Comparison of the microbial population in rabbits and guinea pigs by next generation sequencing

Crowley, Edward J.; King, Julie; Wilkinson, Toby; Worgan, Hilary J.; Huson, Kathryn M.; Rose, Michael T.; McEwan, Neil R.

doi:10.1371/journal.pone.0165779

Cited by 52 publications

(72 citation statements)

References 25 publications

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“…Our results are in agreement with previous work, though the relative abundance of the phyla was different [5]. Euryarchaeota were detected in both samples (1.5 and 0.6% in Cavy 1 and Cavy 2, respectively) (Fig.…”

Section: Resultssupporting

confidence: 93%

“…Those animals eat their own faeces to maintain their intestinal microbes and recover nutrients and vitamins [31]. Bacteroidetes and Firmicutes together formed most of the population in the guinea pig faecal samples, according to the results of two studies [5, 12]. The two most abundant bacterial phyla in guinea pig guts relate to the typical vertebrate gut microbiome, including the human intestine.…”

Section: Introductionmentioning

confidence: 99%

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Microbial Diversity and Organic Acid Production of Guinea Pig Faecal Samples

Ayudthaya

Oost

et al. 2019

Curr Microbiol

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The guinea pig (Cavia porcellus) or cavy is a grass-eating rodent. Its main diet consists of grass or hay, which comprises cellulose, hemicellulose, lignin and their derivatives. Here, the microbial diversity of faecal samples of two guinea pigs and microbial enrichments made with substrates, including starch waste and dried grass, were investigated along with organic acid production profiles. The microbial communities of the faecal samples were dominated by the phyla Bacteroidetes (40%) and Firmicutes (36%). Bacteroidales S24-7 (11% in Cavy 1 and 21% in Cavy 2) was the most abundant order. At genus level, many microorganisms remained unclassified. Different carbon sources were used for organic acid production in faecal enrichments. The dominant bacterial groups in the secondary enrichments with dried grass, starch waste and xylose were closely related to Prevotella and Blautia. Acetate was the predominant organic acid from all enrichments. The organic acid production profiles corresponded to a mixed acid fermentation but differed depending on the substrate. Eight phylogenetically different isolates were obtained, including a novel Streptococcus species, strain Cavy grass 6. This strain had a low abundance (1%) in one of the faecal samples but was enriched in the dried grass enrichment (3%). Cavy grass 6, a fast-growing heterolactic bacterium, ferments cellobiose to lactate, acetate, formate and ethanol. Our results show that cavy faecal samples can be applied as microbial source for organic acid production from complex organic substrates. The cavy gut contains many as-yet-uncultivated bacteria which may be appropriate targets for future studies.Electronic supplementary materialThe online version of this article (10.1007/s00284-019-01630-x) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Microbial Diversity and Organic Acid Production of Guinea Pig Faecal Samples

Ayudthaya

Oost

et al. 2019

Curr Microbiol

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“…Domesticated rabbits have no Treponema in their gut, unlike hares (Lepus spp.) [22,33,34]. Grasscutters and rabbits are both small hindgut fermenters, but they were plotted separately from each other in the PCoA analysis.…”

Section: Discussionmentioning

confidence: 99%

Comparative Analysis of Fecal Microbiota in Grasscutter (Thryonomys swinderianus) and Other Herbivorous Livestock in Ghana

et al. 2020

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The grasscutter (also known as the greater cane rat; Thryonomys swinderianus) is a large rodent native to West Africa that is currently under domestication process for meat production. However, little is known about the physiology of this species. In the present study, aiming to provide information about gut microbiota of the grasscutter and better understand its physiology, we investigated the intestinal microbiota of grasscutters and compared it with that of other livestock (cattle, goat, rabbit, and sheep) using 16S rRNA metagenomics analysis. Similar to the other herbivorous animals, bacteria classified as Bacteroidales, Clostridiales, Ruminococcaceae, and Lachnospiraceae were abundant in the microbiome of grasscutters. However, Prevotella and Treponema bacteria, which have fiber fermentation ability, were especially abundant in grasscutters, where the relative abundance of these genera was higher than that in the other animals. The presence of these genera might confer grasscutters the ability to easily breakdown dietary fibers. Diets for grasscutters should be made from ingredients not consumed by humans to avoid competition for resources and the ability to digest fibers may allow the use of fiber-rich feed materials not used by humans. Our findings serve as reference and support future studies on changes in the gut microbiota of the grasscutter as domestication progresses in order to establish appropriate feeding methods and captivity conditions.

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“…However, 400 g/kg and 250 g/kg NDF groups decreased the diversity of the cecal microbiota ( p = 0.01). Therefore, feeding rabbits with different dietary fiber levels resulted in alteration of the structure of the cecal bacteria community (diversity and relative abundance) (Crowley et al., ). We also noticed that the cecal bacterial diversity increases with age, whereas bacterial abundance maintains a dynamic balance (in this case, increased first and then decreased).…”

Section: Discussionmentioning

confidence: 99%

Effect of dietary fiber levels on bacterial composition with age in the cecum of meat rabbits

Zhou

et al. 2018

MicrobiologyOpen

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This study investigated the influence of dietary fiber levels on the growth performance, digestion, metabolism, and cecal microbial community of rabbits with different diets at different age. The different levels of dietary natural detergent fiber (NDF) were formulated accordingly: 400(A), 350(B), 300(C), 250(D) g/kg original matter basis, respectively; the different ages were 52, 62, and 72 days. With NDF increasing, the average daily feed intake (ADFI) and feed conversion rate (FCR) were increased, whereas average daily gain (ADG) and mortality were decreased (p < 0.05). The stomach relative weight, stomach content relative weight, cecal relative weight, and cecal content weight increased with increasing NDF (p < 0.05). The NH -N concentration of cecum dropped when the dietary NDF increased (p < 0.05). The diversity of the total microbiota increased significantly in Diets B, C (p = 0.011), and reached the lowest in 52 days for all diet groups. The richness index was decreased significantly in Diet A, D (p < 0.05) and in 62 days (p < 0.001), respectively. The phylum Firmicutes was higher (p < 0.01) in rabbits fed Diets B, C than Diets A, D and Bacteroidetes was highest in Diets C, D, and Proteobacteria was the highest in Diet A (p < 0.001). Among the classified genera, there were 14 that had levels of abundance of more than 1% and were commonly shared by all samples. Ruminococcus spp. that produced volatile fatty acid (VFA) abundance was highest from Diets B, C at 52 and 62 days. It is interesting to note that Bifidobacterium from Diet C was the most abundant genus during the entire experimental period (p < 0.01). The data from Venn diagrams, principal component analysis (PCA), and heat map plots of the bacterial communities showed that there were more groups of shared microbiota with aging. The above results indicate the cecal microbiota controlled by the 350 g/kg NDF diet can prevent gastrointestinal distress and exhibit good production performance.

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Comparison of the microbial population in rabbits and guinea pigs by next generation sequencing

Cited by 52 publications

References 25 publications

Microbial Diversity and Organic Acid Production of Guinea Pig Faecal Samples

Microbial Diversity and Organic Acid Production of Guinea Pig Faecal Samples

Comparative Analysis of Fecal Microbiota in Grasscutter (Thryonomys swinderianus) and Other Herbivorous Livestock in Ghana

Effect of dietary fiber levels on bacterial composition with age in the cecum of meat rabbits

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