Comparison of fecal microbiota of three captive carnivore species inhabiting Korea.
Ontology highlight
ABSTRACT:
SUBMITTER: An C
PROVIDER: S-EPMC5383174 | biostudies-literature | 2017 Mar
REPOSITORIES: biostudies-literature
Publications
Comparison of fecal microbiota of three captive carnivore species inhabiting Korea.
An Choa C Okamoto Yumiko Y Xu Siyu S Eo Kyung Yeon KY Kimura Junpei J Yamamoto Naomichi N
The Journal of veterinary medical science 20161230 3
This study aimed at characterizing fecal microbiota of three captive carnivore species of leopard cats Prionailurus bengalensis, Eurasian otters Lutra lutra and raccoon dogs Nyctereutes procyonoides. We used DNA barcoding sequencing to analyze 16S rRNA genes of uncultured bacteria in the feces collected in the Seoul Zoo. The sequencing analyses revealed that: 1) Firmicutes was the most dominant phylum for all three animals; 2) bacterial genus-rank compositions were distinct across species of the ...[more]
Similar Datasets
Project description:The gut microbiota of birds is known to be characterized for different species, although it may change with feeding items. In this study, we compared the gut microbiota of birds with different feeding behaviors in the same habitat. We collected fecal samples from three Arctic species, snow buntings Plectrophenax nivalis, sanderlings Calidris alba, and pink-footed geese Anser brachyrhynchus that are phylogenetically quite distant in different families to evaluate effects of diet on gut microbiota. Also, we characterized the prevalence of fecal bacteria using the Illumina MiSeq platform to sequence bacterial 16S rRNA genes. Our NMDS results showed that fecal bacteria of snow buntings and sanderlings were significantly distant from those of pink-footed geese. Although all three birds were occupied by three bacterial phyla, Proteobacteria, Firmicutes, and Bacteroidetes, dominant taxa still varied among the species. Our bacterial sequences showed that snow buntings and sanderlings were dominated by Firmicutes and Bacteroidetes, while pink-footed geese were dominated by Proteobacteria. In addition, the bacterial diversity in snow buntings and sanderlings was significantly higher than that in pink-footed geese. Our results suggest that insectivorous feeding diet of snow buntings and sanderlings could be responsible for the similar bacterial communities between the two species despite the distant phylogenetic relationship. The distinctive bacterial community in pink-footed geese was discussed to be related with their herbivorous diet.
| S-EPMC7319242 | biostudies-literature
Project description:Diarrhea constitutes one of the most common diseases affecting the survival of captive musk deer and is usually caused by an imbalance in intestinal microbiota. Currently, research regarding the structure and function of intestinal microbiota in diarrheic musk deer is lacking. Therefore, in the present study, high-throughput 16S-rRNA gene sequencing was used to analyze the intestinal microbiota in feces of healthy captive musk deer (HMD) (n = 8) and musk deer with mild (MMD) (n = 8), and severe (n = 5) (SMD) diarrhea to compare the difference in intestinal microbiota of musk deer under various physiological conditions. The results showed that the diversity of HMD fecal microbiota was significantly higher than that of the two diarrhea samples. ? Diversity results indicated that there were extremely significant differences in bacterial communities between the HMD sample and the MMD and SMD samples. However, no significant difference was found between the two diarrhea samples. LefSe analysis showed that the degree of intestinal physiological dysfunction in musk deer was correlated with the types of major pathogens. The main pathogen in the MMD group is Escherichia-Shigella, whereas Fusobacterium is the main pathogen in the SMD group. PICRUSt functional profile prediction indicated that the intestinal microbiota disorder could also lead to changes in the abundance of genes in metabolic pathways of the immune system. Altogether, this study provides a theoretical basis for the exploration of treatments for diarrhea in captive musk deer, which is of considerable significance to the implementation of the musk deer release into the wild program.
