2014] [Indexed: 12/22/2022] Open
Abstract
Background Previously, we demonstrated that dietary protein:carbohydrate ratio dramatically affects the fecal microbial taxonomic structure of kittens using targeted 16S gene sequencing. The present study, using the same fecal samples, applied deep Illumina shotgun sequencing to identify the diet-associated functional potential and analyze taxonomic changes of the feline fecal microbiome. Methodology & Principal Findings Fecal samples from kittens fed one of two diets differing in protein and carbohydrate content (high–protein, low–carbohydrate, HPLC; and moderate-protein, moderate-carbohydrate, MPMC) were collected at 8, 12 and 16 weeks of age (n = 6 per group). A total of 345.3 gigabases of sequence were generated from 36 samples, with 99.75% of annotated sequences identified as bacterial. At the genus level, 26% and 39% of reads were annotated for HPLC- and MPMC-fed kittens, with HPLC-fed cats showing greater species richness and microbial diversity. Two phyla, ten families and fifteen genera were responsible for more than 80% of the sequences at each taxonomic level for both diet groups, consistent with the previous taxonomic study. Significantly different abundances between diet groups were observed for 324 genera (56% of all genera identified) demonstrating widespread diet-induced changes in microbial taxonomic structure. Diversity was not affected over time. Functional analysis identified 2,013 putative enzyme function groups were different (p<0.000007) between the two dietary groups and were associated to 194 pathways, which formed five discrete clusters based on average relative abundance. Of those, ten contained more (p<0.022) enzyme functions with significant diet effects than expected by chance. Six pathways were related to amino acid biosynthesis and metabolism linking changes in dietary protein with functional differences of the gut microbiome. Conclusions These data indicate that feline feces-derived microbiomes have large structural and functional differences relating to the dietary protein:carbohydrate ratio and highlight the impact of diet early in life.
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Affiliation(s)
- Oliver Deusch
- WALTHAM Centre for Pet Nutrition, Waltham-on-the-Wolds, Leicestershire, United Kingdom
| | - Ciaran O’Flynn
- WALTHAM Centre for Pet Nutrition, Waltham-on-the-Wolds, Leicestershire, United Kingdom
| | - Alison Colyer
- WALTHAM Centre for Pet Nutrition, Waltham-on-the-Wolds, Leicestershire, United Kingdom
| | - Penelope Morris
- WALTHAM Centre for Pet Nutrition, Waltham-on-the-Wolds, Leicestershire, United Kingdom
| | - David Allaway
- WALTHAM Centre for Pet Nutrition, Waltham-on-the-Wolds, Leicestershire, United Kingdom
| | - Paul G. Jones
- WALTHAM Centre for Pet Nutrition, Waltham-on-the-Wolds, Leicestershire, United Kingdom
| | - Kelly S. Swanson
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
- Division of Nutritional Sciences, University of Illinois, Urbana, Illinois, United States of America
- Department of Veterinary Clinical Medicine, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
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