Abstract:Intestinal microbes are part of a complex ecosystem. They have a mutual relationship with the host and play an essential role in maintaining the host's health. To optimize the feeding strategies and improve the health status of the dhole, which is an endangered species, we analyzed the structure of fecal microbes in four captive dholes using high-throughput Illumina sequencing targeting the V3-V4 region of the 16S rRNA gene. The diversity indexes and rarefaction curves indicated high microbial diversity in the… Show more
“…As shown in Fig. 2, regions of approximately 468 bp and 394 bp encircling the V3-V4 and V5-V7 hypervariable regions respectively within the 16S rRNA gene was subjected to high-throughput sequencing to maximize the effective length of sequencing reads 18 .Figure 2GoldViewTM Nucleic Acid Stained 1.5% Agarose gel of V3-V4 region of 16S RNA gene sequence (1, 2 and 3) and V5-V7 region of 16S RNA gene (4, 5 and 6) amplified product of eggs, L 3 larvae and adults of H. contortus. Lane 1 and 8: Direct-load™ Star Marker Plus (D2000 Plus); GenStar Biosolutions Co. Ltd, Beijing, China.
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High-throughput sequencing technology has shown tremendous promise for microbial community composition and diversity. Illumina MiSeq platform was exploited to study the microbial community associated with the different stages of the life-cycle of ovine Haemonchus contortus field strains using two distinct amplification primer sets (targeting V3–V4, and V5–V7). Scanning electron microscope and polymerase chain reaction coupled with Illumina MiSeq platform were employed to confirm the absence of any parasite surface contamination by intact bacteria or their DNA products. Results showed 48 (V3–V4 tags) and 28 (V5–V7 tags) bacterial genera comprised the microbial flora of H. contortus microbiome. The dominant bacterial genera belonged to Escherichia-Shigella, Pseudomonas and Ochrobactrum, which were shared in all the stages of the parasite life-cycle using V3–V4 and V5–V7 amplicons. Moreover, the parasite microbiome could reflect the external micro-organisms (i.e. micro- and macro-habitats). There is abundant room for further progress in comparing microbiome of different helminths, which has, and will continue to offer considerable potential for better understanding a wide-variety of devastating animal and human diseases.
“…As shown in Fig. 2, regions of approximately 468 bp and 394 bp encircling the V3-V4 and V5-V7 hypervariable regions respectively within the 16S rRNA gene was subjected to high-throughput sequencing to maximize the effective length of sequencing reads 18 .Figure 2GoldViewTM Nucleic Acid Stained 1.5% Agarose gel of V3-V4 region of 16S RNA gene sequence (1, 2 and 3) and V5-V7 region of 16S RNA gene (4, 5 and 6) amplified product of eggs, L 3 larvae and adults of H. contortus. Lane 1 and 8: Direct-load™ Star Marker Plus (D2000 Plus); GenStar Biosolutions Co. Ltd, Beijing, China.
…”
High-throughput sequencing technology has shown tremendous promise for microbial community composition and diversity. Illumina MiSeq platform was exploited to study the microbial community associated with the different stages of the life-cycle of ovine Haemonchus contortus field strains using two distinct amplification primer sets (targeting V3–V4, and V5–V7). Scanning electron microscope and polymerase chain reaction coupled with Illumina MiSeq platform were employed to confirm the absence of any parasite surface contamination by intact bacteria or their DNA products. Results showed 48 (V3–V4 tags) and 28 (V5–V7 tags) bacterial genera comprised the microbial flora of H. contortus microbiome. The dominant bacterial genera belonged to Escherichia-Shigella, Pseudomonas and Ochrobactrum, which were shared in all the stages of the parasite life-cycle using V3–V4 and V5–V7 amplicons. Moreover, the parasite microbiome could reflect the external micro-organisms (i.e. micro- and macro-habitats). There is abundant room for further progress in comparing microbiome of different helminths, which has, and will continue to offer considerable potential for better understanding a wide-variety of devastating animal and human diseases.
“…) and these organisms facilitate the digestion of cellulose and hemicellulose in food (Wu et al . ). However, the numbers of bacteria from these two phyla were significantly different in the different host groups ( P < 0·01).…”
Aims
The gut microbiota has a great effect on the health and nutrition of the host. Manipulation of the intestinal microbiota may improve animal health and growth performance. The objectives of our study were to characterize the faecal microbiota between wild and captive Tibetan wild asses and discuss the differences and their reasons.
Methods and Results
Through high‐throughput sequencing of the 16S rRNA V4‐V5 region, we studied the gut microbiota composition and structure of Tibetan wild asses in winter, and analysed the differences between wild and captive groups. The results showed that the most common bacterial phylum in Tibetan wild ass faeces samples was Bacteroidetes, while the phylum Firmicutes was dominant in captive Tibetan wild ass faecal samples. The relative abundance of Firmicutes, Tenericutes and Spirochaetes were significantly higher (P < 0·01) than in the wild groups.
Conclusions
Captivity reduces intestinal microbial diversity, evenness and operational taxonomic unit number due to the consumption of industrial food, therefore, increasing the risk of disease prevalence and affecting the health of wildlife.
Significance and Impact of the Study
We studied the effect of the captive environment on intestinal micro‐organisms. This article provides a theoretical basis for the ex‐situ conservation of wild animals in the future.
“…We used the MiSeq PCR conditions described in Wu et al. (), and purified the 16S rRNA amplicons with AMPure XP beads (Beckman, USA), following the manufacturer's instructions. Extracted DNA from each of the 10 samples of each microbiota was pooled in equal concentrations prior to sequencing on an Illumina MiSeq platform (Illumina MiSeq sequencing system, USA).…”
Section: Methodsmentioning
confidence: 99%
“…Within microbiome research, most attention has been directed toward the bacterial communities inhabiting the fish farm environment or within the fish intestine (Indugu, Bittinger, Kumar, Vecchiarelli, & Pitta, ; Sun et al., ; Wu et al., , ; Zhuang et al., ). For example, Stephens et al.…”
The relationship between the internal microbiome of an individual organism and that of its external environment has been little investigated in freshwater ecosystems. Thus, this is an area of interest in freshwater fish biology. Along with the genotype of the fish host, external environment plays an important role in determining the composition of the internal microbiome. Here, we characterized the variability of the microbiome of wild Crucian carp (Carassius auratus), along with those of their surrounding environments (water and mud). We found that each environment had distinct bacterial communities, with varying composition and structure. The primary bacterial phyla identified in the Crucian carp gut were Fusobacteria and Proteobacteria (90% of all bacterial phyla identified); the primary genera identified were Cetobacterium, Aeromonas, and Plesiomonas (85% of all bacterial phyla identified). We identified 1,739 operational taxonomic units (OTUs) in the Crucian carp gut, 1,703 in water, and 5,322 in mud. Each environment had unique OTUs, but the fewest unique OTUs (97) were found in the Crucian carp gut. There were significant differences in the relative abundances of different bacterial phyla in the different environments. It may be that only bacterial phyla vital for efficient fish function (e.g., immune response or metabolism), such as Fusobacteria and Proteobacteria, are retained in the Crucian carp gut.
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