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The duck gastrointestinal tract (GIT) harbors an abundance of microorganisms that play an important role in duck health and production. Here, we constructed the first relatively comprehensive duck gut microbial gene catalog (24 million genes) and 4437 metagenome‐assembled genomes using 375 GIT metagenomic samples from four different duck breeds across five intestinal segments under two distinct rearing conditions. We further characterized the intestinal region‐specific microbial taxonomy and their assigned functions, as well as the temporal development and maturation of the duck gut microbiome. Our metagenomic analysis revealed the similarity within the microbiota of the foregut and hindgut compartments, but distinctive taxonomic and functional differences between distinct intestinal segments. In addition, we found a significant shift in the microbiota composition of newly hatched ducks (3 days), followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days), indicating that the intestinal microbiota develops into a relatively mature and stable community as the host duck matures. Comparing the impact of different rearing conditions (with and without water) on duck cecal microbiota communities and functions, we found that the bacterial capacity for lipopolysaccharide biosynthesis was significantly increased in ducks that had free access to water, leading to the accumulation of pathogenic bacteria and antibiotic‐resistance genes. Taken together, our findings expand the understanding of the microbiome signatures linked to intestinal regional, temporal development, and rearing conditions in ducks, which highlight the significant impact of microbiota on poultry health and production. Highlights: A catalog of microbial genes and metagenome‐assembled genomes from the duck gut microbiome.The microbiota within different duck intestinal segments exhibits both similarities and distinctive taxonomic and functional differences.Significant shifts in microbiota composition have been observed in newly hatched ducks at 3 days of age, followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days).Ducks with free access to water have shown an increased bacterial capacity for lipopolysaccharide biosynthesis, leading to the accumulation of pathogenic bacteria and antibiotic‐resistance genes. [ABSTRACT FROM AUTHOR]

Pig gastrointestinal tracts harbor a heterogeneous and dynamic ecosystem populated with trillions of microbes, enhancing the ability of the host to harvest energy from dietary carbohydrates and contributing to host adipogenesis and fatness. However, the microbial community structure and related mechanisms responsible for the differences between the fatty phenotypes and the lean phenotypes of the pigs remained to be comprehensively elucidated. Herein, we first found significant differences in microbial composition and potential functional capacity among different gut locations in Jinhua pigs with distinct fatness phenotypes. Second, we identified that Jinhua pigs with lower fatness exhibited higher levels of short‐chain fatty acids in the colon, highlighting their enhanced carbohydrate fermentation capacity. Third, we explored the differences in expressed carbohydrate‐active enzyme (CAZyme) in pigs, indicating their involvement in modulating fat storage. Notably, Clostridium butyricum might be a representative bacterial species from Jinhua pigs with lower fatness, and a significantly higher percentage of its genome was dedicated to CAZyme glycoside hydrolase family 13 (GH13). Finally, a subsequent mouse intervention study substantiated the beneficial effects of C. butyricum isolated from experimental pigs, suggesting that it may possess characteristics that promote the utilization of carbohydrates and hinder fat accumulation. Remarkably, when Jinhua pigs were administered C. butyricum, similar alterations in the gut microbiome and host fatness traits were observed, further supporting the potential role of C. butyricum in modulating fatness. Taken together, our findings reveal previously overlooked links between C. butyricum and CAZyme function, providing insight into the basic mechanisms that connect gut microbiome functions to host fatness. Highlight: Significant differences in microbial composition and potential functional capacity among different gut locations were found in Jinhua pigs with distinct fatness phenotypes.Jinhua pigs with lower fatness exhibited higher levels of short‐chain fatty acids in the colon, highlighting their enhanced carbohydrate fermentation capacity.Clostridium butyricum might be a representative bacterial species from Jinhua pigs with lower fatness, and a significantly higher percentage of its genome was dedicated to CAZyme glycoside hydrolase family 13 (GH13).Isolated C. butyricum alleviated fat accumulation and increased the enrichment of GH13 in obese mice. [ABSTRACT FROM AUTHOR]

