Comparative Analysis of Bacterial Diversity between the Liquid Phase and Adherent Fraction within the Donkey Caeco-Colic Ecosystem

Abstract

Donkey hindgut is an enlarged fermentative chamber that harbors a highly complex and extremely abundant community of anaerobic bacteria. It can be divided into two different ecological sites: liquid (Lq) phase and adherent fraction (Ad) colonized by bacteria. However, the Ad bacteria have not previously been specifically collected or directly compared with the Lq bacteria. In the present study, the digesta collected from the caecum, ventral colon and dorsal colon of nine Dezhou donkeys was separated into Lq and Ad fractions. The bacterial community structure was comparatively determined using 16S rRNA gene sequences by Illumina MiSeq. The Ad bacteria had a higher bacterial diversity than Lq bacteria due to the higher Chao and ACE index (p < 0.05). The predominant bacteria at the phylum level were Firmicutes (55.4~74.3%) and Bacteroidota (13.7~32.2%) for both the Lq and Ad fraction. The relative abundance of Bacteroidota, Spirochaetota, Fibrobacterota and Patescibacteria in the Ad fraction was greater than Lq (p < 0.05), suggesting that bacteria associated with feed particles were mainly responsible for plant fiber degradation. At the genus level, the abundance of Lactobacillus in Lq was greater than that in the Ad fraction (p < 0.05), indicating that the bacteria in the Lq fraction were better at hydrolyzing readily fermentable carbohydrates. PICRUSt showed that the activities of enzymes related to fiber degradation in the Ad fraction were also greater than Lq. In addition, the hindgut region also had a significant effect on the bacterial community composition. The relative abundance of Rikenellaceae_RC9_gut_group, Clostridium_sensu_stricto_1, Christensenellaceae_R-7_group and norank_Bacteroidales_BS11_gut_group was increased (p < 0.05) along the donkey hindgut. In summary, the present study provides evidence that bacteria adherent to plant biomass were different to those in the liquid phase within the donkey caeco-colic digesta, and bacteria associated with feed particles may mainly be responsible for plant fiber degradation.

Regulation of the growth performance and the gastrointestinal microbiota community by the addition of defective pear fermentation to feed of small-tailed Han sheep

“…Specifically, group Y had the highest abundance of unclassified_f_Lachnospiraceae but the lowest of Prevotella , suggesting a possible antagonistic relationship between Prevotella and Lachnospiraceae . unclassified_f_Lachnospiraceae , a potential probiotic, played a role in the metabolism of various carbohydrates and the fermentation of intermediate lactate and acetate to butyrate, aiding in maintaining rumen homeostasis and feed digestion (Paz et al, 2018 ; Zhang et al, 2022 ). This aligns with our findings, which revealed a significant positive correlation between unclassified_f_Lachnospiraceae and FCR, but slightly different, the increase of ADG and ADFI in group Y did not have significant effects on slaughter weight and FCR.…”

Could Weaning Remodel the Oral Microbiota Composition in Donkeys? An Exploratory Study

“…Each PCR was performed in total volume of 20 μL with 2 μL of 10 × TaKaRa rTaq buffer, 2 μL of 2.5 mM dNTPs, 0.8 μL of forward and reverse primers, 0.2 μL of TrTaq polymerase, 10 ng template DNA and ultrapure water. The thermal cycling was carried out with initial denaturation at 95 °C for 3 min, 27 cycles of denaturing at 95 °C for 30 s, annealing at 55 °C for 30 s, extension at 72 °C for 45 s, and one final cycle of 72 °C for 10 min [ 9 ]. The resulting PCR product was monitored by electrophoresis on a 2% agarose gel and then purified using the AxyPrep DNA Gel Extraction Kit (Axygen Biosciences, Union City, CA, USA).…”

“…The donkey’s digestive physiology is characterized by a long and intense microbial fermentation in the hindgut. Recently, the donkey hindgut microbiota has been intensively investigated [ 8 , 9 ] and it is well known to perform an important role in the animal’s health and well-being [ 10 , 11 ].…”