Bacterial Diversity in the Cecum of the World’s Largest Living Rodent (Hydrochoerus hydrochaeris)

García-Amado, M. Alexandra; Godoy-Vitorino, Filipa; Piceno, Yvette M.; Tom, Lauren M.; Andersen, Gary L.; Herrera, Emílio; Domínguez-Bello, María Gloria

doi:10.1007/s00248-011-9963-z

Cited by 18 publications

(12 citation statements)

References 31 publications

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“…Early research into lignocellulose digestion in the beaver GI tract identified cellulase activity in ceacal contents [ 19 ], although the microbial basis of this activity was not investigated. Our results demonstrate that the microbial community found in the ceacum and feaces of the beaver is similar to that found in other hindgut fermenters [ 6 , 16 , 17 , 31 ]. These bacterial communities in the beaver are both dominated by Firmicutes and Bacteroidetes; a characteristic that is common within all mammalian guts [ 6 ].…”

Section: Discussionsupporting

confidence: 82%

“…Rodents are primarily herbivores and utilize hind-gut fermentation to break down cellulosic feeds [ 13 ]. With the exception of the mouse ( Mus musculus ) and the lab rat ( Rattus norvegicus ), which serve as model systems for understanding the interactions between host and gut microbiome [ 14 , 15 ], few studies have examined the microbial communities in the ceacum of rodents [ 16 , 17 ]. Of particular interest, the microbial basis of lignocellulose digestion in one of the most iconic Canadian rodents, the beaver (genus Castor ), has not been reported.…”

Section: Introductionmentioning

confidence: 99%

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Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis)

2016

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The North American Beaver (Castor canadensis) is the second largest living rodent and an iconic symbol of Canada. The beaver is a semi-aquatic browser whose diet consists of lignocellulose from a variety of plants. The beaver is a hindgut fermenter and has an enlarged ceacum that houses a complex microbiome. There have been few studies examining the microbial diversity in gastrointestinal tract of hindgut fermenting herbivores. To examine the bacterial and archaeal communities inhabiting the gastrointestinal tract of the beaver, the microbiome of the ceacum and feaces was examined using culture-independent methods. DNA from the microbial community of the ceacum and feaces of 4 adult beavers was extracted, and the16S rRNA gene was sequenced using either bacterial or archaeal specific primers. A total of 1447 and 1435 unique bacterial OTUs were sequenced from the ceacum and feaces, respectively. On average, the majority of OTUs within the ceacum were classified as Bacteroidetes (49.2%) and Firmicutes (47.6%). The feaces was also dominated by OTUs from Bacteroidetes (36.8%) and Firmicutes (58.9%). The composition of bacterial community was not significantly different among animals. The composition of the ceacal and feacal microbiome differed, but this difference is due to changes in the abundance of closely related OTUs, not because of major differences in the taxonomic composition of the communities. Within these communities, known degraders of lignocellulose were identified. In contrast, to the bacterial microbiome, the archaeal community was dominated by a single species of methanogen, Methanosphaera stadtmanae. The data presented here provide the first insight into the microbial community within the hindgut of the beaver.

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Section: Discussionsupporting

confidence: 82%

Section: Introductionmentioning

confidence: 99%

Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis)

2016

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“…Fecal sampling serves as an alternate for more laborious and invasive sampling from, in these circumstances, commercial, domesticated livestock from an active farm. The phyla Firmicutes and Bacteroidetes were identified as the predominant phyla in the microbiota of all the domesticated herbivores in this study; however, this trend has not been universal for other studies and animals (Barker, Gillett, Polkinghorne, & Timms, 2013;García-Amado et al, 2012;Ishaq & Wright, 2012;Li et al, 2013). Ley et al identified Firmicutes and Bacteroidetes as the phyla found most ubiquitous in the vertebrate microbiota .…”

