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

SIMPLE SUMMARY: The bacteria residing in donkey hindgut are clearly divided into two distinct ecological sites: liquid phase (Lq) and adherent fraction (Ad). Though both the Lq and Ad bacteria play an important role in feed digestion, the Ad bacteria have not previously been specifically sampled or directly compared with the Lq bacteria. The present study was conducted to comparatively analyze the bacterial community composition between the Lq and Ad fraction within the donkey caeco-colic ecosystem. The results showed that the relative abundance of Bacteroidota, Spirochaetota, Fibrobacterota and Patescibacteria in the Ad fraction was greater than the Lq fraction, indicating that bacteria associated with plant biomass are mainly responsible for plant fiber degradation. Regarding the genus level, the liquid phase presented higher abundance in Lactobacillus compared to Ad fraction. The activities of enzymes related to fiber degradation were predicted by PICRUSt, and they were also higher in Ad bacteria than Lq. In addition, the bacterial community composition was also distinct within the donkey caecum, ventral colon and dorsal colon. The present study provides evidence that bacteria adherent to feed particles may be better at plant fiber degradation than Lq bacteria due to the greater cellulolytic populations and activities. 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.