Exploration of microbiome diversity of stacked fermented grains by flow cytometry and cell sorting

Multi-omics analyses reveal fecal microbial community and metabolic alterations in finishing cattle fed probiotics-fermented distiller's grains diets

Distiller's grains (DG) are a potential source of animal feeds, and many studies have indicated positive regulatory roles of feeding DG diets in animal breeding. However, there is currently a dearth of research on the actions and underlying mechanisms of probiotics-fermented distiller's grains (FDG)-based diets in cattle breeding. This study aimed to assess the impact of integrating FDG into the diet of finishing cattle on their fecal microbial community and metabolites. Thirty Simmental crossbred cattle (local yellow cattle × Simmental cattle, 8.5 months old, 420.38 ± 68.11 kg) were selected and randomly divided into three dietary treatments, including the basal diet group (CON group), the FDG replacing 10% concentrate (FDG-10%) group, and the FDG replacing 20% concentrate (FDG-20%) group. 16S and ITS sequencing of fecal samples collected from each group on the 30th day of the formal feeding suggested that feeding FDG diets had little effect on the composition and diversity of fecal bacterial and fungal communities in finishing cattle. However, the relative abundance of cellulose-degrading bacteria, including the Christensenellaceae R-7 group and Ruminococcaceae family was significantly higher in both the FDG-20% vs CON comparison and the FDG-20% vs FDG-10% comparison. Besides, the FDG-10% group had a significant drop in the relative abundance of Aspergillus and a noteworthy increase in the relative abundance of Candida when compared to the CON group. Non-targeted metabolomics analysis showed that the addition of FDG modified the levels of organoheterocyclic compounds, lipids and lipid-like molecules, and benzenoids in the feces of finishing cattle and significantly enhanced the metabolic pathway of bile secretion. Further correlation analyses suggested a close association between the significantly differential fecal microbiota and metabolites. In conclusion, these results suggest that FDG supplementation has little effect on the structure and diversity of the fecal microbiota in finishing cattle, but alters intestinal metabolite profiles and influences bile secretion pathways by modulating the relative abundance of genera of fecal bacteria and fungi Christensenellaceae R-7 group, Lachnospiraceae_NK3A20_group, Mucor, and Candida. These findings provide a scientific theoretical basis for the use of FDG in animal feeds.

IMPORTANCE

Probiotics-fermented distiller's grains (FDG) are potential feed sources for livestock. Here, we investigated the effects of partially replacing concentrates with FDG on fecal bacterial and fungal community structure and metabolic profiles in finishing cattle. The results reveal that feeding FDG-based diets alters intestinal metabolite profiles and up-regulates bile secretion pathways through the regulation of relative abundance of certain fecal genera. These findings provide some new insights into clarifying the role and potential mechanisms of FDG diets and also offer a scientific basis for the development of FDG into functional feed resources.

Spatial heterogeneity of microbiota and flavor across different rounds of sauce-flavor baijiu in Northern China

Sauce-flavor baijiu (SFB) is a traditional Chinese distilled liquor crafted through a distinctive brewing process, involving seven rounds of stack fermentation (SF) and pit fermentation (PF). To date, there remains a knowledge gap regarding the microbial succession and flavor throughout all rounds of SFB with distinctive northern characteristics. Through LEfSe analysis, Saccharopolyspora, Virgibacillus, Thermoascus and Thermomyces, and Lactobacillus and Issatchenkia were found to be the most differentially representative genera in SF and PF, respectively. A total of 93 volatile flavor compounds were found in base baijius through the gas-chromatography mass spectrometry. Moreover, 29 volatile flavor substances with significant difference in base baijius of different rounds were revealed using the OPLS-DA model and VIP values and Spearman correlation analysis shows that bacteria have a greater impact on differential flavor compounds than fungi. This study provides a new perspective and insight into the brewing of northern SFB.

A specific and rapid method for detecting Bacillus and Acinetobacter species in Daqu

Daqu is a spontaneous, solid-state cereal fermentation product used for saccharification and as a starter culture for Chinese Baijiu production. Bacillus and Acinetobacter, two dominant microbial genera in Daqu, produce enzymes and organic acids that influence the Daqu quality. However, there are no rapid analytical methods for detecting Bacillus and Acinetobacter. We designed primers specific to the genera Bacillus and Acinetobacter to perform genetic comparisons using the 16 S rRNA. After amplification of polymerase chain reaction using specific primers, high-throughput sequencing was performed to detect strains of Bacillus and Acinetobacter. The results showed that the effective amplification rates for Bacillus and Acinetobacter in Daqu were 86.92% and 79.75%, respectively. Thus, we have devised and assessed a method to accurately identify the species associated with Bacillus and Acinetobacter in Daqu, which can also hold significance for bacterial typing and identification.