BACKGROUND: Efficient utilization of dietary fibers (DFs) is important for optimizing feed resource utilization and animal health. The aim of the current study was to assess the effects of DFs with varying physicochemical properties (bulky, viscous, and fermentable) on fermentation kinetics and microbial composition during in vitro fermentation by fecal inoculum from lactating sow. According to the physicochemical properties, three different DFs, lignocellulose (LC), modified cassava starch (MCS) and konjac flour (KF) were selected as bulky fiber, fermentable fiber and viscous fiber respectively. Gas production, short‐chain fatty acids (SCFAs) profiles and microbial composition were monitored during the fermentation. RESULTS: Results showed that the gas production in 72 h (GP72h) ranked as: KF > MCS > LC (P < 0.05). The halftime of asymptotic gas production ranked as: KF < MCS = LC (P < 0.001). At 36 h of fermentation, MCS group showed higher concentrations of formic acid and lactate than LC and KF groups, whereas KF group showed higher concentrations of propionate and butyrate than LC and MCS groups (P < 0.05). At 72 h of fermentation, KF group showed higher concentrations of formic acid, lactate and propionate than LC and MCS groups, whereas MCS group showed higher concentrations of acetate and butyrate than LC and KF groups (P < 0.05). At 36 h of fermentation, Anaerovibrio and Erysipelatoclostridium abundances were higher in KF group, whereas Proteiniclasticum abundance was higher in MCS group. At 72 h of fermentation, the abundance of Fibrobacter in LC group was higher than that in MCS and KF groups. In addition, we also observed that the abundances of certain specific bacteria (Anaerovibrio and Erysipelatoclostridium) were closely related to the SCFAs production (propionate and butyrate) at different fermentation times. CONCLUSION: Collectively, the present study revealed that KF is a fast fermentation fiber which could produce propionate and butyrate rapidly, whereas LC is difficult to be fermented by bacteria. In addition, the fermentation of DFs with different physicochemical properties had divergent impacts on microbial composition and SCFA production. These findings deepen our understanding of the mechanisms of interaction between DFs and intestinal microbiota, and provide new ideas for the rational use of fiber resources in lactating sows. © 2020 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

To explore the feasibility of using radio frequency ( RF) heating as a method to process kiwi puree, this study compared the effects of RF heating with traditional heat pasteurisation ( TP) on various properties of kiwi puree. RF treatment completely inactivate of microbes in kiwi puree, with total aerobic bacteria counts ( TAC) decreased by 4.81 log CFU mL−1 and yeast and mould counts ( YMC) decreased by 2.62 log CFU mL−1, which are similar to TP treatment. During the 7 weeks' storage, RF-treated puree showed retarded growth of microbes. The pH, titratable acidity and °Brix values of RF-treated samples were significantly different from those of the control. The vitamin C, total phenolic compounds and antioxidant capacity of RF-treated samples were significantly higher than those of TP-treated samples during storage. RF-treated sample retained better colour than TP-treated sample throughout storage. The customer satisfaction analysis indicated that consumers prefer RF-treated kiwi puree than TP-treated samples. These findings suggest that RF heating has potential applications in processing of kiwi puree or similar products. [ABSTRACT FROM AUTHOR]

Fresh fruit is indispensable as a part of a daily diet; however, it commonly harbors large and diverse bacteria populations, including some important human pathogens. To determine the microbial composition on the surface of a strawberry, and structural changes of microbial composition from the field and market, 16SrDNA sequencing of 32 samples collected from production field (B) and market (M), which were divided into Groups I through III, was performed in this study. As a result, the 3,073 operational taxonomic units (OTUs) were clustered, and 5 phyla and 10 genera were dominant across all samples. When comparing I.B with I.M, Acinetobacter, Buchnera, and Bradyrhizobium were higher in I.B (p > 0.05), while Bacteroides, Pseudomonas, and Shewanella were higher in I.M (p > 0.05). Comparing II.B with II.M, Campylobacter was dominant in II.B, while most of the top10 genera decreased in II.M, except Acinetobacter, which presented an overwhelming richness, with an average relative abundance of 65.657 ± 1.071% (p = 0.002). Comparing III.B with III.M, Buchnera decreased in III.M, while Shewanella increased. Additionally, a certain number of opportunistic pathogens that included Acinetobacter were present in some samples. Therefore, analysis of microbial composition changes on the surface of strawberries is important for ensuring the biological safety of strawberries. Practical applications: This paper focused on determining the microbial composition on the surface of strawberry and comparing its structural changes of microbial composition from the field and market. The study results will be helpful for ensuring the biological safety of strawberries as well as a scientific basis for the traceability of microbial contamination of strawberries. [ABSTRACT FROM AUTHOR]