Comparison of the Intestinal Microbial Community in Ducks Reared Differently through High-Throughput Sequencing

Abstract

Birds are an important source of fecal contamination in environment. Many of diseases are spread through water contamination caused by poultry droppings. A study was conducted to compare the intestinal microbial structure of Shaoxing ducks with and without water. Thirty 1-day-old Shaoxing ducks (Qingke No. 3) were randomly divided into two groups; one group had free access to water (CC), while the other one was restricted from water (CT). After 8 months of breeding, caecal samples of 10 birds from each group were obtained on ice for high-throughput sequencing. A total of 1507978 valid sequences were examined and clustered into 1815 operational taxonomic units (OTUs). At phylum level, Firmicutes (41.37%), Bacteroidetes (33.26%), Proteobacteria (13.67%), and Actinobacteria (8.26%) were found to dominate the microbial community in CC birds, while Firmicutes (53.62%), Bacteroidetes (33.06%), and Actinobacteria (11.13%) were uncovered to be the prime phyla in CT ducks. At genus level, Bacteroides (25.02%), Escherichia-Shigella (11.02%), Peptococcus (7.73%) and Parabacteroides (5.86%) were revealed to be the mainly genera in the CC group ducks, while Bacteroides (18.11%), Erysipelatoclostridium (10.94%), Ruminococcaceae_unclassified (10.43%), Lachnospiraceae_unclassified (5.26%), Coriobacteriales_unclassified (5.89%), and Faecalibacterium (4.2%) were detected to staple the microbial flora in the CT birds. One phylum and 13 genera were found to have the significant difference between the two bird groups (p<0.05). At phylum level, Proteobacteria in CT ducks were found to be obviously lower than ducks in CC birds (p<0.05). At genus level, Escherichia-Shigella (p<0.05) and Peptococcus (p<0.05) were found to be notably lower in CT birds, while Erysipelatoclostridium (p<0.05), Ruminococcaceae_unclassified (p<0.01), Coriobacteriales_unclassified (p<0.05), Faecalibacterium (p<0.01), Atopobiaceae_unclassified (p<0.01), Alistipes (p<0.05), Eggerthellaceae_unclassified (p<0.05), Prevotella_7 (<0.05), Rikenellaceae_RC9_gut_group (p<0.05), Prevotellaceae_uncultured (p<0.05), and Shuttleworthia (p<0.05) were observed to be prominently higher in CT ducks. In conclusion, the present study revealed the effects of keeping ducks away from swimming with obvious changes in the microbial community. Though higher microbial richness was found in the ducks without swimming, more pathogenic genera including Eggerthella, Erysipelatoclostridium, Alistipes, Prevotella_7, and Shuttleworthia; zoonotic genera including Eggerthella and Shuttleworthia; inflammatory genus Alistipes; anti-inflammatory Faecalibacterium genus; and tumor genus Rikenellaceae were examined in these ducks. The CT ducks also showed significant changes at genera level regarding the metabolism (Peptococcus, Ruminococcaceae, and Coriobacteriales).

Modulation of the Intestinal Microbiota by the Early Intervention with Clostridium Butyricum in Muscovy Ducks

“…The gastrointestinal tract of poultry is closely linked to the health of the host, especially the composition of the cecum microorganisms [27]. In this study, the dominant phyla detected in the cecum contents were the phyla Bacteroidetes, Firmicutes, and Proteobacteria (Figure 4), which is consistent with previous studies [28,29]. Firmicutes becoming the dominant phylum in the intestines of poultry may be related to the anaerobic environment formed during intestinal development [30].…”

Microbiota populations and short-chain fatty acids production in cecum of immunosuppressed broilers consuming diets containing γ-irradiated Astragalus polysaccharides

“…Genus Negativibacillus in phylum Firmicutes is a kind of bacillus with a Gram-negative cell wall structure ( Ricaboni et al., 2016 ). Zhao et al. (2019) figured out that Negativibacillus performed in line with Ruminococcaceae UCG-014 , both of which were enriched in a growing abundance microecological environment.…”

Dietary supplementation with Bacillus subtilis promotes growth performance of broilers by altering the dominant microbial community

“…Erysipelatoclostridium belongs to the family Erysipelotrichaceae in Firmicutes . It has been reported that high abundance of Erysipelatoclostridium may be related to reducing feed/egg ratio of laying hens ( Guo et al., 2018 ), but Erysipelatoclostridium is also considered to be an opportunistic pathogen ( Zhao et al., 2019 ), which may be associated with diseases such as metabolic syndrome and gout ( Smith et al., 2016 ; Shao et al., 2017 ). In the present study, the genera Parasutterella and Bilophila in Proteobacteria were very abundant in cecum of broilers in the PC group, which were significantly negatively correlated with FCR.…”