| S-EPMC5840195 | biostudies-literature
Project description:BackgroundThe microorganisms populating the gastro-intestinal tract of vertebrates, collectively known as "microbiota", play an essential role in digestion and are important in regulating the immune response. Whereas the intestinal microbiota in humans and model organisms has been studied for many years, much less is known about the microbiota populating the intestinal tract of wild animals.ResultsThe relatively large number of raptors admitted to the Tufts Wildlife Clinic on the Cummings School of Veterinary Medicine at Tufts University campus provided a unique opportunity to investigate the bacterial microbiota in these birds. Opportunistic collection of fecal samples from raptors of 7 different species in the orders Strigiformes, Accipitriformes, and Falconiformes with different medical histories generated a collection of 46 microbiota samples. Based on 16S amplicon sequencing of fecal DNA, large β-diversity values were observed. Many comparisons exceeded weighted UniFrac distances of 0.9. Microbiota diversity did not segregate with the taxonomy of the host; no significant difference between microbiota from Strigiformes and from Accipitriformes/Falconiformes were observed. In contrast, in a sample of 22 birds admitted for rehabilitation, a significant effect of captivity was found. The change in microbiota profile was driven by an expansion of the proportion of Actinobacteria. Based on a small number of raptors treated with anti-microbials, no significant effect of these treatments on microbiota α-diversity was observed.ConclusionsThe concept of "meta-organism conservation", i.e., conservation efforts focused on the host and its intestinal microbiome has recently been proposed. The observed effect of captivity on the fecal microbiota is relevant to understanding the response of wildlife to captivity and optimizing wildlife rehabilitation and conservation efforts.
| S-EPMC7863374 | biostudies-literature
Project description:Fluralaner is a recent external parasiticide, first of a new class of drugs (isoxazoline parasiticides). It is widely used in companion animals both for its wide spectrum (fleas, ticks and other mites) but also for its ease of use (oral tablets given once for 1 to three months). It is known to be eliminated primarily via the feces (>90%) as the unchanged compound. In zoo carnivores, controlling external parasites is also important and there are no specific products with a marketing authorization to control them. The first objective of this study was to evaluate the pharmacokinetic profile of fluralaner in zoo carnivores. The second objective was to demonstrate that fluralaner can be eliminated over a prolonged period of time, thereby raising questions about its potential impact on non-target species such as arthropods. After adjusting the oral dose using allometric equations, animals were dosed and fecal samples were collected on a regular basis for up to three months to determine the fecal elimination curve of fluralaner as a surrogate of plasma kinetics (for ethical and safety reasons, plasma samples were not considered). All samples were analyzed with a validated LC-MSMS technique. Our results show that, despite limitations and a limited number of animals included, most carnivores eliminate fluralaner in their feces for several weeks to months (in Lions, fluralaner was still detectable after 89 days). To our knowledge, this is the first study demonstrating such a long elimination period in animals. Further studies would be required to investigate the risk associated with the presence of active residues in other carnivore feces for the environment, especially in dogs and cats, considering the large use of this class of compounds.
| S-EPMC11362066 | biostudies-literature
Project description:Understanding predator guild niche partitioning using DNA metabarcoding
| PRJNA1103791 | ENA
Project description:gut microbiota in three captive waterfowl Raw sequence reads
| PRJNA1102890 | ENA
Project description:Gut microbiota plays a vital role in maintaining the health and immunity of wild birds. However, less is known about the comparison of fecal microbiota between different ecological groups of wild birds, particularly in the Yellow River National Wetland in Baotou, China, an important transit point for birds migrating all over the East Asia-Australian and Central Asian flyways. In this study, we characterized the fecal microbiota and potential microbial function in nine bird species of raptors, waders, and waterfowl using 16S rRNA gene amplicon sequencing to reveal the microbiota differences and interaction patterns. The results indicated that there was no significant difference in α-diversity, but a significant difference in β-diversity between the three groups of birds. The fecal bacterial microbiota was dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes in all groups of birds. Furthermore, we identified five bacterial genera that were significantly higher in raptors, five genera that were significantly higher in waders, and two genera that were more abundant in waterfowl. The bacterial co-occurrence network results revealed 15 and 26 key genera in raptors and waterfowls, respectively. The microbial network in waterfowl exhibited a stronger correlation pattern than that in raptors. PICRUSt2 predictions indicated that fecal bacterial function was significantly enriched in the antibiotic biosynthesis pathway in all three groups. Metabolic pathways related to cell motility (bacterial chemotaxis and flagellar assembly) were significantly more abundant in raptors than in waders, whereas waders were enriched in lipid metabolism (synthesis and degradation of ketone bodies and fatty acid biosynthesis). The fecal microbiota in waterfowl harbored more abundant vitamin B6 metabolism, RNA polymerase, and tyrosine and tryptophan biosynthesis. This comparative study revealed the microbial community structure, microbial co-occurrence patterns, and potential functions, providing a better understanding of the ecology and conservation of wild birds. Future studies may focus on unraveling metagenomic functions and dynamics along with the migration routine or different seasons by metagenomics or metatranscriptomics.
