The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease

Pilla, Rachel; Suchodolski, Jan S.

doi:10.3389/fvets.2019.00498

Cited by 268 publications

(303 citation statements)

References 116 publications

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“…The genera Succinivibrio, Prevotella, Phascolarctobacterium, Catenibacterium, and Blautia, are recognized short-chain fatty acid (SCFA) producers [53][54][55]. These molecules provide multiple gut health bene ts from reducing in ammation and tumorigenesis to increasing gut motility and secretory activity [2,54,56].…”

Section: Discussionmentioning

confidence: 99%

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Long-Read Metagenomics to Retrieve High-Quality Metagenome-Assembled Genomes from Canine Feces

Cuscó¹,

Pérez²,

Viñes³

et al. 2020

Preprint

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Background. Metagenomics is a powerful and rapidly developing approach that provides new biological insights into the microbes inhabiting underexplored environments, such as canine fecal microbiome. We investigate long-read metagenomics with Nanopore sequencing to profile the fecal microbiome and to retrieve high-quality metagenome-assembled genomes (HQ MAGs) from a healthy dog.Results. More than 99% of total classified reads corresponded to Bacteria. The most abundant phylum was Bacteroidetes (~80% of total reads), followed by Firmicutes, Proteobacteria, and Fusobacteria. Prevotella (>50%) and Bacteroides (>20%) are the more abundant genera, followed by Fusobacterium, Megamonas, Sutterella, and other fecal-related genera, (each representing <5% of the total bacterial composition). We retrieved eight single-contig HQ MAGs and three medium-quality MAGs, after combining several metagenome dataset assemblies. The HQ MAGs corresponded to Succinivibrio, Sutterella, Prevotellamassilia, Phascolarctobacterium, Enterococcus, Blautia, and Catenibacterium genera. Succinivibrio HQ MAG represents a novel candidate bacterial species. Sutterella HQ MAG is potentially the first reported genome assembly for Sutterella stercoricanis, as assigned by 16S rRNA gene similarity. Prevotellamassilia, Phascolarctobacterium, Catenibacterium, and Blautia sp900541345 HQ MAGs improved the contiguity of previously reported genome assemblies in their respective genera, and the number of rRNA genes and tRNA genes. Finally, Enterococcus hirae and Blautia sp003287895 HQ MAGs represented species that already have a complete reference genome. At the technical level, we demonstrated that a high-molecular weight DNA extraction improved the taxonomic classification of the raw unassembled reads, the metagenomics assembly contiguity, and the retrieval of longer and circular contigs, which are potential HQ MAGs. Conclusions. Long-read metagenomics allowed us to recover HQ MAGs from canine feces of a healthy dog. The high-molecular weight DNA extraction to improve contiguity and the correction of the insertions and deletions to reduce frameshift errors ensure the retrieval of complete single-contig HQ MAGs.

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Section: Discussionmentioning

confidence: 99%

“…Previous studies reported similarities between canine and human GI microbiome (See [2][3][4][5] for extensive reviews). Different GI diseases relate to an altered GI microbiome that, on the other hand, can be modulated by diet and dietary complements (such as pre-and probiotics).…”

Section: Introductionmentioning

confidence: 99%

Long-Read Metagenomics to Retrieve High-Quality Metagenome-Assembled Genomes from Canine Feces

Cuscó¹,

Pérez²,

Viñes³

et al. 2020

Preprint

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“…Despite its original carnivorous classification, the domestic dog is currently considered as an omnivorous animal, since commercial pet foods are formulated to provide a balanced nutritional intake yet with the supplementation of high concentrations of fibre and carbohydrates (generally higher than 3% and 30%, respectively; Barry et al ., 2012; Alessandri et al ., 2019a–c), which is necessary to produce extruded dry diet (kibble) (Pilla and Suchodolski, 2019). The domestic cat, on the other hand, with its short colon represents an example of an evolutionary adaptation to a strict carnivorous diet and is still considered an obligate carnivore.…”

Section: The Effect Of Changes In Dietary Habits On Canine and Felinementioning

confidence: 99%

Catching a glimpse of the bacterial gut community of companion animals: a canine and feline perspective

Alessandri

Argentini

Milani

et al. 2020

Microbial Biotechnology

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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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“…Intestinal microorganisms play a dominant role in the nutrition and other vital processes of the bee. There is a dependence of the intestinal microflora of the honeybee on the general health of the insect [93]. This composition of the microbial community can be used as an indicator of the biological health of the insect.…”

Section: Microbiome Of Bumblebees and Honey Bees And The Impact Of Pementioning

confidence: 99%

The Effect of Pesticides on the Microbiome of Animals

et al. 2020

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In recent decades an increase in the use of pesticides to protect plants from pests, diseases and weeds has been observed. There are many studies on the effects of various pesticides on non-target organisms. This review aims to analyze and summarize published scientific data on the effects of pesticides on the animal microbiome. Pesticides can affect various parameters of the animal microbiome, such as the taxonomic composition of bacteria, bacterial biodiversity, and bacterial ratios and modify the microbiome of various organisms from insects to mammals. Pesticide induced changes in the microbiome reducing the animal’s immunity. The negative effects of pesticides could pose a global problem for pollinators. Another possible negative effect of pesticides is the impact of pesticides on the intestinal microbiota of bumblebees and bees that increase the body’s sensitivity to pathogenic microflora, which leads to the death of insects. In addition, pesticides can affect vitality, mating success and characteristics of offspring. The review considers methods for correcting of bee microbiome.

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The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease

Cited by 268 publications

References 116 publications

Long-Read Metagenomics to Retrieve High-Quality Metagenome-Assembled Genomes from Canine Feces

Long-Read Metagenomics to Retrieve High-Quality Metagenome-Assembled Genomes from Canine Feces

Catching a glimpse of the bacterial gut community of companion animals: a canine and feline perspective

The Effect of Pesticides on the Microbiome of Animals

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