Section: Discussioncontrasting

confidence: 52%

“…The phyla Firmicutes and Bacteroidetes were identified as the predominant phyla in the microbiota of all the domesticated herbivores in this study; however, this trend has not been universal for other studies and animals (Barker, Gillett, Polkinghorne, & Timms, ; García‐Amado et al., ; Ishaq & Wright, ; Li et al., ). Ley et al.…”

Section: Discussioncontrasting

confidence: 49%

Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals

et al. 2017

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In this pilot study, we determined the core fecal microbiota composition and overall microbiota diversity of domesticated herbivorous animals of three digestion types: hindgut fermenters, ruminants, and monogastrics. The 42 animals representing 10 animal species were housed on a single farm in Ireland and all the large herbivores consumed similar feed, harmonizing two of the environmental factors that influence the microbiota. Similar to other mammals, the fecal microbiota of all these animals was dominated by the Firmicutes and Bacteroidetes phyla. The fecal microbiota spanning all digestion types comprised 42% of the genera identified. Host phylogeny and, to a lesser extent, digestion type determined the microbiota diversity in these domesticated herbivores. This pilot study forms a platform for future studies into the microbiota of nonbovine and nonequine domesticated herbivorous animals.

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“…Clostridiaceae, the third most abundant family, was not reported as a main bacterial family in rabbits by Massip et al (2012); however, it was present in rabbit caeca (Bäuerl et al, 2014), and was a dominant family in the capybara (García-Amado et al, 2012) and healthy horses (Steelman et al, 2012). Members of the Clostridiaceae family have been found to prefer simpler carbohydrates, rather than the fibrous components utilised by the Lachnospiraceae and Ruminococcaceaea, and its prevalence in the caecum was thus somewhat surprising (Biddle et al, 2013).…”

Section: The Microbiota Profilementioning

confidence: 97%

Composition of rabbit caecal microbiota and the effects of dietary quercetin supplementation and sex thereupon

2019

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The purpose of this study was to add to the current understanding of rabbit caecal microbiota. This involved describing its microbial composition and linking this to live performance parameters, as well as determining the effects of dietary quercetin (Qrc) supplementation (2 g/kg feed) and sex on the microbial population. The weight gain and feed conversion ratio of twelve New Zealand White rabbits was measured from 5 to 12 wk old, blood was sampled at 11 wk old for the determination of serum hormone levels, and the rabbits were slaughtered and caecal samples collected at 13 wk old. Ion 16STM metagenome sequencing was used to determine the microbiota profile. The dominance of Firmicutes (72.01±1.14% of mapped reads), Lachnospiraceae (23.94±1.01%) and Ruminococcaceae (19.71±1.07%) concurred with previous reports, but variation both between studies and individual rabbits was apparent beyond this. Significant correlations between microbial families and live performance parameters were found, suggesting that further research into the mechanisms of these associations could be useful. Negative correlations with the caecal flavonoid content were found, but the latter was not affected by diet, and the effects of quercetin supplementation on the microbiota were very limited, possibly due to the absorption of the quercetin-aglycone from the gastrointestinal tract prior to the caecum. Nonetheless, Clostridiales Family XIII. Incertae Sedis was more abundant in the quercetin-supplemented rabbits (Control: 0.003±0.003%; Qrc: 0.020±0.000; P=0.005), as was the genus Anaerofustis (Control: 0.000±0.002; Qrc: 0.010±0.002; P=0.003). Serum cortisol levels were higher in females, and several microbial families differed between the sexes. Most were more abundant in female rabbits, including the most abundant, the family Eubacteriaceae (Male: 2.93±0.40; Female: 4.73±0.40; P=0.01).

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Bacterial Diversity in the Cecum of the World’s Largest Living Rodent (Hydrochoerus hydrochaeris)

Cited by 18 publications

References 31 publications

Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis)

Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis)

Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals

Composition of rabbit caecal microbiota and the effects of dietary quercetin supplementation and sex thereupon

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