| S-EPMC9393522 | biostudies-literature
Project description:Sequencing of 16S ribosomal RNA (rRNA) gene, which has improved the characterization of microbial community, has made it possible to detect a low level Helicobacter pylori (HP) sequences even in HP-negative subjects which were determined by a combination of conventional methods. This study was conducted to obtain a cutoff value for HP colonization in gastric mucosa biopsies and gastric juices by the pyrosequencing method. Corresponding author: Department of Internal Medicine, Seoul National University Bundang Hospital, Seoungnam, Gyeonggi-do, Korea; Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea (Tel., +82-31-787-7008; e-mail, nayoungkim49@empas.com). Microbial DNA from gastric mucosal samples [gastric antrum (n=63, mucosal biopsy), follow-up sample on gastric antrum (n=16, mucosal biopsy), and gastric body (n=18, mucosal biopsy)] and gastric juices (n=4, not mucosal biopsy) was amplified by nested PCR using universal bacterial primers, and the 16S rRNA genes were pyrosequenced.
2014-09-18 | E-GEOD-61493 | biostudies-arrayexpress
Project description:IntroductionSnub-nosed monkeys are species in danger of extinction due to habitat fragmentation and human activities. Captivity has been suggested as an Auxiliary Conservation Area (ASA) strategy. However, little is known about the adaptation of different species of snub-nosed monkeys to captive environments.MethodsThis study compared the gut microbiota between Rhinopithecus bieti, R. brelichi, and R. roxellana under identical captive conditions to provide insights for improving captive conservation strategies.ResultsThe results showed that these three Rhinopithecus species shared 80.94% of their Operational Taxonomic Unit (OTU), indicating high similarity in gut microbiota composition. The predominant phyla were Firmicutes and Bacteroidetes for all three Rhinopithecus species, but differences were observed in diversity, characteristic bacterial communities, and predicted function. Significant enrichment of cellulolytic families, including Ruminococcaceae, Clostridiales vadinBB60 group, Christensenellaceae, and Erysipelotrichaceae, and pathways involved in propionate and butyrate metabolism in the gut of R. bieti suggested that it may have a superior dietary fiber utilization capacity. In contrast, Bacteroidetes, Ruminoccaceae, and Trichospiraceae were more abundant in R. brelichi and R. roxellana, and were associated with saccharide and glycan metabolic pathways. Moreover, R. brelichi and R. roxellana also had higher similarity in microbiota composition and predicted function.DiscussionIn conclusion, the results demonstrate that host species are associated with the composition and function of the gut microbiota in snub-nosed monkeys. Thus, host species should be considered when formulating nutritional strategies and disease surveillance in captive snub-nosed monkeys.
| S-EPMC10534982 | biostudies-literature
Project description:Fungi in the genus Trichoderma are widely distributed in China, including in Yunnan province. In this study, we report three new soil-inhabiting species in Trichoderma, named as T.kunmingense, T.speciosum and T.zeloharzianum. Their colony and mycelial morphology, including features of asexual states, were described. For each species, their DNA sequences were obtained from three loci, the internal transcribed spacer (ITS) regions of the ribosomal DNA, the translation elongation factor 1-α encoding gene (tef1) and the gene encoding the second largest nuclear RNA polymerase subunit (rpb2). Our analyses indicated that the three new species showed consistent divergence amongst each other and from other known and closely related species. Amongst the three, T.speciosum and T.kunmingense belong to the Viride Clade. Specifically, T.speciosum is related to three species - T.hispanicum, T.samuelsii and T.junci and is characterised by tree-like conidiophores, generally paired branches, curved terminal branches, spindly to fusiform phialides and subglobose to globose conidia. In contrast, T.kunmingense morphologically resembles T.asperellum and T.yunnanense and is distinguished by its pyramidal conidiophores, ampulliform to tapered phialides, discrete branches and ovoidal, occasionally ellipsoid, smooth-walled conidia. The third new species, T.zeloharzianum, is a new member of the Harzianum Clade and is closely associated with T.harzianum, T.lixii and T.simmonsii but distinguished from them by having smaller, subglobose to globose, thin-walled conidia.
| S-EPMC6303281 | biostudies-literature